diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..6e470660bed4db8b05295a49f6300f19aadf00cc
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,22 @@
+log/
+
+*.class
+*/target/
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+/.idea/
+*.iml
+
+*.DS_Store
+
+node_modules
+/admin/src/main/resources/static
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6b63cdd70323f80fe5600b9f7993020cfed22320..de5a3c51e245f629b9ab3473f8340f2c539e1922 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -61,6 +61,8 @@ build_dev:
- docker push "$CI_REGISTRY_IMAGE:$CI_COMMIT_REF_SLUG"
only:
- dev
+ when: manual
+
deploy_master:
@@ -102,6 +104,7 @@ deploy_dev:
url: https://dataportal-dev.edirex.ics.muni.cz/
only:
- dev
+ when: manual
build_tags:
diff --git a/README.md b/README.md
index ee13a8700ab1b127078ce42fa005ff30b4774534..570d43bf080a4196b5a9e874cd19017062ca3309 100644
--- a/README.md
+++ b/README.md
@@ -2,4 +2,3 @@
https://dataportal.europdx.eu
-IDE TO
diff --git a/admin/.classpath b/admin/.classpath
deleted file mode 100644
index 39abf1c5e9102a46b2af14da5d6d536eb2cd121a..0000000000000000000000000000000000000000
--- a/admin/.classpath
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" path="target/generated-sources/annotations">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- <attribute name="ignore_optional_problems" value="true"/>
- <attribute name="m2e-apt" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- <attribute name="ignore_optional_problems" value="true"/>
- <attribute name="m2e-apt" value="true"/>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
diff --git a/admin/.factorypath b/admin/.factorypath
deleted file mode 100644
index d25b2f384001e995e6f0a52be9e1c83366e75dee..0000000000000000000000000000000000000000
--- a/admin/.factorypath
+++ /dev/null
@@ -1,110 +0,0 @@
-<factorypath>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/fasterxml/jackson/core/jackson-core/2.8.10/jackson-core-2.8.10.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/fasterxml/jackson/dataformat/jackson-dataformat-csv/2.8.10/jackson-dataformat-csv-2.8.10.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/fasterxml/jackson/core/jackson-annotations/2.8.0/jackson-annotations-2.8.0.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/fasterxml/jackson/core/jackson-databind/2.8.10/jackson-databind-2.8.10.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-starter-web/1.5.8.RELEASE/spring-boot-starter-web-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-starter/1.5.8.RELEASE/spring-boot-starter-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-starter-logging/1.5.8.RELEASE/spring-boot-starter-logging-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/ch/qos/logback/logback-classic/1.1.11/logback-classic-1.1.11.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/ch/qos/logback/logback-core/1.1.11/logback-core-1.1.11.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/slf4j/jul-to-slf4j/1.7.25/jul-to-slf4j-1.7.25.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/slf4j/log4j-over-slf4j/1.7.25/log4j-over-slf4j-1.7.25.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/yaml/snakeyaml/1.17/snakeyaml-1.17.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-starter-tomcat/1.5.8.RELEASE/spring-boot-starter-tomcat-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/tomcat/embed/tomcat-embed-core/8.5.23/tomcat-embed-core-8.5.23.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/tomcat/tomcat-annotations-api/8.5.23/tomcat-annotations-api-8.5.23.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/tomcat/embed/tomcat-embed-el/8.5.23/tomcat-embed-el-8.5.23.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/tomcat/embed/tomcat-embed-websocket/8.5.23/tomcat-embed-websocket-8.5.23.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-web/4.3.12.RELEASE/spring-web-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-aop/4.3.12.RELEASE/spring-aop-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-beans/4.3.12.RELEASE/spring-beans-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-context/4.3.12.RELEASE/spring-context-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-webmvc/4.3.12.RELEASE/spring-webmvc-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-expression/4.3.12.RELEASE/spring-expression-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-starter-thymeleaf/1.5.8.RELEASE/spring-boot-starter-thymeleaf-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/thymeleaf/thymeleaf-spring4/3.0.2.RELEASE/thymeleaf-spring4-3.0.2.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/thymeleaf/thymeleaf/3.0.2.RELEASE/thymeleaf-3.0.2.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/attoparser/attoparser/2.0.1.RELEASE/attoparser-2.0.1.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/unbescape/unbescape/1.1.4.RELEASE/unbescape-1.1.4.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/nz/net/ultraq/thymeleaf/thymeleaf-layout-dialect/2.1.1/thymeleaf-layout-dialect-2.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/codehaus/groovy/groovy/2.4.12/groovy-2.4.12.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/nz/net/ultraq/thymeleaf/thymeleaf-expression-processor/1.1.2/thymeleaf-expression-processor-1.1.2.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-starter-actuator/1.5.8.RELEASE/spring-boot-starter-actuator-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-actuator/1.5.8.RELEASE/spring-boot-actuator-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/webjars/bootstrap/3.3.7/bootstrap-3.3.7.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/webjars/jquery/1.11.1/jquery-1.11.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/webjars/font-awesome/4.7.0/font-awesome-4.7.0.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/webjars/animate.css/3.5.2/animate.css-3.5.2.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/webjars/bower/amcharts3/3.21.3/amcharts3-3.21.3.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/webjars/webjars-locator/0.32-1/webjars-locator-0.32-1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/webjars/webjars-locator-core/0.32/webjars-locator-core-0.32.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/commons/commons-lang3/3.1/commons-lang3-3.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/commons/commons-compress/1.9/commons-compress-1.9.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-starter-data-neo4j/1.5.8.RELEASE/spring-boot-starter-data-neo4j-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/data/spring-data-neo4j/4.2.8.RELEASE/spring-data-neo4j-4.2.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-tx/4.3.12.RELEASE/spring-tx-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/data/spring-data-commons/1.13.8.RELEASE/spring-data-commons-1.13.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-ogm-core/2.1.5/neo4j-ogm-core-2.1.5.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-ogm-api/2.1.5/neo4j-ogm-api-2.1.5.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/commons-codec/commons-codec/1.10/commons-codec-1.10.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-ogm-compiler/2.1.5/neo4j-ogm-compiler-2.1.5.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/commons/commons-collections4/4.1/commons-collections4-4.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-ogm-http-driver/2.1.5/neo4j-ogm-http-driver-2.1.5.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/httpcomponents/httpclient/4.5.3/httpclient-4.5.3.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/httpcomponents/httpcore/4.4.8/httpcore-4.4.8.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/commons-io/commons-io/2.4/commons-io-2.4.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/spring-core/4.3.12.RELEASE/spring-core-4.3.12.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-devtools/1.5.8.RELEASE/spring-boot-devtools-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot/1.5.8.RELEASE/spring-boot-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/springframework/boot/spring-boot-autoconfigure/1.5.8.RELEASE/spring-boot-autoconfigure-1.5.8.RELEASE.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j/3.1.1/neo4j-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-kernel/3.1.1/neo4j-kernel-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-graphdb-api/3.1.1/neo4j-graphdb-api-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-resource/3.1.1/neo4j-resource-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-common/3.1.1/neo4j-common-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-collections/3.1.1/neo4j-collections-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-primitive-collections/3.1.1/neo4j-primitive-collections-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-unsafe/3.1.1/neo4j-unsafe-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-io/3.1.1/neo4j-io-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-csv/3.1.1/neo4j-csv-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-logging/3.1.1/neo4j-logging-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-lucene-upgrade/3.1.1/neo4j-lucene-upgrade-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/lucene/lucene-backward-codecs/5.5.0/lucene-backward-codecs-5.5.0.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-lucene-index/3.1.1/neo4j-lucene-index-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/lucene/lucene-analyzers-common/5.5.0/lucene-analyzers-common-5.5.0.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/lucene/lucene-core/5.5.0/lucene-core-5.5.0.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/lucene/lucene-queryparser/5.5.0/lucene-queryparser-5.5.0.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/apache/lucene/lucene-codecs/5.5.0/lucene-codecs-5.5.0.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-graph-algo/3.1.1/neo4j-graph-algo-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-udc/3.1.1/neo4j-udc-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-graph-matching/3.1.1/neo4j-graph-matching-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-cypher/3.1.1/neo4j-cypher-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/scala-lang/scala-library/2.11.8/scala-library-2.11.8.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/scala-lang/scala-reflect/2.11.8/scala-reflect-2.11.8.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-codegen/3.1.1/neo4j-codegen-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/ow2/asm/asm/5.0.4/asm-5.0.4.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-cypher-compiler-2.3/2.3.8/neo4j-cypher-compiler-2.3-2.3.8.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-cypher-frontend-2.3/2.3.8/neo4j-cypher-frontend-2.3-2.3.8.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/googlecode/concurrentlinkedhashmap/concurrentlinkedhashmap-lru/1.4.2/concurrentlinkedhashmap-lru-1.4.2.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-cypher-compiler-3.0/3.0.8/neo4j-cypher-compiler-3.0-3.0.8.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-cypher-frontend-3.0/3.0.8/neo4j-cypher-frontend-3.0-3.0.8.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-cypher-compiler-3.1/3.1.1/neo4j-cypher-compiler-3.1-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-cypher-frontend-3.1/3.1.1/neo4j-cypher-frontend-3.1-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/github/ben-manes/caffeine/caffeine/2.3.5/caffeine-2.3.5.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/parboiled/parboiled-scala_2.11/1.1.7/parboiled-scala_2.11-1.1.7.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/parboiled/parboiled-core/1.1.7/parboiled-core-1.1.7.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/net/sf/opencsv/opencsv/2.3/opencsv-2.3.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-jmx/3.1.1/neo4j-jmx-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-consistency-check/3.1.1/neo4j-consistency-check-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-command-line/3.1.1/neo4j-command-line-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-dbms/3.1.1/neo4j-dbms-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/neo4j/neo4j-import-tool/3.1.1/neo4j-import-tool-3.1.1.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/hibernate/hibernate-validator/5.3.5.Final/hibernate-validator-5.3.5.Final.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/javax/validation/validation-api/1.1.0.Final/validation-api-1.1.0.Final.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/org/jboss/logging/jboss-logging/3.3.1.Final/jboss-logging-3.3.1.Final.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/fasterxml/classmate/1.3.4/classmate-1.3.4.jar" enabled="true" runInBatchMode="false"/>
- <factorypathentry kind="VARJAR" id="M2_REPO/com/google/code/gson/gson/2.8.0/gson-2.8.0.jar" enabled="true" runInBatchMode="false"/>
-</factorypath>
diff --git a/admin/.project b/admin/.project
deleted file mode 100644
index 15234ef54b41dbb4ee4fc41fabf8f13f39fa1f76..0000000000000000000000000000000000000000
--- a/admin/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>admin</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- </natures>
-</projectDescription>
diff --git a/admin/pom.xml b/admin/pom.xml
index da7175127267102dc300f1ba7eea6ef9b8b08819..e215943e308a687e1c0c5ca73f2015ecfb901335 100644
--- a/admin/pom.xml
+++ b/admin/pom.xml
@@ -24,6 +24,7 @@
<groupId>org.pdxfinder</groupId>
<artifactId>data-services</artifactId>
</dependency>
+
<dependency>
<groupId>org.pdxfinder</groupId>
<artifactId>data-model</artifactId>
@@ -39,80 +40,22 @@
<artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
- <!--<dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-thymeleaf</artifactId>
- </dependency>
-
- <dependency>
- <groupId>org.webjars</groupId>
- <artifactId>bootstrap</artifactId>
- <version>3.3.7</version>
- </dependency>
-
<dependency>
- <groupId>org.webjars</groupId>
- <artifactId>font-awesome</artifactId>
- <version>4.7.0</version>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j-ogm-bolt-driver</artifactId>
+ <version>3.1.20</version>
</dependency>
<dependency>
- <groupId>org.webjars</groupId>
- <artifactId>animate.css</artifactId>
- <version>3.5.2</version>
+ <!-- WARNING, do not update db engine (stable: 1.4.197) cause compatibility issues, see https://github.com/h2database/h2database/issues/2078 -->
+ <groupId>com.h2database</groupId>
+ <artifactId>h2</artifactId>
+ <version>1.4.197</version>
</dependency>
-
- <dependency>
- <groupId>org.webjars.bower</groupId>
- <artifactId>amcharts3</artifactId>
- <version>3.21.3</version>
- </dependency>
-
- <dependency>
- <groupId>org.webjars</groupId>
- <artifactId>webjars-locator</artifactId>
- </dependency>-->
-
</dependencies>
<build>
<plugins>
- <!--<plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>exec-maven-plugin</artifactId>
- <version>1.6.0</version>
- <executions>
- <execution>
- <id>install-dependencies</id>
- <phase>validate</phase>
- <goals>
- <goal>exec</goal>
- </goals>
- <configuration>
- <executable>${npm.executable}</executable>
- <workingDirectory>src/main/app-ui</workingDirectory>
- <arguments>
- <argument>install</argument>
- </arguments>
- </configuration>
- </execution>
- <execution>
- <id>build-angular-app</id>
- <phase>validate</phase>
- <goals>
- <goal>exec</goal>
- </goals>
- <configuration>
- <executable>ng</executable>
- <workingDirectory>src/main/app-ui</workingDirectory>
- <arguments>
- <argument>build</argument>
- </arguments>
- </configuration>
- </execution>
- </executions>
-
- </plugin>-->
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
@@ -127,21 +70,4 @@
</plugins>
</build>
- <!-- Windows requires different command line -->
- <!--<profiles>
- <profile>
- <id>platform-windows</id>
- <activation>
- <os>
- <family>windows</family>
- </os>
- </activation>
- <properties>
- <npm.executable>npm.cmd</npm.executable>
- <grunt.executable>grunt.cmd</grunt.executable>
- <bower.executable>bower.cmd</bower.executable>
- </properties>
- </profile>
- </profiles>-->
-
</project>
diff --git a/admin/src/main/app-ui/package-lock.json b/admin/src/main/app-ui/package-lock.json
index bd21e67a31740299de89eb6f4c46c68e8fb8c009..1cee6d41766e1c750d1fffff019529143e1a2409 100644
--- a/admin/src/main/app-ui/package-lock.json
+++ b/admin/src/main/app-ui/package-lock.json
@@ -9941,7 +9941,8 @@
},
"ws": {
"version": "1.1.2",
- "resolved": "",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-1.1.2.tgz",
+ "integrity": "sha1-iiRPoFJAHgjJiGz0SoUYnh/UBn8=",
"dev": true,
"requires": {
"options": ">=0.0.5",
diff --git a/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.html b/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.html
index 5baf9aa71b0845d5d9eb3e7cb7df41611894c9eb..ff946ccbae1d5dcee75723607f9049ac8989cfd6 100644
--- a/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.html
+++ b/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.html
@@ -58,51 +58,6 @@
-<div class="wrapper wrapper-content animated fadeInRight">
- <div class="p-w-md m-t-sm col-lg-10 col-lg-offset-1">
-
- <div class="row" style="margin-top: -10px;">
-
- <div class="col-lg-12" *ngIf="dataExists">
-
- <form #mappingForm="ngForm" (ngSubmit)="updateMappingEntity()" novalidate>
- <div class="pdxfinder float-e-margins" style="border: 1px solid rgba(3, 54, 157, 1);">
-
-
- <div class="pdxfinder-content pdxfinder-heading">
- <h3><i class="ti-agenda"></i> <span style="color: #03369D"> {{dataSource | uppercase}} </span> Mapping </h3>
- <small><i class="fa fa-tim"></i> You have 70 unmapped ... and 16 orphaned ...</small>
-
-
- <button *ngIf="report == null" style="float: right; margin-top:-30px;" class="btn btn-primary btn-sm" type="submit">
- <i class="ti-cloud-up"></i> Submit Curation
- </button>
-
- </div>
-
- <div class="pdxfinder-content">
-
- <div *ngIf="report == 'success'" class="alert alert-success alert-dismissable">
- <a aria-hidden="true" class="close" type="button" (click)="toggleReport('success')">Ă—</a>
- Success: <em> The submitted curation was successful, Clear off notification to continue </em> <a class="alert-link"> ... </a>.
- </div>
-
- <div *ngIf="report == 'failed'" class="alert alert-danger alert-dismissable">
- <a aria-hidden="true" class="close" type="button" (click)="toggleReport(null)">Ă—</a>
- OOps!! <em> Failed Request: The submitted curation is invalid, Clear off notification to continue </em> <a class="alert-link"> ... </a>.
- </div>
-
-
-<div class="wrapper wrapper-content animated fadeInRight">
- <div class="p-w-md m-t-sm col-lg-10 col-lg-offset-1">
-
- <div class="row" style="margin-top: -10px;">
-
- <div class="col-lg-12" *ngIf="dataExists">
-
- <form #mappingForm="ngForm" (ngSubmit)="updateMappingEntity()" novalidate>
- <div class="pdxfinder float-e-margins" style="border: 1px solid rgba(3, 54, 157, 1);">
-
<div class="wrapper wrapper-content animated fadeInRight">
@@ -274,4 +229,4 @@
<td> {{ mapping.mappingValues.OriginTissue | uppercase }} </td> -->
<!-- <a [routerLink]="['../'+count]"> {{count }} </a>
-<a [routerLink]="['../']" [queryParams]="{page: count}" > {{count }} </a> {{'curation/'+entityTypeUrl+'/'+dataSource}} +'?page='+count -->
+<a [routerLink]="['../']" [queryParams]="{page: count}" > {{count }} </a> {{'curation/'+entityTypeUrl+'/'+dataSource}} +'?page='+count -->
\ No newline at end of file
diff --git a/admin/src/main/app-ui/src/app/datasource-summary/datasource-summary.component.html b/admin/src/main/app-ui/src/app/datasource-summary/datasource-summary.component.html
index 2baa7f8c8dbab5aad30e5d718feb49e5fc24f6a4..ae0c6cd6870be46ccfa6e80d9913f843c7a7cde6 100644
--- a/admin/src/main/app-ui/src/app/datasource-summary/datasource-summary.component.html
+++ b/admin/src/main/app-ui/src/app/datasource-summary/datasource-summary.component.html
@@ -135,4 +135,4 @@
</div>
</div>
-<!-- use container or blank for small screen and col-lg-10 col-lg-offset-1 for 17 inches upwards swing tada wobble bounceIn (Up,Left,Right,Down) lightSpeedIn , flipInY, rotateInDownRight, rotateInUpLeft, slideInLeft, hinge, rollIn-->
+<!-- use container or blank for small screen and col-lg-10 col-lg-offset-1 for 17 inches upwards swing tada wobble bounceIn (Up,Left,Right,Down) lightSpeedIn , flipInY, rotateInDownRight, rotateInUpLeft, slideInLeft, hinge, rollIn-->
\ No newline at end of file
diff --git a/admin/src/main/app-ui/src/app/mapping.service.ts b/admin/src/main/app-ui/src/app/mapping.service.ts
index bb5eaf3353bc4a03b682c93d88235c548bd32668..b62f5e615ab4b2a0b926e7ec27392b46e6558c01 100644
--- a/admin/src/main/app-ui/src/app/mapping.service.ts
+++ b/admin/src/main/app-ui/src/app/mapping.service.ts
@@ -172,61 +172,11 @@ export class MappingService {
- pushFileToStorage(file: File, entityType: string): Observable<HttpEvent<{}>> {
-
- const formdata: FormData = new FormData();
- formdata.append('uploads', file);
-
- const url = `${this._uploadURL}?entity-type=${entityType}`;
-
- return this.http.post<any>(url, formdata)
- .pipe(
- catchError(this.errorHandler)
- );
-
- }
-
-
-
- connectToDataFlow() {
-
- return fetch('http://localhost:8081/api/mapping/diagnosis?ds=JAX')
- .then((res) => res.json())
- .then((data) => data)
- .catch(error => console.log(error));
- }
-
-
-
- pushFileToStorage(file: File, entityType: string): Observable<HttpEvent<{}>> {
-
- const formdata: FormData = new FormData();
- formdata.append('uploads', file);
-
- const url = `${this._uploadURL}?entity-type=${entityType}`;
-
- return this.http.post<any>(url, formdata)
- .pipe(
- catchError(this.errorHandler)
- );
-
- }
-
-
+}
- connectToDataFlow() {
- return fetch('http://localhost:8081/api/mapping/diagnosis?ds=JAX')
- .then((res) => res.json())
- .then((data) => data)
- .catch(error => console.log(error));
- }
-
-
-
-}
diff --git a/admin/src/main/app-ui/src/pdxfinder/pattern-library/style.css b/admin/src/main/app-ui/src/pdxfinder/pattern-library/style.css
index f1347e48fe0dcf2e21c95c3ddf525ee8f5f3c0f4..99a665cbcf07918c79d200458f030e5d371b1a76 100755
--- a/admin/src/main/app-ui/src/pdxfinder/pattern-library/style.css
+++ b/admin/src/main/app-ui/src/pdxfinder/pattern-library/style.css
@@ -4304,3 +4304,9 @@ a.compose-mail {
margin-bottom: 5px;
margin-right: 5px;
}
+
+
+
+
+
+
diff --git a/admin/src/main/java/org/pdxfinder/controllers/AjaxController.java b/admin/src/main/java/org/pdxfinder/controllers/AjaxController.java
index 0dea840bf01b241cd504d36c7d346e5a08027b88..b534ba22dc6605ad973acf7dbd31212ba6384417 100644
--- a/admin/src/main/java/org/pdxfinder/controllers/AjaxController.java
+++ b/admin/src/main/java/org/pdxfinder/controllers/AjaxController.java
@@ -5,11 +5,11 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.dataformat.csv.CsvMapper;
import com.fasterxml.jackson.dataformat.csv.CsvSchema;
import org.pdxfinder.rdbms.dao.MappingEntity;
-import org.pdxfinder.services.zooma.ZoomaEntity;
import org.pdxfinder.services.MappingService;
import org.pdxfinder.services.UtilityService;
import org.pdxfinder.services.dto.PaginationDTO;
import org.pdxfinder.services.mapping.CSVHandler;
+import org.pdxfinder.services.zooma.ZoomaEntity;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@@ -20,6 +20,7 @@ import org.springframework.web.client.RestTemplate;
import org.springframework.web.multipart.MultipartFile;
import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
import java.util.*;
@@ -127,7 +128,7 @@ public class AjaxController {
* Bulk update of Records
*/
@PutMapping("/mappings")
- public ResponseEntity<?> editListOfEntityMappings(@RequestBody List<MappingEntity> submittedEntities) {
+ public ResponseEntity<?> editListOfEntityMappings(@RequestBody List<MappingEntity> submittedEntities) throws IOException {
List data = mapper.convertValue(submittedEntities, List.class);
log.info(data.toString());
diff --git a/admin/src/main/java/org/pdxfinder/controllers/TransController.java b/admin/src/main/java/org/pdxfinder/controllers/TransController.java
index a01e6d3a044cad360d3f1cf8069836710afebe3b..3e9bac98755916b7b299326b54c5e94eca38d6a2 100644
--- a/admin/src/main/java/org/pdxfinder/controllers/TransController.java
+++ b/admin/src/main/java/org/pdxfinder/controllers/TransController.java
@@ -1,21 +1,21 @@
package org.pdxfinder.controllers;
-import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.collections4.ListUtils;
import org.apache.commons.lang3.StringUtils;
import org.pdxfinder.rdbms.dao.MappingEntity;
-import org.pdxfinder.rdbms.repositories.MappingEntityRepository;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.TransformerService;
import org.pdxfinder.rdbms.dao.PdmrPdxInfo;
import org.pdxfinder.rdbms.dao.PdxInfo;
+import org.pdxfinder.rdbms.repositories.MappingEntityRepository;
+import org.pdxfinder.services.TransformerService;
+import org.pdxfinder.services.UtilityService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.web.client.RestTemplateBuilder;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import org.springframework.web.client.RestTemplate;
@@ -33,6 +33,8 @@ public class TransController {
private final static Logger log = LoggerFactory.getLogger(TransController.class);
private String homeDir = System.getProperty("user.home");
+ private String pdmrRawFileDir = homeDir + "/finderroot/data/PDMR/raw/";
+
private RestTemplate restTemplate = new RestTemplate();
private ObjectMapper mapper = new ObjectMapper();
private TransformerService transformerService;
@@ -42,16 +44,16 @@ public class TransController {
private MappingEntityRepository mappingEntityRepository;
-
- public TransController(TransformerService transformerService, RestTemplateBuilder restTemplateBuilder){
+ public TransController(TransformerService transformerService, RestTemplateBuilder restTemplateBuilder) {
this.transformerService = transformerService;
this.restTemplate = restTemplateBuilder.build();
+
+ this.transformerService.setDataRootDir(System.getProperty("user.home") + "/finderroot/data");
}
@GetMapping("/view-data")
- public PdxInfo getAllPdmr()
- {
+ public PdxInfo getAllPdmr() {
List<PdmrPdxInfo> pdmrPdxInfos = transformerService.getAllPdmr();
PdxInfo pdxInfo = new PdxInfo();
@@ -62,13 +64,12 @@ public class TransController {
@GetMapping("/drugs")
- public String getAllPdmrDrugs()
- {
+ public String getAllPdmrDrugs() {
List<PdmrPdxInfo> pdmrPdxInfos = transformerService.getAllPdmr();
String drugList = "";
- for (PdmrPdxInfo pdmrPdxInfo : pdmrPdxInfos){
+ for (PdmrPdxInfo pdmrPdxInfo : pdmrPdxInfos) {
drugList += transformerService.getDrugs(pdmrPdxInfo);
}
@@ -77,119 +78,52 @@ public class TransController {
}
-
@GetMapping("/transform-pdmr-data")
- public Object connectPdmr(){
+ public Object connectPdmr() {
List<Map<String, String>> mappingList = transformerService.transformDataAndSave();
return mappingList;
}
- /*
- Test Saving Mapping Entity in H2 Database */
-
- @GetMapping("/mapping")
- public List<MappingEntity> saveMapping(){
-
- ArrayList<String> mappingLabels = new ArrayList<>();
- mappingLabels.add("DataSource");
- mappingLabels.add("SampleDiagnosis");
- mappingLabels.add("TumorType");
- mappingLabels.add("OriginTissue");
-
- Map mappingValues = new HashMap();
- mappingValues.put("OriginTissue","blood");
- mappingValues.put("TumorType","primary");
- mappingValues.put("SampleDiagnosis","acute myeloid leukemia");
- mappingValues.put("DataSource","jax");
-
- MappingEntity mappingEntity = new MappingEntity("DIAGNOSIS", mappingLabels, mappingValues);
-
- mappingEntity.setMappedTermLabel("Acute Myeloid Leukemia");
- mappingEntity.setStatus("Created");
- mappingEntity.setDateCreated(new Date());
- mappingEntity.setMappedTermUrl("http://purl.obolibrary.org/obo/NCIT_C3171");
- mappingEntity.setMapType("direct");
- mappingEntity.setJustification("0");
-
- //mappingEntityRepository.save(mappingEntity);
-
- return mappingEntityRepository.findAll();
-
- }
-
@GetMapping("/get-mapping")
- public List<MappingEntity> getMapping(){
+ public List<MappingEntity> getMapping() {
return mappingEntityRepository.findAll();
}
+ @RequestMapping(path = "/pdmr/genomics", method = RequestMethod.GET)
+ public Object transformPdmrGenomicData() {
- @RequestMapping("/rewrite-pdmr-omic-data")
- public Object downloads() {
-
- String omicFile= System.getProperty("user.home") + "/Downloads/NGS-LOADER/ncicancergenepaneldata_MARCH2019.csv";
+ List transformedData = transformerService.transformOncoKB();
- List<Map<String, String>> dataList = utilityService.serializeCSVToMaps(omicFile);
-
-
- List removedList = new ArrayList();
- for (Map<String, String> data : dataList) {
+ String destination = pdmrRawFileDir + "transformed-nci-gene-panel.csv";
- if ( !data.get("Sample_ID").equals("ORIGINATOR") ){
+ utilityService.writeCsvFileGenerics(transformedData, destination);
- String modelID = data.get("Model_ID");
- String sampleID = data.get("Sample_ID");
-
- String passage = transformerService.getPassageByModelIDAndSampleID(modelID, sampleID);
-
- data.put("Passage", passage);
-
- /*if (passage.equals("XXXX")){
- removedList.add(data);
- }*/
- }
-
-
- if ( data.get("hgnc_symbol").equals("None Found") ){
-
- removedList.add(data);
- }
-
- }
-
- dataList.removeAll(removedList);
-
-
- String destination = homeDir+"/Downloads/data.csv";
- utilityService.writeCsvFile(dataList, destination);
-
- return dataList;
+ return transformedData;
}
-
@RequestMapping("/rewrite-ircc-cna-to-json")
public Object irccCNA() {
// Get CNA xls Template
- String cnaFile = System.getProperty("user.home") + "/PDXFinder/data/IRCC-CRC/cna/CNA- IRCC-CRC template.xlsx";
+ String cnaFile = homeDir + "/PDXFinder/data/IRCC-CRC/cna/CNA- IRCC-CRC template.xlsx";
- List<Map<String, String>> dataList = utilityService.serializeExcelDataNoIterator(cnaFile,0,1);
+ List<Map<String, String>> dataList = utilityService.serializeExcelDataNoIterator(cnaFile, 0, 1);
return dataList;
}
-
@RequestMapping("/rewrite-ircc-json")
public Object irccTransformJson() {
- String jsonFile= System.getProperty("user.home") + "/PDXFinder/data/IRCC-CRC/mut/old.json";
+ String jsonFile = homeDir + "/PDXFinder/data/IRCC-CRC/mut/old.json";
List<Map<String, String>> dataList = (List) utilityService.serializeJSONToMaps(jsonFile, "IRCCVariation");
List<Map<String, String>> newDataList = new ArrayList<>();
@@ -206,9 +140,9 @@ public class TransController {
newData.put("Model_ID", data.get("Model ID"));
newData.put("Sample_ID", specimenId);
- if ( specimenId.startsWith(modelId+"H") ){
+ if (specimenId.startsWith(modelId + "H")) {
newData.put("sample_origin", "patient tumor");
- } else if (specimenId.startsWith(modelId+"X")){
+ } else if (specimenId.startsWith(modelId + "X")) {
newData.put("sample_origin", "Xenograft");
}
@@ -237,91 +171,80 @@ public class TransController {
}
-
// Get Exome Template
- String exomeFile = System.getProperty("user.home") + "/PDXFinder/data/IRCC-CRC/exome_IRCC-CRC template.xlsx";
+ String exomeFile = homeDir + "/PDXFinder/data/IRCC-CRC/exome_IRCC-CRC template.xlsx";
- List<Map<String, String>> dataList2 = utilityService.serializeExcelDataNoIterator(exomeFile,0,1);
+ List<Map<String, String>> dataList2 = utilityService.serializeExcelDataNoIterator(exomeFile, 0, 1);
return ListUtils.union(dataList2, newDataList);
}
-
-
-
-
@RequestMapping("/rewrite-curie-lc-cna")
public Object curieTransform() {
- String cnaFile= System.getProperty("user.home") + "/Downloads/curie-cna.xlsx";
+ String cnaFile = homeDir + "/Downloads/curie-cna.xlsx";
- List<Map<String, String>> dataList = utilityService.serializeExcelDataNoIterator(cnaFile,0,1);
+ List<Map<String, String>> dataList = utilityService.serializeExcelDataNoIterator(cnaFile, 0, 1);
for (Map<String, String> data : dataList) {
String modelID = data.get("Model_ID");
- if (modelID.equals("LCF4")){
+ if (modelID.equals("LCF4")) {
- data.put("Sample_ID","LCF4p09/09/2009");
- data.put("sample_origin","engrafted tumor");
- data.put("Passage","4");
- data.put("Platform","CGH array");
+ data.put("Sample_ID", "LCF4p09/09/2009");
+ data.put("sample_origin", "engrafted tumor");
+ data.put("Passage", "4");
+ data.put("Platform", "CGH array");
}
- if (modelID.equals("LCF9")){
+ if (modelID.equals("LCF9")) {
- data.put("Sample_ID","LCF9p16:19/05/2015");
- data.put("sample_origin","engrafted tumor");
- data.put("Passage","16");
- data.put("Platform","CGH array");
+ data.put("Sample_ID", "LCF9p16:19/05/2015");
+ data.put("sample_origin", "engrafted tumor");
+ data.put("Passage", "16");
+ data.put("Platform", "CGH array");
}
- if (modelID.equals("LCF16")){
+ if (modelID.equals("LCF16")) {
- data.put("Sample_ID","LCF16p27:26/08/2016");
- data.put("sample_origin","engrafted tumor");
- data.put("Passage","27");
- data.put("Platform","CGH array");
+ data.put("Sample_ID", "LCF16p27:26/08/2016");
+ data.put("sample_origin", "engrafted tumor");
+ data.put("Passage", "27");
+ data.put("Platform", "CGH array");
}
- if (modelID.equals("LCF26")){
+ if (modelID.equals("LCF26")) {
- data.put("Sample_ID","LCF26p3:23/09/2011");
- data.put("sample_origin","engrafted tumor");
- data.put("Passage","3");
- data.put("Platform","CGH array");
+ data.put("Sample_ID", "LCF26p3:23/09/2011");
+ data.put("sample_origin", "engrafted tumor");
+ data.put("Passage", "3");
+ data.put("Platform", "CGH array");
}
}
- String destination = homeDir+"/Downloads/curie-cna.csv";
+ String destination = homeDir + "/Downloads/curie-cna.csv";
utilityService.writeCsvFile(dataList, destination);
return dataList;
}
-
-
-
-
-
-
// FIX DERIVED DATA SHEET / PDX DETAILS IN CRL DATA
@RequestMapping("/rewrite-crl")
public Object crlTransform() {
// UPDATE DERIVED DATA SHEET
- String templateFile= System.getProperty("user.home") + "/Downloads/DATA/crl.xlsx";
- List<Map<String, String>> derivedDataSheet = utilityService.serializeExcelDataNoIterator(templateFile,6,4);
+ String templateFile = homeDir + "/Downloads/DATA/crl.xlsx";
+ List<Map<String, String>> derivedDataSheet = utilityService.serializeExcelDataNoIterator(templateFile, 6, 4);
List removedList = new ArrayList();
@@ -331,7 +254,7 @@ public class TransController {
String modelID = data.get("Model ID");
// Replace Model Ids with prefix CRL-
- data.put("Model ID","CRL-"+modelID);
+ data.put("Model ID", "CRL-" + modelID);
// Deduct 1 from all passages
String passage = data.get("Passage");
@@ -339,7 +262,7 @@ public class TransController {
String cleanPassage = Integer.toString(Integer.parseInt(passage) - 1);
data.put("Passage", cleanPassage);
- }catch (Exception e){
+ } catch (Exception e) {
log.error("{}'s passage {} is not a meaningful passage data ", modelID, passage);
@@ -348,10 +271,10 @@ public class TransController {
}
// Change Sample Origin to Xenograft
- data.put("Sample origin","xenograft");
+ data.put("Sample origin", "xenograft");
// remove Gene Expression Data
- if ( data.get("Molecular Characterization type").contains("Gene expression") ){
+ if (data.get("Molecular Characterization type").contains("Gene expression")) {
removedList.add(data);
}
@@ -360,23 +283,23 @@ public class TransController {
// Capture Map Keys to use as excel head
List<String> xlsHead = new ArrayList<>();
- for (Map.Entry<String, String> entry : derivedDataSheet.get(0).entrySet() ) {
+ for (Map.Entry<String, String> entry : derivedDataSheet.get(0).entrySet()) {
xlsHead.add(entry.getKey());
}
- String destination = homeDir+"/Downloads/CRL-Derived_dataset_from_tumor.csv";
+ String destination = homeDir + "/Downloads/CRL-Derived_dataset_from_tumor.csv";
utilityService.writeCsvFile(derivedDataSheet, destination);
- utilityService.writeXLSXFile(derivedDataSheet,"CRL-Derived_dataset_from_tumor.xlsx", "Derived_dataset_from_tumor");
+ utilityService.writeXLSXFile(derivedDataSheet, "CRL-Derived_dataset_from_tumor.xlsx", "Derived_dataset_from_tumor");
// UPDATE PDX DETAILS SHEET
- List<Map<String, String>> pdxModelDetailSheet = utilityService.serializeExcelDataNoIterator(templateFile,4,4);
+ List<Map<String, String>> pdxModelDetailSheet = utilityService.serializeExcelDataNoIterator(templateFile, 4, 4);
//pdxModelDetailSheet.remove(pdxModelDetailSheet.get(0));
// Group DerivedDataSheet By ModelID
- Map<String, List<Map<String, String>> > groupedDerivedDataSheet = utilityService.groupDataByColumn(derivedDataSheet,"Model ID");
+ Map<String, List<Map<String, String>>> groupedDerivedDataSheet = utilityService.groupDataByColumn(derivedDataSheet, "Model ID");
// Pull Model from ModelDetailSheet and look Up in DerivedDataSheet using the grouped version, pick the Passages and add to ModelDetailSheet
@@ -392,66 +315,61 @@ public class TransController {
Set<String> derivedDataPassages = new HashSet<>();
derivedDataPassages.add(modelDetailPassage);
- try{
+ try {
- for (Map<String, String> derivedData : derivedDatas ){
+ for (Map<String, String> derivedData : derivedDatas) {
derivedDataPassages.add(derivedData.get("Passage"));
}
modelDetail.put("Passage", StringUtils.join(derivedDataPassages, ','));
- }catch (Exception e){
+ } catch (Exception e) {
- log.error(modelID+" Found in Model Detail, but not in derived data");
+ log.error(modelID + " Found in Model Detail, but not in derived data");
}
}
-
// Capture Map Keys to use as excel head
xlsHead = new ArrayList<>();
- for (Map.Entry<String, String> entry : pdxModelDetailSheet.get(0).entrySet() ) {
+ for (Map.Entry<String, String> entry : pdxModelDetailSheet.get(0).entrySet()) {
xlsHead.add(entry.getKey());
}
- destination = homeDir+"/Downloads/CRL-PDX_Model_detail.csv";
+ destination = homeDir + "/Downloads/CRL-PDX_Model_detail.csv";
utilityService.writeCsvFile(pdxModelDetailSheet, destination);
- utilityService.writeXLSXFile(pdxModelDetailSheet,"CRL-PDX_Model_detail.xlsx", "PDX_Model_detail");
+ utilityService.writeXLSXFile(pdxModelDetailSheet, "CRL-PDX_Model_detail.xlsx", "PDX_Model_detail");
return pdxModelDetailSheet;
}
-
-
-
@RequestMapping("/move-crl-omic-file")
public Object moveFile() {
-
- String templateFile= System.getProperty("user.home") + "/Downloads/template.xlsx";
- List<Map<String, String>> data = utilityService.serializeExcelDataNoIterator(templateFile,6,4);
+ String templateFile = homeDir + "/Downloads/template.xlsx";
+ List<Map<String, String>> data = utilityService.serializeExcelDataNoIterator(templateFile, 6, 4);
data.remove(data.get(0));
- for (Map<String, String> dData : data){
+ for (Map<String, String> dData : data) {
String sampleID = dData.get("sample ID");
String dataType = dData.get("Molecular Characterization type");
String sourceDir = (dataType.equals("Mutation")) ? "Mutation" : "Copy_Numbers";
- String destinationDir = sourceDir+"2";
+ String destinationDir = sourceDir + "2";
String fileSuffix = (dataType.equals("Mutation")) ? "_mutation_list_pdxfinder.csv" : "_cna_list_pdxfinder.csv";
- String source = System.getProperty("user.home") + "/Downloads/TEMP/"+sourceDir+"/"+sampleID+fileSuffix;
+ String source = homeDir + "/Downloads/TEMP/" + sourceDir + "/" + sampleID + fileSuffix;
- String destination = System.getProperty("user.home") + "/Downloads/TEMP/"+destinationDir+"/"+sampleID+fileSuffix;
+ String destination = homeDir + "/Downloads/TEMP/" + destinationDir + "/" + sampleID + fileSuffix;
- utilityService.moveFile(source,destination);
+ utilityService.moveFile(source, destination);
- log.info("Moving {} File ... ",dataType);
+ log.info("Moving {} File ... ", dataType);
}
@@ -459,24 +377,21 @@ public class TransController {
}
-
-
-
@RequestMapping("/clean-crl-omic-files")
public Object cleanCRLOMICFiles() {
- List<String> csvHead = Arrays.asList("datasource","Model_ID","Sample_ID","sample_origin","Passage","host_strain_name","hgnc_symbol","amino_acid_change","nucleotide_change",
- "consequence","read_depth","Allele_frequency","chromosome","seq_start_position","ref_allele","alt_allele","ucsc_gene_id",
- "ncbi_gene_id","ensembl_gene_id","ensembl_transcript_id","rs_id_Variant","genome_assembly","Platform");
+ List<String> csvHead = Arrays.asList("datasource", "Model_ID", "Sample_ID", "sample_origin", "Passage", "host_strain_name", "hgnc_symbol", "amino_acid_change", "nucleotide_change",
+ "consequence", "read_depth", "Allele_frequency", "chromosome", "seq_start_position", "ref_allele", "alt_allele", "ucsc_gene_id",
+ "ncbi_gene_id", "ensembl_gene_id", "ensembl_transcript_id", "rs_id_Variant", "genome_assembly", "Platform");
- String templateFile= homeDir + "/Downloads/template.xlsx";
- List<Map<String, String>> data = utilityService.serializeExcelDataNoIterator(templateFile,6,4);
+ String templateFile = homeDir + "/Downloads/template.xlsx";
+ List<Map<String, String>> data = utilityService.serializeExcelDataNoIterator(templateFile, 6, 4);
data.remove(data.get(0));
- for (Map<String, String> dData : data){
+ for (Map<String, String> dData : data) {
String sampleID = dData.get("sample ID");
String dataType = dData.get("Molecular Characterization type");
@@ -486,10 +401,10 @@ public class TransController {
String fileSuffix = (dataType.equals("Mutation")) ? "_mutation_list_pdxfinder.csv" : "_cna_list_pdxfinder.csv";
- String destinationDir = sourceDir+"-Final";
+ String destinationDir = sourceDir + "-Final";
- String source = homeDir+"/Downloads/TEMP/"+sourceDir+"/"+sampleID+fileSuffix;
+ String source = homeDir + "/Downloads/TEMP/" + sourceDir + "/" + sampleID + fileSuffix;
log.info(source);
@@ -499,11 +414,11 @@ public class TransController {
String modelID = "";
for (Map<String, String> dataRow : dataList) {
- modelID = "CRL-"+dataRow.get("Model_ID");
+ modelID = "CRL-" + dataRow.get("Model_ID");
dataRow.put("Model_ID", modelID);
}
- String destination = homeDir+"/Downloads/TEMP/"+destinationDir+"/"+modelID+".csv";
+ String destination = homeDir + "/Downloads/TEMP/" + destinationDir + "/" + modelID + ".csv";
utilityService.writeCsvFile(dataList, destination);
@@ -515,11 +430,10 @@ public class TransController {
}
-
@RequestMapping("/get-files")
public Object getAllFiles() {
- String source = homeDir+"/Downloads/TEMP/Mutation/";
+ String source = homeDir + "/Downloads/TEMP/Mutation/";
utilityService.listAllFilesInADirectory(source);
@@ -530,9 +444,9 @@ public class TransController {
@RequestMapping("/get-files-size")
public long whenGetReadableSize_thenCorrect() {
- long directorySize = directorySize(homeDir+"/Downloads/TEMP/Mutation2-Final/");
+ long directorySize = directorySize(homeDir + "/Downloads/TEMP/Mutation2-Final/");
- long oneFileSize = oneFileSize(homeDir+"/Downloads/TEMP/Mutation2-Final/CRL-97.csv");
+ long oneFileSize = oneFileSize(homeDir + "/Downloads/TEMP/Mutation2-Final/CRL-97.csv");
// Time taken divided by file size times everything:
@@ -543,7 +457,7 @@ public class TransController {
public long oneFileSize(String fileLink) {
- File file =new File(fileLink);
+ File file = new File(fileLink);
long fileSize = file.length();
@@ -551,7 +465,7 @@ public class TransController {
}
- public long directorySize(String dirLink){
+ public long directorySize(String dirLink) {
long size = 0;
@@ -563,7 +477,8 @@ public class TransController {
.mapToLong(p -> p.toFile().length())
.sum();
- }catch (Exception e){ }
+ } catch (Exception e) {
+ }
return size;
}
diff --git a/admin/src/main/resources/application.properties b/admin/src/main/resources/application.properties
index c9a2b243b9aeee9a31a2cf76dd0f22d2d4076d4b..562756bc12b9a7b83832ac250d75b36495a1bbfb 100644
--- a/admin/src/main/resources/application.properties
+++ b/admin/src/main/resources/application.properties
@@ -17,7 +17,6 @@ spring.thymeleaf.cache=false
server.port=8081
mappings.diagnosis.file = "";
-
mappings.mappedTermUrl=http://localhost/data/mappings.json
## H2 Config
@@ -26,7 +25,6 @@ spring.h2.console.path=/db-admin/console
spring.h2.console.settings.web-allow-others=true
# NON-GRAPH Datasource Config properties
-#${HOME}
spring.datasource.url=jdbc:h2:${data-dir}/h2-db/data;AUTO_SERVER=true;DB_CLOSE_ON_EXIT=FALSE
spring.datasource.username=neo4j
spring.datasource.password=neo5j
@@ -35,8 +33,11 @@ spring.h2.console.settings.trace=true
## Hibernate Config
spring.jpa.hibernate.ddl-auto=update
+# Enable certain actuator endpoints
+management.endpoint.env.enabled=true
+management.endpoints.web.base-path=/manage
+management.endpoints.web.exposure.include=env
# root directory for local data feeds
data-dir=/nfs/web-hx/mouseinformatics/pdx/finderroot
-#${HOME}/PDXFinder
diff --git a/admin/src/main/resources/static/css/animate.css b/admin/src/main/resources/static/css/animate.css
deleted file mode 100644
index cf3eff8c48cbd0b7ee70212631a9faae0c119d7e..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/css/animate.css
+++ /dev/null
@@ -1,3340 +0,0 @@
-@charset "UTF-8";
-
-/*!
- * animate.css -http://daneden.me/animate
- * Version - 3.5.1
- * Licensed under the MIT license - http://opensource.org/licenses/MIT
- *
- * Copyright (c) 2016 Daniel Eden
- */
-
-.animated {
- -webkit-animation-duration: 1s;
- animation-duration: 1s;
- -webkit-animation-fill-mode: both;
- animation-fill-mode: both;
-}
-
-.animated.infinite {
- -webkit-animation-iteration-count: infinite;
- animation-iteration-count: infinite;
-}
-
-.animated.hinge {
- -webkit-animation-duration: 2s;
- animation-duration: 2s;
-}
-
-.animated.flipOutX,
-.animated.flipOutY,
-.animated.bounceIn,
-.animated.bounceOut {
- -webkit-animation-duration: .75s;
- animation-duration: .75s;
-}
-
-@-webkit-keyframes bounce {
- from, 20%, 53%, 80%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- -webkit-transform: translate3d(0,0,0);
- transform: translate3d(0,0,0);
- }
-
- 40%, 43% {
- -webkit-animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- -webkit-transform: translate3d(0, -30px, 0);
- transform: translate3d(0, -30px, 0);
- }
-
- 70% {
- -webkit-animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- -webkit-transform: translate3d(0, -15px, 0);
- transform: translate3d(0, -15px, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(0,-4px,0);
- transform: translate3d(0,-4px,0);
- }
-}
-
-@keyframes bounce {
- from, 20%, 53%, 80%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- -webkit-transform: translate3d(0,0,0);
- transform: translate3d(0,0,0);
- }
-
- 40%, 43% {
- -webkit-animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- -webkit-transform: translate3d(0, -30px, 0);
- transform: translate3d(0, -30px, 0);
- }
-
- 70% {
- -webkit-animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- animation-timing-function: cubic-bezier(0.755, 0.050, 0.855, 0.060);
- -webkit-transform: translate3d(0, -15px, 0);
- transform: translate3d(0, -15px, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(0,-4px,0);
- transform: translate3d(0,-4px,0);
- }
-}
-
-.bounce {
- -webkit-animation-name: bounce;
- animation-name: bounce;
- -webkit-transform-origin: center bottom;
- transform-origin: center bottom;
-}
-
-@-webkit-keyframes flash {
- from, 50%, to {
- opacity: 1;
- }
-
- 25%, 75% {
- opacity: 0;
- }
-}
-
-@keyframes flash {
- from, 50%, to {
- opacity: 1;
- }
-
- 25%, 75% {
- opacity: 0;
- }
-}
-
-.flash {
- -webkit-animation-name: flash;
- animation-name: flash;
-}
-
-/* originally authored by Nick Pettit - https://github.com/nickpettit/glide */
-
-@-webkit-keyframes pulse {
- from {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-
- 50% {
- -webkit-transform: scale3d(1.05, 1.05, 1.05);
- transform: scale3d(1.05, 1.05, 1.05);
- }
-
- to {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-@keyframes pulse {
- from {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-
- 50% {
- -webkit-transform: scale3d(1.05, 1.05, 1.05);
- transform: scale3d(1.05, 1.05, 1.05);
- }
-
- to {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-.pulse {
- -webkit-animation-name: pulse;
- animation-name: pulse;
-}
-
-@-webkit-keyframes rubberBand {
- from {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-
- 30% {
- -webkit-transform: scale3d(1.25, 0.75, 1);
- transform: scale3d(1.25, 0.75, 1);
- }
-
- 40% {
- -webkit-transform: scale3d(0.75, 1.25, 1);
- transform: scale3d(0.75, 1.25, 1);
- }
-
- 50% {
- -webkit-transform: scale3d(1.15, 0.85, 1);
- transform: scale3d(1.15, 0.85, 1);
- }
-
- 65% {
- -webkit-transform: scale3d(.95, 1.05, 1);
- transform: scale3d(.95, 1.05, 1);
- }
-
- 75% {
- -webkit-transform: scale3d(1.05, .95, 1);
- transform: scale3d(1.05, .95, 1);
- }
-
- to {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-@keyframes rubberBand {
- from {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-
- 30% {
- -webkit-transform: scale3d(1.25, 0.75, 1);
- transform: scale3d(1.25, 0.75, 1);
- }
-
- 40% {
- -webkit-transform: scale3d(0.75, 1.25, 1);
- transform: scale3d(0.75, 1.25, 1);
- }
-
- 50% {
- -webkit-transform: scale3d(1.15, 0.85, 1);
- transform: scale3d(1.15, 0.85, 1);
- }
-
- 65% {
- -webkit-transform: scale3d(.95, 1.05, 1);
- transform: scale3d(.95, 1.05, 1);
- }
-
- 75% {
- -webkit-transform: scale3d(1.05, .95, 1);
- transform: scale3d(1.05, .95, 1);
- }
-
- to {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-.rubberBand {
- -webkit-animation-name: rubberBand;
- animation-name: rubberBand;
-}
-
-@-webkit-keyframes shake {
- from, to {
- -webkit-transform: translate3d(0, 0, 0);
- transform: translate3d(0, 0, 0);
- }
-
- 10%, 30%, 50%, 70%, 90% {
- -webkit-transform: translate3d(-10px, 0, 0);
- transform: translate3d(-10px, 0, 0);
- }
-
- 20%, 40%, 60%, 80% {
- -webkit-transform: translate3d(10px, 0, 0);
- transform: translate3d(10px, 0, 0);
- }
-}
-
-@keyframes shake {
- from, to {
- -webkit-transform: translate3d(0, 0, 0);
- transform: translate3d(0, 0, 0);
- }
-
- 10%, 30%, 50%, 70%, 90% {
- -webkit-transform: translate3d(-10px, 0, 0);
- transform: translate3d(-10px, 0, 0);
- }
-
- 20%, 40%, 60%, 80% {
- -webkit-transform: translate3d(10px, 0, 0);
- transform: translate3d(10px, 0, 0);
- }
-}
-
-.shake {
- -webkit-animation-name: shake;
- animation-name: shake;
-}
-
-@-webkit-keyframes headShake {
- 0% {
- -webkit-transform: translateX(0);
- transform: translateX(0);
- }
-
- 6.5% {
- -webkit-transform: translateX(-6px) rotateY(-9deg);
- transform: translateX(-6px) rotateY(-9deg);
- }
-
- 18.5% {
- -webkit-transform: translateX(5px) rotateY(7deg);
- transform: translateX(5px) rotateY(7deg);
- }
-
- 31.5% {
- -webkit-transform: translateX(-3px) rotateY(-5deg);
- transform: translateX(-3px) rotateY(-5deg);
- }
-
- 43.5% {
- -webkit-transform: translateX(2px) rotateY(3deg);
- transform: translateX(2px) rotateY(3deg);
- }
-
- 50% {
- -webkit-transform: translateX(0);
- transform: translateX(0);
- }
-}
-
-@keyframes headShake {
- 0% {
- -webkit-transform: translateX(0);
- transform: translateX(0);
- }
-
- 6.5% {
- -webkit-transform: translateX(-6px) rotateY(-9deg);
- transform: translateX(-6px) rotateY(-9deg);
- }
-
- 18.5% {
- -webkit-transform: translateX(5px) rotateY(7deg);
- transform: translateX(5px) rotateY(7deg);
- }
-
- 31.5% {
- -webkit-transform: translateX(-3px) rotateY(-5deg);
- transform: translateX(-3px) rotateY(-5deg);
- }
-
- 43.5% {
- -webkit-transform: translateX(2px) rotateY(3deg);
- transform: translateX(2px) rotateY(3deg);
- }
-
- 50% {
- -webkit-transform: translateX(0);
- transform: translateX(0);
- }
-}
-
-.headShake {
- -webkit-animation-timing-function: ease-in-out;
- animation-timing-function: ease-in-out;
- -webkit-animation-name: headShake;
- animation-name: headShake;
-}
-
-@-webkit-keyframes swing {
- 20% {
- -webkit-transform: rotate3d(0, 0, 1, 15deg);
- transform: rotate3d(0, 0, 1, 15deg);
- }
-
- 40% {
- -webkit-transform: rotate3d(0, 0, 1, -10deg);
- transform: rotate3d(0, 0, 1, -10deg);
- }
-
- 60% {
- -webkit-transform: rotate3d(0, 0, 1, 5deg);
- transform: rotate3d(0, 0, 1, 5deg);
- }
-
- 80% {
- -webkit-transform: rotate3d(0, 0, 1, -5deg);
- transform: rotate3d(0, 0, 1, -5deg);
- }
-
- to {
- -webkit-transform: rotate3d(0, 0, 1, 0deg);
- transform: rotate3d(0, 0, 1, 0deg);
- }
-}
-
-@keyframes swing {
- 20% {
- -webkit-transform: rotate3d(0, 0, 1, 15deg);
- transform: rotate3d(0, 0, 1, 15deg);
- }
-
- 40% {
- -webkit-transform: rotate3d(0, 0, 1, -10deg);
- transform: rotate3d(0, 0, 1, -10deg);
- }
-
- 60% {
- -webkit-transform: rotate3d(0, 0, 1, 5deg);
- transform: rotate3d(0, 0, 1, 5deg);
- }
-
- 80% {
- -webkit-transform: rotate3d(0, 0, 1, -5deg);
- transform: rotate3d(0, 0, 1, -5deg);
- }
-
- to {
- -webkit-transform: rotate3d(0, 0, 1, 0deg);
- transform: rotate3d(0, 0, 1, 0deg);
- }
-}
-
-.swing {
- -webkit-transform-origin: top center;
- transform-origin: top center;
- -webkit-animation-name: swing;
- animation-name: swing;
-}
-
-@-webkit-keyframes tada {
- from {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-
- 10%, 20% {
- -webkit-transform: scale3d(.9, .9, .9) rotate3d(0, 0, 1, -3deg);
- transform: scale3d(.9, .9, .9) rotate3d(0, 0, 1, -3deg);
- }
-
- 30%, 50%, 70%, 90% {
- -webkit-transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, 3deg);
- transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, 3deg);
- }
-
- 40%, 60%, 80% {
- -webkit-transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, -3deg);
- transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, -3deg);
- }
-
- to {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-@keyframes tada {
- from {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-
- 10%, 20% {
- -webkit-transform: scale3d(.9, .9, .9) rotate3d(0, 0, 1, -3deg);
- transform: scale3d(.9, .9, .9) rotate3d(0, 0, 1, -3deg);
- }
-
- 30%, 50%, 70%, 90% {
- -webkit-transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, 3deg);
- transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, 3deg);
- }
-
- 40%, 60%, 80% {
- -webkit-transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, -3deg);
- transform: scale3d(1.1, 1.1, 1.1) rotate3d(0, 0, 1, -3deg);
- }
-
- to {
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-.tada {
- -webkit-animation-name: tada;
- animation-name: tada;
-}
-
-/* originally authored by Nick Pettit - https://github.com/nickpettit/glide */
-
-@-webkit-keyframes wobble {
- from {
- -webkit-transform: none;
- transform: none;
- }
-
- 15% {
- -webkit-transform: translate3d(-25%, 0, 0) rotate3d(0, 0, 1, -5deg);
- transform: translate3d(-25%, 0, 0) rotate3d(0, 0, 1, -5deg);
- }
-
- 30% {
- -webkit-transform: translate3d(20%, 0, 0) rotate3d(0, 0, 1, 3deg);
- transform: translate3d(20%, 0, 0) rotate3d(0, 0, 1, 3deg);
- }
-
- 45% {
- -webkit-transform: translate3d(-15%, 0, 0) rotate3d(0, 0, 1, -3deg);
- transform: translate3d(-15%, 0, 0) rotate3d(0, 0, 1, -3deg);
- }
-
- 60% {
- -webkit-transform: translate3d(10%, 0, 0) rotate3d(0, 0, 1, 2deg);
- transform: translate3d(10%, 0, 0) rotate3d(0, 0, 1, 2deg);
- }
-
- 75% {
- -webkit-transform: translate3d(-5%, 0, 0) rotate3d(0, 0, 1, -1deg);
- transform: translate3d(-5%, 0, 0) rotate3d(0, 0, 1, -1deg);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes wobble {
- from {
- -webkit-transform: none;
- transform: none;
- }
-
- 15% {
- -webkit-transform: translate3d(-25%, 0, 0) rotate3d(0, 0, 1, -5deg);
- transform: translate3d(-25%, 0, 0) rotate3d(0, 0, 1, -5deg);
- }
-
- 30% {
- -webkit-transform: translate3d(20%, 0, 0) rotate3d(0, 0, 1, 3deg);
- transform: translate3d(20%, 0, 0) rotate3d(0, 0, 1, 3deg);
- }
-
- 45% {
- -webkit-transform: translate3d(-15%, 0, 0) rotate3d(0, 0, 1, -3deg);
- transform: translate3d(-15%, 0, 0) rotate3d(0, 0, 1, -3deg);
- }
-
- 60% {
- -webkit-transform: translate3d(10%, 0, 0) rotate3d(0, 0, 1, 2deg);
- transform: translate3d(10%, 0, 0) rotate3d(0, 0, 1, 2deg);
- }
-
- 75% {
- -webkit-transform: translate3d(-5%, 0, 0) rotate3d(0, 0, 1, -1deg);
- transform: translate3d(-5%, 0, 0) rotate3d(0, 0, 1, -1deg);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.wobble {
- -webkit-animation-name: wobble;
- animation-name: wobble;
-}
-
-@-webkit-keyframes jello {
- from, 11.1%, to {
- -webkit-transform: none;
- transform: none;
- }
-
- 22.2% {
- -webkit-transform: skewX(-12.5deg) skewY(-12.5deg);
- transform: skewX(-12.5deg) skewY(-12.5deg);
- }
-
- 33.3% {
- -webkit-transform: skewX(6.25deg) skewY(6.25deg);
- transform: skewX(6.25deg) skewY(6.25deg);
- }
-
- 44.4% {
- -webkit-transform: skewX(-3.125deg) skewY(-3.125deg);
- transform: skewX(-3.125deg) skewY(-3.125deg);
- }
-
- 55.5% {
- -webkit-transform: skewX(1.5625deg) skewY(1.5625deg);
- transform: skewX(1.5625deg) skewY(1.5625deg);
- }
-
- 66.6% {
- -webkit-transform: skewX(-0.78125deg) skewY(-0.78125deg);
- transform: skewX(-0.78125deg) skewY(-0.78125deg);
- }
-
- 77.7% {
- -webkit-transform: skewX(0.390625deg) skewY(0.390625deg);
- transform: skewX(0.390625deg) skewY(0.390625deg);
- }
-
- 88.8% {
- -webkit-transform: skewX(-0.1953125deg) skewY(-0.1953125deg);
- transform: skewX(-0.1953125deg) skewY(-0.1953125deg);
- }
-}
-
-@keyframes jello {
- from, 11.1%, to {
- -webkit-transform: none;
- transform: none;
- }
-
- 22.2% {
- -webkit-transform: skewX(-12.5deg) skewY(-12.5deg);
- transform: skewX(-12.5deg) skewY(-12.5deg);
- }
-
- 33.3% {
- -webkit-transform: skewX(6.25deg) skewY(6.25deg);
- transform: skewX(6.25deg) skewY(6.25deg);
- }
-
- 44.4% {
- -webkit-transform: skewX(-3.125deg) skewY(-3.125deg);
- transform: skewX(-3.125deg) skewY(-3.125deg);
- }
-
- 55.5% {
- -webkit-transform: skewX(1.5625deg) skewY(1.5625deg);
- transform: skewX(1.5625deg) skewY(1.5625deg);
- }
-
- 66.6% {
- -webkit-transform: skewX(-0.78125deg) skewY(-0.78125deg);
- transform: skewX(-0.78125deg) skewY(-0.78125deg);
- }
-
- 77.7% {
- -webkit-transform: skewX(0.390625deg) skewY(0.390625deg);
- transform: skewX(0.390625deg) skewY(0.390625deg);
- }
-
- 88.8% {
- -webkit-transform: skewX(-0.1953125deg) skewY(-0.1953125deg);
- transform: skewX(-0.1953125deg) skewY(-0.1953125deg);
- }
-}
-
-.jello {
- -webkit-animation-name: jello;
- animation-name: jello;
- -webkit-transform-origin: center;
- transform-origin: center;
-}
-
-@-webkit-keyframes bounceIn {
- from, 20%, 40%, 60%, 80%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- 0% {
- opacity: 0;
- -webkit-transform: scale3d(.3, .3, .3);
- transform: scale3d(.3, .3, .3);
- }
-
- 20% {
- -webkit-transform: scale3d(1.1, 1.1, 1.1);
- transform: scale3d(1.1, 1.1, 1.1);
- }
-
- 40% {
- -webkit-transform: scale3d(.9, .9, .9);
- transform: scale3d(.9, .9, .9);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(1.03, 1.03, 1.03);
- transform: scale3d(1.03, 1.03, 1.03);
- }
-
- 80% {
- -webkit-transform: scale3d(.97, .97, .97);
- transform: scale3d(.97, .97, .97);
- }
-
- to {
- opacity: 1;
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-@keyframes bounceIn {
- from, 20%, 40%, 60%, 80%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- 0% {
- opacity: 0;
- -webkit-transform: scale3d(.3, .3, .3);
- transform: scale3d(.3, .3, .3);
- }
-
- 20% {
- -webkit-transform: scale3d(1.1, 1.1, 1.1);
- transform: scale3d(1.1, 1.1, 1.1);
- }
-
- 40% {
- -webkit-transform: scale3d(.9, .9, .9);
- transform: scale3d(.9, .9, .9);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(1.03, 1.03, 1.03);
- transform: scale3d(1.03, 1.03, 1.03);
- }
-
- 80% {
- -webkit-transform: scale3d(.97, .97, .97);
- transform: scale3d(.97, .97, .97);
- }
-
- to {
- opacity: 1;
- -webkit-transform: scale3d(1, 1, 1);
- transform: scale3d(1, 1, 1);
- }
-}
-
-.bounceIn {
- -webkit-animation-name: bounceIn;
- animation-name: bounceIn;
-}
-
-@-webkit-keyframes bounceInDown {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- 0% {
- opacity: 0;
- -webkit-transform: translate3d(0, -3000px, 0);
- transform: translate3d(0, -3000px, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(0, 25px, 0);
- transform: translate3d(0, 25px, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(0, -10px, 0);
- transform: translate3d(0, -10px, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(0, 5px, 0);
- transform: translate3d(0, 5px, 0);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes bounceInDown {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- 0% {
- opacity: 0;
- -webkit-transform: translate3d(0, -3000px, 0);
- transform: translate3d(0, -3000px, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(0, 25px, 0);
- transform: translate3d(0, 25px, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(0, -10px, 0);
- transform: translate3d(0, -10px, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(0, 5px, 0);
- transform: translate3d(0, 5px, 0);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.bounceInDown {
- -webkit-animation-name: bounceInDown;
- animation-name: bounceInDown;
-}
-
-@-webkit-keyframes bounceInLeft {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- 0% {
- opacity: 0;
- -webkit-transform: translate3d(-3000px, 0, 0);
- transform: translate3d(-3000px, 0, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(25px, 0, 0);
- transform: translate3d(25px, 0, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(-10px, 0, 0);
- transform: translate3d(-10px, 0, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(5px, 0, 0);
- transform: translate3d(5px, 0, 0);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes bounceInLeft {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- 0% {
- opacity: 0;
- -webkit-transform: translate3d(-3000px, 0, 0);
- transform: translate3d(-3000px, 0, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(25px, 0, 0);
- transform: translate3d(25px, 0, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(-10px, 0, 0);
- transform: translate3d(-10px, 0, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(5px, 0, 0);
- transform: translate3d(5px, 0, 0);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.bounceInLeft {
- -webkit-animation-name: bounceInLeft;
- animation-name: bounceInLeft;
-}
-
-@-webkit-keyframes bounceInRight {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- from {
- opacity: 0;
- -webkit-transform: translate3d(3000px, 0, 0);
- transform: translate3d(3000px, 0, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(-25px, 0, 0);
- transform: translate3d(-25px, 0, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(10px, 0, 0);
- transform: translate3d(10px, 0, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(-5px, 0, 0);
- transform: translate3d(-5px, 0, 0);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes bounceInRight {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- from {
- opacity: 0;
- -webkit-transform: translate3d(3000px, 0, 0);
- transform: translate3d(3000px, 0, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(-25px, 0, 0);
- transform: translate3d(-25px, 0, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(10px, 0, 0);
- transform: translate3d(10px, 0, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(-5px, 0, 0);
- transform: translate3d(-5px, 0, 0);
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.bounceInRight {
- -webkit-animation-name: bounceInRight;
- animation-name: bounceInRight;
-}
-
-@-webkit-keyframes bounceInUp {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, 3000px, 0);
- transform: translate3d(0, 3000px, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(0, -20px, 0);
- transform: translate3d(0, -20px, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(0, 10px, 0);
- transform: translate3d(0, 10px, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(0, -5px, 0);
- transform: translate3d(0, -5px, 0);
- }
-
- to {
- -webkit-transform: translate3d(0, 0, 0);
- transform: translate3d(0, 0, 0);
- }
-}
-
-@keyframes bounceInUp {
- from, 60%, 75%, 90%, to {
- -webkit-animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- animation-timing-function: cubic-bezier(0.215, 0.610, 0.355, 1.000);
- }
-
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, 3000px, 0);
- transform: translate3d(0, 3000px, 0);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: translate3d(0, -20px, 0);
- transform: translate3d(0, -20px, 0);
- }
-
- 75% {
- -webkit-transform: translate3d(0, 10px, 0);
- transform: translate3d(0, 10px, 0);
- }
-
- 90% {
- -webkit-transform: translate3d(0, -5px, 0);
- transform: translate3d(0, -5px, 0);
- }
-
- to {
- -webkit-transform: translate3d(0, 0, 0);
- transform: translate3d(0, 0, 0);
- }
-}
-
-.bounceInUp {
- -webkit-animation-name: bounceInUp;
- animation-name: bounceInUp;
-}
-
-@-webkit-keyframes bounceOut {
- 20% {
- -webkit-transform: scale3d(.9, .9, .9);
- transform: scale3d(.9, .9, .9);
- }
-
- 50%, 55% {
- opacity: 1;
- -webkit-transform: scale3d(1.1, 1.1, 1.1);
- transform: scale3d(1.1, 1.1, 1.1);
- }
-
- to {
- opacity: 0;
- -webkit-transform: scale3d(.3, .3, .3);
- transform: scale3d(.3, .3, .3);
- }
-}
-
-@keyframes bounceOut {
- 20% {
- -webkit-transform: scale3d(.9, .9, .9);
- transform: scale3d(.9, .9, .9);
- }
-
- 50%, 55% {
- opacity: 1;
- -webkit-transform: scale3d(1.1, 1.1, 1.1);
- transform: scale3d(1.1, 1.1, 1.1);
- }
-
- to {
- opacity: 0;
- -webkit-transform: scale3d(.3, .3, .3);
- transform: scale3d(.3, .3, .3);
- }
-}
-
-.bounceOut {
- -webkit-animation-name: bounceOut;
- animation-name: bounceOut;
-}
-
-@-webkit-keyframes bounceOutDown {
- 20% {
- -webkit-transform: translate3d(0, 10px, 0);
- transform: translate3d(0, 10px, 0);
- }
-
- 40%, 45% {
- opacity: 1;
- -webkit-transform: translate3d(0, -20px, 0);
- transform: translate3d(0, -20px, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, 2000px, 0);
- transform: translate3d(0, 2000px, 0);
- }
-}
-
-@keyframes bounceOutDown {
- 20% {
- -webkit-transform: translate3d(0, 10px, 0);
- transform: translate3d(0, 10px, 0);
- }
-
- 40%, 45% {
- opacity: 1;
- -webkit-transform: translate3d(0, -20px, 0);
- transform: translate3d(0, -20px, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, 2000px, 0);
- transform: translate3d(0, 2000px, 0);
- }
-}
-
-.bounceOutDown {
- -webkit-animation-name: bounceOutDown;
- animation-name: bounceOutDown;
-}
-
-@-webkit-keyframes bounceOutLeft {
- 20% {
- opacity: 1;
- -webkit-transform: translate3d(20px, 0, 0);
- transform: translate3d(20px, 0, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(-2000px, 0, 0);
- transform: translate3d(-2000px, 0, 0);
- }
-}
-
-@keyframes bounceOutLeft {
- 20% {
- opacity: 1;
- -webkit-transform: translate3d(20px, 0, 0);
- transform: translate3d(20px, 0, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(-2000px, 0, 0);
- transform: translate3d(-2000px, 0, 0);
- }
-}
-
-.bounceOutLeft {
- -webkit-animation-name: bounceOutLeft;
- animation-name: bounceOutLeft;
-}
-
-@-webkit-keyframes bounceOutRight {
- 20% {
- opacity: 1;
- -webkit-transform: translate3d(-20px, 0, 0);
- transform: translate3d(-20px, 0, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(2000px, 0, 0);
- transform: translate3d(2000px, 0, 0);
- }
-}
-
-@keyframes bounceOutRight {
- 20% {
- opacity: 1;
- -webkit-transform: translate3d(-20px, 0, 0);
- transform: translate3d(-20px, 0, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(2000px, 0, 0);
- transform: translate3d(2000px, 0, 0);
- }
-}
-
-.bounceOutRight {
- -webkit-animation-name: bounceOutRight;
- animation-name: bounceOutRight;
-}
-
-@-webkit-keyframes bounceOutUp {
- 20% {
- -webkit-transform: translate3d(0, -10px, 0);
- transform: translate3d(0, -10px, 0);
- }
-
- 40%, 45% {
- opacity: 1;
- -webkit-transform: translate3d(0, 20px, 0);
- transform: translate3d(0, 20px, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, -2000px, 0);
- transform: translate3d(0, -2000px, 0);
- }
-}
-
-@keyframes bounceOutUp {
- 20% {
- -webkit-transform: translate3d(0, -10px, 0);
- transform: translate3d(0, -10px, 0);
- }
-
- 40%, 45% {
- opacity: 1;
- -webkit-transform: translate3d(0, 20px, 0);
- transform: translate3d(0, 20px, 0);
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, -2000px, 0);
- transform: translate3d(0, -2000px, 0);
- }
-}
-
-.bounceOutUp {
- -webkit-animation-name: bounceOutUp;
- animation-name: bounceOutUp;
-}
-
-@-webkit-keyframes fadeIn {
- from {
- opacity: 0;
- }
-
- to {
- opacity: 1;
- }
-}
-
-@keyframes fadeIn {
- from {
- opacity: 0;
- }
-
- to {
- opacity: 1;
- }
-}
-
-.fadeIn {
- -webkit-animation-name: fadeIn;
- animation-name: fadeIn;
-}
-
-@-webkit-keyframes fadeInDown {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, -100%, 0);
- transform: translate3d(0, -100%, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInDown {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, -100%, 0);
- transform: translate3d(0, -100%, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInDown {
- -webkit-animation-name: fadeInDown;
- animation-name: fadeInDown;
-}
-
-@-webkit-keyframes fadeInDownBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, -2000px, 0);
- transform: translate3d(0, -2000px, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInDownBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, -2000px, 0);
- transform: translate3d(0, -2000px, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInDownBig {
- -webkit-animation-name: fadeInDownBig;
- animation-name: fadeInDownBig;
-}
-
-@-webkit-keyframes fadeInLeft {
- from {
- opacity: 0;
- -webkit-transform: translate3d(-100%, 0, 0);
- transform: translate3d(-100%, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInLeft {
- from {
- opacity: 0;
- -webkit-transform: translate3d(-100%, 0, 0);
- transform: translate3d(-100%, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInLeft {
- -webkit-animation-name: fadeInLeft;
- animation-name: fadeInLeft;
-}
-
-@-webkit-keyframes fadeInLeftBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(-2000px, 0, 0);
- transform: translate3d(-2000px, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInLeftBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(-2000px, 0, 0);
- transform: translate3d(-2000px, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInLeftBig {
- -webkit-animation-name: fadeInLeftBig;
- animation-name: fadeInLeftBig;
-}
-
-@-webkit-keyframes fadeInRight {
- from {
- opacity: 0;
- -webkit-transform: translate3d(100%, 0, 0);
- transform: translate3d(100%, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInRight {
- from {
- opacity: 0;
- -webkit-transform: translate3d(100%, 0, 0);
- transform: translate3d(100%, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInRight {
- -webkit-animation-name: fadeInRight;
- animation-name: fadeInRight;
-}
-
-@-webkit-keyframes fadeInRightBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(2000px, 0, 0);
- transform: translate3d(2000px, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInRightBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(2000px, 0, 0);
- transform: translate3d(2000px, 0, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInRightBig {
- -webkit-animation-name: fadeInRightBig;
- animation-name: fadeInRightBig;
-}
-
-@-webkit-keyframes fadeInUp {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, 100%, 0);
- transform: translate3d(0, 100%, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInUp {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, 100%, 0);
- transform: translate3d(0, 100%, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInUp {
- -webkit-animation-name: fadeInUp;
- animation-name: fadeInUp;
-}
-
-@-webkit-keyframes fadeInUpBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, 2000px, 0);
- transform: translate3d(0, 2000px, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes fadeInUpBig {
- from {
- opacity: 0;
- -webkit-transform: translate3d(0, 2000px, 0);
- transform: translate3d(0, 2000px, 0);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.fadeInUpBig {
- -webkit-animation-name: fadeInUpBig;
- animation-name: fadeInUpBig;
-}
-
-@-webkit-keyframes fadeOut {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- }
-}
-
-@keyframes fadeOut {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- }
-}
-
-.fadeOut {
- -webkit-animation-name: fadeOut;
- animation-name: fadeOut;
-}
-
-@-webkit-keyframes fadeOutDown {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, 100%, 0);
- transform: translate3d(0, 100%, 0);
- }
-}
-
-@keyframes fadeOutDown {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, 100%, 0);
- transform: translate3d(0, 100%, 0);
- }
-}
-
-.fadeOutDown {
- -webkit-animation-name: fadeOutDown;
- animation-name: fadeOutDown;
-}
-
-@-webkit-keyframes fadeOutDownBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, 2000px, 0);
- transform: translate3d(0, 2000px, 0);
- }
-}
-
-@keyframes fadeOutDownBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, 2000px, 0);
- transform: translate3d(0, 2000px, 0);
- }
-}
-
-.fadeOutDownBig {
- -webkit-animation-name: fadeOutDownBig;
- animation-name: fadeOutDownBig;
-}
-
-@-webkit-keyframes fadeOutLeft {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(-100%, 0, 0);
- transform: translate3d(-100%, 0, 0);
- }
-}
-
-@keyframes fadeOutLeft {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(-100%, 0, 0);
- transform: translate3d(-100%, 0, 0);
- }
-}
-
-.fadeOutLeft {
- -webkit-animation-name: fadeOutLeft;
- animation-name: fadeOutLeft;
-}
-
-@-webkit-keyframes fadeOutLeftBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(-2000px, 0, 0);
- transform: translate3d(-2000px, 0, 0);
- }
-}
-
-@keyframes fadeOutLeftBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(-2000px, 0, 0);
- transform: translate3d(-2000px, 0, 0);
- }
-}
-
-.fadeOutLeftBig {
- -webkit-animation-name: fadeOutLeftBig;
- animation-name: fadeOutLeftBig;
-}
-
-@-webkit-keyframes fadeOutRight {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(100%, 0, 0);
- transform: translate3d(100%, 0, 0);
- }
-}
-
-@keyframes fadeOutRight {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(100%, 0, 0);
- transform: translate3d(100%, 0, 0);
- }
-}
-
-.fadeOutRight {
- -webkit-animation-name: fadeOutRight;
- animation-name: fadeOutRight;
-}
-
-@-webkit-keyframes fadeOutRightBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(2000px, 0, 0);
- transform: translate3d(2000px, 0, 0);
- }
-}
-
-@keyframes fadeOutRightBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(2000px, 0, 0);
- transform: translate3d(2000px, 0, 0);
- }
-}
-
-.fadeOutRightBig {
- -webkit-animation-name: fadeOutRightBig;
- animation-name: fadeOutRightBig;
-}
-
-@-webkit-keyframes fadeOutUp {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, -100%, 0);
- transform: translate3d(0, -100%, 0);
- }
-}
-
-@keyframes fadeOutUp {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, -100%, 0);
- transform: translate3d(0, -100%, 0);
- }
-}
-
-.fadeOutUp {
- -webkit-animation-name: fadeOutUp;
- animation-name: fadeOutUp;
-}
-
-@-webkit-keyframes fadeOutUpBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, -2000px, 0);
- transform: translate3d(0, -2000px, 0);
- }
-}
-
-@keyframes fadeOutUpBig {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(0, -2000px, 0);
- transform: translate3d(0, -2000px, 0);
- }
-}
-
-.fadeOutUpBig {
- -webkit-animation-name: fadeOutUpBig;
- animation-name: fadeOutUpBig;
-}
-
-@-webkit-keyframes flip {
- from {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -360deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -360deg);
- -webkit-animation-timing-function: ease-out;
- animation-timing-function: ease-out;
- }
-
- 40% {
- -webkit-transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -190deg);
- transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -190deg);
- -webkit-animation-timing-function: ease-out;
- animation-timing-function: ease-out;
- }
-
- 50% {
- -webkit-transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -170deg);
- transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -170deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- 80% {
- -webkit-transform: perspective(400px) scale3d(.95, .95, .95);
- transform: perspective(400px) scale3d(.95, .95, .95);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- to {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-}
-
-@keyframes flip {
- from {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -360deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -360deg);
- -webkit-animation-timing-function: ease-out;
- animation-timing-function: ease-out;
- }
-
- 40% {
- -webkit-transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -190deg);
- transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -190deg);
- -webkit-animation-timing-function: ease-out;
- animation-timing-function: ease-out;
- }
-
- 50% {
- -webkit-transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -170deg);
- transform: perspective(400px) translate3d(0, 0, 150px) rotate3d(0, 1, 0, -170deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- 80% {
- -webkit-transform: perspective(400px) scale3d(.95, .95, .95);
- transform: perspective(400px) scale3d(.95, .95, .95);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- to {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-}
-
-.animated.flip {
- -webkit-backface-visibility: visible;
- backface-visibility: visible;
- -webkit-animation-name: flip;
- animation-name: flip;
-}
-
-@-webkit-keyframes flipInX {
- from {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- opacity: 0;
- }
-
- 40% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- 60% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, 10deg);
- transform: perspective(400px) rotate3d(1, 0, 0, 10deg);
- opacity: 1;
- }
-
- 80% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, -5deg);
- transform: perspective(400px) rotate3d(1, 0, 0, -5deg);
- }
-
- to {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-}
-
-@keyframes flipInX {
- from {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- opacity: 0;
- }
-
- 40% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- 60% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, 10deg);
- transform: perspective(400px) rotate3d(1, 0, 0, 10deg);
- opacity: 1;
- }
-
- 80% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, -5deg);
- transform: perspective(400px) rotate3d(1, 0, 0, -5deg);
- }
-
- to {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-}
-
-.flipInX {
- -webkit-backface-visibility: visible !important;
- backface-visibility: visible !important;
- -webkit-animation-name: flipInX;
- animation-name: flipInX;
-}
-
-@-webkit-keyframes flipInY {
- from {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- opacity: 0;
- }
-
- 40% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -20deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -20deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- 60% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, 10deg);
- transform: perspective(400px) rotate3d(0, 1, 0, 10deg);
- opacity: 1;
- }
-
- 80% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -5deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -5deg);
- }
-
- to {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-}
-
-@keyframes flipInY {
- from {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- opacity: 0;
- }
-
- 40% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -20deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -20deg);
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
- }
-
- 60% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, 10deg);
- transform: perspective(400px) rotate3d(0, 1, 0, 10deg);
- opacity: 1;
- }
-
- 80% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -5deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -5deg);
- }
-
- to {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-}
-
-.flipInY {
- -webkit-backface-visibility: visible !important;
- backface-visibility: visible !important;
- -webkit-animation-name: flipInY;
- animation-name: flipInY;
-}
-
-@-webkit-keyframes flipOutX {
- from {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-
- 30% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- opacity: 1;
- }
-
- to {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- opacity: 0;
- }
-}
-
-@keyframes flipOutX {
- from {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-
- 30% {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- transform: perspective(400px) rotate3d(1, 0, 0, -20deg);
- opacity: 1;
- }
-
- to {
- -webkit-transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- transform: perspective(400px) rotate3d(1, 0, 0, 90deg);
- opacity: 0;
- }
-}
-
-.flipOutX {
- -webkit-animation-name: flipOutX;
- animation-name: flipOutX;
- -webkit-backface-visibility: visible !important;
- backface-visibility: visible !important;
-}
-
-@-webkit-keyframes flipOutY {
- from {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-
- 30% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -15deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -15deg);
- opacity: 1;
- }
-
- to {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- opacity: 0;
- }
-}
-
-@keyframes flipOutY {
- from {
- -webkit-transform: perspective(400px);
- transform: perspective(400px);
- }
-
- 30% {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, -15deg);
- transform: perspective(400px) rotate3d(0, 1, 0, -15deg);
- opacity: 1;
- }
-
- to {
- -webkit-transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- transform: perspective(400px) rotate3d(0, 1, 0, 90deg);
- opacity: 0;
- }
-}
-
-.flipOutY {
- -webkit-backface-visibility: visible !important;
- backface-visibility: visible !important;
- -webkit-animation-name: flipOutY;
- animation-name: flipOutY;
-}
-
-@-webkit-keyframes lightSpeedIn {
- from {
- -webkit-transform: translate3d(100%, 0, 0) skewX(-30deg);
- transform: translate3d(100%, 0, 0) skewX(-30deg);
- opacity: 0;
- }
-
- 60% {
- -webkit-transform: skewX(20deg);
- transform: skewX(20deg);
- opacity: 1;
- }
-
- 80% {
- -webkit-transform: skewX(-5deg);
- transform: skewX(-5deg);
- opacity: 1;
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-@keyframes lightSpeedIn {
- from {
- -webkit-transform: translate3d(100%, 0, 0) skewX(-30deg);
- transform: translate3d(100%, 0, 0) skewX(-30deg);
- opacity: 0;
- }
-
- 60% {
- -webkit-transform: skewX(20deg);
- transform: skewX(20deg);
- opacity: 1;
- }
-
- 80% {
- -webkit-transform: skewX(-5deg);
- transform: skewX(-5deg);
- opacity: 1;
- }
-
- to {
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-.lightSpeedIn {
- -webkit-animation-name: lightSpeedIn;
- animation-name: lightSpeedIn;
- -webkit-animation-timing-function: ease-out;
- animation-timing-function: ease-out;
-}
-
-@-webkit-keyframes lightSpeedOut {
- from {
- opacity: 1;
- }
-
- to {
- -webkit-transform: translate3d(100%, 0, 0) skewX(30deg);
- transform: translate3d(100%, 0, 0) skewX(30deg);
- opacity: 0;
- }
-}
-
-@keyframes lightSpeedOut {
- from {
- opacity: 1;
- }
-
- to {
- -webkit-transform: translate3d(100%, 0, 0) skewX(30deg);
- transform: translate3d(100%, 0, 0) skewX(30deg);
- opacity: 0;
- }
-}
-
-.lightSpeedOut {
- -webkit-animation-name: lightSpeedOut;
- animation-name: lightSpeedOut;
- -webkit-animation-timing-function: ease-in;
- animation-timing-function: ease-in;
-}
-
-@-webkit-keyframes rotateIn {
- from {
- -webkit-transform-origin: center;
- transform-origin: center;
- -webkit-transform: rotate3d(0, 0, 1, -200deg);
- transform: rotate3d(0, 0, 1, -200deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: center;
- transform-origin: center;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-@keyframes rotateIn {
- from {
- -webkit-transform-origin: center;
- transform-origin: center;
- -webkit-transform: rotate3d(0, 0, 1, -200deg);
- transform: rotate3d(0, 0, 1, -200deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: center;
- transform-origin: center;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-.rotateIn {
- -webkit-animation-name: rotateIn;
- animation-name: rotateIn;
-}
-
-@-webkit-keyframes rotateInDownLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, -45deg);
- transform: rotate3d(0, 0, 1, -45deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-@keyframes rotateInDownLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, -45deg);
- transform: rotate3d(0, 0, 1, -45deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-.rotateInDownLeft {
- -webkit-animation-name: rotateInDownLeft;
- animation-name: rotateInDownLeft;
-}
-
-@-webkit-keyframes rotateInDownRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, 45deg);
- transform: rotate3d(0, 0, 1, 45deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-@keyframes rotateInDownRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, 45deg);
- transform: rotate3d(0, 0, 1, 45deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-.rotateInDownRight {
- -webkit-animation-name: rotateInDownRight;
- animation-name: rotateInDownRight;
-}
-
-@-webkit-keyframes rotateInUpLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, 45deg);
- transform: rotate3d(0, 0, 1, 45deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-@keyframes rotateInUpLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, 45deg);
- transform: rotate3d(0, 0, 1, 45deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-.rotateInUpLeft {
- -webkit-animation-name: rotateInUpLeft;
- animation-name: rotateInUpLeft;
-}
-
-@-webkit-keyframes rotateInUpRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, -90deg);
- transform: rotate3d(0, 0, 1, -90deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-@keyframes rotateInUpRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, -90deg);
- transform: rotate3d(0, 0, 1, -90deg);
- opacity: 0;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: none;
- transform: none;
- opacity: 1;
- }
-}
-
-.rotateInUpRight {
- -webkit-animation-name: rotateInUpRight;
- animation-name: rotateInUpRight;
-}
-
-@-webkit-keyframes rotateOut {
- from {
- -webkit-transform-origin: center;
- transform-origin: center;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: center;
- transform-origin: center;
- -webkit-transform: rotate3d(0, 0, 1, 200deg);
- transform: rotate3d(0, 0, 1, 200deg);
- opacity: 0;
- }
-}
-
-@keyframes rotateOut {
- from {
- -webkit-transform-origin: center;
- transform-origin: center;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: center;
- transform-origin: center;
- -webkit-transform: rotate3d(0, 0, 1, 200deg);
- transform: rotate3d(0, 0, 1, 200deg);
- opacity: 0;
- }
-}
-
-.rotateOut {
- -webkit-animation-name: rotateOut;
- animation-name: rotateOut;
-}
-
-@-webkit-keyframes rotateOutDownLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, 45deg);
- transform: rotate3d(0, 0, 1, 45deg);
- opacity: 0;
- }
-}
-
-@keyframes rotateOutDownLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, 45deg);
- transform: rotate3d(0, 0, 1, 45deg);
- opacity: 0;
- }
-}
-
-.rotateOutDownLeft {
- -webkit-animation-name: rotateOutDownLeft;
- animation-name: rotateOutDownLeft;
-}
-
-@-webkit-keyframes rotateOutDownRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, -45deg);
- transform: rotate3d(0, 0, 1, -45deg);
- opacity: 0;
- }
-}
-
-@keyframes rotateOutDownRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, -45deg);
- transform: rotate3d(0, 0, 1, -45deg);
- opacity: 0;
- }
-}
-
-.rotateOutDownRight {
- -webkit-animation-name: rotateOutDownRight;
- animation-name: rotateOutDownRight;
-}
-
-@-webkit-keyframes rotateOutUpLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, -45deg);
- transform: rotate3d(0, 0, 1, -45deg);
- opacity: 0;
- }
-}
-
-@keyframes rotateOutUpLeft {
- from {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: left bottom;
- transform-origin: left bottom;
- -webkit-transform: rotate3d(0, 0, 1, -45deg);
- transform: rotate3d(0, 0, 1, -45deg);
- opacity: 0;
- }
-}
-
-.rotateOutUpLeft {
- -webkit-animation-name: rotateOutUpLeft;
- animation-name: rotateOutUpLeft;
-}
-
-@-webkit-keyframes rotateOutUpRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, 90deg);
- transform: rotate3d(0, 0, 1, 90deg);
- opacity: 0;
- }
-}
-
-@keyframes rotateOutUpRight {
- from {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- opacity: 1;
- }
-
- to {
- -webkit-transform-origin: right bottom;
- transform-origin: right bottom;
- -webkit-transform: rotate3d(0, 0, 1, 90deg);
- transform: rotate3d(0, 0, 1, 90deg);
- opacity: 0;
- }
-}
-
-.rotateOutUpRight {
- -webkit-animation-name: rotateOutUpRight;
- animation-name: rotateOutUpRight;
-}
-
-@-webkit-keyframes hinge {
- 0% {
- -webkit-transform-origin: top left;
- transform-origin: top left;
- -webkit-animation-timing-function: ease-in-out;
- animation-timing-function: ease-in-out;
- }
-
- 20%, 60% {
- -webkit-transform: rotate3d(0, 0, 1, 80deg);
- transform: rotate3d(0, 0, 1, 80deg);
- -webkit-transform-origin: top left;
- transform-origin: top left;
- -webkit-animation-timing-function: ease-in-out;
- animation-timing-function: ease-in-out;
- }
-
- 40%, 80% {
- -webkit-transform: rotate3d(0, 0, 1, 60deg);
- transform: rotate3d(0, 0, 1, 60deg);
- -webkit-transform-origin: top left;
- transform-origin: top left;
- -webkit-animation-timing-function: ease-in-out;
- animation-timing-function: ease-in-out;
- opacity: 1;
- }
-
- to {
- -webkit-transform: translate3d(0, 700px, 0);
- transform: translate3d(0, 700px, 0);
- opacity: 0;
- }
-}
-
-@keyframes hinge {
- 0% {
- -webkit-transform-origin: top left;
- transform-origin: top left;
- -webkit-animation-timing-function: ease-in-out;
- animation-timing-function: ease-in-out;
- }
-
- 20%, 60% {
- -webkit-transform: rotate3d(0, 0, 1, 80deg);
- transform: rotate3d(0, 0, 1, 80deg);
- -webkit-transform-origin: top left;
- transform-origin: top left;
- -webkit-animation-timing-function: ease-in-out;
- animation-timing-function: ease-in-out;
- }
-
- 40%, 80% {
- -webkit-transform: rotate3d(0, 0, 1, 60deg);
- transform: rotate3d(0, 0, 1, 60deg);
- -webkit-transform-origin: top left;
- transform-origin: top left;
- -webkit-animation-timing-function: ease-in-out;
- animation-timing-function: ease-in-out;
- opacity: 1;
- }
-
- to {
- -webkit-transform: translate3d(0, 700px, 0);
- transform: translate3d(0, 700px, 0);
- opacity: 0;
- }
-}
-
-.hinge {
- -webkit-animation-name: hinge;
- animation-name: hinge;
-}
-
-/* originally authored by Nick Pettit - https://github.com/nickpettit/glide */
-
-@-webkit-keyframes rollIn {
- from {
- opacity: 0;
- -webkit-transform: translate3d(-100%, 0, 0) rotate3d(0, 0, 1, -120deg);
- transform: translate3d(-100%, 0, 0) rotate3d(0, 0, 1, -120deg);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-@keyframes rollIn {
- from {
- opacity: 0;
- -webkit-transform: translate3d(-100%, 0, 0) rotate3d(0, 0, 1, -120deg);
- transform: translate3d(-100%, 0, 0) rotate3d(0, 0, 1, -120deg);
- }
-
- to {
- opacity: 1;
- -webkit-transform: none;
- transform: none;
- }
-}
-
-.rollIn {
- -webkit-animation-name: rollIn;
- animation-name: rollIn;
-}
-
-/* originally authored by Nick Pettit - https://github.com/nickpettit/glide */
-
-@-webkit-keyframes rollOut {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(100%, 0, 0) rotate3d(0, 0, 1, 120deg);
- transform: translate3d(100%, 0, 0) rotate3d(0, 0, 1, 120deg);
- }
-}
-
-@keyframes rollOut {
- from {
- opacity: 1;
- }
-
- to {
- opacity: 0;
- -webkit-transform: translate3d(100%, 0, 0) rotate3d(0, 0, 1, 120deg);
- transform: translate3d(100%, 0, 0) rotate3d(0, 0, 1, 120deg);
- }
-}
-
-.rollOut {
- -webkit-animation-name: rollOut;
- animation-name: rollOut;
-}
-
-@-webkit-keyframes zoomIn {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.3, .3, .3);
- transform: scale3d(.3, .3, .3);
- }
-
- 50% {
- opacity: 1;
- }
-}
-
-@keyframes zoomIn {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.3, .3, .3);
- transform: scale3d(.3, .3, .3);
- }
-
- 50% {
- opacity: 1;
- }
-}
-
-.zoomIn {
- -webkit-animation-name: zoomIn;
- animation-name: zoomIn;
-}
-
-@-webkit-keyframes zoomInDown {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.1, .1, .1) translate3d(0, -1000px, 0);
- transform: scale3d(.1, .1, .1) translate3d(0, -1000px, 0);
- -webkit-animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(.475, .475, .475) translate3d(0, 60px, 0);
- transform: scale3d(.475, .475, .475) translate3d(0, 60px, 0);
- -webkit-animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- }
-}
-
-@keyframes zoomInDown {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.1, .1, .1) translate3d(0, -1000px, 0);
- transform: scale3d(.1, .1, .1) translate3d(0, -1000px, 0);
- -webkit-animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(.475, .475, .475) translate3d(0, 60px, 0);
- transform: scale3d(.475, .475, .475) translate3d(0, 60px, 0);
- -webkit-animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- }
-}
-
-.zoomInDown {
- -webkit-animation-name: zoomInDown;
- animation-name: zoomInDown;
-}
-
-@-webkit-keyframes zoomInLeft {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.1, .1, .1) translate3d(-1000px, 0, 0);
- transform: scale3d(.1, .1, .1) translate3d(-1000px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(.475, .475, .475) translate3d(10px, 0, 0);
- transform: scale3d(.475, .475, .475) translate3d(10px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- }
-}
-
-@keyframes zoomInLeft {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.1, .1, .1) translate3d(-1000px, 0, 0);
- transform: scale3d(.1, .1, .1) translate3d(-1000px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(.475, .475, .475) translate3d(10px, 0, 0);
- transform: scale3d(.475, .475, .475) translate3d(10px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- }
-}
-
-.zoomInLeft {
- -webkit-animation-name: zoomInLeft;
- animation-name: zoomInLeft;
-}
-
-@-webkit-keyframes zoomInRight {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.1, .1, .1) translate3d(1000px, 0, 0);
- transform: scale3d(.1, .1, .1) translate3d(1000px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(.475, .475, .475) translate3d(-10px, 0, 0);
- transform: scale3d(.475, .475, .475) translate3d(-10px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- }
-}
-
-@keyframes zoomInRight {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.1, .1, .1) translate3d(1000px, 0, 0);
- transform: scale3d(.1, .1, .1) translate3d(1000px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(.475, .475, .475) translate3d(-10px, 0, 0);
- transform: scale3d(.475, .475, .475) translate3d(-10px, 0, 0);
- -webkit-animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- animation-timing-function: cubic-bezier(0.175, 0.885, 0.320, 1);
- }
-}
-
-.zoomInRight {
- -webkit-animation-name: zoomInRight;
- animation-name: zoomInRight;
-}
-
-@-webkit-keyframes zoomInUp {
- from {
- opacity: 0;
- -webkit-transform: scale3d(.1, .1, .1) translate3d(0, 1000px, 0);
- transform: scale3d(.1, .1, .1) translate3d(0, 1000px, 0);
- -webkit-animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- animation-timing-function: cubic-bezier(0.550, 0.055, 0.675, 0.190);
- }
-
- 60% {
- opacity: 1;
- -webkit-transform: scale3d(.475, .475, .475) translate3d(0, -60px, 0);
- transform: scale3d(.475, .475, .475) translate3d(0, -60px, 0);
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diff --git a/admin/src/main/resources/static/css/bootstrap.css b/admin/src/main/resources/static/css/bootstrap.css
deleted file mode 100644
index bc4fe8fd8862bb31f37b0bedd0b05f5699d42084..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/css/bootstrap.css
+++ /dev/null
@@ -1,6757 +0,0 @@
-/*!
- * Bootstrap v3.3.7 (http://getbootstrap.com)
- * Copyright 2011-2016 Twitter, Inc.
- * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
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-/*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */
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diff --git a/admin/src/main/resources/static/css/font-awesome.css b/admin/src/main/resources/static/css/font-awesome.css
deleted file mode 100644
index 38260c37baf7cd657dadb87d9c937abf94d56b94..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/css/font-awesome.css
+++ /dev/null
@@ -1,2337 +0,0 @@
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diff --git a/admin/src/main/resources/static/css/style.css b/admin/src/main/resources/static/css/style.css
deleted file mode 100755
index 5508ad65f89b2178bc03c2a87d5f767a8c211fbe..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/css/style.css
+++ /dev/null
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-@media only screen and (min-width: 768px) {
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- .vertical-timeline-content p {
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- border-color: transparent;
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- .center-orientation .vertical-timeline-content .btn {
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- .center-orientation .vertical-timeline-content .vertical-date {
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- top: 2px;
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- .center-orientation .vertical-timeline-block:nth-child(even) .vertical-timeline-content {
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-@media (max-width: 767px) {
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- .tabs-container .nav-tabs > li.active > a {
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-/* jsvectormap */
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- height: 100%;
- position: relative;
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-}
-.jvectormap-tip {
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-.jvectormap-zoomin,
-.jvectormap-zoomout,
-.jvectormap-goback {
- position: absolute;
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-.jvectormap-zoomin {
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-.jvectormap-zoomout {
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-.jvectormap-spinner {
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- display: block;
- background: #007C82;
- padding: 9px 8px;
- text-align: center;
- color: #fff;
- border-radius: 50%;
-}
-.open-small-chat:hover {
- color: white;
- background: #007C82;
-}
-.small-chat-box {
- display: none;
- position: fixed;
- bottom: 20px;
- right: 75px;
- background: #fff;
- border: 1px solid #e7eaec;
- width: 230px;
- height: 320px;
- border-radius: 4px;
-}
-.small-chat-box.ng-small-chat {
- display: block;
-}
-.body-small .small-chat-box {
- bottom: 70px;
- right: 20px;
-}
-.small-chat-box.active {
- display: block;
-}
-.small-chat-box .heading {
- background: #2f4050;
- padding: 8px 15px;
- font-weight: bold;
- color: #fff;
-}
-.small-chat-box .chat-date {
- opacity: 0.6;
- font-size: 10px;
- font-weight: normal;
-}
-.small-chat-box .content {
- padding: 15px 15px;
-}
-.small-chat-box .content .author-name {
- font-weight: bold;
- margin-bottom: 3px;
- font-size: 11px;
-}
-.small-chat-box .content > div {
- padding-bottom: 20px;
-}
-.small-chat-box .content .chat-message {
- padding: 5px 10px;
- border-radius: 6px;
- font-size: 11px;
- line-height: 14px;
- max-width: 80%;
- background: #f3f3f4;
- margin-bottom: 10px;
-}
-.small-chat-box .content .chat-message.active {
- background: #007C82;
- color: #fff;
-}
-.small-chat-box .content .left {
- text-align: left;
- clear: both;
-}
-.small-chat-box .content .left .chat-message {
- float: left;
-}
-.small-chat-box .content .right {
- text-align: right;
- clear: both;
-}
-.small-chat-box .content .right .chat-message {
- float: right;
-}
-.small-chat-box .form-chat {
- padding: 10px 10px;
-}
-/*
- * metismenu - v2.0.2
- * A jQuery menu plugin
- * https://github.com/onokumus/metisMenu
- *
- * Made by Osman Nuri Okumus
- * Under MIT License
- */
-.metismenu .plus-minus,
-.metismenu .plus-times {
- float: right;
-}
-.metismenu .arrow {
- float: right;
- line-height: 1.42857;
-}
-.metismenu .glyphicon.arrow:before {
- content: "\e079";
-}
-.metismenu .active > a > .glyphicon.arrow:before {
- content: "\e114";
-}
-.metismenu .fa.arrow:before {
- content: "\f104";
-}
-.metismenu .active > a > .fa.arrow:before {
- content: "\f107";
-}
-.metismenu .ion.arrow:before {
- content: "\f3d2";
-}
-.metismenu .active > a > .ion.arrow:before {
- content: "\f3d0";
-}
-.metismenu .fa.plus-minus:before,
-.metismenu .fa.plus-times:before {
- content: "\f067";
-}
-.metismenu .active > a > .fa.plus-times {
- -webkit-transform: rotate(45deg);
- -ms-transform: rotate(45deg);
- transform: rotate(45deg);
-}
-.metismenu .active > a > .fa.plus-minus:before {
- content: "\f068";
-}
-.metismenu .collapse {
- display: none;
-}
-.metismenu .collapse.in {
- display: block;
-}
-.metismenu .collapsing {
- position: relative;
- height: 0;
- overflow: hidden;
- -webkit-transition-timing-function: ease;
- transition-timing-function: ease;
- -webkit-transition-duration: .35s;
- transition-duration: .35s;
- -webkit-transition-property: height, visibility;
- transition-property: height, visibility;
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-rotating-plane"></div>
- *
- */
-.sk-spinner-rotating-plane.sk-spinner {
- width: 30px;
- height: 30px;
- background-color: #007C82;
- margin: 0 auto;
- -webkit-animation: sk-rotatePlane 1.2s infinite ease-in-out;
- animation: sk-rotatePlane 1.2s infinite ease-in-out;
-}
-@-webkit-keyframes sk-rotatePlane {
- 0% {
- -webkit-transform: perspective(120px) rotateX(0deg) rotateY(0deg);
- transform: perspective(120px) rotateX(0deg) rotateY(0deg);
- }
- 50% {
- -webkit-transform: perspective(120px) rotateX(-180.1deg) rotateY(0deg);
- transform: perspective(120px) rotateX(-180.1deg) rotateY(0deg);
- }
- 100% {
- -webkit-transform: perspective(120px) rotateX(-180deg) rotateY(-179.9deg);
- transform: perspective(120px) rotateX(-180deg) rotateY(-179.9deg);
- }
-}
-@keyframes sk-rotatePlane {
- 0% {
- -webkit-transform: perspective(120px) rotateX(0deg) rotateY(0deg);
- transform: perspective(120px) rotateX(0deg) rotateY(0deg);
- }
- 50% {
- -webkit-transform: perspective(120px) rotateX(-180.1deg) rotateY(0deg);
- transform: perspective(120px) rotateX(-180.1deg) rotateY(0deg);
- }
- 100% {
- -webkit-transform: perspective(120px) rotateX(-180deg) rotateY(-179.9deg);
- transform: perspective(120px) rotateX(-180deg) rotateY(-179.9deg);
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-double-bounce">
- * <div class="sk-double-bounce1"></div>
- * <div class="sk-double-bounce2"></div>
- * </div>
- *
- */
-.sk-spinner-double-bounce.sk-spinner {
- width: 40px;
- height: 40px;
- position: relative;
- margin: 0 auto;
-}
-.sk-spinner-double-bounce .sk-double-bounce1,
-.sk-spinner-double-bounce .sk-double-bounce2 {
- width: 100%;
- height: 100%;
- border-radius: 50%;
- background-color: #007C82;
- opacity: 0.6;
- position: absolute;
- top: 0;
- left: 0;
- -webkit-animation: sk-doubleBounce 2s infinite ease-in-out;
- animation: sk-doubleBounce 2s infinite ease-in-out;
-}
-.sk-spinner-double-bounce .sk-double-bounce2 {
- -webkit-animation-delay: -1s;
- animation-delay: -1s;
-}
-@-webkit-keyframes sk-doubleBounce {
- 0%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 50% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-@keyframes sk-doubleBounce {
- 0%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 50% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-wave">
- * <div class="sk-rect1"></div>
- * <div class="sk-rect2"></div>
- * <div class="sk-rect3"></div>
- * <div class="sk-rect4"></div>
- * <div class="sk-rect5"></div>
- * </div>
- *
- */
-.sk-spinner-wave.sk-spinner {
- margin: 0 auto;
- width: 50px;
- height: 30px;
- text-align: center;
- font-size: 10px;
-}
-.sk-spinner-wave div {
- background-color: #007C82;
- height: 100%;
- width: 6px;
- display: inline-block;
- -webkit-animation: sk-waveStretchDelay 1.2s infinite ease-in-out;
- animation: sk-waveStretchDelay 1.2s infinite ease-in-out;
-}
-.sk-spinner-wave .sk-rect2 {
- -webkit-animation-delay: -1.1s;
- animation-delay: -1.1s;
-}
-.sk-spinner-wave .sk-rect3 {
- -webkit-animation-delay: -1s;
- animation-delay: -1s;
-}
-.sk-spinner-wave .sk-rect4 {
- -webkit-animation-delay: -0.9s;
- animation-delay: -0.9s;
-}
-.sk-spinner-wave .sk-rect5 {
- -webkit-animation-delay: -0.8s;
- animation-delay: -0.8s;
-}
-@-webkit-keyframes sk-waveStretchDelay {
- 0%,
- 40%,
- 100% {
- -webkit-transform: scaleY(0.4);
- transform: scaleY(0.4);
- }
- 20% {
- -webkit-transform: scaleY(1);
- transform: scaleY(1);
- }
-}
-@keyframes sk-waveStretchDelay {
- 0%,
- 40%,
- 100% {
- -webkit-transform: scaleY(0.4);
- transform: scaleY(0.4);
- }
- 20% {
- -webkit-transform: scaleY(1);
- transform: scaleY(1);
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-wandering-cubes">
- * <div class="sk-cube1"></div>
- * <div class="sk-cube2"></div>
- * </div>
- *
- */
-.sk-spinner-wandering-cubes.sk-spinner {
- margin: 0 auto;
- width: 32px;
- height: 32px;
- position: relative;
-}
-.sk-spinner-wandering-cubes .sk-cube1,
-.sk-spinner-wandering-cubes .sk-cube2 {
- background-color: #007C82;
- width: 10px;
- height: 10px;
- position: absolute;
- top: 0;
- left: 0;
- -webkit-animation: sk-wanderingCubeMove 1.8s infinite ease-in-out;
- animation: sk-wanderingCubeMove 1.8s infinite ease-in-out;
-}
-.sk-spinner-wandering-cubes .sk-cube2 {
- -webkit-animation-delay: -0.9s;
- animation-delay: -0.9s;
-}
-@-webkit-keyframes sk-wanderingCubeMove {
- 25% {
- -webkit-transform: translateX(42px) rotate(-90deg) scale(0.5);
- transform: translateX(42px) rotate(-90deg) scale(0.5);
- }
- 50% {
- /* Hack to make FF rotate in the right direction */
- -webkit-transform: translateX(42px) translateY(42px) rotate(-179deg);
- transform: translateX(42px) translateY(42px) rotate(-179deg);
- }
- 50.1% {
- -webkit-transform: translateX(42px) translateY(42px) rotate(-180deg);
- transform: translateX(42px) translateY(42px) rotate(-180deg);
- }
- 75% {
- -webkit-transform: translateX(0px) translateY(42px) rotate(-270deg) scale(0.5);
- transform: translateX(0px) translateY(42px) rotate(-270deg) scale(0.5);
- }
- 100% {
- -webkit-transform: rotate(-360deg);
- transform: rotate(-360deg);
- }
-}
-@keyframes sk-wanderingCubeMove {
- 25% {
- -webkit-transform: translateX(42px) rotate(-90deg) scale(0.5);
- transform: translateX(42px) rotate(-90deg) scale(0.5);
- }
- 50% {
- /* Hack to make FF rotate in the right direction */
- -webkit-transform: translateX(42px) translateY(42px) rotate(-179deg);
- transform: translateX(42px) translateY(42px) rotate(-179deg);
- }
- 50.1% {
- -webkit-transform: translateX(42px) translateY(42px) rotate(-180deg);
- transform: translateX(42px) translateY(42px) rotate(-180deg);
- }
- 75% {
- -webkit-transform: translateX(0px) translateY(42px) rotate(-270deg) scale(0.5);
- transform: translateX(0px) translateY(42px) rotate(-270deg) scale(0.5);
- }
- 100% {
- -webkit-transform: rotate(-360deg);
- transform: rotate(-360deg);
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-pulse"></div>
- *
- */
-.sk-spinner-pulse.sk-spinner {
- width: 40px;
- height: 40px;
- margin: 0 auto;
- background-color: #007C82;
- border-radius: 100%;
- -webkit-animation: sk-pulseScaleOut 1s infinite ease-in-out;
- animation: sk-pulseScaleOut 1s infinite ease-in-out;
-}
-@-webkit-keyframes sk-pulseScaleOut {
- 0% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 100% {
- -webkit-transform: scale(1);
- transform: scale(1);
- opacity: 0;
- }
-}
-@keyframes sk-pulseScaleOut {
- 0% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 100% {
- -webkit-transform: scale(1);
- transform: scale(1);
- opacity: 0;
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-chasing-dots">
- * <div class="sk-dot1"></div>
- * <div class="sk-dot2"></div>
- * </div>
- *
- */
-.sk-spinner-chasing-dots.sk-spinner {
- margin: 0 auto;
- width: 40px;
- height: 40px;
- position: relative;
- text-align: center;
- -webkit-animation: sk-chasingDotsRotate 2s infinite linear;
- animation: sk-chasingDotsRotate 2s infinite linear;
-}
-.sk-spinner-chasing-dots .sk-dot1,
-.sk-spinner-chasing-dots .sk-dot2 {
- width: 60%;
- height: 60%;
- display: inline-block;
- position: absolute;
- top: 0;
- background-color: #007C82;
- border-radius: 100%;
- -webkit-animation: sk-chasingDotsBounce 2s infinite ease-in-out;
- animation: sk-chasingDotsBounce 2s infinite ease-in-out;
-}
-.sk-spinner-chasing-dots .sk-dot2 {
- top: auto;
- bottom: 0;
- -webkit-animation-delay: -1s;
- animation-delay: -1s;
-}
-@-webkit-keyframes sk-chasingDotsRotate {
- 100% {
- -webkit-transform: rotate(360deg);
- transform: rotate(360deg);
- }
-}
-@keyframes sk-chasingDotsRotate {
- 100% {
- -webkit-transform: rotate(360deg);
- transform: rotate(360deg);
- }
-}
-@-webkit-keyframes sk-chasingDotsBounce {
- 0%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 50% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-@keyframes sk-chasingDotsBounce {
- 0%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 50% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-three-bounce">
- * <div class="sk-bounce1"></div>
- * <div class="sk-bounce2"></div>
- * <div class="sk-bounce3"></div>
- * </div>
- *
- */
-.sk-spinner-three-bounce.sk-spinner {
- margin: 0 auto;
- width: 70px;
- text-align: center;
-}
-.sk-spinner-three-bounce div {
- width: 18px;
- height: 18px;
- background-color: #007C82;
- border-radius: 100%;
- display: inline-block;
- -webkit-animation: sk-threeBounceDelay 1.4s infinite ease-in-out;
- animation: sk-threeBounceDelay 1.4s infinite ease-in-out;
- /* Prevent first frame from flickering when animation starts */
- -webkit-animation-fill-mode: both;
- animation-fill-mode: both;
-}
-.sk-spinner-three-bounce .sk-bounce1 {
- -webkit-animation-delay: -0.32s;
- animation-delay: -0.32s;
-}
-.sk-spinner-three-bounce .sk-bounce2 {
- -webkit-animation-delay: -0.16s;
- animation-delay: -0.16s;
-}
-@-webkit-keyframes sk-threeBounceDelay {
- 0%,
- 80%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 40% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-@keyframes sk-threeBounceDelay {
- 0%,
- 80%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 40% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-circle">
- * <div class="sk-circle1 sk-circle"></div>
- * <div class="sk-circle2 sk-circle"></div>
- * <div class="sk-circle3 sk-circle"></div>
- * <div class="sk-circle4 sk-circle"></div>
- * <div class="sk-circle5 sk-circle"></div>
- * <div class="sk-circle6 sk-circle"></div>
- * <div class="sk-circle7 sk-circle"></div>
- * <div class="sk-circle8 sk-circle"></div>
- * <div class="sk-circle9 sk-circle"></div>
- * <div class="sk-circle10 sk-circle"></div>
- * <div class="sk-circle11 sk-circle"></div>
- * <div class="sk-circle12 sk-circle"></div>
- * </div>
- *
- */
-.sk-spinner-circle.sk-spinner {
- margin: 0 auto;
- width: 22px;
- height: 22px;
- position: relative;
-}
-.sk-spinner-circle .sk-circle {
- width: 100%;
- height: 100%;
- position: absolute;
- left: 0;
- top: 0;
-}
-.sk-spinner-circle .sk-circle:before {
- content: '';
- display: block;
- margin: 0 auto;
- width: 20%;
- height: 20%;
- background-color: #007C82;
- border-radius: 100%;
- -webkit-animation: sk-circleBounceDelay 1.2s infinite ease-in-out;
- animation: sk-circleBounceDelay 1.2s infinite ease-in-out;
- /* Prevent first frame from flickering when animation starts */
- -webkit-animation-fill-mode: both;
- animation-fill-mode: both;
-}
-.sk-spinner-circle .sk-circle2 {
- -webkit-transform: rotate(30deg);
- -ms-transform: rotate(30deg);
- transform: rotate(30deg);
-}
-.sk-spinner-circle .sk-circle3 {
- -webkit-transform: rotate(60deg);
- -ms-transform: rotate(60deg);
- transform: rotate(60deg);
-}
-.sk-spinner-circle .sk-circle4 {
- -webkit-transform: rotate(90deg);
- -ms-transform: rotate(90deg);
- transform: rotate(90deg);
-}
-.sk-spinner-circle .sk-circle5 {
- -webkit-transform: rotate(120deg);
- -ms-transform: rotate(120deg);
- transform: rotate(120deg);
-}
-.sk-spinner-circle .sk-circle6 {
- -webkit-transform: rotate(150deg);
- -ms-transform: rotate(150deg);
- transform: rotate(150deg);
-}
-.sk-spinner-circle .sk-circle7 {
- -webkit-transform: rotate(180deg);
- -ms-transform: rotate(180deg);
- transform: rotate(180deg);
-}
-.sk-spinner-circle .sk-circle8 {
- -webkit-transform: rotate(210deg);
- -ms-transform: rotate(210deg);
- transform: rotate(210deg);
-}
-.sk-spinner-circle .sk-circle9 {
- -webkit-transform: rotate(240deg);
- -ms-transform: rotate(240deg);
- transform: rotate(240deg);
-}
-.sk-spinner-circle .sk-circle10 {
- -webkit-transform: rotate(270deg);
- -ms-transform: rotate(270deg);
- transform: rotate(270deg);
-}
-.sk-spinner-circle .sk-circle11 {
- -webkit-transform: rotate(300deg);
- -ms-transform: rotate(300deg);
- transform: rotate(300deg);
-}
-.sk-spinner-circle .sk-circle12 {
- -webkit-transform: rotate(330deg);
- -ms-transform: rotate(330deg);
- transform: rotate(330deg);
-}
-.sk-spinner-circle .sk-circle2:before {
- -webkit-animation-delay: -1.1s;
- animation-delay: -1.1s;
-}
-.sk-spinner-circle .sk-circle3:before {
- -webkit-animation-delay: -1s;
- animation-delay: -1s;
-}
-.sk-spinner-circle .sk-circle4:before {
- -webkit-animation-delay: -0.9s;
- animation-delay: -0.9s;
-}
-.sk-spinner-circle .sk-circle5:before {
- -webkit-animation-delay: -0.8s;
- animation-delay: -0.8s;
-}
-.sk-spinner-circle .sk-circle6:before {
- -webkit-animation-delay: -0.7s;
- animation-delay: -0.7s;
-}
-.sk-spinner-circle .sk-circle7:before {
- -webkit-animation-delay: -0.6s;
- animation-delay: -0.6s;
-}
-.sk-spinner-circle .sk-circle8:before {
- -webkit-animation-delay: -0.5s;
- animation-delay: -0.5s;
-}
-.sk-spinner-circle .sk-circle9:before {
- -webkit-animation-delay: -0.4s;
- animation-delay: -0.4s;
-}
-.sk-spinner-circle .sk-circle10:before {
- -webkit-animation-delay: -0.3s;
- animation-delay: -0.3s;
-}
-.sk-spinner-circle .sk-circle11:before {
- -webkit-animation-delay: -0.2s;
- animation-delay: -0.2s;
-}
-.sk-spinner-circle .sk-circle12:before {
- -webkit-animation-delay: -0.1s;
- animation-delay: -0.1s;
-}
-@-webkit-keyframes sk-circleBounceDelay {
- 0%,
- 80%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 40% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-@keyframes sk-circleBounceDelay {
- 0%,
- 80%,
- 100% {
- -webkit-transform: scale(0);
- transform: scale(0);
- }
- 40% {
- -webkit-transform: scale(1);
- transform: scale(1);
- }
-}
-/*
- * Usage:
- *
- * <div class="sk-spinner sk-spinner-cube-grid">
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * <div class="sk-cube"></div>
- * </div>
- *
- */
-.sk-spinner-cube-grid {
- /*
- * Spinner positions
- * 1 2 3
- * 4 5 6
- * 7 8 9
- */
-}
-.sk-spinner-cube-grid.sk-spinner {
- width: 30px;
- height: 30px;
- margin: 0 auto;
-}
-.sk-spinner-cube-grid .sk-cube {
- width: 33%;
- height: 33%;
- background-color: #007C82;
- float: left;
- -webkit-animation: sk-cubeGridScaleDelay 1.3s infinite ease-in-out;
- animation: sk-cubeGridScaleDelay 1.3s infinite ease-in-out;
-}
-.sk-spinner-cube-grid .sk-cube:nth-child(1) {
- -webkit-animation-delay: 0.2s;
- animation-delay: 0.2s;
-}
-.sk-spinner-cube-grid .sk-cube:nth-child(2) {
- -webkit-animation-delay: 0.3s;
- animation-delay: 0.3s;
-}
-.sk-spinner-cube-grid .sk-cube:nth-child(3) {
- -webkit-animation-delay: 0.4s;
- animation-delay: 0.4s;
-}
-.sk-spinner-cube-grid .sk-cube:nth-child(4) {
- -webkit-animation-delay: 0.1s;
- animation-delay: 0.1s;
-}
-.sk-spinner-cube-grid .sk-cube:nth-child(5) {
- -webkit-animation-delay: 0.2s;
- animation-delay: 0.2s;
-}
-.sk-spinner-cube-grid .sk-cube:nth-child(6) {
- -webkit-animation-delay: 0.3s;
- animation-delay: 0.3s;
-}
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diff --git a/admin/src/main/resources/static/fonts/FontAwesome.otf b/admin/src/main/resources/static/fonts/FontAwesome.otf
deleted file mode 100755
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Binary files a/admin/src/main/resources/static/fonts/FontAwesome.otf and /dev/null differ
diff --git a/admin/src/main/resources/static/fonts/fontawesome-webfont.eot b/admin/src/main/resources/static/fonts/fontawesome-webfont.eot
deleted file mode 100755
index 33b2bb80055cc480e797de704925acaba4ba7d7d..0000000000000000000000000000000000000000
Binary files a/admin/src/main/resources/static/fonts/fontawesome-webfont.eot and /dev/null differ
diff --git a/admin/src/main/resources/static/fonts/fontawesome-webfont.svg b/admin/src/main/resources/static/fonts/fontawesome-webfont.svg
deleted file mode 100755
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diff --git a/admin/src/main/resources/static/js/jquery-2.1.1.js b/admin/src/main/resources/static/js/jquery-2.1.1.js
deleted file mode 100755
index 9ed2acc66dc4b8573176fe94b636e98799cee014..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/jquery-2.1.1.js
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diff --git a/admin/src/main/resources/static/js/pdxAdmin.js b/admin/src/main/resources/static/js/pdxAdmin.js
deleted file mode 100755
index 54fa468adf3879891ab663c795ac79a090e76f88..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/pdxAdmin.js
+++ /dev/null
@@ -1,294 +0,0 @@
-
-$(document).ready(function () {
-
-
- // Add body-small class if window less than 768px
- if ($(this).width() < 769) {
- $('body').addClass('body-small')
- } else {
- $('body').removeClass('body-small')
- }
-
- // MetsiMenu
- $('#side-menu').metisMenu();
-
- // Collapse ibox function
- $('.collapse-link').click(function () {
- var ibox = $(this).closest('div.ibox');
- var button = $(this).find('i');
- var content = ibox.find('div.ibox-content');
- content.slideToggle(200);
- button.toggleClass('fa-chevron-up').toggleClass('fa-chevron-down');
- ibox.toggleClass('').toggleClass('border-bottom');
- setTimeout(function () {
- ibox.resize();
- ibox.find('[id^=map-]').resize();
- }, 50);
- });
-
- // Close ibox function
- $('.close-link').click(function () {
- var content = $(this).closest('div.ibox');
- content.remove();
- });
-
- // Fullscreen ibox function
- $('.fullscreen-link').click(function () {
- var ibox = $(this).closest('div.ibox');
- var button = $(this).find('i');
- $('body').toggleClass('fullscreen-ibox-mode');
- button.toggleClass('fa-expand').toggleClass('fa-compress');
- ibox.toggleClass('fullscreen');
- setTimeout(function () {
- $(window).trigger('resize');
- }, 100);
- });
-
- // Close menu in canvas mode
- $('.close-canvas-menu').click(function () {
- $("body").toggleClass("mini-navbar");
- SmoothlyMenu();
- });
-
- // Run menu of canvas
- $('body.canvas-menu .sidebar-collapse').slimScroll({
- height: '100%',
- railOpacity: 0.9
- });
-
- // Open close right sidebar
- $('.right-sidebar-toggle').click(function () {
- $('#right-sidebar').toggleClass('sidebar-open');
- });
-
- // Initialize slimscroll for right sidebar
- $('.sidebar-container').slimScroll({
- height: '100%',
- railOpacity: 0.4,
- wheelStep: 10
- });
-
- // Open close small chat
- $('.open-small-chat').click(function () {
- $(this).children().toggleClass('fa-comments').toggleClass('fa-remove');
- $('.small-chat-box').toggleClass('active');
- });
-
- // Initialize slimscroll for small chat
- $('.small-chat-box .content').slimScroll({
- height: '234px',
- railOpacity: 0.4
- });
-
- // Small todo handler
- $('.check-link').click(function () {
- var button = $(this).find('i');
- var label = $(this).next('span');
- button.toggleClass('fa-check-square').toggleClass('fa-square-o');
- label.toggleClass('todo-completed');
- return false;
- });
-
- // Append config box / Only for demo purpose
- // Uncomment on server mode to enable XHR calls
- //$.get("skin-config.html", function (data) {
- // if (!$('body').hasClass('no-skin-config'))
- // $('body').append(data);
- //});
-
- // Minimalize menu
- $('.navbar-minimalize').click(function () {
- $("body").toggleClass("mini-navbar");
- SmoothlyMenu();
-
- });
-
- // Tooltips demo
- $('.tooltip-demo').tooltip({
- selector: "[data-toggle=tooltip]",
- container: "body"
- });
-
- // Move modal to body
- // Fix Bootstrap backdrop issu with animation.css
- $('.modal').appendTo("body");
-
- // Full height of sidebar
- function fix_height() {
- var heightWithoutNavbar = $("body > #wrapper").height() - 61;
- $(".sidebard-panel").css("min-height", heightWithoutNavbar + "px");
-
- var navbarHeigh = $('nav.navbar-default').height();
- var wrapperHeigh = $('#page-wrapper').height();
-
- if (navbarHeigh > wrapperHeigh) {
- $('#page-wrapper').css("min-height", navbarHeigh + "px");
- }
-
- if (navbarHeigh < wrapperHeigh) {
- $('#page-wrapper').css("min-height", $(window).height() + "px");
- }
-
- if ($('body').hasClass('fixed-nav')) {
- if (navbarHeigh > wrapperHeigh) {
- $('#page-wrapper').css("min-height", navbarHeigh - 60 + "px");
- } else {
- $('#page-wrapper').css("min-height", $(window).height() - 60 + "px");
- }
- }
-
- }
-
- fix_height();
-
- // Fixed Sidebar
- $(window).bind("load", function () {
- if ($("body").hasClass('fixed-sidebar')) {
- $('.sidebar-collapse').slimScroll({
- height: '100%',
- railOpacity: 0.9
- });
- }
- });
-
- // Move right sidebar top after scroll
- $(window).scroll(function () {
- if ($(window).scrollTop() > 0 && !$('body').hasClass('fixed-nav')) {
- $('#right-sidebar').addClass('sidebar-top');
- } else {
- $('#right-sidebar').removeClass('sidebar-top');
- }
- });
-
- $(window).bind("load resize scroll", function () {
- if (!$("body").hasClass('body-small')) {
- fix_height();
- }
- });
-
- $("[data-toggle=popover]")
- .popover();
-
- // Add slimscroll to element
- $('.full-height-scroll').slimscroll({
- height: '100%'
- })
-});
-
-
-// Minimalize menu when screen is less than 768px
-$(window).bind("resize", function () {
- if ($(this).width() < 769) {
- $('body').addClass('body-small')
- } else {
- $('body').removeClass('body-small')
- }
-});
-
-// Local Storage functions
-// Set proper body class and plugins based on user configuration
-$(document).ready(function () {
- if (localStorageSupport) {
-
- var collapse = localStorage.getItem("collapse_menu");
- var fixedsidebar = localStorage.getItem("fixedsidebar");
- var fixednavbar = localStorage.getItem("fixednavbar");
- var boxedlayout = localStorage.getItem("boxedlayout");
- var fixedfooter = localStorage.getItem("fixedfooter");
-
- var body = $('body');
-
- if (fixedsidebar == 'on') {
- body.addClass('fixed-sidebar');
- $('.sidebar-collapse').slimScroll({
- height: '100%',
- railOpacity: 0.9
- });
- }
-
- if (collapse == 'on') {
- if (body.hasClass('fixed-sidebar')) {
- if (!body.hasClass('body-small')) {
- body.addClass('mini-navbar');
- }
- } else {
- if (!body.hasClass('body-small')) {
- body.addClass('mini-navbar');
- }
-
- }
- }
-
- if (fixednavbar == 'on') {
- $(".navbar-static-top").removeClass('navbar-static-top').addClass('navbar-fixed-top');
- body.addClass('fixed-nav');
- }
-
- if (boxedlayout == 'on') {
- body.addClass('boxed-layout');
- }
-
- if (fixedfooter == 'on') {
- $(".footer").addClass('fixed');
- }
- }
-});
-
-// check if browser support HTML5 local storage
-function localStorageSupport() {
- return (('localStorage' in window) && window['localStorage'] !== null)
-}
-
-// For demo purpose - animation css script
-function animationHover(element, animation) {
- element = $(element);
- element.hover(
- function () {
- element.addClass('animated ' + animation);
- },
- function () {
- //wait for animation to finish before removing classes
- window.setTimeout(function () {
- element.removeClass('animated ' + animation);
- }, 2000);
- });
-}
-
-function SmoothlyMenu() {
- if (!$('body').hasClass('mini-navbar') || $('body').hasClass('body-small')) {
- // Hide menu in order to smoothly turn on when maximize menu
- $('#side-menu').hide();
- // For smoothly turn on menu
- setTimeout(
- function () {
- $('#side-menu').fadeIn(400);
- }, 200);
- } else if ($('body').hasClass('fixed-sidebar')) {
- $('#side-menu').hide();
- setTimeout(
- function () {
- $('#side-menu').fadeIn(400);
- }, 100);
- } else {
- // Remove all inline style from jquery fadeIn function to reset menu state
- $('#side-menu').removeAttr('style');
- }
-}
-
-// Dragable panels
-function WinMove() {
- var element = "[class*=col]";
- var handle = ".ibox-title";
- var connect = "[class*=col]";
- $(element).sortable(
- {
- handle: handle,
- connectWith: connect,
- tolerance: 'pointer',
- forcePlaceholderSize: true,
- opacity: 0.8
- })
- .disableSelection();
-}
-
-
diff --git a/admin/src/main/resources/static/js/plugins/chart/3dbar.js b/admin/src/main/resources/static/js/plugins/chart/3dbar.js
deleted file mode 100755
index 27836c1a21563740a4df0f7587dd5f8db0205d9b..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/chart/3dbar.js
+++ /dev/null
@@ -1,110 +0,0 @@
-var chart = AmCharts.makeChart("chartdiv", {
- "theme": "light",
- "type": "serial",
- "startDuration": 2,
- "dataProvider": [{
- "country": "Breast Cancer",
- "visits": 4025,
- "color": "#FF0F00"
- }, {
- "country": "Pancreatic",
- "visits": 1882,
- "color": "#FF6600"
- }, {
- "country": "Rectum",
- "visits": 1809,
- "color": "#FF9E01"
- }, {
- "country": "Bile Duct",
- "visits": 1322,
- "color": "#FCD202"
- }, {
- "country": "Liver",
- "visits": 1122,
- "color": "#F8FF01"
- }, {
- "country": "Salivary Gland",
- "visits": 1114,
- "color": "#B0DE09"
- }, {
- "country": "tonsil",
- "visits": 984,
- "color": "#04D215"
- }, {
- "country": "anal",
- "visits": 711,
- "color": "#0D8ECF"
- }, {
- "country": "Stomach",
- "visits": 665,
- "color": "#0D52D1"
- }, {
- "country": "appendix",
- "visits": 580,
- "color": "#2A0CD0"
- }, {
- "country": "esophageal",
- "visits": 443,
- "color": "#8A0CCF"
- }, {
- "country": "duodenum",
- "visits": 441,
- "color": "#CD0D74"
- }, {
- "country": "lung ",
- "visits": 395,
- "color": "#754DEB"
- }, {
- "country": "Brain",
- "visits": 386,
- "color": "#DDDDDD"
- }, {
- "country": "adrenal gland",
- "visits": 384,
- "color": "#999999"
- }, {
- "country": "Breast",
- "visits": 338,
- "color": "#333333"
- }, {
- "country": "Skin",
- "visits": 328,
- "color": "#000000"
- }],
- "valueAxes": [{
- "position": "left",
- "title": "Visitors"
- }],
- "graphs": [{
- "balloonText": "[[category]]: <b>[[value]]</b>",
- "fillColorsField": "color",
- "fillAlphas": 1,
- "lineAlpha": 0.1,
- "type": "column",
- "valueField": "visits",
- "showHandOnHover": true
- }],
- "depth3D": 20,
- "angle": 30,
- "chartCursor": {
- "categoryBalloonEnabled": false,
- "cursorAlpha": 0,
- "zoomable": true
- },
- "categoryField": "country",
- "categoryAxis": {
- "gridPosition": "start",
- "labelRotation": 0
- },
- "listeners": [{
- "event": "clickGraphItem",
- "method": function(event) {
- var drillDownLink = 'http://www.pdxfinder.org/data/search?cancer_system='+event.item.category;
- window.open(drillDownLink,'_blank');
- }
- }],
- "export": {
- "enabled": true
- }
-
-});
\ No newline at end of file
diff --git a/admin/src/main/resources/static/js/plugins/chart/amcharts.js b/admin/src/main/resources/static/js/plugins/chart/amcharts.js
deleted file mode 100755
index 0b5e4944311fdf82e33471174ad34fe8da182fb5..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/chart/amcharts.js
+++ /dev/null
@@ -1,55 +0,0 @@
-(function(){var d;window.AmCharts?d=window.AmCharts:(d={},window.AmCharts=d,d.themes={},d.maps={},d.inheriting={},d.charts=[],d.onReadyArray=[],d.useUTC=!1,d.updateRate=60,d.uid=0,d.lang={},d.translations={},d.mapTranslations={},d.windows={},d.initHandlers=[],d.amString="am",d.pmString="pm");d.Class=function(a){var b=function(){arguments[0]!==d.inheriting&&(this.events={},this.construct.apply(this,arguments))};a.inherits?(b.prototype=new a.inherits(d.inheriting),b.base=a.inherits.prototype,delete a.inherits):(b.prototype.createEvents=function(){for(var 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d=window.AmCharts;d.AxisBase=d.Class({construct:function(a){this.createEvents("clickItem","rollOverItem","rollOutItem","rollOverGuide","rollOutGuide","clickGuide");this.titleDY=this.y=this.x=this.dy=this.dx=0;this.axisThickness=1;this.axisColor="#000000";this.axisAlpha=1;this.gridCount=this.tickLength=5;this.gridAlpha=.15;this.gridThickness=1;this.gridColor="#000000";this.dashLength=0;this.labelFrequency=1;this.showLastLabel=this.showFirstLabel=!0;this.fillColor="#FFFFFF";this.fillAlpha=0;this.labelsEnabled=!0;this.labelRotation=0;this.autoGridCount=!0;this.offset=0;this.guides=[];this.visible=!0;this.counter=0;this.guides=[];this.ignoreAxisWidth=this.inside=!1;this.minHorizontalGap=75;this.minVerticalGap=35;this.titleBold=!0;this.minorGridEnabled=!1;this.minorGridAlpha=.07;this.autoWrap=!1;this.titleAlign="middle";this.labelOffset=0;this.bcn="axis-";this.centerLabels=!1;this.firstDayOfWeek=1;this.centerLabelOnFullPeriod=this.markPeriodChange=this.boldPeriodBeginning=!0;this.periods=[{period:"fff",count:1},{period:"fff",count:5},{period:"fff",count:10},{period:"fff",count:50},{period:"fff",count:100},{period:"fff",count:500},{period:"ss",count:1},{period:"ss",count:5},{period:"ss",count:10},{period:"ss",count:30},{period:"mm",count:1},{period:"mm",count:5},{period:"mm",count:10},{period:"mm",count:30},{period:"hh",count:1},{period:"hh",count:3},{period:"hh",count:6},{period:"hh",count:12},{period:"DD",count:1},{period:"DD",count:2},{period:"DD",count:3},{period:"DD",count:4},{period:"DD",count:5},{period:"WW",count:1},{period:"MM",count:1},{period:"MM",count:2},{period:"MM",count:3},{period:"MM",count:6},{period:"YYYY",count:1},{period:"YYYY",count:2},{period:"YYYY",count:5},{period:"YYYY",count:10},{period:"YYYY",count:50},{period:"YYYY",count:100}];this.dateFormats=[{period:"fff",format:"NN:SS.QQQ"},{period:"ss",format:"JJ:NN:SS"},{period:"mm",format:"JJ:NN"},{period:"hh",format:"JJ:NN"},{period:"DD",format:"MMM DD"},{period:"WW",format:"MMM DD"},{period:"MM",format:"MMM"},{period:"YYYY",format:"YYYY"}];this.nextPeriod={fff:"ss",ss:"mm",mm:"hh",hh:"DD",DD:"MM",MM:"YYYY"};d.applyTheme(this,a,"AxisBase")},zoom:function(a,b){this.start=a;this.end=b;this.dataChanged=!0;this.draw()},fixAxisPosition:function(){var a=this.position;"H"==this.orientation?("left"==a&&(a="bottom"),"right"==a&&(a="top")):("bottom"==a&&(a="left"),"top"==a&&(a="right"));this.position=a},init:function(){this.createBalloon()},draw:function(){var a=this.chart;this.prevBY=this.prevBX=NaN;this.allLabels=[];this.counter=0;this.destroy();this.fixAxisPosition();this.setBalloonBounds();this.labels=[];var b=a.container,c=b.set();a.gridSet.push(c);this.set=c;b=b.set();a.axesLabelsSet.push(b);this.labelsSet=b;this.axisLine=new this.axisRenderer(this);this.autoGridCount?("V"==this.orientation?(a=this.height/this.minVerticalGap,3>a&&(a=3)):a=this.width/this.minHorizontalGap,this.gridCountR=Math.max(a,1)):this.gridCountR=this.gridCount;this.axisWidth=this.axisLine.axisWidth;this.addTitle()},setOrientation:function(a){this.orientation=a?"H":"V"},addTitle:function(){var a=this.title;this.titleLabel=null;if(a){var b=this.chart,c=this.titleColor;void 0===c&&(c=b.color);var e=this.titleFontSize;isNaN(e)&&(e=b.fontSize+1);a=d.text(b.container,a,c,b.fontFamily,e,this.titleAlign,this.titleBold);d.setCN(b,a,this.bcn+"title");this.titleLabel=a}},positionTitle:function(){var a=this.titleLabel;if(a){var b,c,e=this.labelsSet,h={};0<e.length()?h=e.getBBox():(h.x=0,h.y=0,h.width=this.width,h.height=this.height,d.VML&&(h.y+=this.y,h.x+=this.x));e.push(a);var e=h.x,f=h.y;d.VML&&(f-=this.y,e-=this.x);var g=h.width,h=h.height,k=this.width,l=this.height,m=0,p=a.getBBox().height/2,q=this.inside,n=this.titleAlign;switch(this.position){case"top":b="left"==n?-1:"right"==n?k:k/2;c=f-10-p;break;case"bottom":b="left"==n?-1:"right"==n?k:k/2;c=f+h+10+p;break;case"left":b=e-10-p;q&&(b-=5);m=-90;c=("left"==n?l+1:"right"==n?-1:l/2)+this.titleDY;break;case"right":b=e+g+10+p,q&&(b+=7),c=("left"==n?l+2:"right"==n?-2:l/2)+this.titleDY,m=-90}this.marginsChanged?(a.translate(b,c),this.tx=b,this.ty=c):a.translate(this.tx,this.ty);this.marginsChanged=!1;isNaN(this.titleRotation)||(m=this.titleRotation);0!==m&&a.rotate(m)}},pushAxisItem:function(a,b){var c=this,e=a.graphics();0<e.length()&&(b?c.labelsSet.push(e):c.set.push(e));if(e=a.getLabel())c.labelsSet.push(e),e.click(function(b){c.handleMouse(b,a,"clickItem")}).touchend(function(b){c.handleMouse(b,a,"clickItem")}).mouseover(function(b){c.handleMouse(b,a,"rollOverItem")}).mouseout(function(b){c.handleMouse(b,a,"rollOutItem")})},handleMouse:function(a,b,c){this.fire({type:c,value:b.value,serialDataItem:b.serialDataItem,axis:this,target:b.label,chart:this.chart,event:a})},addGuide:function(a){for(var b=this.guides,c=!1,e=b.length,h=0;h<b.length;h++)b[h]==a&&(c=!0,e=h);a=d.processObject(a,d.Guide,this.theme);a.id||(a.id="guideAuto"+e+"_"+(new Date).getTime());c||b.push(a)},removeGuide:function(a){var b=this.guides,c;for(c=0;c<b.length;c++)b[c]==a&&b.splice(c,1)},handleGuideOver:function(a){clearTimeout(this.chart.hoverInt);var b=a.graphics.getBBox(),c=this.x+b.x+b.width/2,b=this.y+b.y+b.height/2,e=a.fillColor;void 0===e&&(e=a.lineColor);this.chart.showBalloon(a.balloonText,e,!0,c,b);this.fire({type:"rollOverGuide",guide:a,chart:this.chart})},handleGuideOut:function(a){this.chart.hideBalloon();this.fire({type:"rollOutGuide",guide:a,chart:this.chart})},handleGuideClick:function(a){this.chart.hideBalloon();this.fire({type:"clickGuide",guide:a,chart:this.chart})},addEventListeners:function(a,b){var c=this;a.mouseover(function(){c.handleGuideOver(b)});a.mouseup(function(){c.handleGuideClick(b)});a.touchstart(function(){c.handleGuideOver(b)});a.mouseout(function(){c.handleGuideOut(b)})},getBBox:function(){var a;this.labelsSet&&(a=this.labelsSet.getBBox());a?d.VML||(a={x:a.x+this.x,y:a.y+this.y,width:a.width,height:a.height}):a={x:0,y:0,width:0,height:0};return a},destroy:function(){d.remove(this.set);d.remove(this.labelsSet);var a=this.axisLine;a&&d.remove(a.axisSet);d.remove(this.grid0)},chooseMinorFrequency:function(a){for(var b=10;0<b;b--)if(a/
-b==Math.round(a/b))return a/b},parseDatesDraw:function(){var a,b=this.chart,c=this.showFirstLabel,e=this.showLastLabel,h,f="",g=d.extractPeriod(this.minPeriod),k=d.getPeriodDuration(g.period,g.count),l,m,p,q,n,t=this.firstDayOfWeek,r=this.boldPeriodBeginning;a=this.minorGridEnabled;var w,z=this.gridAlpha,x,u=this.choosePeriod(0),A=u.period,u=u.count,y=d.getPeriodDuration(A,u);y<k&&(A=g.period,u=g.count,y=k);g=A;"WW"==g&&(g="DD");this.stepWidth=this.getStepWidth(this.timeDifference);var B=Math.ceil(this.timeDifference/
-y)+5,D=l=d.resetDateToMin(new Date(this.startTime-y),A,u,t).getTime();if(g==A&&1==u&&this.centerLabelOnFullPeriod||this.autoWrap||this.centerLabels)p=y*this.stepWidth,this.autoWrap&&!this.centerLabels&&(p=-p);this.cellWidth=k*this.stepWidth;q=Math.round(l/y);k=-1;q/2==Math.round(q/2)&&(k=-2,l-=y);q=this.firstTime;var C=0,I=0;a&&1<u&&(w=this.chooseMinorFrequency(u),x=d.getPeriodDuration(A,w),"DD"==A&&(x+=d.getPeriodDuration("hh")),"fff"==A&&(x=1));if(0<this.gridCountR)for(B-5-k>this.autoRotateCount&&!isNaN(this.autoRotateAngle)&&(this.labelRotationR=this.autoRotateAngle),a=k;a<=B;a++){n=q+y*(a+Math.floor((D-q)/y))-C;"DD"==A&&(n+=36E5);n=d.resetDateToMin(new Date(n),A,u,t).getTime();"MM"==A&&(h=(n-l)/y,1.5<=(n-l)/y&&(n=n-(h-1)*y+d.getPeriodDuration("DD",3),n=d.resetDateToMin(new Date(n),A,1).getTime(),C+=y));h=(n-this.startTime)*this.stepWidth;if("radar"==b.type){if(h=this.axisWidth-h,0>h||h>this.axisWidth)continue}else this.rotate?"date"==this.type&&"middle"==this.gridPosition&&(I=-y*this.stepWidth/
-2):"date"==this.type&&(h=this.axisWidth-h);f=!1;this.nextPeriod[g]&&(f=this.checkPeriodChange(this.nextPeriod[g],1,n,l,g));l=!1;f&&this.markPeriodChange?(f=this.dateFormatsObject[this.nextPeriod[g]],this.twoLineMode&&(f=this.dateFormatsObject[g]+"\n"+f,f=d.fixBrakes(f)),l=!0):f=this.dateFormatsObject[g];r||(l=!1);this.currentDateFormat=f;f=d.formatDate(new Date(n),f,b);if(a==k&&!c||a==B&&!e)f=" ";this.labelFunction&&(f=this.labelFunction(f,new Date(n),this,A,u,m).toString());this.boldLabels&&(l=!0);m=new this.axisItemRenderer(this,h,f,!1,p,I,!1,l);this.pushAxisItem(m);m=l=n;if(!isNaN(w))for(h=1;h<u;h+=w)this.gridAlpha=this.minorGridAlpha,f=n+x*h,f=d.resetDateToMin(new Date(f),A,w,t).getTime(),f=new this.axisItemRenderer(this,(f-this.startTime)*this.stepWidth,void 0,void 0,void 0,void 0,void 0,void 0,void 0,!0),this.pushAxisItem(f);this.gridAlpha=z}},choosePeriod:function(a){var b=d.getPeriodDuration(this.periods[a].period,this.periods[a].count),c=this.periods;return this.timeDifference<b&&0<a?c[a-1]:Math.ceil(this.timeDifference/b)<=this.gridCountR?c[a]:a+1<c.length?this.choosePeriod(a+1):c[a]},getStepWidth:function(a){var b;this.startOnAxis?(b=this.axisWidth/(a-1),1==a&&(b=this.axisWidth)):b=this.axisWidth/a;return b},timeZoom:function(a,b){this.startTime=a;this.endTime=b},minDuration:function(){var a=d.extractPeriod(this.minPeriod);return d.getPeriodDuration(a.period,a.count)},checkPeriodChange:function(a,b,c,e,h){c=new Date(c);var f=new Date(e),g=this.firstDayOfWeek;e=b;"DD"==a&&(b=1);c=d.resetDateToMin(c,a,b,g).getTime();b=d.resetDateToMin(f,a,b,g).getTime();return"DD"==a&&"hh"!=h&&c-b<d.getPeriodDuration(a,e)-d.getPeriodDuration("hh",1)?!1:c!=b?!0:!1},generateDFObject:function(){this.dateFormatsObject={};var a;for(a=0;a<this.dateFormats.length;a++){var b=this.dateFormats[a];this.dateFormatsObject[b.period]=b.format}},hideBalloon:function(){this.balloon&&this.balloon.hide&&this.balloon.hide();this.prevBY=this.prevBX=NaN},formatBalloonText:function(a){return a},showBalloon:function(a,b,c,e){var d=this.offset;switch(this.position){case"bottom":b=this.height+d;break;case"top":b=-d;break;case"left":a=-d;break;case"right":a=this.width+d}c||(c=this.currentDateFormat);if("V"==this.orientation){if(0>b||b>this.height)return;if(isNaN(b)){this.hideBalloon();return}b=this.adjustBalloonCoordinate(b,e);e=this.coordinateToValue(b)}else{if(0>a||a>this.width)return;if(isNaN(a)){this.hideBalloon();return}a=this.adjustBalloonCoordinate(a,e);e=this.coordinateToValue(a)}var f;if(d=this.chart.chartCursor)f=d.index;if(this.balloon&&void 0!==e&&this.balloon.enabled){if(this.balloonTextFunction){if("date"==this.type||!0===this.parseDates)e=new Date(e);e=this.balloonTextFunction(e)}else this.balloonText?e=this.formatBalloonText(this.balloonText,f,c):isNaN(e)||(e=this.formatValue(e,c));if(a!=this.prevBX||b!=this.prevBY)this.balloon.setPosition(a,b),this.prevBX=a,this.prevBY=b,e&&this.balloon.showBalloon(e)}},adjustBalloonCoordinate:function(a){return a},createBalloon:function(){var a=this.chart,b=a.chartCursor;b&&(b=b.cursorPosition,"mouse"!=b&&(this.stickBalloonToCategory=!0),"start"==b&&(this.stickBalloonToStart=!0),"ValueAxis"==this.cname&&(this.stickBalloonToCategory=!1));this.balloon&&(this.balloon.destroy&&this.balloon.destroy(),d.extend(this.balloon,a.balloon,!0))},setBalloonBounds:function(){var a=this.balloon;if(a){var b=this.chart;a.cornerRadius=0;a.shadowAlpha=0;a.borderThickness=1;a.borderAlpha=1;a.adjustBorderColor=!1;a.showBullet=!1;this.balloon=a;a.chart=b;a.mainSet=b.plotBalloonsSet;a.pointerWidth=this.tickLength;if(this.parseDates||"date"==this.type)a.pointerWidth=0;a.className=this.id;b="V";"V"==this.orientation&&(b="H");this.stickBalloonToCategory||(a.animationDuration=0);var c,e,d,f,g=this.inside,k=this.width,l=this.height;switch(this.position){case"bottom":c=0;e=k;g?(d=0,f=l):(d=l,f=l+1E3);break;case"top":c=0;e=k;g?(d=0,f=l):(d=-1E3,f=0);break;case"left":d=0;f=l;g?(c=0,e=k):(c=-1E3,e=0);break;case"right":d=0,f=l,g?(c=0,e=k):(c=k,e=k+1E3)}a.drop||(a.pointerOrientation=b);a.setBounds(c,d,e,f)}}})})();(function(){var d=window.AmCharts;d.ValueAxis=d.Class({inherits:d.AxisBase,construct:function(a){this.cname="ValueAxis";this.createEvents("axisChanged","logarithmicAxisFailed","axisZoomed","axisIntZoomed");d.ValueAxis.base.construct.call(this,a);this.dataChanged=!0;this.stackType="none";this.position="left";this.unitPosition="right";this.includeAllValues=this.recalculateToPercents=this.includeHidden=this.includeGuidesInMinMax=this.integersOnly=!1;this.durationUnits={DD:"d. ",hh:":",mm:":",ss:""};this.scrollbar=!1;this.baseValue=0;this.radarCategoriesEnabled=!0;this.axisFrequency=1;this.gridType="polygons";this.useScientificNotation=!1;this.axisTitleOffset=10;this.pointPosition="axis";this.minMaxMultiplier=1;this.logGridLimit=2;this.totalTextOffset=this.treatZeroAs=0;this.minPeriod="ss";this.relativeStart=0;this.relativeEnd=1;d.applyTheme(this,a,this.cname)},updateData:function(){0>=this.gridCountR&&(this.gridCountR=1);this.totals=[];this.data=this.chart.chartData;var a=this.chart;"xy"!=a.type&&(this.stackGraphs("smoothedLine"),this.stackGraphs("line"),this.stackGraphs("column"),this.stackGraphs("step"));this.recalculateToPercents&&this.recalculate();this.synchronizationMultiplier&&this.synchronizeWith?(d.isString(this.synchronizeWith)&&(this.synchronizeWith=a.getValueAxisById(this.synchronizeWith)),this.synchronizeWith&&(this.synchronizeWithAxis(this.synchronizeWith),this.foundGraphs=!0)):(this.foundGraphs=!1,this.getMinMax(),0===this.start&&this.end==this.data.length-1&&isNaN(this.minZoom)&&isNaN(this.maxZoom)&&(this.fullMin=this.min,this.fullMax=this.max,"date"!=this.type&&this.strictMinMax&&(isNaN(this.minimum)||(this.fullMin=this.minimum),isNaN(this.maximum)||(this.fullMax=this.maximum)),this.logarithmic&&(this.fullMin=this.logMin,0===this.fullMin&&(this.fullMin=this.treatZeroAs)),"date"==this.type&&(this.minimumDate||(this.fullMin=this.minRR),this.maximumDate||(this.fullMax=this.maxRR),this.strictMinMax&&(this.minimumDate&&(this.fullMin=this.minimumDate.getTime()),this.maximumDate&&(this.fullMax=this.maximumDate.getTime())))))},draw:function(){d.ValueAxis.base.draw.call(this);var a=this.chart,b=this.set;this.labelRotationR=this.labelRotation;d.setCN(a,this.set,"value-axis value-axis-"+this.id);d.setCN(a,this.labelsSet,"value-axis value-axis-"+this.id);d.setCN(a,this.axisLine.axisSet,"value-axis value-axis-"+this.id);var c=this.type;"duration"==c&&(this.duration="ss");!0===this.dataChanged&&(this.updateData(),this.dataChanged=!1);"date"==c&&(this.logarithmic=!1,this.min=this.minRR,this.max=this.maxRR,this.reversed=!1,this.getDateMinMax());if(this.logarithmic){var e=this.treatZeroAs,h=this.getExtremes(0,this.data.length-1).min;!isNaN(this.minimum)&&this.minimum<h&&(h=this.minimum);this.logMin=h;this.minReal<h&&(this.minReal=h);isNaN(this.minReal)&&(this.minReal=h);0<e&&0===h&&(this.minReal=h=e);if(0>=h||0>=this.minimum){this.fire({type:"logarithmicAxisFailed",chart:a});return}}this.grid0=null;var f,g,k=a.dx,l=a.dy,e=!1,h=this.logarithmic;if(isNaN(this.min)||isNaN(this.max)||!this.foundGraphs||Infinity==this.min||-Infinity==this.max)e=!0;else{"date"==this.type&&this.min==this.max&&(this.max+=this.minDuration(),this.min-=this.minDuration());var m=this.labelFrequency,p=this.showFirstLabel,q=this.showLastLabel,n=1,t=0;this.minCalc=this.min;this.maxCalc=this.max;if(this.strictMinMax&&(isNaN(this.minimum)||(this.min=this.minimum),isNaN(this.maximum)||(this.max=this.maximum),this.min==this.max))return;isNaN(this.minZoom)||(this.minReal=this.min=this.minZoom);isNaN(this.maxZoom)||(this.max=this.maxZoom);if(this.logarithmic){g=this.fullMin;var r=this.fullMax;isNaN(this.minimum)||(g=this.minimum);isNaN(this.maximum)||(r=this.maximum);var r=Math.log(r)*Math.LOG10E-Math.log(g)*Math.LOG10E,w=Math.log(this.max)/Math.LN10-Math.log(g)*Math.LOG10E;this.relativeStart=d.roundTo((Math.log(this.minReal)/Math.LN10-Math.log(g)*Math.LOG10E)/r,5);this.relativeEnd=d.roundTo(w/r,5)}else this.relativeStart=d.roundTo(d.fitToBounds((this.min-this.fullMin)/(this.fullMax-this.fullMin),0,1),5),this.relativeEnd=
-d.roundTo(d.fitToBounds((this.max-this.fullMin)/(this.fullMax-this.fullMin),0,1),5);var r=Math.round((this.maxCalc-this.minCalc)/this.step)+1,z;!0===h?(z=Math.log(this.max)*Math.LOG10E-Math.log(this.minReal)*Math.LOG10E,this.stepWidth=this.axisWidth/z,z>this.logGridLimit&&(r=Math.ceil(Math.log(this.max)*Math.LOG10E)+1,t=Math.round(Math.log(this.minReal)*Math.LOG10E),r>this.gridCountR&&(n=Math.ceil(r/this.gridCountR)))):this.stepWidth=this.axisWidth/(this.max-this.min);var x=0;1>this.step&&-1<this.step&&
-(x=d.getDecimals(this.step));this.integersOnly&&(x=0);x>this.maxDecCount&&(x=this.maxDecCount);w=this.precision;isNaN(w)||(x=w);isNaN(this.maxZoom)&&(this.max=d.roundTo(this.max,this.maxDecCount),this.min=d.roundTo(this.min,this.maxDecCount));g={};g.precision=x;g.decimalSeparator=a.nf.decimalSeparator;g.thousandsSeparator=a.nf.thousandsSeparator;this.numberFormatter=g;var u;this.exponential=!1;for(g=t;g<r;g+=n){var A=d.roundTo(this.step*g+this.min,x);-1!=String(A).indexOf("e")&&(this.exponential=!0)}this.duration&&(this.maxInterval=d.getMaxInterval(this.max,this.duration));var x=this.step,y,A=this.minorGridAlpha;this.minorGridEnabled&&(y=this.getMinorGridStep(x,this.stepWidth*x));if(this.autoGridCount||0!==this.gridCount)if("date"==c)this.generateDFObject(),this.timeDifference=this.max-this.min,this.maxTime=this.lastTime=this.max,this.startTime=this.firstTime=this.min,this.parseDatesDraw();else for(r>=this.autoRotateCount&&!isNaN(this.autoRotateAngle)&&(this.labelRotationR=this.autoRotateAngle),c=this.minCalc,h&&(r++,c=this.maxCalc-r*x),this.gridCountReal=r,g=this.startCount=t;g<r;g+=n)if(t=x*g+c,t=d.roundTo(t,this.maxDecCount+1),!this.integersOnly||Math.round(t)==t)if(isNaN(w)||Number(d.toFixed(t,w))==t){if(!0===h)if(z>this.logGridLimit)t=Math.pow(10,g);else if(0>=t&&(t=c+x*g+x/2,0>=t))continue;u=this.formatValue(t,!1,g);Math.round(g/m)!=g/m&&(u=void 0);if(0===g&&!p||g==r-1&&!q)u=" ";f=this.getCoordinate(t);var B;this.rotate&&this.autoWrap&&(B=this.stepWidth*x-10);u=new this.axisItemRenderer(this,f,u,void 0,B,void 0,void 0,this.boldLabels);this.pushAxisItem(u);if(t==this.baseValue&&"radar"!=a.type){var D,C,I=this.width,H=this.height;"H"==this.orientation?0<=f&&f<=I+1&&(D=[f,f,f+k],C=[H,0,l]):0<=f&&f<=H+1&&(D=[0,I,I+k],C=[f,f,f+l]);D&&(f=d.fitToBounds(2*this.gridAlpha,0,1),isNaN(this.zeroGridAlpha)||(f=this.zeroGridAlpha),f=d.line(a.container,D,C,this.gridColor,f,1,this.dashLength),f.translate(this.x,this.y),this.grid0=f,a.axesSet.push(f),f.toBack(),d.setCN(a,f,this.bcn+"zero-grid-"+this.id),d.setCN(a,f,this.bcn+"zero-grid"))}if(!isNaN(y)&&0<A&&g<r-1){f=x/y;h&&(y=x*(g+n)+this.minCalc,y=d.roundTo(y,this.maxDecCount+1),z>this.logGridLimit&&(y=Math.pow(10,g+n)),f=9,y=(y-t)/f);I=this.gridAlpha;this.gridAlpha=this.minorGridAlpha;for(H=1;H<f;H++){var Q=this.getCoordinate(t+y*H),Q=new this.axisItemRenderer(this,Q,"",!1,0,0,!1,!1,0,!0);this.pushAxisItem(Q)}this.gridAlpha=I}}z=this.guides;B=z.length;if(0<B){D=this.fillAlpha;for(g=this.fillAlpha=0;g<B;g++)C=z[g],k=NaN,y=C.above,isNaN(C.toValue)||
-(k=this.getCoordinate(C.toValue),u=new this.axisItemRenderer(this,k,"",!0,NaN,NaN,C),this.pushAxisItem(u,y)),l=NaN,isNaN(C.value)||(l=this.getCoordinate(C.value),u=new this.axisItemRenderer(this,l,C.label,!0,NaN,(k-l)/2,C),this.pushAxisItem(u,y)),isNaN(k)&&(l-=3,k=l+3),u&&(m=u.label)&&this.addEventListeners(m,C),isNaN(k-l)||0>l&&0>k||(k=new this.guideFillRenderer(this,l,k,C),this.pushAxisItem(k,y),y=k.graphics(),C.graphics=y,this.addEventListeners(y,C));this.fillAlpha=D}u=this.baseValue;this.min>
-this.baseValue&&this.max>this.baseValue&&(u=this.min);this.min<this.baseValue&&this.max<this.baseValue&&(u=this.max);h&&u<this.minReal&&(u=this.minReal);this.baseCoord=this.getCoordinate(u,!0);u={type:"axisChanged",target:this,chart:a};u.min=h?this.minReal:this.min;u.max=this.max;this.fire(u);this.axisCreated=!0}h=this.axisLine.set;u=this.labelsSet;b.translate(this.x,this.y);u.translate(this.x,this.y);this.positionTitle();"radar"!=a.type&&h.toFront();!this.visible||e?(b.hide(),h.hide(),u.hide()):(b.show(),h.show(),u.show());this.axisY=this.y;this.axisX=this.x},getDateMinMax:function(){this.minimumDate&&(this.minimumDate instanceof Date||(this.minimumDate=d.getDate(this.minimumDate,this.chart.dataDateFormat,"fff")),this.min=this.minimumDate.getTime());this.maximumDate&&(this.maximumDate instanceof Date||(this.maximumDate=d.getDate(this.maximumDate,this.chart.dataDateFormat,"fff")),this.max=this.maximumDate.getTime())},formatValue:function(a,b,c){var e=this.exponential,h=this.logarithmic,f=this.numberFormatter,g=this.chart;if(f)return!0===this.logarithmic&&(e=-1!=String(a).indexOf("e")?!0:!1),this.useScientificNotation&&(e=!0),this.usePrefixes&&(e=!1),e?(c=-1==String(a).indexOf("e")?a.toExponential(15):String(a),e=c.split("e"),c=Number(e[0]),e=Number(e[1]),c=d.roundTo(c,14),b||isNaN(this.precision)||(c=d.roundTo(c,this.precision)),10==c&&(c=1,e+=1),c=c+"e"+e,0===a&&(c="0"),1==a&&(c="1")):(h&&(e=String(a).split("."),e[1]?(f.precision=e[1].length,0>c&&(f.precision=Math.abs(c)),b&&1<a&&(f.precision=0),b||isNaN(this.precision)||(f.precision=this.precision)):f.precision=-1),c=this.usePrefixes?d.addPrefix(a,g.prefixesOfBigNumbers,g.prefixesOfSmallNumbers,f,!b):d.formatNumber(a,f,f.precision)),this.duration&&(b&&(f.precision=0),c=d.formatDuration(a,this.duration,"",this.durationUnits,this.maxInterval,f)),"date"==this.type&&(c=d.formatDate(new Date(a),this.currentDateFormat,g)),this.recalculateToPercents?c+="%":(b=this.unit)&&(c="left"==this.unitPosition?b+c:c+b),this.labelFunction&&(c="date"==this.type?this.labelFunction(c,new Date(a),this).toString():this.labelFunction(a,c,this).toString()),c},getMinorGridStep:function(a,b){var c=[5,4,2];60>b&&c.shift();for(var e=Math.floor(Math.log(Math.abs(a))*Math.LOG10E),d=0;d<c.length;d++){var f=a/c[d],g=Math.floor(Math.log(Math.abs(f))*Math.LOG10E);if(!(1<Math.abs(e-g)))if(1>a){if(g=Math.pow(10,-g)*f,g==Math.round(g))return f}else if(f==Math.round(f))return f}},stackGraphs:function(a){var b=this.stackType;"stacked"==b&&(b="regular");"line"==b&&(b="none");"100% stacked"==b&&(b="100%");this.stackType=b;var c=[],e=[],h=[],f=[],g,k=this.chart.graphs,l,m,p,q,n,t=this.baseValue,r=!1;if("line"==a||"step"==a||"smoothedLine"==a)r=!0;if(r&&("regular"==b||"100%"==b))for(q=0;q<k.length;q++)p=k[q],p.stackGraph=null,p.hidden||(m=p.type,p.chart==this.chart&&p.valueAxis==this&&a==m&&p.stackable&&(l&&(p.stackGraph=l),l=p));p=this.start-10;l=this.end+10;q=this.data.length-1;p=d.fitToBounds(p,0,q);l=d.fitToBounds(l,0,q);for(n=p;n<=l;n++){var w=0;for(q=0;q<k.length;q++)if(p=k[q],p.hidden)p.newStack&&(h[n]=NaN,e[n]=NaN);else if(m=p.type,p.chart==this.chart&&p.valueAxis==this&&a==m&&p.stackable)if(m=this.data[n].axes[this.id].graphs[p.id],g=m.values.value,isNaN(g))p.newStack&&(h[n]=NaN,e[n]=NaN);else{var z=d.getDecimals(g);w<z&&(w=z);isNaN(f[n])?f[n]=Math.abs(g):f[n]+=Math.abs(g);f[n]=d.roundTo(f[n],w);z=p.fillToGraph;r&&z&&(z=this.data[n].axes[this.id].graphs[z.id])&&(m.values.open=z.values.value);"regular"==b&&(r&&(isNaN(c[n])?(c[n]=g,m.values.close=g,m.values.open=this.baseValue):(isNaN(g)?m.values.close=c[n]:m.values.close=g+c[n],m.values.open=c[n],c[n]=m.values.close)),"column"==a&&(p.newStack&&(h[n]=NaN,e[n]=NaN),m.values.close=g,0>g?(m.values.close=g,isNaN(e[n])?m.values.open=t:(m.values.close+=e[n],m.values.open=e[n]),e[n]=m.values.close):(m.values.close=g,isNaN(h[n])?m.values.open=t:(m.values.close+=h[n],m.values.open=h[n]),h[n]=m.values.close)))}}for(n=this.start;n<=this.end;n++)for(q=0;q<k.length;q++)(p=k[q],p.hidden)?p.newStack&&(h[n]=NaN,e[n]=NaN):(m=p.type,p.chart==this.chart&&p.valueAxis==this&&a==m&&p.stackable&&(m=this.data[n].axes[this.id].graphs[p.id],g=m.values.value,isNaN(g)||(c=g/f[n]*100,m.values.percents=c,m.values.total=f[n],p.newStack&&(h[n]=NaN,e[n]=NaN),"100%"==b&&(isNaN(e[n])&&(e[n]=0),isNaN(h[n])&&(h[n]=0),0>c?(m.values.close=d.fitToBounds(c+e[n],-100,100),m.values.open=e[n],e[n]=m.values.close):(m.values.close=d.fitToBounds(c+h[n],-100,100),m.values.open=h[n],h[n]=m.values.close)))))},recalculate:function(){var a=this.chart,b=a.graphs,c;for(c=0;c<b.length;c++){var e=b[c];if(e.valueAxis==this){var h="value";if("candlestick"==e.type||"ohlc"==e.type)h="open";var f,g,k=this.end+2,k=d.fitToBounds(this.end+1,0,this.data.length-1),l=this.start;0<l&&l--;var m;g=this.start;e.compareFromStart&&(g=0);if(!isNaN(a.startTime)&&(m=a.categoryAxis)){var p=m.minDuration(),p=new Date(a.startTime+p/2),q=d.resetDateToMin(new Date(a.startTime),m.minPeriod).getTime();d.resetDateToMin(new Date(p),m.minPeriod).getTime()>q&&g++}if(m=a.recalculateFromDate)m=d.getDate(m,a.dataDateFormat,"fff"),g=a.getClosestIndex(a.chartData,"time",m.getTime(),!0,0,a.chartData.length),k=a.chartData.length-1;for(m=g;m<=k&&(g=this.data[m].axes[this.id].graphs[e.id],f=g.values[h],e.recalculateValue&&(f=g.dataContext[e.valueField+e.recalculateValue]),isNaN(f));m++);this.recBaseValue=f;for(h=l;h<=k;h++){g=this.data[h].axes[this.id].graphs[e.id];g.percents={};var l=g.values,n;for(n in l)g.percents[n]="percents"!=n?l[n]/f*100-100:l[n]}}}},getMinMax:function(){var a=!1,b=this.chart,c=b.graphs,e;for(e=0;e<c.length;e++){var h=c[e].type;("line"==h||"step"==h||"smoothedLine"==h)&&this.expandMinMax&&(a=!0)}a&&(0<this.start&&this.start--,this.end<this.data.length-1&&this.end++);"serial"==b.type&&(!0!==b.categoryAxis.parseDates||a||this.end<this.data.length-1&&this.end++);this.includeAllValues&&(this.start=0,this.end=this.data.length-1);a=this.minMaxMultiplier;b=this.getExtremes(this.start,this.end);this.min=b.min;this.max=b.max;this.minRR=this.min;this.maxRR=this.max;a=(this.max-this.min)*(a-1);this.min-=a;this.max+=a;a=this.guides.length;if(this.includeGuidesInMinMax&&0<a)for(b=0;b<a;b++)c=this.guides[b],c.toValue<this.min&&(this.min=c.toValue),c.value<this.min&&(this.min=c.value),c.toValue>this.max&&(this.max=c.toValue),c.value>this.max&&(this.max=c.value);isNaN(this.minimum)||(this.min=this.minimum);isNaN(this.maximum)||(this.max=this.maximum);"date"==this.type&&this.getDateMinMax();this.min>this.max&&(a=this.max,this.max=this.min,this.min=a);isNaN(this.minZoom)||(this.min=this.minZoom);isNaN(this.maxZoom)||(this.max=this.maxZoom);this.minCalc=this.min;this.maxCalc=this.max;this.minReal=this.min;this.maxReal=this.max;0===this.min&&0===this.max&&(this.max=9);this.min>this.max&&(this.min=this.max-1);a=this.min;b=this.max;c=this.max-this.min;e=0===c?Math.pow(10,Math.floor(Math.log(Math.abs(this.max))*Math.LOG10E))/10:Math.pow(10,Math.floor(Math.log(Math.abs(c))*Math.LOG10E))/10;isNaN(this.maximum)&&(this.max=Math.ceil(this.max/e)*e+e);isNaN(this.minimum)&&(this.min=
-Math.floor(this.min/e)*e-e);0>this.min&&0<=a&&(this.min=0);0<this.max&&0>=b&&(this.max=0);"100%"==this.stackType&&(this.min=0>this.min?-100:0,this.max=0>this.max?0:100);c=this.max-this.min;e=Math.pow(10,Math.floor(Math.log(Math.abs(c))*Math.LOG10E))/10;this.step=Math.ceil(c/this.gridCountR/e)*e;c=Math.pow(10,Math.floor(Math.log(Math.abs(this.step))*Math.LOG10E));c=d.fixStepE(c);e=Math.ceil(this.step/c);5<e&&(e=10);5>=e&&2<e&&(e=5);this.step=Math.ceil(this.step/(c*e))*c*e;isNaN(this.setStep)||(this.step=
-this.setStep);1>c?(this.maxDecCount=Math.abs(Math.log(Math.abs(c))*Math.LOG10E),this.maxDecCount=Math.round(this.maxDecCount),this.step=d.roundTo(this.step,this.maxDecCount+1)):this.maxDecCount=0;this.min=this.step*Math.floor(this.min/this.step);this.max=this.step*Math.ceil(this.max/this.step);0>this.min&&0<=a&&(this.min=0);0<this.max&&0>=b&&(this.max=0);1<this.minReal&&1<this.max-this.minReal&&(this.minReal=Math.floor(this.minReal));c=Math.pow(10,Math.floor(Math.log(Math.abs(this.minReal))*Math.LOG10E));0===this.min&&(this.minReal=c);0===this.min&&1<this.minReal&&(this.minReal=1);0<this.min&&0<this.minReal-this.step&&(this.minReal=this.min+this.step<this.minReal?this.min+this.step:this.min);this.logarithmic&&(2<Math.log(b)*Math.LOG10E-Math.log(a)*Math.LOG10E?(this.minReal=this.min=Math.pow(10,Math.floor(Math.log(Math.abs(a))*Math.LOG10E)),this.maxReal=this.max=Math.pow(10,Math.ceil(Math.log(Math.abs(b))*Math.LOG10E))):(a=Math.pow(10,Math.floor(Math.log(Math.abs(a))*Math.LOG10E))/10,Math.pow(10,Math.floor(Math.log(Math.abs(this.min))*
-Math.LOG10E))/10<a&&(this.minReal=this.min=10*a)))},getExtremes:function(a,b){var c,e,d;for(d=a;d<=b;d++){var f=this.data[d].axes[this.id].graphs,g;for(g in f)if(f.hasOwnProperty(g)){var k=this.chart.graphsById[g];if(k.includeInMinMax&&(!k.hidden||this.includeHidden)){isNaN(c)&&(c=Infinity);isNaN(e)&&(e=-Infinity);this.foundGraphs=!0;k=f[g].values;this.recalculateToPercents&&(k=f[g].percents);var l;if(this.minMaxField)l=k[this.minMaxField],l<c&&(c=l),l>e&&(e=l);else for(var m in k)k.hasOwnProperty(m)&&
-"percents"!=m&&"total"!=m&&"error"!=m&&(l=k[m],l<c&&(c=l),l>e&&(e=l))}}}return{min:c,max:e}},zoomOut:function(a){this.maxZoom=this.minZoom=NaN;this.zoomToRelativeValues(0,1,a)},zoomToRelativeValues:function(a,b,c){if(this.reversed){var e=a;a=1-b;b=1-e}var d=this.fullMax,e=this.fullMin,f=e+(d-e)*a,g=e+(d-e)*b;0<=this.minimum&&0>f&&(f=0);this.logarithmic&&(isNaN(this.minimum)||(e=this.minimum),isNaN(this.maximum)||(d=this.maximum),d=Math.log(d)*Math.LOG10E-Math.log(e)*Math.LOG10E,f=Math.pow(10,d*a+
-Math.log(e)*Math.LOG10E),g=Math.pow(10,d*b+Math.log(e)*Math.LOG10E));return this.zoomToValues(f,g,c)},zoomToValues:function(a,b,c){if(b<a){var e=b;b=a;a=e}var h=this.fullMax,e=this.fullMin;this.relativeStart=d.roundTo((a-e)/(h-e),9);this.relativeEnd=d.roundTo((b-e)/(h-e),9);if(this.logarithmic){isNaN(this.minimum)||(e=this.minimum);isNaN(this.maximum)||(h=this.maximum);var h=Math.log(h)*Math.LOG10E-Math.log(e)*Math.LOG10E,f=Math.log(b)/Math.LN10-Math.log(e)*Math.LOG10E;this.relativeStart=d.roundTo((Math.log(a)/
-Math.LN10-Math.log(e)*Math.LOG10E)/h,9);this.relativeEnd=d.roundTo(f/h,9)}if(this.minZoom!=a||this.maxZoom!=b)return this.minZoom=a,this.maxZoom=b,e={type:"axisZoomed"},e.chart=this.chart,e.valueAxis=this,e.startValue=a,e.endValue=b,e.relativeStart=this.relativeStart,e.relativeEnd=this.relativeEnd,this.prevStartValue==a&&this.prevEndValue==b||this.fire(e),this.prevStartValue=a,this.prevEndValue=b,c||(a={},d.copyProperties(e,a),a.type="axisIntZoomed",this.fire(a)),0===this.relativeStart&&1==this.relativeEnd&&
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b=document.createElement("div"),c=b.style;c.overflow="hidden";c.position="relative";c.textAlign="left";this.chartDiv=b;b=document.createElement("div");c=b.style;c.overflow="hidden";c.position="relative";c.textAlign="left";this.legendDiv=b;this.titleHeight=0;this.hideBalloonTime=150;this.handDrawScatter=2;this.cssScale=this.handDrawThickness=1;this.cssAngle=0;this.prefixesOfBigNumbers=[{number:1E3,prefix:"k"},{number:1E6,prefix:"M"},{number:1E9,prefix:"G"},{number:1E12,prefix:"T"},{number:1E15,prefix:"P"},{number:1E18,prefix:"E"},{number:1E21,prefix:"Z"},{number:1E24,prefix:"Y"}];this.prefixesOfSmallNumbers=[{number:1E-24,prefix:"y"},{number:1E-21,prefix:"z"},{number:1E-18,prefix:"a"},{number:1E-15,prefix:"f"},{number:1E-12,prefix:"p"},{number:1E-9,prefix:"n"},{number:1E-6,prefix:"\u03bc"},{number:.001,prefix:"m"}];this.panEventsEnabled=!0;this.product="amcharts";this.animations=[];this.balloon=new 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a="http://www."+a,e=c=0,d=this.realWidth,f=this.realHeight,g=this.type;if("serial"==g||"xy"==g||"gantt"==g)c=this.marginLeftReal,e=this.marginTopReal,d=c+this.plotAreaWidth,f=e+this.plotAreaHeight;var g=a+"/javascript-charts/",k="JavaScript charts",l="JS chart by amCharts";"ammap"==this.product&&(g=a+"/javascript-maps/",k="Interactive JavaScript maps",l="JS map by amCharts");a=document.createElement("a");l=document.createTextNode(l);a.setAttribute("href",g);a.setAttribute("title",k);this.urlTarget&&a.setAttribute("target",this.urlTarget);a.appendChild(l);this.chartDiv.appendChild(a);this.amLink=a;g=a.style;g.position="absolute";g.textDecoration="none";g.color=this.color;g.fontFamily=this.fontFamily;g.fontSize="11px";g.opacity=.7;g.display="block";var 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0===a.bulletAlpha&&(a.bulletAlpha=a.lineAlpha);if("step"==c||d.VML)a.noRounding=!1;var c=b.type;"gantt"==c&&(c="serial");clearTimeout(a.playedTO);if(!isNaN(a.valueAxis.min)&&!isNaN(a.valueAxis.max)){switch(c){case"serial":a.categoryAxis&&(a.createSerialGraph(),"candlestick"==a.type&&1>a.valueAxis.minMaxMultiplier&&a.positiveClip(a.set));break;case"radar":a.createRadarGraph();break;case"xy":a.createXYGraph()}a.playedTO=setTimeout(function(){a.setAnimationPlayed.call(a)},500*a.chart.startDuration)}},setAnimationPlayed:function(){this.animationPlayed=!0},createXYGraph:function(){var a=[],b=[],c=this.xAxis,e=this.yAxis;this.pmh=e.height;this.pmw=c.width;this.pmy=this.pmx=0;var d;for(d=this.start;d<=this.end;d++){var f=this.data[d].axes[c.id].graphs[this.id],g=f.values,k=g.x,l=g.y,g=c.getCoordinate(k,this.noRounding),m=e.getCoordinate(l,this.noRounding);if(!isNaN(k)&&!isNaN(l)&&(a.push(g),b.push(m),f.x=g,f.y=m,k=this.createBullet(f,g,m,d),l=this.labelText)){var l=this.createLabel(f,l),p=0;k&&(p=k.size);this.positionLabel(f,g,m,l,p)}}this.drawLineGraph(a,b);this.launchAnimation()},createRadarGraph:function(){var a=this.valueAxis.stackType,b=[],c=[],e=[],d=[],f,g,k,l,m;for(m=this.start;m<=this.end;m++){var p=this.data[m].axes[this.valueAxis.id].graphs[this.id],q,n;"none"==a||"3d"==a?q=p.values.value:(q=p.values.close,n=p.values.open);if(isNaN(q))this.connect||(this.drawLineGraph(b,c,e,d),b=[],c=[],e=[],d=[]);else{var t=this.valueAxis.getCoordinate(q,this.noRounding)-this.height,t=t*this.valueAxis.rMultiplier,r=-360/(this.end-this.start+1)*m;"middle"==this.valueAxis.pointPosition&&(r-=180/(this.end-this.start+1));q=t*Math.sin(r/180*Math.PI);t*=Math.cos(r/180*Math.PI);b.push(q);c.push(t);if(!isNaN(n)){var w=this.valueAxis.getCoordinate(n,this.noRounding)-this.height,w=w*this.valueAxis.rMultiplier,z=w*Math.sin(r/180*Math.PI),r=w*Math.cos(r/180*Math.PI);e.push(z);d.push(r);isNaN(k)&&(k=z);isNaN(l)&&(l=r)}r=this.createBullet(p,q,t,m);p.x=q;p.y=t;if(z=this.labelText)z=this.createLabel(p,z),w=0,r&&(w=r.size),this.positionLabel(p,q,t,z,w);isNaN(f)&&(f=q);isNaN(g)&&(g=t)}}b.push(f);c.push(g);isNaN(k)||(e.push(k),d.push(l));this.drawLineGraph(b,c,e,d);this.launchAnimation()},positionLabel:function(a,b,c,e,d){if(e){var f=this.chart,g=this.valueAxis,k="middle",l=!1,m=this.labelPosition,p=e.getBBox(),q=this.chart.rotate,n=a.isNegative,t=this.fontSize;void 0===t&&(t=this.chart.fontSize);c-=p.height/2-t/2-1;void 0!==a.labelIsNegative&&(n=a.labelIsNegative);switch(m){case"right":m=q?n?"left":"right":"right";break;case"top":m=q?"top":n?"bottom":"top";break;case"bottom":m=q?"bottom":n?"top":"bottom";break;case"left":m=q?n?"right":"left":"left"}var t=a.columnGraphics,r=0,w=0;t&&(r=t.x,w=t.y);var z=this.labelOffset;switch(m){case"right":k="start";b+=d/2+z;break;case"top":c=g.reversed?c+(d/2+p.height/2+z):c-(d/2+p.height/2+z);break;case"bottom":c=g.reversed?c-(d/2+p.height/2+z):c+(d/2+p.height/2+z);break;case"left":k="end";b-=d/2+z;break;case"inside":"column"==this.type&&(l=!0,q?n?(k="end",b=r-3-z):(k="start",b=r+3+z):c=n?w+7+z:w-10-z);break;case"middle":"column"==this.type&&(l=!0,q?b-=(b-r)/2+z-3:c-=(c-w)/2+z-3)}"auto"!=this.labelAnchor&&(k=this.labelAnchor);e.attr({"text-anchor":k});this.labelRotation&&e.rotate(this.labelRotation);e.translate(b,c);!this.showAllValueLabels&&t&&l&&(p=e.getBBox(),p.height>a.columnHeight||p.width>a.columnWidth)&&(e.remove(),e=null);if(e&&"radar"!=f.type)if(q){if(0>c||c>this.height)e.remove(),e=null;!this.showAllValueLabels&&e&&(0>b||b>this.width)&&(e.remove(),e=null)}else{if(0>b||b>this.width)e.remove(),
-e=null;!this.showAllValueLabels&&e&&(0>c||c>this.height)&&(e.remove(),e=null)}e&&this.allBullets.push(e);return e}},getGradRotation:function(){var a=270;"horizontal"==this.gradientOrientation&&(a=0);return this.gradientRotation=a},createSerialGraph:function(){this.dashLengthSwitched=this.fillColorsSwitched=this.lineColorSwitched=void 0;var a=this.chart,b=this.id,c=this.index,e=this.data,h=this.chart.container,f=this.valueAxis,g=this.type,k=this.columnWidthReal,l=this.showBulletsAt;isNaN(this.columnWidth)||(k=this.columnWidth);isNaN(k)&&(k=.8);var m=this.useNegativeColorIfDown,p=this.width,q=this.height,n=this.y,t=this.rotate,r=this.columnCount,w=d.toCoordinate(this.cornerRadiusTop,k/2),z=this.connect,x=[],u=[],A,y,B,D,C=this.chart.graphs.length,I,H=this.dx/this.tcc,Q=this.dy/this.tcc,M=f.stackType,P=this.start,ia=this.end,J=this.scrollbar,aa="graph-column-";J&&(aa="scrollbar-graph-column-");var ma=this.categoryAxis,na=this.baseCoord,Pa=this.negativeBase,Z=this.columnIndex,da=this.lineThickness,X=this.lineAlpha,xa=this.lineColorR,ea=this.dashLength,fa=this.set,Ba,ga=this.getGradRotation(),V=this.chart.columnSpacing,Y=ma.cellWidth,Da=(Y*k-r)/r;V>Da&&(V=Da);var G,v,oa,ha=q,Qa=p,ca=0,tb=0,ub=0,vb=0,gb=0,hb=0,wb=this.fillColorsR,Ra=this.negativeFillColors,Ja=this.negativeLineColor,Ya=this.fillAlphas,Za=this.negativeFillAlphas;"object"==typeof Ya&&(Ya=Ya[0]);"object"==typeof Za&&(Za=Za[0]);var xb=this.noRounding;"step"==g&&(xb=!1);var ib=f.getCoordinate(f.min);f.logarithmic&&(ib=f.getCoordinate(f.minReal));this.minCoord=
-ib;this.resetBullet&&(this.bullet="none");if(!(J||"line"!=g&&"smoothedLine"!=g&&"step"!=g||(1==e.length&&"step"!=g&&"none"==this.bullet&&(this.bullet="round",this.resetBullet=!0),!Ra&&void 0==Ja||m))){var Ua=Pa;Ua>f.max&&(Ua=f.max);Ua<f.min&&(Ua=f.min);f.logarithmic&&(Ua=f.minReal);var Ka=f.getCoordinate(Ua),Mb=f.getCoordinate(f.max);t?(ha=q,Qa=Math.abs(Mb-Ka),ub=q,vb=Math.abs(ib-Ka),hb=tb=0,f.reversed?(ca=0,gb=Ka):(ca=Ka,gb=0)):(Qa=p,ha=Math.abs(Mb-Ka),vb=p,ub=Math.abs(ib-Ka),gb=ca=0,f.reversed?(hb=n,tb=Ka):hb=Ka)}var La=Math.round;this.pmx=La(ca);this.pmy=La(tb);this.pmh=La(ha);this.pmw=La(Qa);this.nmx=La(gb);this.nmy=La(hb);this.nmh=La(ub);this.nmw=La(vb);d.isModern||(this.nmy=this.nmx=0,this.nmh=this.height);this.clustered||(r=1);k="column"==g?(Y*k-V*(r-1))/r:Y*k;1>k&&(k=1);var Nb=this.fixedColumnWidth;isNaN(Nb)||(k=Nb);var L;if("line"==g||"step"==g||"smoothedLine"==g){if(0<P){for(L=P-1;-1<L;L--)if(G=e[L],v=G.axes[f.id].graphs[b],oa=v.values.value,!isNaN(oa)){P=L;break}if(this.lineColorField)for(L=
-P;-1<L;L--)if(G=e[L],v=G.axes[f.id].graphs[b],v.lineColor){this.lineColorSwitched=v.lineColor;void 0===this.bulletColor&&(this.bulletColorSwitched=this.lineColorSwitched);break}if(this.fillColorsField)for(L=P;-1<L;L--)if(G=e[L],v=G.axes[f.id].graphs[b],v.fillColors){this.fillColorsSwitched=v.fillColors;break}if(this.dashLengthField)for(L=P;-1<L;L--)if(G=e[L],v=G.axes[f.id].graphs[b],!isNaN(v.dashLength)){this.dashLengthSwitched=v.dashLength;break}}if(ia<e.length-1)for(L=ia+1;L<e.length;L++)if(G=e[L],v=G.axes[f.id].graphs[b],oa=v.values.value,!isNaN(oa)){ia=L;break}}ia<e.length-1&&ia++;var T=[],U=[],Ma=!1;if("line"==g||"step"==g||"smoothedLine"==g)if(this.stackable&&"regular"==M||"100%"==M||this.fillToGraph)Ma=!0;var Ob=this.noStepRisers,jb=-1E3,kb=-1E3,lb=this.minDistance,Sa=!0,$a=!1;for(L=P;L<=ia;L++){G=e[L];v=G.axes[f.id].graphs[b];v.index=L;var ab,Ta=NaN;if(m&&void 0==this.openField)for(var yb=L+1;yb<e.length&&(!e[yb]||!(ab=e[L+1].axes[f.id].graphs[b])||!ab.values||(Ta=ab.values.value,isNaN(Ta)));yb++);var S,R,K,ba,ja=NaN,E=NaN,F=NaN,O=NaN,N=NaN,qa=NaN,ra=NaN,sa=NaN,ta=NaN,ya=NaN,Ea=NaN,ka=NaN,la=NaN,W=NaN,zb=NaN,Ab=NaN,ua=NaN,va=void 0,Na=wb,Va=Ya,Ha=xa,Ca,za,Bb=this.proCandlesticks,mb=this.topRadius,Fa=q-1,pa=p-1,bb=this.pattern;void 0!=v.pattern&&(bb=v.pattern);isNaN(v.alpha)||(Va=v.alpha);isNaN(v.dashLength)||(ea=v.dashLength);var Ia=v.values;f.recalculateToPercents&&(Ia=v.percents);"none"==M&&(Z=isNaN(v.columnIndex)?this.columnIndex:v.columnIndex);if(Ia){W=this.stackable&&"none"!=M&&"3d"!=M?Ia.close:Ia.value;if("candlestick"==g||"ohlc"==g)W=Ia.close,Ab=Ia.low,ra=f.getCoordinate(Ab),zb=Ia.high,ta=f.getCoordinate(zb);ua=Ia.open;F=f.getCoordinate(W,xb);isNaN(ua)||(N=f.getCoordinate(ua,xb),m&&"regular"!=M&&"100%"!=M&&(Ta=ua,ua=N=NaN));m&&(void 0==this.openField?ab&&(ab.isNegative=Ta<W?!0:!1,isNaN(Ta)&&(v.isNegative=!Sa)):v.isNegative=Ta>W?!0:!1);if(!J)switch(this.showBalloonAt){case"close":v.y=F;break;case"open":v.y=N;break;case"high":v.y=ta;break;case"low":v.y=ra}var ja=G.x[ma.id],Wa=this.periodSpan-1;"step"!=g||isNaN(G.cellWidth)||(Y=G.cellWidth);var wa=Math.floor(Y/2)+Math.floor(Wa*Y/2),Ga=wa,nb=0;"left"==this.stepDirection&&(nb=(2*Y+Wa*Y)/2,ja-=nb);"center"==this.stepDirection&&(nb=Y/2,ja-=nb);"start"==this.pointPosition&&(ja-=Y/2+Math.floor(Wa*Y/2),wa=0,Ga=Math.floor(Y)+Math.floor(Wa*Y));"end"==this.pointPosition&&(ja+=Y/2+Math.floor(Wa*Y/2),wa=Math.floor(Y)+Math.floor(Wa*Y),Ga=0);if(Ob){var Cb=this.columnWidth;isNaN(Cb)||(wa*=Cb,Ga*=Cb)}J||(v.x=ja);-1E5>ja&&(ja=-1E5);
-ja>p+1E5&&(ja=p+1E5);t?(E=F,O=N,N=F=ja,isNaN(ua)&&!this.fillToGraph&&(O=na),qa=ra,sa=ta):(O=E=ja,isNaN(ua)&&!this.fillToGraph&&(N=na));if(!Bb&&W<ua||Bb&&W<Ba)v.isNegative=!0,Ra&&(Na=Ra),Za&&(Va=Za),void 0!=Ja&&(Ha=Ja);$a=!1;isNaN(W)||(m?W>Ta?(Sa&&($a=!0),Sa=!1):(Sa||($a=!0),Sa=!0):v.isNegative=W<Pa?!0:!1,Ba=W);var Pb=!1;J&&a.chartScrollbar.ignoreCustomColors&&(Pb=!0);Pb||(void 0!=v.color&&(Na=v.color),v.fillColors&&(Na=v.fillColors));F=d.fitToBounds(F,-3E4,3E4);switch(g){case"line":if(isNaN(W))z||(this.drawLineGraph(x,u,T,U),x=[],u=[],T=[],U=[]);else{if(Math.abs(E-jb)>=lb||Math.abs(F-kb)>=lb)x.push(E),u.push(F),jb=E,kb=F;ya=E;Ea=F;ka=E;la=F;!Ma||isNaN(N)||isNaN(O)||(T.push(O),U.push(N));if($a||void 0!=v.lineColor&&v.lineColor!=this.lineColorSwitched||void 0!=v.fillColors&&v.fillColors!=this.fillColorsSwitched||!isNaN(v.dashLength))this.drawLineGraph(x,u,T,U),x=[E],u=[F],T=[],U=[],!Ma||isNaN(N)||isNaN(O)||(T.push(O),U.push(N)),m?(Sa?(this.lineColorSwitched=xa,this.fillColorsSwitched=wb):(this.lineColorSwitched=Ja,this.fillColorsSwitched=Ra),void 0===this.bulletColor&&(this.bulletColorSwitched=xa)):(this.lineColorSwitched=v.lineColor,this.fillColorsSwitched=v.fillColors,void 0===this.bulletColor&&(this.bulletColorSwitched=this.lineColorSwitched)),this.dashLengthSwitched=v.dashLength;v.gap&&(this.drawLineGraph(x,u,T,U),x=[],u=[],T=[],U=[])}break;case"smoothedLine":if(isNaN(W))z||(this.drawSmoothedGraph(x,u,T,U),x=[],u=[],T=[],U=[]);else{if(Math.abs(E-jb)>=lb||Math.abs(F-kb)>=lb)x.push(E),u.push(F),jb=E,kb=F;ya=E;Ea=F;ka=E;la=F;!Ma||isNaN(N)||isNaN(O)||(T.push(O),U.push(N));void 0==v.lineColor&&void 0==v.fillColors&&isNaN(v.dashLength)||(this.drawSmoothedGraph(x,u,T,U),x=[E],u=[F],T=[],U=[],!Ma||isNaN(N)||isNaN(O)||(T.push(O),U.push(N)),this.lineColorSwitched=v.lineColor,this.fillColorsSwitched=v.fillColors,this.dashLengthSwitched=v.dashLength);v.gap&&(this.drawSmoothedGraph(x,u,T,U),x=[],u=[],T=[],U=[])}break;case"step":if(!isNaN(W)){t?(isNaN(A)||(x.push(A),u.push(F-wa)),u.push(F-wa),x.push(E),u.push(F+Ga),x.push(E),!Ma||isNaN(N)||isNaN(O)||(isNaN(B)||(T.push(B),U.push(N-wa)),T.push(O),U.push(N-wa),T.push(O),U.push(N+Ga))):(isNaN(y)||(u.push(y),x.push(E-wa)),x.push(E-wa),u.push(F),x.push(E+Ga),u.push(F),!Ma||isNaN(N)||isNaN(O)||(isNaN(D)||(T.push(O-wa),U.push(D)),T.push(O-wa),U.push(N),T.push(O+Ga),U.push(N)));A=E;y=F;B=O;D=N;ya=E;Ea=F;ka=E;la=F;if($a||void 0!=v.lineColor||void 0!=v.fillColors||!isNaN(v.dashLength)){var Db=x[x.length-2],dc=u[u.length-2];x.pop();u.pop();T.pop();U.pop();this.drawLineGraph(x,u,T,U);x=[Db];u=[dc];T=[];U=[];Ma&&(T=[Db,Db+wa+Ga],U=[D,D]);t?(u.push(F+Ga),x.push(E)):(x.push(E+Ga),u.push(F));this.lineColorSwitched=v.lineColor;this.fillColorsSwitched=v.fillColors;this.dashLengthSwitched=v.dashLength;m&&(Sa?(this.lineColorSwitched=xa,this.fillColorsSwitched=wb):(this.lineColorSwitched=Ja,this.fillColorsSwitched=Ra))}if(Ob||v.gap)A=y=NaN,this.drawLineGraph(x,u,T,U),x=[],u=[],T=[],U=[]}else if(!z){if(1>=this.periodSpan||1<this.periodSpan&&E-A>wa+Ga)A=y=NaN;this.drawLineGraph(x,u,T,U);x=[];u=[];T=[];U=[]}break;case"column":Ca=Ha;void 0!=v.lineColor&&(Ca=v.lineColor);if(!isNaN(W)){m||(v.isNegative=W<Pa?!0:!1);v.isNegative&&(Ra&&(Na=Ra),void 0!=Ja&&(Ca=Ja));var Qb=f.min,Rb=f.max,ob=ua;isNaN(ob)&&(ob=Pa);if(!(W<Qb&&ob<Qb||W>Rb&&ob>Rb)){var Aa;if(t){"3d"==M?(R=F-(r/2-this.depthCount+1)*(k+V)+V/2+Q*Z,S=O+H*Z,Aa=Z):(R=Math.floor(F-(r/2-Z)*(k+V)+V/2),S=O,Aa=0);K=k;ya=E;Ea=R+k/2;ka=E;la=R+k/2;R+K>q+Aa*Q&&(K=q-R+Aa*Q);R<Aa*Q&&(K+=R,R=Aa*Q);ba=E-O;var ec=S;S=d.fitToBounds(S,0,p);ba+=ec-S;ba=d.fitToBounds(ba,-S,p-S+H*Z);v.labelIsNegative=0>ba?!0:!1;0===ba&&1/W===1/-0&&(v.labelIsNegative=!0);isNaN(G.percentWidthValue)||(K=this.height*G.percentWidthValue/100,R=ja-K/2,Ea=R+K/2);K=d.roundTo(K,2);ba=d.roundTo(ba,2);R<q&&0<K&&(va=new d.Cuboid(h,ba,K,H-a.d3x,Q-a.d3y,Na,Va,da,Ca,X,ga,w,t,ea,bb,mb,aa),v.columnWidth=Math.abs(ba),v.columnHeight=Math.abs(K))}else{"3d"==M?(S=E-(r/2-this.depthCount+1)*(k+V)+V/2+H*Z,R=N+Q*Z,Aa=Z):(S=E-(r/2-Z)*(k+V)+V/2,R=N,Aa=0);K=k;ya=S+k/2;Ea=F;ka=S+k/2;la=F;S+K>p+Aa*H&&(K=p-S+Aa*H);S<Aa*H&&(K+=S-Aa*H,S=Aa*H);ba=F-N;v.labelIsNegative=0<ba?!0:!1;0===ba&&1/W!==1/Math.abs(W)&&(v.labelIsNegative=!0);var fc=R;R=d.fitToBounds(R,this.dy,q);ba+=fc-R;ba=d.fitToBounds(ba,-R+Q*Aa,q-R);isNaN(G.percentWidthValue)||(K=this.width*G.percentWidthValue/100,S=ja-K/2,ya=S+K/2);K=d.roundTo(K,2);ba=d.roundTo(ba,2);S<p+Z*H&&0<K&&(this.showOnAxis&&(R-=Q/2),va=new d.Cuboid(h,K,ba,H-a.d3x,Q-a.d3y,Na,Va,da,Ca,this.lineAlpha,ga,w,t,ea,bb,mb,aa),v.columnHeight=Math.abs(ba),v.columnWidth=Math.abs(K))}}if(va){za=va.set;d.setCN(a,va.set,"graph-"+this.type);d.setCN(a,va.set,"graph-"+this.id);v.className&&d.setCN(a,va.set,v.className,!0);v.columnGraphics=za;S=d.roundTo(S,2);R=d.roundTo(R,2);za.translate(S,R);(v.url||this.showHandOnHover)&&za.setAttr("cursor","pointer");if(!J){"none"==M&&(I=t?(this.end+1-L)*C-c:C*L+c);"3d"==M&&(t?(I=(this.end+1-L)*C-c-1E3*this.depthCount,ya+=H*Z,ka+=H*Z,v.y+=H*Z):(I=(C-c)*(L+1)+1E3*this.depthCount,Ea+=Q*Z,la+=Q*Z,v.y+=Q*Z));if("regular"==M||"100%"==M)I=t?0<Ia.value?(this.end+1-L)*C+c:(this.end+1-L)*C-c:0<Ia.value?C*L+c:C*L-c;this.columnsArray.push({column:va,depth:I});v.x=t?R+K/2:S+K/2;this.ownColumns.push(va);this.animateColumns(va,L,E,O,F,N);this.addListeners(za,v);void 0!==this.tabIndex&&za.setAttr("tabindex",this.tabIndex)}this.columnsSet.push(za)}}break;case"candlestick":if(!isNaN(ua)&&!isNaN(W)){var Xa,cb;Ca=Ha;void 0!=v.lineColor&&(Ca=v.lineColor);ya=E;la=Ea=F;ka=E;if(t){"open"==l&&(ka=O);"high"==l&&(ka=sa);"low"==l&&(ka=qa);E=d.fitToBounds(E,0,pa);O=d.fitToBounds(O,0,pa);qa=d.fitToBounds(qa,0,pa);sa=d.fitToBounds(sa,0,pa);if(0===E&&0===O&&0===qa&&0===sa)continue;if(E==pa&&O==pa&&qa==pa&&sa==pa)continue;R=F-k/2;S=O;K=k;R+K>q&&(K=q-R);0>R&&(K+=R,R=0);if(R<q&&0<K){var Eb,Fb;W>ua?(Eb=[E,sa],Fb=[O,qa]):(Eb=[O,sa],Fb=[E,qa]);!isNaN(sa)&&!isNaN(qa)&&F<q&&0<F&&(Xa=d.line(h,Eb,[F,F],Ca,X,da),cb=d.line(h,Fb,[F,F],Ca,X,da));ba=E-O;va=new d.Cuboid(h,ba,K,H,Q,Na,Ya,da,Ca,X,ga,w,t,ea,bb,mb,aa)}}else{"open"==l&&(la=N);"high"==l&&(la=ta);"low"==l&&(la=ra);F=d.fitToBounds(F,0,Fa);N=d.fitToBounds(N,0,Fa);ra=d.fitToBounds(ra,0,Fa);ta=d.fitToBounds(ta,0,Fa);if(0===F&&0===N&&0===ra&&0===ta)continue;if(F==Fa&&N==Fa&&ra==Fa&&ta==Fa)continue;S=E-k/2;R=N+da/2;K=k;S+K>p&&(K=p-S);0>S&&(K+=S,S=0);ba=F-N;if(S<p&&0<K){Bb&&W>=ua&&(Va=0);var va=new d.Cuboid(h,K,ba,H,Q,Na,Va,da,Ca,X,ga,w,t,ea,bb,mb,aa),Gb,Hb;W>ua?(Gb=[F,ta],Hb=[N,ra]):(Gb=[N,ta],Hb=[F,ra]);!isNaN(ta)&&!isNaN(ra)&&E<p&&0<E&&(Xa=d.line(h,[E,E],Gb,Ca,X,da),cb=d.line(h,[E,E],Hb,Ca,X,da),d.setCN(a,Xa,this.bcn+"line-high"),v.className&&d.setCN(a,Xa,v.className,!0),d.setCN(a,cb,this.bcn+"line-low"),v.className&&d.setCN(a,cb,v.className,!0))}}va&&(za=va.set,v.columnGraphics=za,fa.push(za),za.translate(S,R-da/2),(v.url||this.showHandOnHover)&&za.setAttr("cursor","pointer"),Xa&&(fa.push(Xa),fa.push(cb)),J||(v.x=t?R+K/2:S+K/2,this.animateColumns(va,L,E,O,F,N),this.addListeners(za,v),void 0!==this.tabIndex&&za.setAttr("tabindex",this.tabIndex)))}break;case"ohlc":if(!(isNaN(ua)||isNaN(zb)||isNaN(Ab)||isNaN(W))){var Sb=h.set();fa.push(Sb);W<ua&&(v.isNegative=!0,void 0!=Ja&&(Ha=Ja));void 0!=v.lineColor&&(Ha=v.lineColor);var pb,qb,rb;if(t){la=F;ka=E;"open"==l&&(ka=O);"high"==l&&(ka=sa);"low"==l&&(ka=qa);qa=d.fitToBounds(qa,0,pa);sa=d.fitToBounds(sa,0,pa);if(0===E&&0===O&&0===qa&&0===sa)continue;if(E==pa&&O==pa&&qa==pa&&sa==pa)continue;var Ib=F-k/2,Ib=d.fitToBounds(Ib,0,q),Tb=d.fitToBounds(F,0,q),Jb=F+k/2,Jb=d.fitToBounds(Jb,0,q);0<=O&&O<=pa&&(qb=d.line(h,[O,O],[Ib,Tb],Ha,X,da,ea));0<F&&F<q&&(pb=d.line(h,[qa,sa],[F,F],Ha,X,da,ea));0<=E&&E<=pa&&(rb=d.line(h,[E,E],[Tb,Jb],Ha,X,da,ea))}else{la=F;"open"==l&&(la=N);"high"==l&&(la=ta);"low"==l&&(la=ra);var ka=E,ra=d.fitToBounds(ra,0,Fa),ta=d.fitToBounds(ta,0,Fa),Kb=E-k/2,Kb=d.fitToBounds(Kb,0,p),Ub=d.fitToBounds(E,0,p),Lb=E+k/2,Lb=d.fitToBounds(Lb,0,p);0<=N&&N<=Fa&&(qb=d.line(h,[Kb,Ub],[N,N],Ha,X,da,ea));0<E&&E<p&&(pb=d.line(h,[E,E],[ra,ta],Ha,X,da,ea));0<=F&&F<=Fa&&(rb=d.line(h,[Ub,Lb],[F,F],Ha,X,da,ea))}fa.push(qb);fa.push(pb);fa.push(rb);d.setCN(a,qb,this.bcn+"stroke-open");d.setCN(a,rb,this.bcn+"stroke-close");d.setCN(a,pb,this.bcn+"stroke");v.className&&d.setCN(a,Sb,v.className,!0);ya=E;Ea=F}}if(!J&&!isNaN(W)){var Vb=this.hideBulletsCount;if(this.end-this.start<=Vb||0===Vb){var Wb=this.createBullet(v,ka,la,L),Xb=this.labelText;if(Xb&&!isNaN(ya)&&!isNaN(ya)){var gc=this.createLabel(v,Xb),Yb=0;Wb&&(Yb=Wb.size);this.positionLabel(v,ya,Ea,gc,Yb)}if("regular"==M||"100%"==M){var Zb=f.totalText;if(Zb){var Oa=this.createLabel(v,Zb,f.totalTextColor);d.setCN(a,Oa,this.bcn+"label-total");this.allBullets.push(Oa);if(Oa){var $b=Oa.getBBox(),ac=$b.width,bc=$b.height,db,eb,sb=f.totalTextOffset,cc=f.totals[L];cc&&cc.remove();var fb=0;"column"!=g&&(fb=this.bulletSize);t?(eb=Ea,db=0>W?E-ac/2-2-fb-sb:E+ac/2+3+fb+sb):(db=ya,eb=0>W?F+bc/2+fb+sb:F-bc/2-3-fb-sb);Oa.translate(db,eb);f.totals[L]=Oa;t?(0>eb||eb>q)&&Oa.remove():(0>db||db>p)&&Oa.remove()}}}}}}}this.lastDataItem=v;if("line"==g||"step"==g||"smoothedLine"==g)"smoothedLine"==g?this.drawSmoothedGraph(x,u,T,U):this.drawLineGraph(x,u,T,U),J||this.launchAnimation();this.bulletsHidden&&this.hideBullets();this.customBulletsHidden&&this.hideCustomBullets()},animateColumns:function(a,b){var c=this,e=c.chart.startDuration;0<e&&!c.animationPlayed&&(c.seqAn?(a.set.hide(),c.animationArray.push(a),e=setTimeout(function(){c.animate.call(c)},e/(c.end-c.start+1)*(b-c.start)*1E3),c.timeOuts.push(e)):c.animate(a),c.chart.animatable.push(a))},createLabel:function(a,b,c){var e=this.chart,h=a.labelColor;h||(h=this.color);h||(h=e.color);c&&(h=c);c=this.fontSize;void 0===c&&(this.fontSize=c=e.fontSize);var f=this.labelFunction;b=e.formatString(b,a);b=d.cleanFromEmpty(b);f&&(b=f(a,b));if(void 0!==b&&""!==b)return a=d.text(this.container,b,h,e.fontFamily,c),a.node.style.pointerEvents="none",d.setCN(e,a,this.bcn+"label"),this.bulletSet.push(a),a},positiveClip:function(a){a.clipRect(this.pmx,this.pmy,this.pmw,this.pmh)},negativeClip:function(a){a.clipRect(this.nmx,this.nmy,this.nmw,this.nmh)},drawLineGraph:function(a,b,c,e){var h=this;if(1<a.length){var f=h.noRounding,g=h.set,k=h.chart,l=h.container,m=l.set(),p=l.set();g.push(p);g.push(m);var q=h.lineAlpha,n=h.lineThickness,g=h.fillAlphas,t=h.lineColorR,r=h.negativeLineAlpha;isNaN(r)&&(r=q);var w=h.lineColorSwitched;w&&(t=w);var w=h.fillColorsR,z=h.fillColorsSwitched;z&&(w=z);var x=h.dashLength;(z=h.dashLengthSwitched)&&(x=z);var z=h.negativeLineColor,u=h.negativeFillColors,A=h.negativeFillAlphas,y=h.baseCoord;0!==h.negativeBase&&(y=h.valueAxis.getCoordinate(h.negativeBase,f),y>h.height&&(y=h.height),0>y&&(y=0));q=d.line(l,a,b,t,q,n,x,!1,!0,f);q.node.setAttribute("stroke-linejoin","round");d.setCN(k,q,h.bcn+"stroke");m.push(q);m.click(function(a){h.handleGraphEvent(a,"clickGraph")}).mouseover(function(a){h.handleGraphEvent(a,"rollOverGraph")}).mouseout(function(a){h.handleGraphEvent(a,"rollOutGraph")}).touchmove(function(a){h.chart.handleMouseMove(a)}).touchend(function(a){h.chart.handleTouchEnd(a)});void 0===z||h.useNegativeColorIfDown||(n=d.line(l,a,b,z,r,n,x,!1,!0,f),n.node.setAttribute("stroke-linejoin","round"),d.setCN(k,n,h.bcn+"stroke"),d.setCN(k,n,h.bcn+"stroke-negative"),p.push(n));if(0<g||0<A)if(n=a.join(";").split(";"),r=b.join(";").split(";"),q=k.type,"serial"==q||"radar"==q?0<c.length?(c.reverse(),e.reverse(),n=a.concat(c),r=b.concat(e)):"radar"==q?(r.push(0),n.push(0)):h.rotate?(r.push(r[r.length-1]),n.push(y),r.push(r[0]),n.push(y),r.push(r[0]),n.push(n[0])):(n.push(n[n.length-1]),r.push(y),n.push(n[0]),r.push(y),n.push(a[0]),r.push(r[0])):"xy"==q&&(b=h.fillToAxis)&&(d.isString(b)&&(b=k.getValueAxisById(b)),"H"==b.orientation?(y="top"==b.position?0:b.height,n.push(n[n.length-1]),r.push(y),n.push(n[0]),r.push(y),n.push(a[0]),r.push(r[0])):(y="left"==b.position?0:b.width,r.push(r[r.length-1]),n.push(y),r.push(r[0]),n.push(y),r.push(r[0]),n.push(n[0]))),a=h.gradientRotation,0<g&&(b=d.polygon(l,n,r,w,g,1,"#000",0,a,f),b.pattern(h.pattern,NaN,k.path),d.setCN(k,b,h.bcn+"fill"),m.push(b)),u||void 0!==z)isNaN(A)&&(A=g),u||(u=z),f=d.polygon(l,n,r,u,A,1,"#000",0,a,f),d.setCN(k,f,h.bcn+"fill"),d.setCN(k,f,h.bcn+"fill-negative"),f.pattern(h.pattern,NaN,k.path),p.push(f),p.click(function(a){h.handleGraphEvent(a,"clickGraph")}).mouseover(function(a){h.handleGraphEvent(a,"rollOverGraph")}).mouseout(function(a){h.handleGraphEvent(a,"rollOutGraph")}).touchmove(function(a){h.chart.handleMouseMove(a)}).touchend(function(a){h.chart.handleTouchEnd(a)});h.applyMask(p,m)}},applyMask:function(a,b){var c=a.length();"serial"!=this.chart.type||this.scrollbar||(this.positiveClip(b),0<c&&this.negativeClip(a))},drawSmoothedGraph:function(a,b,c,e){if(1<a.length){var h=this.set,f=this.chart,g=this.container,k=g.set(),l=g.set();h.push(l);h.push(k);var m=this.lineAlpha,p=this.lineThickness,h=this.dashLength,q=this.fillAlphas,n=this.lineColorR,t=this.fillColorsR,r=this.negativeLineColor,w=this.negativeFillColors,z=this.negativeFillAlphas,x=this.baseCoord,u=this.lineColorSwitched;u&&(n=u);(u=this.fillColorsSwitched)&&(t=u);var A=this.negativeLineAlpha;isNaN(A)&&(A=m);u=this.getGradRotation();m=new d.Bezier(g,a,b,n,m,p,t,0,h,void 0,u);d.setCN(f,m,this.bcn+"stroke");k.push(m.path);void 0!==r&&(p=new d.Bezier(g,a,b,r,A,p,t,0,h,void 0,u),d.setCN(f,p,this.bcn+"stroke"),d.setCN(f,p,this.bcn+"stroke-negative"),l.push(p.path));0<q&&(p=a.join(";").split(";"),m=b.join(";").split(";"),n="",0<c.length?(c.push("M"),e.push("M"),c.reverse(),e.reverse(),p=a.concat(c),m=b.concat(e)):(this.rotate?(n+=" L"+x+","+b[b.length-1],n+=" L"+x+","+b[0]):(n+=" L"+a[a.length-1]+","+
-x,n+=" L"+a[0]+","+x),n+=" L"+a[0]+","+b[0]),a=new d.Bezier(g,p,m,NaN,0,0,t,q,h,n,u),d.setCN(f,a,this.bcn+"fill"),a.path.pattern(this.pattern,NaN,f.path),k.push(a.path),w||void 0!==r)&&(z||(z=q),w||(w=r),g=new d.Bezier(g,p,m,NaN,0,0,w,z,h,n,u),g.path.pattern(this.pattern,NaN,f.path),d.setCN(f,g,this.bcn+"fill"),d.setCN(f,g,this.bcn+"fill-negative"),l.push(g.path));this.applyMask(l,k)}},launchAnimation:function(){var a=this,b=a.chart.startDuration;if(0<b&&!a.animationPlayed){var c=a.set,e=a.bulletSet;d.VML||(c.attr({opacity:a.startAlpha}),e.attr({opacity:a.startAlpha}));c.hide();e.hide();a.seqAn?(b=setTimeout(function(){a.animateGraphs.call(a)},a.index*b*1E3),a.timeOuts.push(b)):a.animateGraphs()}},animateGraphs:function(){var a=this.chart,b=this.set,c=this.bulletSet,e=this.x,d=this.y;b.show();c.show();var f=a.startDuration,g=a.startEffect;b&&(this.rotate?(b.translate(-1E3,d),c.translate(-1E3,d)):(b.translate(e,-1E3),c.translate(e,-1E3)),b.animate({opacity:1,translate:e+","+d},f,g),c.animate({opacity:1,translate:e+","+d},f,g),a.animatable.push(b))},animate:function(a){var b=this.chart,c=this.animationArray;!a&&0<c.length&&(a=c[0],c.shift());c=d[d.getEffect(b.startEffect)];b=b.startDuration;a&&(this.rotate?a.animateWidth(b,c):a.animateHeight(b,c),a.set.show())},legendKeyColor:function(){var a=this.legendColor,b=this.lineAlpha;void 0===a&&(a=this.lineColorR,0===b&&(b=this.fillColorsR)&&(a="object"==typeof b?b[0]:b));return a},legendKeyAlpha:function(){var a=this.legendAlpha;void 0===a&&(a=this.lineAlpha,this.fillAlphas>a&&(a=this.fillAlphas),0===a&&(a=this.bulletAlpha),0===a&&(a=1));return a},createBullet:function(a,b,c){if(!isNaN(b)&&!isNaN(c)&&("none"!=this.bullet||this.customBullet||a.bullet||a.customBullet)){var e=this.chart,h=this.container,f=this.bulletOffset,g=this.bulletSize;isNaN(a.bulletSize)||(g=a.bulletSize);var k=a.values.value,l=this.maxValue,m=this.minValue,p=this.maxBulletSize,q=this.minBulletSize;isNaN(l)||(isNaN(k)||(g=(k-m)/(l-m)*(p-q)+q),m==l&&(g=p));l=g;this.bulletAxis&&(g=a.values.error,
-isNaN(g)||(k=g),g=this.bulletAxis.stepWidth*k);g<this.minBulletSize&&(g=this.minBulletSize);this.rotate?b=a.isNegative?b-f:b+f:c=a.isNegative?c+f:c-f;q=this.bulletColorR;a.lineColor&&void 0===this.bulletColor&&(this.bulletColorSwitched=a.lineColor);this.bulletColorSwitched&&(q=this.bulletColorSwitched);a.isNegative&&void 0!==this.bulletColorNegative&&(q=this.bulletColorNegative);void 0!==a.color&&(q=a.color);var n;"xy"==e.type&&this.valueField&&(n=this.pattern,a.pattern&&(n=a.pattern));f=this.bullet;a.bullet&&(f=a.bullet);var k=this.bulletBorderThickness,m=this.bulletBorderColorR,p=this.bulletBorderAlpha,t=this.bulletAlpha;m||(m=q);this.useLineColorForBulletBorder&&(m=this.lineColorR,a.isNegative&&this.negativeLineColor&&(m=this.negativeLineColor),this.lineColorSwitched&&(m=this.lineColorSwitched));var r=a.alpha;isNaN(r)||(t=r);n=d.bullet(h,f,g,q,t,k,m,p,l,0,n,e.path);l=this.customBullet;a.customBullet&&(l=a.customBullet);l&&(n&&n.remove(),"function"==typeof l?(l=new l,l.chart=e,a.bulletConfig&&(l.availableSpace=c,l.graph=this,l.graphDataItem=a,l.bulletY=c,a.bulletConfig.minCoord=this.minCoord-c,l.bulletConfig=a.bulletConfig),l.write(h),n&&l.showBullet&&l.set.push(n),a.customBulletGraphics=l.cset,n=l.set):(n=h.set(),l=h.image(l,0,0,g,g),n.push(l),this.centerCustomBullets&&l.translate(-g/2,-g/2)));if(n){(a.url||this.showHandOnHover)&&n.setAttr("cursor","pointer");if("serial"==e.type||"gantt"==e.type)if(-.5>b||b>this.width||c<-g/2||c>this.height)n.remove(),n=null;n&&(this.bulletSet.push(n),n.translate(b,c),this.addListeners(n,a),this.allBullets.push(n));a.bx=b;a.by=c;d.setCN(e,n,this.bcn+"bullet");a.className&&d.setCN(e,n,a.className,!0)}if(n){n.size=g||0;if(e=this.bulletHitAreaSize)h=d.circle(h,e,"#FFFFFF",.001,0),h.translate(b,c),a.hitBullet=h,this.bulletSet.push(h),this.addListeners(h,a);a.bulletGraphics=n;void 0!==this.tabIndex&&n.setAttr("tabindex",this.tabIndex)}else n={size:0};n.graphDataItem=a;return n}},showBullets:function(){var a=this.allBullets,b;this.bulletsHidden=!1;for(b=0;b<a.length;b++)a[b].show()},hideBullets:function(){var a=this.allBullets,b;this.bulletsHidden=!0;for(b=0;b<a.length;b++)a[b].hide()},showCustomBullets:function(){var a=this.allBullets,b;this.customBulletsHidden=!1;for(b=0;b<a.length;b++){var c=a[b].graphDataItem;c&&c.customBulletGraphics&&c.customBulletGraphics.show()}},hideCustomBullets:function(){var a=this.allBullets,b;this.customBulletsHidden=!0;for(b=0;b<a.length;b++){var c=a[b].graphDataItem;c&&c.customBulletGraphics&&c.customBulletGraphics.hide()}},addListeners:function(a,b){var c=this;a.mouseover(function(a){c.handleRollOver(b,a)}).mouseout(function(a){c.handleRollOut(b,a)}).touchend(function(a){c.handleRollOver(b,a);c.chart.panEventsEnabled&&c.handleClick(b,a)}).touchstart(function(a){c.handleRollOver(b,a)}).click(function(a){c.handleClick(b,a)}).dblclick(function(a){c.handleDoubleClick(b,a)}).contextmenu(function(a){c.handleRightClick(b,a)});var e=c.chart;if(e.accessible&&c.accessibleLabel){var d=e.formatString(c.accessibleLabel,b);e.makeAccessible(a,d)}},handleRollOver:function(a,b){this.handleGraphEvent(b,"rollOverGraph");if(a){var c=this.chart;a.bulletConfig&&(c.isRolledOverBullet=!0);var e={type:"rollOverGraphItem",item:a,index:a.index,graph:this,target:this,chart:this.chart,event:b};this.fire(e);c.fire(e);clearTimeout(c.hoverInt);(c=c.chartCursor)&&c.valueBalloonsEnabled||this.showGraphBalloon(a,"V",!0)}},handleRollOut:function(a,b){var c=this.chart;if(a){var e={type:"rollOutGraphItem",item:a,index:a.index,graph:this,target:this,chart:this.chart,event:b};this.fire(e);c.fire(e);c.isRolledOverBullet=!1}this.handleGraphEvent(b,"rollOutGraph");(c=c.chartCursor)&&c.valueBalloonsEnabled||this.hideBalloon()},handleClick:function(a,b){if(!this.chart.checkTouchMoved()&&this.chart.checkTouchDuration(b)){if(a){var c={type:"clickGraphItem",item:a,index:a.index,graph:this,target:this,chart:this.chart,event:b};this.fire(c);this.chart.fire(c);d.getURL(a.url,this.urlTarget)}this.handleGraphEvent(b,"clickGraph")}},handleGraphEvent:function(a,b){var c={type:b,graph:this,target:this,chart:this.chart,event:a};this.fire(c);this.chart.fire(c)},handleRightClick:function(a,b){if(a){var c={type:"rightClickGraphItem",item:a,index:a.index,graph:this,target:this,chart:this.chart,event:b};this.fire(c);this.chart.fire(c)}},handleDoubleClick:function(a,b){if(a){var c={type:"doubleClickGraphItem",item:a,index:a.index,graph:this,target:this,chart:this.chart,event:b};this.fire(c);this.chart.fire(c)}},zoom:function(a,b){this.start=a;this.end=b;this.draw()},changeOpacity:function(a){var b=this.set;b&&b.setAttr("opacity",a);if(b=this.ownColumns){var c;for(c=0;c<b.length;c++){var e=b[c].set;e&&e.setAttr("opacity",a)}}(b=this.bulletSet)&&b.setAttr("opacity",a)},destroy:function(){d.remove(this.set);d.remove(this.bulletSet);var a=this.timeOuts;if(a){var b;for(b=0;b<a.length;b++)clearTimeout(a[b])}this.timeOuts=[]},createBalloon:function(){var a=this.chart;this.balloon?this.balloon.destroy&&this.balloon.destroy():this.balloon={};var b=this.balloon;d.extend(b,a.balloon,!0);b.chart=a;b.mainSet=a.plotBalloonsSet;b.className=this.id},hideBalloon:function(){var a=this,b=a.chart;b.chartCursor?b.chartCursor.valueBalloonsEnabled||b.hideBalloon():b.hideBalloon();clearTimeout(a.hoverInt);a.hoverInt=setTimeout(function(){a.hideBalloonReal.call(a)},b.hideBalloonTime)},hideBalloonReal:function(){this.balloon&&this.balloon.hide();this.fixBulletSize()},fixBulletSize:function(){if(d.isModern){var a=this.resizedDItem;if(a){var b=a.bulletGraphics;if(b&&!b.doNotScale){b.translate(a.bx,a.by,1);var c=this.bulletAlpha;isNaN(a.alpha)||(c=a.alpha);b.setAttr("fill-opacity",c);b.setAttr("stroke-opacity",this.bulletBorderAlpha)}}this.resizedDItem=null}},showGraphBalloon:function(a,b,c,e,h){if(a){var f=this.chart,g=this.balloon,k=0,l=0,m=f.chartCursor,p=!0;m?m.valueBalloonsEnabled||(g=f.balloon,k=this.x,l=this.y,p=!1):(g=f.balloon,k=this.x,l=this.y,p=!1);clearTimeout(this.hoverInt);if(f.chartCursor&&(this.currentDataItem=a,"serial"==f.type&&f.isRolledOverBullet&&f.chartCursor.valueBalloonsEnabled)){this.hideBalloonReal();return}this.resizeBullet(a,e,h);if(g&&g.enabled&&this.showBalloon&&!this.hidden){var m=f.formatString(this.balloonText,a,!0),q=this.balloonFunction;q&&(m=q(a,a.graph));m&&(m=d.cleanFromEmpty(m));m&&""!==m?(e=f.getBalloonColor(this,a),g.drop||(g.pointerOrientation=b),b=a.x,h=a.y,f.rotate&&(b=a.y,h=a.x),b+=k,h+=l,isNaN(b)||isNaN(h)?this.hideBalloonReal():(a=this.width,q=this.height,p&&g.setBounds(k,l,a+k,q+l),g.changeColor(e),g.setPosition(b,h),g.fixPrevious(),g.fixedPosition&&(c=!1),!c&&"radar"!=f.type&&(b<k||b>a+k||h<l-.5||h>q+l)?(g.showBalloon(m),g.hide(0)):(g.followCursor(c),g.showBalloon(m)))):(this.hideBalloonReal(),g.hide(),this.resizeBullet(a,e,h))}else this.hideBalloonReal()}},resizeBullet:function(a,b,c){this.fixBulletSize();if(a&&d.isModern&&(1!=b||!isNaN(c))){var e=a.bulletGraphics;e&&!e.doNotScale&&(e.translate(a.bx,a.by,b),isNaN(c)||(e.setAttr("fill-opacity",c),e.setAttr("stroke-opacity",c)),this.resizedDItem=a)}}})})();(function(){var d=window.AmCharts;d.ChartCursor=d.Class({construct:function(a){this.cname="ChartCursor";this.createEvents("changed","zoomed","onHideCursor","onShowCursor","draw","selected","moved","panning","zoomStarted");this.enabled=!0;this.cursorAlpha=1;this.selectionAlpha=.2;this.cursorColor="#CC0000";this.categoryBalloonAlpha=1;this.color="#FFFFFF";this.type="cursor";this.zoomed=!1;this.zoomable=!0;this.pan=!1;this.categoryBalloonDateFormat="MMM DD, YYYY";this.categoryBalloonText="[[category]]";this.categoryBalloonEnabled=this.valueBalloonsEnabled=!0;this.rolledOver=!1;this.cursorPosition="middle";this.bulletsEnabled=this.skipZoomDispatch=!1;this.bulletSize=8;this.selectWithoutZooming=this.oneBalloonOnly=!1;this.graphBulletSize=1.7;this.animationDuration=.3;this.zooming=!1;this.adjustment=0;this.avoidBalloonOverlapping=!0;this.leaveCursor=!1;this.leaveAfterTouch=!0;this.valueZoomable=!1;this.balloonPointerOrientation="horizontal";this.hLineEnabled=this.vLineEnabled=!0;this.vZoomEnabled=this.hZoomEnabled=!1;d.applyTheme(this,a,this.cname)},draw:function(){this.destroy();var a=this.chart;a.panRequired=!0;var b=a.container;this.rotate=a.rotate;this.container=b;this.prevLineHeight=this.prevLineWidth=NaN;b=b.set();b.translate(this.x,this.y);this.set=b;a.cursorSet.push(b);this.createElements();d.isString(this.limitToGraph)&&(this.limitToGraph=d.getObjById(a.graphs,this.limitToGraph),this.fullWidth=!1,this.cursorPosition="middle");this.pointer=this.balloonPointerOrientation.substr(0,1).toUpperCase();this.isHidden=!1;this.hideLines();this.valueLineAxis||(this.valueLineAxis=a.valueAxes[0])},createElements:function(){var a=this,b=a.chart,c=b.dx,e=b.dy,h=a.width,f=a.height,g,k,l=a.cursorAlpha,m=a.valueLineAlpha;a.rotate?(g=m,k=l):(k=m,g=l);"xy"==b.type&&(k=l,void 0!==m&&(k=m),g=l);a.vvLine=d.line(a.container,[c,0,0],[e,0,f],a.cursorColor,g,1);d.setCN(b,a.vvLine,"cursor-line");d.setCN(b,a.vvLine,"cursor-line-vertical");a.hhLine=d.line(a.container,[0,h,h+c],[0,0,e],a.cursorColor,k,1);d.setCN(b,a.hhLine,"cursor-line");d.setCN(b,a.hhLine,"cursor-line-horizontal");a.vLine=a.rotate?a.vvLine:a.hhLine;a.set.push(a.vvLine);a.set.push(a.hhLine);a.set.node.style.pointerEvents="none";a.fullLines=a.container.set();b=b.cursorLineSet;b.push(a.fullLines);b.translate(a.x,a.y);b.clipRect(-1,-1,h+2,f+2);void 0!==a.tabIndex&&(b.setAttr("tabindex",a.tabIndex),b.keyup(function(b){a.handleKeys(b)}).focus(function(b){a.showCursor()}).blur(function(b){a.hideCursor()}));a.set.clipRect(0,0,h,f)},handleKeys:function(a){var b=this.prevIndex,c=this.chart;if(c){var e=c.chartData;e&&(isNaN(b)&&(b=e.length-1),37!=a.keyCode&&40!=a.keyCode||b--,39!=a.keyCode&&38!=a.keyCode||b++,b=d.fitToBounds(b,c.startIndex,c.endIndex),(a=this.chart.chartData[b])&&this.setPosition(a.x.categoryAxis),this.prevIndex=b)}},update:function(){var a=this.chart;if(a){var b=a.mouseX-this.x,c=a.mouseY-this.y;this.mouseX=b;this.mouseY=c;this.mouse2X=a.mouse2X-this.x;this.mouse2Y=a.mouse2Y-this.y;var e;if(a.chartData&&0<a.chartData.length){this.mouseIsOver()?(this.hideGraphBalloons=!1,this.rolledOver=e=!0,this.updateDrawing(),this.vvLine&&isNaN(this.fx)&&(a.rotate||!this.limitToGraph)&&this.vvLine.translate(b,0),!this.hhLine||!isNaN(this.fy)||a.rotate&&this.limitToGraph||this.hhLine.translate(0,c),isNaN(this.mouse2X)?this.dispatchMovedEvent(b,c):e=!1):this.forceShow||this.hideCursor();if(this.zooming){if(!isNaN(this.mouse2X)){isNaN(this.mouse2X0)||this.dispatchPanEvent();return}if(this.pan){this.dispatchPanEvent();return}(this.hZoomEnabled||this.vZoomEnabled)&&this.zooming&&this.updateSelection()}e&&this.showCursor()}}},updateDrawing:function(){this.drawing&&this.chart.setMouseCursor("crosshair");if(this.drawingNow&&(d.remove(this.drawingLine),1<Math.abs(this.drawStartX-this.mouseX)||1<Math.abs(this.drawStartY-this.mouseY))){var a=this.chart,b=a.marginTop,a=a.marginLeft;this.drawingLine=d.line(this.container,[this.drawStartX+a,this.mouseX+a],[this.drawStartY+b,this.mouseY+b],this.cursorColor,1,1)}},fixWidth:function(a){if(this.fullWidth&&this.prevLineWidth!=a){var b=this.vvLine,c=0;b&&(b.remove(),c=b.x);b=this.container.set();b.translate(c,0);c=d.rect(this.container,a,this.height,this.cursorColor,this.cursorAlpha,this.cursorAlpha,this.cursorColor);d.setCN(this.chart,c,"cursor-fill");c.translate(-a/2-1,0);b.push(c);this.vvLine=b;this.fullLines.push(b);this.prevLineWidth=a}},fixHeight:function(a){if(this.fullWidth&&this.prevLineHeight!=a){var b=this.hhLine,c=0;b&&(b.remove(),c=b.y);b=this.container.set();b.translate(0,c);c=d.rect(this.container,this.width,a,this.cursorColor,this.cursorAlpha);c.translate(0,-a/2);b.push(c);this.fullLines.push(b);this.hhLine=b;this.prevLineHeight=a}},fixVLine:function(a,b){if(!isNaN(a)){if(isNaN(this.prevLineX)){var c=0,e=this.mouseX;if(this.limitToGraph){var d=this.chart.categoryAxis;d&&(this.chart.rotate||(c="bottom"==d.position?this.height:-this.height),e=a)}this.vvLine.translate(e,c)}else this.prevLineX!=a&&this.vvLine.translate(this.prevLineX,this.prevLineY);this.fx=a;this.prevLineX!=a&&(c=this.animationDuration,this.zooming&&(c=0),this.vvLine.stop(),this.vvLine.animate({translate:a+","+b},c,"easeOutSine"),this.prevLineX=a,this.prevLineY=b)}},fixHLine:function(a,b){if(!isNaN(a)){if(isNaN(this.prevLineY)){var c=0,e=this.mouseY;if(this.limitToGraph){var d=this.chart.categoryAxis;d&&(this.chart.rotate&&(c="right"==d.position?this.width:-this.width),e=a)}this.hhLine.translate(c,e)}else this.prevLineY!=a&&this.hhLine.translate(this.prevLineX,this.prevLineY);this.fy=a;this.prevLineY!=a&&(c=this.animationDuration,this.zooming&&(c=0),this.hhLine.stop(),this.hhLine.animate({translate:b+","+a},c,"easeOutSine"),this.prevLineY=a,this.prevLineX=b)}},hideCursor:function(a){this.forceShow=!1;this.chart.wasTouched&&this.leaveAfterTouch||this.isHidden||this.leaveCursor||(this.hideCursorReal(),a?this.chart.handleCursorHide():this.fire({target:this,chart:this.chart,type:"onHideCursor"}),this.chart.setMouseCursor("auto"))},hideCursorReal:function(){this.hideLines();this.isHidden=!0;this.index=this.prevLineY=this.prevLineX=this.mouseY0=this.mouseX0=this.fy=this.fx=NaN},hideLines:function(){this.vvLine&&this.vvLine.hide();this.hhLine&&this.hhLine.hide();this.fullLines&&this.fullLines.hide();this.isHidden=!0;this.chart.handleCursorHide()},showCursor:function(a){!this.drawing&&this.enabled&&(this.vLineEnabled&&this.vvLine&&this.vvLine.show(),this.hLineEnabled&&this.hhLine&&this.hhLine.show(),this.isHidden=!1,this.updateFullLine(),a||this.fire({target:this,chart:this.chart,type:"onShowCursor"}),this.pan&&this.chart.setMouseCursor("move"))},updateFullLine:function(){this.zooming&&this.fullWidth&&this.selection&&(this.rotate?0<this.selection.height&&this.hhLine.hide():0<this.selection.width&&this.vvLine.hide())},updateSelection:function(){if(!this.pan&&this.enabled){var a=this.mouseX,b=this.mouseY;isNaN(this.fx)||(a=this.fx);isNaN(this.fy)||(b=this.fy);this.clearSelection();var c=this.mouseX0,e=this.mouseY0,h=this.width,f=this.height,a=d.fitToBounds(a,0,h),b=d.fitToBounds(b,0,f),g;a<c&&(g=a,a=c,c=g);b<e&&(g=b,b=e,e=g);this.hZoomEnabled?h=a-c:c=0;this.vZoomEnabled?f=b-e:e=0;isNaN(this.mouse2X)&&0<Math.abs(h)&&0<Math.abs(f)&&(a=this.chart,b=d.rect(this.container,h,f,this.cursorColor,this.selectionAlpha),d.setCN(a,b,"cursor-selection"),b.width=h,b.height=f,b.translate(c,e),this.set.push(b),this.selection=b);this.updateFullLine()}},mouseIsOver:function(){var a=this.mouseX,b=this.mouseY;if(this.justReleased)return this.justReleased=!1,!0;if(this.mouseIsDown)return!0;if(!this.chart.mouseIsOver)return this.handleMouseOut(),!1;if(0<a&&a<this.width&&0<b&&b<this.height)return!0;this.handleMouseOut()},fixPosition:function(){this.prevY=this.prevX=NaN},handleMouseDown:function(){this.update();if(this.mouseIsOver())if(this.mouseIsDown=!0,this.mouseX0=this.mouseX,this.mouseY0=this.mouseY,this.mouse2X0=this.mouse2X,this.mouse2Y0=this.mouse2Y,this.drawing)this.drawStartY=this.mouseY,this.drawStartX=this.mouseX,this.drawingNow=!0;else if(this.dispatchMovedEvent(this.mouseX,this.mouseY),!this.pan&&isNaN(this.mouse2X0)&&(isNaN(this.fx)||(this.mouseX0=this.fx),isNaN(this.fy)||(this.mouseY0=this.fy)),this.hZoomEnabled||this.vZoomEnabled){this.zooming=!0;var a={chart:this.chart,target:this,type:"zoomStarted"};a.x=this.mouseX/this.width;a.y=this.mouseY/this.height;this.index0=a.index=this.index;this.timestamp0=this.timestamp;this.fire(a)}},registerInitialMouse:function(){},handleReleaseOutside:function(){this.mouseIsDown=!1;if(this.drawingNow){this.drawingNow=!1;d.remove(this.drawingLine);var a=this.drawStartX,b=this.drawStartY,c=this.mouseX,e=this.mouseY,h=this.chart;(2<Math.abs(a-c)||2<Math.abs(b-e))&&this.fire({type:"draw",target:this,chart:h,initialX:a,initialY:b,finalX:c,finalY:e})}this.zooming&&(this.zooming=!1,this.selectWithoutZooming?this.dispatchZoomEvent("selected"):(this.hZoomEnabled||this.vZoomEnabled)&&this.dispatchZoomEvent("zoomed"),this.rolledOver&&this.dispatchMovedEvent(this.mouseX,this.mouseY));this.mouse2Y0=this.mouse2X0=this.mouseY0=this.mouseX0=NaN},dispatchZoomEvent:function(a){if(!this.pan){var b=this.selection;if(b&&3<Math.abs(b.width)&&3<Math.abs(b.height)){var c=Math.min(this.index,this.index0),e=Math.max(this.index,this.index0),d=c,f=e,g=this.chart,k=g.chartData,l=g.categoryAxis;l&&l.parseDates&&!l.equalSpacing&&(d=k[c]?k[c].time:Math.min(this.timestamp0,this.timestamp),f=k[e]?g.getEndTime(k[e].time):Math.max(this.timestamp0,this.timestamp));var b={type:a,chart:this.chart,target:this,end:f,start:d,startIndex:c,endIndex:e,selectionHeight:b.height,selectionWidth:b.width,selectionY:b.y,selectionX:b.x},m;this.hZoomEnabled&&4<Math.abs(this.mouseX0-
-this.mouseX)&&(b.startX=this.mouseX0/this.width,b.endX=this.mouseX/this.width,m=!0);this.vZoomEnabled&&4<Math.abs(this.mouseY0-this.mouseY)&&(b.startY=1-this.mouseY0/this.height,b.endY=1-this.mouseY/this.height,m=!0);m&&(this.prevY=this.prevX=NaN,this.fire(b),"selected"!=a&&this.clearSelection());this.hideCursor()}}},dispatchMovedEvent:function(a,b,c,e){a=Math.round(a);b=Math.round(b);if(!this.isHidden&&(a!=this.prevX||b!=this.prevY||"changed"==c)){c||(c="moved");var d=this.fx,f=this.fy;isNaN(d)&&(d=a);isNaN(f)&&(f=b);var g=!1;this.zooming&&this.pan&&(g=!0);g={hidden:this.isHidden,type:c,chart:this.chart,target:this,x:a,y:b,finalX:d,finalY:f,zooming:this.zooming,panning:g,mostCloseGraph:this.mostCloseGraph,index:this.index,skip:e,hideBalloons:this.hideGraphBalloons};this.prevIndex=this.index;this.rotate?(g.position=b,g.finalPosition=f):(g.position=a,g.finalPosition=d);this.prevX=a;this.prevY=b;e?this.chart.handleCursorMove(g):(this.fire(g),"changed"==c&&this.chart.fire(g))}},dispatchPanEvent:function(){if(this.mouseIsDown){var a=d.roundTo((this.mouseX-this.mouseX0)/this.width,3),b=d.roundTo((this.mouseY-this.mouseY0)/this.height,3),c=d.roundTo((this.mouse2X-this.mouse2X0)/this.width,3),e=d.roundTo((this.mouse2Y-this.mouse2Y0)/this.height,2),h=!1;0!==Math.abs(a)&&0!==Math.abs(b)&&(h=!0);if(this.prevDeltaX==a||this.prevDeltaY==b)h=!1;isNaN(c)||isNaN(e)||(0!==Math.abs(c)&&0!==Math.abs(e)&&(h=!0),this.prevDelta2X!=c&&this.prevDelta2Y!=e)||(h=!1);h&&(this.hideLines(),this.fire({type:"panning",chart:this.chart,target:this,deltaX:a,
-deltaY:b,delta2X:c,delta2Y:e,index:this.index}),this.prevDeltaX=a,this.prevDeltaY=b,this.prevDelta2X=c,this.prevDelta2Y=e)}},clearSelection:function(){var a=this.selection;a&&(a.width=0,a.height=0,a.remove())},destroy:function(){this.clear();d.remove(this.selection);this.selection=null;clearTimeout(this.syncTO);d.remove(this.set)},clear:function(){},setTimestamp:function(a){this.timestamp=a},setIndex:function(a,b){a!=this.index&&(this.index=a,b||this.isHidden||this.dispatchMovedEvent(this.mouseX,this.mouseY,"changed"))},handleMouseOut:function(){this.enabled&&this.rolledOver&&(this.leaveCursor||this.setIndex(void 0),this.forceShow=!1,this.hideCursor(),this.rolledOver=!1)},showCursorAt:function(a){var b=this.chart.categoryAxis;b&&this.setPosition(b.categoryToCoordinate(a),a)},setPosition:function(a,b){var c=this.chart,e=c.categoryAxis;if(e){var d,f;void 0===b&&(b=e.coordinateToValue(a));e.showBalloonAt(b,a);this.forceShow=!0;e.stickBalloonToCategory?c.rotate?this.fixHLine(a,0):this.fixVLine(a,0):(this.showCursor(),c.rotate?this.hhLine.translate(0,a):this.vvLine.translate(a,0));c.rotate?d=a:f=a;c.rotate?(this.vvLine&&this.vvLine.hide(),this.hhLine&&this.hhLine.show()):(this.hhLine&&this.hhLine.hide(),this.vvLine&&this.vvLine.show());this.updateFullLine();this.isHidden=!1;this.dispatchMovedEvent(f,d,"moved",!0)}},enableDrawing:function(a){this.enabled=!a;this.hideCursor();this.drawing=a},syncWithCursor:function(a,b){clearTimeout(this.syncTO);a&&(a.isHidden?this.hideCursor(!0):this.syncWithCursorReal(a,b))},isZooming:function(a){this.zooming=a},syncWithCursorReal:function(a,b){var c=a.vvLine,e=a.hhLine;this.index=a.index;this.forceShow=!0;this.zooming&&this.pan||this.showCursor(!0);this.hideGraphBalloons=b;this.justReleased=a.justReleased;this.zooming=a.zooming;this.index0=a.index0;this.mouseX0=a.mouseX0;this.mouseY0=a.mouseY0;this.mouse2X0=a.mouse2X0;this.mouse2Y0=a.mouse2Y0;this.timestamp0=a.timestamp0;this.prevDeltaX=a.prevDeltaX;this.prevDeltaY=a.prevDeltaY;this.prevDelta2X=a.prevDelta2X;this.prevDelta2Y=a.prevDelta2Y;this.fx=a.fx;this.fy=a.fy;a.zooming&&this.updateSelection();var d=a.mouseX,f=a.mouseY;this.rotate?(d=NaN,this.vvLine&&this.vvLine.hide(),this.hhLine&&e&&(isNaN(a.fy)?this.hhLine.translate(0,a.mouseY):this.fixHLine(a.fy,0))):(f=NaN,this.hhLine&&this.hhLine.hide(),this.vvLine&&c&&(isNaN(a.fx)?this.vvLine.translate(a.mouseX,0):this.fixVLine(a.fx,0)));this.dispatchMovedEvent(d,f,"moved",!0)}})})();(function(){var d=window.AmCharts;d.SimpleChartScrollbar=d.Class({construct:function(a){this.createEvents("zoomed","zoomStarted","zoomEnded");this.backgroundColor="#D4D4D4";this.backgroundAlpha=1;this.selectedBackgroundColor="#EFEFEF";this.scrollDuration=this.selectedBackgroundAlpha=1;this.resizeEnabled=!0;this.hideResizeGrips=!1;this.scrollbarHeight=20;this.updateOnReleaseOnly=!1;9>document.documentMode&&(this.updateOnReleaseOnly=!0);this.dragIconHeight=this.dragIconWidth=35;this.dragIcon="dragIconRoundBig";this.dragCursorHover="cursor: move; cursor: grab; cursor: -moz-grab; cursor: -webkit-grab;";this.dragCursorDown="cursor: move; cursor: grab; cursor: -moz-grabbing; cursor: -webkit-grabbing;";this.vResizeCursor="ns-resize";this.hResizeCursor="ew-resize";this.enabled=!0;this.percentStart=this.offset=0;this.percentEnd=1;d.applyTheme(this,a,"SimpleChartScrollbar")},getPercents:function(){var a=this.getDBox(),b=a.x,c=a.y,e=a.width,a=a.height;this.rotate?(b=1-c/this.height,c=1-(c+a)/this.height):(c=b/this.width,
-b=(b+e)/this.width);this.percentStart=c;this.percentEnd=b},draw:function(){var a=this;a.destroy();if(a.enabled){var b=a.chart.container,c=a.rotate,e=a.chart;e.panRequired=!0;var h=b.set();a.set=h;c?d.setCN(e,h,"scrollbar-vertical"):d.setCN(e,h,"scrollbar-horizontal");e.scrollbarsSet.push(h);var f,g;c?(f=a.scrollbarHeight,g=e.plotAreaHeight):(g=a.scrollbarHeight,f=e.plotAreaWidth);a.width=f;if((a.height=g)&&f){var k=d.rect(b,f,g,a.backgroundColor,a.backgroundAlpha,1,a.backgroundColor,a.backgroundAlpha);
-d.setCN(e,k,"scrollbar-bg");a.bg=k;h.push(k);k=d.rect(b,f,g,"#000",.005);h.push(k);a.invisibleBg=k;k.click(function(){a.handleBgClick()}).mouseover(function(){a.handleMouseOver()}).mouseout(function(){a.handleMouseOut()}).touchend(function(){a.handleBgClick()});k=d.rect(b,f,g,a.selectedBackgroundColor,a.selectedBackgroundAlpha);d.setCN(e,k,"scrollbar-bg-selected");a.selectedBG=k;h.push(k);f=d.rect(b,f,g,"#000",.005);a.dragger=f;h.push(f);f.mousedown(function(b){a.handleDragStart(b)}).mouseup(function(){a.handleDragStop()}).mouseover(function(){a.handleDraggerOver()}).mouseout(function(){a.handleMouseOut()}).touchstart(function(b){a.handleDragStart(b)}).touchend(function(){a.handleDragStop()});g=e.pathToImages;var l,k=a.dragIcon.replace(/\.[a-z]*$/i,"");d.isAbsolute(k)&&(g="");c?(l=g+k+"H"+e.extension,g=a.dragIconWidth,c=a.dragIconHeight):(l=g+k+e.extension,c=a.dragIconWidth,g=a.dragIconHeight);k=b.image(l,0,0,c,g);d.setCN(e,k,"scrollbar-grip-left");l=b.image(l,0,0,c,g);d.setCN(e,l,"scrollbar-grip-right");var m=10,p=20;e.panEventsEnabled&&(m=25,p=a.scrollbarHeight);var q=d.rect(b,m,p,"#000",.005),n=d.rect(b,m,p,"#000",.005);n.translate(-(m-c)/2,-(p-g)/2);q.translate(-(m-c)/2,-(p-g)/2);
-c=b.set([k,n]);b=b.set([l,q]);a.iconLeft=c;h.push(a.iconLeft);a.iconRight=b;h.push(b);a.updateGripCursor(!1);e.makeAccessible(c,a.accessibleLabel);e.makeAccessible(b,a.accessibleLabel);e.makeAccessible(f,a.accessibleLabel);c.setAttr("role","menuitem");b.setAttr("role","menuitem");f.setAttr("role","menuitem");void 0!==a.tabIndex&&(c.setAttr("tabindex",a.tabIndex),c.keyup(function(b){a.handleKeys(b,1,0)}));void 0!==a.tabIndex&&(f.setAttr("tabindex",a.tabIndex),f.keyup(function(b){a.handleKeys(b,1,1)}));void 0!==a.tabIndex&&(b.setAttr("tabindex",a.tabIndex),b.keyup(function(b){a.handleKeys(b,0,1)}));c.mousedown(function(){a.leftDragStart()}).mouseup(function(){a.leftDragStop()}).mouseover(function(){a.iconRollOver()}).mouseout(function(){a.iconRollOut()}).touchstart(function(){a.leftDragStart()}).touchend(function(){a.leftDragStop()});b.mousedown(function(){a.rightDragStart()}).mouseup(function(){a.rightDragStop()}).mouseover(function(){a.iconRollOver()}).mouseout(function(){a.iconRollOut()}).touchstart(function(){a.rightDragStart()}).touchend(function(){a.rightDragStop()});d.ifArray(e.chartData)?h.show():h.hide();a.hideDragIcons();a.clipDragger(!1)}h.translate(a.x,a.y);h.node.style.msTouchAction="none";h.node.style.touchAction="none"}},handleKeys:function(a,b,c){this.getPercents();var e=this.percentStart,d=this.percentEnd;if(this.rotate)var f=d,d=e,e=f;if(37==a.keyCode||40==a.keyCode)e-=.02*b,d-=.02*c;if(39==a.keyCode||38==a.keyCode)e+=.02*b,d+=.02*c;this.rotate&&(a=d,d=e,e=a);isNaN(d)||isNaN(e)||this.percentZoom(e,d,!0)},updateScrollbarSize:function(a,b){if(!isNaN(a)&&!isNaN(b)){a=Math.round(a);b=Math.round(b);var c=this.dragger,e,d,f,g,k;this.rotate?(e=0,d=a,f=this.width+1,g=b-a,c.setAttr("height",b-a),c.setAttr("y",d)):(e=a,d=0,f=b-a,g=this.height+1,k=b-a,c.setAttr("x",e),c.setAttr("width",k));this.clipAndUpdate(e,d,f,g)}},update:function(){var a,b=!1,c,e,d=this.x,f=this.y,g=this.dragger,k=this.getDBox();if(k){c=k.x+d;e=k.y+f;var l=k.width,k=k.height,m=this.rotate,p=this.chart,q=this.width,n=this.height,t=p.mouseX,p=p.mouseY;a=this.initialMouse;this.forceClip&&this.clipDragger(!0);if(this.dragging){var r=this.initialCoord;m?(a=r+(p-a),0>a&&(a=0),r=n-k,a>r&&(a=r),g.setAttr("y",a)):(a=r+(t-a),0>a&&(a=0),r=q-l,a>r&&(a=r),g.setAttr("x",a));this.clipDragger(!0)}if(this.resizingRight){if(m)if(a=p-e,!isNaN(this.maxHeight)&&a>this.maxHeight&&(a=this.maxHeight),a+e>n+f&&(a=n-e+f),0>a)this.resizingRight=!1,b=this.resizingLeft=!0;else{if(0===a||isNaN(a))a=.1;g.setAttr("height",a)}else if(a=t-c,!isNaN(this.maxWidth)&&a>this.maxWidth&&(a=this.maxWidth),a+c>q+d&&(a=q-c+d),0>a)this.resizingRight=!1,b=this.resizingLeft=!0;else{if(0===a||isNaN(a))a=.1;g.setAttr("width",a)}this.clipDragger(!0)}if(this.resizingLeft){if(m)if(c=e,e=p,e<f&&(e=f),isNaN(e)&&(e=f),e>n+f&&(e=n+f),a=!0===b?c-e:k+c-e,!isNaN(this.maxHeight)&&a>this.maxHeight&&(a=this.maxHeight,e=c),0>a)this.resizingRight=!0,this.resizingLeft=!1,g.setAttr("y",c+k-f);else{if(0===a||isNaN(a))a=.1;g.setAttr("y",e-f);g.setAttr("height",a)}else if(e=t,e<d&&(e=d),isNaN(e)&&(e=d),e>q+d&&(e=q+d),a=!0===b?c-e:l+c-e,!isNaN(this.maxWidth)&&a>this.maxWidth&&(a=this.maxWidth,e=c),0>a)this.resizingRight=!0,this.resizingLeft=!1,g.setAttr("x",c+l-d);else{if(0===a||isNaN(a))a=.1;g.setAttr("x",e-d);g.setAttr("width",a)}this.clipDragger(!0)}}},stopForceClip:function(){this.animating=this.forceClip=!1},clipDragger:function(a){var b=this.getDBox();if(b){var c=b.x,e=b.y,d=b.width,b=b.height,f=!1;if(this.rotate){if(c=0,d=this.width+1,this.clipY!=e||this.clipH!=b)f=!0}else if(e=0,b=this.height+1,this.clipX!=c||this.clipW!=d)f=!0;f&&(this.clipAndUpdate(c,e,d,b),a&&(this.updateOnReleaseOnly||this.dispatchScrollbarEvent()))}},maskGraphs:function(){},clipAndUpdate:function(a,b,c,d){this.clipX=a;this.clipY=b;this.clipW=c;this.clipH=d;this.selectedBG.setAttr("width",c);this.selectedBG.setAttr("height",d);this.selectedBG.translate(a,b);this.updateDragIconPositions();this.maskGraphs(a,b,c,d)},dispatchScrollbarEvent:function(){if(this.skipEvent)this.skipEvent=!1;else{var a=this.chart;a.hideBalloon();var b=this.getDBox(),c=b.x,d=b.y,h=b.width,b=b.height;this.getPercents();this.rotate?(c=d,h=this.height/b):h=this.width/h;this.fire({type:"zoomed",position:c,chart:a,target:this,multiplier:h,relativeStart:this.percentStart,relativeEnd:this.percentEnd})}},updateDragIconPositions:function(){var a=this.getDBox(),b=a.x,c=a.y,d=this.iconLeft,h=this.iconRight,f,g,k=this.scrollbarHeight;this.rotate?(f=this.dragIconWidth,g=this.dragIconHeight,d.translate((k-g)/2,c-f/2),h.translate((k-g)/2,c+a.height-f/2)):(f=this.dragIconHeight,
-g=this.dragIconWidth,d.translate(b-g/2,(k-f)/2),h.translate(b-g/2+a.width,(k-f)/2))},showDragIcons:function(){this.resizeEnabled&&(this.iconLeft.show(),this.iconRight.show())},hideDragIcons:function(){if(!this.resizingLeft&&!this.resizingRight&&!this.dragging){if(this.hideResizeGrips||!this.resizeEnabled)this.iconLeft.hide(),this.iconRight.hide();this.removeCursors()}},removeCursors:function(){this.chart.setMouseCursor("auto")},fireZoomEvent:function(a){this.fire({type:a,chart:this.chart,target:this})},
-percentZoom:function(a,b,c){a=d.fitToBounds(a,0,b);b=d.fitToBounds(b,a,1);if(this.dragger&&this.enabled){this.dragger.stop();isNaN(a)&&(a=0);isNaN(b)&&(b=1);var e,h;this.rotate?(e=this.height,b=e-e*b,h=e-e*a):(e=this.width,h=e*b,b=e*a);this.updateScrollbarSize(b,h);this.clipDragger(!1);this.getPercents();c&&this.dispatchScrollbarEvent()}},destroy:function(){this.clear();d.remove(this.set);d.remove(this.iconRight);d.remove(this.iconLeft)},clear:function(){},handleDragStart:function(){if(this.enabled){this.fireZoomEvent("zoomStarted");var a=this.chart;this.dragger.stop();this.removeCursors();d.isModern&&(this.dragger.node.style.cssText=this.dragCursorDown);this.dragging=!0;var b=this.getDBox();this.rotate?(this.initialCoord=b.y,this.initialMouse=a.mouseY):(this.initialCoord=b.x,this.initialMouse=a.mouseX)}},handleDragStop:function(){this.updateOnReleaseOnly&&(this.update(),this.skipEvent=!1,this.dispatchScrollbarEvent());this.dragging=!1;this.mouseIsOver&&this.removeCursors();d.isModern&&(this.dragger.node.style.cssText=this.dragCursorHover);this.update();this.fireZoomEvent("zoomEnded")},handleDraggerOver:function(){this.handleMouseOver();d.isModern&&(this.dragger.node.style.cssText=this.dragCursorHover)},leftDragStart:function(){this.fireZoomEvent("zoomStarted");this.dragger.stop();this.resizingLeft=!0;this.updateGripCursor(!0)},updateGripCursor:function(a){d.isModern&&(a=this.rotate?a?this.vResizeCursorDown:this.vResizeCursorHover:a?this.hResizeCursorDown:this.hResizeCursorHover)&&(this.iconRight&&(this.iconRight.node.style.cssText=a),this.iconLeft&&(this.iconLeft.node.style.cssText=a))},leftDragStop:function(){this.resizingLeft&&(this.resizingLeft=!1,this.mouseIsOver||this.removeCursors(),this.updateOnRelease(),this.fireZoomEvent("zoomEnded"));this.updateGripCursor(!1)},rightDragStart:function(){this.fireZoomEvent("zoomStarted");this.dragger.stop();this.resizingRight=!0;this.updateGripCursor(!0)},rightDragStop:function(){this.resizingRight&&(this.resizingRight=!1,this.mouseIsOver||this.removeCursors(),this.updateOnRelease(),this.fireZoomEvent("zoomEnded"));this.updateGripCursor(!1)},iconRollOut:function(){this.removeCursors()},iconRollOver:function(){this.rotate?this.vResizeCursor&&this.chart.setMouseCursor(this.vResizeCursor):this.hResizeCursor&&this.chart.setMouseCursor(this.hResizeCursor);this.handleMouseOver()},getDBox:function(){if(this.dragger)return this.dragger.getBBox()},handleBgClick:function(){var a=this;if(!a.resizingRight&&!a.resizingLeft){a.zooming=!0;var b,c,e=a.scrollDuration,h=a.dragger;b=a.getDBox();var f=b.height,g=b.width;c=a.chart;var k=a.y,l=a.x,m=a.rotate;m?(b="y",c=c.mouseY-f/2-k,c=d.fitToBounds(c,0,a.height-f)):(b="x",c=c.mouseX-g/2-l,c=d.fitToBounds(c,0,a.width-g));a.updateOnReleaseOnly?(a.skipEvent=!1,h.setAttr(b,c),a.dispatchScrollbarEvent(),a.clipDragger()):(a.animating=!0,c=Math.round(c),m?h.animate({y:c},e,">"):h.animate({x:c},e,">"),a.forceClip=!0,clearTimeout(a.forceTO),a.forceTO=setTimeout(function(){a.stopForceClip.call(a)},5E3*e))}},updateOnRelease:function(){this.updateOnReleaseOnly&&(this.update(),this.skipEvent=!1,this.dispatchScrollbarEvent())},handleReleaseOutside:function(){if(this.set){if(this.resizingLeft||this.resizingRight||this.dragging)this.dragging=this.resizingRight=this.resizingLeft=!1,this.updateOnRelease(),this.removeCursors();this.animating=this.mouseIsOver=!1;this.hideDragIcons();this.update()}},handleMouseOver:function(){this.mouseIsOver=!0;this.showDragIcons()},handleMouseOut:function(){this.mouseIsOver=!1;this.hideDragIcons();this.removeCursors()}})})();(function(){var d=window.AmCharts;d.ChartScrollbar=d.Class({inherits:d.SimpleChartScrollbar,construct:function(a){this.cname="ChartScrollbar";d.ChartScrollbar.base.construct.call(this,a);this.graphLineColor="#BBBBBB";this.graphLineAlpha=0;this.graphFillColor="#BBBBBB";this.graphFillAlpha=1;this.selectedGraphLineColor="#888888";this.selectedGraphLineAlpha=0;this.selectedGraphFillColor="#888888";this.selectedGraphFillAlpha=1;this.gridCount=0;this.gridColor="#FFFFFF";this.gridAlpha=.7;this.skipEvent=this.autoGridCount=!1;this.color="#FFFFFF";this.scrollbarCreated=!1;this.oppositeAxis=!0;this.accessibleLabel="Zoom chart using cursor arrows";d.applyTheme(this,a,this.cname)},init:function(){var a=this.categoryAxis,b=this.chart,c=this.gridAxis;a||("CategoryAxis"==this.gridAxis.cname?(this.catScrollbar=!0,a=new d.CategoryAxis,a.id="scrollbar"):(a=new d.ValueAxis,a.data=b.chartData,a.id=c.id,a.type=c.type,a.maximumDate=c.maximumDate,a.minimumDate=c.minimumDate,a.minPeriod=c.minPeriod,a.minMaxField=c.minMaxField),this.categoryAxis=a);a.chart=b;var e=b.categoryAxis;e&&(a.firstDayOfWeek=e.firstDayOfWeek);a.dateFormats=c.dateFormats;a.markPeriodChange=c.markPeriodChange;a.boldPeriodBeginning=c.boldPeriodBeginning;a.labelFunction=c.labelFunction;a.axisItemRenderer=d.RecItem;a.axisRenderer=d.RecAxis;a.guideFillRenderer=d.RecFill;a.inside=!0;a.fontSize=this.fontSize;a.tickLength=0;a.axisAlpha=0;d.isString(this.graph)&&(this.graph=d.getObjById(b.graphs,this.graph));(a=this.graph)&&this.catScrollbar&&(c=this.valueAxis,c||(this.valueAxis=c=new d.ValueAxis,c.visible=!1,c.scrollbar=!0,c.axisItemRenderer=d.RecItem,c.axisRenderer=d.RecAxis,c.guideFillRenderer=d.RecFill,c.labelsEnabled=!1,c.chart=b),b=this.unselectedGraph,b||(b=new d.AmGraph,b.scrollbar=!0,this.unselectedGraph=b,b.negativeBase=a.negativeBase,b.noStepRisers=a.noStepRisers),b=this.selectedGraph,b||(b=new d.AmGraph,b.scrollbar=!0,this.selectedGraph=b,b.negativeBase=a.negativeBase,b.noStepRisers=a.noStepRisers));this.scrollbarCreated=!0},draw:function(){var a=this;d.ChartScrollbar.base.draw.call(a);if(a.enabled){a.scrollbarCreated||a.init();var b=a.chart,c=b.chartData,e=a.categoryAxis,h=a.rotate,f=a.x,g=a.y,k=a.width,l=a.height,m=a.gridAxis,p=a.set;e.setOrientation(!h);e.parseDates=m.parseDates;"ValueAxis"==a.categoryAxis.cname&&(e.rotate=!h);e.equalSpacing=m.equalSpacing;e.minPeriod=m.minPeriod;e.startOnAxis=m.startOnAxis;e.width=k-1;e.height=l;e.gridCount=a.gridCount;e.gridColor=a.gridColor;e.gridAlpha=a.gridAlpha;e.color=a.color;e.tickLength=0;e.axisAlpha=0;e.autoGridCount=a.autoGridCount;e.parseDates&&!e.equalSpacing&&e.timeZoom(b.firstTime,b.lastTime);e.minimum=a.gridAxis.fullMin;e.maximum=a.gridAxis.fullMax;e.strictMinMax=!0;e.zoom(0,c.length-1);if((m=a.graph)&&a.catScrollbar){var q=a.valueAxis,n=m.valueAxis;q.id=n.id;q.rotate=h;q.setOrientation(h);q.width=k;q.height=l;q.dataProvider=c;q.reversed=n.reversed;q.logarithmic=n.logarithmic;q.gridAlpha=0;q.axisAlpha=0;p.push(q.set);h?(q.y=g,q.x=0):(q.x=f,q.y=0);var f=Infinity,g=-Infinity,t;for(t=0;t<c.length;t++){var r=c[t].axes[n.id].graphs[m.id].values,w;for(w in r)if(r.hasOwnProperty(w)&&"percents"!=w&&"total"!=w){var z=r[w];z<f&&(f=z);z>g&&(g=z)}}Infinity!=f&&(q.minimum=f);-Infinity!=g&&(q.maximum=g+.1*(g-f));f==g&&(--q.minimum,q.maximum+=1);void 0!==a.minimum&&(q.minimum=a.minimum);void 0!==a.maximum&&(q.maximum=a.maximum);q.zoom(0,c.length-1);w=a.unselectedGraph;w.id=m.id;w.bcn="scrollbar-graph-";w.rotate=h;w.chart=b;w.data=c;w.valueAxis=q;w.chart=m.chart;w.categoryAxis=a.categoryAxis;w.periodSpan=m.periodSpan;w.valueField=m.valueField;w.openField=m.openField;w.closeField=m.closeField;w.highField=m.highField;w.lowField=m.lowField;w.lineAlpha=a.graphLineAlpha;w.lineColorR=a.graphLineColor;w.fillAlphas=a.graphFillAlpha;w.fillColorsR=a.graphFillColor;w.connect=m.connect;w.hidden=m.hidden;w.width=k;w.height=l;w.pointPosition=m.pointPosition;w.stepDirection=m.stepDirection;w.periodSpan=m.periodSpan;n=a.selectedGraph;n.id=m.id;n.bcn=w.bcn+"selected-";n.rotate=h;n.chart=b;n.data=c;n.valueAxis=q;n.chart=m.chart;n.categoryAxis=e;n.periodSpan=m.periodSpan;n.valueField=m.valueField;n.openField=m.openField;n.closeField=m.closeField;n.highField=m.highField;n.lowField=m.lowField;n.lineAlpha=a.selectedGraphLineAlpha;n.lineColorR=a.selectedGraphLineColor;n.fillAlphas=a.selectedGraphFillAlpha;n.fillColorsR=a.selectedGraphFillColor;n.connect=m.connect;n.hidden=m.hidden;n.width=k;n.height=l;n.pointPosition=m.pointPosition;n.stepDirection=m.stepDirection;n.periodSpan=m.periodSpan;b=a.graphType;b||(b=m.type);w.type=b;n.type=b;c=c.length-1;w.zoom(0,c);n.zoom(0,c);n.set.click(function(){a.handleBackgroundClick()}).mouseover(function(){a.handleMouseOver()}).mouseout(function(){a.handleMouseOut()});w.set.click(function(){a.handleBackgroundClick()}).mouseover(function(){a.handleMouseOver()}).mouseout(function(){a.handleMouseOut()});p.push(w.set);p.push(n.set)}p.push(e.set);p.push(e.labelsSet);a.bg.toBack();a.invisibleBg.toFront();a.dragger.toFront();a.iconLeft.toFront();a.iconRight.toFront()}},timeZoom:function(a,b,c){this.startTime=a;this.endTime=b;this.timeDifference=b-a;this.skipEvent=!d.toBoolean(c);this.zoomScrollbar();this.dispatchScrollbarEvent()},zoom:function(a,b){this.start=a;this.end=b;this.skipEvent=!0;this.zoomScrollbar()},dispatchScrollbarEvent:function(){if(this.categoryAxis&&"ValueAxis"==this.categoryAxis.cname)d.ChartScrollbar.base.dispatchScrollbarEvent.call(this);else if(this.skipEvent)this.skipEvent=!1;else{var a=this.chart.chartData,b,c,e=this.dragger.getBBox();b=e.x;var h=e.y,f=e.width,e=e.height,g=this.chart;this.rotate?(b=h,c=e):c=f;f={type:"zoomed",target:this};f.chart=g;var k=this.categoryAxis,l=this.stepWidth,h=g.minSelectedTime,e=g.maxSelectedTime,m=!1;if(k.parseDates&&!k.equalSpacing){if(a=g.lastTime,g=g.firstTime,k=Math.round(b/l)+g,b=this.dragging?k+this.timeDifference:Math.round((b+c)/l)+g,k>b&&(k=b),0<h&&b-k<h&&(b=Math.round(k+(b-k)/2),m=Math.round(h/2),k=b-m,b+=m,m=!0),0<e&&b-k>e&&(b=Math.round(k+(b-k)/2),m=Math.round(e/2),k=b-m,b+=m,m=!0),b>a&&(b=
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a=this.chart.mouseX-this.offsetX*this.deltaSignX-this.sdx,b=this.chart.mouseY-this.sdy;this.pointToX=a;this.pointToY=b;if(a!=this.previousX||b!=this.previousY)if(this.previousX=a,this.previousY=b,0===this.cornerRadius)this.draw();else{var c=this.set;if(c){var d=c.getBBox(),a=a-d.width/2,h=b-d.height-10;a<this.l&&(a=this.l);a>this.r-d.width&&(a=this.r-d.width);h<this.t&&(h=b+10);c.translate(a,h);b=this.textDiv.style;b.left=a+this.horizontalPadding+"px";b.top=h+this.verticalPadding+"px"}}}},changeColor:function(a){this.balloonColor=a},setBounds:function(a,b,c,d){this.l=a;this.t=b;this.r=c;this.b=d;this.destroyTO&&clearTimeout(this.destroyTO)},showBalloon:function(a){if(this.text!=a||this.positionChanged)this.text=a,this.isHiding=!1,this.show=!0,this.destroyTO&&clearTimeout(this.destroyTO),a=this.chart,this.fadeAnim1&&a.stopAnim(this.fadeAnim1),this.fadeAnim2&&a.stopAnim(this.fadeAnim2),this.draw(),this.positionChanged=!1},hide:function(a){var b=this;b.text=void 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a=this.textDiv.parentNode;a&&a.removeChild(this.textDiv)}},destroy:function(){clearInterval(this.interval);d.remove(this.set);this.removeDiv();this.set=null}})})();(function(){var d=window.AmCharts;d.AmCoordinateChart=d.Class({inherits:d.AmChart,construct:function(a){d.AmCoordinateChart.base.construct.call(this,a);this.theme=a;this.createEvents("rollOverGraphItem","rollOutGraphItem","clickGraphItem","doubleClickGraphItem","rightClickGraphItem","clickGraph","rollOverGraph","rollOutGraph");this.startAlpha=1;this.startDuration=0;this.startEffect="elastic";this.sequencedAnimation=!0;this.colors="#FF6600 #FCD202 #B0DE09 #0D8ECF #2A0CD0 #CD0D74 #CC0000 #00CC00 #0000CC #DDDDDD #999999 #333333 #990000".split(" ");this.balloonDateFormat="MMM DD, YYYY";this.valueAxes=[];this.graphs=[];this.guides=[];this.gridAboveGraphs=!1;d.applyTheme(this,a,"AmCoordinateChart")},initChart:function(){d.AmCoordinateChart.base.initChart.call(this);this.drawGraphs=!0;var a=this.categoryAxis;a&&(this.categoryAxis=d.processObject(a,d.CategoryAxis,this.theme));this.processValueAxes();this.createValueAxes();this.processGraphs();this.processGuides();d.VML&&(this.startAlpha=1);this.setLegendData(this.graphs);this.gridAboveGraphs&&(this.gridSet.toFront(),this.bulletSet.toFront(),this.balloonsSet.toFront())},createValueAxes:function(){if(0===this.valueAxes.length){var a=new d.ValueAxis;this.addValueAxis(a)}},parseData:function(){this.processValueAxes();this.processGraphs()},parseSerialData:function(a){this.chartData=[];if(a)if(0<this.processTimeout){1>this.processCount&&(this.processCount=1);var b=a.length/this.processCount;this.parseCount=Math.ceil(b)-1;for(var c=0;c<b;c++)this.delayParseSerialData(a,c)}else this.parseCount=0,this.parsePartSerialData(a,0,a.length,0);else this.onDataUpdated()},delayParseSerialData:function(a,b){var c=this,d=c.processCount;setTimeout(function(){c.parsePartSerialData.call(c,a,b*d,(b+1)*d,b)},c.processTimeout)},parsePartSerialData:function(a,b,c,e){c>a.length&&(c=a.length);var h=this.graphs,f={},g=this.seriesIdField;g||(g=this.categoryField);var k=!1,l,m=this.categoryAxis,p,q,n;m&&(k=m.parseDates,p=m.forceShowField,n=m.classNameField,q=m.labelColorField,l=m.categoryFunction);var t,r,w={},z;k&&(t=d.extractPeriod(m.minPeriod),r=t.period,t=t.count,z=d.getPeriodDuration(r,t));var x={};this.lookupTable=x;var u,A=this.dataDateFormat,y={};for(u=b;u<c;u++){var B={},D=a[u];b=D[this.categoryField];B.dataContext=D;B.category=l?l(b,D,m):String(b);p&&(B.forceShow=D[p]);n&&(B.className=D[n]);q&&(B.labelColor=D[q]);x[D[g]]=B;if(k&&(m.categoryFunction?b=m.categoryFunction(b,D,m):(!A||b instanceof Date||(b=b.toString()+" |"),b=d.getDate(b,A,m.minPeriod)),b=d.resetDateToMin(b,r,t,m.firstDayOfWeek),B.category=b,B.time=b.getTime(),isNaN(B.time)))continue;var C=this.valueAxes;B.axes={};B.x={};var I;for(I=0;I<C.length;I++){var H=C[I].id;B.axes[H]={};B.axes[H].graphs={};var Q;for(Q=0;Q<h.length;Q++){b=h[Q];var M=b.id,P=1.1;isNaN(b.gapPeriod)||(P=b.gapPeriod);var ia=b.periodValue;if(b.valueAxis.id==H){B.axes[H].graphs[M]={};var J={};J.index=u;var aa=D;b.dataProvider&&(aa=f);J.values=this.processValues(aa,b,ia);if(!b.connect||b.forceGap&&!isNaN(b.gapPeriod))if(y&&y[M]&&0<P&&B.time-w[M]>=z*P&&(y[M].gap=!0),b.forceGap){var P=0,ma;for(ma in J.values)P++;0<P&&(w[M]=B.time,y[M]=J)}else w[M]=B.time,y[M]=J;this.processFields(b,J,aa);J.category=B.category;J.serialDataItem=B;J.graph=b;B.axes[H].graphs[M]=J}}}this.chartData[u]=B}if(this.parseCount==e){for(a=0;a<h.length;a++)b=h[a],b.dataProvider&&this.parseGraphData(b);this.dataChanged=!1;this.dispatchDataUpdated=!0;this.onDataUpdated()}},processValues:function(a,b,c){var e={},h,f=!1;"candlestick"!=b.type&&"ohlc"!=b.type||""===c||(f=!0);for(var g="value error open close low high".split(" "),k=0;k<g.length;k++){var l=g[k];"value"!=l&&"error"!=l&&f&&(c=l.charAt(0).toUpperCase()+l.slice(1));var m=a[b[l+"Field"]+c];null!==m&&(h=Number(m),isNaN(h)||(e[l]=h),"date"==b.valueAxis.type&&void 0!==m&&(h=d.getDate(m,b.chart.dataDateFormat),e[l]=h.getTime()))}return e},parseGraphData:function(a){var b=a.dataProvider,c=a.seriesIdField;c||(c=this.seriesIdField);c||(c=this.categoryField);var d;for(d=0;d<b.length;d++){var h=b[d],f=this.lookupTable[String(h[c])],g=a.valueAxis.id;f&&(g=f.axes[g].graphs[a.id],g.serialDataItem=f,g.values=this.processValues(h,a,a.periodValue),this.processFields(a,g,h))}},addValueAxis:function(a){a.chart=this;this.valueAxes.push(a);this.validateData()},removeValueAxesAndGraphs:function(){var a=this.valueAxes,b;for(b=a.length-1;-1<b;b--)this.removeValueAxis(a[b])},removeValueAxis:function(a){var b=this.graphs,c;for(c=b.length-1;0<=c;c--){var 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diff --git a/admin/src/main/resources/static/js/plugins/chart/export.css b/admin/src/main/resources/static/js/plugins/chart/export.css
deleted file mode 100755
index 7ff4aa1716987247d4cd3eb210440ad5c89a9e44..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/chart/export.css
+++ /dev/null
@@ -1 +0,0 @@
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ease-out;-moz-transition:opacity 0.5s ease-out;-ms-transition:opacity 0.5s ease-out;-o-transition:opacity 0.5s ease-out;transition:opacity 0.5s ease-out;}.amcharts-export-canvas.dropbox .canvas-container{opacity:0.5;}.amcharts-export-menu .export-drawing-shape a{font:0/0 a;text-shadow:none;color:transparent;}.amcharts-export-menu li img{height:20px;}.amcharts-export-menu .export-drawing-width a{text-align:center;}.amcharts-export-menu .export-drawing-width span{display:block;margin:0 auto;}.amcharts-export-menu .export-drawing-width span>span{display:block;background:#000;border-radius:100%;}.amcharts-export-menu .export-drawing-shape a:hover img,.amcharts-export-menu .export-drawing-shape.active a img{-webkit-filter:invert(100%);filter:invert(100%);}
diff --git a/admin/src/main/resources/static/js/plugins/chart/export.min.js b/admin/src/main/resources/static/js/plugins/chart/export.min.js
deleted file mode 100755
index b26964a9f70e9b123d834e42cf7711620077c1e7..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/chart/export.min.js
+++ /dev/null
@@ -1 +0,0 @@
-AmCharts.translations.export||(AmCharts.translations.export={}),AmCharts.translations.export.en||(AmCharts.translations.export.en={"fallback.save.text":"CTRL + C to copy the data into the clipboard.","fallback.save.image":"Rightclick -> Save picture as... to save the image.","capturing.delayed.menu.label":"{{duration}}","capturing.delayed.menu.title":"Click to cancel","menu.label.print":"Print","menu.label.undo":"Undo","menu.label.redo":"Redo","menu.label.cancel":"Cancel","menu.label.save.image":"Download as ...","menu.label.save.data":"Save as ...","menu.label.draw":"Annotate ...","menu.label.draw.change":"Change ...","menu.label.draw.add":"Add ...","menu.label.draw.shapes":"Shape ...","menu.label.draw.colors":"Color ...","menu.label.draw.widths":"Size ...","menu.label.draw.opacities":"Opacity ...","menu.label.draw.text":"Text","menu.label.draw.modes":"Mode ...","menu.label.draw.modes.pencil":"Pencil","menu.label.draw.modes.line":"Line","menu.label.draw.modes.arrow":"Arrow","label.saved.from":"Saved from: "}),function(){AmCharts.export=function(e,t){var a,i={name:"export",version:"1.4.72",libs:{async:!0,autoLoad:!0,reload:!1,resources:["fabric.js/fabric.min.js","FileSaver.js/FileSaver.min.js",{"jszip/jszip.min.js":["xlsx/xlsx.min.js"],"pdfmake/pdfmake.min.js":["pdfmake/vfs_fonts.js"]}],namespaces:{"pdfmake.min.js":"pdfMake","jszip.min.js":"JSZip","xlsx.min.js":"XLSX","fabric.min.js":"fabric","FileSaver.min.js":"saveAs"},loadTimeout:1e4},config:{},setup:{chart:e,hasBlob:!1,wrapper:!1,isIE:!!window.document.documentMode,IEversion:window.document.documentMode,hasTouch:"object"==typeof window.Touch,focusedMenuItem:void 0},drawing:{enabled:!1,undos:[],redos:[],buffer:{position:{x1:0,y1:0,x2:0,y2:0,xD:0,yD:0}},handler:{undo:function(e,t){var a=i.drawing.undos.pop();if(a){a.selectable=!0,i.drawing.redos.push(a),"added"==a.action&&i.setup.fabric.remove(a.target);var r=JSON.parse(a.state);a.target.set(r),a.target instanceof fabric.Group&&i.drawing.handler.change({color:r.cfg.color,width:r.cfg.width,opacity:r.cfg.opacity},!0,a.target),i.setup.fabric.renderAll()}},redo:function(e,t){var a=i.drawing.redos.pop();if(a){a.selectable=!0,i.drawing.undos.push(a),"added"==a.action&&i.setup.fabric.add(a.target);var r=JSON.parse(a.state);a.target.recentState=a.state,a.target.set(r),a.target instanceof fabric.Group&&i.drawing.handler.change({color:r.cfg.color,width:r.cfg.width,opacity:r.cfg.opacity},!0,a.target),i.setup.fabric.renderAll()}},done:function(e){i.drawing.enabled=!1,i.drawing.buffer.enabled=!1,i.drawing.undos=[],i.drawing.redos=[],i.createMenu(i.config.menu),i.setup.fabric.deactivateAll(),i.isElement(i.setup.wrapper)&&i.isElement(i.setup.wrapper.parentNode)&&i.setup.wrapper.parentNode.removeChild&&(i.setup.wrapper.parentNode.removeChild(i.setup.wrapper),i.setup.wrapper=!1)},add:function(e){var t=i.deepMerge({top:i.setup.fabric.height/2,left:i.setup.fabric.width/2},e||{});(-1!=t.url.indexOf(".svg")?fabric.loadSVGFromURL:fabric.Image.fromURL)(t.url,function(e,a){var r=void 0!==a?fabric.util.groupSVGElements(e,a):e,n=!1;(r.height>i.setup.fabric.height||r.width>i.setup.fabric.width)&&(n=i.setup.fabric.height/2/r.height),t.top>i.setup.fabric.height&&(t.top=i.setup.fabric.height/2),t.left>i.setup.fabric.width&&(t.left=i.setup.fabric.width/2),i.drawing.buffer.isDrawing=!0,r.set({originX:"center",originY:"center",top:t.top,left:t.left,width:n?r.width*n:r.width,height:n?r.height*n:r.height,fill:i.drawing.color}),i.setup.fabric.add(r)})},change:function(e,t,a){var r,n,o,s=i.deepMerge({},e||{}),l=a||i.drawing.buffer.target,d=l?l._objects?l._objects:[l]:null;if(s.mode&&(i.drawing.mode=s.mode),s.width&&(i.drawing.width=s.width,i.drawing.fontSize=s.fontSize=3*s.width,1==i.drawing.width&&(i.drawing.fontSize=s.fontSize=i.defaults.fabric.drawing.fontSize)),s.fontSize&&(i.drawing.fontSize=s.fontSize),s.color&&(i.drawing.color=s.color),s.opacity&&(i.drawing.opacity=s.opacity),(o=i.getRGBA(i.drawing.color)).pop(),o.push(i.drawing.opacity),i.drawing.color="rgba("+o.join()+")",i.setup.fabric.freeDrawingBrush.color=i.drawing.color,i.setup.fabric.freeDrawingBrush.width=i.drawing.width,l){for((r=JSON.parse(l.recentState).cfg)&&(s.color=s.color||r.color,s.width=s.width||r.width,s.opacity=s.opacity||r.opacity,s.fontSize=s.fontSize||r.fontSize,(o=i.getRGBA(s.color)).pop(),o.push(s.opacity),s.color="rgba("+o.join()+")"),n=0;n<d.length;n++)d[n]instanceof fabric.Text||d[n]instanceof fabric.PathGroup||d[n]instanceof fabric.Triangle?((s.color||s.opacity)&&d[n].set({fill:s.color}),s.fontSize&&d[n].set({fontSize:s.fontSize})):(d[n]instanceof fabric.Path||d[n]instanceof fabric.Line)&&(l instanceof fabric.Group?(s.color||s.opacity)&&d[n].set({stroke:s.color}):((s.color||s.opacity)&&d[n].set({stroke:s.color}),s.width&&d[n].set({strokeWidth:s.width})));t||(r=JSON.stringify(i.deepMerge(l.saveState()._stateProperties,{cfg:{color:s.color,width:s.width,opacity:s.opacity}})),l.recentState=r,i.drawing.redos=[],i.drawing.undos.push({action:"modified",target:l,state:r})),i.setup.fabric.renderAll()}},text:function(e){var t=i.deepMerge({text:i.i18l("menu.label.draw.text"),top:i.setup.fabric.height/2,left:i.setup.fabric.width/2,fontSize:i.drawing.fontSize,fontFamily:i.setup.chart.fontFamily||"Verdana",fill:i.drawing.color},e||{});t.click=function(){};var a=new fabric.IText(t.text,t);return i.drawing.buffer.isDrawing=!0,i.setup.fabric.add(a),i.setup.fabric.setActiveObject(a),a.selectAll(),a.enterEditing(),a},line:function(e){var t,a,r,n,o=i.deepMerge({x1:i.setup.fabric.width/2-i.setup.fabric.width/10,x2:i.setup.fabric.width/2+i.setup.fabric.width/10,y1:i.setup.fabric.height/2,y2:i.setup.fabric.height/2,angle:90,strokeLineCap:i.drawing.lineCap,arrow:i.drawing.arrow,color:i.drawing.color,width:i.drawing.width,group:[]},e||{}),s=new fabric.Line([o.x1,o.y1,o.x2,o.y2],{stroke:o.color,strokeWidth:o.width,strokeLineCap:o.strokeLineCap});if(o.group.push(s),o.arrow&&(o.angle=o.angle?o.angle:i.getAngle(o.x1,o.y1,o.x2,o.y2),"start"==o.arrow?(r=o.y1+o.width/2,n=o.x1+o.width/2):"middle"==o.arrow?(r=o.y2+o.width/2-(o.y2-o.y1)/2,n=o.x2+o.width/2-(o.x2-o.x1)/2):(r=o.y2+o.width/2,n=o.x2+o.width/2),a=new fabric.Triangle({top:r,left:n,fill:o.color,height:7*o.width,width:7*o.width,angle:o.angle,originX:"center",originY:"bottom"}),o.group.push(a)),i.drawing.buffer.isDrawing=!0,"config"!=o.action){if(o.arrow){var l=new fabric.Group(o.group);return l.set({cfg:o,fill:o.color,action:o.action,selectable:!0,known:"change"==o.action}),"change"==o.action&&i.setup.fabric.setActiveObject(l),i.setup.fabric.add(l),l}return i.setup.fabric.add(s),s}for(t=0;t<o.group.length;t++)o.group[t].ignoreUndo=!0,i.setup.fabric.add(o.group[t]);return o}}},defaults:{position:"top-right",fileName:"amCharts",action:"download",overflow:!0,path:(e.path||"")+"plugins/export/",formats:{JPG:{mimeType:"image/jpg",extension:"jpg",capture:!0},PNG:{mimeType:"image/png",extension:"png",capture:!0},SVG:{mimeType:"text/xml",extension:"svg",capture:!0},PDF:{mimeType:"application/pdf",extension:"pdf",capture:!0},CSV:{mimeType:"text/plain",extension:"csv"},JSON:{mimeType:"text/plain",extension:"json"},XLSX:{mimeType:"application/octet-stream",extension:"xlsx"}},fabric:{backgroundColor:"#FFFFFF",removeImages:!0,forceRemoveImages:!1,selection:!1,loadTimeout:5e3,drawing:{enabled:!0,arrow:"end",lineCap:"butt",mode:"pencil",modes:["pencil","line","arrow"],color:"#000000",colors:["#000000","#FFFFFF","#FF0000","#00FF00","#0000FF"],shapes:["11.svg","14.svg","16.svg","17.svg","20.svg","27.svg"],width:1,fontSize:11,widths:[1,5,10,15],opacity:1,opacities:[1,.8,.6,.4,.2],menu:void 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i.gatherClassName(e.parentNode,t,a,r+1);n&&(n=e)}return n},gatherElements:function(e,t,a){var r,n;for(r=0;r<e.children.length;r++){var o=e.children[r];if("clipPath"==o.tagName){var s={},l=fabric.parseTransformAttribute(i.gatherAttribute(o,"transform"));for(n=0;n<o.childNodes.length;n++)o.childNodes[n].setAttribute("fill","transparent"),s={x:i.pxToNumber(o.childNodes[n].getAttribute("x")),y:i.pxToNumber(o.childNodes[n].getAttribute("y")),width:i.pxToNumber(o.childNodes[n].getAttribute("width")),height:i.pxToNumber(o.childNodes[n].getAttribute("height"))};e.clippings[o.id]={svg:o,bbox:s,transform:l}}else if("pattern"==o.tagName){var 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a=fabric.parseAttributes(e,fabric.Text.ATTRIBUTE_NAMES);(t=fabric.util.object.extend(t?fabric.util.object.clone(t):{},a)).top=t.top||0,t.left=t.left||0,"dx"in a&&(t.left+=a.dx),"dy"in a&&(t.top+=a.dy),"fontSize"in t||(t.fontSize=fabric.Text.DEFAULT_SVG_FONT_SIZE),t.originX||(t.originX="left");var i="",r=[];if("textContent"in e)if(e.childNodes)for(var n=0;n<e.childNodes.length;n++)r.push(e.childNodes[n].textContent);else r.push(e.textContent);else"firstChild"in e&&null!==e.firstChild&&"data"in e.firstChild&&null!==e.firstChild.data&&r.push(e.firstChild.data);i=r.join("\n");var o=new fabric.Text(i,t),s=0;return"left"===o.originX&&(s=o.getWidth()/2),"right"===o.originX&&(s=-o.getWidth()/2),r.length>1?o.set({left:o.getLeft()+s,top:o.getTop()+o.fontSize*(r.length-1)*(.18+o._fontSizeFraction),textAlign:t.originX,lineHeight:r.length>1?.965:1.16}):o.set({left:o.getLeft()+s,top:o.getTop()-o.getHeight()/2+o.fontSize*(.18+o._fontSizeFraction)}),o}},capture:function(e,t){var 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d=i.setup.chart.containerDiv.getElementsByTagName("svg");for(a=0;a<d.length;a++)(p={svg:d[a],parent:d[a].parentNode,children:d[a].getElementsByTagName("*"),offset:{x:0,y:0},patterns:{},clippings:{},has:{legend:!1,panel:!1,scrollbar:!1}}).has.legend=i.gatherClassName(p.parent,i.setup.chart.classNamePrefix+"-legend-div",1),p.has.panel=i.gatherClassName(p.parent,i.setup.chart.classNamePrefix+"-stock-panel-div"),p.has.scrollbar=i.gatherClassName(p.parent,i.setup.chart.classNamePrefix+"-scrollbar-chart-div"),p=i.gatherElements(p,r,s),n.push(p);if(i.config.legend){if("stock"==i.setup.chart.type)for(a=0;a<i.setup.chart.panels.length;a++)i.setup.chart.panels[a].stockLegend&&i.setup.chart.panels[a].stockLegend.divId&&l.items.push(i.setup.chart.panels[a].stockLegend);else i.setup.chart.legend&&i.setup.chart.legend.divId&&l.items.push(i.setup.chart.legend);for(a=0;a<l.items.length;a++){var c=l.items[a],p={svg:c.container.container,parent:c.container.container.parentNode,children:c.container.container.getElementsByTagName("*"),offset:{x:0,y:0},legend:{id:a,type:-1!=["top","left"].indexOf(i.config.legend.position)?"unshift":"push",position:i.config.legend.position,width:i.config.legend.width?i.config.legend.width:c.container.div.offsetWidth,height:i.config.legend.height?i.config.legend.height:c.container.div.offsetHeight},patterns:{},clippings:{},has:{legend:!1,panel:!1,scrollbar:!1}};l.width+=p.legend.width,l.height+=p.legend.height,l.maxWidth=p.legend.width>l.maxWidth?p.legend.width:l.maxWidth,l.maxHeight=p.legend.height>l.maxHeight?p.legend.height:l.maxHeight,p=i.gatherElements(p,r,s),n[p.legend.type](p)}-1!=["top","bottom"].indexOf(i.config.legend.position)?(o.width=l.maxWidth>o.width?l.maxWidth:o.width,o.height+=l.height):-1!=["left","right"].indexOf(i.config.legend.position)?(o.width+=l.maxWidth,o.height=l.height>o.height?l.height:o.height):(o.height+=l.height,o.width+=l.maxWidth)}if(i.drawing.enabled=r.drawing.enabled="draw"==r.action,i.drawing.buffer.enabled=i.drawing.enabled,i.setup.wrapper=document.createElement("div"),i.setup.wrapper.setAttribute("class",i.setup.chart.classNamePrefix+"-export-canvas"),i.setup.chart.containerDiv.appendChild(i.setup.wrapper),"stock"==i.setup.chart.type){var f={top:0,right:0,bottom:0,left:0};i.setup.chart.leftContainer&&(o.width-=i.setup.chart.leftContainer.offsetWidth,f.left=i.setup.chart.leftContainer.offsetWidth+2*i.setup.chart.panelsSettings.panelSpacing),i.setup.chart.rightContainer&&(o.width-=i.setup.chart.rightContainer.offsetWidth,f.right=i.setup.chart.rightContainer.offsetWidth+2*i.setup.chart.panelsSettings.panelSpacing),i.setup.chart.periodSelector&&-1!=["top","bottom"].indexOf(i.setup.chart.periodSelector.position)&&(o.height-=i.setup.chart.periodSelector.offsetHeight+i.setup.chart.panelsSettings.panelSpacing,f[i.setup.chart.periodSelector.position]+=i.setup.chart.periodSelector.offsetHeight+i.setup.chart.panelsSettings.panelSpacing),i.setup.chart.dataSetSelector&&-1!=["top","bottom"].indexOf(i.setup.chart.dataSetSelector.position)&&(o.height-=i.setup.chart.dataSetSelector.offsetHeight,f[i.setup.chart.dataSetSelector.position]+=i.setup.chart.dataSetSelector.offsetHeight),i.setup.wrapper.style.paddingTop=i.numberToPx(f.top),i.setup.wrapper.style.paddingRight=i.numberToPx(f.right),i.setup.wrapper.style.paddingBottom=i.numberToPx(f.bottom),i.setup.wrapper.style.paddingLeft=i.numberToPx(f.left)}i.setup.canvas=document.createElement("canvas"),i.setup.wrapper.appendChild(i.setup.canvas);var u=i.removeFunctionsFromObject(i.deepMerge({width:o.width,height:o.height,isDrawingMode:!0},r));for(i.setup.fabric=new fabric.Canvas(i.setup.canvas,u),i.deepMerge(i.setup.fabric,r),i.deepMerge(i.setup.fabric.freeDrawingBrush,r.drawing),i.deepMerge(i.drawing,r.drawing),i.drawing.handler.change(r.drawing),i.setup.fabric.on("mouse:down",function(e){i.gatherPosition(e.e,1);i.drawing.buffer.pressedTS=Number(new Date),i.isPressed(e.e),i.drawing.buffer.isDrawing=!1,i.drawing.buffer.isDrawingTimer=setTimeout(function(){i.drawing.buffer.isSelected||(i.drawing.buffer.isDrawing=!0)},200)}),i.setup.fabric.on("mouse:move",function(e){var t=i.gatherPosition(e.e,2);if(i.isPressed(e.e),i.drawing.buffer.isPressed&&!i.drawing.buffer.isSelected&&(i.drawing.buffer.isDrawing=!0,!i.drawing.buffer.line&&"pencil"!=i.drawing.mode&&(t.xD>5||t.yD>5)&&(i.setup.fabric.isDrawingMode=!1,i.setup.fabric._isCurrentlyDrawing=!1,i.drawing.buffer.ignoreUndoOnMouseUp=!0,i.setup.fabric.freeDrawingBrush.onMouseUp(),i.setup.fabric.remove(i.setup.fabric._objects.pop()),i.drawing.buffer.line=i.drawing.handler.line({x1:t.x1,y1:t.y1,x2:t.x2,y2:t.y2,arrow:"line"!=i.drawing.mode&&i.drawing.arrow,action:"config"}))),i.drawing.buffer.isSelected&&(i.setup.fabric.isDrawingMode=!1),i.drawing.buffer.line){var r,n,o,s=i.drawing.buffer.line;for(s.x2=t.x2,s.y2=t.y2,a=0;a<s.group.length;a++)(r=s.group[a])instanceof fabric.Line?r.set({x2:s.x2,y2:s.y2}):r instanceof fabric.Triangle&&(s.angle=i.getAngle(s.x1,s.y1,s.x2,s.y2)+90,"start"==s.arrow?(n=s.y1+s.width/2,o=s.x1+s.width/2):"middle"==s.arrow?(n=s.y2+s.width/2-(s.y2-s.y1)/2,o=s.x2+s.width/2-(s.x2-s.x1)/2):(n=s.y2+s.width/2,o=s.x2+s.width/2),r.set({top:n,left:o,angle:s.angle}));i.setup.fabric.renderAll()}}),i.setup.fabric.on("mouse:up",function(e){if(!i.drawing.buffer.isDrawing){var t=i.setup.fabric.findTarget(e.e);t&&t.selectable&&i.setup.fabric.setActiveObject(t)}if(i.drawing.buffer.line){for(a=0;a<i.drawing.buffer.line.group.length;a++)i.drawing.buffer.line.group[a].remove();delete i.drawing.buffer.line.action,delete i.drawing.buffer.line.group,i.drawing.handler.line(i.drawing.buffer.line)}i.drawing.buffer.line=!1,i.drawing.buffer.hasLine=!1,i.drawing.buffer.isPressed=!1,clearTimeout(i.drawing.buffer.isDrawingTimer),i.drawing.buffer.isDrawing=!1}),i.setup.fabric.on("object:selected",function(e){i.drawing.buffer.isSelected=!0,i.drawing.buffer.target=e.target,i.setup.fabric.isDrawingMode=!1}),i.setup.fabric.on("selection:cleared",function(e){i.drawing.buffer.target=!1,i.drawing.buffer.isSelected&&(i.setup.fabric._isCurrentlyDrawing=!1),i.drawing.buffer.isSelected=!1,i.setup.fabric.isDrawingMode=!0}),i.setup.fabric.on("path:created",function(e){var t=e.path;if(!i.drawing.buffer.isDrawing||i.drawing.buffer.hasLine)return i.setup.fabric.remove(t),void i.setup.fabric.renderAll()}),i.setup.fabric.on("object:added",function(e){var 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a,r,n,o,s=i.deepMerge({data:[],titles:{},dateFields:[],dataFields:[],dataFieldsMap:{},exportTitles:i.config.exportTitles,exportFields:i.config.exportFields,exportSelection:i.config.exportSelection,columnNames:i.config.columnNames},e||{},!0),l=["valueField","openField","closeField","highField","lowField","xField","yField"];if(0==s.data.length)if("stock"==i.setup.chart.type){for(s.data=i.cloneObject(i.setup.chart.mainDataSet.dataProvider),t(i.setup.chart.mainDataSet.categoryField),s.dateFields.push(i.setup.chart.mainDataSet.categoryField),a=0;a<i.setup.chart.mainDataSet.fieldMappings.length;a++){u=i.setup.chart.mainDataSet.fieldMappings[a];for(r=0;r<i.setup.chart.panels.length;r++){var d=i.setup.chart.panels[r];for(n=0;n<d.stockGraphs.length;n++){v=d.stockGraphs[n];for(i4=0;i4<l.length;i4++)v[l[i4]]==u.toField&&t(u.fromField,v.title,l[i4])}}}if(i.setup.chart.comparedGraphs.length){for(o=[],a=0;a<s.data.length;a++)o.push(s.data[a][i.setup.chart.mainDataSet.categoryField]);for(a=0;a<i.setup.chart.comparedGraphs.length;a++){v=i.setup.chart.comparedGraphs[a];for(r=0;r<v.dataSet.dataProvider.length;r++){var c=v.dataSet.categoryField,p=v.dataSet.dataProvider[r][c],f=o.indexOf(p);if(-1!=f)for(n=0;n<v.dataSet.fieldMappings.length;n++){var u=v.dataSet.fieldMappings[n],g=v.dataSet.id+"_"+u.toField;s.data[f][g]=v.dataSet.dataProvider[r][u.fromField],s.titles[g]||t(g,v.dataSet.title)}}}}}else if("gantt"==i.setup.chart.type){t(i.setup.chart.categoryField);var h=i.setup.chart.segmentsField;for(a=0;a<i.setup.chart.dataProvider.length;a++){var m=i.setup.chart.dataProvider[a];if(m[h])for(r=0;r<m[h].length;r++)m[h][r][i.setup.chart.categoryField]=m[i.setup.chart.categoryField],s.data.push(m[h][r])}for(a=0;a<i.setup.chart.graphs.length;a++){v=i.setup.chart.graphs[a];for(r=0;r<l.length;r++){var b=v[w=l[r]];v.title;t(b,v.title,w)}}}else if(-1!=["pie","funnel"].indexOf(i.setup.chart.type))s.data=i.setup.chart.dataProvider,t(i.setup.chart.titleField),s.dateFields.push(i.setup.chart.titleField),t(i.setup.chart.valueField);else if("map"!=i.setup.chart.type)for(s.data=i.setup.chart.dataProvider,i.setup.chart.categoryAxis&&(t(i.setup.chart.categoryField,i.setup.chart.categoryAxis.title),!1!==i.setup.chart.categoryAxis.parseDates&&s.dateFields.push(i.setup.chart.categoryField)),a=0;a<i.setup.chart.graphs.length;a++){var v=i.setup.chart.graphs[a];for(r=0;r<l.length;r++){var w=l[r];t(b=v[w],v.title,w)}}return i.processData(s)},getAnnotations:function(e,t){var a,r=i.deepMerge({},e||{},!0),n=[];for(a=0;a<i.setup.fabric._objects.length;a++)if(!i.setup.fabric._objects[a].isCoreElement){var o=i.setup.fabric._objects[a].toJSON();i.handleCallback(r.reviver,o,a),n.push(o)}return i.handleCallback(t,n),n},setAnnotations:function(e,t){var a=i.deepMerge({data:[]},e||{},!0);return fabric.util.enlivenObjects(a.data,function(e){e.forEach(function(e,t){i.handleCallback(a.reviver,e,t),i.setup.fabric.add(e)}),i.handleCallback(t,a)}),a.data},processData:function(t){var a,r,n=i.deepMerge({data:[],titles:{},dateFields:[],dataFields:[],dataFieldsMap:{},dataFieldsTitlesMap:{},dataDateFormat:i.setup.chart.dataDateFormat,dateFormat:i.config.dateFormat||i.setup.chart.dataDateFormat||"YYYY-MM-DD",exportTitles:i.config.exportTitles,exportFields:i.config.exportFields,exportSelection:i.config.exportSelection,columnNames:i.config.columnNames,processData:i.config.processData},t||{},!0);if(n.data.length){for(a=0;a<n.data.length;a++)for(r in n.data[a])-1==n.dataFields.indexOf(r)&&(n.dataFields.push(r),n.dataFieldsMap[r]=r);void 0!==n.exportFields&&(n.dataFields=n.exportFields.filter(function(e){return-1!=n.dataFields.indexOf(e)}));var o=[];for(a=0;a<n.data.length;a++){var s={},l=!1;for(r=0;r<n.dataFields.length;r++){var d=n.dataFields[r],c=n.dataFieldsMap[d],p=n.columnNames&&n.columnNames[d]||n.titles[d]||d,f=n.data[a][c];null==f&&(f=void 0),n.exportTitles&&"gantt"!=i.setup.chart.type&&p in s&&(p+=["( ",d," )"].join("")),-1!=n.dateFields.indexOf(c)&&(n.dataDateFormat&&(f instanceof String||"string"==typeof f)?f=AmCharts.stringToDate(f,n.dataDateFormat):n.dateFormat&&(f instanceof Number||"number"==typeof f)&&(f=new Date(f)),n.exportSelection&&(f instanceof Date?(f<e.startDate||f>e.endDate)&&(l=!0):(a<e.startIndex||a>e.endIndex)&&(l=!0)),n.dateFormat&&"dateObject"!=n.dateFormat&&f instanceof Date&&(f=AmCharts.formatDate(f,n.dateFormat))),n.dataFieldsTitlesMap[c]=p,s[p]=f}l||o.push(s)}n.data=o}return void 0!==n.processData&&(n.data=i.handleCallback(n.processData,n.data,n)),n.data},capitalize:function(e){return e.charAt(0).toUpperCase()+e.slice(1).toLowerCase()},createMenu:function(t,a){function r(t,a){var o,s,l=document.createElement("ul");for(o=0;o<t.length;o++){var d="string"==typeof t[o]?{format:t[o]}:t[o],c=document.createElement("li"),p=document.createElement("a"),f=document.createElement("img"),u=document.createElement("span"),g=String(d.action?d.action:d.format).toLowerCase();if(d.format=String(d.format).toUpperCase(),c.addEventListener("mouseleave",function(e){this.classList.remove("active")}),p.addEventListener("focus",function(e){if(!i.setup.hasTouch){i.setup.focusedMenuItem=this;var t=this.parentNode;"UL"!=t.tagName&&(t=t.parentNode);var 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if(!d.populated&&d.action&&-1!=d.action.indexOf("draw.")){var h=d.action.split(".")[1],m=d[h]||i.config.fabric.drawing[h]||[];for(d.menu=[],d.populated=!0,s=0;s<m.length;s++){var b={label:m[s]};if("shapes"==h){var v=-1==m[s].indexOf("//"),w=(v?i.config.path+"shapes/":"")+m[s];b.action="add",b.url=w,b.icon=w,b.ignore=v,b.class="export-drawing-shape"}else"colors"==h?(b.style="background-color: "+m[s],b.action="change",b.color=m[s],b.class="export-drawing-color"):"widths"==h?(b.action="change",b.width=m[s],b.label=document.createElement("span"),b.label.style.width=i.numberToPx(m[s]),b.label.style.height=i.numberToPx(m[s]),b.class="export-drawing-width"):"opacities"==h?(b.style="opacity: "+m[s],b.action="change",b.opacity=m[s],b.label=100*m[s]+"%",b.class="export-drawing-opacity"):"modes"==h&&(b.label=i.i18l("menu.label.draw.modes."+m[s]),b.click=function(e){return function(){i.drawing.mode=e}}(m[s]),b.class="export-drawing-mode");d.menu.push(b)}}else d.click||d.menu||d.items||(i.drawing.handler[g]instanceof Function?(d.action=g,d.click=function(e){return function(){this.drawing.handler[e.action](e),"cancel"!=e.action&&this.createMenu(this.config.fabric.drawing.menu)}}(d)):i.drawing.enabled?d.click=function(e){return function(){this.config.drawing.autoClose&&this.drawing.handler.done(),this["to"+e.format](e,function(t){"download"==e.action&&this.download(t,e.mimeType,[e.fileName,e.extension].join("."))})}}(d):"UNDEFINED"!=d.format&&(d.click=function(e){return function(){if(e.capture||"print"==e.action||"PRINT"==e.format)this.capture(e,function(){this.drawing.handler.done(),this["to"+e.format](e,function(t){"download"==e.action&&(this.download(t,e.mimeType,[e.fileName,e.extension].join(".")),this.createMenu(this.config.menu))})});else{if(!this["to"+e.format])throw new Error("Invalid format. Could not determine output type.");this["to"+e.format](e,function(t){this.download(t,e.mimeType,[e.fileName,e.extension].join(".")),this.createMenu(this.config.menu)})}}}(d)));(void 0===d.menu||d.menu.length)&&(p.setAttribute("href","#"),i.setup.hasTouch&&c.classList?(p.addEventListener("touchend",function(e,t){return function(a){a.preventDefault();var r=[a,t];if(("draw"==t.action||"PRINT"==t.format||"UNDEFINED"!=t.format&&t.capture)&&!i.drawing.enabled&&(!isNaN(t.delay)||!isNaN(i.config.delay)))return t.delay=isNaN(t.delay)?i.config.delay:t.delay,void i.delay(t,e);e.apply(i,r)}}(d.click||function(e){e.preventDefault()},d)),p.addEventListener("touchend",function(e){return function(t){function a(e){return e.classList.contains("export-main")||e.classList.contains("export-drawing")}t.preventDefault();var r=e.elements.li,s=function(e){var t=e.parentNode.parentNode,a=t.classList;return!("LI"!=t.tagName||!a.contains("active"))}(r),l=(function(e){var 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i.delay(t,e);e.apply(i,r)}}(d.click||function(e){e.preventDefault()},d)),c.appendChild(p),i.isElement(d.label)?u.appendChild(d.label):u.innerHTML=d.label,d.class&&(c.className=d.class),d.style&&c.setAttribute("style",d.style),d.icon&&(f.setAttribute("src",(d.ignore||-1!=d.icon.slice(0,10).indexOf("//")?"":e.pathToImages)+d.icon),p.appendChild(f)),d.label&&p.appendChild(u),d.title&&p.setAttribute("title",d.title),i.config.menuReviver&&(c=i.config.menuReviver.apply(i,[d,c])),d.elements={li:c,a:p,img:f,span:u},(d.menu||d.items)&&"draw"!=d.action?r(d.menu||d.items,c).childNodes.length&&l.appendChild(c):l.appendChild(c))}}return l.childNodes.length&&a.appendChild(l),l}var n=[];return a||("string"==typeof i.config.divId?i.config.divId=a=document.getElementById(i.config.divId):a=i.isElement(i.config.divId)?i.config.divId:i.setup.chart.containerDiv),i.isElement(i.setup.menu)?i.setup.menu.innerHTML="":i.setup.menu=document.createElement("div"),i.setup.menu.setAttribute("class",i.setup.chart.classNamePrefix+"-export-menu "+i.setup.chart.classNamePrefix+"-export-menu-"+i.config.position+" amExportButton"),i.config.menuWalker&&(r=i.config.menuWalker),r.apply(this,[t,i.setup.menu]),i.setup.menu.childNodes.length&&a.appendChild(i.setup.menu),i.setup.menu},delay:function(e,t){var a,r,n=i.deepMerge({delay:3,precision:2},e||{}),o=Number(new Date),s=i.createMenu([{label:i.i18l("capturing.delayed.menu.label").replace("{{duration}}",AmCharts.toFixed(n.delay,n.precision)),title:i.i18l("capturing.delayed.menu.title"),class:"export-delayed-capturing",click:function(){clearTimeout(a),clearTimeout(r),i.createMenu(i.config.menu)}}]).getElementsByTagName("a")[0];a=setInterval(function(){var e=n.delay-(Number(new Date)-o)/1e3;e<=0?(clearTimeout(a),"draw"!=n.action&&i.createMenu(i.config.menu)):s&&(s.innerHTML=i.i18l("capturing.delayed.menu.label").replace("{{duration}}",AmCharts.toFixed(e,2)))},AmCharts.updateRate),r=setTimeout(function(){t.apply(i,arguments)},1e3*n.delay)},migrateSetup:function(e){function t(e){var i;for(i in e){var r=e[i];"export"==i.slice(0,6)&&r?a.menu.push(i.slice(6)):"userCFG"==i?t(r):"menuItems"==i?a.menu=r:"libs"==i?a.libs=r:"string"==typeof i&&(a[i]=r)}}var a={enabled:!0,migrated:!0,libs:{autoLoad:!0},menu:[]};return t(e),a},clear:function(){var e,t;for(void 0!==i.setup.fabric&&i.setup.fabric.removeListeners(),e=0;e<i.listenersToRemove.length;e++)(t=i.listenersToRemove[e]).node.removeEventListener(t.event,t.method);i.isElement(i.setup.wrapper)&&i.isElement(i.setup.wrapper.parentNode)&&i.setup.wrapper.parentNode.removeChild&&i.setup.wrapper.parentNode.removeChild(i.setup.wrapper),i.isElement(i.setup.menu)&&i.isElement(i.setup.wrapper.parentNode)&&i.setup.wrapper.parentNode.removeChild&&i.setup.menu.parentNode.removeChild(i.setup.menu),i.listenersToRemove=[],i.setup.chart.AmExport=void 0,i.setup.chart.export=void 0,i.setup=void 0},loadListeners:function(){function e(e){e&&(e.set({top:e.top+10,left:e.left+10}),i.setup.fabric.add(e))}i.config.keyListener&&"attached"!=i.config.keyListener&&(i.docListener=function(t){function a(e,t){for(i1=0;i1<e.length;i1++){var a=e[i1];a.parentNode.classList.remove("active"),0!=i1||t||a.focus()}}function r(e){i.setup.focusedMenuItem&&i.setup.focusedMenuItem.nextSibling&&(i.setup.focusedMenuItem.parentNode.classList.add("active"),a(i.setup.focusedMenuItem.nextSibling.getElementsByTagName("a"),e))}function n(e){i.setup.focusedMenuItem&&i.setup.focusedMenuItem.parentNode.parentNode.parentNode&&(i.setup.focusedMenuItem.parentNode.classList.add("active"),a(i.setup.focusedMenuItem.parentNode.parentNode.parentNode.getElementsByTagName("a"),e))}var o=i.drawing.buffer.target,s=[37,38,39,40,13,9,27],l=(["top-left","bottom-left"].indexOf(i.config.position),-1!=["top-right","bottom-right"].indexOf(i.config.position));if(i.setup.focusedMenuItem&&-1!=s.indexOf(t.keyCode)){if(9==t.keyCode)return void(i.setup.focusedMenuItem.nextSibling?t.shiftKey&&i.setup.focusedMenuItem.parentNode.classList.remove("active"):(i.setup.focusedMenuItem.parentNode.classList.remove("active"),i.setup.focusedMenuItem.parentNode.nextSibling||(i.setup.focusedMenuItem.parentNode.classList.remove("active"),i.setup.focusedMenuItem.parentNode.parentNode.parentNode.classList.remove("active"))));13==t.keyCode&&i.setup.focusedMenuItem.nextSibling&&r(),37==t.keyCode&&(l?r():n()),39==t.keyCode&&(l?n():r()),40==t.keyCode&&function(e){i.setup.focusedMenuItem&&i.setup.focusedMenuItem.parentNode.nextSibling&&(i.setup.focusedMenuItem.parentNode.classList.remove("active"),a(i.setup.focusedMenuItem.parentNode.nextSibling.getElementsByTagName("a"),e))}(),38==t.keyCode&&function(e){i.setup.focusedMenuItem&&i.setup.focusedMenuItem.parentNode.previousSibling&&(i.setup.focusedMenuItem.parentNode.classList.remove("active"),a(i.setup.focusedMenuItem.parentNode.previousSibling.getElementsByTagName("a"),e))}(),27==t.keyCode&&function(){function e(t){i.isElement(t)&&(t.blur(),t.parentNode&&t.parentNode.classList.remove("active"),t.classList.contains("amExportButton")||e(t.parentNode))}i.setup.focusedMenuItem&&(e(i.setup.focusedMenuItem),i.setup.focusedMenuItem=void 0)}()}8!=t.keyCode&&46!=t.keyCode||!o?27==t.keyCode&&i.drawing.enabled?(t.preventDefault(),i.drawing.buffer.isSelected?i.setup.fabric.discardActiveObject():i.drawing.handler.done()):67==t.keyCode&&(t.metaKey||t.ctrlKey)&&o?i.drawing.buffer.copy=o:88==t.keyCode&&(t.metaKey||t.ctrlKey)&&o?(i.drawing.buffer.copy=o,i.setup.fabric.remove(o)):86==t.keyCode&&(t.metaKey||t.ctrlKey)?i.drawing.buffer.copy&&e(i.drawing.buffer.copy.clone(e)):90==t.keyCode&&(t.metaKey||t.ctrlKey)&&(t.preventDefault(),t.shiftKey?i.drawing.handler.redo():i.drawing.handler.undo()):(t.preventDefault(),i.setup.fabric.remove(o))},i.config.keyListener="attached",document.addEventListener("keydown",i.docListener),i.addListenerToRemove("keydown",document,i.docListener)),i.config.fileListener&&(i.setup.chart.containerDiv.addEventListener("dragover",i.handleDropbox),i.addListenerToRemove("dragover",i.setup.chart.containerDiv,i.handleDropbox),i.setup.chart.containerDiv.addEventListener("dragleave",i.handleDropbox),i.addListenerToRemove("dragleave",i.setup.chart.containerDiv,i.handleDropbox),i.setup.chart.containerDiv.addEventListener("drop",i.handleDropbox),i.addListenerToRemove("drop",i.setup.chart.containerDiv,i.handleDropbox))},init:function(){clearTimeout(a),a=setInterval(function(){i.setup&&i.setup.chart.containerDiv&&(clearTimeout(a),i.config.enabled&&(i.setup.chart.AmExport=i,i.config.overflow&&(i.setup.chart.div.style.overflow="visible"),i.loadListeners(),i.createMenu(i.config.menu),i.handleReady(i.config.onReady)))},AmCharts.updateRate)},construct:function(){i.drawing.handler.cancel=i.drawing.handler.done;try{i.setup.hasBlob=!!new Blob}catch(e){}window.safari=window.safari?window.safari:{},i.defaults.fabric.drawing.fontSize=i.setup.chart.fontSize||11,i.config.drawing=i.deepMerge(i.defaults.fabric.drawing,i.config.drawing||{},!0),i.config.border&&(i.config.border=i.deepMerge(i.defaults.fabric.border,i.config.border||{},!0)),i.deepMerge(i.defaults.fabric,i.config,!0),i.deepMerge(i.defaults.fabric,i.config.fabric||{},!0),i.deepMerge(i.defaults.pdfMake,i.config,!0),i.deepMerge(i.defaults.pdfMake,i.config.pdfMake||{},!0),i.deepMerge(i.libs,i.config.libs||{},!0),i.config.drawing=i.defaults.fabric.drawing,i.config.fabric=i.defaults.fabric,i.config.pdfMake=i.defaults.pdfMake,i.config=i.deepMerge(i.defaults,i.config,!0),i.config.fabric.drawing.enabled&&void 0===i.config.fabric.drawing.menu&&(i.config.fabric.drawing.menu=[],i.deepMerge(i.config.fabric.drawing.menu,[{class:"export-drawing",menu:[{label:i.i18l("menu.label.draw.add"),menu:[{label:i.i18l("menu.label.draw.shapes"),action:"draw.shapes"},{label:i.i18l("menu.label.draw.text"),action:"text"}]},{label:i.i18l("menu.label.draw.change"),menu:[{label:i.i18l("menu.label.draw.modes"),action:"draw.modes"},{label:i.i18l("menu.label.draw.colors"),action:"draw.colors"},{label:i.i18l("menu.label.draw.widths"),action:"draw.widths"},{label:i.i18l("menu.label.draw.opacities"),action:"draw.opacities"},"UNDO","REDO"]},{label:i.i18l("menu.label.save.image"),menu:["PNG","JPG","SVG","PDF"]},"PRINT","CANCEL"]}])),void 0===i.config.menu&&(i.config.menu=[],i.deepMerge(i.config,{menu:[{class:"export-main",menu:[{label:i.i18l("menu.label.save.image"),menu:["PNG","JPG","SVG","PDF"]},{label:i.i18l("menu.label.save.data"),menu:["CSV","XLSX","JSON"]},{label:i.i18l("menu.label.draw"),action:"draw",menu:i.config.fabric.drawing.menu},{format:"PRINT",label:i.i18l("menu.label.print")}]}]})),i.libs.path||(i.libs.path=i.config.path+"libs/"),i.isSupported()&&(i.loadDependencies(i.libs.resources,i.libs.reload),i.setup.chart.addClassNames=!0,i.setup.chart[i.name]=i,i.init())}};if(t)i.config=t;else if(i.setup.chart[i.name])i.config=i.setup.chart[i.name];else{if(!i.setup.chart.amExport&&!i.setup.chart.exportConfig)return;i.config=i.migrateSetup(i.setup.chart.amExport||i.setup.chart.exportConfig)}return i.construct(),i.deepMerge(this,i)}}(),AmCharts.addInitHandler(function(e){new AmCharts.export(e)},["pie","serial","xy","funnel","radar","gauge","stock","map","gantt"]);
diff --git a/admin/src/main/resources/static/js/plugins/chart/light.js b/admin/src/main/resources/static/js/plugins/chart/light.js
deleted file mode 100755
index 5ef906abc075106fba39b01b1e65252f70784d3e..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/chart/light.js
+++ /dev/null
@@ -1 +0,0 @@
-AmCharts.themes.light={themeName:"light",AmChart:{color:"#000000",backgroundColor:"#FFFFFF"},AmCoordinateChart:{colors:["#67b7dc","#fdd400","#84b761","#cc4748","#cd82ad","#2f4074","#448e4d","#b7b83f","#b9783f","#b93e3d","#913167"]},AmStockChart:{colors:["#67b7dc","#fdd400","#84b761","#cc4748","#cd82ad","#2f4074","#448e4d","#b7b83f","#b9783f","#b93e3d","#913167"]},AmSlicedChart:{colors:["#67b7dc","#fdd400","#84b761","#cc4748","#cd82ad","#2f4074","#448e4d","#b7b83f","#b9783f","#b93e3d","#913167"],outlineAlpha:1,outlineThickness:2,labelTickColor:"#000000",labelTickAlpha:0.3},AmRectangularChart:{zoomOutButtonColor:'#000000',zoomOutButtonRollOverAlpha:0.15,zoomOutButtonImage:"lens"},AxisBase:{axisColor:"#000000",axisAlpha:0.3,gridAlpha:0.1,gridColor:"#000000"},ChartScrollbar:{backgroundColor:"#000000",backgroundAlpha:0.12,graphFillAlpha:0.5,graphLineAlpha:0,selectedBackgroundColor:"#FFFFFF",selectedBackgroundAlpha:0.4,gridAlpha:0.15},ChartCursor:{cursorColor:"#000000",color:"#FFFFFF",cursorAlpha:0.5},AmLegend:{color:"#000000"},AmGraph:{lineAlpha:0.9},GaugeArrow:{color:"#000000",alpha:0.8,nailAlpha:0,innerRadius:"40%",nailRadius:15,startWidth:15,borderAlpha:0.8,nailBorderAlpha:0},GaugeAxis:{tickColor:"#000000",tickAlpha:1,tickLength:15,minorTickLength:8,axisThickness:3,axisColor:'#000000',axisAlpha:1,bandAlpha:0.8},TrendLine:{lineColor:"#c03246",lineAlpha:0.8},AreasSettings:{alpha:0.8,color:"#67b7dc",colorSolid:"#003767",unlistedAreasAlpha:0.4,unlistedAreasColor:"#000000",outlineColor:"#FFFFFF",outlineAlpha:0.5,outlineThickness:0.5,rollOverColor:"#3c5bdc",rollOverOutlineColor:"#FFFFFF",selectedOutlineColor:"#FFFFFF",selectedColor:"#f15135",unlistedAreasOutlineColor:"#FFFFFF",unlistedAreasOutlineAlpha:0.5},LinesSettings:{color:"#000000",alpha:0.8},ImagesSettings:{alpha:0.8,labelColor:"#000000",color:"#000000",labelRollOverColor:"#3c5bdc"},ZoomControl:{buttonFillAlpha:0.7,buttonIconColor:"#a7a7a7"},SmallMap:{mapColor:"#000000",rectangleColor:"#f15135",backgroundColor:"#FFFFFF",backgroundAlpha:0.7,borderThickness:1,borderAlpha:0.8},PeriodSelector:{color:"#000000"},PeriodButton:{color:"#000000",background:"transparent",opacity:0.7,border:"1px solid rgba(0, 0, 0, .3)",MozBorderRadius:"5px",borderRadius:"5px",margin:"1px",outline:"none",boxSizing:"border-box"},PeriodButtonSelected:{color:"#000000",backgroundColor:"#b9cdf5",border:"1px solid rgba(0, 0, 0, .3)",MozBorderRadius:"5px",borderRadius:"5px",margin:"1px",outline:"none",opacity:1,boxSizing:"border-box"},PeriodInputField:{color:"#000000",background:"transparent",border:"1px solid rgba(0, 0, 0, .3)",outline:"none"},DataSetSelector:{color:"#000000",selectedBackgroundColor:"#b9cdf5",rollOverBackgroundColor:"#a8b0e4"},DataSetCompareList:{color:"#000000",lineHeight:"100%",boxSizing:"initial",webkitBoxSizing:"initial",border:"1px solid rgba(0, 0, 0, .3)"},DataSetSelect:{border:"1px solid rgba(0, 0, 0, .3)",outline:"none"}};
diff --git a/admin/src/main/resources/static/js/plugins/chart/serial.js b/admin/src/main/resources/static/js/plugins/chart/serial.js
deleted file mode 100755
index 56d7a841b9f6cb5da36a8eb0dbfeee9911c562db..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/chart/serial.js
+++ /dev/null
@@ -1,15 +0,0 @@
-(function(){var f=window.AmCharts;f.AmRectangularChart=f.Class({inherits:f.AmCoordinateChart,construct:function(a){f.AmRectangularChart.base.construct.call(this,a);this.theme=a;this.createEvents("zoomed","changed");this.marginRight=this.marginBottom=this.marginTop=this.marginLeft=20;this.depth3D=this.angle=0;this.plotAreaFillColors="#FFFFFF";this.plotAreaFillAlphas=0;this.plotAreaBorderColor="#000000";this.plotAreaBorderAlpha=0;this.maxZoomFactor=20;this.zoomOutButtonImageSize=19;this.zoomOutButtonImage="lens";this.zoomOutText="Show all";this.zoomOutButtonColor="#e5e5e5";this.zoomOutButtonAlpha=0;this.zoomOutButtonRollOverAlpha=1;this.zoomOutButtonPadding=8;this.trendLines=[];this.autoMargins=!0;this.marginsUpdated=!1;this.autoMarginOffset=10;f.applyTheme(this,a,"AmRectangularChart")},initChart:function(){f.AmRectangularChart.base.initChart.call(this);this.updateDxy();!this.marginsUpdated&&this.autoMargins&&(this.resetMargins(),this.drawGraphs=!1);this.processScrollbars();this.updateMargins();this.updatePlotArea();this.updateScrollbars();this.updateTrendLines();this.updateChartCursor();this.updateValueAxes();this.scrollbarOnly||this.updateGraphs()},drawChart:function(){f.AmRectangularChart.base.drawChart.call(this);this.drawPlotArea();if(f.ifArray(this.chartData)){var a=this.chartCursor;a&&a.draw()}},resetMargins:function(){var a={},b;if("xy"==this.type){var c=this.xAxes,d=this.yAxes;for(b=0;b<c.length;b++){var g=c[b];g.ignoreAxisWidth||(g.setOrientation(!0),g.fixAxisPosition(),a[g.position]=!0)}for(b=0;b<d.length;b++)c=d[b],c.ignoreAxisWidth||(c.setOrientation(!1),c.fixAxisPosition(),a[c.position]=!0)}else{d=this.valueAxes;for(b=0;b<d.length;b++)c=d[b],c.ignoreAxisWidth||(c.setOrientation(this.rotate),c.fixAxisPosition(),a[c.position]=!0);(b=this.categoryAxis)&&!b.ignoreAxisWidth&&(b.setOrientation(!this.rotate),b.fixAxisPosition(),b.fixAxisPosition(),a[b.position]=!0)}a.left&&(this.marginLeft=0);a.right&&(this.marginRight=0);a.top&&(this.marginTop=0);a.bottom&&(this.marginBottom=0);this.fixMargins=a},measureMargins:function(){var a=this.valueAxes,b,c=this.autoMarginOffset,d=this.fixMargins,g=this.realWidth,h=this.realHeight,e=c,f=c,k=g;b=h;var m;for(m=0;m<a.length;m++)a[m].handleSynchronization(),b=this.getAxisBounds(a[m],e,k,f,b),e=Math.round(b.l),k=Math.round(b.r),f=Math.round(b.t),b=Math.round(b.b);if(a=this.categoryAxis)b=this.getAxisBounds(a,e,k,f,b),e=Math.round(b.l),k=Math.round(b.r),f=Math.round(b.t),b=Math.round(b.b);d.left&&e<c&&(this.marginLeft=Math.round(-e+c),!isNaN(this.minMarginLeft)&&this.marginLeft<this.minMarginLeft&&(this.marginLeft=this.minMarginLeft));d.right&&k>=g-c&&(this.marginRight=Math.round(k-g+c),!isNaN(this.minMarginRight)&&this.marginRight<this.minMarginRight&&(this.marginRight=this.minMarginRight));d.top&&f<c+this.titleHeight&&(this.marginTop=Math.round(this.marginTop-f+c+this.titleHeight),!isNaN(this.minMarginTop)&&this.marginTop<this.minMarginTop&&(this.marginTop=this.minMarginTop));d.bottom&&b>h-c&&(this.marginBottom=Math.round(this.marginBottom+b-h+c),!isNaN(this.minMarginBottom)&&this.marginBottom<this.minMarginBottom&&(this.marginBottom=this.minMarginBottom));this.initChart()},getAxisBounds:function(a,b,c,d,g){if(!a.ignoreAxisWidth){var h=a.labelsSet,e=a.tickLength;a.inside&&(e=0);if(h)switch(h=a.getBBox(),a.position){case"top":a=h.y;d>a&&(d=a);break;case"bottom":a=h.y+h.height;g<a&&(g=a);break;case"right":a=h.x+h.width+e+3;c<a&&(c=a);break;case"left":a=h.x-e,b>a&&(b=a)}}return{l:b,t:d,r:c,b:g}},drawZoomOutButton:function(){var a=this;if(!a.zbSet){var b=a.container.set();a.zoomButtonSet.push(b);var c=a.color,d=a.fontSize,g=a.zoomOutButtonImageSize,h=a.zoomOutButtonImage.replace(/\.[a-z]*$/i,""),e=a.langObj.zoomOutText||a.zoomOutText,l=a.zoomOutButtonColor,k=a.zoomOutButtonAlpha,m=a.zoomOutButtonFontSize,p=a.zoomOutButtonPadding;isNaN(m)||(d=m);(m=a.zoomOutButtonFontColor)&&(c=m);var m=a.zoomOutButton,n;m&&(m.fontSize&&(d=m.fontSize),m.color&&(c=m.color),m.backgroundColor&&(l=m.backgroundColor),isNaN(m.backgroundAlpha)||(a.zoomOutButtonRollOverAlpha=m.backgroundAlpha));var u=m=0,u=a.pathToImages;if(h){if(f.isAbsolute(h)||void 0===u)u="";n=a.container.image(u+h+a.extension,0,0,g,g);f.setCN(a,n,"zoom-out-image");b.push(n);n=n.getBBox();m=n.width+5}void 0!==e&&(c=f.text(a.container,e,c,a.fontFamily,d,"start"),f.setCN(a,c,"zoom-out-label"),d=c.getBBox(),u=n?n.height/2-3:d.height/2,c.translate(m,u),b.push(c));n=b.getBBox();c=1;f.isModern||(c=0);l=f.rect(a.container,n.width+2*p+5,n.height+2*p-2,l,1,1,l,c);l.setAttr("opacity",k);l.translate(-p,-p);f.setCN(a,l,"zoom-out-bg");b.push(l);l.toBack();a.zbBG=l;n=l.getBBox();b.translate(a.marginLeftReal+a.plotAreaWidth-n.width+p,a.marginTopReal+p);b.hide();b.mouseover(function(){a.rollOverZB()}).mouseout(function(){a.rollOutZB()}).click(function(){a.clickZB()}).touchstart(function(){a.rollOverZB()}).touchend(function(){a.rollOutZB();a.clickZB()});for(k=0;k<b.length;k++)b[k].attr({cursor:"pointer"});void 0!==a.zoomOutButtonTabIndex&&(b.setAttr("tabindex",a.zoomOutButtonTabIndex),b.setAttr("role","menuitem"),b.keyup(function(b){13==b.keyCode&&a.clickZB()}));a.zbSet=b}},rollOverZB:function(){this.rolledOverZB=!0;this.zbBG.setAttr("opacity",this.zoomOutButtonRollOverAlpha)},rollOutZB:function(){this.rolledOverZB=!1;this.zbBG.setAttr("opacity",this.zoomOutButtonAlpha)},clickZB:function(){this.rolledOverZB=!1;this.zoomOut()},zoomOut:function(){this.zoomOutValueAxes()},drawPlotArea:function(){var a=this.dx,b=this.dy,c=this.marginLeftReal,d=this.marginTopReal,g=this.plotAreaWidth-1,h=this.plotAreaHeight-1,e=this.plotAreaFillColors,l=this.plotAreaFillAlphas,k=this.plotAreaBorderColor,m=this.plotAreaBorderAlpha;"object"==typeof l&&(l=l[0]);e=f.polygon(this.container,[0,g,g,0,0],[0,0,h,h,0],e,l,1,k,m,this.plotAreaGradientAngle);f.setCN(this,e,"plot-area");e.translate(c+a,d+b);this.set.push(e);0!==a&&0!==b&&(e=this.plotAreaFillColors,"object"==typeof e&&(e=e[0]),e=f.adjustLuminosity(e,-.15),g=f.polygon(this.container,[0,a,g+a,g,0],[0,b,b,0,0],e,l,1,k,m),f.setCN(this,g,"plot-area-bottom"),g.translate(c,d+h),this.set.push(g),a=f.polygon(this.container,[0,0,a,a,0],[0,h,h+b,b,0],e,l,1,k,m),f.setCN(this,a,"plot-area-left"),a.translate(c,d),this.set.push(a));(c=this.bbset)&&this.scrollbarOnly&&c.remove()},updatePlotArea:function(){var a=this.updateWidth(),b=this.updateHeight(),c=this.container;this.realWidth=a;this.realWidth=b;c&&this.container.setSize(a,b);var c=this.marginLeftReal,d=this.marginTopReal,a=a-c-this.marginRightReal-this.dx,b=b-d-this.marginBottomReal;1>a&&(a=1);1>b&&(b=1);this.plotAreaWidth=Math.round(a);this.plotAreaHeight=Math.round(b);this.plotBalloonsSet.translate(c,d)},updateDxy:function(){this.dx=Math.round(this.depth3D*Math.cos(this.angle*Math.PI/180));this.dy=Math.round(-this.depth3D*Math.sin(this.angle*Math.PI/180));this.d3x=Math.round(this.columnSpacing3D*Math.cos(this.angle*Math.PI/180));this.d3y=Math.round(-this.columnSpacing3D*Math.sin(this.angle*Math.PI/180))},updateMargins:function(){var a=this.getTitleHeight();this.titleHeight=a;this.marginTopReal=this.marginTop-this.dy;this.fixMargins&&!this.fixMargins.top&&(this.marginTopReal+=a);this.marginBottomReal=this.marginBottom;this.marginLeftReal=this.marginLeft;this.marginRightReal=this.marginRight},updateValueAxes:function(){var a=this.valueAxes,b;for(b=0;b<a.length;b++){var c=a[b];this.setAxisRenderers(c);this.updateObjectSize(c)}},setAxisRenderers:function(a){a.axisRenderer=f.RecAxis;a.guideFillRenderer=f.RecFill;a.axisItemRenderer=f.RecItem;a.marginsChanged=!0},updateGraphs:function(){var a=this.graphs,b;for(b=0;b<a.length;b++){var c=a[b];c.index=b;c.rotate=this.rotate;this.updateObjectSize(c)}},updateObjectSize:function(a){a.width=this.plotAreaWidth-1;a.height=this.plotAreaHeight-1;a.x=this.marginLeftReal;a.y=this.marginTopReal;a.dx=this.dx;a.dy=this.dy},updateChartCursor:function(){var a=this.chartCursor;a&&(a=f.processObject(a,f.ChartCursor,this.theme),this.updateObjectSize(a),this.addChartCursor(a),a.chart=this)},processScrollbars:function(){var a=this.chartScrollbar;a&&(a=f.processObject(a,f.ChartScrollbar,this.theme),this.addChartScrollbar(a))},updateScrollbars:function(){},removeChartCursor:function(){f.callMethod("destroy",[this.chartCursor]);this.chartCursor=null},zoomTrendLines:function(){var a=this.trendLines,b;for(b=0;b<a.length;b++){var c=a[b];c.valueAxis.recalculateToPercents?c.set&&c.set.hide():(c.x=this.marginLeftReal,c.y=this.marginTopReal,c.draw())}},handleCursorValueZoom:function(){},addTrendLine:function(a){this.trendLines.push(a)},zoomOutValueAxes:function(){for(var a=this.valueAxes,b=0;b<a.length;b++)a[b].zoomOut()},removeTrendLine:function(a){var b=this.trendLines,c;for(c=b.length-1;0<=c;c--)b[c]==a&&b.splice(c,1)},adjustMargins:function(a,b){var c=a.position,d=a.scrollbarHeight+a.offset;a.enabled&&("top"==c?b?this.marginLeftReal+=d:this.marginTopReal+=d:b?this.marginRightReal+=d:this.marginBottomReal+=d)},getScrollbarPosition:function(a,b,c){var d="bottom",g="top";a.oppositeAxis||(g=d,d="top");a.position=b?"bottom"==c||"left"==c?d:g:"top"==c||"right"==c?d:g},updateChartScrollbar:function(a,b){if(a){a.rotate=b;var c=this.marginTopReal,d=this.marginLeftReal,g=a.scrollbarHeight,h=this.dx,e=this.dy,f=a.offset;"top"==a.position?b?(a.y=c,a.x=d-g-f):(a.y=c-g+e-f,a.x=d+h):b?(a.y=c+e,a.x=d+this.plotAreaWidth+h+f):(a.y=c+this.plotAreaHeight+f,a.x=this.marginLeftReal)}},showZB:function(a){var b=this.zbSet;a&&(b=this.zoomOutText,""!==b&&b&&this.drawZoomOutButton());if(b=this.zbSet)this.zoomButtonSet.push(b),a?b.show():b.hide(),this.rollOutZB()},handleReleaseOutside:function(a){f.AmRectangularChart.base.handleReleaseOutside.call(this,a);(a=this.chartCursor)&&a.handleReleaseOutside&&a.handleReleaseOutside()},handleMouseDown:function(a){f.AmRectangularChart.base.handleMouseDown.call(this,a);var b=this.chartCursor;b&&b.handleMouseDown&&!this.rolledOverZB&&b.handleMouseDown(a)},update:function(){f.AmRectangularChart.base.update.call(this);this.chartCursor&&this.chartCursor.update&&this.chartCursor.update()},handleScrollbarValueZoom:function(a){this.relativeZoomValueAxes(a.target.valueAxes,a.relativeStart,a.relativeEnd);this.zoomAxesAndGraphs()},zoomValueScrollbar:function(a){if(a&&a.enabled){var b=a.valueAxes[0],c=b.relativeStart,d=b.relativeEnd;b.reversed&&(d=1-c,c=1-b.relativeEnd);a.percentZoom(c,d)}},zoomAxesAndGraphs:function(){if(!this.scrollbarOnly){var a=this.valueAxes,b;for(b=0;b<a.length;b++)a[b].zoom(this.start,this.end);a=this.graphs;for(b=0;b<a.length;b++)a[b].zoom(this.start,this.end);(b=this.chartCursor)&&b.clearSelection();this.zoomTrendLines()}},handleValueAxisZoomReal:function(a,b){var c=a.relativeStart,d=a.relativeEnd;if(c>d)var g=c,c=d,d=g;this.relativeZoomValueAxes(b,c,d);this.updateAfterValueZoom()},updateAfterValueZoom:function(){this.zoomAxesAndGraphs();this.zoomScrollbar()},relativeZoomValueAxes:function(a,b,c){this.hideBalloonReal();b=f.fitToBounds(b,0,1);c=f.fitToBounds(c,0,1);if(b>c){var d=b;b=c;c=d}var d=1/this.maxZoomFactor,g=f.getDecimals(d)+4;c-b<d&&(c=b+(c-b)/2,b=c-d/2,c+=d/2,1<c&&(b-=c-1,c=1),0>b&&(b=0,c=d));b=f.roundTo(b,g);c=f.roundTo(c,g);d=!1;if(a){for(g=0;g<a.length;g++){var h=a[g].zoomToRelativeValues(b,c,!0);h&&(d=h)}this.showZB()}return d},addChartCursor:function(a){f.callMethod("destroy",
-[this.chartCursor]);a&&(this.listenTo(a,"moved",this.handleCursorMove),this.listenTo(a,"zoomed",this.handleCursorZoom),this.listenTo(a,"zoomStarted",this.handleCursorZoomStarted),this.listenTo(a,"panning",this.handleCursorPanning),this.listenTo(a,"onHideCursor",this.handleCursorHide));this.chartCursor=a},handleCursorChange:function(){},handleCursorMove:function(a){var b,c=this.valueAxes;for(b=0;b<c.length;b++)if(!a.panning){var d=c[b];d&&d.showBalloon&&d.showBalloon(a.x,a.y)}},handleCursorZoom:function(a){if(this.skipZoomed)this.skipZoomed=!1;else{var b=this.startX0,c=this.endX0,d=this.endY0,g=this.startY0,h=a.startX,e=a.endX,f=a.startY,k=a.endY;this.startX0=this.endX0=this.startY0=this.endY0=NaN;this.handleCursorZoomReal(b+h*(c-b),b+e*(c-b),g+f*(d-g),g+k*(d-g),a)}},handleCursorHide:function(){var a,b=this.valueAxes;for(a=0;a<b.length;a++)b[a].hideBalloon();b=this.graphs;for(a=0;a<b.length;a++)b[a].hideBalloonReal()}})})();(function(){var f=window.AmCharts;f.AmSerialChart=f.Class({inherits:f.AmRectangularChart,construct:function(a){this.type="serial";f.AmSerialChart.base.construct.call(this,a);this.cname="AmSerialChart";this.theme=a;this.columnSpacing=5;this.columnSpacing3D=0;this.columnWidth=.8;var b=new f.CategoryAxis(a);b.chart=this;this.categoryAxis=b;this.zoomOutOnDataUpdate=!0;this.mouseWheelZoomEnabled=this.mouseWheelScrollEnabled=this.rotate=this.skipZoom=!1;this.minSelectedTime=0;f.applyTheme(this,a,this.cname)},initChart:function(){f.AmSerialChart.base.initChart.call(this);this.updateCategoryAxis(this.categoryAxis,this.rotate,"categoryAxis");if(this.dataChanged)this.parseData();else this.onDataUpdated();this.drawGraphs=!0},onDataUpdated:function(){var a=this.countColumns(),b=this.chartData,c=this.graphs,d;for(d=0;d<c.length;d++){var g=c[d];g.data=b;g.columnCount=a}0<b.length&&(this.firstTime=this.getStartTime(b[0].time),this.lastTime=this.getEndTime(b[b.length-1].time));this.drawChart();this.autoMargins&&!this.marginsUpdated?(this.marginsUpdated=!0,this.measureMargins()):this.dispDUpd()},syncGrid:function(){if(this.synchronizeGrid){var a=this.valueAxes,b,c;if(0<a.length){var d=0;for(c=0;c<a.length;c++)b=a[c],d<b.gridCountReal&&(d=b.gridCountReal);var g=!1;for(c=0;c<a.length;c++)if(b=a[c],b.gridCountReal<d){var h=(d-b.gridCountReal)/2,e=g=h;0!==h-Math.round(h)&&(g-=.5,e+=.5);0<=b.min&&0>b.min-g*b.step&&(e+=g,g=0);0>=b.max&&0<b.max+e*b.step&&(g+=e,e=0);h=f.getDecimals(b.step);b.minimum=f.roundTo(b.min-
-g*b.step,h);b.maximum=f.roundTo(b.max+e*b.step,h);b.setStep=b.step;g=b.strictMinMax=!0}g&&this.updateAfterValueZoom();for(c=0;c<a.length;c++)b=a[c],b.minimum=NaN,b.maximum=NaN,b.setStep=NaN,b.strictMinMax=!1}}},handleWheelReal:function(a,b){if(!this.wheelBusy){var c=this.categoryAxis,d=c.parseDates,g=c.minDuration(),h=1,e=1;this.mouseWheelZoomEnabled?b||(h=-1):b&&(h=-1);var f=this.chartCursor;if(f){var k=f.mouseX,f=f.mouseY;h!=e&&(k=this.rotate?f/this.plotAreaHeight:k/this.plotAreaWidth,h*=k,e*=1-
-k);k=.05*(this.end-this.start);d&&(k=.05*(this.endTime-this.startTime)/g);1>k&&(k=1);h*=k;e*=k;if(!d||c.equalSpacing)h=Math.round(h),e=Math.round(e)}f=this.chartData.length;c=this.lastTime;k=this.firstTime;0>a?d?(f=this.endTime-this.startTime,d=this.startTime+h*g,g=this.endTime+e*g,0<e&&0<h&&g>=c&&(g=c,d=c-f),this.zoomToDates(new Date(d),new Date(g))):(0<e&&0<h&&this.end>=f-1&&(h=e=0),d=this.start+h,g=this.end+e,this.zoomToIndexes(d,g)):d?(f=this.endTime-this.startTime,d=this.startTime-h*g,g=this.endTime-
-e*g,0<e&&0<h&&d<=k&&(d=k,g=k+f),this.zoomToDates(new Date(d),new Date(g))):(0<e&&0<h&&1>this.start&&(h=e=0),d=this.start-h,g=this.end-e,this.zoomToIndexes(d,g))}},validateData:function(a){this.marginsUpdated=!1;this.zoomOutOnDataUpdate&&!a&&(this.endTime=this.end=this.startTime=this.start=NaN);var b=a=!1,c=!1,d=this.chartScrollbar;d&&(d.dragging&&(a=!0,d.handleDragStop()),d.resizingRight&&(c=!0,d.rightDragStop()),d.resizingLeft&&(b=!0,d.leftDragStop()));f.AmSerialChart.base.validateData.call(this);a&&d.handleDragStart();c&&d.rightDragStart();b&&d.leftDragStart()},drawChart:function(){if(0<this.realWidth&&0<this.realHeight){f.AmSerialChart.base.drawChart.call(this);var a=this.chartData;if(f.ifArray(a)){var b=this.chartScrollbar;!b||!this.marginsUpdated&&this.autoMargins||b.draw();(b=this.valueScrollbar)&&b.draw();var b=a.length-1,c,d;c=this.categoryAxis;if(c.parseDates&&!c.equalSpacing){if(c=this.startTime,d=this.endTime,isNaN(c)||isNaN(d))c=this.firstTime,d=this.lastTime}else{c=this.start;d=this.end;if(isNaN(c)||isNaN(d))d=c=NaN;isNaN(c)&&(isNaN(this.startTime)||(c=this.getClosestIndex(a,"time",this.startTime,!0,0,a.length)));isNaN(d)&&(isNaN(this.endTime)||(d=this.getClosestIndex(a,"time",this.endTime,!1,0,a.length)));if(isNaN(c)||isNaN(d))c=0,d=b}this.endTime=this.startTime=this.end=this.start=void 0;this.zoom(c,d)}}else this.cleanChart()},cleanChart:function(){f.callMethod("destroy",[this.valueAxes,this.graphs,this.categoryAxis,this.chartScrollbar,this.chartCursor,this.valueScrollbar])},updateCategoryAxis:function(a,b,c){a.chart=this;a.id=c;a.rotate=b;a.setOrientation(!this.rotate);a.init();this.setAxisRenderers(a);this.updateObjectSize(a)},updateValueAxes:function(){f.AmSerialChart.base.updateValueAxes.call(this);var a=this.valueAxes,b;for(b=0;b<a.length;b++){var c=a[b],d=this.rotate;c.rotate=d;c.setOrientation(d);d=this.categoryAxis;if(!d.startOnAxis||d.parseDates)c.expandMinMax=!0}},getStartTime:function(a){var b=this.categoryAxis;return f.resetDateToMin(new Date(a),b.minPeriod,1,b.firstDayOfWeek).getTime()},getEndTime:function(a){var b=f.extractPeriod(this.categoryAxis.minPeriod);return f.changeDate(new Date(a),b.period,b.count,!0).getTime()-1},updateMargins:function(){f.AmSerialChart.base.updateMargins.call(this);var a=this.chartScrollbar;a&&(this.getScrollbarPosition(a,this.rotate,this.categoryAxis.position),this.adjustMargins(a,this.rotate));if(a=this.valueScrollbar)this.getScrollbarPosition(a,!this.rotate,this.valueAxes[0].position),this.adjustMargins(a,!this.rotate)},updateScrollbars:function(){f.AmSerialChart.base.updateScrollbars.call(this);this.updateChartScrollbar(this.chartScrollbar,this.rotate);this.updateChartScrollbar(this.valueScrollbar,!this.rotate)},zoom:function(a,b){var c=this.categoryAxis;c.parseDates&&!c.equalSpacing?(this.timeZoom(a,b),isNaN(a)&&this.zoomOutValueAxes()):this.indexZoom(a,b);(c=this.chartCursor)&&(c.pan||c.hideCursorReal());this.updateLegendValues()},timeZoom:function(a,b){var c=this.maxSelectedTime;isNaN(c)||(b!=this.endTime&&b-
-a>c&&(a=b-c),a!=this.startTime&&b-a>c&&(b=a+c));var d=this.minSelectedTime;if(0<d&&b-a<d){var g=Math.round(a+(b-a)/2),d=Math.round(d/2);a=g-d;b=g+d}d=this.chartData;g=this.categoryAxis;if(f.ifArray(d)&&(a!=this.startTime||b!=this.endTime)){var h=g.minDuration(),e=this.firstTime,l=this.lastTime;a||(a=e,isNaN(c)||(a=l-c));b||(b=l);a>l&&(a=l);b<e&&(b=e);a<e&&(a=e);b>l&&(b=l);b<a&&(b=a+h);b-a<h/5&&(b<l?b=a+h/5:a=b-h/5);this.startTime=a;this.endTime=b;c=d.length-1;h=this.getClosestIndex(d,"time",a,!0,
-0,c);d=this.getClosestIndex(d,"time",b,!1,h,c);g.timeZoom(a,b);g.zoom(h,d);this.start=f.fitToBounds(h,0,c);this.end=f.fitToBounds(d,0,c);this.zoomAxesAndGraphs();this.zoomScrollbar();this.fixCursor();this.showZB();this.syncGrid();this.updateColumnsDepth();this.dispatchTimeZoomEvent()}},showZB:function(){var a,b=this.categoryAxis;b&&b.parseDates&&!b.equalSpacing&&(this.startTime>this.firstTime&&(a=!0),this.endTime<this.lastTime&&(a=!0));0<this.start&&(a=!0);this.end<this.chartData.length-1&&(a=!0);if(b=this.valueAxes)b=b[0],isNaN(b.relativeStart)||(0!==f.roundTo(b.relativeStart,3)&&(a=!0),1!=f.roundTo(b.relativeEnd,3)&&(a=!0));f.AmSerialChart.base.showZB.call(this,a)},updateAfterValueZoom:function(){f.AmSerialChart.base.updateAfterValueZoom.call(this);this.updateColumnsDepth()},indexZoom:function(a,b){var c=this.maxSelectedSeries,d=!1;isNaN(c)||(b!=this.end&&b-a>c&&(a=b-c,d=!0),a!=this.start&&b-a>c&&(b=a+c,d=!0));if(d&&(d=this.chartScrollbar)&&d.dragger){var g=d.dragger.getBBox();d.maxWidth=g.width;d.maxHeight=g.height}if(a!=this.start||b!=this.end)d=this.chartData.length-1,isNaN(a)&&(a=0,isNaN(c)||(a=d-c)),isNaN(b)&&(b=d),b<a&&(b=a),b>d&&(b=d),a>d&&(a=d-1),0>a&&(a=0),this.start=a,this.end=b,this.categoryAxis.zoom(a,b),this.zoomAxesAndGraphs(),this.zoomScrollbar(),this.fixCursor(),0!==a||b!=this.chartData.length-1?this.showZB(!0):this.showZB(!1),this.syncGrid(),this.updateColumnsDepth(),this.dispatchIndexZoomEvent()},updateGraphs:function(){f.AmSerialChart.base.updateGraphs.call(this);var a=this.graphs,b;for(b=0;b<a.length;b++){var c=a[b];c.columnWidthReal=this.columnWidth;c.categoryAxis=this.categoryAxis;f.isString(c.fillToGraph)&&(c.fillToGraph=this.graphsById[c.fillToGraph])}},zoomAxesAndGraphs:function(){f.AmSerialChart.base.zoomAxesAndGraphs.call(this);this.updateColumnsDepth()},updateColumnsDepth:function(){if(0!==this.depth3D||0!==this.angle){var a,b=this.graphs,c;this.columnsArray=[];for(a=0;a<b.length;a++){c=b[a];var d=c.columnsArray;if(d){var g;for(g=0;g<d.length;g++)this.columnsArray.push(d[g])}}this.columnsArray.sort(this.compareDepth);b=this.columnsSet;if(0<this.columnsArray.length){d=this.container.set();this.columnSet.push(d);for(a=0;a<this.columnsArray.length;a++)d.push(this.columnsArray[a].column.set);c&&d.translate(c.x,c.y);this.columnsSet=d}f.remove(b)}},compareDepth:function(a,b){return a.depth>b.depth?1:-1},zoomScrollbar:function(){var a=this.chartScrollbar,b=this.categoryAxis;if(a){if(!this.zoomedByScrollbar){var c=a.dragger;c&&c.stop()}this.zoomedByScrollbar=!1;b.parseDates&&!b.equalSpacing?a.timeZoom(this.startTime,this.endTime):a.zoom(this.start,this.end)}this.zoomValueScrollbar(this.valueScrollbar)},updateTrendLines:function(){var a=this.trendLines,b;for(b=0;b<a.length;b++){var c=a[b],c=f.processObject(c,f.TrendLine,this.theme);a[b]=c;c.chart=this;c.id||(c.id="trendLineAuto"+b+"_"+(new Date).getTime());f.isString(c.valueAxis)&&(c.valueAxis=this.getValueAxisById(c.valueAxis));c.valueAxis||(c.valueAxis=this.valueAxes[0]);c.categoryAxis=this.categoryAxis}},countColumns:function(){var a=0,b=this.valueAxes.length,c=this.graphs.length,d,g,f=!1,e,l;for(l=0;l<b;l++){g=this.valueAxes[l];var k=g.stackType,m=0;if("100%"==k||"regular"==k)for(f=!1,e=0;e<c;e++)d=this.graphs[e],d.tcc=1,d.valueAxis==g&&"column"==d.type&&(!f&&d.stackable&&(a++,f=!0),(!d.stackable&&d.clustered||d.newStack&&0!==m)&&a++,d.columnIndex=a-1,d.clustered||(d.columnIndex=0),m++);if("none"==k||"3d"==k){f=!1;for(e=0;e<c;e++)d=this.graphs[e],d.valueAxis==g&&"column"==d.type&&(d.clustered?(d.tcc=1,d.newStack&&(a=0),d.hidden||(d.columnIndex=a,a++)):d.hidden||(f=!0,d.tcc=1,d.columnIndex=0));f&&0===a&&(a=1)}if("3d"==k){g=1;for(l=0;l<c;l++)d=this.graphs[l],d.newStack&&g++,d.depthCount=g,d.tcc=a;a=g}}return a},parseData:function(){f.AmSerialChart.base.parseData.call(this);this.parseSerialData(this.dataProvider)},getCategoryIndexByValue:function(a){var b=this.chartData,c;for(c=0;c<b.length;c++)if(b[c].category==a)return c},handleScrollbarZoom:function(a){this.zoomedByScrollbar=!0;this.zoom(a.start,a.end)},dispatchTimeZoomEvent:function(){if(this.drawGraphs&&(this.prevStartTime!=this.startTime||this.prevEndTime!=this.endTime)){var a={type:"zoomed"};a.startDate=new Date(this.startTime);a.endDate=new Date(this.endTime);a.startIndex=this.start;a.endIndex=this.end;this.startIndex=this.start;this.endIndex=this.end;this.startDate=a.startDate;this.endDate=a.endDate;this.prevStartTime=this.startTime;this.prevEndTime=this.endTime;var b=this.categoryAxis,c=f.extractPeriod(b.minPeriod).period,b=b.dateFormatsObject[c];a.startValue=f.formatDate(a.startDate,b,this);a.endValue=f.formatDate(a.endDate,b,this);a.chart=this;a.target=this;this.fire(a)}},dispatchIndexZoomEvent:function(){if(this.drawGraphs&&(this.prevStartIndex!=this.start||this.prevEndIndex!=this.end)){this.startIndex=this.start;this.endIndex=this.end;var a=this.chartData;if(f.ifArray(a)&&!isNaN(this.start)&&!isNaN(this.end)){var b={chart:this,target:this,type:"zoomed"};b.startIndex=this.start;b.endIndex=this.end;b.startValue=a[this.start].category;b.endValue=a[this.end].category;this.categoryAxis.parseDates&&(this.startTime=a[this.start].time,this.endTime=a[this.end].time,b.startDate=new Date(this.startTime),b.endDate=new Date(this.endTime));this.prevStartIndex=this.start;this.prevEndIndex=this.end;this.fire(b)}}},updateLegendValues:function(){this.legend&&this.legend.updateValues()},getClosestIndex:function(a,b,c,d,g,f){0>g&&(g=0);f>a.length-1&&(f=a.length-1);var e=g+Math.round((f-g)/2),l=a[e][b];return c==l?e:1>=f-g?d?g:Math.abs(a[g][b]-c)<Math.abs(a[f][b]-c)?g:f:c==l?e:c<l?this.getClosestIndex(a,b,
-c,d,g,e):this.getClosestIndex(a,b,c,d,e,f)},zoomToIndexes:function(a,b){var c=this.chartData;if(c){var d=c.length;0<d&&(0>a&&(a=0),b>d-1&&(b=d-1),d=this.categoryAxis,d.parseDates&&!d.equalSpacing?this.zoom(c[a].time,this.getEndTime(c[b].time)):this.zoom(a,b))}},zoomToDates:function(a,b){var c=this.chartData;if(c)if(this.categoryAxis.equalSpacing){var d=this.getClosestIndex(c,"time",a.getTime(),!0,0,c.length);b=f.resetDateToMin(b,this.categoryAxis.minPeriod,1);c=this.getClosestIndex(c,"time",b.getTime(),!1,0,c.length);this.zoom(d,c)}else this.zoom(a.getTime(),b.getTime())},zoomToCategoryValues:function(a,b){this.chartData&&this.zoom(this.getCategoryIndexByValue(a),this.getCategoryIndexByValue(b))},formatPeriodString:function(a,b){if(b){b.periodDataItem={};b.periodPercentDataItem={};var c=["value","open","low","high","close"],d="value open low high close average sum count".split(" "),g=b.valueAxis,h=this.chartData,e=b.numberFormatter;e||(e=this.nf);for(var l=0;l<c.length;l++){for(var k=c[l],m=0,p=0,n=0,u=0,v,x,E,t,r,B,q,w,y,C,F=this.start;F<=this.end;F++){var D=h[F];if(D){var A=D.axes[g.id].graphs[b.id];if(A){if(A.values){var z=A.values[k],D=D.x.categoryAxis;if(this.rotate){if(0>D||D>A.graph.height)z=NaN}else if(0>D||D>A.graph.width)z=NaN;if(!isNaN(z)){isNaN(v)&&(v=z);x=z;if(isNaN(E)||E>z)E=z;if(isNaN(t)||t<z)t=z;r=f.getDecimals(m);D=f.getDecimals(z);m+=z;m=f.roundTo(m,Math.max(r,D));p++;r=m/p}}if(A.percents&&(A=A.percents[k],!isNaN(A))){isNaN(B)&&(B=A);q=A;if(isNaN(w)||w>A)w=A;if(isNaN(y)||y<A)y=A;C=f.getDecimals(n);z=f.getDecimals(A);n+=A;n=f.roundTo(n,Math.max(C,z));u++;C=n/u}}}}m={open:v,close:x,high:t,low:E,average:r,sum:m,count:p};n={open:B,close:q,high:y,low:w,average:C,sum:n,count:u};a=f.formatValue(a,m,d,e,k+"\\.",this.usePrefixes,this.prefixesOfSmallNumbers,this.prefixesOfBigNumbers);a=f.formatValue(a,n,d,this.pf,"percents\\."+k+"\\.");b.periodDataItem[k]=m;b.periodPercentDataItem[k]=n}}return a=f.cleanFromEmpty(a)},formatString:function(a,b,c){if(b){var d=b.graph;if(void 0!==a){if(-1!=a.indexOf("[[category]]")){var g=b.serialDataItem.category;if(this.categoryAxis.parseDates){var h=this.balloonDateFormat,e=this.chartCursor;e&&e.categoryBalloonDateFormat&&(h=e.categoryBalloonDateFormat);h=f.formatDate(g,h,this);-1!=h.indexOf("fff")&&(h=f.formatMilliseconds(h,g));g=h}a=a.replace(/\[\[category\]\]/g,String(g.replace("$","$$$")))}g=d.numberFormatter;g||(g=this.nf);h=b.graph.valueAxis;(e=h.duration)&&!isNaN(b.values.value)&&(e=f.formatDuration(b.values.value,e,"",h.durationUnits,h.maxInterval,g),a=a.replace(RegExp("\\[\\[value\\]\\]","g"),e));"date"==h.type&&(h=f.formatDate(new Date(b.values.value),d.dateFormat,this),e=RegExp("\\[\\[value\\]\\]","g"),a=a.replace(e,h),h=f.formatDate(new Date(b.values.open),d.dateFormat,this),e=RegExp("\\[\\[open\\]\\]","g"),a=a.replace(e,h));d="value open low high close total".split(" ");h=this.pf;a=f.formatValue(a,b.percents,d,h,"percents\\.");a=f.formatValue(a,b.values,d,g,"",this.usePrefixes,this.prefixesOfSmallNumbers,this.prefixesOfBigNumbers);a=f.formatValue(a,b.values,["percents"],h);-1!=a.indexOf("[[")&&(a=f.formatDataContextValue(a,b.dataContext));-1!=a.indexOf("[[")&&b.graph.customData&&(a=f.formatDataContextValue(a,b.graph.customData));a=f.AmSerialChart.base.formatString.call(this,a,b,c)}return a}},updateChartCursor:function(){f.AmSerialChart.base.updateChartCursor.call(this);var a=this.chartCursor,b=this.categoryAxis;if(a){var c=a.categoryBalloonAlpha,d=a.categoryBalloonColor,g=a.color;void 0===d&&(d=a.cursorColor);var h=a.valueZoomable,e=a.zoomable,l=a.valueLineEnabled;this.rotate?(a.vLineEnabled=l,a.hZoomEnabled=h,a.vZoomEnabled=e):(a.hLineEnabled=l,a.vZoomEnabled=h,a.hZoomEnabled=e);if(a.valueLineBalloonEnabled)for(l=0;l<this.valueAxes.length;l++)h=this.valueAxes[l],(e=h.balloon)||(e={}),e=f.extend(e,this.balloon,!0),e.fillColor=d,e.balloonColor=d,e.fillAlpha=c,e.borderColor=d,e.color=g,h.balloon=e;else for(e=0;e<this.valueAxes.length;e++)h=this.valueAxes[e],h.balloon&&(h.balloon=null);b&&(b.balloonTextFunction=a.categoryBalloonFunction,a.categoryLineAxis=b,b.balloonText=a.categoryBalloonText,a.categoryBalloonEnabled&&((e=b.balloon)||(e={}),e=f.extend(e,this.balloon,!0),e.fillColor=d,e.balloonColor=d,e.fillAlpha=c,e.borderColor=d,e.color=g,b.balloon=e),b.balloon&&(b.balloon.enabled=a.categoryBalloonEnabled))}},addChartScrollbar:function(a){f.callMethod("destroy",[this.chartScrollbar]);a&&(a.chart=this,this.listenTo(a,"zoomed",this.handleScrollbarZoom));this.rotate?void 0===a.width&&(a.width=a.scrollbarHeight):void 0===a.height&&(a.height=a.scrollbarHeight);a.gridAxis=this.categoryAxis;this.chartScrollbar=a},addValueScrollbar:function(a){f.callMethod("destroy",[this.valueScrollbar]);a&&(a.chart=this,this.listenTo(a,"zoomed",this.handleScrollbarValueZoom),this.listenTo(a,"zoomStarted",this.handleCursorZoomStarted));var b=a.scrollbarHeight;this.rotate?void 0===a.height&&(a.height=b):void 0===a.width&&(a.width=b);a.gridAxis||(a.gridAxis=this.valueAxes[0]);a.valueAxes=this.valueAxes;this.valueScrollbar=a},removeChartScrollbar:function(){f.callMethod("destroy",[this.chartScrollbar]);this.chartScrollbar=null},removeValueScrollbar:function(){f.callMethod("destroy",[this.valueScrollbar]);this.valueScrollbar=null},handleReleaseOutside:function(a){f.AmSerialChart.base.handleReleaseOutside.call(this,a);f.callMethod("handleReleaseOutside",[this.chartScrollbar,this.valueScrollbar])},update:function(){f.AmSerialChart.base.update.call(this);this.chartScrollbar&&this.chartScrollbar.update&&this.chartScrollbar.update();this.valueScrollbar&&this.valueScrollbar.update&&this.valueScrollbar.update()},processScrollbars:function(){f.AmSerialChart.base.processScrollbars.call(this);var a=this.valueScrollbar;a&&(a=f.processObject(a,f.ChartScrollbar,this.theme),a.id="valueScrollbar",this.addValueScrollbar(a))},handleValueAxisZoom:function(a){this.handleValueAxisZoomReal(a,this.valueAxes)},zoomOut:function(){f.AmSerialChart.base.zoomOut.call(this);this.zoom();this.syncGrid()},getNextItem:function(a){var b=a.index,c=this.chartData,d=a.graph;if(b+1<c.length)for(b+=1;b<c.length;b++)if(a=c[b])if(a=a.axes[d.valueAxis.id].graphs[d.id],!isNaN(a.y))return a},handleCursorZoomReal:function(a,b,c,d,g){var f=g.target,e,l;this.rotate?(isNaN(a)||isNaN(b)||this.relativeZoomValueAxes(this.valueAxes,a,b)&&this.updateAfterValueZoom(),f.vZoomEnabled&&(e=g.start,l=g.end)):(isNaN(c)||isNaN(d)||this.relativeZoomValueAxes(this.valueAxes,c,d)&&this.updateAfterValueZoom(),f.hZoomEnabled&&(e=g.start,l=g.end));isNaN(e)||isNaN(l)||(a=this.categoryAxis,a.parseDates&&!a.equalSpacing?this.zoomToDates(new Date(e),new Date(l)):this.zoomToIndexes(e,l))},handleCursorZoomStarted:function(){var a=this.valueAxes;if(a){var a=a[0],b=a.relativeStart,c=a.relativeEnd;a.reversed&&(b=1-a.relativeEnd,c=1-a.relativeStart);this.rotate?(this.startX0=b,this.endX0=c):(this.startY0=b,this.endY0=c)}this.categoryAxis&&(this.start0=this.start,this.end0=this.end,this.startTime0=this.startTime,this.endTime0=this.endTime)},fixCursor:function(){this.chartCursor&&this.chartCursor.fixPosition();this.prevCursorItem=null},handleCursorMove:function(a){f.AmSerialChart.base.handleCursorMove.call(this,a);var b=a.target,c=this.categoryAxis;if(a.panning)this.handleCursorHide(a);else if(this.chartData&&!b.isHidden){var d=this.graphs;if(d){var g;g=c.xToIndex(this.rotate?a.y:a.x);if(g=this.chartData[g]){var h,e,l,k;if(b.oneBalloonOnly&&b.valueBalloonsEnabled){var m=Infinity;for(h=d.length-1;0<=h;h--)if(e=d[h],e.balloon.enabled&&e.showBalloon&&!e.hidden){l=e.valueAxis.id;l=g.axes[l].graphs[e.id];if(b.showNextAvailable&&isNaN(l.y)&&(l=this.getNextItem(l),!l))continue;l=l.y;"top"==e.showBalloonAt&&(l=0);"bottom"==e.showBalloonAt&&(l=this.height);var p=b.mouseX,n=b.mouseY;l=this.rotate?Math.abs(p-l):Math.abs(n-l);l<m&&(m=l,k=e)}b.mostCloseGraph=k}if(this.prevCursorItem!=g||k!=this.prevMostCloseGraph){m=[];for(h=0;h<d.length;h++){e=d[h];l=e.valueAxis.id;l=g.axes[l].graphs[e.id];if(b.showNextAvailable&&isNaN(l.y)&&(l=this.getNextItem(l),!l&&e.balloon)){e.balloon.hide();continue}k&&e!=k?(e.showGraphBalloon(l,b.pointer,!1,b.graphBulletSize,b.graphBulletAlpha),e.balloon.hide(0)):b.valueBalloonsEnabled?(e.balloon.showBullet=b.bulletsEnabled,e.balloon.bulletSize=b.bulletSize/2,a.hideBalloons||(e.showGraphBalloon(l,b.pointer,!1,b.graphBulletSize,b.graphBulletAlpha),e.balloon.set&&m.push({balloon:e.balloon,y:e.balloon.pointToY}))):(e.currentDataItem=l,e.resizeBullet(l,b.graphBulletSize,b.graphBulletAlpha))}b.avoidBalloonOverlapping&&this.arrangeBalloons(m);this.prevCursorItem=g}this.prevMostCloseGraph=k}}c.showBalloon(a.x,a.y,b.categoryBalloonDateFormat,a.skip);this.updateLegendValues()}},handleCursorHide:function(a){f.AmSerialChart.base.handleCursorHide.call(this,a);a=this.categoryAxis;this.prevCursorItem=null;this.updateLegendValues();a&&a.hideBalloon();a=this.graphs;var 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c=this;c.animationFinished=!1;c.easing=b;c.totalFrames=a*f.updateRate;c.rh=c.h;c.frame=0;c.height(1);setTimeout(function(){c.updateHeight.call(c)},1E3/f.updateRate)},updateHeight:function(){var a=this;a.frame++;var b=a.totalFrames;a.frame<=b?(b=a.easing(0,a.frame,1,a.rh-1,b),a.height(b),window.requestAnimationFrame?window.requestAnimationFrame(function(){a.updateHeight.call(a)}):setTimeout(function(){a.updateHeight.call(a)},1E3/f.updateRate)):(a.height(a.rh),a.animationFinished=!0)},animateWidth:function(a,b){var c=this;c.animationFinished=!1;c.easing=b;c.totalFrames=a*f.updateRate;c.rw=c.w;c.frame=0;c.width(1);setTimeout(function(){c.updateWidth.call(c)},1E3/f.updateRate)},updateWidth:function(){var a=this;a.frame++;var b=a.totalFrames;a.frame<=b?(b=a.easing(0,a.frame,1,a.rw-1,b),a.width(b),window.requestAnimationFrame?window.requestAnimationFrame(function(){a.updateWidth.call(a)}):setTimeout(function(){a.updateWidth.call(a)},1E3/f.updateRate)):(a.width(a.rw),a.animationFinished=!0)}})})();(function(){var f=window.AmCharts;f.CategoryAxis=f.Class({inherits:f.AxisBase,construct:function(a){this.cname="CategoryAxis";f.CategoryAxis.base.construct.call(this,a);this.minPeriod="DD";this.equalSpacing=this.parseDates=!1;this.position="bottom";this.startOnAxis=!1;this.gridPosition="middle";this.safeDistance=30;this.stickBalloonToCategory=!1;f.applyTheme(this,a,this.cname)},draw:function(){f.CategoryAxis.base.draw.call(this);this.generateDFObject();var a=this.chart.chartData;this.data=a;this.labelRotationR=this.labelRotation;this.type=null;if(f.ifArray(a)){var b,c=this.chart;"scrollbar"!=this.id?(f.setCN(c,this.set,"category-axis"),f.setCN(c,this.labelsSet,"category-axis"),f.setCN(c,this.axisLine.axisSet,"category-axis")):this.bcn=this.id+"-";var d=this.start,g=this.labelFrequency,h=0,e=this.end-d+1,l=this.gridCountR,k=this.showFirstLabel,m=this.showLastLabel,p,n="",n=f.extractPeriod(this.minPeriod),u=f.getPeriodDuration(n.period,n.count),v,x,E,t,r,B=this.rotate,q=this.firstDayOfWeek,w=this.boldPeriodBeginning;b=f.resetDateToMin(new Date(a[a.length-1].time+1.05*u),this.minPeriod,1,q).getTime();this.firstTime=c.firstTime;this.endTime>b&&(this.endTime=b);r=this.minorGridEnabled;x=this.gridAlpha;var y=0,C=0;if(this.widthField)for(b=this.start;b<=this.end;b++)if(t=this.data[b]){var F=Number(this.data[b].dataContext[this.widthField]);isNaN(F)||(y+=F,t.widthValue=F)}if(this.parseDates&&!this.equalSpacing)this.lastTime=a[a.length-1].time,this.maxTime=f.resetDateToMin(new 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u=0,D=n;for(b=e;b<C;b++)t=this.data[b].time,this.checkPeriodChange(g,v,t,D)&&(u++,2<=u&&(F=b,b=C),D=t)}r&&1<v&&(t=this.chooseMinorFrequency(v),f.getPeriodDuration(g,t));if(0<this.gridCountR)for(b=e;b<C;b++)if(t=this.data[b].time,this.checkPeriodChange(g,v,t,n)&&b>=F){e=this.getCoordinate(b-this.start);r=!1;this.nextPeriod[x]&&(r=this.checkPeriodChange(this.nextPeriod[x],1,t,n,x))&&f.resetDateToMin(new Date(t),this.nextPeriod[x],1,q).getTime()!=t&&(r=!1);u=!1;r&&this.markPeriodChange?(r=this.dateFormatsObject[this.nextPeriod[x]],u=!0):r=this.dateFormatsObject[x];n=f.formatDate(new Date(t),r,c);if(b==d&&!k||b==l&&!m)n=" ";a?a=!1:(w||(u=!1),e-this.previousPos>this.safeDistance*Math.cos(this.labelRotationR*Math.PI/180)&&(this.labelFunction&&(n=this.labelFunction(n,new Date(t),this,g,v,E)),this.boldLabels&&(u=!0),p=new this.axisItemRenderer(this,e,n,void 0,void 0,void 0,void 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-r)/2,p=!0,k.toDate&&(p=!1),p="H"==this.orientation?new this.axisItemRenderer(this,r,k.label,p,2*q,NaN,k):new this.axisItemRenderer(this,r,k.label,!1,NaN,q,k),this.pushAxisItem(p,m)),p&&(q=p.label)&&this.addEventListeners(q,k),0<d||0<r){q=!1;if(this.rotate){if(d<this.height||r<this.height)q=!0}else if(d<this.width||r<this.width)q=!0;q&&(d=new this.guideFillRenderer(this,r,d,k),r=d.graphics(),this.pushAxisItem(d,m),k.graphics=r,r.index=b,this.addEventListeners(r,k))}if(c=c.chartCursor)B?c.fixHeight(this.cellWidth):
-(c.fixWidth(this.cellWidth),c.fullWidth&&this.balloon&&(this.balloon.minWidth=this.cellWidth));this.previousHeight=A}this.axisCreated=!0;this.set.translate(this.x,this.y);this.labelsSet.translate(this.x,this.y);this.labelsSet.show();this.positionTitle();(B=this.axisLine.set)&&B.toFront();var A=this.getBBox().height;2<A-this.previousHeight&&this.autoWrap&&!this.parseDates&&(this.axisCreated=this.chart.marginsUpdated=!1)},xToIndex:function(a){var b=this.data,c=this.chart,d=c.rotate,g=this.stepWidth,h;if(this.parseDates&&!this.equalSpacing)a=this.startTime+Math.round(a/g)-this.minDuration()/2,h=c.getClosestIndex(b,"time",a,!1,this.start,this.end+1);else if(this.widthField)for(c=Infinity,g=this.start;g<=this.end;g++){var e=this.data[g];e&&(e=Math.abs(e.x[this.id]-a),e<c&&(c=e,h=g))}else this.startOnAxis||(a-=g/2),h=this.start+Math.round(a/g);h=f.fitToBounds(h,0,b.length-1);var l;b[h]&&(l=b[h].x[this.id]);d?l>this.height+1&&h--:l>this.width+1&&h--;0>l&&h++;return h=f.fitToBounds(h,0,b.length-1)},
-dateToCoordinate:function(a){return this.parseDates&&!this.equalSpacing?(a.getTime()-this.startTime)*this.stepWidth:this.parseDates&&this.equalSpacing?(a=this.chart.getClosestIndex(this.data,"time",a.getTime(),!1,0,this.data.length-1),this.getCoordinate(a-this.start)):NaN},categoryToCoordinate:function(a){if(this.chart){if(this.parseDates)return this.dateToCoordinate(new Date(a));a=this.chart.getCategoryIndexByValue(a);if(!isNaN(a))return this.getCoordinate(a-this.start)}else return NaN},coordinateToDate:function(a){return this.equalSpacing?(a=this.xToIndex(a),new Date(this.data[a].time)):new Date(this.startTime+a/this.stepWidth)},coordinateToValue:function(a){a=this.xToIndex(a);if(a=this.data[a])return this.parseDates?a.time:a.category},getCoordinate:function(a){a*=this.stepWidth;this.startOnAxis||(a+=this.stepWidth/2);return Math.round(a)},formatValue:function(a,b){b||(b=this.currentDateFormat);this.parseDates&&(a=f.formatDate(new Date(a),b,this.chart));return a},showBalloonAt:function(a,b){void 0===b&&(b=this.parseDates?this.dateToCoordinate(new Date(a)):this.categoryToCoordinate(a));return this.adjustBalloonCoordinate(b)},formatBalloonText:function(a,b,c){var d="",g="",h=this.chart,e=this.data[b];if(e)if(this.parseDates)d=f.formatDate(e.category,c,h),b=f.changeDate(new Date(e.category),this.minPeriod,1),g=f.formatDate(b,c,h),-1!=d.indexOf("fff")&&(d=f.formatMilliseconds(d,e.category),g=f.formatMilliseconds(g,b));else{var l;this.data[b+1]&&(l=this.data[b+1]);d=f.fixNewLines(e.category);l&&(g=f.fixNewLines(l.category))}a=a.replace(/\[\[category\]\]/g,String(d));return a=a.replace(/\[\[toCategory\]\]/g,String(g))},adjustBalloonCoordinate:function(a,b){var c=this.xToIndex(a),d=this.chart.chartCursor;if(this.stickBalloonToCategory){var f=this.data[c];f&&(a=f.x[this.id]);this.stickBalloonToStart&&(a-=this.cellWidth/2);var h=0;if(d){var e=d.limitToGraph;if(e){var l=e.valueAxis.id;e.hidden||(h=f.axes[l].graphs[e.id].y)}this.rotate?("left"==this.position?(e&&(h-=d.width),0<h&&(h=0)):0>h&&(h=0),d.fixHLine(a,h)):("top"==this.position?(e&&(h-=d.height),0<h&&(h=0)):0>h&&(h=0),d.fullWidth&&(a+=1),d.fixVLine(a,h))}}d&&!b&&(d.setIndex(c),this.parseDates&&d.setTimestamp(this.coordinateToDate(a).getTime()));return a}})})();
diff --git a/admin/src/main/resources/static/js/plugins/metisMenu/jquery.metisMenu.js b/admin/src/main/resources/static/js/plugins/metisMenu/jquery.metisMenu.js
deleted file mode 100755
index 6f22effccf6efa30ec697bdcd497ec61d36f256a..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/metisMenu/jquery.metisMenu.js
+++ /dev/null
@@ -1,10 +0,0 @@
-/*
- * metismenu - v2.0.2
- * A jQuery menu plugin
- * https://github.com/onokumus/metisMenu
- *
- * Made by Osman Nuri Okumus
- * Under MIT License
- */
-
-!function(a){"use strict";function b(){var a=document.createElement("mm"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in b)if(void 0!==a.style[c])return{end:b[c]};return!1}function c(b){return this.each(function(){var c=a(this),d=c.data("mm"),f=a.extend({},e.DEFAULTS,c.data(),"object"==typeof b&&b);d||c.data("mm",d=new e(this,f)),"string"==typeof b&&d[b]()})}a.fn.emulateTransitionEnd=function(b){var c=!1,e=this;a(this).one("mmTransitionEnd",function(){c=!0});var f=function(){c||a(e).trigger(d.end)};return setTimeout(f,b),this};var d=b();d&&(a.event.special.mmTransitionEnd={bindType:d.end,delegateType:d.end,handle:function(b){return a(b.target).is(this)?b.handleObj.handler.apply(this,arguments):void 0}});var e=function(b,c){this.$element=a(b),this.options=a.extend({},e.DEFAULTS,c),this.transitioning=null,this.init()};e.TRANSITION_DURATION=350,e.DEFAULTS={toggle:!0,doubleTapToGo:!1,activeClass:"active"},e.prototype.init=function(){var b=this,c=this.options.activeClass;this.$element.find("li."+c).has("ul").children("ul").addClass("collapse in"),this.$element.find("li").not("."+c).has("ul").children("ul").addClass("collapse"),this.options.doubleTapToGo&&this.$element.find("li."+c).has("ul").children("a").addClass("doubleTapToGo"),this.$element.find("li").has("ul").children("a").on("click.metisMenu",function(d){var e=a(this),f=e.parent("li"),g=f.children("ul");return d.preventDefault(),f.hasClass(c)?b.hide(g):b.show(g),b.options.doubleTapToGo&&b.doubleTapToGo(e)&&"#"!==e.attr("href")&&""!==e.attr("href")?(d.stopPropagation(),void(document.location=e.attr("href"))):void 0})},e.prototype.doubleTapToGo=function(a){var b=this.$element;return a.hasClass("doubleTapToGo")?(a.removeClass("doubleTapToGo"),!0):a.parent().children("ul").length?(b.find(".doubleTapToGo").removeClass("doubleTapToGo"),a.addClass("doubleTapToGo"),!1):void 0},e.prototype.show=function(b){var c=this.options.activeClass,f=a(b),g=f.parent("li");if(!this.transitioning&&!f.hasClass("in")){g.addClass(c),this.options.toggle&&this.hide(g.siblings().children("ul.in")),f.removeClass("collapse").addClass("collapsing").height(0),this.transitioning=1;var h=function(){f.removeClass("collapsing").addClass("collapse in").height(""),this.transitioning=0};return d?void f.one("mmTransitionEnd",a.proxy(h,this)).emulateTransitionEnd(e.TRANSITION_DURATION).height(f[0].scrollHeight):h.call(this)}},e.prototype.hide=function(b){var c=this.options.activeClass,f=a(b);if(!this.transitioning&&f.hasClass("in")){f.parent("li").removeClass(c),f.height(f.height())[0].offsetHeight,f.addClass("collapsing").removeClass("collapse").removeClass("in"),this.transitioning=1;var g=function(){this.transitioning=0,f.removeClass("collapsing").addClass("collapse")};return d?void f.height(0).one("mmTransitionEnd",a.proxy(g,this)).emulateTransitionEnd(e.TRANSITION_DURATION):g.call(this)}};var f=a.fn.metisMenu;a.fn.metisMenu=c,a.fn.metisMenu.Constructor=e,a.fn.metisMenu.noConflict=function(){return a.fn.metisMenu=f,this}}(jQuery);
\ No newline at end of file
diff --git a/admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.js b/admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.js
deleted file mode 100755
index 9c3b4dde266cbe590353cc6dfe12b1835e8b6b12..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.js
+++ /dev/null
@@ -1,470 +0,0 @@
-/*! Copyright (c) 2011 Piotr Rochala (http://rocha.la)
- * Dual licensed under the MIT (http://www.opensource.org/licenses/mit-license.php)
- * and GPL (http://www.opensource.org/licenses/gpl-license.php) licenses.
- *
- * Version: 1.3.6
- *
- */
-(function($) {
-
- $.fn.extend({
- slimScroll: function(options) {
-
- var defaults = {
-
- // width in pixels of the visible scroll area
- width : 'auto',
-
- // height in pixels of the visible scroll area
- height : '250px',
-
- // width in pixels of the scrollbar and rail
- size : '7px',
-
- // scrollbar color, accepts any hex/color value
- color: '#000',
-
- // scrollbar position - left/right
- position : 'right',
-
- // distance in pixels between the side edge and the scrollbar
- distance : '1px',
-
- // default scroll position on load - top / bottom / $('selector')
- start : 'top',
-
- // sets scrollbar opacity
- opacity : .4,
-
- // enables always-on mode for the scrollbar
- alwaysVisible : false,
-
- // check if we should hide the scrollbar when user is hovering over
- disableFadeOut : false,
-
- // sets visibility of the rail
- railVisible : false,
-
- // sets rail color
- railColor : '#333',
-
- // sets rail opacity
- railOpacity : .2,
-
- // whether we should use jQuery UI Draggable to enable bar dragging
- railDraggable : true,
-
- // defautlt CSS class of the slimscroll rail
- railClass : 'slimScrollRail',
-
- // defautlt CSS class of the slimscroll bar
- barClass : 'slimScrollBar',
-
- // defautlt CSS class of the slimscroll wrapper
- wrapperClass : 'slimScrollDiv',
-
- // check if mousewheel should scroll the window if we reach top/bottom
- allowPageScroll : false,
-
- // scroll amount applied to each mouse wheel step
- wheelStep : 20,
-
- // scroll amount applied when user is using gestures
- touchScrollStep : 200,
-
- // sets border radius
- borderRadius: '7px',
-
- // sets border radius of the rail
- railBorderRadius : '7px'
- };
-
- var o = $.extend(defaults, options);
-
- // do it for every element that matches selector
- this.each(function(){
-
- var isOverPanel, isOverBar, isDragg, queueHide, touchDif,
- barHeight, percentScroll, lastScroll,
- divS = '<div></div>',
- minBarHeight = 30,
- releaseScroll = false;
-
- // used in event handlers and for better minification
- var me = $(this);
-
- // ensure we are not binding it again
- if (me.parent().hasClass(o.wrapperClass))
- {
- // start from last bar position
- var offset = me.scrollTop();
-
- // find bar and rail
- bar = me.closest('.' + o.barClass);
- rail = me.closest('.' + o.railClass);
-
- getBarHeight();
-
- // check if we should scroll existing instance
- if ($.isPlainObject(options))
- {
- // Pass height: auto to an existing slimscroll object to force a resize after contents have changed
- if ( 'height' in options && options.height == 'auto' ) {
- me.parent().css('height', 'auto');
- me.css('height', 'auto');
- var height = me.parent().parent().height();
- me.parent().css('height', height);
- me.css('height', height);
- }
-
- if ('scrollTo' in options)
- {
- // jump to a static point
- offset = parseInt(o.scrollTo);
- }
- else if ('scrollBy' in options)
- {
- // jump by value pixels
- offset += parseInt(o.scrollBy);
- }
- else if ('destroy' in options)
- {
- // remove slimscroll elements
- bar.remove();
- rail.remove();
- me.unwrap();
- return;
- }
-
- // scroll content by the given offset
- scrollContent(offset, false, true);
- }
-
- return;
- }
- else if ($.isPlainObject(options))
- {
- if ('destroy' in options)
- {
- return;
- }
- }
-
- // optionally set height to the parent's height
- o.height = (o.height == 'auto') ? me.parent().height() : o.height;
-
- // wrap content
- var wrapper = $(divS)
- .addClass(o.wrapperClass)
- .css({
- position: 'relative',
- overflow: 'hidden',
- width: o.width,
- height: o.height
- });
-
- // update style for the div
- me.css({
- overflow: 'hidden',
- width: o.width,
- height: o.height
- });
-
- // create scrollbar rail
- var rail = $(divS)
- .addClass(o.railClass)
- .css({
- width: o.size,
- height: '100%',
- position: 'absolute',
- top: 0,
- display: (o.alwaysVisible && o.railVisible) ? 'block' : 'none',
- 'border-radius': o.railBorderRadius,
- background: o.railColor,
- opacity: o.railOpacity,
- zIndex: 90
- });
-
- // create scrollbar
- var bar = $(divS)
- .addClass(o.barClass)
- .css({
- background: o.color,
- width: o.size,
- position: 'absolute',
- top: 0,
- opacity: o.opacity,
- display: o.alwaysVisible ? 'block' : 'none',
- 'border-radius' : o.borderRadius,
- BorderRadius: o.borderRadius,
- MozBorderRadius: o.borderRadius,
- WebkitBorderRadius: o.borderRadius,
- zIndex: 99
- });
-
- // set position
- var posCss = (o.position == 'right') ? { right: o.distance } : { left: o.distance };
- rail.css(posCss);
- bar.css(posCss);
-
- // wrap it
- me.wrap(wrapper);
-
- // append to parent div
- me.parent().append(bar);
- me.parent().append(rail);
-
- // make it draggable and no longer dependent on the jqueryUI
- if (o.railDraggable){
- bar.bind("mousedown", function(e) {
- var $doc = $(document);
- isDragg = true;
- t = parseFloat(bar.css('top'));
- pageY = e.pageY;
-
- $doc.bind("mousemove.slimscroll", function(e){
- currTop = t + e.pageY - pageY;
- bar.css('top', currTop);
- scrollContent(0, bar.position().top, false);// scroll content
- });
-
- $doc.bind("mouseup.slimscroll", function(e) {
- isDragg = false;hideBar();
- $doc.unbind('.slimscroll');
- });
- return false;
- }).bind("selectstart.slimscroll", function(e){
- e.stopPropagation();
- e.preventDefault();
- return false;
- });
- }
-
- // on rail over
- rail.hover(function(){
- showBar();
- }, function(){
- hideBar();
- });
-
- // on bar over
- bar.hover(function(){
- isOverBar = true;
- }, function(){
- isOverBar = false;
- });
-
- // show on parent mouseover
- me.hover(function(){
- isOverPanel = true;
- showBar();
- hideBar();
- }, function(){
- isOverPanel = false;
- hideBar();
- });
-
- // support for mobile
- me.bind('touchstart', function(e,b){
- if (e.originalEvent.touches.length)
- {
- // record where touch started
- touchDif = e.originalEvent.touches[0].pageY;
- }
- });
-
- me.bind('touchmove', function(e){
- // prevent scrolling the page if necessary
- if(!releaseScroll)
- {
- e.originalEvent.preventDefault();
- }
- if (e.originalEvent.touches.length)
- {
- // see how far user swiped
- var diff = (touchDif - e.originalEvent.touches[0].pageY) / o.touchScrollStep;
- // scroll content
- scrollContent(diff, true);
- touchDif = e.originalEvent.touches[0].pageY;
- }
- });
-
- // set up initial height
- getBarHeight();
-
- // check start position
- if (o.start === 'bottom')
- {
- // scroll content to bottom
- bar.css({ top: me.outerHeight() - bar.outerHeight() });
- scrollContent(0, true);
- }
- else if (o.start !== 'top')
- {
- // assume jQuery selector
- scrollContent($(o.start).position().top, null, true);
-
- // make sure bar stays hidden
- if (!o.alwaysVisible) { bar.hide(); }
- }
-
- // attach scroll events
- attachWheel(this);
-
- function _onWheel(e)
- {
- // use mouse wheel only when mouse is over
- if (!isOverPanel) { return; }
-
- var e = e || window.event;
-
- var delta = 0;
- if (e.wheelDelta) { delta = -e.wheelDelta/120; }
- if (e.detail) { delta = e.detail / 3; }
-
- var target = e.target || e.srcTarget || e.srcElement;
- if ($(target).closest('.' + o.wrapperClass).is(me.parent())) {
- // scroll content
- scrollContent(delta, true);
- }
-
- // stop window scroll
- if (e.preventDefault && !releaseScroll) { e.preventDefault(); }
- if (!releaseScroll) { e.returnValue = false; }
- }
-
- function scrollContent(y, isWheel, isJump)
- {
- releaseScroll = false;
- var delta = y;
- var maxTop = me.outerHeight() - bar.outerHeight();
-
- if (isWheel)
- {
- // move bar with mouse wheel
- delta = parseInt(bar.css('top')) + y * parseInt(o.wheelStep) / 100 * bar.outerHeight();
-
- // move bar, make sure it doesn't go out
- delta = Math.min(Math.max(delta, 0), maxTop);
-
- // if scrolling down, make sure a fractional change to the
- // scroll position isn't rounded away when the scrollbar's CSS is set
- // this flooring of delta would happened automatically when
- // bar.css is set below, but we floor here for clarity
- delta = (y > 0) ? Math.ceil(delta) : Math.floor(delta);
-
- // scroll the scrollbar
- bar.css({ top: delta + 'px' });
- }
-
- // calculate actual scroll amount
- percentScroll = parseInt(bar.css('top')) / (me.outerHeight() - bar.outerHeight());
- delta = percentScroll * (me[0].scrollHeight - me.outerHeight());
-
- if (isJump)
- {
- delta = y;
- var offsetTop = delta / me[0].scrollHeight * me.outerHeight();
- offsetTop = Math.min(Math.max(offsetTop, 0), maxTop);
- bar.css({ top: offsetTop + 'px' });
- }
-
- // scroll content
- me.scrollTop(delta);
-
- // fire scrolling event
- me.trigger('slimscrolling', ~~delta);
-
- // ensure bar is visible
- showBar();
-
- // trigger hide when scroll is stopped
- hideBar();
- }
-
- function attachWheel(target)
- {
- if (window.addEventListener)
- {
- target.addEventListener('DOMMouseScroll', _onWheel, false );
- target.addEventListener('mousewheel', _onWheel, false );
- }
- else
- {
- document.attachEvent("onmousewheel", _onWheel)
- }
- }
-
- function getBarHeight()
- {
- // calculate scrollbar height and make sure it is not too small
- barHeight = Math.max((me.outerHeight() / me[0].scrollHeight) * me.outerHeight(), minBarHeight);
- bar.css({ height: barHeight + 'px' });
-
- // hide scrollbar if content is not long enough
- var display = barHeight == me.outerHeight() ? 'none' : 'block';
- bar.css({ display: display });
- }
-
- function showBar()
- {
- // recalculate bar height
- getBarHeight();
- clearTimeout(queueHide);
-
- // when bar reached top or bottom
- if (percentScroll == ~~percentScroll)
- {
- //release wheel
- releaseScroll = o.allowPageScroll;
-
- // publish approporiate event
- if (lastScroll != percentScroll)
- {
- var msg = (~~percentScroll == 0) ? 'top' : 'bottom';
- me.trigger('slimscroll', msg);
- }
- }
- else
- {
- releaseScroll = false;
- }
- lastScroll = percentScroll;
-
- // show only when required
- if(barHeight >= me.outerHeight()) {
- //allow window scroll
- releaseScroll = true;
- return;
- }
- bar.stop(true,true).fadeIn('fast');
- if (o.railVisible) { rail.stop(true,true).fadeIn('fast'); }
- }
-
- function hideBar()
- {
- // only hide when options allow it
- if (!o.alwaysVisible)
- {
- queueHide = setTimeout(function(){
- if (!(o.disableFadeOut && isOverPanel) && !isOverBar && !isDragg)
- {
- bar.fadeOut('slow');
- rail.fadeOut('slow');
- }
- }, 1000);
- }
- }
-
- });
-
- // maintain chainability
- return this;
- }
- });
-
- $.fn.extend({
- slimscroll: $.fn.slimScroll
- });
-
-})(jQuery);
\ No newline at end of file
diff --git a/admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.min.js b/admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.min.js
deleted file mode 100755
index 7ecb25283652098ee59d270d36aad4daf973a121..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.min.js
+++ /dev/null
@@ -1,16 +0,0 @@
-/*! Copyright (c) 2011 Piotr Rochala (http://rocha.la)
- * Dual licensed under the MIT (http://www.opensource.org/licenses/mit-license.php)
- * and GPL (http://www.opensource.org/licenses/gpl-license.php) licenses.
- *
- * Version: 1.3.6
- *
- */
-(function(e){e.fn.extend({slimScroll:function(g){var a=e.extend({width:"auto",height:"250px",size:"7px",color:"#000",position:"right",distance:"1px",start:"top",opacity:.4,alwaysVisible:!1,disableFadeOut:!1,railVisible:!1,railColor:"#333",railOpacity:.2,railDraggable:!0,railClass:"slimScrollRail",barClass:"slimScrollBar",wrapperClass:"slimScrollDiv",allowPageScroll:!1,wheelStep:20,touchScrollStep:200,borderRadius:"7px",railBorderRadius:"7px"},g);this.each(function(){function v(d){if(r){d=d||window.event;
- var c=0;d.wheelDelta&&(c=-d.wheelDelta/120);d.detail&&(c=d.detail/3);e(d.target||d.srcTarget||d.srcElement).closest("."+a.wrapperClass).is(b.parent())&&m(c,!0);d.preventDefault&&!k&&d.preventDefault();k||(d.returnValue=!1)}}function m(d,e,g){k=!1;var f=d,h=b.outerHeight()-c.outerHeight();e&&(f=parseInt(c.css("top"))+d*parseInt(a.wheelStep)/100*c.outerHeight(),f=Math.min(Math.max(f,0),h),f=0<d?Math.ceil(f):Math.floor(f),c.css({top:f+"px"}));l=parseInt(c.css("top"))/(b.outerHeight()-c.outerHeight());
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- h.hover(function(){w()},function(){p()});c.hover(function(){y=!0},function(){y=!1});b.hover(function(){r=!0;w();p()},function(){r=!1;p()});b.bind("touchstart",function(a,b){a.originalEvent.touches.length&&(A=a.originalEvent.touches[0].pageY)});b.bind("touchmove",function(b){k||b.originalEvent.preventDefault();b.originalEvent.touches.length&&(m((A-b.originalEvent.touches[0].pageY)/a.touchScrollStep,!0),A=b.originalEvent.touches[0].pageY)});x();"bottom"===a.start?(c.css({top:b.outerHeight()-c.outerHeight()}),
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\ No newline at end of file
diff --git a/admin/src/main/resources/templates/fragments/components.html b/admin/src/main/resources/templates/fragments/components.html
deleted file mode 100644
index 79d5263cad62f13fbb0f1c6895bc410b1159b6d2..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/templates/fragments/components.html
+++ /dev/null
@@ -1,34 +0,0 @@
-<!DOCTYPE html>
-<html xmlns:th="http://www.thymeleaf.org">
-<head lang="en">
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
- <title>PDX Finder Admin Curator</title>
-</head>
-<body>
-
- <!-- ICONS COMPONENT -->
- <div th:fragment="icons(title, image, link)" class="col-lg-2 col-md-3 col-sm-4 col-xs-6">
-
- <div class="ibox">
- <div class="ibox-content" style="padding-bottom:10px;">
- <a href="#" th:href="${link}" > <img th:src="'images/icons/' + ${image}" class="icon"> </a>
- <div class='text-navy pdx-singleLine' th:text="${title}"> RAW DATA </div>
- </div>
- </div>
- </div>
-
-
-
- <!-- PROGRESS BAR COMPONENT -->
- <li th:fragment="progressBar(num, desc, type, size)">
- <h3 class="no-margins" th:text="${num}"> ... </h3>
- <small th:text="${desc}"> ... </small>
- <div class="progress progress-mini">
- <div class="progress-bar" th:classappend="'progress-bar-'+ ${type}" th:style="'width:'+ ${size}">></div>
- </div>
- </li>
-
-
-
-</body>
-</html>
\ No newline at end of file
diff --git a/admin/src/main/resources/templates/fragments/footer.html b/admin/src/main/resources/templates/fragments/footer.html
deleted file mode 100644
index 710a7fcfc47fa7f03b097cd13273f1564ed20ff9..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/templates/fragments/footer.html
+++ /dev/null
@@ -1,29 +0,0 @@
-<!DOCTYPE html>
-<html xmlns:th="http://www.thymeleaf.org">
-<head lang="en"></head>
-<body>
-
- <div th:fragment="footer">
-
- <!-- Mainly scripts -->
- <script th:src="@{/js/jquery-2.1.1.js}"></script>
- <script th:src="@{/js/bootstrap.min.js}"></script>
- <script th:src="@{/js/plugins/metisMenu/jquery.metisMenu.js}"></script>
- <script th:src="@{/js/plugins/slimscroll/jquery.slimscroll.min.js}"></script>
-
- <!-- Custom and plugin javascript -->
- <script src="/js/pdxAdmin.js"></script>
-
-
- <!-- Am Chart Dependencies Start -->
- <link rel="stylesheet" href="/js/plugins/chart/export.css" type="text/css" media="all" />
- <script th:src="@{/js/plugins/chart/amcharts.js}"></script>
- <script th:src="@{/js/plugins/chart/serial.js}"></script>
- <script th:src="@{/js/plugins/chart/export.min.js}"></script>
- <script th:src="@{/js/plugins/chart/light.js}"></script>
- <!-- Am Chart Dependencies Ends -->
- <script type="application/javascript" th:src="@{/js/plugins/chart/3dbar.js}"></script>
-
- </div>
-</body>
-</html>
\ No newline at end of file
diff --git a/admin/src/main/resources/templates/fragments/header.html b/admin/src/main/resources/templates/fragments/header.html
deleted file mode 100644
index e1a9ddd00fd5c1b9bdd68781ea0cc3f927eefa6c..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/templates/fragments/header.html
+++ /dev/null
@@ -1,20 +0,0 @@
-<!DOCTYPE html>
-<html xmlns:th="http://www.thymeleaf.org">
-<head lang="en" th:fragment="header">
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
- <title>PDX Finder Admin</title>
-
- <!--<link th:href="@{/webjars//bootstrap/css/bootstrap.css}" href="//cdn.jsdelivr.net/webjars/org.webjars/bootstrap/3.3.7/css/bootstrap.css" rel="stylesheet" media="screen"/>
- <link th:href="@{/webjars//animate.css/animate.css}" href="//cdn.jsdelivr.net/webjars/org.webjars/animate.css/3.5.2/animate.css" rel="stylesheet" media="screen"/>
- <link th:href="@{/webjars//font-awesome/css/font-awesome.css}" href="//cdn.jsdelivr.net/webjars/org.webjars/font-awesome/4.7.0/css/font-awesome.css" rel="stylesheet" media="screen"/>-->
- <link th:href="@{/css/bootstrap.css}" href="../static/css/bootstrap.css" rel="stylesheet"/>
- <link th:href="@{/css/animate.css}" href="../static/css/animate.css" rel="stylesheet"/>
- <link th:href="@{/css/font-awesome.css}" href="../static/css/font-awesome.css" rel="stylesheet"/>
- <link th:href="@{/css/style.css}" href="../static/css/style.css" rel="stylesheet"/>
-
-
-</head>
-<body>
-
-</body>
-</html>
\ No newline at end of file
diff --git a/admin/src/main/resources/templates/fragments/sidenav.html b/admin/src/main/resources/templates/fragments/sidenav.html
deleted file mode 100644
index 6b70b600a6aa0f5ae85e80c73dc13dc8e6fc351c..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/templates/fragments/sidenav.html
+++ /dev/null
@@ -1,75 +0,0 @@
-<!DOCTYPE html>
-<html xmlns:th="http://www.thymeleaf.org">
-<head lang="en">
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
- <title>PDX Finder Admin Curator</title>
-</head>
-<body>
-
- <nav th:fragment="side-navigation-menu" class="navbar-default navbar-static-side" role="navigation">
-
- <div class="sidebar-collapse">
- <a class="close-canvas-menu"><i class="fa fa-times"></i></a>
- <ul class="nav metismenu" id="side-menu">
- <li class="nav-header">
- <div class="dropdown profile-element"> <span>
- <img alt="image" class="img-circle" src="images/profile_small.jpg" />
- </span>
- <a data-toggle="dropdown" class="dropdown-toggle" href="#">
- <span class="clear"> <span class="block m-t-xs"> <strong class="font-bold">Nathalie Conte</strong>
- </span> <span class="text-muted text-xs block">Bioinformatician <b class="caret"></b></span> </span>
- </a>
- </div>
- <div class="logo-element">
- PDX+
- </div>
- </li>
- <li class="active">
- <a href="#"><i class="fa fa-th-large"></i> <span class="nav-label">Tool Box</span> <span class="fa arrow"></span></a>
- <ul class="nav nav-second-level">
- <li class="active"><a href="#" class="active">Zooma Mappings</a></li>
- <li><a href="#">PDX Finder Jira <span class="label label-primary pull-right">8</span></a></li>
- <li><a href="#">Raw Data <span class="label label-primary pull-right">2</span></a></li>
- <li><a href="#">Reports </a></li>
- <li><a href="#">SOPs & Methods </a></li>
- <li><a href="#">Finder </a></li>
- <li><a href="#">Github </a></li>
- <li><a href="#">Community Contacts </a></li>
- </ul>
- </li>
- <li> <a href="#"><i class="fa fa-database"></i> <span class="nav-label">Manage IRCC Data</span></a> </li>
- <li> <a href="#"><i class="fa fa-database"></i> <span class="nav-label">Manage JAX Data</span></a> </li>
- <li>
- <a href="#"><i class="fa fa-flask"></i> <span class="nav-label">PDX Models</span><span class="fa arrow"></span></a>
- <ul class="nav nav-second-level collapse">
- <li><a href="#">Mouse Models <span class="label label-primary pull-right">Catalog</span></a></li>
- <li><a href="#">Histopathological Data</a></li>
- <li><a href="#">Host-Mouse Metadata</a></li>
- <li><a href="#">Genomic Data <span class="label label-primary pull-right">435</span></a></li>
- <li><a href="#">Chemotherapeutic</a></li>
- <li><a href="#">Image Data</a></li>
- </ul>
- </li>
- <li><a href="#"><i class="fa fa-pie-chart"></i> <span class="nav-label">PDX Model Request</span> </a></li>
- <li><a href="#"><i class="fa fa-pie-chart"></i> <span class="nav-label">API Access Request</span> </a></li>
-
- <li>
- <a href="#"><i class="fa fa-search-minus"></i> <span class="nav-label">User Search Report</span></a>
- </li>
-
- <li class="landing_link">
- <a target="_blank" href="landing.html"><i class="fa fa-desktop"></i> <span class="nav-label">PDX Finder Website</span> </a>
- </li>
- <li class="special_link">
- <a href="package.html"><i class="fa fa-database"></i> <span class="nav-label">Neo4j Database</span></a>
- </li>
- </ul>
-
- </div>
-
- </nav>
-
-
-
-</body>
-</html>
\ No newline at end of file
diff --git a/admin/src/main/resources/templates/fragments/topnav.html b/admin/src/main/resources/templates/fragments/topnav.html
deleted file mode 100644
index 38c6e72a40d326d28c9092db7d1f5c5d1330ff96..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/templates/fragments/topnav.html
+++ /dev/null
@@ -1,56 +0,0 @@
-<!DOCTYPE html>
-<html xmlns:th="http://www.thymeleaf.org">
-<head lang="en">
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
- <title>PDX Finder Admin Curator</title>
-</head>
-<body>
-
-
- <div th:fragment="top-navigation-menu" class="row border-bottom">
-
- <nav class="navbar navbar-static-top white-bg" role="navigation" style="margin-bottom: 0">
- <div class="navbar-header">
- <a class="navbar-minimalize minimalize-styl-2 btn btn-primary " href="#"><i class="fa fa-bars"></i> </a>
- <form role="search" class="navbar-form-custom" action="search_results.html">
- <div class="form-group">
- <input type="text" placeholder="Search for PDX Models..." class="form-control" name="top-search" id="top-search">
- </div>
- </form>
- </div>
- <ul class="nav navbar-top-links navbar-right">
- <li>
- <span class="m-r-sm text-muted welcome-message">Welcome to PDX-Curator+ Admin</span>
- </li>
- <li class="dropdown">
- <a class="dropdown-toggle count-info" data-toggle="dropdown" href="#">
- <i class="fa fa-envelope"></i> <span class="label label-warning">6</span>
- </a>
- </li>
- <li class="dropdown">
- <a class="dropdown-toggle count-info" data-toggle="dropdown" href="#">
- <i class="fa fa-bell"></i> <span class="label label-primary">8</span>
- </a>
- </li>
-
-
- <li>
- <a href="index.html">
- <i class="fa fa-sign-out"></i> Log out
- </a>
- </li>
- <li>
- <a class="right-sidebar-toggle">
- <i class="fa fa-tasks"></i>
- </a>
- </li>
- </ul>
-
- </nav>
-
- </div>
-
-
-
-</body>
-</html>
\ No newline at end of file
diff --git a/admin/src/main/resources/templates/index.html b/admin/src/main/resources/templates/index.html
deleted file mode 100644
index f2767277f7ba3d77715ad8b2497a8b177ccd9f88..0000000000000000000000000000000000000000
--- a/admin/src/main/resources/templates/index.html
+++ /dev/null
@@ -1,128 +0,0 @@
-<!DOCTYPE html>
-<html xmlns:th="http://www.thymeleaf.org">
-<head>
- <!--/*/ <th:block th:include="fragments/header :: header"></th:block> /*/-->
-</head>
-
-<body class="md-skin canvas-menu">
-<div id="wrapper">
-
- <!-- Side Navigation menu here-->
- <!--/*/ <th:block th:replace="fragments/sidenav :: side-navigation-menu"></th:block> /*/-->
-
-
-
-
- <div id="page-wrapper" class="gray-bg">
-
- <!-- Top Navigation Menu here -->
- <!--/*/ <th:block th:replace="fragments/topnav :: top-navigation-menu"></th:block> /*/-->
-
-
- <div class="wrapper wrapper-content animated fadeIn">
- <div class="p-w-md m-t-sm container">
-
-
-
-
- <div class="row" style="margin-top:-20px;">
-
-
- <div class="col-lg-12">
- <div class="ibox float-e-margins">
- <div class="ibox-content" >
-
-
- <div>
- <span class="pull-right text-right">
- <small>PDX Finder contains more than 800 PDX models from : <strong>JAX and IRCC</strong></small>
- <br/>
- All Models: 162,862
- </span>
- <h3 class="font-bold no-margins">
- PDX Finder cancer by tissue
- </h3>
- <small>From all data sources.</small>
- </div>
-
- <div class="m-t-sm">
-
- <div class="row" style="margin-top:-10px;">
- <div class="col-md-8">
- <div id="chartdiv" style="width: 100%; height:280px;"></div>
- </div>
- <div class="col-md-4" style="margin-top:20px;">
- <ul class="stat-list m-t-lg">
-
- <!--/*/ <th:block th:replace="fragments/components :: progressBar(num='2,346', desc='IRCC PDX Mouse Data', type='danger', size='30%')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: progressBar(num='4,422', desc='JAX PDX Mouse Data', type='info', size='36%')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: progressBar(num='2,912', desc='PDX Search last month', type='primary', size='80%')"></th:block> /*/-->
-
- </ul>
- </div>
- </div>
-
- </div>
-
- <div class="m-t-md">
- <small class="pull-right">
- <i class="fa fa-clock-o"> </i>
- Updated on 30.07.2017
- </small>
- <small>
- <strong> PDX report summary :</strong> The report has been changed over time, and last month reached a level over 50,000 counts
- </small>
- </div>
-
- </div>
- </div>
- </div>
-
- </div>
-
-
-
-
- <div class="row">
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='ZOOMA MAPPINGS ' , image='zoomaa.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='RAW DATA' , image='vms.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='PDXFinder JIRA' , image='jira2.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='REPORTS' , image='Reports-icon.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='SOPs & METHODS' , image='SOPs.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='FINDER' , image='finder.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='GITHUB' , image='github.jpg', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='COMMUNITY CONTACTS' , image='contact.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='SOPs & METHODS' , image='SOPs.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='FINDER' , image='finder.png', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='GITHUB' , image='github.jpg', link='')"></th:block> /*/-->
-
- <!--/*/ <th:block th:replace="fragments/components :: icons (title='COMMUNITY CONTACTS' , image='contact.png', link='')"></th:block> /*/-->
-
- </div>
-
-
- </div>
- </div>
- </div>
-
-</div>
-
-
-
-<!--/*/ <th:block th:include="fragments/footer :: footer"></th:block> /*/-->
-
-</body>
-</html>
\ No newline at end of file
diff --git a/data-model/pom.xml b/data-model/pom.xml
index 35c7cdd72a98c1a960fcc5d353c026164ca4a329..4741d6583aa68d24a11a11b5858e52b9cadd80a7 100644
--- a/data-model/pom.xml
+++ b/data-model/pom.xml
@@ -3,6 +3,21 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
+ <dependencies>
+ <dependency>
+ <groupId>com.google.code.gson</groupId>
+ <artifactId>gson</artifactId>
+ <version>2.8.2</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j-ogm-embedded-driver</artifactId>
+ <version>3.1.20</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
<parent>
<groupId>org.pdxfinder</groupId>
@@ -14,20 +29,4 @@
<artifactId>data-model</artifactId>
<packaging>jar</packaging>
- <dependencies>
-
- <dependency>
- <groupId>org.neo4j</groupId>
- <artifactId>neo4j-ogm-embedded-driver</artifactId>
- <scope>test</scope>
- <version>2.1.1</version>
- </dependency>
-
-<!-- <dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-data-rest</artifactId>
- </dependency>-->
-
- </dependencies>
-
</project>
\ No newline at end of file
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/CurrentTreatment.java b/data-model/src/main/java/org/pdxfinder/graph/dao/CurrentTreatment.java
index fabbd404c60f6c73720e10627eb30594f9f63ac1..d5601bc0051caa7864f5f8ed831080d4f4a59234 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/CurrentTreatment.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/CurrentTreatment.java
@@ -1,6 +1,7 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import org.neo4j.ogm.annotation.NodeEntity;
/*
@@ -9,7 +10,7 @@ import org.neo4j.ogm.annotation.NodeEntity;
@NodeEntity
public class CurrentTreatment {
- @GraphId
+ @Id @GeneratedValue
private Long id;
private String name;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/DataProjection.java b/data-model/src/main/java/org/pdxfinder/graph/dao/DataProjection.java
index 33c35dc792c5019eca5ab97ea33581e5905d9c1c..a39208093accf6b8ed6555fb84a7f9810a060806 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/DataProjection.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/DataProjection.java
@@ -1,6 +1,7 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import org.neo4j.ogm.annotation.NodeEntity;
/*
@@ -9,7 +10,7 @@ import org.neo4j.ogm.annotation.NodeEntity;
@NodeEntity
public class DataProjection {
- @GraphId
+ @Id @GeneratedValue
private Long id;
private String label;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Drug.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Drug.java
index b8912a04620b0f107343c02884d6e079d0203c65..59722b815d84c6dcb947d4aa9577182b58b2d705 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Drug.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Drug.java
@@ -1,6 +1,7 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import org.neo4j.ogm.annotation.NodeEntity;
/*
@@ -18,7 +19,7 @@ public class Drug {
* @param synonyms Synonyms of the drug
*/
- @GraphId
+ @Id @GeneratedValue
private Long id;
private String name;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalDataSource.java b/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalDataSource.java
index e90314721650da3e2418e26889901c576194733d..de9b83a86810f64f537bf269abea6b6281e8686c 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalDataSource.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalDataSource.java
@@ -1,6 +1,7 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import org.neo4j.ogm.annotation.NodeEntity;
import java.util.Date;
@@ -12,7 +13,7 @@ import java.util.List;
@NodeEntity
public class ExternalDataSource {
- @GraphId
+ @Id @GeneratedValue
private Long id;
private String name;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalUrl.java b/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalUrl.java
index 7ded1e7c4712551dca7a4264b711c881ffdeccb8..3d075a81593feec58eddc9749dd55b061ef0c164 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalUrl.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/ExternalUrl.java
@@ -1,7 +1,8 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import org.neo4j.ogm.annotation.NodeEntity;
/**
@@ -10,7 +11,7 @@ import org.neo4j.ogm.annotation.NodeEntity;
@NodeEntity
public class ExternalUrl {
- @GraphId
+ @Id @GeneratedValue
private Long id;
private String type;
private String url;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Histology.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Histology.java
index 30793938cdeee6a2b818ad89dc501091cb450e27..6405dfa2b3dcb722765b8ad25fa28f40c03bb843 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Histology.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Histology.java
@@ -1,6 +1,7 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
@@ -13,7 +14,7 @@ import java.util.Set;
@NodeEntity
public class Histology {
- @GraphId
+ @Id @GeneratedValue
Long id;
@Relationship(type = "HAS_IMAGE")
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Image.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Image.java
index 47b5c0796ba993663764b864a2004dbd6b9f19d3..f9f9569df098c1d1fe8623c0bc4143ea4dc500a3 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Image.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Image.java
@@ -1,6 +1,7 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import org.neo4j.ogm.annotation.NodeEntity;
/**
@@ -9,7 +10,7 @@ import org.neo4j.ogm.annotation.NodeEntity;
@NodeEntity
public class Image {
- @GraphId
+ @Id @GeneratedValue
Long id;
private String url;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java
index 47604229d284539b48efa3950ba8668dd29a61e7..8fb821c00074c531b11c6476940229bb62b13240 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java
@@ -3,9 +3,9 @@ package org.pdxfinder.graph.dao;
import org.apache.commons.lang3.StringUtils;
import org.neo4j.ogm.annotation.Index;
import org.neo4j.ogm.annotation.NodeEntity;
+
import javax.persistence.GeneratedValue;
import javax.persistence.Id;
-import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java b/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java
index b8c016558a27a2cf8387f7f33cec194a7cc8e1d7..55eaa9830523b9190f14fe8da050b76dba018b31 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java
@@ -24,7 +24,7 @@ public class MarkerAssociation {
private String molecularDataString;
private int dataPoints = 0;
- private List<MolecularData> molecularDataList = new ArrayList<>();
+ private List<MolecularData> molecularDataList;
public MarkerAssociation() {
molecularDataList = new ArrayList<>();
@@ -39,7 +39,8 @@ public class MarkerAssociation {
}
public void encodeMolecularData(){
- molecularDataString = new Gson().toJson(molecularDataList);
+ Gson gson = new Gson();
+ molecularDataString = gson.toJson(molecularDataList);
dataPoints = molecularDataList.size();
molecularDataList = Collections.emptyList();
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/OntologyTerm.java b/data-model/src/main/java/org/pdxfinder/graph/dao/OntologyTerm.java
index 5f85bd4709b948cf257b02f6b39dbad6d1ff617c..f8b40110596a327607ec8def1e693e9be4a0f10d 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/OntologyTerm.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/OntologyTerm.java
@@ -1,10 +1,11 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.Index;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import java.util.HashSet;
import java.util.Set;
@@ -14,7 +15,8 @@ import java.util.Set;
@NodeEntity
public class OntologyTerm {
- @GraphId
+ @Id
+ @GeneratedValue
private Long id;
@Index
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/PatientSnapshot.java b/data-model/src/main/java/org/pdxfinder/graph/dao/PatientSnapshot.java
index ad4e48ec882e79057c16e9525e0dd6cae310d74b..2baefc17c419ca18216001a6e945a11f5cd43bcd 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/PatientSnapshot.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/PatientSnapshot.java
@@ -1,10 +1,12 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.cypher.internal.frontend.v2_3.SemanticDirection;
-import org.neo4j.ogm.annotation.GraphId;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import java.util.HashSet;
import java.util.Set;
@@ -14,7 +16,8 @@ import java.util.Set;
@NodeEntity
public class PatientSnapshot {
- @GraphId
+ @Id
+ @GeneratedValue
private Long id;
private String ageAtCollection;
@@ -90,7 +93,7 @@ public class PatientSnapshot {
if (ageInteger <= 23) {
return "0-23 months";
} else {
- return getAgeBin(ageInteger / 24);
+ return getAgeBin(ageInteger / 12);
}
}
catch (Exception e){
@@ -246,4 +249,31 @@ public class PatientSnapshot {
return String.format("[%s at age %s]", getPatient().getExternalId(), getAgeAtCollection());
}
+ @Override
+ public boolean equals(Object o) {
+ if (this == o) return true;
+
+ if (o == null || getClass() != o.getClass()) return false;
+
+ PatientSnapshot that = (PatientSnapshot) o;
+
+ return new EqualsBuilder()
+ .append(getAgeAtCollection(), that.getAgeAtCollection())
+ .append(getDateAtCollection(), that.getDateAtCollection())
+ .append(getCollectionEvent(), that.getCollectionEvent())
+ .append(getElapsedTime(), that.getElapsedTime())
+ .append(getPatient(), that.getPatient())
+ .isEquals();
+ }
+
+ @Override
+ public int hashCode() {
+ return new HashCodeBuilder(17, 37)
+ .append(getAgeAtCollection())
+ .append(getDateAtCollection())
+ .append(getCollectionEvent())
+ .append(getElapsedTime())
+ .append(getPatient())
+ .toHashCode();
+ }
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Platform.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Platform.java
index 2eeeeca81411ed220b43e2c54029a9b73718dc8d..6edd4b8223909266bd33c199a748735e572f2666 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Platform.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Platform.java
@@ -1,9 +1,10 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import java.util.Set;
/**
@@ -12,7 +13,8 @@ import java.util.Set;
@NodeEntity
public class Platform {
- @GraphId
+ @Id
+ @GeneratedValue
private Long id;
private String name;
private String url;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/PlatformAssociation.java b/data-model/src/main/java/org/pdxfinder/graph/dao/PlatformAssociation.java
index 5c9cce67f8aab28ca176a4302a424b444bc68a77..a7e8673490c7be16192e17292146433ed96f78f9 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/PlatformAssociation.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/PlatformAssociation.java
@@ -1,16 +1,19 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
+
/**
* Created by jmason on 21/07/2017.
*/
@NodeEntity
public class PlatformAssociation {
- @GraphId
+ @Id
+ @GeneratedValue
Long id;
private String exon;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/QualityAssurance.java b/data-model/src/main/java/org/pdxfinder/graph/dao/QualityAssurance.java
index 2b91449c3219e709739724a08a6f7ad36deb1555..68511dee299d60e565b78159c73fe6660ef629c4 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/QualityAssurance.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/QualityAssurance.java
@@ -1,7 +1,8 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
/**
* Created by jmason on 17/03/2017.
@@ -9,7 +10,8 @@ import org.neo4j.ogm.annotation.NodeEntity;
@NodeEntity
public class QualityAssurance {
- @GraphId
+ @Id
+ @GeneratedValue
Long id;
private String technology;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Response.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Response.java
index 7ce6cfcdaa2b139d45e822d1d67435a71acab14c..f83084c44da12be2fa13044c69e0075f8199d35a 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Response.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Response.java
@@ -1,8 +1,9 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
/*
* Created by csaba on 20/10/2017.
@@ -10,7 +11,8 @@ import org.neo4j.ogm.annotation.Relationship;
@NodeEntity
public class Response {
- @GraphId
+ @Id
+ @GeneratedValue
private Long id;
private String description;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Sample.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Sample.java
index 2db4431f6a209de51a9fcca9d15ed33b0e420488..b05dba5224aeaa8e9d3b5526d8f8d27ba95f731d 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Sample.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Sample.java
@@ -3,6 +3,7 @@ package org.pdxfinder.graph.dao;
import org.apache.commons.collections4.CollectionUtils;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+
import javax.persistence.GeneratedValue;
import javax.persistence.Id;
import java.util.HashSet;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/SampleToOntologyRelationship.java b/data-model/src/main/java/org/pdxfinder/graph/dao/SampleToOntologyRelationship.java
index e0828412370639c9010cb73dbf58a847879d9b60..9586d443c0b63558727f567451c0fc9e8ff7968c 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/SampleToOntologyRelationship.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/SampleToOntologyRelationship.java
@@ -2,6 +2,8 @@ package org.pdxfinder.graph.dao;
import org.neo4j.ogm.annotation.*;
import org.springframework.beans.factory.annotation.Autowired;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
/*
* Created by csaba on 16/11/2017.
@@ -9,8 +11,9 @@ import org.springframework.beans.factory.annotation.Autowired;
@RelationshipEntity(type="MAPPED_TO")
public class SampleToOntologyRelationship {
- @GraphId
- private Long relationshipId;
+ @Id
+ @GeneratedValue
+ private Long id;
@Property
private String type;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Specimen.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Specimen.java
index 5e4bbc559f489c1b6a854e1d93897e1998aab002..979d11f5d84eab841d2772db0f8535d1f9ca661c 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Specimen.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Specimen.java
@@ -6,7 +6,6 @@ import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
import javax.persistence.GeneratedValue;
import javax.persistence.Id;
-import java.util.StringJoiner;
/**
* Created by jmason on 06/06/2017.
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Treatment.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Treatment.java
index 21b6294fac92992ceb22764afee05eacc8345623..8a548a0d3a511780fc1a64881a8941d11266c39c 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/Treatment.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/Treatment.java
@@ -1,8 +1,9 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
/*
* Created by csaba on 08/05/2019.
@@ -11,7 +12,8 @@ import org.neo4j.ogm.annotation.Relationship;
public class Treatment {
- @GraphId
+ @Id
+ @GeneratedValue
private Long id;
private String name;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentComponent.java b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentComponent.java
index a6ac343a3484b67ef01934680ad4eaf3c8c6d109..69b608713ff52b809c929cc822bdf78a878c656b 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentComponent.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentComponent.java
@@ -1,8 +1,9 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
/*
* Created by csaba on 23/05/2018.
@@ -10,7 +11,8 @@ import org.neo4j.ogm.annotation.Relationship;
@NodeEntity
public class TreatmentComponent {
- @GraphId
+ @Id
+ @GeneratedValue
private Long id;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProtocol.java b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProtocol.java
index 2ba3c61adf66bd87b5f99dc0e76a055ef264aa94..d570d666c8dd932b8d30dfdec11a110b82ec11b8 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProtocol.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProtocol.java
@@ -3,6 +3,7 @@ package org.pdxfinder.graph.dao;
import org.apache.commons.lang3.StringUtils;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
+
import javax.persistence.GeneratedValue;
import javax.persistence.Id;
import java.util.ArrayList;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentSummary.java b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentSummary.java
index 3a2ae4500a9f81743dcc0c63176b6d2dd791c188..2d9a03c03e0f1c05702ef62ab7296061b65b2bdb 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentSummary.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentSummary.java
@@ -1,13 +1,12 @@
package org.pdxfinder.graph.dao;
-import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;
import org.neo4j.ogm.annotation.Relationship;
-
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
import java.util.ArrayList;
-import java.util.HashSet;
import java.util.List;
-import java.util.Set;
+
/**
* TreatmentSummary represents a summary of the application of a treatment protocol to a sample (either Human or Xenograft)
@@ -16,7 +15,8 @@ import java.util.Set;
@NodeEntity
public class TreatmentSummary {
- @GraphId
+ @Id
+ @GeneratedValue
Long id;
//url to a page that describes the treatment
String url;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentToOntologyRelationship.java b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentToOntologyRelationship.java
index 04aa63cf87ec8bd9f2d74f82e183662197552348..afe5566f3258bbfc4cb38223a7e7fecd001ab993 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentToOntologyRelationship.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentToOntologyRelationship.java
@@ -1,6 +1,8 @@
package org.pdxfinder.graph.dao;
import org.neo4j.ogm.annotation.*;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
/*
* Created by csaba on 08/05/2019.
@@ -8,8 +10,9 @@ import org.neo4j.ogm.annotation.*;
@RelationshipEntity(type="MAPPED_TO")
public class TreatmentToOntologyRelationship {
- @GraphId
- private Long relationshipId;
+ @Id
+ @GeneratedValue
+ private Long id;
@Property
private String type;
diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/ValidationTechniques.java b/data-model/src/main/java/org/pdxfinder/graph/dao/ValidationTechniques.java
deleted file mode 100644
index 2f8f4a0556f48b0efc20b31a1e619bc4a3b9289e..0000000000000000000000000000000000000000
--- a/data-model/src/main/java/org/pdxfinder/graph/dao/ValidationTechniques.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package org.pdxfinder.graph.dao;
-
-/**
- * Created by jmason on 06/06/2017.
- */
-public enum ValidationTechniques {
- NOT_SPECIFIED("Not specified"),
- FINGERPRINT("Fingerprint"),
- FINGERPRINT_HISTOLOGY("Histology/STR"),
- HISTOLOGY("Histology"),
- HEALTH_CHECK("Health-check");
-
- private String technique;
-
- private ValidationTechniques(String s) {
- technique = s;
- }
-
- public String getTechnique() {
- return technique;
- }
-
-
-}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/DataProjectionRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/DataProjectionRepository.java
index f374f18228a723bd2a4880a860b57898f1dffcd3..0a321c6e3abbbac90ec2206100215c59a7beeef2 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/DataProjectionRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/DataProjectionRepository.java
@@ -7,7 +7,6 @@ import org.springframework.data.neo4j.repository.Neo4jRepository;
import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
-import java.util.Set;
/*
* Created by csaba on 09/03/2018.
@@ -18,33 +17,4 @@ public interface DataProjectionRepository extends Neo4jRepository<DataProjection
@Query("MATCH (dp:DataProjection) WHERE dp.label = {label} return dp ")
DataProjection findByLabel(@Param("label") String label);
-
-
-
-
-
-
- //VALIDATION QUERIES
-
- //find nodes that are not linked to anything
- @Query("MATCH (n) WHERE NOT (n)--() RETURN n")
- Set<Object> findUnlinkedNodes();
-
-
- //find patients that have multiple treatment summaries
- @Query("MATCH (p:Patient)--(ps:PatientSnapshot)--(ts1:TreatmentSummary) " +
- "WITH p, ps, ts1 " +
- "MATCH (ps)--(ts2:TreatmentSummary) " +
- "WHERE ts1 <> ts2 " +
- "RETURN p")
- Set<Object> findPatientsWithMultipleTreatmentSummaries();
-
-
- @Query("MATCH (pl:Platform) " +
- "WHERE NOT exists(pl.url) " +
- "OR pl.url = \"\" " +
- "RETURN pl")
- Set<Object> findPlatformsWithoutUrl();
-
-
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/DrugRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/DrugRepository.java
deleted file mode 100644
index db9a7aa216e597ee69d508eaaa7971d0377ce902..0000000000000000000000000000000000000000
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/DrugRepository.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package org.pdxfinder.graph.repositories;
-
-import org.neo4j.ogm.model.Result;
-import org.pdxfinder.graph.dao.Drug;
-import org.pdxfinder.graph.dao.ModelCreation;
-import org.springframework.data.neo4j.annotation.Query;
-import org.springframework.data.neo4j.repository.Neo4jRepository;
-import org.springframework.data.repository.query.Param;
-import org.springframework.stereotype.Repository;
-
-import java.util.List;
-import java.util.Set;
-
-/*
- * Created by csaba on 23/05/2018.
- */
-@Repository
-public interface DrugRepository extends Neo4jRepository<Drug, Long> {
-
- @Query("MATCH (d:Drug) RETURN DISTINCT d.name")
- List<String> findDistinctDrugNames();
-
-
- @Query("MATCH (mod:ModelCreation)--(ts:TreatmentSummary)-[tpr:TREATMENT_PROTOCOL]-(tp)-[tcr:TREATMENT_COMPONENT]-(tc:TreatmentComponent)-[dr:TREATMENT]-(drug:Drug) " +
- "RETURN drug.name AS drug_name, COUNT(DISTINCT mod.sourcePdxId) as model_count " +
- "ORDER BY model_count DESC")
- Result countModelsByDrug();
-
- @Query("MATCH (mod:ModelCreation)--(ts:TreatmentSummary)-[tpr:TREATMENT_PROTOCOL]-(tp)-[tcr:TREATMENT_COMPONENT]-(tc:TreatmentComponent)-[dr:DRUG]-(drug:Drug) " +
- "WHERE tc.type = {type} " +
- "RETURN drug.name AS drug_name, COUNT(DISTINCT mod.sourcePdxId) as model_count " +
- "ORDER BY model_count DESC")
- Result countModelsByDrugAndComponentType(@Param("type") String type);
-
-
-
-}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/ExternalUrlRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/ExternalUrlRepository.java
index 7df0046fd1862e723e3a89b2b19bf531461338c3..211341ac93d49b350ab58116610afd5e4559f644 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/ExternalUrlRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/ExternalUrlRepository.java
@@ -5,18 +5,10 @@ import org.springframework.data.neo4j.annotation.Query;
import org.springframework.data.repository.PagingAndSortingRepository;
import org.springframework.data.repository.query.Param;
-import java.util.List;
-
public interface ExternalUrlRepository extends PagingAndSortingRepository<ExternalUrl, Long> {
@Query("MATCH (u:ExternalUrl) WHERE u.type = {type} AND u.url = {url} RETURN u")
ExternalUrl findByTypeAndUrl(@Param("type") String type, @Param("url") String url);
- @Query("MATCH (exturl:ExternalUrl) RETURN DISTINCT exturl.type ORDER BY exturl.type")
- List<String> findAllTypes();
-
- @Query("MATCH (exturl:ExternalUrl) RETURN DISTINCT exturl.url ORDER BY exturl.url")
- List<String> findAllUrls();
-
}
\ No newline at end of file
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/HostStrainRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/HostStrainRepository.java
index 56f08947e1a8a4e723b00c40fd6911d304c6b7fe..3e6a84e652a36c27173ec71002c8643499acac66 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/HostStrainRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/HostStrainRepository.java
@@ -18,7 +18,4 @@ public interface HostStrainRepository extends PagingAndSortingRepository<HostStr
@Query("MATCH (t:HostStrain) WHERE t.name = {name} RETURN t")
HostStrain findByName(@Param("name") String name);
- @Query("MATCH (t:HostStrain) WHERE t.name = {name} AND t.symbol = {symbol} RETURN t")
- HostStrain findByNameAndSymbol(@Param("name") String name, @Param("symbol") String symbol);
-
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerAssociationRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerAssociationRepository.java
index 0320342fdd7ce39134798c579ec59f56a6c8e973..cc3db8f882e2b29c2bc7590f230c1c013d03d16c 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerAssociationRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerAssociationRepository.java
@@ -7,7 +7,6 @@ import org.springframework.data.repository.PagingAndSortingRepository;
import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
-import java.util.List;
import java.util.Set;
/**
@@ -16,26 +15,9 @@ import java.util.Set;
@Repository
public interface MarkerAssociationRepository extends PagingAndSortingRepository<MarkerAssociation, Long>{
- //TODO: Verify cypher
- @Query("MATCH (n:MarkerAssociation)-[]-(m:Marker) where n.description = {type} and m.hgncSymbol={symbol} return n")
- MarkerAssociation findByTypeAndMarkerSymbol(@Param("type") String type, @Param("symbol") String symbol);
-
- @Query("MATCH (n:MarkerAssociation)-[]-(m:Marker) where n.description = {type} and m.name={name} return n")
- MarkerAssociation findByTypeAndMarkerName(@Param("type") String type, @Param("name") String name);
-
@Query("MATCH (mc:MolecularCharacterization)--(ma:MarkerAssociation) WHERE id(mc) = {mc} RETURN ma")
Set<MarkerAssociation> findMutationByMolChar(@Param("mc") MolecularCharacterization mc);
@Query("MATCH (mc:MolecularCharacterization)--(ma:MarkerAssociation) WHERE id(mc) = {mc} RETURN ma")
Set<MarkerAssociation> findByMolChar(@Param("mc") MolecularCharacterization mc);
-
- @Query("MATCH (mc:MolecularCharacterization)-[awr:ASSOCIATED_WITH]-(ma:MarkerAssociation) " +
- "WHERE ID(mc) = {id} " +
- "RETURN count(ma)")
- int getMarkerAssociationCountByMolCharId(@Param("id") Long id);
-
- @Query("MATCH (mc:MolecularCharacterization)-[awr:ASSOCIATED_WITH]-(ma:MarkerAssociation)-[mr:MARKER]-(m:Marker) " +
- "WHERE ID(mc) = {id} " +
- "RETURN ma, mr, m SKIP {from} LIMIT {to}")
- List<MarkerAssociation> findAssociationsByMolCharIdFromTo(@Param("id") Long id, @Param("from") int from, @Param("to") int to);
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerRepository.java
index e68c76ede8f7590622b22c91bfe05a59922cd2bb..0b1a7b624e5df760579be393386d5d19d217fa50 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerRepository.java
@@ -1,17 +1,14 @@
package org.pdxfinder.graph.repositories;
-import org.neo4j.ogm.model.Result;
import org.pdxfinder.graph.dao.Marker;
-import org.pdxfinder.graph.dao.MarkerAssociation;
-import org.pdxfinder.graph.queryresults.MutatedMarkerData;
+
import org.springframework.data.neo4j.annotation.Query;
import org.springframework.data.repository.PagingAndSortingRepository;
import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
import java.util.Collection;
-import java.util.List;
-import java.util.Set;
+
/**
* Interface for Markers
@@ -24,52 +21,17 @@ public interface MarkerRepository extends PagingAndSortingRepository<Marker, Lon
@Query("MATCH (t:Marker) WHERE t.name = {name} RETURN t")
Marker findByName(@Param("name") String name);
-
- @Query("MATCH (t:Marker) WHERE t.ensembleId = {id} RETURN t")
- Marker findByEnsemblId(@Param("id") String id);
@Query("MATCH (t:Marker) WHERE t.ncbiGeneId = {id} return t")
Marker findByNcbiGeneId(@Param("id") String id);
- @Query("MATCH (m:Marker) RETURN m")
- Collection<Marker> findAllMarkers();
-
@Query("MATCH (m:Marker) RETURN count(m)")
Integer countAllMarkers();
-
@Query("MATCH (m:Marker) " +
"RETURN m")
Collection<Marker> findAllHumanMarkers();
- @Query("MATCH (s:Sample)--(:MolecularCharacterization)--(:MarkerAssociation)--(m:Marker) WHERE s.sourceSampleId = {sampleId} return m")
- Collection<Marker> findAllBySampleId(@Param("sampleId") String sampleId);
-
- @Query("MATCH (ma:MarkerAssociation)--(m:Marker) WHERE id(ma) = {ma} RETURN m")
- Marker findByMarkerAssociation(@Param("ma") MarkerAssociation ma);
-
-
-
- @Query("MATCH (mod:ModelCreation)--(spec:Specimen)--(msamp:Sample)--(molchar:MolecularCharacterization)-->(mAss:MarkerAssociation)--(marker:Marker) " +
- "RETURN marker.hgncSymbol AS gene_name, COUNT(DISTINCT mod.sourcePdxId) as number_of_models " +
- "ORDER BY number_of_models DESC")
- List<MutatedMarkerData> countModelsByMarker();
-
-
- @Query("MATCH (m:Marker) WHERE {synonym} IN m.aliasSymbols RETURN m")
- List<Marker> findBySynonym(@Param("synonym") String synonym);
-
- @Query("MATCH (m:Marker) WHERE {synonym} IN m.prevSymbols RETURN m")
- List<Marker> findByPrevSymbol(@Param("synonym") String synonym);
-
- @Query("MATCH (m:Marker) WHERE NOT (m)--() DELETE m")
- void deleteMarkersWithoutRelationships();
-
- @Query("MATCH (mc:MolecularCharacterization)-[awr:ASSOCIATED_WITH]-(ma:MarkerAssociation) " +
- "WHERE ID(mc) = {id} " +
- "RETURN DISTINCT m")
- Set<Marker> findDistinctByMolCharId(@Param("id") Long id);
-
@Query("MATCH (m:Marker) return count(m)")
int getMarkerCount();
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java
index c55eb3c260d24b1475fd2d0db0d7fb52ddcc6b72..54837b1ddfdcedca517acc3f6b8653559c5a6de5 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java
@@ -128,56 +128,6 @@ public interface ModelCreationRepository extends Neo4jRepository<ModelCreation,
Collection<ModelCreation> findAllModelsPlatforms();
-
- @Query("MATCH (mc:ModelCreation)--(psamp:Sample)-[char:CHARACTERIZED_BY]-(molch:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation)-[aw:MARKER]-(m:Marker) " +
- " WHERE mc.dataSource = {dataSource} " +
- " AND mc.sourcePdxId = {modelId} " +
- "WITH mc, psamp, char, molch, assoc, mAss, aw, m " +
- "MATCH (molch)-[pu:PLATFORM_USED]-(pl:Platform) " +
-
- " WHERE (pl.name = {tech} OR {tech} = '' ) " +
-
- " OR toLower(m.hgncSymbol) CONTAINS toLower({search}) " +
- " OR any( property in keys(mAss) where toLower(mAss[property]) CONTAINS toLower({search}) ) " +
- " RETURN count(*) ")
- Integer variationCountByDataSourceAndPdxIdAndPlatform(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("tech") String tech,
- @Param("search") String search);
-
-
- @Query("MATCH (mc:ModelCreation)--(psamp:Sample)-[char:CHARACTERIZED_BY]-(molch:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation)-[aw:MARKER]-(m:Marker) " +
-
- " WHERE mc.dataSource = {dataSource} " +
- " AND mc.sourcePdxId = {modelId} " +
- "WITH mc, psamp, char, molch, assoc, mAss, aw, m " +
- "MATCH (molch)-[pu:PLATFORM_USED]-(pl:Platform) " +
-
- " WHERE (pl.name = {tech} OR {tech} = '' ) " +
-
-
- " OR toLower(m.hgncSymbol) CONTAINS toLower({search})" +
- " OR any( property in keys(mAss) where toLower(mAss[property]) CONTAINS toLower({search}) ) " +
-
- " RETURN mc,psamp,char,molch,mAss,m, pu, pl SKIP {skip} LIMIT {lim} ")
- ModelCreation findVariationBySourcePdxIdAndPlatform(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("tech") String tech,
- @Param("search") String search,
- @Param("skip") int skip,
- @Param("lim") int lim);
-
- @Query("MATCH (mc)-[msr:MODEL_SAMPLE_RELATION]-(s:Sample)-[cbr:CHARACTERIZED_BY]-(molChar:MolecularCharacterization)-[pur:PLATFORM_USED]-(p:Platform) " +
- "WHERE mc.sourcePdxId={sourcePdxId} AND p.name={platform} AND mc.dataSource = {dataSource} " +
- "WITH mc, msr, s, cbr, molChar, pur, p " +
-
- "OPTIONAL MATCH (molChar)-[assW:ASSOCIATED_WITH]-(mAss:MarkerAssociation) " +
- "RETURN count(mAss) ")
- Integer countMarkerAssociationBySourcePdxId(@Param("sourcePdxId") String sourcePdxId,
- @Param("dataSource") String dataSource,
- @Param("platform") String platform);
-
-
@Query("MATCH (model:ModelCreation)--(s:Sample)--(molch:MolecularCharacterization) " +
"WHERE id(molch) = {mc} " +
"RETURN model")
@@ -208,19 +158,21 @@ public interface ModelCreationRepository extends Neo4jRepository<ModelCreation,
List<ModelCreation> findModelPlatformSampleByDS(@Param("dataSource") String dataSource);
- @Query("MATCH (mod:ModelCreation) WHERE toLower(mod.dataSource) = toLower({dataSource}) and mod.sourcePdxId = {modelId} " +
+ @Query("MATCH (mod:ModelCreation) WHERE toLower(mod.dataSource) = toLower({dataSource}) " +
"WITH mod " +
- "OPTIONAL MATCH (mod)-[iir:IMPLANTED_IN]-(psamp:Sample)-[cbr:CHARACTERIZED_BY]-(mc:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation) " +
+ "MATCH (mod)--(samp:Sample)-[cbr:CHARACTERIZED_BY]-(mc:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation) " +
"WHERE mc.type = {type} "+
- "WITH mod, iir, psamp, cbr, mc, assoc, mAss " +
+ "WITH mod, samp, cbr, mc, assoc, mAss " +
+ "OPTIONAL MATCH (mod)-[iir:IMPLANTED_IN]-(psamp:Sample) " +
+ "WITH iir, psamp, mod, samp, cbr, mc, assoc, mAss " +
"OPTIONAL MATCH (mod)-[spr:SPECIMENS]-(sp:Specimen)-[sfr:SAMPLED_FROM]-(s:Sample)-[cbr2:CHARACTERIZED_BY]-(mc2:MolecularCharacterization)-[assoc2:ASSOCIATED_WITH]->(mAss2:MarkerAssociation) " +
"WHERE mc2.type = {type} "+
- "WITH mod, iir, psamp, spr, sp, sfr, s, cbr, mc, mc2, cbr2, assoc, mAss, assoc2, mAss2 " +
+ "WITH iir, psamp, mod, samp, spr, sp, sfr, s, cbr, mc, mc2, cbr2, assoc, mAss, assoc2, mAss2 " +
"OPTIONAL MATCH (sp)-[hsr:HOST_STRAIN]-(hs:HostStrain) " +
"OPTIONAL MATCH (mc)-[pur:PLATFORM_USED]-(pl:Platform) " +
"OPTIONAL MATCH (mc2)-[pur2:PLATFORM_USED]-(pl2:Platform) " +
- "RETURN mod, iir, psamp, spr, sp, sfr, s, cbr, mc, mc2, cbr2, pur, pl, pur2, pl2, assoc, mAss, assoc2, mAss2, hsr, hs ")
- ModelCreation findModelWithMolecularDataByDSAndIdAndMolcharType(@Param("dataSource") String dataSource, @Param("modelId") String modelId, @Param("type") String type);
+ "RETURN mod, iir, psamp, samp, spr, sp, sfr, s, cbr, mc, mc2, cbr2, pur, pl, pur2, pl2, assoc, mAss, assoc2, mAss2, hsr, hs ")
+ List<ModelCreation> findModelsWithMolecularDataByDSAndMolcharType(@Param("dataSource") String dataSource, @Param("type") String type);
@Query("MATCH (mod:ModelCreation) WHERE toLower(mod.dataSource) = toLower({dataSource}) " +
"WITH mod SKIP {from} LIMIT {to}" +
@@ -259,10 +211,6 @@ public interface ModelCreationRepository extends Neo4jRepository<ModelCreation,
"RETURN model, spr, sp, hsr, hs, sfr, s, psamp, ir, cbr, mc, pur, pl, cbr2, mc2, pur2, pl2")
ModelCreation findBySourcePdxIdAndDataSourceWithSamplesAndSpecimensAndHostStrain(@Param("modelId") String modelId, @Param("dataSource") String dataSource);
- @Query("CREATE INDEX ON :ModelCreation(dataSource, sourcePdxId)")
- void createIndex();
-
-
@Query("MATCH (model:ModelCreation)-[msr:MODEL_SAMPLE_RELATION]-(samp:Sample)-[cby:CHARACTERIZED_BY]-(molchar:MolecularCharacterization)-[asw:ASSOCIATED_WITH]-(massoc:MarkerAssociation)-[mark:MARKER]-(marker:Marker) WHERE molchar.type={molcharType} " +
"RETURN model, msr, samp, cby, molchar, asw, massoc, mark, marker")
List<ModelCreation> findByMolcharType(@Param("molcharType") String molcharType);
@@ -272,6 +220,19 @@ public interface ModelCreationRepository extends Neo4jRepository<ModelCreation,
"RETURN mod, tsr, ts, tpr, tp, tcr, tc, dr, d, mt, ot")
Set<ModelCreation> getModelsTreatmentsAndDrugs(@Param("type") String type);
+ @Query("MATCH (model:ModelCreation)-[ii:IMPLANTED_IN]-(samp:Sample)--(ps:PatientSnapshot)-[tsr:SUMMARY_OF_TREATMENT]-(ts:TreatmentSummary)-[tpr:TREATMENT_PROTOCOL]-(tp:TreatmentProtocol)-[tcr:TREATMENT_COMPONENT]-(tc:TreatmentComponent)-[dr:TREATMENT]-(d:Treatment) " +
+ "WHERE model.dataSource = {dataSource} " +
+ "WITH model, ii, samp, ps, tsr, ts, tpr, tp, tcr, tc, dr, d " +
+ "OPTIONAL MATCH (tp)-[resp:RESPONSE]-(res:Response) " +
+ "RETURN model, ii, samp, ps, tsr, ts, tpr, tp, tcr, tc, dr, d,resp, res")
+ List<ModelCreation> findModelFromPatienSnapshotWithTreatmentSummaryByDataSource(@Param("dataSource")String dataSource);
+
+ @Query("MATCH(model:ModelCreation)-[tsr:SUMMARY_OF_TREATMENT]-(ts:TreatmentSummary)-[tpr:TREATMENT_PROTOCOL]-(tp:TreatmentProtocol)-[tcr:TREATMENT_COMPONENT]-(tc:TreatmentComponent)-[dr:TREATMENT]-(d:Treatment) " +
+ "WHERE toLower(model.dataSource) = toLower({dataSource}) " +
+ "WITH model,tsr, ts, tpr, tp, tcr, tc, dr, d " +
+ "OPTIONAL MATCH (tp)-[resp:RESPONSE]-(res:Response) " +
+ "RETURN model,tsr, ts, tpr, tp, tcr, tc, dr, d, res, resp" )
+ List<ModelCreation> findModelsWithTreatmentSummaryByDataSource(@Param("dataSource") String dataSource);
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/MolecularCharacterizationRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/MolecularCharacterizationRepository.java
index 06dd72e217663f7ab9dc869a119beb73816d9069..9b8a9e66fed4e627cd4dbb4d4a826508addb16c8 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/MolecularCharacterizationRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/MolecularCharacterizationRepository.java
@@ -29,16 +29,6 @@ public interface MolecularCharacterizationRepository extends PagingAndSortingRep
List<MolecularCharacterization> findPatientPlatformByModelId(@Param("dataSource") String dataSource, @Param("modelId") String modelId);
- @Query("MATCH (molch:MolecularCharacterization) " +
- "WHERE molch.type = {type} " +
- "WITH molch " +
- "MATCH (molch)-[awr:ASSOCIATED_WITH]-(mAss:MarkerAssociation) " +
- "WHERE exists(mAss.aminoAcidChange) " +
- "WITH molch, awr, mAss " +
- "MATCH (mAss)-[mr:MARKER]-(m:Marker) " +
- "RETURN distinct molch, awr, mAss, mr, m")
- Collection<MolecularCharacterization> getAllDistinctByType(@Param("type") String type);
-
@Query("MATCH (molch:MolecularCharacterization) " +
"WHERE molch.type = {type} " +
"OPTIONAL MATCH (molch)-[plr:PLATFORM_USED]-(pl:Platform) " +
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/OntologyTermRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/OntologyTermRepository.java
index 3f13b26761b717ff8085150ff737f1573b456c2f..b8387e9bd8abcb1fe0e91c1ef009d1e2dd74c0cb 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/OntologyTermRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/OntologyTermRepository.java
@@ -8,7 +8,6 @@ import org.springframework.stereotype.Repository;
import java.util.Collection;
import java.util.List;
-import java.util.Set;
/**
* Created by csaba on 07/06/2017.
@@ -40,25 +39,12 @@ public interface OntologyTermRepository extends PagingAndSortingRepository<Ontol
@Query("MATCH (ot:OntologyTerm) RETURN ot")
Collection<OntologyTerm> findAll();
- @Query("MATCH (st:OntologyTerm)<-[*]-(term:OntologyTerm) " +
- "WHERE st.label = {label} " +
- "RETURN sum(term.indirectMappedSamplesNumber)")
- int getIndirectMappingNumber(@Param("label") String label);
-
- @Query("MATCH (st:OntologyTerm)<-[*]-(term:OntologyTerm) " +
- "WHERE st.label = {label} " +
- "RETURN term, st")
- Set<OntologyTerm> getDistinctSubTreeNodes(@Param("label") String label);
-
@Query("MATCH (o:OntologyTerm) RETURN count(o)")
int getOntologyTermNumber();
@Query("MATCH (o:OntologyTerm) WHERE o.type = {type} RETURN count(o)")
int getOntologyTermNumberByType(@Param("type") String type);
- @Query("match (o:OntologyTerm) RETURN o SKIP {from} LIMIT {to}")
- Collection<OntologyTerm> findAllFromTo(@Param("from") int from, @Param("to") int to);
-
@Query("match (o:OntologyTerm) WHERE o.type = {type} RETURN o SKIP {from} LIMIT {to}")
Collection<OntologyTerm> findAllByTypeFromTo(@Param("type") String type, @Param("from") int from, @Param("to") int to);
@@ -67,7 +53,6 @@ public interface OntologyTermRepository extends PagingAndSortingRepository<Ontol
"RETURN parent")
Collection<OntologyTerm> findAllDirectParents(@Param("url") String url);
-
@Query("MATCH (o:OntologyTerm) WHERE o.directMappedSamplesNumber > 0 RETURN o")
Collection<OntologyTerm> findAllWithNotZeroDirectMappingNumber();
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientRepository.java
index 87be07334931f61c3619214d657fb500a1fefbf0..c641d8f390bf1840572f95d23da8887b8995b8fe 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientRepository.java
@@ -32,22 +32,6 @@ public interface PatientRepository extends Neo4jRepository<Patient, Long> {
"RETURN p, patRel, ps, sf, s, ii, mod, o, t, ot, tt, ssr, ss ORDER BY p.externalId")
List<Patient> findPatientTumorAtCollectionDataByDS(@Param("g") Group g);
-
-
- @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) " +
- "MATCH (s:Sample)-[sf:SAMPLED_FROM]-(ps:PatientSnapshot)-[pt:PATIENT]-(p:Patient) " +
- "WHERE mod.sourcePdxId = {modelId} " +
- "RETURN mod, ii, s, ps, p, sf, pt")
- Patient findByModelId(@Param("modelId") String modelId);
-
-
- @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) " +
- "MATCH (s:Sample)--(ps:PatientSnapshot)--(p:Patient) " +
- "WHERE s.sourceSampleId = {sampleId} " +
- "RETURN mod, ii, s, ps, p")
- Patient findBySampleId(@Param("sampleId") String sampleId);
-
-
@Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) " +
"WHERE mod.sourcePdxId = {modelId} " +
"AND toLower(mod.dataSource) = toLower({dataSource}) "+
@@ -58,43 +42,6 @@ public interface PatientRepository extends Neo4jRepository<Patient, Long> {
Patient findByDataSourceAndModelId(@Param("dataSource") String dataSource, @Param("modelId") String modelId);
- @Query("MATCH(pat:Patient)-[patRel:COLLECTION_EVENT]-(ps:PatientSnapshot)-[sfrm:SAMPLED_FROM]-(psamp:Sample)-[char:CHARACTERIZED_BY]-(molch:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation)-[aw:MARKER]-(m:Marker) " +
- "WITH pat,patRel,ps,sfrm,psamp,char,molch,mAss,m " +
- "Match (psamp)-[imp:IMPLANTED_IN]-(mc:ModelCreation) " +
- " WHERE psamp.dataSource = {dataSource} " +
- " AND mc.sourcePdxId = {modelId} " +
- " AND (mc.technology = {tech} OR {tech} = '' ) " +
-
-
- " OR toLower(m.hgncSymbol) CONTAINS toLower({search})" +
- " OR toLower(mc.technology) CONTAINS toLower({search})" +
- " OR any( property in keys(mAss) where toLower(mAss[property]) CONTAINS toLower({search}) ) " +
-
- " RETURN pat,patRel,ps,sfrm,psamp,char,molch,mAss,m SKIP {skip} LIMIT {lim} ")
- Set<Patient> findSpecimenBySourcePdxIdAndPlatform(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("tech") String tech,
- @Param("search") String search,
- @Param("skip") int skip,
- @Param("lim") int lim);
-
-
- @Query("MATCH(pat:Patient)-[patRel:PATIENT]-(ps:PatientSnapshot)-[sfrm:SAMPLED_FROM]-(psamp:Sample)-[char:CHARACTERIZED_BY]-(molch:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation)-[aw:MARKER]-(m:Marker) " +
- "WITH pat,patRel,ps,sfrm,psamp,char,molch,mAss,m " +
- "Match (psamp)-[imp:IMPLANTED_IN]-(mc:ModelCreation) " +
- " WHERE psamp.dataSource = {dataSource} " +
- " AND mc.sourcePdxId = {modelId} " +
- " AND (mc.technology = {tech} OR {tech} = '' ) " +
-
- " OR toLower(m.hgncSymbol) CONTAINS toLower({search}) " +
- " OR toLower(mc.technology) CONTAINS toLower({search}) " +
- " OR any( property in keys(mAss) where toLower(mAss[property]) CONTAINS toLower({search}) ) " +
- " RETURN count(*) ")
- Integer countByBySourcePdxIdAndPlatform(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("tech") String tech,
- @Param("search") String search);
-
@Query("MATCH (p:Patient)--(ps:PatientSnapshot)--(s:Sample)--(mod:ModelCreation) " +
"WHERE mod.dataSource = {dataSource} " +
"AND mod.sourcePdxId = {modelId} " +
@@ -141,6 +88,7 @@ public interface PatientRepository extends Neo4jRepository<Patient, Long> {
"AND samp.sourceSampleId = {sourceSampleId} " +
" RETURN mod.sourcePdxId ")
String getModelIdByDataSourceAndPatientSampleId(@Param("dataSource") String dataSource,
- @Param("sourceSampleId") String modelId);
+ @Param("sourceSampleId") String modelId);
}
+
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientSnapshotRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientSnapshotRepository.java
index 78b836ab64b7023d67e73ea7d3bbe290ec42be93..ec66329335ce13e03dbd6d12f97d920a31fe186b 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientSnapshotRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/PatientSnapshotRepository.java
@@ -6,7 +6,6 @@ import org.springframework.data.neo4j.repository.Neo4jRepository;
import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
-import java.util.List;
import java.util.Set;
@Repository
@@ -15,25 +14,6 @@ public interface PatientSnapshotRepository extends Neo4jRepository<PatientSnapsh
@Query("MATCH (ps:PatientSnapshot)--(p:Patient) WHERE p.externalId = {patientId} RETURN ps")
Set<PatientSnapshot> findByPatient(@Param("patientId") String patientId);
- @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample)-[sf:SAMPLED_FROM]-(ps:PatientSnapshot)-[pr:PATIENT]-(p:Patient) \n" +
- "WHERE mod.sourcePdxId = {modelId} " +
- "WITH mod, ii, s, sf, ps, pr, p " +
- "OPTIONAL MATCH (s)-[ot:ORIGIN_TISSUE]-(t1:Tissue) " +
- "OPTIONAL MATCH (s)-[ss:SAMPLE_SITE]-(t2:Tissue) " +
-
- "RETURN mod,ii,s,sf,ps, p, pr, t1, t2, ot, ss")
- PatientSnapshot findByModelId(@Param("modelId") String modelId);
-
- @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample)-[sf:SAMPLED_FROM]-(ps:PatientSnapshot)-[pr:PATIENT]-(p:Patient) " +
- "WHERE mod.sourcePdxId = {modelId} " +
- "AND toLower(s.dataSource) = toLower({dataSource}) "+
- "WITH mod, ii, s, sf, ps, pr, p " +
- "OPTIONAL MATCH (s)-[ot:ORIGIN_TISSUE]-(t1:Tissue) " +
- "OPTIONAL MATCH (s)-[ss:SAMPLE_SITE]-(t2:Tissue) " +
-
- "RETURN mod,ii,s,sf,ps, p, pr, t1, t2, ot, ss")
- List<PatientSnapshot> findByDataSourceAndModelId(@Param("dataSource") String dataSource, @Param("modelId") String modelId);
-
@Query("MATCH (p:Patient)--(ps:PatientSnapshot) " +
"WHERE p.externalId = {patientId} " +
"AND p.dataSource = {dataSource} " +
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/PlatformAssociationRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/PlatformAssociationRepository.java
index bdd61ec9ec60cda8d0b2263ae484e97983683305..56f1dbe7d498f5cf076c964781d96fb99b970ec4 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/PlatformAssociationRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/PlatformAssociationRepository.java
@@ -14,8 +14,6 @@ import java.util.Set;
@Repository
public interface PlatformAssociationRepository extends PagingAndSortingRepository<PlatformAssociation, Long> {
- Set<PlatformAssociation> findAllByPlatform_Name(@Param("name") String name);
-
@Query("MATCH (pa:PlatformAssociation), (p:Platform), (ds:Group) WHERE (pa)--(p)--(ds) AND ds.name = {name} AND ds.type='Provider' RETURN pa")
Set<PlatformAssociation> findByPlatform_ExternalDataSource_Name(@Param("name") String name);
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/QualityAssuranceRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/QualityAssuranceRepository.java
index ec294cb3eb635d4d1a40db1cb7fffda8de6bde0c..8cd98ede7c7fa55d844dda3dfe9245a4ecbb3bb5 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/QualityAssuranceRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/QualityAssuranceRepository.java
@@ -1,6 +1,7 @@
package org.pdxfinder.graph.repositories;
import org.pdxfinder.graph.dao.QualityAssurance;
+import org.springframework.data.neo4j.annotation.Query;
import org.springframework.data.neo4j.repository.Neo4jRepository;
import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
@@ -9,6 +10,7 @@ import org.springframework.stereotype.Repository;
@Repository
public interface QualityAssuranceRepository extends Neo4jRepository<QualityAssurance, Long> {
- QualityAssurance findFirstByTechnologyAndDescription(@Param("technology") String technology, @Param("description") String description);
+ @Query("MATCH (qa:QualityAssurance) WHERE qa.technology = {technology} AND qa.description = {description} AND qa.passage = {passage} RETURN qa")
+ QualityAssurance findByTechnologyAndDescriptionAndPassage(@Param("technology") String technology, @Param("description") String description, @Param("passage") String passage);
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/ResponseRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/ResponseRepository.java
index 4f931cb64879377dd0efe526e7d2f5e1afc1ddbc..9f8aa697748589a138b44fa46d48c3023cbb5f72 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/ResponseRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/ResponseRepository.java
@@ -13,9 +13,6 @@ import java.util.List;
@Repository
public interface ResponseRepository extends PagingAndSortingRepository<Response, Long>{
- @Query("MATCH (r:Response) RETURN DISTINCT r.description")
- List<String> findAllResponses();
-
@Query("MATCH (m:ModelCreation)--(ts:TreatmentSummary)--(tp:TreatmentProtocol)--(r:Response) RETURN DISTINCT r.description")
List<String> findAllSpecimenDrugResponses();
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/SampleRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/SampleRepository.java
index f6cb8bfb31f980cb62013c0f96b44e3d5ee0a033..c1163101e9e8c1f12f4c0ea5c5a9b3f869baf411 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/SampleRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/SampleRepository.java
@@ -1,16 +1,11 @@
package org.pdxfinder.graph.repositories;
-
-import org.pdxfinder.graph.dao.ModelCreation;
import org.pdxfinder.graph.dao.Sample;
import org.springframework.data.neo4j.annotation.Query;
import org.springframework.data.repository.PagingAndSortingRepository;
import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
-
import java.util.Collection;
-import java.util.List;
-import java.util.Set;
/**
* Repository for managing creating, finding, and deleting sample objects
@@ -21,71 +16,9 @@ public interface SampleRepository extends PagingAndSortingRepository<Sample, Lon
@Query("MATCH (s:Sample) WHERE s.sourceSampleId = {sourceSampleId} AND s.dataSource = {dataSource} return s")
Sample findBySourceSampleIdAndDataSource(@Param("sourceSampleId") String sourceSampleId, @Param("dataSource") String dataSource) ;
- Set<Sample> findByDataSource(String dataSource);
-
- @Query("MATCH (s:Sample)-[o:ORIGIN_TISSUE]-(t:Tissue) where s.diagnosis contains {diag} return s,o,t order by s.diagnosis limit 30")
- Collection<Sample> findByDiagnosisContains(@Param("diag") String diag);
-
- @Query("MATCH (s:Sample)-[o:ORIGIN_TISSUE]-(t:Tissue) " +
- "MATCH (s:Sample)--(:MolecularCharacterization)--(:MarkerAssociation)--(m:Marker) " +
- "WHERE toLower(s.diagnosis) CONTAINS toLower({diag}) " +
- "AND m.name IN {markers} return s,o,t")
- Collection<Sample> findByDiagnosisContainsAndHaveMarkers(@Param("diag") String diag, @Param("markers") String[] markers);
-
-
- @Query("MATCH (s:Sample)-[o:ORIGIN_TISSUE]-(t:Tissue) " +
- "MATCH (s:Sample)-[cb:CHARACTERIZED_BY]-(mc:MolecularCharacterization)-[aw:ASSOCIATED_WITH]-(ma:MarkerAssociation)-[mar:MARKER]-(m:Marker) " +
- "MATCH (s:Sample)-[ot:OF_TYPE]-(tt:TumorType) " +
- "MATCH (s:Sample)-[ii:IMPLANTED_IN]-(mod:ModelCreation) "+
- "WHERE (toLower(s.diagnosis) CONTAINS toLower({diag}) OR {diag}='') " +
- "AND (m.name IN {markers} OR {markers}=[]) " +
- "AND (s.dataSource IN {dataSource} OR {dataSource}=[]) " +
- "AND (tt.name IN {tumorType} OR {tumorType}=[]) " +
- "RETURN s,o,t,ot, tt, mc, ma, m, mar, cb, aw, ii, mod")
- Collection<Sample> findByMultipleFilters(@Param("diag") String diag, @Param("markers") String[] markers,
- @Param("dataSource") String[] dataSource, @Param("tumorType") String[] tumorType);
-
-
-
- @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) " +
- "WHERE mod.sourcePdxId = {sourcePdxId} " +
- "WITH s, mod, ii " +
- "OPTIONAL MATCH (s)-[o:ORIGIN_TISSUE]-(t:Tissue) " +
- "OPTIONAL MATCH (s)-[cb:CHARACTERIZED_BY]-(mc:MolecularCharacterization)-[aw:ASSOCIATED_WITH]-(ma:MarkerAssociation)-[mar:MARKER]-(m:Marker) " +
- "OPTIONAL MATCH (s)-[ot:OF_TYPE]-(tt:TumorType) " +
- "RETURN mod,ii,s,o,t,ot, tt, mc, ma, m, mar, cb, aw")
- Sample findBySourcePdxId(@Param("sourcePdxId") String sourcePdxId);
-
-
- @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) " +
- "WHERE mod.sourcePdxId = {sourcePdxId} " +
- "AND toLower(s.dataSource) = toLower({dataSource}) " +
- "WITH s, mod, ii " +
- "OPTIONAL MATCH (s)-[o:ORIGIN_TISSUE]-(t:Tissue) " +
- "OPTIONAL MATCH (s)-[ssr:SAMPLE_SITE]-(ss:Tissue) " +
-
- "OPTIONAL MATCH (s)-[cb:CHARACTERIZED_BY]-(mc:MolecularCharacterization)-[aw:ASSOCIATED_WITH]-(ma:MarkerAssociation)-[mar:MARKER]-(m:Marker) " +
- "OPTIONAL MATCH (s)-[ot:OF_TYPE]-(tt:TumorType) " +
- "OPTIONAL MATCH (s)-[mapped:MAPPED_TO]-(oterm:OntologyTerm) " +
- "RETURN mod,ii,s,o,t,ot, tt, mc, ma, m, mar, cb, aw, mapped, oterm, ssr, ss")
- Sample findByDataSourceAndPdxId(@Param("dataSource") String dataSource, @Param("sourcePdxId") String sourcePdxId);
-
-
- @Query("MATCH (p:Patient--(ps:PatientSnapshot)--(s:Sample) " +
- "WHERE p.externalId = {patientId} " +
- "AND p.dataSource = {dataSource} " +
- "AND s.sourceSampleId = {sampleId} " +
- "RETURN s")
- Sample findHumanSampleByPatientIdAndDataSourceAndSampleId(@Param("patientId") String patientId,
- @Param("dataSource") String dataSource,
- @Param("sampleId") String sampleId);
-
@Query("MATCH (ps:PatientSnapshot)--(s:Sample) WHERE s.dataSource = {dataSource} AND s.sourceSampleId = {sampleId} RETURN s")
Sample findHumanSampleBySampleIdAndDataSource(@Param("sampleId") String sampleId, @Param("dataSource") String dataSource);
- @Query("MATCH (sp:Specimen)--(s:Sample) WHERE s.sourceSampleId = {sampleId} AND s.dataSource = {dataSource} RETURN s")
- Sample findMouseSampleBySampleIdAndDataSource(@Param("sampleId") String sampleId, @Param("dataSource") String dataSource);
-
@Query("MATCH (ps:PatientSnapshot)--(s:Sample) RETURN count(s)")
int findHumanSamplesNumber();
@@ -96,45 +29,9 @@ public interface SampleRepository extends PagingAndSortingRepository<Sample, Lon
"RETURN s, ot,t, oft, tt SKIP {from} LIMIT {to}")
Collection<Sample> findHumanSamplesFromTo(@Param("from") int from, @Param("to") int to);
- @Query("MATCH (ps:PatientSnapshot)-[sf:SAMPLED_FROM]-(s:Sample) WHERE NOT (s)-[:MAPPED_TO]-() " +
- "WITH s " +
- "OPTIONAL MATCH (s)-[ot:ORIGIN_TISSUE]-(ti:Tissue) " +
- "OPTIONAL MATCH (s)-[oft:OF_TYPE]-(t:TumorType) " +
- "RETURN DISTINCT s, ti, t, ot, oft ORDER BY s.diagnosis")
- Collection<Sample> findSamplesWithoutOntologyMapping();
-
-
@Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) WHERE mod.sourcePdxId = {modelId} AND mod.dataSource = {ds} RETURN s")
Sample findHumanSampleByModelIdAndDS(@Param("modelId") String modelId, @Param("ds") String ds);
- @Query("MATCH (mod:ModelCreation)--(sp:Specimen)--(s:Sample)" +
- "WHERE mod.sourcePdxId = {modelId} " +
- "AND mod.dataSource = {ds} " +
- "AND sp.externalId = {specimenId} " +
- "RETURN s")
- Sample findMouseSampleByModelIdAndDataSourceAndSpecimenId(@Param("modelId") String modelId, @Param("ds") String dataSource, @Param("specimenId") String specimenId);
-
-
- @Query("MATCH (ps:PatientSnapshot)-[sf:SAMPLED_FROM]-(s:Sample) " +
- "WHERE NOT (s)-[:MAPPED_TO]-() " +
- "AND s.dataSource = {ds}" +
- "WITH s " +
- "OPTIONAL MATCH (s)-[ot:ORIGIN_TISSUE]-(ti:Tissue) " +
- "OPTIONAL MATCH (s)-[oft:OF_TYPE]-(t:TumorType) " +
- "RETURN DISTINCT s, ti, t, ot, oft ORDER BY s.diagnosis")
- Collection<Sample> findSamplesWithoutOntologyMappingByDataSource(@Param("ds") String dataSource);
-
-
- @Query("MATCH (mod:ModelCreation)--(sp:Specimen)--(s:Sample) " +
- "WHERE mod.sourcePdxId = {modelId} " +
- "AND mod.dataSource = {ds} " +
- "AND s.sourceSampleId = {sampleId} " +
- "WITH s " +
- "OPTIONAL MATCH (s)-[cb:CHARACTERIZED_BY]-(mc:MolecularCharacterization) " +
- "RETURN s, cb, mc"
- )
- Sample findMouseSampleWithMolcharByModelIdAndDataSourceAndSampleId(@Param("modelId") String modelId, @Param("ds") String ds, @Param("sampleId") String sampleId);
-
@Query("MATCH (mod:ModelCreation)--(s:Sample)--(ps:PatientSnapshot) " +
"WHERE mod.sourcePdxId = {modelId} " +
@@ -146,17 +43,7 @@ public interface SampleRepository extends PagingAndSortingRepository<Sample, Lon
Sample findHumanSampleWithMolcharByModelIdAndDataSource(@Param("modelId") String modelId, @Param("ds") String ds);
- @Query("MATCH (mod:ModelCreation)--(sp:Specimen)--(hs:HostStrain) " +
- "WHERE mod.sourcePdxId = {modelId} " +
- "AND mod.dataSource = {ds} " +
- "AND hs.symbol = {nomenclature} " +
- "AND sp.passage = {passage}" +
- "WITH sp " +
- "MATCH (sp)--(s:Sample) " +
- "RETURN s")
- Sample findMouseSampleByModelIdAndDataSourceAndPassageAndNomenclature(@Param("modelId") String modelId, @Param("ds") String dataSource, @Param("passage") String passage, @Param("nomenclature") String nomenclature);
-
-@Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) " +
+ @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(s:Sample) " +
"WHERE mod.sourcePdxId = {sourcePdxId} " +
"AND toLower(mod.dataSource) = toLower({dataSource}) " +
"WITH s " +
@@ -173,17 +60,4 @@ public interface SampleRepository extends PagingAndSortingRepository<Sample, Lon
"RETURN s")
Sample findSampleByMolcharId(@Param("id") Long id);
-
- @Query("MATCH (mod:ModelCreation)-[ii:IMPLANTED_IN]-(samp:Sample) " +
- "-[char:CHARACTERIZED_BY]-(molchar:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation)-[aw:MARKER]-(m:Marker) WHERE molchar.type={molcharType} " +
- " WITH mod, ii, samp, char,molchar, assoc,mAss, aw,m " +
- " MATCH (molchar)-[pl:PLATFORM_USED]-(tech:Platform) " +
- " WHERE mod.dataSource = {dataSource} " +
- " AND mod.sourcePdxId = {modelId} " +
-
- " RETURN ii, samp, char,molchar, assoc,mAss, aw,m,pl,tech ")
- Sample findHumanSampleBySourcePdxIdAndMolcharType(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("molcharType") String molcharType);
-
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/SpecimenRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/SpecimenRepository.java
index 0c53c3fe80a8e77f8aeccdc3041c9476d1444b92..34763b4bc9692541050146ffe44f34a1d0ffa4ed 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/SpecimenRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/SpecimenRepository.java
@@ -40,43 +40,6 @@ public interface SpecimenRepository extends Neo4jRepository<Specimen, Long> {
@Param("specimenId") String specimenId,
@Param("passage") String passage);
- @Query("MATCH (mod:ModelCreation)--(spec:Specimen) " +
- "WHERE mod.dataSource = {dataSource} " +
- "AND mod.sourcePdxId = {modelId} " +
- "AND spec.passage = {passage} " +
- "RETURN spec")
- List<Specimen> findByModelIdAndDataSourceAndAndPassage(
- @Param("modelId") String modelId,
- @Param("dataSource") String dataSource,
- @Param("passage") String passage);
-
-
- @Query("MATCH (mod:ModelCreation)-[sp:SPECIMENS]-(spec:Specimen)-[sfrm:SAMPLED_FROM]-(msamp:Sample)" +
- "-[char:CHARACTERIZED_BY]-(molchar:MolecularCharacterization)-[assoc:ASSOCIATED_WITH]->(mAss:MarkerAssociation)-[aw:MARKER]-(m:Marker) WHERE molchar.type={molcharType} " +
- " WITH mod, sp, spec, sfrm,msamp, char,molchar, assoc,mAss, aw,m " +
- " MATCH (molchar)-[pl:PLATFORM_USED]-(tech:Platform) " +
-
- " WHERE mod.dataSource = {dataSource} " +
- " AND mod.sourcePdxId = {modelId} " +
-
- " RETURN spec, sp, sfrm,msamp, char,molchar, assoc,mAss, aw,m,pl,tech ")
- List<Specimen> findSpecimenBySourcePdxId(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("molcharType") String molcharType);
-
-
-
- @Query("MATCH (mod:ModelCreation)-[spr:SPECIMENS]-(sp:Specimen) " +
- "WHERE mod.dataSource = {dataSource} " +
- "AND mod.sourcePdxId = {modelId} " +
- "WITH sp " +
- "OPTIONAL MATCH (sp)-[etr:ENGRAFTMENT_TYPE]-(et:EngraftmentType) " +
- "OPTIONAL MATCH (sp)-[esr:ENGRAFTMENT_SITE]-(es:EngraftmentSite) " +
- "OPTIONAL MATCH (sp)-[emr:ENGRAFTMENT_MATERIAL]-(em:EngraftmentMaterial) " +
- "OPTIONAL MATCH (sp)-[hsr:HOST_STRAIN]-(hs:HostStrain) " +
- "RETURN sp, etr, et, esr, es, emr, em, hsr, hs")
- List<Specimen> findByDataSourceAndModelId(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId);
@Query("MATCH (mod:ModelCreation)-[sp:SPECIMENS]-(spec:Specimen)-[sfrm:SAMPLED_FROM]-(msamp:Sample) " +
" -[char:CHARACTERIZED_BY]-(molchar:MolecularCharacterization) " +
@@ -92,52 +55,6 @@ public interface SpecimenRepository extends Neo4jRepository<Specimen, Long> {
@Param("modelId") String modelId,
@Param("tech") String tech);
-
-
- @Query("MATCH (mod:ModelCreation)--(spec:Specimen)--(msamp:Sample)--(molchar:MolecularCharacterization)-->(mAss:MarkerAssociation)--(m:Marker) " +
- " WITH mod,spec,msamp,molchar,mAss,m " +
- " MATCH (molchar)--(tech:Platform) " +
-
- " WHERE mod.dataSource = {dataSource} " +
- " AND mod.sourcePdxId = {modelId} " +
- " AND (tech.name = {tech} OR {tech} = '' ) " +
- " AND (spec.passage = {passage} OR {passage} = '' )" +
-
- " AND ( toLower(spec.externalId) CONTAINS toLower({search})" +
- " OR toLower(m.hgncSymbol) CONTAINS toLower({search})" +
- " OR toLower(tech.name) CONTAINS toLower({search})" +
- " OR any( property in keys(mAss) where toLower(mAss[property]) CONTAINS toLower({search}) ) ) " +
- " RETURN count(*) ")
- Integer countBySearchParameterAndPlatform(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("tech") String tech,
- @Param("passage") String passage,
- @Param("search") String search);
-
-
-
- @Query("MATCH (mod:ModelCreation)--(spec:Specimen)--(msamp:Sample)--(molchar:MolecularCharacterization)-->(mAss:MarkerAssociation)--(m:Marker) " +
- " WITH mod,spec,msamp,molchar,mAss,m " +
- " MATCH (molchar)--(tech:Platform) " +
-
- " WHERE mod.dataSource = {dataSource} " +
- " AND mod.sourcePdxId = {modelId} " +
- " AND (tech.name = {tech} OR {tech} = '' ) " +
- " AND (spec.passage = {passage} OR {passage} = '' )" +
-
- " RETURN count(*) ")
- Integer countByPlatform(@Param("dataSource") String dataSource,
- @Param("modelId") String modelId,
- @Param("tech") String tech,
- @Param("passage") String passage);
-
-
- @Query("MATCH (mod:ModelCreation)--(sp:Specimen) WHERE mod.sourcePdxId = {modelId} AND mod.dataSource = {dataSource} RETURN sp")
- List<Specimen> findByModelIdAndDataSource(@Param("modelId") String modelId, @Param("dataSource") String dataSource);
-
-
-
-
@Query("MATCH (mod:ModelCreation)--(sp:Specimen)--(hs:HostStrain) " +
"WHERE id(mod) = {model} " +
"AND sp.passage = {passage} " +
@@ -147,7 +64,6 @@ public interface SpecimenRepository extends Neo4jRepository<Specimen, Long> {
"RETURN sp, sfr, s, cbr, mc, pur, pl")
Specimen findByModelAndPassageAndNomenClature(@Param("model") ModelCreation modelCreation, @Param("passage") String passage, @Param("symbol") String nomenclature);
-
@Query("MATCH (sp:Specimen)--(s:Sample)--(mc:MolecularCharacterization) " +
"WHERE id(mc) = {mc} " +
"RETURN sp")
@@ -159,8 +75,4 @@ public interface SpecimenRepository extends Neo4jRepository<Specimen, Long> {
"OPTIONAL MATCH (sp)-[sfr:SAMPLED_FROM]-(s:Sample)-[cbr:CHARACTERIZED_BY]-(mc:MolecularCharacterization)-[pur:PLATFORM_USED]-(pl:Platform) " +
"RETURN sp, sfr, s, cbr, mc, pur, pl")
List<Specimen> findAllWithMolcharDataByModel(@Param("model") ModelCreation model);
-
-
-
-
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentProtocolRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentProtocolRepository.java
index 904dcb88bec6c949daf6efdc77a2907b9c73e30f..b8165dc4741b8dfbec2ba6b68a59c3071df95016 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentProtocolRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentProtocolRepository.java
@@ -1,11 +1,9 @@
package org.pdxfinder.graph.repositories;
import org.pdxfinder.graph.dao.TreatmentProtocol;
-import org.springframework.data.neo4j.annotation.Query;
import org.springframework.data.neo4j.repository.Neo4jRepository;
import org.springframework.stereotype.Repository;
-import java.util.List;
/*
* Created by csaba on 23/10/2017.
@@ -14,11 +12,4 @@ import java.util.List;
public interface TreatmentProtocolRepository extends Neo4jRepository<TreatmentProtocol, Long> {
-
- @Query("MATCH (tp:TreatmentProtocol) RETURN DISTINCT tp.drug")
- List<List<String>> findDrugNames();
-
-
-
-
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentRepository.java
index bd6ccc1465abe7bace422cf2ace0ac3e484fd705..a8c116bb16bb158427508b58be7ab5af00abb703 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentRepository.java
@@ -23,15 +23,6 @@ public interface TreatmentRepository extends Neo4jRepository<Treatment, Long> {
int findPatientTreatmentNumberByDS(@Param("ds") String ds);
- @Query("MATCH (mod:ModelCreation)--(ts:TreatmentSummary) RETURN count(ts) ")
- int findModelTreatmentNumber();
-
- @Query("MATCH (mod:ModelCreation)--(ts:TreatmentSummary) " +
- "WHERE mod.dataSource = {ds} "+
- "RETURN count(ts) ")
- int findModelTreatmentNumberByDS(@Param("ds") String ds);
-
-
@Query("MATCH (ps:PatientSnapshot)--(ts:TreatmentSummary)" +
"WITH ts SKIP {from} LIMIT {batch}"+
"MATCH (ts)-[tpr:TREATMENT_PROTOCOL]-(tp:TreatmentProtocol)-[tcr:TREATMENT_COMPONENT]-(tc:TreatmentComponent)--(tr:Treatment) "+
@@ -63,6 +54,4 @@ public interface TreatmentRepository extends Neo4jRepository<Treatment, Long> {
"return COLLECT(distinct gr.abbreviation+ '___' + toLower(t.name)) as abbrAndTreatmentName")
TreatmentMappingData getUnmappedPatientTreatments();
-
-
}
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentSummaryRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentSummaryRepository.java
index 700de6d1876b4366905b3af816203f1d1560d378..7faf61058acf0d841ff715eeaa378aa35f169e90 100644
--- a/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentSummaryRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentSummaryRepository.java
@@ -39,11 +39,6 @@ public interface TreatmentSummaryRepository extends Neo4jRepository<TreatmentSum
@Query("MATCH (mod:ModelCreation)--(ts:TreatmentSummary) WHERE toLower(mod.dataSource) = toLower({dataSource}) AND EXISTS(ts.url) RETURN ts.url LIMIT 1")
String findPlatformUrlByDataSource(@Param("dataSource") String dataSource);
- @Query("MATCH (ts:TreatmentSummary)-[tpr:TREATMENT_PROTOCOL]-(tp:TreatmentProtocol)-[tcr:TREATMENT_COMPONENT]-(tc:TreatmentComponent)-[dr:TREATMENT]-(d:Treatment) " +
- "MATCH (tp)-[rr:RESPONSE]-(r:Response) " +
- "RETURN ts, tpr, tp, tcr, tc, dr, d, rr, r")
- List<TreatmentSummary> findAllWithDrugData();
-
@Query("MATCH (mod:ModelCreation)--(ts:TreatmentSummary)-[tpr:TREATMENT_PROTOCOL]-(tp:TreatmentProtocol)-[tcr:TREATMENT_COMPONENT]-(tc:TreatmentComponent)-[dr:TREATMENT]-(d:Treatment)-[mtr:MAPPED_TO]-(ot:OntologyTerm) " +
"MATCH (tp)-[rr:RESPONSE]-(r:Response) " +
"OPTIONAL MATCH (ot)-[sor:SUBCLASS_OF]-(ot2:OntologyTerm) " +
diff --git a/data-model/src/main/java/org/pdxfinder/rdbms/dao/MappingEntity.java b/data-model/src/main/java/org/pdxfinder/rdbms/dao/MappingEntity.java
index a200150b972787ae570e265b7e3d1d2ba1c4b30d..329d199e6a1d88eb76dbbbbea6bb4818355b0474 100644
--- a/data-model/src/main/java/org/pdxfinder/rdbms/dao/MappingEntity.java
+++ b/data-model/src/main/java/org/pdxfinder/rdbms/dao/MappingEntity.java
@@ -109,7 +109,7 @@ public class MappingEntity {
* The unique String that identifies a Mapping
*/
@JsonIgnore
- @Column(unique = true, nullable = false, columnDefinition="Text")
+ @Column(nullable = false, columnDefinition="Text")
private String mappingKey;
diff --git a/data-model/src/main/java/org/pdxfinder/rdbms/repositories/MappingEntityRepository.java b/data-model/src/main/java/org/pdxfinder/rdbms/repositories/MappingEntityRepository.java
index eb3bcba371613120628018eeafcf8d203cd54987..1809dd6f93e8e3f1cecd8ae9966434e7200ef845 100644
--- a/data-model/src/main/java/org/pdxfinder/rdbms/repositories/MappingEntityRepository.java
+++ b/data-model/src/main/java/org/pdxfinder/rdbms/repositories/MappingEntityRepository.java
@@ -9,7 +9,6 @@ import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
import java.util.List;
-import java.util.Map;
import java.util.Optional;
@@ -46,19 +45,15 @@ public interface MappingEntityRepository extends JpaRepository<MappingEntity, Lo
Pageable pageable);
-
@Query(value = "select me from MappingEntity me JOIN me.mappingValues mv WHERE KEY(mv) = :dataKey AND mv = :dataValue ")
List<MappingEntity> findByAttributeAndValue(@Param("dataKey") String dataKey,
@Param("dataValue") String dataValue);
-
List<MappingEntity> findByEntityTypeAndMapTypeIsNotNull(String entityType);
List<MappingEntity> findByEntityTypeAndStatusIsNot(String entityType, String statusIsNot);
-
-
-
+ boolean existsByEntityId(Long entityId);
@Query("SELECT distinct lower(mv), " +
" count(case when me.status = 'unmapped' THEN 1 END) as unmapped, " +
diff --git a/data-model/src/test/java/org/pdxfinder/BaseTestWithPersistence.java b/data-model/src/test/java/org/pdxfinder/BaseTestWithPersistence.java
deleted file mode 100644
index 21c2647449522a8e9c50d72cbe9b1c35f8021992..0000000000000000000000000000000000000000
--- a/data-model/src/test/java/org/pdxfinder/BaseTestWithPersistence.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package org.pdxfinder;
-
-import org.junit.Ignore;
-import org.junit.runner.RunWith;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.TestPropertySource;
-import org.springframework.test.context.junit4.SpringRunner;
-import org.springframework.transaction.annotation.Transactional;
-
-@RunWith(SpringRunner.class)
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.NONE)
-@ContextConfiguration(classes = {TestConfigWithPersistence.class})
-@TestPropertySource(locations = {"classpath:ogm.properties"})
-@Transactional
-@Ignore
-public class BaseTestWithPersistence {
-
-}
diff --git a/data-model/src/test/java/org/pdxfinder/TestConfig.java b/data-model/src/test/java/org/pdxfinder/TestConfig.java
index 47c6166c99277adb1e196562256a257a20499828..f07a6fc8a44b8437d1fc0fd10bab992c386edde3 100644
--- a/data-model/src/test/java/org/pdxfinder/TestConfig.java
+++ b/data-model/src/test/java/org/pdxfinder/TestConfig.java
@@ -19,7 +19,7 @@ public class TestConfig{
@Bean
public org.neo4j.ogm.config.Configuration getConfiguration() {
- return new org.neo4j.ogm.config.Configuration();
+ return new org.neo4j.ogm.config.Configuration.Builder().build();
}
@Bean
diff --git a/data-model/src/test/java/org/pdxfinder/TestConfigWithPersistence.java b/data-model/src/test/java/org/pdxfinder/TestConfigWithPersistence.java
deleted file mode 100644
index ba46bc22a7ef35253ef93ecc9ae6898744efc5b8..0000000000000000000000000000000000000000
--- a/data-model/src/test/java/org/pdxfinder/TestConfigWithPersistence.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package org.pdxfinder;
-
-import org.neo4j.ogm.session.SessionFactory;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.data.neo4j.repository.config.EnableNeo4jRepositories;
-import org.springframework.data.neo4j.transaction.Neo4jTransactionManager;
-import org.springframework.transaction.annotation.EnableTransactionManagement;
-
-import java.nio.file.Paths;
-
-@Configuration
-@EnableTransactionManagement
-@ComponentScan(value = "org.pdxfinder")
-@EnableNeo4jRepositories("org.pdxfinder.graph.repositories")
-public class TestConfigWithPersistence {
-
- @Bean
- public org.neo4j.ogm.config.Configuration getConfiguration() {
- org.neo4j.ogm.config.Configuration config = new org.neo4j.ogm.config.Configuration();
-
- String pathToDb = Paths.get(".").toAbsolutePath().normalize().toString() + "/target/test_graph.db";
- config
- .driverConfiguration()
- .setDriverClassName("org.neo4j.ogm.drivers.embedded.driver.EmbeddedDriver")
- .setURI("file://" + pathToDb);
-
- System.out.println(config);
-
- return config;
- }
-
- @Bean
- public SessionFactory sessionFactory() {
- return new SessionFactory(getConfiguration(), "org.pdxfinder");
- }
-
- @Bean
- public Neo4jTransactionManager transactionManager() {
- return new Neo4jTransactionManager(sessionFactory());
- }
-
-}
-
-
diff --git a/data-model/src/test/java/org/pdxfinder/graph/dao/DataProjectionsTimeTest.java b/data-model/src/test/java/org/pdxfinder/graph/dao/DataProjectionsTimeTest.java
index 2f19158e8340c219aeee727e56cd4e8ec5dd5d6b..33187f84346b4f7a622ab4b1ef392d25ae588bdb 100644
--- a/data-model/src/test/java/org/pdxfinder/graph/dao/DataProjectionsTimeTest.java
+++ b/data-model/src/test/java/org/pdxfinder/graph/dao/DataProjectionsTimeTest.java
@@ -3,7 +3,7 @@ package org.pdxfinder.graph.dao;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
-import org.pdxfinder.BaseTestWithPersistence;
+import org.pdxfinder.BaseTest;
import org.pdxfinder.graph.repositories.DataProjectionRepository;
import org.springframework.beans.factory.annotation.Autowired;
@@ -12,7 +12,7 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Random;
-public class DataProjectionsTimeTest extends BaseTestWithPersistence {
+public class DataProjectionsTimeTest extends BaseTest {
private static final String LABEL = "TEST";
diff --git a/data-model/src/test/java/org/pdxfinder/graph/dao/MarkerAssociationTest.java b/data-model/src/test/java/org/pdxfinder/graph/dao/MarkerAssociationTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..d4c6abda3979074a8facd644e2ae9604aef1f60b
--- /dev/null
+++ b/data-model/src/test/java/org/pdxfinder/graph/dao/MarkerAssociationTest.java
@@ -0,0 +1,27 @@
+package org.pdxfinder.graph.dao;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.Collections;
+
+public class MarkerAssociationTest {
+
+
+
+ @Test
+ public void Given_MarkerAssociation_When_EncodeIsCalled_Then_DataInRightFormat(){
+
+ MarkerAssociation ma = new MarkerAssociation();
+ MolecularData md = new MolecularData();
+ md.setMarker("KRAS");
+
+ ma.setMolecularDataList(Collections.singletonList(md));
+
+ ma.encodeMolecularData();
+
+ Assert.assertEquals(1, ma.getDataPoints());
+
+ }
+
+}
diff --git a/data-model/src/test/java/org/pdxfinder/graph/dao/PatientSnapshotTest.java b/data-model/src/test/java/org/pdxfinder/graph/dao/PatientSnapshotTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c052a6ae189141b829ce420f3b95159565f9b89b
--- /dev/null
+++ b/data-model/src/test/java/org/pdxfinder/graph/dao/PatientSnapshotTest.java
@@ -0,0 +1,48 @@
+package org.pdxfinder.graph.dao;
+
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.HashSet;
+
+
+public class PatientSnapshotTest {
+
+ @Test
+ public void given_PatientSnapshot_when_PaediatricAge_then_AgeBinCorrect(){
+ Patient patient = new Patient("test1", new Group());
+
+ PatientSnapshot patientSnapshot1 = new PatientSnapshot(patient, "1", new HashSet<>(), new TreatmentSummary());
+ PatientSnapshot patientSnapshot2 = new PatientSnapshot(patient, "12mo", new HashSet<>());
+ patientSnapshot2.addSample(new Sample("sample123"));
+ PatientSnapshot patientSnapshot3 = new PatientSnapshot(patient, "26mo", "", "", "");
+ PatientSnapshot patientSnapshot4 = new PatientSnapshot(patient, "5", "", "", "");
+ PatientSnapshot patientSnapshot5 = new PatientSnapshot(patient, "15", "", "", "");
+ PatientSnapshot patientSnapshot6 = new PatientSnapshot(patient, "25", "", "", "");
+ PatientSnapshot patientSnapshot7 = new PatientSnapshot(patient, "35", "", "", "");
+ PatientSnapshot patientSnapshot8 = new PatientSnapshot(patient, "45", "", "", "");
+ PatientSnapshot patientSnapshot9 = new PatientSnapshot(patient, "55", "", "", "");
+ PatientSnapshot patientSnapshot10 = new PatientSnapshot(patient, "65", "", "", "");
+ PatientSnapshot patientSnapshot11 = new PatientSnapshot(patient, "75", "", "", "");
+ PatientSnapshot patientSnapshot12 = new PatientSnapshot(patient, "85", "", "", "");
+ PatientSnapshot patientSnapshot13 = new PatientSnapshot(patient, "95", "", "", "");
+
+
+ Assert.assertEquals(patientSnapshot1.getAgeBin(), "0-23 months");
+ Assert.assertEquals(patientSnapshot2.getAgeBin(), "0-23 months");
+ Assert.assertEquals(patientSnapshot3.getAgeBin(), "2-9");
+ Assert.assertEquals(patientSnapshot4.getAgeBin(), "2-9");
+ Assert.assertEquals(patientSnapshot5.getAgeBin(), "10-19");
+ Assert.assertEquals(patientSnapshot6.getAgeBin(), "20-29");
+ Assert.assertEquals(patientSnapshot7.getAgeBin(), "30-39");
+ Assert.assertEquals(patientSnapshot8.getAgeBin(), "40-49");
+ Assert.assertEquals(patientSnapshot9.getAgeBin(), "50-59");
+ Assert.assertEquals(patientSnapshot10.getAgeBin(), "60-69");
+ Assert.assertEquals(patientSnapshot11.getAgeBin(), "70-79");
+ Assert.assertEquals(patientSnapshot12.getAgeBin(), "80-89");
+ Assert.assertEquals(patientSnapshot13.getAgeBin(), "90+");
+ Assert.assertEquals(false, patientSnapshot2.equals(patientSnapshot3));
+ }
+
+}
diff --git a/data-model/src/test/java/org/pdxfinder/graph/repositories/AllLookupNodeRepositoriesTest.java b/data-model/src/test/java/org/pdxfinder/graph/repositories/AllLookupNodeRepositoriesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..86aeea9bc607ff4c2bd8622cb7f6d33c16b09000
--- /dev/null
+++ b/data-model/src/test/java/org/pdxfinder/graph/repositories/AllLookupNodeRepositoriesTest.java
@@ -0,0 +1,138 @@
+package org.pdxfinder.graph.repositories;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.transaction.BeforeTransaction;
+
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Tests for the Sample Type repository
+ */
+public class AllLookupNodeRepositoriesTest extends BaseTest {
+
+ private final static Logger log = LoggerFactory.getLogger(AllLookupNodeRepositoriesTest.class);
+
+ private static final String TISSUE_NAME = "TEST_TISSUE";
+ private static final String BACKGROUND_STRAIN = "TEST_BACKGROUND_STRAIN";
+ private static final String IMPLANTATION_TYPE = "TEST_IMPLANTATION_TYPE";
+ private static final String IMPLANTATION_SITE = "TEST_IMPLANTATION_SITE";
+
+ @Autowired
+ private
+ TumorTypeRepository tumorTypeRepository;
+
+ @Autowired
+ private TissueRepository tissueRepository;
+
+ @Autowired
+ private HostStrainRepository hostStrainRepository;
+
+ @Autowired
+ private EngraftmentSiteRepository engraftmentSiteRepository;
+
+ @Autowired
+ private EngraftmentTypeRepository engraftmentTypeRepository;
+
+
+ @Before
+ public void setupDb() {
+ }
+
+ @Rollback(false)
+ @BeforeTransaction
+ public void cleanDb() {
+ tumorTypeRepository.deleteAll();
+ tissueRepository.deleteAll();
+ }
+
+
+ @Test
+ public void createTumorTypes() throws Exception {
+
+ List<String> types = Arrays.asList("Metastasis", "Metastatic", "Not Specified", "Primary Malignancy", "Recurrent/Relapse");
+
+ for (String type : types) {
+ TumorType foundType = tumorTypeRepository.findByName(type);
+ if (foundType == null) {
+ log.debug("Sample type {} not found. Creating", type);
+ foundType = new TumorType(type);
+ tumorTypeRepository.save(foundType);
+ }
+
+ foundType = tumorTypeRepository.findByName(type);
+ log.info(" Found Sample type {}", foundType.getName());
+
+ assert (foundType.getName().equals(type));
+
+ }
+
+ }
+
+ @Test
+ public void createTissue() {
+
+ Tissue tissue = tissueRepository.findByName(TISSUE_NAME);
+ if (tissue == null) {
+ log.debug("Tissue {} not found. Creating", TISSUE_NAME);
+ tissue = new Tissue(TISSUE_NAME);
+ tissueRepository.save(tissue);
+ }
+
+ Assert.assertNotNull(tissueRepository.findByName(TISSUE_NAME));
+ log.info(" Found Tissue {}", tissueRepository.findByName(TISSUE_NAME).getName());
+
+ }
+
+ @Test
+ public void createBackgroundStrain() {
+
+ HostStrain bgStrain = hostStrainRepository.findBySymbol(BACKGROUND_STRAIN);
+ if (bgStrain == null) {
+ log.debug("Background strain {} not found. Creating", BACKGROUND_STRAIN);
+ bgStrain = new HostStrain(BACKGROUND_STRAIN);
+ hostStrainRepository.save(bgStrain);
+ }
+
+ Assert.assertNotNull(hostStrainRepository.findBySymbol(BACKGROUND_STRAIN));
+ log.info(" Found Background Strain {}", hostStrainRepository.findBySymbol(BACKGROUND_STRAIN).getSymbol());
+ }
+
+ @Test
+ public void createImplantationSite() {
+
+ EngraftmentSite site = engraftmentSiteRepository.findByName(IMPLANTATION_SITE);
+ if (site == null) {
+ log.debug("Implantation site {} not found. Creating", IMPLANTATION_SITE);
+ site = new EngraftmentSite(IMPLANTATION_SITE);
+ engraftmentSiteRepository.save(site);
+ }
+
+ Assert.assertNotNull(engraftmentSiteRepository.findByName(IMPLANTATION_SITE));
+ log.info(" Found Implantation Site {}", engraftmentSiteRepository.findByName(IMPLANTATION_SITE).getName());
+ }
+
+ @Test
+ public void createImplantationType() {
+
+ EngraftmentType type = engraftmentTypeRepository.findByName(IMPLANTATION_TYPE);
+ if (type == null) {
+ log.debug("Implantation type {} not found. Creating", IMPLANTATION_TYPE);
+ type = new EngraftmentType(IMPLANTATION_TYPE);
+ engraftmentTypeRepository.save(type);
+ }
+
+ Assert.assertNotNull(engraftmentTypeRepository.findByName(IMPLANTATION_TYPE));
+ log.info(" Found Implantation Type {}", engraftmentTypeRepository.findByName(IMPLANTATION_TYPE).getName());
+
+ }
+
+}
\ No newline at end of file
diff --git a/data-model/src/test/java/org/pdxfinder/graph/repositories/PatientRepositoryTest.java b/data-model/src/test/java/org/pdxfinder/graph/repositories/PatientRepositoryTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c4666365af72caadb48bd6eab1671fc94aeb5eef
--- /dev/null
+++ b/data-model/src/test/java/org/pdxfinder/graph/repositories/PatientRepositoryTest.java
@@ -0,0 +1,68 @@
+package org.pdxfinder.graph.repositories;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.Group;
+import org.pdxfinder.graph.dao.Patient;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.sql.Date;
+import java.time.Instant;
+
+/**
+ * Tests for the Patient data repository
+ */
+
+public class PatientRepositoryTest extends BaseTest {
+
+ private final static Logger log = LoggerFactory.getLogger(PatientRepositoryTest.class);
+ private String extDsName = "TEST_SOURCE";
+ private String extDsAbbrev = "TS";
+
+ @Autowired
+ private GroupRepository groupRepository;
+
+ @Autowired
+ private PatientRepository patientRepository;
+
+ @Before
+ public void setupDb() {
+
+ patientRepository.deleteAll();
+ groupRepository.deleteAll();
+
+ Group ds = groupRepository.findByNameAndType(extDsName, "Provider");
+ if(ds == null){
+ log.info("Group not found. Creating", extDsName);
+
+ ds = new Group(extDsName, extDsAbbrev, "Provider");
+ groupRepository.save(ds);
+
+ }
+ }
+
+ @Test
+ public void persistedPatientShouldBeRetrievableFromGraphDb() throws Exception {
+
+ Group group = groupRepository.findByNameAndType(extDsName, "Provider");
+
+ Patient femalePatient = new Patient("-9999", "F", null, null, group);
+ patientRepository.save(femalePatient);
+
+ Patient foundFemalePatient = patientRepository.findBySex("F").iterator().next();
+ assert (foundFemalePatient != null);
+ assert (foundFemalePatient.getSex().equals("F"));
+
+ log.info(foundFemalePatient.toString());
+
+ patientRepository.delete(patientRepository.findByExternalIdAndGroup("-9999", group));
+ Patient notFoundFemalePatient = patientRepository.findByExternalIdAndGroup("-9999", group);
+ assert (notFoundFemalePatient == null);
+
+
+ }
+
+}
\ No newline at end of file
diff --git a/data-model/src/test/java/org/pdxfinder/graph/repositories/PlatformRepositoryTest.java b/data-model/src/test/java/org/pdxfinder/graph/repositories/PlatformRepositoryTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..804070571e46066dd3a19a8d298afcf4612776a0
--- /dev/null
+++ b/data-model/src/test/java/org/pdxfinder/graph/repositories/PlatformRepositoryTest.java
@@ -0,0 +1,85 @@
+package org.pdxfinder.graph.repositories;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.sql.Date;
+import java.time.Instant;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Testing repository for managing tumor objects
+ */
+public class PlatformRepositoryTest extends BaseTest {
+
+ private final static Logger log = LoggerFactory.getLogger(PlatformRepositoryTest.class);
+ private String extDsName = "TEST_SOURCE";
+ private String extDsAbbrev = "TS";
+ @Autowired
+ private PlatformRepository platformRepository;
+
+ @Autowired
+ private PlatformAssociationRepository platformAssociationRepository;
+
+ @Autowired
+ private GroupRepository groupRepository;
+
+ @Autowired
+ private MarkerRepository markerRepository;
+
+ @Before
+ public void cleanDb() {
+
+ platformRepository.deleteAll();
+ platformAssociationRepository.deleteAll();
+ groupRepository.deleteAll();
+ markerRepository.deleteAll();
+
+ Group ds = groupRepository.findByNameAndType(extDsName, "Provider");
+ if(ds == null){
+ log.info("Group not found. Creating", extDsName);
+
+ ds = new Group(extDsName, extDsAbbrev, "Provider");
+ groupRepository.save(ds);
+
+ }
+
+ }
+
+ @Test
+ public void createPlatformAndAssociateMarkers() throws Exception {
+
+ Set<PlatformAssociation> pas = new HashSet<>();
+
+ for (int i = 0; i < 10; i++) {
+ Marker marker = new Marker();
+ marker.setHgncName("Marker" + i);
+
+ PlatformAssociation p = new PlatformAssociation();
+ p.setMarker(marker);
+ p.setExon("exon " + i);
+ pas.add(p);
+
+ }
+
+ Platform p = new Platform();
+ p.setPlatformAssociations(pas);
+ p.setName("Gene Panel");
+ p.setGroup(groupRepository.findByNameAndType(extDsName, "Provider"));
+
+ platformRepository.save(p);
+
+ assert (platformAssociationRepository.findByPlatform_ExternalDataSource_Name(extDsName).size() > 0);
+ assert platformRepository.findByName("Gene Panel").getPlatformAssociations().stream().count() > 5;
+
+
+ }
+
+
+}
diff --git a/data-model/src/test/java/org/pdxfinder/graph/repositories/SampleRepositoryTest.java b/data-model/src/test/java/org/pdxfinder/graph/repositories/SampleRepositoryTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..0d09e4239af9e0d6863886ac28d8947db4483c34
--- /dev/null
+++ b/data-model/src/test/java/org/pdxfinder/graph/repositories/SampleRepositoryTest.java
@@ -0,0 +1,145 @@
+package org.pdxfinder.graph.repositories;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.sql.Date;
+import java.time.Instant;
+
+/**
+ * Testing repository for managing tumor objects
+ */
+public class SampleRepositoryTest extends BaseTest {
+
+ private final static Logger log = LoggerFactory.getLogger(SampleRepositoryTest.class);
+ private String tumorTypeName = "TEST_TUMORTYPE";
+ private String extDsName = "TEST_SOURCE";
+ private String extDsAbbrev = "TS";
+ private String tissueName = "TEST_TISSUE";
+
+ @Autowired
+ private SampleRepository sampleRepository;
+
+ @Autowired
+ private TissueRepository tissueRepository;
+
+ @Autowired
+ private TumorTypeRepository tumorTypeRepository;
+
+ @Autowired
+ private PatientRepository patientRepository;
+
+ @Autowired
+ private GroupRepository groupRepository;
+
+ @Before
+ public void cleanDb() {
+
+ sampleRepository.deleteAll();
+ patientRepository.deleteAll();
+ groupRepository.deleteAll();
+ tissueRepository.deleteAll();
+
+ TumorType tumorType = tumorTypeRepository.findByName(tumorTypeName);
+ if (tumorType == null) {
+ log.debug("Sample type {} not found. Creating", tumorTypeName);
+ tumorType = new TumorType(tumorTypeName);
+ tumorTypeRepository.save(tumorType);
+ }
+
+ Group ds = groupRepository.findByNameAndType(extDsName, "Provider");
+ if(ds == null){
+ log.info("Group not found. Creating", extDsName);
+
+ ds = new Group(extDsName, extDsAbbrev, "Provider");
+ groupRepository.save(ds);
+
+ }
+
+ Tissue tissue = tissueRepository.findByName(tissueName);
+ if (tissue == null) {
+ log.debug("Tissue {} not found. Creating", extDsName);
+ tissue = new Tissue(tissueName);
+ tissueRepository.save(tissue);
+ }
+
+ }
+
+ @Test
+ public void createTumorInGraphDb() throws Exception {
+
+ // Sample:
+ // String sourceTumorId
+ // TumorType type
+ // String diagnosis
+ // Tissue originTissue
+ // Tissue tumorSite
+ // String classification
+ // ExternalDataSource externalDataSource
+
+ TumorType tumorType = tumorTypeRepository.findByName(tumorTypeName);
+ Tissue tissue = tissueRepository.findByName(tissueName);
+ Group group = groupRepository.findByNameAndType(extDsName, "Provider");
+
+ String TEST_TUMOR_ID = "TESTID-1";
+ generateTumor(tumorType, tissue, group, TEST_TUMOR_ID);
+
+ Sample foundSample = sampleRepository.findBySourceSampleIdAndDataSource(TEST_TUMOR_ID, group.getAbbreviation());
+ Assert.assertNotNull(foundSample);
+
+
+ }
+
+ @Test
+ public void deleteTumor() throws Exception {
+
+ TumorType tumorType = tumorTypeRepository.findByName(tumorTypeName);
+ Tissue tissue = tissueRepository.findByName(tissueName);
+ Group ds = groupRepository.findByNameAndType(extDsName, "Provider");
+
+ String testTumorId = "DELETE_TESTID-1";
+ generateTumor(tumorType, tissue, ds, testTumorId);
+
+ Sample foundSample = sampleRepository.findBySourceSampleIdAndDataSource(testTumorId, ds.getAbbreviation());
+ Assert.assertNotNull(foundSample);
+
+ sampleRepository.delete(foundSample);
+ foundSample = sampleRepository.findBySourceSampleIdAndDataSource(testTumorId, ds.getAbbreviation());
+ Assert.assertNull(foundSample);
+ }
+
+
+ @Test
+ public void deleteMultipleTumorsByDatasource() throws Exception {
+
+ TumorType tumorType = tumorTypeRepository.findByName(tumorTypeName);
+ Tissue tissue = tissueRepository.findByName(tissueName);
+ Group ds = groupRepository.findByNameAndType(extDsName, "Provider");
+
+ for (Integer i = 0; i < 20; i++) {
+ String testTumorId = "TESTID-" + i;
+ generateTumor(tumorType, tissue, ds, testTumorId);
+ }
+
+ Sample foundSample = sampleRepository.findBySourceSampleIdAndDataSource("TESTID-12", ds.getAbbreviation());
+ Assert.assertNotNull(foundSample);
+
+ // Added 20 tumors, count should be 20
+ Assert.assertEquals(20, sampleRepository.count());
+
+
+ }
+//String sourceSampleId, TumorType type, String diagnosis, Tissue originTissue, Tissue sampleSite, String extractionMethod, String classification, Boolean normalTissue
+ private void generateTumor(TumorType tumorType, Tissue tissue, Group group, String TEST_TUMOR_ID) {
+ Sample sample = new Sample(TEST_TUMOR_ID, tumorType, "TEST_DIAGNOSIS", tissue, tissue, "Surgical Resection", "TEST_CLASSIFICATION", false, group.getAbbreviation());
+ sampleRepository.save(sample);
+ }
+
+
+}
diff --git a/data-model/src/test/resources/logback.xml b/data-model/src/test/resources/logback.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6a89304411c6f7825c0392d1c5b6318dc0e688c1
--- /dev/null
+++ b/data-model/src/test/resources/logback.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+ <include resource="org/springframework/boot/logging/logback/base.xml"/>
+ <logger name="org.springframework" level="WARN"/>
+ <logger name="org.springframework.data.neo4j.mapping.Neo4jPersistentProperty" level="ERROR"/>
+ <logger name="org.neo4j" level="WARN"/>
+</configuration>
\ No newline at end of file
diff --git a/indexer/src/test/resources/ogm.properties b/data-model/src/test/resources/ogm.properties
similarity index 55%
rename from indexer/src/test/resources/ogm.properties
rename to data-model/src/test/resources/ogm.properties
index a19ce84a6387ea17c01eedf517d270c3e287df72..e0d9ac7939a5d88c2fe886acb2cb2d0c94ee5640 100644
--- a/indexer/src/test/resources/ogm.properties
+++ b/data-model/src/test/resources/ogm.properties
@@ -1 +1,4 @@
+#
+# Configuration for embedded neo4j for tests
+#
driver=org.neo4j.ogm.drivers.embedded.driver.EmbeddedDriver
diff --git a/data-services/pom.xml b/data-services/pom.xml
index ce9ca9623755b0398334c4f244c547c5b61e3324..d61dc5f0278111a26dae972db21171305679921f 100644
--- a/data-services/pom.xml
+++ b/data-services/pom.xml
@@ -23,15 +23,16 @@
</dependency>
<dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
- <groupId>com.h2database</groupId>
- <artifactId>h2</artifactId>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-core</artifactId>
</dependency>
+
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-csv</artifactId>
@@ -42,13 +43,6 @@
<artifactId>jackson-databind</artifactId>
</dependency>
- <dependency>
- <groupId>org.neo4j</groupId>
- <artifactId>neo4j-ogm-embedded-driver</artifactId>
- <scope>test</scope>
- <version>2.1.1</version>
- </dependency>
-
<dependency>
<groupId>com.google.zxing</groupId>
<artifactId>core</artifactId>
@@ -61,26 +55,25 @@
<version>3.3.0</version>
</dependency>
- <!-- For loading excel documents -->
- <dependency>
- <groupId>org.apache.poi</groupId>
- <artifactId>poi-ooxml</artifactId>
- <version>3.15</version>
- </dependency>
- <dependency>
- <groupId>org.apache.poi</groupId>
- <artifactId>poi</artifactId>
- <version>3.15</version>
- </dependency>
-
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>3.4.2</version>
</dependency>
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j-ogm-embedded-driver</artifactId>
+ <version>3.1.20</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <!-- WARNING, do not update db engine (stable: 1.4.197) cause compatibility issues, see https://github.com/h2database/h2database/issues/2078 -->
+ <groupId>com.h2database</groupId>
+ <artifactId>h2</artifactId>
+ <version>1.4.197</version>
+ </dependency>
</dependencies>
-
</project>
\ No newline at end of file
diff --git a/data-services/src/main/java/org/pdxfinder/services/AutoCompleteService.java b/data-services/src/main/java/org/pdxfinder/services/AutoCompleteService.java
index 3448d647dc4e1f5cc6e7a5b0abf857aec159db18..e35a9e0931a3b6111365f0a0f5445db1444a79eb 100644
--- a/data-services/src/main/java/org/pdxfinder/services/AutoCompleteService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/AutoCompleteService.java
@@ -1,17 +1,11 @@
package org.pdxfinder.services;
-import org.pdxfinder.graph.dao.DataProjection;
import org.pdxfinder.graph.dao.OntologyTerm;
-import org.pdxfinder.graph.repositories.DataProjectionRepository;
import org.pdxfinder.graph.repositories.OntologyTermRepository;
import org.pdxfinder.services.ds.AutoCompleteOption;
-import org.pdxfinder.services.ds.ModelForQuery;
-import org.pdxfinder.services.ds.SearchDS;
import org.springframework.stereotype.Service;
-
import java.util.*;
-import java.util.stream.Collectors;
/*
* Created by csaba on 05/02/2018.
@@ -139,7 +133,6 @@ public class AutoCompleteService {
Set<String> termsToRemove = new HashSet<>(Arrays.asList(doNotDisplay));
-
Collection<OntologyTerm> ontologyTerms = ontologyTermRepository.findAllWithMappings();
List<String> autoSuggestList = new ArrayList<>();
@@ -157,142 +150,9 @@ public class AutoCompleteService {
}
Collections.sort(autoSuggestList);
- return autoSuggestList;
- }
-
- public List<String> getAutoSuggestions(List<String> ids){
- String[] doNotDisplay = {"Neoplasm by Morphology",
- "Neoplasm by Site",
- "Glandular Cell Neoplasm",
- "Digestive System Neoplasm",
- "Intestinal Neoplasm",
- "Colorectal Neoplasm",
- "Melanocytic Neoplasm",
- "Respiratory Tract Neoplasm",
- "Thoracic Neoplasm",
- "Lung Neoplasm",
- "Breast Neoplasm",
- "Colon Neoplasm",
- "Skin Neoplasm",
- "Melanocytic Skin Neoplasm",
- "Urinary System Neoplasm",
- "Nervous System Neoplasm",
- "Central Nervous System Neoplasm",
- "Astrocytic Tumor",
- "Bladder Neoplasm",
- "Pancreatic Neoplasm",
- "Bone Marrow Neoplasm",
- "Pancreatic Exocrine Neoplasm",
- "Breast Carcinoma by Gene Expression Profile",
- "Reproductive System Neoplasm",
- "Endocrine Neoplasm",
- "Myomatous Neoplasm",
- "Female Reproductive System Neoplasm",
- "Sarcoma by NCI Grade",
- "Sarcoma NCI Grade 3",
- "Ovarian Neoplasm",
- "Ovarian Epithelial Tumor",
- "Head and Neck Neoplasm",
- "Bone Neoplasm",
- "Skeletal Muscle Neoplasm",
- "Ovarian Serous Tumor",
- "Sarcoma by FNCLCC Grade",
- "FNCLCC Sarcoma Grade 3",
- "Kidney and Ureter Neoplasm",
- "Kidney Neoplasm",
- "Rectal Neoplasm",
- "Smooth Muscle Neoplasm",
- "Soft Tissue Neoplasm",
- "Hepatobiliary Neoplasm",
- "Intraductal Breast Neoplasm",
- "Ampulla of Vater Neoplasm",
- "Intraepithelial Neoplasia",
- "Eye Neoplasm",
- "Male Reproductive System Neoplasm",
- "Uterine Neoplasm",
- "Glandular Cell Intraepithelial Neoplasia",
- "High Grade Glandular Intraepithelial Neoplasia",
- "Uterine Corpus Neoplasm",
- "Uveal Neoplasm",
- "Grade III Glandular Intraepithelial Neoplasia",
- "Soft Tissue Tumor of Uncertain Differentiation",
- "Malignant Soft Tissue Tumor of Uncertain Differentiation",
- "Cecum Neoplasm",
- "Breast Cancer by AJCC v6 Stage",
- "Breast Cancer by AJCC v7 Stage",
- "Stage 0 Breast Cancer AJCC v6 and v7",
- "High Grade Intraepithelial Neoplasia",
- "Neck Neoplasm",
- "Salivary Gland Neoplasm",
- "Acute Myeloid Leukemia Not Otherwise Specified",
- "Lipomatous Neoplasm",
- "Prostate Neoplasm",
- "Appendix Neoplasm",
- "Gastric Neoplasm",
- "Anal Neoplasm",
- "Intraductal Proliferative Lesion of the Breast",
- "Intraductal Papillary Breast Neoplasm",
- "Breast Cancer by AJCC v8 Stage",
- "Breast Cancer by AJCC v8 Anatomic Stage",
- "Anatomic Stage 0 Breast Cancer AJCC v8",
- "Pharyngeal Neoplasm",
- "Oropharyngeal Neoplasm",
- "Tonsillar Neoplasm",
- "Liver and Intrahepatic Bile Duct Epithelial Neoplasm",
- "Malignant Mesothelioma",
- "Peritoneal and Retroperitoneal Neoplasms",
- "Peripheral Nervous System Neoplasm",
- "Intracranial Neoplasm",
- "Oral Neoplasm",
- "Mixed Mesodermal (Mullerian) Tumor",
- "Brain Neoplasm",
- "Retroperitoneal Neoplasm",
- "Nerve Sheath Neoplasm",
- "Stromal Neoplasm",
- "Chondrogenic Neoplasm",
- "Lobular Neoplasia",
- "Primary Brain Neoplasm",
- "Testicular Neoplasm",
- "Esophageal Neoplasm",
- "Oral Cavity Neoplasm",
- "Small Intestinal Neoplasm",
- "Duodenal Neoplasm",
- "Glioblastoma, IDH-Wildtype",
- "Uterine Corpus Smooth Muscle Neoplasm",
- "Testicular Germ Cell Tumor",
- "Testicular Pure Germ Cell Tumor",
- "Testicular Non-Seminomatous Germ Cell Tumor",
- "Adult Acute Lymphoblastic Leukemia",
- "Adrenal Gland Neoplasm",
- "Adrenal Medulla Neoplasm",
- "Childhood Kidney Neoplasm",
- "Tongue Neoplasm"};
-
- Set<String> termsToRemove = new HashSet<>(Arrays.asList(doNotDisplay));
-
-
- Collection<OntologyTerm> ontologyTerms = ontologyTermRepository.findAllWithMappings();
-
- List<String> autoSuggestList = new ArrayList<>();
-
- for (OntologyTerm ontologyTerm : ontologyTerms) {
- if (ontologyTerm.getLabel() != null) {
-
- if(!termsToRemove.contains(ontologyTerm.getLabel()) || ontologyTerm.getDirectMappedSamplesNumber() > 0){
-
- //autoSuggestList.add(new AutoCompleteOption(ontologyTerm.getLabel(), "OntologyTerm"));
- autoSuggestList.add(ontologyTerm.getLabel());
- }
-
- }
- }
-
- Collections.sort(autoSuggestList);
- autoSuggestList.addAll(ids);
return autoSuggestList;
}
-
}
diff --git a/data-services/src/main/java/org/pdxfinder/services/DataImportService.java b/data-services/src/main/java/org/pdxfinder/services/DataImportService.java
index 60a5ad5d44f69a4e8452d999823807c60cab23cc..12e73337b491cc8e79ae39df50a747b24fdabe12 100644
--- a/data-services/src/main/java/org/pdxfinder/services/DataImportService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/DataImportService.java
@@ -1,10 +1,9 @@
package org.pdxfinder.services;
+import com.github.openjson.JSONArray;
+import com.github.openjson.JSONObject;
import org.apache.commons.lang3.StringUtils;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.graph.queryresults.MutatedMarkerData;
import org.pdxfinder.graph.queryresults.TreatmentMappingData;
import org.pdxfinder.graph.repositories.*;
import org.pdxfinder.services.ds.Standardizer;
@@ -16,8 +15,6 @@ import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Component;
import org.springframework.util.Assert;
-import org.springframework.cache.annotation.Cacheable;
-
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@@ -53,7 +50,6 @@ public class DataImportService {
private TreatmentProtocolRepository treatmentProtocolRepository;
private CurrentTreatmentRepository currentTreatmentRepository;
private ExternalUrlRepository externalUrlRepository;
- private DrugRepository drugRepository;
private TreatmentRepository treatmentRepository;
private final static Logger log = LoggerFactory.getLogger(DataImportService.class);
@@ -88,7 +84,6 @@ public class DataImportService {
TreatmentProtocolRepository treatmentProtocolRepository,
CurrentTreatmentRepository currentTreatmentRepository,
ExternalUrlRepository externalUrlRepository,
- DrugRepository drugRepository,
TreatmentRepository treatmentRepository) {
Assert.notNull(tumorTypeRepository, "tumorTypeRepository cannot be null");
@@ -131,7 +126,6 @@ public class DataImportService {
this.treatmentProtocolRepository = treatmentProtocolRepository;
this.currentTreatmentRepository = currentTreatmentRepository;
this.externalUrlRepository = externalUrlRepository;
- this.drugRepository = drugRepository;
this.treatmentRepository = treatmentRepository;
@@ -141,20 +135,6 @@ public class DataImportService {
}
- public Group getGroup(String name, String abbrev, String type){
-
- Group g = groupRepository.findByNameAndType(name, type);
-
- if(g == null){
- log.info("Group not found. Creating {}", name);
-
- g = new Group(name, abbrev, type);
- groupRepository.save(g);
-
- }
-
- return g;
- }
public Group getProviderGroup(String name, String abbrev, String description, String providerType, String contact, String url){
@@ -299,10 +279,6 @@ public class DataImportService {
return modelCreationRepository.findAllModelsPlatforms();
}
- public int countMarkerAssociationBySourcePdxId(String modelId, String dataSource, String platformName){
-
- return modelCreationRepository.countMarkerAssociationBySourcePdxId(modelId, dataSource, platformName);
- }
public Collection<ModelCreation> findModelsWithPatientData(){
@@ -324,9 +300,17 @@ public class DataImportService {
return modelCreationRepository.findModelPlatformSampleByDS(ds);
}
- public ModelCreation findModelWithMolecularDataByDSAndIdAndMolcharType(String dataSource, String modelId, String molcharType){
+ public List<ModelCreation> findModelsWithMolecularDataByDSAndMolcharType(String dataSource, String molcharType){
+
+ return modelCreationRepository.findModelsWithMolecularDataByDSAndMolcharType(dataSource, molcharType);
+ }
+
+ public List<ModelCreation> findModelsWithTreatmentSummaryByDS(String datasource){
+ return modelCreationRepository.findModelsWithTreatmentSummaryByDataSource(datasource);
+ }
- return modelCreationRepository.findModelWithMolecularDataByDSAndIdAndMolcharType(dataSource, modelId, molcharType);
+ public List<ModelCreation> findModelFromPatienSnapshotWithTreatmentSummaryByDS(String datasource){
+ return modelCreationRepository.findModelFromPatienSnapshotWithTreatmentSummaryByDataSource(datasource);
}
public List<ModelCreation> findModelsWithSharingAndContactByDS(String ds){
@@ -363,10 +347,6 @@ public class DataImportService {
return modelCreationRepository.findModelWithSampleByMolChar(mc);
}
- public int getModelCount(){
-
- return modelCreationRepository.countAllModels();
- }
public int getModelCountByDataSource(String dataSource){
@@ -518,24 +498,6 @@ public class DataImportService {
return ps;
}
-
-
- public Patient getPatient(String externalId, String sex, String race, String ethnicity, Group group) {
-
- Patient patient = patientRepository.findByExternalIdAndGroup(externalId, group);
-
- if (patient == null) {
- log.info("Patient '{}' not found. Creating", externalId);
-
- patient = new Patient(externalId, sex, race, ethnicity, group);
-
- patientRepository.save(patient);
- }
-
- return patient;
- }
-
-
public Sample getSample(String sourceSampleId, String typeStr, String diagnosis, String originStr, String sampleSiteStr, String extractionMethod, String classification, Boolean normalTissue, String dataSource) {
TumorType type = this.getTumorType(typeStr);
@@ -597,44 +559,6 @@ public class DataImportService {
}
-
- public Sample findSampleByDataSourceAndSourceSampleId(String dataSource, String sampleId){
-
- return sampleRepository.findBySourceSampleIdAndDataSource(sampleId, dataSource);
- }
-
- public Collection<Sample> findSamplesWithoutOntologyMapping(){
-
- return sampleRepository.findSamplesWithoutOntologyMapping();
- }
-
- public Sample getMouseSample(ModelCreation model, String specimenId, String dataSource, String passage, String sampleId){
-
- Specimen specimen = this.getSpecimen(model, specimenId, dataSource, passage);
- Sample sample;
-
- if(specimen.getSample() == null){
- sample = new Sample();
- sample.setSourceSampleId(sampleId);
- sample.setDataSource(dataSource);
- sampleRepository.save(sample);
- }
- else{
-
- sample = specimen.getSample();
- }
-
- return sample;
- }
-
- //public findSampleWithMolcharBySpecimen
-
-
- public Sample findMouseSampleWithMolcharByModelIdAndDataSourceAndSampleId(String modelId, String dataSource, String sampleId){
-
- return sampleRepository.findMouseSampleWithMolcharByModelIdAndDataSourceAndSampleId(modelId, dataSource, sampleId);
- }
-
public Sample findHumanSampleWithMolcharByModelIdAndDataSource(String modelId, String dataSource){
return sampleRepository.findHumanSampleWithMolcharByModelIdAndDataSource(modelId, dataSource);
@@ -658,30 +582,12 @@ public class DataImportService {
return molecularCharacterizationRepository.findByIds(ids);
}
- public Sample getHumanSample(String sampleId, String dataSource){
-
-
- return sampleRepository.findHumanSampleBySampleIdAndDataSource(sampleId, dataSource);
- }
-
public Sample findHumanSample(String modelId, String dsAbbrev){
return sampleRepository.findHumanSampleByModelIdAndDS(modelId, dsAbbrev);
}
- public Sample findXenograftSample(String modelId, String dataSource, String specimenId){
-
- return sampleRepository.findMouseSampleByModelIdAndDataSourceAndSpecimenId(modelId, dataSource, specimenId);
- }
-
- public Sample findXenograftSample(String modelId, String dataSource, String passage, String nomenclature){
-
-
- return sampleRepository.findMouseSampleByModelIdAndDataSourceAndPassageAndNomenclature(modelId, dataSource, passage, nomenclature);
- }
-
-
public int getHumanSamplesNumber(){
return sampleRepository.findHumanSamplesNumber();
@@ -789,12 +695,6 @@ public class DataImportService {
return hostStrain;
}
- public HostStrain findHostStrain(String symbol){
-
- return hostStrainRepository.findBySymbol(symbol);
- }
-
-
// is this bad? ... probably..
public Marker getMarker(String symbol) {
log.error("MARKER METHOD WAS CALLED!");
@@ -815,11 +715,6 @@ public class DataImportService {
return marker;
}
- public List<MutatedMarkerData> getFrequentlyMutatedGenes(){
-
- return markerRepository.countModelsByMarker();
- }
-
public Set<MarkerAssociation> findMarkerAssocsByMolChar(MolecularCharacterization mc){
return markerAssociationRepository.findByMolChar(mc);
@@ -837,9 +732,13 @@ public class DataImportService {
return molecularCharacterizationRepository.save(mc);
}
+ public void saveMolecularCharacterizations(List<MolecularCharacterization> mc){
+ molecularCharacterizationRepository.saveAll(mc);
+ }
+
public void saveQualityAssurance(QualityAssurance qa) {
if (qa != null) {
- if (null == qualityAssuranceRepository.findFirstByTechnologyAndDescription(qa.getTechnology(), qa.getDescription())) {
+ if (null == qualityAssuranceRepository.findByTechnologyAndDescriptionAndPassage(qa.getTechnology(), qa.getDescription(), qa.getPassages())) {
qualityAssuranceRepository.save(qa);
}
}
@@ -850,12 +749,6 @@ public class DataImportService {
return molecularCharacterizationRepository.findAllByType(type);
}
-
- public List<Specimen> findSpecimenByPassage(ModelCreation model, String passage){
-
- return specimenRepository.findByModelIdAndDataSourceAndAndPassage(model.getSourcePdxId(), model.getDataSource(), passage);
- }
-
public Specimen getSpecimen(ModelCreation model, String specimenId, String dataSource, String passage){
Specimen specimen = specimenRepository.findByModelIdAndDataSourceAndSpecimenIdAndPassage(model.getSourcePdxId(), dataSource, specimenId, passage);
@@ -877,13 +770,6 @@ public class DataImportService {
return specimenRepository.findByModelAndPassageAndNomenClature(modelCreation, passage, nomenclature);
}
-
- public List<Specimen> getAllSpecimenByModel(String modelId, String dataSource){
-
- return specimenRepository.findByModelIdAndDataSource(modelId, dataSource);
- }
-
-
public Specimen findSpecimenByMolChar(MolecularCharacterization mc){
return specimenRepository.findByMolChar(mc);
@@ -910,10 +796,6 @@ public class DataImportService {
return ontologyTermRepository.findByUrl(url);
}
- public OntologyTerm findOntologyTermByLabel(String label){
- return ontologyTermRepository.findByLabel(label);
- }
-
public OntologyTerm findOntologyTermByLabelAndType(String label, String type){
return ontologyTermRepository.findByLabelAndType(label, type);
}
@@ -923,12 +805,6 @@ public class DataImportService {
return ontologyTermRepository.findByUrl(url);
}
- public Collection<OntologyTerm> getAllOntologyTerms() {
-
- return ontologyTermRepository.findAll();
-
- }
-
public Collection<OntologyTerm> getAllOntologyTermsWithNotZeroDirectMapping(){
return ontologyTermRepository.findAllWithNotZeroDirectMappingNumber();
@@ -939,28 +815,6 @@ public class DataImportService {
return ontologyTermRepository.findAllDirectParents(termUrl);
}
- public int getIndirectMappingNumber(String label) {
-
- return ontologyTermRepository.getIndirectMappingNumber(label);
- }
-
- public int findDirectMappingNumber(String label) {
-
-
- Set<OntologyTerm> otset = ontologyTermRepository.getDistinctSubTreeNodes(label);
- int mapNum = 0;
- for (OntologyTerm ot : otset) {
- mapNum += ot.getDirectMappedSamplesNumber();
- }
- return mapNum;
- }
-
- public Collection<OntologyTerm> getAllOntologyTermsFromTo(int from, int to) {
-
- return ontologyTermRepository.findAllFromTo(from, to);
-
- }
-
public Collection<OntologyTerm> getAllOntologyTermsByTypeFromTo(String type, int from, int to) {
return ontologyTermRepository.findAllByTypeFromTo(type, from, to);
@@ -1003,11 +857,7 @@ public class DataImportService {
}
public void saveAllMarkers(Collection<Marker> markers) {
- markerRepository.save(markers);
- }
-
- public Collection<Marker> getAllMarkers() {
- return markerRepository.findAllMarkers();
+ markerRepository.saveAll(markers);
}
public Integer countAllMarkers() {
@@ -1022,11 +872,6 @@ public class DataImportService {
return markerRepository.findAllHumanMarkers();
}
- public Set<Marker> findAllDistinctMarkersByMolCharId(Long id){
-
- return markerRepository.findDistinctByMolCharId(id);
- }
-
public Platform getPlatform(String name, String type, Group group) {
//remove special characters from platform name
@@ -1095,13 +940,9 @@ public class DataImportService {
return pa;
}
- public void savePlatformAssociation(PlatformAssociation pa){
- platformAssociationRepository.save(pa);
- }
-
- public void saveDataProjection(DataProjection dp){
+ public DataProjection saveDataProjection(DataProjection dp){
- dataProjectionRepository.save(dp);
+ return dataProjectionRepository.save(dp);
}
public DataProjection findDataProjectionByLabel(String label){
@@ -1138,21 +979,6 @@ public class DataImportService {
}
- public int findModelTreatmentNumber(String dataSource){
-
- if(dataSource == null || dataSource.isEmpty()){
-
- return treatmentRepository.findModelTreatmentNumber();
- }
- else{
-
- return treatmentRepository.findModelTreatmentNumberByDS(dataSource);
- }
-
-
- }
-
-
public Collection<Treatment> getPatientTreatmentFrom(int from, int batch, String dataSource){
if(dataSource == null || dataSource.isEmpty()){
@@ -1163,8 +989,6 @@ public class DataImportService {
return treatmentRepository.getPatientTreatmentFromByDS(from, batch, dataSource);
}
-
-
}
@@ -1178,7 +1002,6 @@ public class DataImportService {
return treatmentRepository.getModelTreatmentFromByDS(from, batch, dataSource);
}
-
}
@@ -1231,12 +1054,6 @@ public class DataImportService {
return ct;
}
-
- public void createDrug(Drug d){
- drugRepository.save(d);
- }
-
-
/**
*
* @param drugString
@@ -1390,37 +1207,11 @@ public class DataImportService {
}
-
-
-
-
public TreatmentSummary findTreatmentSummaryByPatientSnapshot(PatientSnapshot ps){
return treatmentSummaryRepository.findByPatientSnapshot(ps);
-
- }
-
-
-
-
-
- public Set<Object> findUnlinkedNodes(){
-
- return dataProjectionRepository.findUnlinkedNodes();
- }
-
- public Set<Object> findPatientsWithMultipleSummaries(){
-
- return dataProjectionRepository.findPatientsWithMultipleTreatmentSummaries();
}
- public Set<Object> findPlatformsWithoutUrl(){
-
- return dataProjectionRepository.findPlatformsWithoutUrl();
- }
-
-
-
public QualityAssurance getQualityAssurance(JSONObject data, String ds) throws Exception{
QualityAssurance qa = new QualityAssurance();
@@ -1512,24 +1303,6 @@ public class DataImportService {
return qa;
}
- @Cacheable
- public Marker getMarkerBySymbol(String symbol){
-
- return markerRepository.findBySymbol(symbol);
- }
-
- @Cacheable
- public List<Marker> getMarkerByPrevSymbol(String symbol){
-
- return markerRepository.findByPrevSymbol(symbol);
- }
-
- @Cacheable
- public List<Marker> getMarkerBySynonym(String symbol){
-
- return markerRepository.findBySynonym(symbol);
- }
-
private void initializeMarkers(){
int markerCount = markerRepository.getMarkerCount();
diff --git a/data-services/src/main/java/org/pdxfinder/services/DetailsService.java b/data-services/src/main/java/org/pdxfinder/services/DetailsService.java
index 52926a22cb879ab67c29acdcf4906271024fca6c..6e62c2abb62b92255330661fb7467df2741737c0 100644
--- a/data-services/src/main/java/org/pdxfinder/services/DetailsService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/DetailsService.java
@@ -1,15 +1,13 @@
package org.pdxfinder.services;
-import org.apache.commons.collections4.ListUtils;
import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.text.WordUtils;
import org.pdxfinder.graph.dao.*;
import org.pdxfinder.graph.repositories.*;
import org.pdxfinder.services.dto.*;
import org.pdxfinder.services.dto.pdxgun.Reference;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import org.springframework.data.domain.Sort;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.*;
@@ -27,17 +25,14 @@ public class DetailsService {
private SampleRepository sampleRepository;
private PatientRepository patientRepository;
- private PatientSnapshotRepository patientSnapshotRepository;
+
private ModelCreationRepository modelCreationRepository;
private SpecimenRepository specimenRepository;
private MolecularCharacterizationRepository molecularCharacterizationRepository;
private PlatformRepository platformRepository;
private TreatmentSummaryRepository treatmentSummaryRepository;
- private MarkerAssociationRepository markerAssociationRepository;
- private GraphService graphService;
- private Map<String, List<String>> facets = new HashMap<>();
- private PlatformService platformService;
+
private DrugService drugService;
private PatientService patientService;
private PublicationService publicationService;
@@ -45,36 +40,30 @@ public class DetailsService {
private final static Logger log = LoggerFactory.getLogger(DetailsService.class);
private ReferenceDbService referenceDbService;
-
+ @Autowired
public DetailsService(SampleRepository sampleRepository,
PatientRepository patientRepository,
- PatientSnapshotRepository patientSnapshotRepository,
+
ModelCreationRepository modelCreationRepository,
SpecimenRepository specimenRepository,
MolecularCharacterizationRepository molecularCharacterizationRepository,
PlatformRepository platformRepository,
TreatmentSummaryRepository treatmentSummaryRepository,
- GraphService graphService,
- PlatformService platformService,
DrugService drugService,
PatientService patientService,
- MarkerAssociationRepository markerAssociationRepository,
PublicationService publicationService,
ReferenceDbService referenceDbService) {
this.sampleRepository = sampleRepository;
this.patientRepository = patientRepository;
- this.patientSnapshotRepository = patientSnapshotRepository;
+
this.modelCreationRepository = modelCreationRepository;
this.molecularCharacterizationRepository = molecularCharacterizationRepository;
this.specimenRepository = specimenRepository;
this.platformRepository = platformRepository;
this.treatmentSummaryRepository = treatmentSummaryRepository;
- this.graphService = graphService;
- this.platformService = platformService;
this.drugService = drugService;
this.patientService = patientService;
- this.markerAssociationRepository = markerAssociationRepository;
this.publicationService = publicationService;
this.referenceDbService = referenceDbService;
@@ -352,17 +341,7 @@ public class DetailsService {
mde.setDataAvailableLabel(mc.getPlatform().getName());
mde.setDataAvailableUrl("");
mde.setPlatformUsedLabel(mc.getPlatform().getName());
-
- // mde.setPlatformUsedUrl(mc.getPlatform().getUrl());
-
- // temp solution, ToDo: solve properly via appropriate url redirection - /platform/sth/ -> /platform/sth
- String auxStr = mc.getPlatform().getUrl();
- if (auxStr != null && auxStr.length() > 1 && auxStr.charAt(auxStr.length() - 1) == '/') {
- auxStr = auxStr.substring(0, auxStr.length() - 1);
- }
- mde.setPlatformUsedUrl(auxStr);
-
- mde.setRawDataLabel("Not available");
+ mde.setPlatformUsedUrl(mc.getPlatform().getUrl());
mde.setMolcharId(mc.getId().toString());
setRawDataLabelAndLink(mde, xenoSample);
@@ -419,10 +398,14 @@ public class DetailsService {
}
- public MolecularDataTableDTO getMolecularDataTable(String id){
+ public MolecularCharacterization getMolcharData(String id){
+ return molecularCharacterizationRepository.getMolecularDataById(Long.valueOf(id));
+ }
+
+ public MolecularDataTableDTO getMolecularDataTable(String id, boolean forceReturn){
MolecularDataTableDTO dto = new MolecularDataTableDTO();
- MolecularCharacterization mc = molecularCharacterizationRepository.getMolecularDataById(Long.valueOf(id));
+ MolecularCharacterization mc = getMolcharData(id);
if(mc == null){
@@ -439,6 +422,15 @@ public class DetailsService {
dto.setMolecularDataRows(new ArrayList<>());
return dto;
}
+ else if(mc.getFirstMarkerAssociation() != null && mc.getFirstMarkerAssociation().getDataPoints() > 300 && !forceReturn){
+
+ List<String> dataRow = new ArrayList<>();
+ dataRow.add("This dataset is too big to display, please click on the download results button to view data.");
+ dto.setVisible(true);
+ dto.setReports(dataRow);
+ dto.setMolecularDataRows(new ArrayList<>());
+ return dto;
+ }
else {
Sample sample = sampleRepository.findSampleByMolcharId(Long.valueOf(id));
diff --git a/data-services/src/main/java/org/pdxfinder/services/EmailService.java b/data-services/src/main/java/org/pdxfinder/services/EmailService.java
index 8562a06385b3ec5600c7f3c57ac43d32bb0c7318..fb19d781ce6f6c98beace05384b510f0b36d1e8f 100644
--- a/data-services/src/main/java/org/pdxfinder/services/EmailService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/EmailService.java
@@ -1,6 +1,5 @@
package org.pdxfinder.services;
-import org.neo4j.cypher.internal.frontend.v2_3.ast.functions.Str;
import org.pdxfinder.services.email.Mail;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -10,7 +9,7 @@ import org.springframework.mail.javamail.JavaMailSender;
import org.springframework.mail.javamail.MimeMessageHelper;
import org.springframework.stereotype.Service;
import org.thymeleaf.context.Context;
-import org.thymeleaf.spring4.SpringTemplateEngine;
+import org.thymeleaf.spring5.SpringTemplateEngine;
import javax.mail.internet.InternetAddress;
import javax.mail.internet.MimeMessage;
@@ -50,7 +49,7 @@ public class EmailService {
mail.setSubject(subject);
- Map<String, Object> model = new HashMap<String, Object>();
+ Map<String, Object> model = new HashMap<>();
model.put("date", "xxxx");
model.put("count", missingCount);
mail.setModel(model);
diff --git a/data-services/src/main/java/org/pdxfinder/services/GraphService.java b/data-services/src/main/java/org/pdxfinder/services/GraphService.java
index 078446482eb244ee887e822a5bc1639bbb283080..77b4291bc2d60dc9b060489d302af4bcd52953b1 100644
--- a/data-services/src/main/java/org/pdxfinder/services/GraphService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/GraphService.java
@@ -1,7 +1,7 @@
package org.pdxfinder.services;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.JSONArray;
+import com.github.openjson.JSONObject;
import org.pdxfinder.graph.dao.DataProjection;
import org.pdxfinder.graph.dao.OntologyTerm;
import org.pdxfinder.graph.dao.Sample;
diff --git a/data-services/src/main/java/org/pdxfinder/services/MappingService.java b/data-services/src/main/java/org/pdxfinder/services/MappingService.java
index d2b2f0cead5f6a11e287f7f251ff220571d1b3db..9b769e41276e254b428f22bff79ff91b617c8a7b 100644
--- a/data-services/src/main/java/org/pdxfinder/services/MappingService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/MappingService.java
@@ -3,19 +3,18 @@ package org.pdxfinder.services;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.gson.Gson;
+import com.github.openjson.JSONArray;
+import com.github.openjson.JSONException;
+import com.github.openjson.JSONObject;
import org.apache.commons.lang3.StringUtils;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONException;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.services.mapping.MappingContainer;
import org.pdxfinder.graph.dao.OntologyTerm;
import org.pdxfinder.graph.repositories.OntologyTermRepository;
-import org.pdxfinder.rdbms.dao.MappingEntity;
import org.pdxfinder.graph.repositories.SampleRepository;
+import org.pdxfinder.rdbms.dao.MappingEntity;
import org.pdxfinder.rdbms.repositories.MappingEntityRepository;
import org.pdxfinder.services.dto.PaginationDTO;
import org.pdxfinder.services.mapping.CSV;
+import org.pdxfinder.services.mapping.MappingContainer;
import org.pdxfinder.services.mapping.MappingEntityType;
import org.pdxfinder.services.mapping.Status;
import org.pdxfinder.services.zooma.*;
@@ -31,7 +30,10 @@ import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Sort;
import org.springframework.stereotype.Service;
-import java.io.*;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
import java.util.*;
import java.util.stream.Collectors;
@@ -55,7 +57,6 @@ public class MappingService {
@Value("${data-dir}")
private String rootDir;
-
@Value("${mappings.mappedTermUrl}")
private String knowledgBaseURL;
@@ -122,10 +123,7 @@ public class MappingService {
Map<String, List<MappingEntity>> mappings = new HashMap<>();
mappings.put("mappings", maprules);
- Gson gson = new Gson();
- String json = gson.toJson(mappings);
-
-
+ String json = JSONObject.wrap(mappings).toString();
try {
BufferedWriter writer = new BufferedWriter(new FileWriter(fileName, false));
@@ -664,7 +662,9 @@ public class MappingService {
for (String mappingLabel : mappingLabels) {
/* ZOOMA PROPERTY DATA */
- Property property = new Property(mappingLabel, StringUtils.upperCase(mappingValues.get(mappingLabel)));
+ Property property = new org.pdxfinder.services.zooma.Property(
+ mappingLabel,
+ StringUtils.upperCase(mappingValues.get(mappingLabel)));
List<String> annotations = new ArrayList<>();
@@ -809,36 +809,42 @@ public class MappingService {
public void writeMappingsToFile(String entityType) {
+ if (!containsSpecialCharacters(entityType)) throw new IllegalArgumentException("EntityType contains illegal characters");
+ else {
+ String jsonKey = "mappings";
+ String mappingFile = rootDir + "/mapping/" + entityType + "_mappings.json";
- String jsonKey = "mappings";
-
- String mappingFile = rootDir + "/mapping/" + entityType + "_mappings.json";
-
- // Generate Unique name to back up previous mapping file
- String backupPreviousMappingFile = rootDir + "/mapping/backup/" + entityType + "/" +
- (new Date()).toString().replaceAll(" ", "-") + "-" + entityType + "_mappings.json";
+ // Generate Unique name to back up previous mapping file
+ String baseDirectory = rootDir + "/mapping/backup/";
+ String backupPreviousMappingFile = baseDirectory + entityType + "/" +
+ (new Date()).toString().replaceAll(" ", "-") + "-" + entityType + "_mappings.json";
- // Back up previous mapping file before replacement
- utilityService.moveFile(mappingFile, backupPreviousMappingFile);
+ // Back up previous mapping file before replacement
+ utilityService.moveFile(mappingFile, backupPreviousMappingFile);
- // Get Latest mapped terms from the data base
- List<MappingEntity> mappingEntities = mappingEntityRepository.findByEntityTypeAndStatusIsNot(entityType, "unmapped");
- Map dataMap = new HashMap();
+ // Get Latest mapped terms from the data base
+ List<MappingEntity> mappingEntities = mappingEntityRepository.findByEntityTypeAndStatusIsNot(entityType, "unmapped");
- dataMap.put(jsonKey, mappingEntities);
+ Map dataMap = new HashMap();
+ dataMap.put(jsonKey, mappingEntities);
- // Write latest mapped terms to the file system
- try {
+ // Write latest mapped terms to the file system
+ try {
- String newFile = mapper.writeValueAsString(dataMap);
- utilityService.writeToFile(newFile, mappingFile, false);
+ String newFile = mapper.writeValueAsString(dataMap);
+ utilityService.writeToFile(newFile, mappingFile, false);
- } catch (JsonProcessingException e) {
+ } catch (JsonProcessingException e) {
+ }
}
}
+ private boolean containsSpecialCharacters(String input){
+ return input.matches("^[A-Za-z0-9-_]*$");
+ }
+
public PaginationDTO search(int page,
int size,
@@ -861,7 +867,9 @@ public class MappingService {
// requested page is either +ve or forced to default page
int start = (page > 0) ? page - 1 : 0;
- pageable = new PageRequest(start, size, direction, sortColumn);
+ Sort sort = Sort.by(direction, sortColumn);
+
+ pageable = PageRequest.of(start, size, sort);
Page<MappingEntity> mappingEntityPage = mappingEntityRepository.findByMultipleFilters(entityType, mappingLabel, mappingValue, mappedTermLabel, mapType, mappedTermsOnly, status, pageable);
@@ -952,7 +960,7 @@ public class MappingService {
public boolean checkExistence(Long entityId) {
- return mappingEntityRepository.exists(entityId);
+ return mappingEntityRepository.existsByEntityId(entityId);
}
@@ -1049,11 +1057,10 @@ public class MappingService {
});
return savedEntities;
-
}
-
-
-
+ public void setRootDir(String rootDir) {
+ this.rootDir = rootDir;
+ }
}
diff --git a/data-services/src/main/java/org/pdxfinder/services/OmicTransformationService.java b/data-services/src/main/java/org/pdxfinder/services/OmicTransformationService.java
index f29ba339c33a627e6af372860c1f0529dc3cc5a1..7101769bd02bd01e5da1936d270351bb90a7f4bc 100644
--- a/data-services/src/main/java/org/pdxfinder/services/OmicTransformationService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/OmicTransformationService.java
@@ -63,13 +63,18 @@ public class OmicTransformationService {
}
public String ncbiGeneIdToHgncSymbol(String ncbiGene) {
- String hgncSymbol = geneIdCache.get(ncbiGene);
- if (hgncSymbol == null) {
- Marker marker = dataImportService.getMarkerbyNcbiGeneId(ncbiGene);
- if (marker.hasHgncSymbol()) {
- hgncSymbol = marker.getHgncSymbol();
- geneIdCache.put(ncbiGene, hgncSymbol);
- } else { log.warn("No marker found for NCBI gene Id {} Cannot generate Hgnc symbol", ncbiGene); }
+ String hgncSymbol = "";
+ if (!ncbiGene.isEmpty()) {
+ hgncSymbol = geneIdCache.get(ncbiGene);
+ if (hgncSymbol == null) {
+ Marker marker = dataImportService.getMarkerbyNcbiGeneId(ncbiGene);
+ if (marker != null && marker.hasHgncSymbol()) {
+ hgncSymbol = marker.getHgncSymbol();
+ geneIdCache.put(ncbiGene, hgncSymbol);
+ } else {
+ log.warn("No marker found for NCBI gene Id {} Cannot generate Hgnc symbol", ncbiGene);
+ }
+ }
}
return hgncSymbol;
}
diff --git a/data-services/src/main/java/org/pdxfinder/services/PlatformService.java b/data-services/src/main/java/org/pdxfinder/services/PlatformService.java
index 190d1c6b17b23f65be615406a01c0f1a5f0fcef5..fae5f001e63c1fd68d85a2c8d604b47955b40371 100644
--- a/data-services/src/main/java/org/pdxfinder/services/PlatformService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/PlatformService.java
@@ -1,7 +1,6 @@
package org.pdxfinder.services;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.graph.dao.*;
import org.pdxfinder.graph.repositories.DataProjectionRepository;
import org.pdxfinder.graph.repositories.ModelCreationRepository;
diff --git a/data-services/src/main/java/org/pdxfinder/services/PublicationService.java b/data-services/src/main/java/org/pdxfinder/services/PublicationService.java
index 4e8e7adf628e739789f14765ffbb35edcd132b93..ee0631bcaddaf0d9b84712dfd43fd9906854f239 100644
--- a/data-services/src/main/java/org/pdxfinder/services/PublicationService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/PublicationService.java
@@ -5,7 +5,9 @@ import org.pdxfinder.services.dto.europepmc.Publication;
import org.springframework.stereotype.Service;
import org.springframework.web.client.RestTemplate;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
@Service
public class PublicationService {
@@ -24,7 +26,7 @@ public class PublicationService {
pubMedIds = sanitizePubMedIds(pubMedIds);
List<Publication> publications = new ArrayList<>();
pubMedIds.forEach(pubMedId->{
- String api = String.format("%s?query=%s&resultType=core&format=json", DataUrl.EUROPE_PMC_URL.get(), pubMedId);
+ String api = String.format("%s?query=ext_id:%s&resultType=core&format=json", DataUrl.EUROPE_PMC_URL.get(), pubMedId);
publications.add(restTemplate.getForObject(api, Publication.class));
});
@@ -36,6 +38,7 @@ public class PublicationService {
public List<String> sanitizePubMedIds(List<String> pubMedIds){
List<String> cleanedPubMedIds = new ArrayList<>();
pubMedIds.forEach(pubMedId -> {
+ pubMedId = pubMedId.toUpperCase();
pubMedId = pubMedId.replace(PUBLICATION_PREFIX, EMPTY_STRING);
pubMedId = pubMedId.replaceAll("\\s+",EMPTY_STRING);
if (pubMedId.contains(";")){
diff --git a/data-services/src/main/java/org/pdxfinder/services/SearchService.java b/data-services/src/main/java/org/pdxfinder/services/SearchService.java
index 1a9f6623f767412c1c099549dafd5ec6c91a1430..85a690f3db6111f0b50fada0c7e8e72b19db6e03 100644
--- a/data-services/src/main/java/org/pdxfinder/services/SearchService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/SearchService.java
@@ -45,7 +45,7 @@ public class SearchService {
List<String> sampleTumorTypeOptions = new ArrayList<>();
List<String> dataAvailableOptions = new ArrayList<>();
- private static List<String> modelsIDsForAutoSuggest;
+
public SearchService(ModelCreationRepository modelCreationRepository,
@@ -64,8 +64,6 @@ public class SearchService {
this.drugService = drugService;
this.searchDS = searchDS;
-
-
facets.put("datasource_options", datasourceOptions);
facets.put("patient_age_options", patientAgeOptions);
facets.put("patient_gender_options", patientGenderOptions);
@@ -73,11 +71,6 @@ public class SearchService {
facets.put("data_available_options", dataAvailableOptions);
facets.put("sample_tumor_type_options", sampleTumorTypeOptions);
-
- Set<ModelForQuery> modelsForAutoSuggest = searchDS.search(getFacetMap(Optional.empty(),Optional.empty(),Optional.empty(),Optional.empty(),Optional.empty(),Optional.empty(), Optional.empty(),Optional.empty(),Optional.empty(), Optional.empty(),Optional.empty(),Optional.empty(), Optional.empty(),Optional.empty(),Optional.empty(),Optional.empty(),Optional.empty(),Optional.empty(), Optional.empty()));
-
- modelsIDsForAutoSuggest = modelsForAutoSuggest.stream().map(ModelForQuery::getExternalId).collect(Collectors.toList());
-
}
@@ -103,6 +96,7 @@ public class SearchService {
Optional<List<String>> copy_number_alteration,
Optional<List<String>> gene_expression,
Optional<List<String>> cytogenetics,
+ Optional<List<String>> model_id,
Integer page,
Integer size){
@@ -126,7 +120,8 @@ public class SearchService {
access_modalities,
copy_number_alteration,
gene_expression,
- cytogenetics
+ cytogenetics,
+ model_id
);
WebSearchDTO wsDTO = new WebSearchDTO();
@@ -177,8 +172,7 @@ public class SearchService {
wsDTO.setTextSearchDescription(textSearchDescription);
wsDTO.setTotalResults(searchDS.getModels().size());
- wsDTO.setMainSearchFieldOptions(autoCompleteService.getAutoSuggestions(modelsIDsForAutoSuggest));
-
+ wsDTO.setMainSearchFieldOptions(autoCompleteService.getAutoSuggestions());
List<ModelForQuery> resultSet = new ArrayList<>(results).subList((page - 1) * size, Math.min(((page - 1) * size) + size, results.size()));
wsDTO.setResults(resultSet);
@@ -210,7 +204,8 @@ public class SearchService {
Optional<List<String>> access_modalities,
Optional<List<String>> copy_number_alteration,
Optional<List<String>> gene_expression,
- Optional<List<String>> cytogenetics){
+ Optional<List<String>> cytogenetics,
+ Optional<List<String>> model_id){
Map<SearchFacetName, List<String>> configuredFacets = getFacetMap(
query,
@@ -231,7 +226,8 @@ public class SearchService {
access_modalities,
copy_number_alteration,
gene_expression,
- cytogenetics
+ cytogenetics,
+ model_id
);
@@ -244,7 +240,7 @@ public class SearchService {
- public Map<SearchFacetName, List<String>> getFacetMap(
+ private Map<SearchFacetName, List<String>> getFacetMap(
Optional<String> query,
Optional<List<String>> datasource,
Optional<List<String>> diagnosis,
@@ -263,8 +259,8 @@ public class SearchService {
Optional<List<String>> access_modalities,
Optional<List<String>> copy_number_alteration,
Optional<List<String>> gene_expression,
- Optional<List<String>> cytogenetics
-
+ Optional<List<String>> cytogenetics,
+ Optional<List<String>> model_id
) {
@@ -402,6 +398,13 @@ public class SearchService {
}
}
+ if (model_id.isPresent() && !model_id.get().isEmpty()) {
+ configuredFacets.put(SearchFacetName.model_id, new ArrayList<>());
+ for (String s : model_id.get()) {
+ configuredFacets.get(SearchFacetName.model_id).add(s);
+ }
+ }
+
return configuredFacets;
}
diff --git a/data-services/src/main/java/org/pdxfinder/services/Statistics.java b/data-services/src/main/java/org/pdxfinder/services/Statistics.java
index 9c5f58f9cbf518422c040c2cae3d5c32be61b90d..c67d3df946a57be911b0540d4f565f363c9e463e 100644
--- a/data-services/src/main/java/org/pdxfinder/services/Statistics.java
+++ b/data-services/src/main/java/org/pdxfinder/services/Statistics.java
@@ -131,10 +131,12 @@ public class Statistics {
// Populate the chartData category List
categories.add(StatisticsDTO.getCategory());
-
- StatisticsDTO.getDataCounts().forEach(CountDTO -> {
- dataMap.get(CountDTO.getKey()).add(CountDTO.getValue());
- });
+ if(StatisticsDTO.getDataCounts()!= null){
+ StatisticsDTO.getDataCounts().forEach(CountDTO -> {
+ if(CountDTO != null && CountDTO.getKey() != null && dataMap.containsKey(CountDTO.getKey()))
+ dataMap.get(CountDTO.getKey()).add(CountDTO.getValue());
+ });
+ }
});
diff --git a/data-services/src/main/java/org/pdxfinder/services/TransformerService.java b/data-services/src/main/java/org/pdxfinder/services/TransformerService.java
index f93696d4fbdfa9ccf0665a2c3278a323f284d0cb..0473b49b2adec84264b3b762b0f8de8f03173f1c 100644
--- a/data-services/src/main/java/org/pdxfinder/services/TransformerService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/TransformerService.java
@@ -2,16 +2,9 @@ package org.pdxfinder.services;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
-import org.pdxfinder.rdbms.dao.PdmrPdxInfo;
-import org.pdxfinder.rdbms.dao.Sample;
-import org.pdxfinder.rdbms.dao.Treatment;
-import org.pdxfinder.rdbms.dao.Validation;
-import org.pdxfinder.rdbms.repositories.TransPdxInfoRepository;
-import org.pdxfinder.rdbms.repositories.TransSampleRepository;
-import org.pdxfinder.rdbms.repositories.TransTreatmentRepository;
-import org.pdxfinder.rdbms.repositories.TransValidationRepository;
-import org.pdxfinder.services.constants.OmicCSVColumn;
-import org.pdxfinder.services.constants.PdmrOmicCol;
+import org.pdxfinder.rdbms.dao.*;
+import org.pdxfinder.rdbms.repositories.*;
+import org.pdxfinder.services.constants.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
@@ -514,19 +507,19 @@ public class TransformerService {
for (Treatment treatment: treatments){
treatment.setPdmrPdxInfo(pdmrPdxInfo);
}
- transTreatmentRepository.save(treatments);
+ transTreatmentRepository.saveAll(treatments);
// Update the Foreign Key pdxinfo_id for the corresponding validations
for (Validation validation : validations){
validation.setPdmrPdxInfo(pdmrPdxInfo);
}
- transValidationRepository.save(validations);
+ transValidationRepository.saveAll(validations);
// Update the Foreign key pdxinfo_id for the corresponding samples
for (Sample sample : sampleList){
sample.setPdmrPdxInfo(pdmrPdxInfo);
}
- transSampleRepository.save(sampleList);
+ transSampleRepository.saveAll(sampleList);
log.info("Loaded Record for Patient" + specimenSearch.get("PATIENTID"));
diff --git a/data-services/src/main/java/org/pdxfinder/services/UtilityService.java b/data-services/src/main/java/org/pdxfinder/services/UtilityService.java
index 5e28ead7f0eb9e27ceec7073677b7e8a36996e93..f3f09c341878c4ebd92ba0d2ecd8850724bd851d 100644
--- a/data-services/src/main/java/org/pdxfinder/services/UtilityService.java
+++ b/data-services/src/main/java/org/pdxfinder/services/UtilityService.java
@@ -2,22 +2,20 @@ package org.pdxfinder.services;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.MappingIterator;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.dataformat.csv.CsvMapper;
import com.fasterxml.jackson.dataformat.csv.CsvSchema;
-import org.apache.poi.hssf.usermodel.HSSFCell;
-import org.apache.poi.hssf.usermodel.HSSFRow;
-import org.apache.poi.hssf.usermodel.HSSFSheet;
-import org.apache.poi.hssf.usermodel.HSSFWorkbook;
import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import org.apache.poi.ss.usermodel.*;
import org.apache.poi.xssf.usermodel.XSSFCell;
import org.apache.poi.xssf.usermodel.XSSFRow;
import org.apache.poi.xssf.usermodel.XSSFSheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
+import org.springframework.util.StringUtils;
+import org.springframework.web.multipart.MultipartFile;
import java.io.*;
import java.net.HttpURLConnection;
@@ -30,10 +28,6 @@ import java.util.*;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Stream;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-import org.springframework.util.StringUtils;
-import org.springframework.web.multipart.MultipartFile;
-
/*
* Created by abayomi on 12/02/2019.
*/
@@ -50,7 +44,30 @@ public class UtilityService {
private static final String COMMA_DELIMITER = ",";
private static final String NEW_LINE_SEPARATOR = "\n";
+ /*************************************************************************************************************
+ * DATA SERIALIZER METHODS SECTION *
+ ************************************************************************************************************/
+
+ public List<Map<String, String>> serializeDataToMaps(String fileName) {
+
+
+ String fileExtension = getFileExtension(fileName);
+
+ List<Map<String, String>> csvMaps;
+
+ if (fileExtension.equals("csv")) {
+
+ csvMaps = serializeCSVToMaps(fileName);
+ }else if (fileExtension.equals("json")) {
+
+ csvMaps = (List) serializeJSONToMaps(fileName);
+ } else {
+
+ csvMaps = serializeExcelDataNoIterator(fileName,0,1);
+ }
+ return csvMaps;
+ }
public String serializeToCsvWithIncludeNonEmpty(List<?> pojoList) throws IOException {
@@ -79,33 +96,6 @@ public class UtilityService {
return csvMapper.writer(schema).writeValueAsString(csvData);
}
- /*************************************************************************************************************
- * DATA SERIALIZER METHODS SECTION *
- ************************************************************************************************************/
-
- public List<Map<String, String>> serializeDataToMaps(String fileName) {
-
-
- String fileExtension = getFileExtension(fileName);
-
- List<Map<String, String>> csvMaps;
-
- if (fileExtension.equals("csv")) {
-
- csvMaps = serializeCSVToMaps(fileName);
- }else if (fileExtension.equals("json")) {
-
- csvMaps = (List) serializeJSONToMaps(fileName);
- } else {
-
- csvMaps = serializeExcelDataNoIterator(fileName,0,1);
- }
-
- return csvMaps;
- }
-
-
-
public Map<String, List<Map<String, String>> > serializeAndGroupFileContent(String fileName, String groupColumn) {
String fileExtension = getFileExtension(fileName);
@@ -163,73 +153,17 @@ public class UtilityService {
return groupedMap;
}
-
-
-
-
-
-
-
-
-
-
/*************************************************************************************************************
* MICROSOFT EXCEL FILE HANDLER SECTION *
************************************************************************************************************/
-
-
- // EXCEL FILE READER : READ EXCEL FILE USING ITERATOR, NOT VERY SAFE FOR EMPTY/FORMATTED CELLS
- public List<Map<String, String>> serializeExcelData(String excelURL) {
-
- FileInputStream inputStream = convertFileToStream(excelURL);
-
- int dataRow = 0;
- List<String> tableHead = new ArrayList<>();
- List<Map<String, String>> csvMap = new ArrayList<>();
-
- try(Workbook workbook = WorkbookFactory.create(inputStream)) {
- Row row;
- Sheet spreadsheet = workbook.getSheetAt(0);
- Iterator<Row> rowIterator = spreadsheet.iterator();
-
- while (rowIterator.hasNext()) // Read the rows
- {
- row = rowIterator.next();
- Iterator<Cell> cellIterator = row.cellIterator();
-
- if (dataRow == 0) {
- tableHead = getXlsTableHeadData(cellIterator);
-
- } else {
- Map<String, String> rowMap = getXlsCellData(cellIterator, tableHead);
- csvMap.add(rowMap);
- }
- dataRow++;
- }
-
- inputStream.close();
- } catch (IOException | InvalidFormatException ex) {
- log.warn(ex.getMessage());
- }
-
- return csvMap;
- }
-
-
-
-
// EXCEL FILE READER : READ EXCEL FILE WITHOUT USING ITERATOR, SAFER LOADING FOR EMPTY CELLS
public List<Map<String, String>> serializeExcelDataNoIterator(String excelURL, int sheet, int startRow) {
-
FileInputStream inputStream = convertFileToStream(excelURL);
-
return serializeExcelDataNoIterator(inputStream, sheet, startRow);
-
}
public List<Map<String, String>> serializeExcelDataNoIterator(InputStream inputStream, int sheet, int startRow) {
-
List<String> tableHead = new ArrayList<>();
List<Map<String, String>> csvMap = new ArrayList<>();
@@ -299,11 +233,6 @@ public class UtilityService {
return csvMap;
}
-
-
-
-
- // EXCEL WRITER : CREATE .XLSX FILE
public void writeXLSXFile(List<Map<String, String>> dataList,String fileName, String sheetName) {
String excelFileName = homeDir+"/Downloads/"+fileName;
@@ -356,70 +285,6 @@ public class UtilityService {
}
-
-
- // EXCEL WRITER : CREATE .XLS FILE
- public void writeXLSFile() throws IOException {
-
- String excelFileName = "";//name of excel file
-
- String sheetName = "Sheet1";//name of sheet
-
- try (HSSFWorkbook wb = new HSSFWorkbook()) {
- HSSFSheet sheet = wb.createSheet(sheetName);
-
- //iterating r number of rows
- for (int r = 0; r < 5; r++) {
- HSSFRow row = sheet.createRow(r);
-
- //iterating c number of columns
- for (int c = 0; c < 5; c++) {
- HSSFCell cell = row.createCell(c);
-
- cell.setCellValue("Cell " + r + " " + c);
- }
- }
-
- FileOutputStream fileOut = new FileOutputStream(excelFileName);
-
- //write this workbook to an Outputstream.
- wb.write(fileOut);
- fileOut.flush();
- fileOut.close();
- }
- }
-
-
-
- // GET SMALL SECTIONS OF EXCEL: RETRIEVE FIRST ROW OF EXCEL SHEET
- public List<String> getXlsHead(String excelURL, int sheet) {
-
- FileInputStream inputStream = convertFileToStream(excelURL);
-
- List<String> tableHead = new ArrayList<>();
-
- try(Workbook workbook = WorkbookFactory.create(inputStream)) {
- Row row;
- Sheet spreadsheet = workbook.getSheetAt(sheet);
- Iterator<Row> rowIterator = spreadsheet.iterator();
-
- while (rowIterator.hasNext())
- {
- row = rowIterator.next();
-
- Iterator<Cell> cellIterator = row.cellIterator();
- tableHead = getXlsTableHeadData(cellIterator);
- break;
- }
-
- }catch (Exception e){
- log.warn(e.getMessage());
- }
-
- return tableHead;
- }
-
-
// GET SMALL SECTIONS OF EXCEL: RETRIEVE FIRST ROW OF EXCEL SHEET
public List<String> getXlsTableHeadData(Iterator<Cell> cellIterator){
@@ -437,31 +302,6 @@ public class UtilityService {
return data;
}
-
-
-
- // GET SMALL SECTIONS OF EXCEL: RETRIEVE BODY ROWS OF EXCEL SHEET
- private Map<String, String> getXlsCellData(Iterator<Cell> cellIterator, List<String> tableHead){
-
- Map<String, String> rowMap = new HashMap();
-
- int column = 0;
- while (cellIterator.hasNext())
- {
- Cell cell = cellIterator.next();
-
- if (cell.getCellType() == Cell.CELL_TYPE_NUMERIC){
- rowMap.put(tableHead.get(column).trim(), cell.getNumericCellValue() + "");
- }else {
- rowMap.put(tableHead.get(column).trim(), cell.getStringCellValue() + "");
- }
- column++;
- }
- return rowMap;
- }
-
-
-
// EXCEL CUSTOMIZER : SET EXCEL CELL FONT SIZE AND COLOR
private CellStyle setXLSFont(Workbook wb, int fontSize, IndexedColors colors){
@@ -478,49 +318,34 @@ public class UtilityService {
return headerCellStyle;
}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
/*************************************************************************************************************
* CSV FILE HANDLER SECTION *
************************************************************************************************************/
public List<Map<String, String>> serializeMultipartFile(MultipartFile multipartFile) {
-
- String[] stringArr = multipartFile.getOriginalFilename().split("\\.");
- String type = stringArr[stringArr.length - 1];
-
- // multipartFile.getContentType()
-
- InputStream inputStream = null;
List<Map<String, String>> dataList = new ArrayList<>();
+ if(multipartFile.getOriginalFilename() != null) {
- try {
- inputStream = multipartFile.getInputStream();
- } catch (IOException e) {
- log.warn(e.getMessage());
- }
+ InputStream inputStream = null;
+ String type = "";
+ try {
+ String[] stringArr = multipartFile.getOriginalFilename().split("\\.");
+ type = stringArr[stringArr.length - 1];
- if (type.equals("xlsx")) {
+ inputStream = multipartFile.getInputStream();
+ } catch (Exception e) {
+ log.warn(e.getMessage());
+ }
+ if (type.equals("xlsx")) {
- dataList = serializeExcelDataNoIterator(inputStream, 0, 1);
+ dataList = serializeExcelDataNoIterator(inputStream, 0, 1);
- } else if (type.equals("csv")) {
+ } else if (type.equals("csv")) {
- assert inputStream != null;
- DataInputStream csvData = new DataInputStream(inputStream);
- dataList = serializeCSVToMaps(csvData);
+ assert inputStream != null;
+ DataInputStream csvData = new DataInputStream(inputStream);
+ dataList = serializeCSVToMaps(csvData);
+ }
}
return dataList;
@@ -709,14 +534,6 @@ public class UtilityService {
// write to csv at the specified destination
writeCsvFile(stringMapList, destination);
}
-
-
-
-
-
-
-
-
/*************************************************************************************************************
* JSON FILE HANDLER SECTION *
************************************************************************************************************/
diff --git a/data-services/src/main/java/org/pdxfinder/services/constants/DataProvider.java b/data-services/src/main/java/org/pdxfinder/services/constants/DataProvider.java
index 47c48a758b0610e85772df331f084481f0c6c2be..81969fbb4ce806b5e036b8efe48acc8012a15412 100644
--- a/data-services/src/main/java/org/pdxfinder/services/constants/DataProvider.java
+++ b/data-services/src/main/java/org/pdxfinder/services/constants/DataProvider.java
@@ -3,13 +3,13 @@ package org.pdxfinder.services.constants;
public enum DataProvider {
Test_Minimal("Test-Minimal"),
- PDXNet_HCI_BCM("PDXNet-HCI-BCM"),
+ HCI_BCM("HCI-BCM"),
IRCC_CRC("IRCC-CRC"),
JAX("JAX"),
- PDXNet_MDAnderson("PDXNet-MDAnderson"),
+ MDAnderson("MDAnderson"),
PDMR("PDMR"),
- PDXNet_Wistar_MDAnderson_Penn("PDXNet-Wistar-MDAnderson-Penn"),
- PDXNet_WUSTL("PDXNet-WUSTL"),
+ Wistar_MDAnderson_Penn("Wistar-MDAnderson-Penn"),
+ WUSTL("WUSTL"),
CRL("CRL"),
Curie_BC("Curie-BC"),
Curie_LC("Curie-LC"),
@@ -23,12 +23,13 @@ public enum DataProvider {
VHIO_CRC("VHIO-CRC"),
DFCI_CPDM("DFCI-CPDM"),
NKI("NKI"),
- PIPELINE("PIPELINE"),
JAX_XDOG("JAX-XDOG"),
SJCRH("SJCRH"),
UMCG("UMCG"),
VHIO_PC("VHIO-PC"),
- LIH("LIH");
+ LIH("LIH"),
+ PPTC("PPTC"),
+ PIPELINE("PIPELINE");
private String name;
DataProvider(String name) {
@@ -40,3 +41,4 @@ public enum DataProvider {
return name;
}
}
+
diff --git a/data-services/src/main/java/org/pdxfinder/services/constants/DataProviderGroup.java b/data-services/src/main/java/org/pdxfinder/services/constants/DataProviderGroup.java
index 599c609d36679f2cf7a588966bf14f28c4a79b9c..a36de1cac1775c49a0e45e5aa18696c100bf0891 100644
--- a/data-services/src/main/java/org/pdxfinder/services/constants/DataProviderGroup.java
+++ b/data-services/src/main/java/org/pdxfinder/services/constants/DataProviderGroup.java
@@ -1,12 +1,14 @@
package org.pdxfinder.services.constants;
import java.util.Arrays;
+import java.util.Collections;
import java.util.EnumMap;
import java.util.List;
public enum DataProviderGroup {
All,
EurOPDX,
+ PDXNet,
UPDOG,
CustomLoaders;
@@ -15,14 +17,6 @@ public enum DataProviderGroup {
EnumMap<DataProviderGroup, List<DataProvider>> map = new EnumMap<>(DataProviderGroup.class);
map.put(DataProviderGroup.All, Arrays.asList(DataProvider.values()));
-
- // DS: temp
- /*
- map.put(DataProviderGroup.EurOPDX, Arrays.asList(
- DataProvider.Curie_LC
- ));
- */
-
map.put(DataProviderGroup.EurOPDX, Arrays.asList(
DataProvider.Curie_BC,
DataProvider.Curie_LC,
@@ -35,13 +29,12 @@ public enum DataProviderGroup {
DataProvider.VHIO_BC,
DataProvider.VHIO_CRC,
DataProvider.NKI,
- DataProvider.PIPELINE,
DataProvider.UMCG,
DataProvider.VHIO_PC,
- DataProvider.LIH
+ DataProvider.LIH,
+ DataProvider.PPTC
));
-
map.put(DataProviderGroup.UPDOG, Arrays.asList(
DataProvider.IRCC_GC,
DataProvider.IRCC_CRC,
@@ -63,15 +56,23 @@ public enum DataProviderGroup {
DataProvider.SJCRH,
DataProvider.UMCG,
DataProvider.VHIO_PC,
- DataProvider.LIH
+ DataProvider.LIH,
+ DataProvider.PPTC,
+ DataProvider.WUSTL,
+ DataProvider.MDAnderson,
+ DataProvider.Wistar_MDAnderson_Penn,
+ DataProvider.HCI_BCM
+ ));
+
+ map.put(DataProviderGroup.PDXNet, Arrays.asList(
+ DataProvider.WUSTL,
+ DataProvider.MDAnderson,
+ DataProvider.Wistar_MDAnderson_Penn,
+ DataProvider.HCI_BCM
));
- map.put(DataProviderGroup.CustomLoaders, Arrays.asList(
- DataProvider.JAX,
- DataProvider.PDXNet_MDAnderson,
- DataProvider.PDXNet_HCI_BCM,
- DataProvider.PDXNet_Wistar_MDAnderson_Penn,
- DataProvider.PDXNet_WUSTL
+ map.put(DataProviderGroup.CustomLoaders, Collections.singletonList(
+ DataProvider.JAX
));
return map.get(group);
diff --git a/data-services/src/main/java/org/pdxfinder/services/constants/DataUrl.java b/data-services/src/main/java/org/pdxfinder/services/constants/DataUrl.java
index 338dd892eec20a6ba9a5d766b1df9814cd158f89..f464cf145163531f314778bea875a4cf0f9b7e5e 100644
--- a/data-services/src/main/java/org/pdxfinder/services/constants/DataUrl.java
+++ b/data-services/src/main/java/org/pdxfinder/services/constants/DataUrl.java
@@ -16,7 +16,7 @@ public enum DataUrl {
private String value;
- private DataUrl(String val) {
+ DataUrl(String val) {
value = val;
}
diff --git a/data-services/src/main/java/org/pdxfinder/services/constants/OmicCSVColumn.java b/data-services/src/main/java/org/pdxfinder/services/constants/OmicCSVColumn.java
index f9b2c6fd52530a6e675e6451fe99f11cc13b962b..5045c0f18145c94cbf374909eb5aca5f0d1a88dc 100644
--- a/data-services/src/main/java/org/pdxfinder/services/constants/OmicCSVColumn.java
+++ b/data-services/src/main/java/org/pdxfinder/services/constants/OmicCSVColumn.java
@@ -32,7 +32,7 @@ public enum OmicCSVColumn {
private String value;
- private OmicCSVColumn(String val) {
+ OmicCSVColumn(String val) {
value = val;
}
diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java b/data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java
index 90e813dff5c13801dad763e6142fb7988d5c0d45..9d809e92432bf73082f4ce92dab30289450a8a4f 100644
--- a/data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java
+++ b/data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java
@@ -1,18 +1,9 @@
package org.pdxfinder.services.ds;
-import org.apache.commons.lang3.StringUtils;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.graph.dao.QualityAssurance;
+import com.github.openjson.*;
import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
import org.springframework.beans.factory.annotation.Autowired;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
public class Harmonizer {
diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java b/data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java
index a87d9eec7792e494a31ed6977f1bf77bf2498c13..ac88ec6156cdfb6a724dc7d23058c89f428a1d7f 100644
--- a/data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java
+++ b/data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java
@@ -2,13 +2,9 @@ package org.pdxfinder.services.ds;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONException;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.graph.dao.DataProjection;
import org.pdxfinder.graph.repositories.DataProjectionRepository;
-import org.pdxfinder.services.search.WebFacetSection;
-import org.pdxfinder.services.search.WebFacetContainer;
import org.pdxfinder.services.search.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -16,12 +12,10 @@ import org.springframework.cache.annotation.Cacheable;
import org.springframework.stereotype.Component;
import org.springframework.util.Assert;
-import java.lang.reflect.Array;
import java.util.*;
import java.util.function.Predicate;
import java.util.stream.Collectors;
-
import static java.lang.Long.parseLong;
@@ -251,6 +245,9 @@ public class SearchDS {
pdxModelSection.addComponent(datasource);
facetOptionMap.put("datasource", datasourceOptions);
+ OneParamTextFilter modelId = new OneParamTextFilter("MODEL ID", "model_id", false,
+ FilterType.OneParamTextFilter.get(), "MODEL", getUniqueModelIds(), new ArrayList<>());
+ pdxModelSection.addComponent(modelId);
//project filter def
Set<String> projectsSet = new HashSet<>();
@@ -614,21 +611,8 @@ public class SearchDS {
switch(facet){
case query:
-
- /*
- Set<ModelForQuery> result_2 = oneParamCheckboxSearch.searchOnCollection_model(filters.get(SearchFacetName.query), result);
- if (result_2.size() == 0) {
- result = oneParamCheckboxSearch.searchOnCollection(facetOptionMap.get("query"), filters.get(SearchFacetName.query), result, ModelForQuery::getAllOntologyTermAncestors);
- } else {
- result = result_2;
- }
- */
-
- Set<ModelForQuery> result_2 = oneParamCheckboxSearch.searchOnCollection_model(filters.get(SearchFacetName.query), result);
+ //List<String> searchParams, Set<ModelForQuery> mfqSet, Function<ModelForQuery, List<String>> searchFunc
result = oneParamCheckboxSearch.searchOnCollection(facetOptionMap.get("query"), filters.get(SearchFacetName.query), result, ModelForQuery::getAllOntologyTermAncestors);
-
- result.addAll(result_2);
-
break;
//We don't need to provide a replacement string list for datasource, since it is already using the datasource abbrev as key!
@@ -727,6 +711,9 @@ public class SearchDS {
result = cytogeneticsSearch.search(filters.get(SearchFacetName.cytogenetics), result, ModelForQuery::addCytogenetics);
break;
+ case model_id:
+ result = oneParamCheckboxSearch.searchOnString(null, filters.get(SearchFacetName.model_id), result, ModelForQuery::getExternalId);
+
default:
//undexpected filter option
log.warn("Unrecognised facet {} passed to search, skipping", facet.getName());
@@ -760,8 +747,15 @@ public class SearchDS {
this.models = models;
}
+ public List<String> getModelIds(){
+ return models.stream().distinct().map(s->s.getExternalId()).collect(Collectors.toList());
+ }
+ public List<String> getUniqueModelIds(){
+
+ return getModelIds().stream().distinct().collect(Collectors.toList());
+ }
/**
* This method loads the ModelForQuery Data Projection object and initializes the models
@@ -1271,4 +1265,4 @@ public class SearchDS {
}
-}
+}
\ No newline at end of file
diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java b/data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java
index 29125cac267165bd0728e207dc8391bb9deb820d..74844b1b59119d5b01499c49a51641cf9ba51164 100644
--- a/data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java
+++ b/data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java
@@ -25,7 +25,8 @@ public enum SearchFacetName {
copy_number_alteration,
patient_treatment,
gene_expression,
- cytogenetics;
+ cytogenetics,
+ model_id;
public String getName() {
return name();
diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java b/data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java
index 61bbd5269d02cd7edaaf034f18f9e97df39bc7c9..70bf753f6d0e4fba0fb1f3dbfec89d52a898b749 100644
--- a/data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java
+++ b/data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java
@@ -1,20 +1,9 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
package org.pdxfinder.services.ds;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.graph.dao.Drug;
-import org.pdxfinder.graph.dao.Response;
-import org.pdxfinder.graph.dao.TreatmentComponent;
-import org.pdxfinder.graph.dao.TreatmentProtocol;
+
+import com.github.openjson.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import java.security.spec.ECField;
-import java.util.ArrayList;
-
/**
*
* @author sbn
diff --git a/data-services/src/main/java/org/pdxfinder/services/dto/LoaderDTO.java b/data-services/src/main/java/org/pdxfinder/services/dto/LoaderDTO.java
index 4af5ab5e832fb421ab0aea576de9164b736fb60b..dcb293ccced38584a1997d9ec081c5335df86dad 100644
--- a/data-services/src/main/java/org/pdxfinder/services/dto/LoaderDTO.java
+++ b/data-services/src/main/java/org/pdxfinder/services/dto/LoaderDTO.java
@@ -1,6 +1,6 @@
package org.pdxfinder.services.dto;
-import org.neo4j.ogm.json.JSONArray;
+import com.github.openjson.JSONArray;
import org.pdxfinder.graph.dao.*;
import java.util.HashMap;
diff --git a/data-services/src/main/java/org/pdxfinder/services/dto/europepmc/Publication.java b/data-services/src/main/java/org/pdxfinder/services/dto/europepmc/Publication.java
index ec724d73a57860d8cce2553cb8fcff87efc501fb..16d8928b288409e8da8f97aec74d7c18707436b3 100644
--- a/data-services/src/main/java/org/pdxfinder/services/dto/europepmc/Publication.java
+++ b/data-services/src/main/java/org/pdxfinder/services/dto/europepmc/Publication.java
@@ -2,7 +2,9 @@ package org.pdxfinder.services.dto.europepmc;
import com.fasterxml.jackson.annotation.JsonInclude;
-import java.util.*;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
@JsonInclude(JsonInclude.Include.NON_NULL)
public class Publication {
diff --git a/data-services/src/main/java/org/pdxfinder/services/dto/pdxgun/Reference.java b/data-services/src/main/java/org/pdxfinder/services/dto/pdxgun/Reference.java
index 784b3cd7305570251561f95d3ff7d9946611a502..dc22f2bb8a120325e8eb18d6c8cc1804ce8de5f0 100644
--- a/data-services/src/main/java/org/pdxfinder/services/dto/pdxgun/Reference.java
+++ b/data-services/src/main/java/org/pdxfinder/services/dto/pdxgun/Reference.java
@@ -1,7 +1,5 @@
package org.pdxfinder.services.dto.pdxgun;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
import java.util.Map;
public class Reference {
diff --git a/data-services/src/main/java/org/pdxfinder/services/graphqlclient/Operator.java b/data-services/src/main/java/org/pdxfinder/services/graphqlclient/Operator.java
index 04726731a0ef2494c8ba2f65c154f1312ab5ec1d..3ecbb76eede378a79e9fd5323d504b0a9c2d7b6f 100644
--- a/data-services/src/main/java/org/pdxfinder/services/graphqlclient/Operator.java
+++ b/data-services/src/main/java/org/pdxfinder/services/graphqlclient/Operator.java
@@ -6,7 +6,7 @@ public enum Operator {
IN("_in:");
private String value;
- private Operator(String val) {
+ Operator(String val) {
value = val;
}
public String get() {
diff --git a/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadMarkers.java b/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadMarkers.java
index 9e0acaf180e402f38f8b7b132330d036e0374cef..84620f4f37f2079ccf51fed6211cd6a277405e5d 100644
--- a/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadMarkers.java
+++ b/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadMarkers.java
@@ -7,11 +7,16 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
-import java.time.*;
-import java.util.*;
+import java.time.Duration;
+import java.time.Instant;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
@Service
public class LoadMarkers {
@@ -27,7 +32,7 @@ public class LoadMarkers {
public void loadGenes(String dataURL) {
Instant start = Instant.now();
- log.info("Downloading latest marker data from {}...", dataURL);
+ log.info("Downloading latest marker data from {}...", dataURL.substring(0, 50));
BufferedReader reader = downloadDataFromURL(dataURL);
List<Marker> markers = parseMarkers(reader);
dataImportService.saveAllMarkers(markers);
diff --git a/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadNCIT.java b/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadNCIT.java
index 52870761d20419e82cef1438fd42cb2d2167aef9..f661d799a19bd63bc65dd1c7d823f74f90feb46a 100644
--- a/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadNCIT.java
+++ b/data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadNCIT.java
@@ -1,7 +1,6 @@
package org.pdxfinder.services.loader.envload;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.graph.dao.OntologyTerm;
import org.pdxfinder.services.DataImportService;
import org.pdxfinder.services.UtilityService;
@@ -10,16 +9,10 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.UnsupportedEncodingException;
+import java.io.*;
import java.net.URLEncoder;
-import java.time.Duration;
-import java.time.Instant;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
+import java.time.*;
+import java.util.*;
@Service
public class LoadNCIT {
diff --git a/data-services/src/main/java/org/pdxfinder/services/ontology/Ontolia.java b/data-services/src/main/java/org/pdxfinder/services/ontology/Ontolia.java
index 878e4d2742cec7f8c3035bcca9789815469da68f..6b5ba9fd88b61e3c1514ad0f88e1c2112bd3097b 100644
--- a/data-services/src/main/java/org/pdxfinder/services/ontology/Ontolia.java
+++ b/data-services/src/main/java/org/pdxfinder/services/ontology/Ontolia.java
@@ -1,7 +1,6 @@
package org.pdxfinder.services.ontology;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.graph.dao.OntologyTerm;
import org.pdxfinder.services.DataImportService;
import org.pdxfinder.services.UtilityService;
diff --git a/data-services/src/main/java/org/pdxfinder/services/pdf/Label.java b/data-services/src/main/java/org/pdxfinder/services/pdf/Label.java
index 36ef7d1045ef4948f8f1c7074bd10684c5436b7f..49672b0b83d22638ea58d710d34f37aa36b09032 100755
--- a/data-services/src/main/java/org/pdxfinder/services/pdf/Label.java
+++ b/data-services/src/main/java/org/pdxfinder/services/pdf/Label.java
@@ -81,7 +81,7 @@ public enum Label {
private String value;
- private Label(String val) {
+ Label(String val) {
value = val;
}
diff --git a/data-services/src/main/java/org/pdxfinder/services/search/OneParamCheckboxSearch.java b/data-services/src/main/java/org/pdxfinder/services/search/OneParamCheckboxSearch.java
index 59a9b9f4afa333b059735aa8835f1ca438449bd9..03ea63a70ab63ecedfe6adeb79cb36a0412e6ebe 100644
--- a/data-services/src/main/java/org/pdxfinder/services/search/OneParamCheckboxSearch.java
+++ b/data-services/src/main/java/org/pdxfinder/services/search/OneParamCheckboxSearch.java
@@ -58,28 +58,6 @@ public class OneParamCheckboxSearch extends GeneralSearch{
}
- public Set<ModelForQuery> searchOnCollection_model(List<String> searchParams, Set<ModelForQuery> mfqSet){
-
- Set<ModelForQuery> results = new HashSet<>();
-
- List<String> queryItems = Arrays.asList(searchParams.get(0).split(","));
-
- for(ModelForQuery mfq: mfqSet) {
-
- if (queryItems.contains(mfq.getExternalId())) {
- results.add(mfq);
- }
-
- /*
- if (mfq.getExternalId().equals(searchParams.get(0))) {
- results.add(mfq);
- }
- */
- }
- return results;
- }
-
-
/**
* Performs a search on a selected ModelForQuery field that's type is List of Strings
@@ -93,8 +71,7 @@ public class OneParamCheckboxSearch extends GeneralSearch{
List<String> decodedSearchParams = new ArrayList<>();
if(replacementStrings == null){
- // decodedSearchParams = searchParams;
- decodedSearchParams = Arrays.asList(searchParams.get(0).split(","));
+ decodedSearchParams = searchParams;
}
else{
diff --git a/data-services/src/test/java/org/pdxfinder/DataImportServiceTests.java b/data-services/src/test/java/org/pdxfinder/DataImportServiceTests.java
index fd59244e40f02cefa441fc4d303540e517879a8d..195567d69d7a28ad38120789e5ce9b1d92b2718e 100644
--- a/data-services/src/test/java/org/pdxfinder/DataImportServiceTests.java
+++ b/data-services/src/test/java/org/pdxfinder/DataImportServiceTests.java
@@ -1,5 +1,6 @@
package org.pdxfinder;
+import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.when;
import org.junit.Assert;
@@ -8,11 +9,11 @@ import org.junit.Test;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Spy;
+import org.pdxfinder.graph.dao.DataProjection;
import org.pdxfinder.graph.dao.Group;
import org.pdxfinder.graph.dao.Patient;
import org.pdxfinder.graph.dao.PatientSnapshot;
-import org.pdxfinder.graph.repositories.PatientRepository;
-import org.pdxfinder.graph.repositories.PatientSnapshotRepository;
+import org.pdxfinder.graph.repositories.*;
import org.pdxfinder.services.DataImportService;
import org.springframework.beans.factory.annotation.Autowired;
@@ -20,11 +21,31 @@ import java.util.HashSet;
public class DataImportServiceTests extends BaseTest {
- @Mock
- private PatientSnapshotRepository patientSnapshotRepository;
-
- @Mock
- private PatientRepository patientRepository;
+ @Mock private TumorTypeRepository tumorTypeRepository;
+ @Mock private HostStrainRepository hostStrainRepository;
+ @Mock private EngraftmentTypeRepository engraftmentTypeRepository;
+ @Mock private EngraftmentSiteRepository engraftmentSiteRepository;
+ @Mock private EngraftmentMaterialRepository engraftmentMaterialRepository;
+ @Mock private GroupRepository groupRepository;
+ @Mock private PatientRepository patientRepository;
+ @Mock private ModelCreationRepository modelCreationRepository;
+ @Mock private TissueRepository tissueRepository;
+ @Mock private PatientSnapshotRepository patientSnapshotRepository;
+ @Mock private SampleRepository sampleRepository;
+ @Mock private MarkerRepository markerRepository;
+ @Mock private MarkerAssociationRepository markerAssociationRepository;
+ @Mock private MolecularCharacterizationRepository molecularCharacterizationRepository;
+ @Mock private QualityAssuranceRepository qualityAssuranceRepository;
+ @Mock private OntologyTermRepository ontologyTermRepository;
+ @Mock private SpecimenRepository specimenRepository;
+ @Mock private PlatformRepository platformRepository;
+ @Mock private PlatformAssociationRepository platformAssociationRepository;
+ @Mock private DataProjectionRepository dataProjectionRepository;
+ @Mock private TreatmentSummaryRepository treatmentSummaryRepository;
+ @Mock private TreatmentProtocolRepository treatmentProtocolRepository;
+ @Mock private CurrentTreatmentRepository currentTreatmentRepository;
+ @Mock private ExternalUrlRepository externalUrlRepository;
+ @Mock private TreatmentRepository treatmentRepository;
@Spy
@InjectMocks
@@ -109,22 +130,6 @@ public class DataImportServiceTests extends BaseTest {
Assert.assertEquals(ELAPSED_TIME, actualSnapshot.getDateAtCollection());
}
- @Test
- public void Given_GetPatientSnapshot6Param_When_PatientInDB_Then_ReturnNewPSforPatient(){
-
- when(patientRepository.findByExternalIdAndGroup(EXTERNAL_ID, GROUP))
- .thenReturn(PATIENT);
-
- when(dataImportService.getPatientSnapshot(PATIENT, AGE_AT_COLLECTION))
- .thenReturn(actualSnapshot);
-
- actualSnapshot = dataImportService.getPatientSnapshot(EXTERNAL_ID, SEX, RACE,
- ETHNICITY, AGE_AT_COLLECTION, GROUP);
-
- Assert.assertEquals(PATIENT, actualSnapshot.getPatient());
- Assert.assertEquals(AGE_AT_COLLECTION, actualSnapshot.getAgeAtCollection());
- }
-
@Test
public void Given_getPatientSnapshot6Param_When_ValidArgAndNoPatientInDB_Then_ReturnMatchingPS(){
@@ -154,5 +159,16 @@ public class DataImportServiceTests extends BaseTest {
}
+ @Test
+ public void Given_DataProjection_When_Save_Then_Saved(){
+
+ DataProjection dataProjection = new DataProjection();
+ dataProjection.setLabel("test");
+ when(dataProjectionRepository.save(any())).thenReturn(dataProjection);
+ Assert.assertEquals("test", dataImportService.saveDataProjection(dataProjection).getLabel());
+ }
+
}
+
+
diff --git a/data-services/src/test/java/org/pdxfinder/TestConfig.java b/data-services/src/test/java/org/pdxfinder/TestConfig.java
index 265845167d5957275a2f3d85156865a003e6f457..ca06792597007118f8af3e0faea8dfbedd49dc87 100755
--- a/data-services/src/test/java/org/pdxfinder/TestConfig.java
+++ b/data-services/src/test/java/org/pdxfinder/TestConfig.java
@@ -2,9 +2,11 @@ package org.pdxfinder;
import org.neo4j.ogm.session.SessionFactory;
+import org.pdxfinder.configurations.DataServicesConfig;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.FilterType;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.data.neo4j.repository.config.EnableNeo4jRepositories;
import org.springframework.data.neo4j.transaction.Neo4jTransactionManager;
@@ -14,11 +16,12 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import org.springframework.web.client.RestTemplate;
-import org.thymeleaf.spring4.SpringTemplateEngine;
-import org.thymeleaf.spring4.templateresolver.SpringResourceTemplateResolver;
+import org.thymeleaf.spring5.SpringTemplateEngine;
+import org.thymeleaf.spring5.templateresolver.SpringResourceTemplateResolver;
import javax.sql.DataSource;
import java.nio.charset.StandardCharsets;
+import java.nio.file.Paths;
/**
@@ -27,7 +30,7 @@ import java.nio.charset.StandardCharsets;
*/
@Configuration
@EnableTransactionManagement
-@ComponentScan(value = "org.pdxfinder")
+@ComponentScan(value = "org.pdxfinder", excludeFilters = @ComponentScan.Filter(type= FilterType.ASSIGNABLE_TYPE, classes = DataServicesConfig.class))
@EnableNeo4jRepositories("org.pdxfinder.graph.repositories")
@EnableJpaRepositories(basePackages = "org.pdxfinder.rdbms.repositories")
public class TestConfig {
@@ -35,16 +38,11 @@ public class TestConfig {
@Bean
public org.neo4j.ogm.config.Configuration getConfiguration() {
- org.neo4j.ogm.config.Configuration config = new org.neo4j.ogm.config.Configuration();
+ org.neo4j.ogm.config.Configuration config = new org.neo4j.ogm.config.Configuration.Builder().build();
- // To persist the database, uncomment this section
- // String pathToDb = Paths.get(".").toAbsolutePath().normalize().toString() + "/target/test_graph.db";
- // config
- // .driverConfiguration()
- // .setDriverClassName("org.neo4j.ogm.drivers.embedded.driver.EmbeddedDriver")
- // .setURI("file://" + pathToDb);
- //
- // System.out.println(config);
+ org.neo4j.ogm.config.Configuration configWithPersistance = new org.neo4j.ogm.config.Configuration.Builder()
+ .uri("file://" + Paths.get(".").toAbsolutePath().normalize().toString() + "/target/test_graph.db")
+ .build();
return config;
}
@@ -109,3 +107,4 @@ public class TestConfig {
}
+
diff --git a/data-services/src/test/java/org/pdxfinder/services/DetailsServiceTest.java b/data-services/src/test/java/org/pdxfinder/services/DetailsServiceTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..785623571d710560a62b21321d39dc10eecb3107
--- /dev/null
+++ b/data-services/src/test/java/org/pdxfinder/services/DetailsServiceTest.java
@@ -0,0 +1,106 @@
+package org.pdxfinder.services;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.MockitoAnnotations;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.MarkerAssociation;
+import org.pdxfinder.graph.dao.MolecularCharacterization;
+import org.pdxfinder.graph.dao.MolecularData;
+import org.pdxfinder.graph.dao.Sample;
+import org.pdxfinder.graph.repositories.MolecularCharacterizationRepository;
+import org.pdxfinder.graph.repositories.SampleRepository;
+import org.pdxfinder.services.dto.MolecularDataTableDTO;
+import static org.mockito.Mockito.*;
+import java.util.HashMap;
+import java.util.Map;
+
+public class DetailsServiceTest extends BaseTest {
+
+ @InjectMocks
+ private DetailsService detailsService;
+
+ @Mock
+ MolecularCharacterizationRepository molecularCharacterizationRepository;
+
+ @Mock
+ SampleRepository sampleRepository;
+
+ @Mock
+ ReferenceDbService referenceDbService;
+
+ Map<String, MolecularCharacterization> molchars;
+ Sample sample;
+
+ @Before
+ public void init(){
+ MockitoAnnotations.initMocks(this);
+ molchars = initMolchars();
+ sample = new Sample();
+ sample.setSourceSampleId("test");
+ }
+
+ @Test
+ public void given_MolcharId_When_GetMolcharTable_Then_CorrectContentReturned(){
+ when(detailsService.getMolcharData("1")).thenReturn(molchars.get("1"));
+ when(detailsService.getMolcharData("2")).thenReturn(molchars.get("2"));
+ when(detailsService.getMolcharData("3")).thenReturn(molchars.get("3"));
+ when(sampleRepository.findSampleByMolcharId(anyLong())).thenReturn(sample);
+ when(referenceDbService.getReferenceData(any(), any())).thenReturn(new HashMap<>());
+ MolecularDataTableDTO table1 = detailsService.getMolecularDataTable("1", false);
+ MolecularDataTableDTO table2 = detailsService.getMolecularDataTable("2", false);
+ MolecularDataTableDTO table3 = detailsService.getMolecularDataTable("3", false);
+
+ Assert.assertEquals(3, table1.getMolecularDataRows().size());
+ Assert.assertEquals(0, table2.getMolecularDataRows().size());
+ Assert.assertEquals(0, table3.getMolecularDataRows().size());
+
+ }
+
+
+
+
+ private Map<String, MolecularCharacterization> initMolchars(){
+
+ Map<String, MolecularCharacterization> molecularCharacterizationMap = new HashMap();
+
+ MolecularCharacterization mc1 = new MolecularCharacterization();
+ MarkerAssociation ma1 = new MarkerAssociation();
+ ma1.setMolecularDataString("[{\"cytogeneticsResult\":\"postive\",\"marker\":\"ESR1\"},{\"cytogeneticsResult\":\"postive\",\"marker\":\"PGR\"},{\"cytogeneticsResult\":\"negative\",\"marker\":\"ERBB2\"}]");
+ ma1.setDataPoints(3);
+ mc1.addMarkerAssociation(ma1);
+ mc1.setVisible(true);
+
+ MolecularCharacterization mc2 = new MolecularCharacterization();
+ MarkerAssociation ma2 = new MarkerAssociation();
+ ma2.setMolecularDataString("[{\"cytogeneticsResult\":\"postive\",\"marker\":\"ESR1\"},{\"cytogeneticsResult\":\"postive\",\"marker\":\"PGR\"},{\"cytogeneticsResult\":\"negative\",\"marker\":\"ERBB2\"}]");
+ ma2.setDataPoints(3);
+ mc2.addMarkerAssociation(ma2);
+ mc2.setVisible(false);
+
+ MolecularCharacterization mc3 = new MolecularCharacterization();
+ MarkerAssociation ma3 = new MarkerAssociation();
+ ma3.setDataPoints(400);
+ mc3.setVisible(true);
+
+ for(int i=0;i<400;i++){
+ MolecularData md = new MolecularData();
+ md.setMarker("ABC");
+ md.setCytogeneticsResult("negative");
+ ma3.addMolecularData(md);
+ }
+ ma3.encodeMolecularData();
+ mc3.addMarkerAssociation(ma3);
+
+
+ molecularCharacterizationMap.put("1", mc1);
+ molecularCharacterizationMap.put("2", mc2);
+ molecularCharacterizationMap.put("3", mc3);
+
+ return molecularCharacterizationMap;
+ }
+
+}
diff --git a/data-services/src/test/java/org/pdxfinder/services/MappingServiceTest.java b/data-services/src/test/java/org/pdxfinder/services/MappingServiceTest.java
index 0ff27f56f3878cae2bac490f9dc9a0a62e7a4f4e..11f675f0191096614da46aa59eedcbf6591a8aa6 100644
--- a/data-services/src/test/java/org/pdxfinder/services/MappingServiceTest.java
+++ b/data-services/src/test/java/org/pdxfinder/services/MappingServiceTest.java
@@ -6,6 +6,7 @@ import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.pdxfinder.BaseTest;
import org.pdxfinder.rdbms.repositories.MappingEntityRepository;
+
import static org.mockito.Mockito.*;
public class MappingServiceTest extends BaseTest {
@@ -13,6 +14,9 @@ public class MappingServiceTest extends BaseTest {
@Mock
private MappingEntityRepository mappingEntityRepository;
+ @Mock
+ private UtilityService utilityService;
+
@InjectMocks
private MappingService mappingService;
@@ -32,6 +36,21 @@ public class MappingServiceTest extends BaseTest {
}
+ @Test(expected = IllegalArgumentException.class)
+ public void given_directoryAttack_when_entityIsWrittenToFile_Then_throwArgumentException() {
+ mappingService.setRootDir("/tmp");
+ String attackVector = "../../..";
+ mappingService.writeMappingsToFile(attackVector);
+ }
+
+ @Test
+ public void given_AplhaNumericAndHyphenatedDir_when_entityIsWrittenToFile_Then_doNotThrowArgumentException() {
+ mappingService.setRootDir("/tmp");
+ String normalEntity= "TReatment-90_90-HELLO--";
+ mappingService.writeMappingsToFile(normalEntity);
+ }
+
+
}
diff --git a/data-services/src/test/java/org/pdxfinder/services/MolcharTableTest.java b/data-services/src/test/java/org/pdxfinder/services/MolcharTableTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..3308248925ec8b360c19d85cd4aae63aa9a23cd4
--- /dev/null
+++ b/data-services/src/test/java/org/pdxfinder/services/MolcharTableTest.java
@@ -0,0 +1,87 @@
+package org.pdxfinder.services;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.repositories.MolecularCharacterizationRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.List;
+
+/*
+ * Created by csaba on 18/03/2019.
+ */
+public class MolcharTableTest extends BaseTest{
+
+
+ private final static Logger log = LoggerFactory.getLogger(MolcharTableTest.class);
+
+ @Autowired
+ private MolecularCharacterizationRepository molecularCharacterizationRepository;
+
+ List<Long> molcharNodeIds;
+
+ @Before
+ public void setUp(){
+ //log.info("Getting molchar node ids");
+ //molcharNodeIds = molecularCharacterizationRepository.getAllMolCharIDs();
+
+ //log.info("Found "+molcharNodeIds.size()+ " molchar nodes");
+ }
+
+
+
+ @Test
+ public void visitAllMolcharUrls(){
+
+/*
+
+ for(Long id: molcharNodeIds){
+
+ }
+
+ try{
+
+ String url = "/getmoleculardata/"+molcharNodeIds.get(0);
+ log.info("Getting data from: "+url);
+ String response = getText(url);
+
+ System.out.println(response);
+
+ }
+ catch (Exception e){
+ e.printStackTrace();
+ }
+
+
+
+*/
+ }
+
+
+ public static String getText(String url) throws Exception {
+ URL website = new URL(url);
+ URLConnection connection = website.openConnection();
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(
+ connection.getInputStream()));
+
+ StringBuilder response = new StringBuilder();
+ String inputLine;
+
+ while ((inputLine = in.readLine()) != null)
+ response.append(inputLine);
+
+ in.close();
+
+ return response.toString();
+
+ }
+
+}
diff --git a/data-services/src/test/java/org/pdxfinder/services/PublicationServiceTest.java b/data-services/src/test/java/org/pdxfinder/services/PublicationServiceTest.java
index 7180c511bcf87cedb224093ca0fde9fc46a60f76..9a04319602172486857f17670f0191e95dde8ea8 100644
--- a/data-services/src/test/java/org/pdxfinder/services/PublicationServiceTest.java
+++ b/data-services/src/test/java/org/pdxfinder/services/PublicationServiceTest.java
@@ -1,13 +1,8 @@
package org.pdxfinder.services;
-import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.node.ObjectNode;
import org.junit.Before;
import org.junit.Test;
-import org.mockito.InjectMocks;
-import org.mockito.Mock;
-import org.mockito.Mockito;
import org.pdxfinder.BaseTest;
import org.pdxfinder.services.constants.DataUrl;
import org.pdxfinder.services.dto.europepmc.Publication;
@@ -18,7 +13,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpMethod;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
-import org.springframework.http.ResponseEntity;
import org.springframework.test.web.client.ExpectedCount;
import org.springframework.test.web.client.MockRestServiceServer;
import org.springframework.web.client.RestTemplate;
@@ -30,10 +24,9 @@ import java.util.List;
import java.util.Map;
import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-
-import static org.springframework.test.web.client.match.MockRestRequestMatchers.*;
-import static org.springframework.test.web.client.response.MockRestResponseCreators.*;
+import static org.springframework.test.web.client.match.MockRestRequestMatchers.method;
+import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
+import static org.springframework.test.web.client.response.MockRestResponseCreators.withStatus;
public class PublicationServiceTest extends BaseTest {
@@ -62,7 +55,7 @@ public class PublicationServiceTest extends BaseTest {
// given
String pubMedId = "29245952";
- String apiUrl = String.format("%s?query=%s&resultType=core&format=json", DataUrl.EUROPE_PMC_URL.get(), pubMedId);
+ String apiUrl = String.format("%s?query=ext_id:%s&resultType=core&format=json", DataUrl.EUROPE_PMC_URL.get(), pubMedId);
String expectedTitle= "The humanized anti-human AMHRII mAb 3C23K exerts an anti-tumor activity against human ovarian cancer through tumor-associated macrophages.";
String expectedAuthors= "Bougherara H, Némati F, Nicolas A, Massonnet G, Pugnière M, Ngô C, Le Frère-Belda MA";
diff --git a/data-services/src/test/java/org/pdxfinder/services/SearchServiceTest.java b/data-services/src/test/java/org/pdxfinder/services/SearchServiceTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..96609da7d45059103ad3cb3fabefc0df9485ac3d
--- /dev/null
+++ b/data-services/src/test/java/org/pdxfinder/services/SearchServiceTest.java
@@ -0,0 +1,41 @@
+package org.pdxfinder.services;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.repositories.SampleRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.util.Assert;
+
+/**
+ * Created by jmason on 06/07/2017.
+ */
+public class SearchServiceTest extends BaseTest {
+
+ private final static Logger log = LoggerFactory.getLogger(SearchServiceTest.class);
+
+ @MockBean
+ private SampleRepository sampleRepository;
+
+ @Before
+ public void setup() {
+ // Preload the base data in the graph for testing the service
+ log.info("Set up");
+ }
+
+ @Test
+ public void searchForBreastCancerModels() throws Exception {
+
+ log.info("Testing mock sample repository");
+ Assert.notNull(sampleRepository, "Sample repo is null");
+
+ }
+
+ @Test
+ public void anotherTest() {
+ log.info("This is another test");
+ }
+
+}
\ No newline at end of file
diff --git a/data-services/src/test/java/org/pdxfinder/services/UtilityServiceTest.java b/data-services/src/test/java/org/pdxfinder/services/UtilityServiceTest.java
index 4c2ae3ced2e570cc46b4be09bbba442cc63fd737..278fc52350d7af8237046fc73cc294e6fe1145cc 100644
--- a/data-services/src/test/java/org/pdxfinder/services/UtilityServiceTest.java
+++ b/data-services/src/test/java/org/pdxfinder/services/UtilityServiceTest.java
@@ -1,6 +1,5 @@
package org.pdxfinder.services;
-import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;
@@ -15,18 +14,13 @@ import org.mockito.InjectMocks;
import org.pdxfinder.BaseTest;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.mock.web.MockMultipartFile;
+import org.springframework.web.multipart.MultipartFile;
-import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
-import java.net.MalformedURLException;
import java.nio.file.Files;
-import java.nio.file.NoSuchFileException;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
+import java.util.*;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.Assert.*;
@@ -280,4 +274,16 @@ public class UtilityServiceTest extends BaseTest {
// Then
assertEquals(expected, actual);
}
+
+ @Test
+ public void given_CSV_When_Serialize_Then_FormatIsCorrect() throws Exception{
+
+ String mails = "test@example.com,test@example.net,john.doe@example.org";
+ MultipartFile mockFile = new MockMultipartFile("mockFile", "test.csv", "text/csv", mails.getBytes("utf-8"));
+
+ List<Map<String, String>> data = utilityService.serializeMultipartFile(mockFile);
+ Assert.assertEquals("text/csv", mockFile.getContentType());
+
+
+ }
}
\ No newline at end of file
diff --git a/data-services/src/test/java/org/pdxfinder/services/constants/DataProviderTest.java b/data-services/src/test/java/org/pdxfinder/services/constants/DataProviderTest.java
deleted file mode 100644
index 6b3049d0320b38d6d340a426c764bcabd540b5e1..0000000000000000000000000000000000000000
--- a/data-services/src/test/java/org/pdxfinder/services/constants/DataProviderTest.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package org.pdxfinder.services.constants;
-
-import org.junit.Test;
-import org.pdxfinder.BaseTest;
-
-import static org.junit.Assert.assertTrue;
-
-public class DataProviderTest extends BaseTest {
-
- private final static String ASSERTION_ERROR = "Unknown Data Provider Found: ";
-
- @Test
- public void given_DataProviders_When_EnumListIsChanged_Then_Error() {
-
- boolean expected = true;
- String message = "";
-
- for (DataProvider option : DataProvider.values()) {
-
- switch (option) {
- case Test_Minimal:
- break;
- case PDXNet_HCI_BCM:
- break;
- case IRCC_CRC:
- break;
- case JAX:
- break;
- case PDXNet_MDAnderson:
- break;
- case PDMR:
- break;
- case PDXNet_Wistar_MDAnderson_Penn:
- break;
- case PDXNet_WUSTL:
- break;
- case CRL:
- break;
- case Curie_BC:
- break;
- case Curie_LC:
- break;
- case Curie_OC:
- break;
- case IRCC_GC:
- break;
- case PMLB:
- break;
- case TRACE:
- break;
- case UOC_BC:
- break;
- case UOM_BC:
- break;
- case VHIO_BC:
- break;
- case VHIO_CRC:
- break;
- case DFCI_CPDM:
- break;
- case NKI:
- break;
- case PIPELINE:
- break;
- case JAX_XDOG:
- break;
- case SJCRH:
- break;
- case UMCG:
- break;
- case VHIO_PC:
- break;
- case LIH:
- break;
- default:
- message = String.format("%s %s", ASSERTION_ERROR, option);
- expected = false;
- }
-
- assertTrue(message, expected);
- }
-
- }
-
-}
diff --git a/data-services/src/test/java/org/pdxfinder/services/ds/SearchDSTest.java b/data-services/src/test/java/org/pdxfinder/services/ds/SearchDSTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..8308e893601d835d1f4ebe19e8708e9abf524adb
--- /dev/null
+++ b/data-services/src/test/java/org/pdxfinder/services/ds/SearchDSTest.java
@@ -0,0 +1,140 @@
+package org.pdxfinder.services.ds;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.DataProjection;
+import org.pdxfinder.graph.repositories.DataProjectionRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.*;
+import java.util.function.Predicate;
+import java.util.stream.Collectors;
+
+import static org.hamcrest.CoreMatchers.is;
+import static org.junit.Assert.assertThat;
+
+public class SearchDSTest extends BaseTest {
+
+ private final static Logger log = LoggerFactory.getLogger(SearchDSTest.class);
+
+ @Autowired
+ SearchDS searchDS;
+
+ @Autowired
+ DataProjectionRepository dataProjectionRepository;
+
+
+ private Set<ModelForQuery> models = new HashSet<>();
+
+ @Before
+ public void setUp() {
+
+ ModelForQuery m = new ModelForQuery();
+ m.setModelId(1L);
+ m.setPatientAge("TEST FILTER");
+ m.setPatientGender("Male");
+ models.add(m);
+
+ m = new ModelForQuery();
+ m.setModelId(2L);
+ m.setPatientAge("TEST FILTER 2");
+ m.setPatientGender("Female");
+ models.add(m);
+
+ m = new ModelForQuery();
+ m.setModelId(3L);
+ m.setPatientAge("TEST FILTER 3");
+ m.setPatientGender("Male");
+ models.add(m);
+
+ m = new ModelForQuery();
+ m.setModelId(4L);
+ m.setPatientAge("TEST FILTER 4");
+ m.setPatientGender("Male");
+ models.add(m);
+
+ DataProjection dp = new DataProjection();
+ dp.setLabel("ModelForQuery");
+ dp.setValue("[" +
+ "{\"modelId\":164005,\"datasource\":\"PDXNet-WUSTL\",\"externalId\":\"WUSTL 911-06\",\"patientAge\":\"30-39\",\"patientGender\":\"Female\",\"sampleOriginTissue\":\"Not Specified\",\"sampleSampleSite\":\"Not Specified\",\"sampleExtractionMethod\":\"surgical sample\",\"sampleClassification\":\"ypT3/N1b/M1a/G1/G2\",\"sampleTumorType\":\"Primary\",\"cancerSystem\":[\"Unclassified\"],\"diagnosis\":\"Adenocarcinoma\",\"mappedOntologyTerm\":\"Adenocarcinoma\",\"treatmentHistory\":\"Not Specified\",\"allOntologyTermAncestors\":[\"Adenocarcinoma\",\"Carcinoma\",\"Epithelial Neoplasm\",\"Cancer\",\"Glandular Cell Neoplasm\",\"Neoplasm by Morphology\"]}," +
+ "{\"modelId\":158929,\"datasource\":\"JAX\",\"externalId\":\"J000104117\",\"patientAge\":\"60-69\",\"patientGender\":\"Female\",\"sampleOriginTissue\":\"Colon\",\"sampleSampleSite\":\"Abdominal wall\",\"sampleExtractionMethod\":\"Biopsy (type unspecified)\",\"sampleClassification\":\"AJCC IV/\",\"sampleTumorType\":\"Metastatic\",\"cancerSystem\":[\"Digestive System Cancer\"],\"diagnosis\":\"colon adenocarcinoma\",\"mappedOntologyTerm\":\"Colon Adenocarcinoma\",\"treatmentHistory\":\"Not Specified\",\"dataAvailable\":[\"CTP\"],\"allOntologyTermAncestors\":[\"Adenocarcinoma\",\"Colorectal Adenocarcinoma\",\"Colorectal Neoplasm\",\"Carcinoma\",\"Colon Neoplasm\",\"Colorectal Cancer\",\"Digestive System Carcinoma\",\"Colon Carcinoma\",\"Intestinal Cancer\",\"Neoplasm by Morphology\",\"Neoplasm by Site\",\"Colorectal Carcinoma\",\"Colon Cancer\",\"Intestinal Neoplasm\",\"Epithelial Neoplasm\",\"Digestive System Cancer\",\"Colon Adenocarcinoma\",\"Digestive System Neoplasm\",\"Glandular Cell Neoplasm\",\"Cancer\"]}" +
+ "]");
+
+ DataProjection mutDP = new DataProjection();
+ mutDP.setLabel("PlatformMarkerVariantModel");
+ mutDP.setValue("{\"TargetedNGS_MUT\":{\"RB1\":{\"N123D\":[10411],\"Q383E\":[10940],\"E323Q\":[16519],\"G38S\":[12539]}}}");
+
+
+ DataProjection drugDP = new DataProjection();
+ drugDP.setLabel("DrugResponse");
+ drugDP.setValue("{}");
+
+ dataProjectionRepository.save(dp);
+ dataProjectionRepository.save(mutDP);
+ dataProjectionRepository.save(drugDP);
+
+ assertThat(models.size(), is(4));
+
+ }
+
+ @Test
+ public void getExactMatchDisjunctionPredicateTest() {
+
+ List<String> filters = Arrays.asList("TEST FILTER", "TEST FILTER 2");
+ Predicate pred = searchDS.getExactMatchDisjunctionPredicate(filters);
+
+ Set<ModelForQuery> results = new HashSet<>(models);
+ Set<ModelForQuery> filteredResults = results.stream().filter(x -> pred.test(x.getPatientAge())).collect(Collectors.toSet());
+ assertThat(filteredResults.size(), is(2));
+
+ }
+
+ @Test
+ public void testCombinedFilters() {
+
+ List<String> patientAgefilters = Arrays.asList("TEST FILTER", "TEST FILTER 2");
+ Predicate predAge = searchDS.getExactMatchDisjunctionPredicate(patientAgefilters);
+
+ List<String> patientGenderfilters = Arrays.asList("Female");
+ Predicate predGender = searchDS.getExactMatchDisjunctionPredicate(patientGenderfilters);
+
+
+ Set<ModelForQuery> results = new HashSet<>(models);
+
+ Set<ModelForQuery> filteredResults = results.stream().filter(x -> predAge.test(x.getPatientAge())).collect(Collectors.toSet());
+ assertThat(filteredResults.size(), is(2));
+
+ filteredResults = filteredResults.stream().filter(x -> predGender.test(x.getPatientGender())).collect(Collectors.toSet());
+ assertThat(filteredResults.size(), is(1));
+
+
+ // Test applying the filters in another order to ensure the same result comes a the end
+
+ filteredResults = results.stream().filter(x -> predGender.test(x.getPatientGender())).collect(Collectors.toSet());
+ assertThat(filteredResults.size(), is(1));
+
+ filteredResults = filteredResults.stream().filter(x -> predAge.test(x.getPatientAge())).collect(Collectors.toSet());
+ assertThat(filteredResults.size(), is(1));
+
+ assertThat(new ArrayList<>(filteredResults).get(0).getModelId(), is(2L));
+
+ log.info("Result after filtering is ", filteredResults);
+
+
+ }
+
+ @Test
+ public void testGetDiagnosisCounts() {
+ searchDS.init();
+ Map<String, Integer> diagnosisCounts = searchDS.getDiagnosisCounts();
+ System.out.println(diagnosisCounts);
+ assertThat(diagnosisCounts.get("Adenocarcinoma"), is(2));
+ assertThat(diagnosisCounts.get("Colon Adenocarcinoma"), is(1));
+
+ }
+
+
+}
\ No newline at end of file
diff --git a/data-services/src/test/java/org/pdxfinder/services/loader/LoadMarkerTest.java b/data-services/src/test/java/org/pdxfinder/services/loader/LoadMarkerTest.java
index 7cdd518668981efc7b125539363cec5f406919a7..2e2664ddf9be50e841bb77a640093b8511f431d7 100644
--- a/data-services/src/test/java/org/pdxfinder/services/loader/LoadMarkerTest.java
+++ b/data-services/src/test/java/org/pdxfinder/services/loader/LoadMarkerTest.java
@@ -10,10 +10,9 @@ import org.pdxfinder.services.DataImportService;
import org.pdxfinder.services.constants.DataUrl;
import org.pdxfinder.services.loader.envload.LoadMarkers;
-import java.io.IOException;
-
import static org.mockito.Matchers.anyListOf;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.doReturn;
+import static org.mockito.Mockito.verify;
public class LoadMarkerTest extends BaseTest {
diff --git a/data-services/src/test/resources/logback.xml b/data-services/src/test/resources/logback.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6a89304411c6f7825c0392d1c5b6318dc0e688c1
--- /dev/null
+++ b/data-services/src/test/resources/logback.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+ <include resource="org/springframework/boot/logging/logback/base.xml"/>
+ <logger name="org.springframework" level="WARN"/>
+ <logger name="org.springframework.data.neo4j.mapping.Neo4jPersistentProperty" level="ERROR"/>
+ <logger name="org.neo4j" level="WARN"/>
+</configuration>
\ No newline at end of file
diff --git a/data-services/src/test/resources/ogm.properties b/data-services/src/test/resources/ogm.properties
new file mode 100644
index 0000000000000000000000000000000000000000..5cb8c7a63424763060cc283b3477637d1d2f1a81
--- /dev/null
+++ b/data-services/src/test/resources/ogm.properties
@@ -0,0 +1,4 @@
+#
+# Configuration for embedded neo4j for tests
+#
+driver=org.neo4j.ogm.drivers.embedded.driver.EmbeddedDriver
\ No newline at end of file
diff --git a/data-services/target/maven-archiver/pom.properties b/data-services/target/maven-archiver/pom.properties
deleted file mode 100644
index f1e8bfe9c686f50755faa26fa588c6dd1b6dad25..0000000000000000000000000000000000000000
--- a/data-services/target/maven-archiver/pom.properties
+++ /dev/null
@@ -1,5 +0,0 @@
-#Generated by Apache Maven
-#Mon Sep 23 13:05:56 CEST 2019
-groupId=org.pdxfinder
-artifactId=data-services
-version=1.0.0
diff --git a/data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst b/data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst
deleted file mode 100644
index 9c35f3d90108207a41390f8ecc20c254f2ccdfea..0000000000000000000000000000000000000000
--- a/data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst
+++ /dev/null
@@ -1,120 +0,0 @@
-org/pdxfinder/services/PaginationService.class
-org/pdxfinder/services/search/OneParamTextFilter.class
-org/pdxfinder/services/dto/LoaderDTO.class
-org/pdxfinder/services/ds/SearchDS.class
-org/pdxfinder/services/UtilityService.class
-org/pdxfinder/services/Statistics.class
-org/pdxfinder/services/highchart/HexColors.class
-org/pdxfinder/services/pdf/Lists.class
-org/pdxfinder/services/search/TwoParamUnlinkedFilter.class
-org/pdxfinder/services/search/OneParamCheckboxSearch.class
-org/pdxfinder/services/dto/MolecularDataTableDTO.class
-org/pdxfinder/services/highchart/Column.class
-org/pdxfinder/services/dto/QualityControlDTO.class
-org/pdxfinder/services/PdfService.class
-org/pdxfinder/services/dto/VariationDataDTO.class
-org/pdxfinder/services/reporting/MarkerLogEntity.class
-org/pdxfinder/services/pdf/PdfHelper.class
-org/pdxfinder/services/ds/AutoCompleteOption.class
-org/pdxfinder/services/search/WebFacetContainer.class
-org/pdxfinder/services/mapping/CSV.class
-org/pdxfinder/services/ds/SearchDS$6.class
-org/pdxfinder/services/search/OneParamTextSearch.class
-org/pdxfinder/services/ds/SearchFacetName.class
-org/pdxfinder/services/search/OneParamLinkedFilter.class
-org/pdxfinder/services/PlatformService.class
-org/pdxfinder/services/highchart/Marker.class
-org/pdxfinder/services/ds/ModelForQuery$1.class
-org/pdxfinder/services/dto/StatisticsDTO.class
-org/pdxfinder/services/DrugService.class
-org/pdxfinder/services/mapping/MappingEntityType.class
-org/pdxfinder/services/dto/KeyValuePairDTO.class
-org/pdxfinder/services/pdf/Table.class
-org/pdxfinder/services/MolCharService.class
-org/pdxfinder/services/highchart/Labels.class
-org/pdxfinder/services/SearchService.class
-org/pdxfinder/services/highchart/Title.class
-org/pdxfinder/services/search/FilterType.class
-org/pdxfinder/services/dto/DetailsDTO.class
-org/pdxfinder/services/highchart/SeriesType.class
-org/pdxfinder/services/highchart/ToolTip.class
-org/pdxfinder/services/highchart/XAxis.class
-org/pdxfinder/services/search/OneParamLinkedSearch.class
-org/pdxfinder/services/PatientService.class
-org/pdxfinder/services/SearchService$1.class
-org/pdxfinder/services/ds/Standardizer.class
-org/pdxfinder/utils/DamerauLevenshteinAlgorithm.class
-org/pdxfinder/services/search/ThreeParamLinkedSearch.class
-org/pdxfinder/services/dto/TreatmentSummaryDTO.class
-org/pdxfinder/services/ontology/OntoliaMatrix.class
-org/pdxfinder/services/search/TwoParamUnlinkedSearch.class
-org/pdxfinder/services/pdf/Column.class
-org/pdxfinder/services/search/OneParamCheckboxFilter.class
-org/pdxfinder/services/email/EmailConfig.class
-org/pdxfinder/services/highchart/Chart.class
-org/pdxfinder/services/search/ComparisonOperator.class
-org/pdxfinder/services/ds/Harmonizer.class
-org/pdxfinder/services/dto/PaginationDTO.class
-org/pdxfinder/services/EmailService.class
-org/pdxfinder/services/ds/SearchDS$1.class
-org/pdxfinder/services/highchart/DataLabels.class
-org/pdxfinder/services/highchart/Style.class
-org/pdxfinder/services/highchart/Subtitle.class
-org/pdxfinder/services/ds/SearchDS$5.class
-org/pdxfinder/services/search/ThreeParamLinkedFilter.class
-org/pdxfinder/services/search/TwoParamLinkedFilter.class
-org/pdxfinder/services/mapping/Status.class
-org/pdxfinder/services/pdf/Text.class
-org/pdxfinder/services/highchart/PieData.class
-org/pdxfinder/services/highchart/Item.class
-org/pdxfinder/services/highchart/ChartStrings.class
-org/pdxfinder/services/dto/PatientDTO.class
-org/pdxfinder/services/reporting/LogEntityType.class
-org/pdxfinder/services/pdf/Label.class
-org/pdxfinder/services/dto/DrugSummaryDTO.class
-org/pdxfinder/services/dto/NodeSuggestionDTO.class
-org/pdxfinder/services/ds/ModelForQueryExport.class
-org/pdxfinder/services/search/OneParamFilter.class
-org/pdxfinder/services/email/EmailConstant.class
-org/pdxfinder/services/search/WebFacetSection.class
-org/pdxfinder/services/dto/CountDTO.class
-org/pdxfinder/services/highchart/ChartHelper.class
-org/pdxfinder/services/dto/CollectionEventsDTO.class
-org/pdxfinder/services/highchart/Options3d.class
-org/pdxfinder/services/dto/EngraftmentDataDTO.class
-org/pdxfinder/services/search/FourParamLinkedFilter.class
-org/pdxfinder/services/pdf/TableLayout.class
-org/pdxfinder/services/ds/SearchDS$2.class
-org/pdxfinder/services/pdf/Report.class
-org/pdxfinder/services/reporting/LogEntity.class
-org/pdxfinder/services/MappingService.class
-org/pdxfinder/services/highchart/YAxis.class
-org/pdxfinder/services/search/TwoParamLinkedSearch.class
-org/pdxfinder/services/dto/SearchDTO.class
-org/pdxfinder/services/highchart/ChartData.class
-org/pdxfinder/services/highchart/PlotOptions.class
-org/pdxfinder/services/dto/DataAvailableDTO.class
-org/pdxfinder/services/DetailsService.class
-org/pdxfinder/services/ds/SearchDS$3.class
-org/pdxfinder/services/search/GeneralSearch.class
-org/pdxfinder/services/email/Mail.class
-org/pdxfinder/services/ontology/Ontolia.class
-org/pdxfinder/services/dto/PlatformDataDTO.class
-org/pdxfinder/services/dto/ExportDTO.class
-org/pdxfinder/services/mapping/CSVHandler.class
-org/pdxfinder/services/highchart/Series.class
-org/pdxfinder/services/GraphService.class
-org/pdxfinder/services/ds/FacetOption.class
-org/pdxfinder/services/AutoCompleteService.class
-org/pdxfinder/services/DataImportService.class
-org/pdxfinder/services/search/OneParamSearch.class
-org/pdxfinder/services/pdf/CanvasLine.class
-org/pdxfinder/services/ontology/OntoliaMatrixRow.class
-org/pdxfinder/services/dto/MolecularDataEntryDTO.class
-org/pdxfinder/services/pdf/Style.class
-org/pdxfinder/services/dto/WebSearchDTO.class
-org/pdxfinder/services/ds/ModelForQuery.class
-org/pdxfinder/services/search/FourParamLinkedSearch.class
-org/pdxfinder/services/highchart/Pie.class
-org/pdxfinder/services/ds/SearchDS$4.class
-org/pdxfinder/services/search/GeneralFilter.class
diff --git a/data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst b/data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst
deleted file mode 100644
index 5633912428684bea337943cb8b051f2bcaa7281b..0000000000000000000000000000000000000000
--- a/data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst
+++ /dev/null
@@ -1,112 +0,0 @@
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/AutoCompleteOption.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/DrugService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamCheckboxSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/CanvasLine.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamTextFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/SearchDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/PdfService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/FilterType.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/CollectionEventsDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/Lists.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/mapping/CSV.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/ThreeParamLinkedSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/PaginationDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/utils/DamerauLevenshteinAlgorithm.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/GraphService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/ExportDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/reporting/LogEntityType.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/UtilityService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/XAxis.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/ModelForQuery.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/PieData.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamLinkedSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/PaginationService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/Statistics.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/Text.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/EmailService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/FourParamLinkedFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/TwoParamLinkedSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/CountDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamCheckboxFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/PatientService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamLinkedFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/WebSearchDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/ChartData.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Marker.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/TwoParamUnlinkedSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/QualityControlDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/PatientDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/StatisticsDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Labels.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/TwoParamUnlinkedFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/ChartHelper.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/ToolTip.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/VariationDataDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/AutoCompleteService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/ComparisonOperator.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/GeneralSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/ChartStrings.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Style.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/DataImportService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/MolecularDataEntryDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Column.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/MolCharService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/GeneralFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/Table.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ontology/OntoliaMatrix.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/LoaderDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/PlatformDataDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Chart.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/WebFacetSection.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/Label.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/PdfHelper.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/email/Mail.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/FacetOption.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/email/EmailConfig.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/DetailsService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/PlotOptions.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/mapping/MappingEntityType.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/EngraftmentDataDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/PlatformService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/DataAvailableDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Title.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/HexColors.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ontology/Ontolia.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/YAxis.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/email/EmailConstant.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/TreatmentSummaryDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/TwoParamLinkedFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Subtitle.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/DataLabels.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/Column.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Options3d.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/WebFacetContainer.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/ThreeParamLinkedFilter.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/SearchService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Pie.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/FourParamLinkedSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/mapping/Status.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Series.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/Style.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/DetailsDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/reporting/LogEntity.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/NodeSuggestionDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/SeriesType.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/MolecularDataTableDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/Report.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/search/OneParamTextSearch.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ontology/OntoliaMatrixRow.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/mapping/CSVHandler.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/KeyValuePairDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/highchart/Item.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/dto/DrugSummaryDTO.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/MappingService.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/pdf/TableLayout.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/reporting/MarkerLogEntity.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java
-/home/luboslav/Desktop/dataportal-sourcecode/data-services/src/main/java/org/pdxfinder/services/ds/ModelForQueryExport.java
diff --git a/dependencies/pom.xml b/dependencies/pom.xml
index a0fb4cc472e141773278ec26bba0d42333f82dbd..85202eaeb97b42d46fbfe3051310bc91e040427c 100644
--- a/dependencies/pom.xml
+++ b/dependencies/pom.xml
@@ -3,6 +3,12 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-parent</artifactId>
+ <version>2.3.3.RELEASE</version>
+ <relativePath/>
+ </parent>
<groupId>org.pdxfinder</groupId>
<artifactId>dependencies</artifactId>
@@ -12,17 +18,10 @@
<properties>
<pdxfinder.version>${project.version}</pdxfinder.version>
<java.version>1.8</java.version>
- <thymeleaf.version>3.0.2.RELEASE</thymeleaf.version>
+ <neo4j.version>3.1.8</neo4j.version>
<thymeleaf-layout-dialect.version>2.1.1</thymeleaf-layout-dialect.version>
</properties>
- <parent>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-parent</artifactId>
- <version>1.5.8.RELEASE</version>
- <relativePath/>
- <!-- lookup parent from repository -->
- </parent>
<repositories>
<repository>
<id>spring-milestones</id>
@@ -43,17 +42,11 @@
<dependencies>
-
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
- <dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-data-neo4j</artifactId>
- </dependency>
-
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
@@ -66,43 +59,69 @@
<optional>true</optional>
</dependency>
+ <dependency>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-mail</artifactId>
+ </dependency>
- <!-- Override neo4j version -->
<dependency>
- <groupId>org.neo4j</groupId>
- <artifactId>neo4j</artifactId>
- <version>3.1.1</version>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
- <!-- Include javax.validation package -->
<dependency>
- <groupId>org.hibernate</groupId>
- <artifactId>hibernate-validator</artifactId>
+ <groupId>com.github.openjson</groupId>
+ <artifactId>openjson</artifactId>
+ <version>1.0.11</version>
</dependency>
<dependency>
- <groupId>com.google.code.gson</groupId>
- <artifactId>gson</artifactId>
- <version>2.8.0</version>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi-ooxml</artifactId>
+ <version>3.15</version>
</dependency>
- <!-- Include java mail dependencies -->
<dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-mail</artifactId>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi</artifactId>
+ <version>3.15</version>
</dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.6</version>
+ </dependency>
+
+
+
<dependency>
<groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-thymeleaf</artifactId>
+ <artifactId>spring-boot-starter-data-neo4j</artifactId>
</dependency>
+
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j</artifactId>
+ <version>3.5.20</version>
+ <scope>runtime</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j-ogm-core</artifactId>
+ <version>3.1.20</version>
+ </dependency>
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j-ogm-api</artifactId>
+ <version>3.1.20</version>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
- <!-- version management for project internal dependencies -->
<dependency>
<groupId>org.pdxfinder</groupId>
<artifactId>data-model</artifactId>
diff --git a/documentation/details_pdxfinder.pdf b/documentation/details_pdxfinder.pdf
deleted file mode 100644
index 2122f224158249bf606a5ad023772d59ed8e8709..0000000000000000000000000000000000000000
Binary files a/documentation/details_pdxfinder.pdf and /dev/null differ
diff --git a/documentation/homepage_pdxfinder.pdf b/documentation/homepage_pdxfinder.pdf
deleted file mode 100644
index 99aa2661a3a71d073ef48466a4689ea6d876f5e7..0000000000000000000000000000000000000000
Binary files a/documentation/homepage_pdxfinder.pdf and /dev/null differ
diff --git a/documentation/search_pdxfinder.pdf b/documentation/search_pdxfinder.pdf
deleted file mode 100644
index 2d2661cf9e9c1030689e068990600ed35c1b5e01..0000000000000000000000000000000000000000
Binary files a/documentation/search_pdxfinder.pdf and /dev/null differ
diff --git a/dp-quick-run.sh b/dp-quick-run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..337a7c45876d3dd568efd6f8f08120599c8002f8
--- /dev/null
+++ b/dp-quick-run.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+mvn clean package -DskipTests
+java -jar web/target/web-1.0.0.jar
+#goto http://localhost:8080/data/search
diff --git a/indexer/pom.xml b/indexer/pom.xml
index ee4b5edb3bcbb44808ba3a2e534978511c36cf21..474cd2b1a27cff3b8cb76594dc9a23b0d22900b1 100644
--- a/indexer/pom.xml
+++ b/indexer/pom.xml
@@ -21,32 +21,27 @@
</dependency>
<dependency>
- <groupId>commons-cli</groupId>
- <artifactId>commons-cli</artifactId>
- <version>1.3.1</version>
+ <groupId>org.pdxfinder</groupId>
+ <artifactId>data-services</artifactId>
</dependency>
<dependency>
- <groupId>org.neo4j</groupId>
- <artifactId>neo4j-ogm-embedded-driver</artifactId>
- <version>2.1.1</version>
+ <groupId>commons-cli</groupId>
+ <artifactId>commons-cli</artifactId>
+ <version>1.3.1</version>
</dependency>
- <!-- For command line option parsing -->
<dependency>
<groupId>net.sf.jopt-simple</groupId>
<artifactId>jopt-simple</artifactId>
<version>4.8</version>
</dependency>
+
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli-spring-boot-starter</artifactId>
<version>4.0.4</version>
</dependency>
- <dependency>
- <groupId>org.pdxfinder</groupId>
- <artifactId>data-services</artifactId>
- </dependency>
<dependency>
<groupId>tech.tablesaw</groupId>
@@ -54,6 +49,17 @@
<version>LATEST</version>
</dependency>
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j-ogm-embedded-driver</artifactId>
+ <version>3.1.20</version>
+ </dependency>
+ <dependency>
+ <!-- WARNING, do not update db engine (stable: 1.4.197) cause compatibility issues, see https://github.com/h2database/h2database/issues/2078 -->
+ <groupId>com.h2database</groupId>
+ <artifactId>h2</artifactId>
+ <version>1.4.197</version>
+ </dependency>
</dependencies>
<build>
diff --git a/indexer/src/main/java/org/pdxfinder/DatasourceConfig.java b/indexer/src/main/java/org/pdxfinder/DatasourceConfig.java
deleted file mode 100644
index b27d5dc89729b2d22353641321145765a94b34e3..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/DatasourceConfig.java
+++ /dev/null
@@ -1,134 +0,0 @@
-package org.pdxfinder;
-
-import org.apache.commons.io.FileUtils;
-import org.neo4j.ogm.session.SessionFactory;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.autoconfigure.jdbc.DataSourceBuilder;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Primary;
-import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
-import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
-import org.springframework.data.neo4j.repository.config.EnableNeo4jRepositories;
-import org.springframework.data.neo4j.transaction.Neo4jTransactionManager;
-import org.springframework.data.transaction.ChainedTransactionManager;
-import org.springframework.orm.jpa.JpaTransactionManager;
-import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.annotation.EnableTransactionManagement;
-
-import javax.sql.DataSource;
-import java.io.File;
-import java.io.IOException;
-
-@Configuration
-@EnableNeo4jRepositories(basePackages = "org.pdxfinder.graph")
-@EnableJpaRepositories(basePackages = "org.pdxfinder.rdbms", transactionManagerRef = "h2TransactionManager")
-@EnableTransactionManagement
-public class DatasourceConfig {
-
- private Logger log = LoggerFactory.getLogger(DatasourceConfig.class);
-
- /*************************************************************************************************************
- * NEO4J GRAPH DATABASE CONFIGURATION *
- **************************************************/
-
- @Value("${spring.data.neo4j.uri}")
- private String embeddedDataDir;
-
- @Value("${db-cache-dir}")
- private String cacheDataDir;
-
- @Value("${db-refresh}")
- private boolean embeddedDbRefresh;
-
- @Primary
- @Bean
- public SessionFactory sessionFactory() throws IOException {
-
- this.refreshEmbeddedDBFromCache();
- org.neo4j.ogm.config.Configuration config = new org.neo4j.ogm.config.Configuration();
- config
- .driverConfiguration()
- .setDriverClassName("org.neo4j.ogm.drivers.embedded.driver.EmbeddedDriver")
- .setURI(embeddedDataDir);
- config.autoIndexConfiguration().setAutoIndex("assert");
- return new SessionFactory(config, "org.pdxfinder.graph");
- }
-
-
- @Primary
- @Bean(name = "neo4jTransactionManager")
- public Neo4jTransactionManager transactionManager() throws IOException {
- return new Neo4jTransactionManager(sessionFactory());
- }
-
-
- /*************************************************************************************************************
- * RELATIONAL DATABASE CONFIGURATION *
- **************************************************/
-
- @Bean(name = "dataSource")
- @ConfigurationProperties(prefix = "spring.datasource")
- public DataSource dataSource() {
- return DataSourceBuilder
- .create().build();
- }
-
- @Bean
- public PersistenceExceptionTranslationPostProcessor exceptionTranslation() {
- return new PersistenceExceptionTranslationPostProcessor();
- }
-
- @Autowired
- @Bean(name = "h2TransactionManager")
- public JpaTransactionManager h2TransactionManager(LocalContainerEntityManagerFactoryBean entityManagerFactory)
- throws Exception {
- return new JpaTransactionManager(entityManagerFactory.getObject());
- }
-
-
- /*************************************************************************************************************
- * CHAINED TRANSACTION MANAGER FOR MULTIPLE DATA SOURCES *
- *******************************************************************/
-
- @Autowired
- @Bean(name = "transactionManager")
- public PlatformTransactionManager transactionManager(Neo4jTransactionManager neo4jTransactionManager,
- JpaTransactionManager h2TransactionManager) {
- return new ChainedTransactionManager(
- h2TransactionManager,
- neo4jTransactionManager
- );
- }
-
-
- private void refreshEmbeddedDBFromCache() throws IOException{
-
- boolean dataDeleted = false;
- String dataDir = embeddedDataDir.replace("file://", "");
-
- if (embeddedDbRefresh) {
- File data = new File(dataDir);
- File cache = new File(cacheDataDir);
-
- if (data.isDirectory()){
- FileUtils.cleanDirectory(data);
- dataDeleted = true;
- }
-
- if (cache.isDirectory() && dataDeleted){
- FileUtils.copyDirectory(cache, data);
- }
- }
- }
-
-
-
-}
-
-
diff --git a/indexer/src/main/java/org/pdxfinder/LoadDiseaseOntology.java b/indexer/src/main/java/org/pdxfinder/LoadDiseaseOntology.java
index dd7852e9673169ad41f61b840d50867f442313c3..34bc8dc4216f4e05aaee89172fd1518dd6f58109 100644
--- a/indexer/src/main/java/org/pdxfinder/LoadDiseaseOntology.java
+++ b/indexer/src/main/java/org/pdxfinder/LoadDiseaseOntology.java
@@ -2,8 +2,7 @@ package org.pdxfinder;
import joptsimple.OptionParser;
import joptsimple.OptionSet;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.graph.dao.OntologyTerm;
import org.pdxfinder.services.DataImportService;
import org.pdxfinder.services.UtilityService;
diff --git a/indexer/src/main/java/org/pdxfinder/Loader.java b/indexer/src/main/java/org/pdxfinder/Loader.java
index 3ef84967ecfffd7b6bf7abfd0dff8e537a7e6968..edbeac4b5c09b4adabe572ed32567e1417885236 100644
--- a/indexer/src/main/java/org/pdxfinder/Loader.java
+++ b/indexer/src/main/java/org/pdxfinder/Loader.java
@@ -1,45 +1,16 @@
-
package org.pdxfinder;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.SpringApplication;
+import org.springframework.boot.WebApplicationType;
import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.data.neo4j.repository.config.EnableNeo4jRepositories;
-import org.springframework.transaction.annotation.EnableTransactionManagement;
+import org.springframework.boot.builder.SpringApplicationBuilder;
@SpringBootApplication
-@EnableNeo4jRepositories
-@EnableTransactionManagement
public class Loader {
- private final static Logger log = LoggerFactory.getLogger(Loader.class);
-
public static void main(String[] args) throws Exception {
-
- if (args.length == 0) {
- Options options = new Options();
- HelpFormatter formatter = new HelpFormatter();
-
- Option createOpt = Option.builder("create")
- .desc("Process all data and re-creates the base graph database" +
- " with the basic nodes pre loaded" +
- " (standard tissues, implantation details, background strains, etc.")
- .build();
- Option loadOpt = Option.builder("load").desc("load command ").build();
- Option jaxOpt = Option.builder("loadJAX").desc("Load JAX PDX models from file.").build();
-
- options.addOption(createOpt);
- options.addOption(loadOpt);
- options.addOption(jaxOpt);
-
- formatter.printHelp("Application", options);
- } else {
- SpringApplication.run(Loader.class, args);
- }
+ new SpringApplicationBuilder(Loader.class)
+ .web(WebApplicationType.NONE)
+ .run(args);
}
}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TSV.java b/indexer/src/main/java/org/pdxfinder/TSV.java
similarity index 69%
rename from indexer/src/main/java/org/pdxfinder/dataloaders/updog/TSV.java
rename to indexer/src/main/java/org/pdxfinder/TSV.java
index e992f45eb9a99f25b7126c977407e227db102a60..fcf53ebab98f472aa21fd14aae9834a118aeadcc 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TSV.java
+++ b/indexer/src/main/java/org/pdxfinder/TSV.java
@@ -1,4 +1,4 @@
-package org.pdxfinder.dataloaders.updog;
+package org.pdxfinder;
public class TSV {
@@ -167,4 +167,65 @@ public class TSV {
model_id
}
+ public enum providerFileNames{
+ metadata,
+ sampleplatform,
+ cna,
+ mut,
+ expression,
+ patienttreatment,
+ cytogenetics,
+ drugdosing
+ }
+
+
+ public enum metadataSheetNames{
+ checklist,
+ patient,
+ sample,
+ model,
+ model_validation,
+ sharing,
+ loader
+ }
+
+ //Sample Platform sheet, these are the internal strings in the DB
+ public enum molecular_characterisation_type{
+
+ cyto("cytogenetics"),
+ expression("expression"),
+ mut("mutation"),
+ cna("copy number alteration");
+
+ public final String mcType;
+
+ molecular_characterisation_type(String mcType) { this.mcType = mcType; }
+ }
+
+ public enum numberOfMetadataSheets{
+ numberSheets(6);
+ public final int count;
+ numberOfMetadataSheets(int count) {
+ this.count = count;
+ }
+ }
+
+ public enum templateNames{
+ metadata_template("metadata_template.xlsx"),
+ sampleplatform_template("sampleplatform_template.xlsx"),
+ patienttreatment_template("patienttreatment_template.xlsx"),
+ cna_template("cna_template.xlsx"),
+ expression_template("expression_template.xlsx"),
+ cytogenetics_template("cytogenetics_template.xlsx"),
+ mutation_template("mutation_template.xlsx"),
+ drugdosing_template("drugdosing_template.xlsx");
+
+ public final String fileName;
+
+ templateNames(String fileName) {
+ this.fileName = fileName;
+ }
+
+ }
+
}
\ No newline at end of file
diff --git a/indexer/src/main/java/org/pdxfinder/ValidateGeneSymbols.java b/indexer/src/main/java/org/pdxfinder/ValidateGeneSymbols.java
index 7dd7f4012ecc7257a4d14bca4765ad609a9f923c..eb0fb233a5192707c76223a0b9eee98f7c231f9a 100644
--- a/indexer/src/main/java/org/pdxfinder/ValidateGeneSymbols.java
+++ b/indexer/src/main/java/org/pdxfinder/ValidateGeneSymbols.java
@@ -1,10 +1,6 @@
package org.pdxfinder;
-import joptsimple.OptionParser;
-import joptsimple.OptionSet;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONException;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.accessionidtatamodel.AccessionData;
import org.pdxfinder.graph.dao.ModelCreation;
import org.pdxfinder.services.DataImportService;
@@ -13,9 +9,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.CommandLineRunner;
import org.springframework.core.annotation.Order;
-import org.springframework.stereotype.Component;
import org.springframework.stereotype.Service;
import java.io.BufferedReader;
diff --git a/indexer/src/main/java/org/pdxfinder/commandline/FinderCommandLine.java b/indexer/src/main/java/org/pdxfinder/commandline/FinderCommandLine.java
index 4f773a93c3feb7e9e070f2835e0fb2f6c25d9c90..4ff71473d1b3434c130c6c6fbcb18ff3a083b236 100644
--- a/indexer/src/main/java/org/pdxfinder/commandline/FinderCommandLine.java
+++ b/indexer/src/main/java/org/pdxfinder/commandline/FinderCommandLine.java
@@ -9,9 +9,9 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.annotation.Order;
import org.springframework.stereotype.Component;
import picocli.CommandLine;
+import picocli.CommandLine.ArgGroup;
import picocli.CommandLine.Command;
import picocli.CommandLine.Option;
-import picocli.CommandLine.ArgGroup;
import java.io.File;
import java.io.IOException;
@@ -27,6 +27,7 @@ import java.util.concurrent.Callable;
subcommands = {
FinderCommandLine.Load.class,
FinderCommandLine.Export.class,
+ FinderCommandLine.ExportMappings.class,
FinderCommandLine.Transform.class,
CommandLine.HelpCommand.class
}
@@ -150,14 +151,90 @@ public class FinderCommandLine implements Callable<Integer> {
@Override
public String toString() {
- return new StringJoiner("\n", Load.class.getSimpleName() + "[\n", "\n]")
- .add("dataDirectory=" + dataDirectory)
- .add("clearCacheRequested=" + loadCacheRequested)
- .add("datasetRequested=" + getListOfRequestedProviders())
- .toString();
+ return new StringJoiner(", ", Load.class.getSimpleName() + "[", "]")
+ .add("dataDirectory=" + dataDirectory)
+ .add("initializeMappingDB=" + initializeMappingDB)
+ .add("validateOnlyRequested=" + validateOnlyRequested)
+ .add("postLoadRequested=" + postLoadRequested)
+ .add("springDataNeo4jUri='" + springDataNeo4jUri + "'")
+ .add("debReload='" + debReload + "'")
+ .add("springDatasourceUrl='" + springDatasourceUrl + "'")
+ .toString();
}
}
+ @Component
+ @Order(value = -100)
+ @Command(name = "exportMapping",
+ description = "Exports a subset of mappings defined by a group",
+ mixinStandardHelpOptions = true,
+ exitCodeOnExecutionException = 34)
+ static class ExportMappings implements Callable<Integer>{
+
+ @Option(
+ names = {"-d", "--data-dir"},
+ required = true,
+ description = "Path of the PDX Finder data directory " +
+ "(default: [${DEFAULT-VALUE}], set in application.properties)")
+ private File dataDirectory;
+
+ @ArgGroup(multiplicity = "0..1")
+ ExportMappings.Exclusive datasetRequested = new ExportMappings.Exclusive();
+
+ static class Exclusive {
+
+ @Option(names = {"-g", "--group"}, arity = "1",
+ description = "Load the data for groups of dataProvider (default: [${DEFAULT-VALUE}]). " +
+ "Accepted Values: [@|cyan ${COMPLETION-CANDIDATES} |@]")
+ private DataProviderGroup dataProviderGroup;
+
+ @Option(names = {"-o", "--only"}, arity = "1..*",
+ description = "Load only the data for the listed dataProvider. " +
+ "Accepted Values: [@|cyan ${COMPLETION-CANDIDATES} |@]")
+ private DataProvider[] dataProvider;
+
+ public DataProviderGroup getDataProviderGroup() {
+ return dataProviderGroup;
+ }
+
+ public DataProvider[] getDataProvider() {
+ return dataProvider;
+ }
+ }
+
+ @Autowired
+ FinderMappingExporter finderMappingExporter;
+
+ @Override
+ public Integer call() throws Exception {
+
+ List<DataProvider> providersRequested = getListOfRequestedProviders();
+ finderMappingExporter.run(dataDirectory, providersRequested);
+ return 0;
+ }
+
+
+
+ List<DataProvider> getListOfRequestedProviders() {
+
+ Optional<DataProvider[]> dataProviders = Optional.ofNullable(
+ datasetRequested.getDataProvider()
+ );
+
+ Optional<DataProviderGroup> dataProviderGroup = Optional.ofNullable(
+ datasetRequested.getDataProviderGroup()
+ );
+
+ if (dataProviders.isPresent()) {
+ return Arrays.asList(dataProviders.get());
+ } else if (dataProviderGroup.isPresent()) {
+ return DataProviderGroup.getProvidersFrom(dataProviderGroup.get());
+ } else {
+ return new ArrayList<>();
+ }
+ }
+
+ }
@Component
@Order(value = -100)
@@ -169,13 +246,19 @@ public class FinderCommandLine implements Callable<Integer> {
@Autowired
private FinderExporter finderExporter;
-
@Option(
names = {"-d", "--data-dir"},
description = "Path of the PDX Finder data directory " +
"(default: [${DEFAULT-VALUE}], set in application.properties)")
private File dataDirectory;
+ @Option(
+ names = {"-o", "--harmonized"},
+ description = "Exports the NCIT ontology information"
+ )
+ private boolean isHarmonized;
+
+
@ArgGroup(multiplicity = "0..1")
Export.Exclusive datasetRequested = new Export.Exclusive();
static class Exclusive{
@@ -193,8 +276,8 @@ public class FinderCommandLine implements Callable<Integer> {
private boolean loadAll;
- public DataProvider getProvider() {
- return provider;
+ public String getProvider() {
+ return Objects.nonNull(provider) ? provider.toString() : "";
}
public boolean isLoadAll() {
@@ -203,7 +286,7 @@ public class FinderCommandLine implements Callable<Integer> {
}
@Override
public Integer call() throws IOException {
- finderExporter.run(dataDirectory, datasetRequested.provider.toString(), datasetRequested.isLoadAll());
+ finderExporter.run(dataDirectory, datasetRequested.getProvider(), datasetRequested.isLoadAll(), isHarmonized);
return 0;
}
@@ -213,6 +296,7 @@ public class FinderCommandLine implements Callable<Integer> {
.add("dataDirectory=" + dataDirectory)
.add("Export provider" + datasetRequested.getProvider())
.add("Load all" + datasetRequested.isLoadAll())
+ .add("Unharmonized" + isHarmonized)
.toString();
}
}
diff --git a/indexer/src/main/java/org/pdxfinder/commandline/FinderExporter.java b/indexer/src/main/java/org/pdxfinder/commandline/FinderExporter.java
index 3308d9fd22aa812a98677c7633be84ce6543840f..9cda96d830094ec7e6866e1f5d6840336c2576a3 100644
--- a/indexer/src/main/java/org/pdxfinder/commandline/FinderExporter.java
+++ b/indexer/src/main/java/org/pdxfinder/commandline/FinderExporter.java
@@ -4,7 +4,6 @@ import org.apache.commons.lang3.StringUtils;
import org.pdxfinder.dataexport.UniversalDataExporter;
import org.pdxfinder.graph.dao.Group;
import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@@ -24,21 +23,21 @@ public class FinderExporter {
private File rootDir;
private static final Logger log = LoggerFactory.getLogger(FinderExporter.class);
- private UtilityService utilityService;
private DataImportService dataImportService;
+ private UniversalDataExporter universalDataExporter;
@Autowired
- FinderExporter(UtilityService utilityService, DataImportService dataImportService){
- this.utilityService = utilityService;
+ FinderExporter(DataImportService dataImportService, UniversalDataExporter universalDataExporter){
this.dataImportService = dataImportService;
+ this.universalDataExporter = universalDataExporter;
}
- public void run(File dataDirectory, String provider, boolean loadAll) throws IOException {
+ public void run(File dataDirectory, String provider, boolean loadAll, boolean isHarmonized) throws IOException {
resolveRootDir(dataDirectory);
if(loadAll){
- exportAllGroups(rootDir);
+ exportAllGroups(rootDir, isHarmonized);
}
else if (StringUtils.isNotEmpty(provider)) {
- export(rootDir, provider);
+ export(rootDir, provider, isHarmonized);
}
}
@@ -52,26 +51,24 @@ public class FinderExporter {
}
}
- public void exportAllGroups(File rootDir){
+ public void exportAllGroups(File rootDir, boolean isUnharmonized){
List<Group> allProviders = dataImportService.getAllProviderGroups();
allProviders.forEach(g -> {
try {
- export(rootDir, g.getAbbreviation());
+ export(rootDir, g.getAbbreviation(),isUnharmonized);
} catch (IOException e) {
log.error(Arrays.toString(e.getStackTrace()));
}
});
}
- public void export(File rootDir, String dataSourceAbbrev) throws IOException {
+ public void export(File rootDir, String dataSourceAbbrev, boolean isHarmonized) throws IOException {
Group ds = dataImportService.findProviderGroupByAbbrev(dataSourceAbbrev);
if(ds == null) {
log.error("Datasource {} not found. ",dataSourceAbbrev);
return;
}
- UniversalDataExporter downDog = new UniversalDataExporter(dataImportService, utilityService);
- downDog.init(rootDir + "/template", ds);
- downDog.export(rootDir + "/export");
+ universalDataExporter.exportAllFromGroup(rootDir.getAbsolutePath() + "/export", ds, isHarmonized, rootDir + "/template");
}
public void setDefaultDirectory(String defaultDirectory) {
diff --git a/indexer/src/main/java/org/pdxfinder/commandline/FinderLoader.java b/indexer/src/main/java/org/pdxfinder/commandline/FinderLoader.java
index 428e9cabea995c4583b2e7e63f4030766ec28f53..b3679361de97d034ca4d63727a3c42ce6c708ccb 100644
--- a/indexer/src/main/java/org/pdxfinder/commandline/FinderLoader.java
+++ b/indexer/src/main/java/org/pdxfinder/commandline/FinderLoader.java
@@ -1,14 +1,13 @@
package org.pdxfinder.commandline;
import org.apache.commons.collections4.CollectionUtils;
-import org.pdxfinder.dataloaders.*;
+import org.pdxfinder.dataloaders.LoadJAXData;
import org.pdxfinder.dataloaders.updog.Updog;
import org.pdxfinder.mapping.InitMappingDatabase;
import org.pdxfinder.mapping.LinkSamplesToNCITTerms;
import org.pdxfinder.mapping.LinkTreatmentsToNCITTerms;
import org.pdxfinder.postload.CreateDataProjections;
import org.pdxfinder.postload.SetDataVisibility;
-import org.pdxfinder.postload.ValidateDB;
import org.pdxfinder.services.DataImportService;
import org.pdxfinder.services.constants.DataProvider;
import org.pdxfinder.services.constants.DataProviderGroup;
@@ -37,20 +36,14 @@ public class FinderLoader {
private LoadNCIT loadNCIT;
// DataProvider Loading Components
- private LoadHCI loadHCI;
private LoadJAXData loadJAXData;
- private LoadMDAnderson loadMDAnderson;
- private LoadWISTAR loadWISTAR;
- private LoadWUSTL loadWUSTL;
private Updog updog;
// PostLoad Components
- private LoadAdditionalDatasets loadAdditionalDatasets;
private LinkSamplesToNCITTerms linkSamplesToNCITTerms;
private LinkTreatmentsToNCITTerms linkTreatmentsToNCITTerms;
private CreateDataProjections createDataProjections;
private SetDataVisibility setDataVisibility;
- private ValidateDB validateDB;
private InitMappingDatabase initMappingDatabase;
@@ -60,21 +53,13 @@ public class FinderLoader {
public FinderLoader(LoadMarkers loadMarkers,
LoadNCITDrugs loadNCITDrugs,
LoadNCIT loadNCIT,
-
- LoadHCI loadHCI,
LoadJAXData loadJAXData,
- LoadMDAnderson loadMDAnderson,
- LoadPDMRData loadPDMRData,
- LoadWISTAR loadWISTAR,
- LoadWUSTL loadWUSTL,
Updog updog,
- LoadAdditionalDatasets loadAdditionalDatasets,
LinkSamplesToNCITTerms linkSamplesToNCITTerms,
LinkTreatmentsToNCITTerms linkTreatmentsToNCITTerms,
CreateDataProjections createDataProjections,
SetDataVisibility setDataVisibility,
- ValidateDB validateDB,
DataImportService dataImportService,
ApplicationContext applicationContext,
InitMappingDatabase initMappingDatabase) {
@@ -83,19 +68,13 @@ public class FinderLoader {
this.loadNCITDrugs = loadNCITDrugs;
this.loadNCIT = loadNCIT;
- this.loadHCI = loadHCI;
this.loadJAXData = loadJAXData;
- this.loadMDAnderson = loadMDAnderson;
- this.loadWISTAR = loadWISTAR;
- this.loadWUSTL = loadWUSTL;
this.updog = updog;
- this.loadAdditionalDatasets = loadAdditionalDatasets;
this.linkSamplesToNCITTerms = linkSamplesToNCITTerms;
this.linkTreatmentsToNCITTerms = linkTreatmentsToNCITTerms;
this.createDataProjections = createDataProjections;
this.setDataVisibility = setDataVisibility;
- this.validateDB = validateDB;
this.initMappingDatabase = initMappingDatabase;
@@ -181,23 +160,10 @@ public class FinderLoader {
) {
List<DataProvider> updogProviders = DataProviderGroup.getProvidersFrom(DataProviderGroup.UPDOG);
try {
- switch (dataProvider) {
- case PDXNet_HCI_BCM:
- loadHCI.run();
- break;
- case JAX:
- loadJAXData.run();
- break;
- case PDXNet_MDAnderson:
- loadMDAnderson.run();
- break;
- case PDXNet_Wistar_MDAnderson_Penn:
- loadWISTAR.run();
- break;
- case PDXNet_WUSTL:
- loadWUSTL.run();
- break;
- default:
+ if (dataProvider.equals(DataProvider.JAX)) {
+ loadJAXData.run();
+ }
+ else{
if (updogProviders.contains(dataProvider)) {
Path updogDirectory = Paths.get(
dataDirectory.toString(),
@@ -222,7 +188,6 @@ public class FinderLoader {
linkTreatmentsToNCITTerms.run();
createDataProjections.run();
setDataVisibility.run();
- validateDB.run();
}
}
diff --git a/indexer/src/main/java/org/pdxfinder/commandline/FinderMappingExporter.java b/indexer/src/main/java/org/pdxfinder/commandline/FinderMappingExporter.java
new file mode 100644
index 0000000000000000000000000000000000000000..8b95a9d56cdaf92e19abe8659260d093694d821b
--- /dev/null
+++ b/indexer/src/main/java/org/pdxfinder/commandline/FinderMappingExporter.java
@@ -0,0 +1,41 @@
+package org.pdxfinder.commandline;
+
+import org.pdxfinder.services.MappingService;
+import org.pdxfinder.services.constants.DataProvider;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+@Component
+public class FinderMappingExporter {
+
+ @Autowired
+ MappingService mappingService;
+
+ public void run(File dataDirectory, List<DataProvider> dataProviders){
+
+ System.out.println("OK");
+ List<String> dataSourcesToExport = new ArrayList<>();
+
+ for(DataProvider dp: dataProviders)
+ dataSourcesToExport.add(dp.toString());
+
+ String diagnosisFileName = String.format("%s/mappings_out/diagnosis_mappings.json", dataDirectory.getPath());
+ String treatmentFileName = String.format("%s/mappings_out/treatment_mappings.json", dataDirectory.getPath());
+
+
+ mappingService.saveMappingsToFile(
+ diagnosisFileName,
+ mappingService.getMappingsByDSAndType(dataSourcesToExport, "diagnosis").getEntityList()
+ );
+
+ mappingService.saveMappingsToFile(
+ treatmentFileName,
+ mappingService.getMappingsByDSAndType(dataSourcesToExport, "treatment").getEntityList()
+ );
+
+ }
+}
diff --git a/indexer/src/main/java/org/pdxfinder/configuration/H2Configuration.java b/indexer/src/main/java/org/pdxfinder/configuration/H2Configuration.java
new file mode 100644
index 0000000000000000000000000000000000000000..582b69cbeab398b2197ca7253d68fea58f9740de
--- /dev/null
+++ b/indexer/src/main/java/org/pdxfinder/configuration/H2Configuration.java
@@ -0,0 +1,64 @@
+package org.pdxfinder.configuration;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.jdbc.DataSourceBuilder;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
+import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.data.neo4j.transaction.Neo4jTransactionManager;
+import org.springframework.data.transaction.ChainedTransactionManager;
+import org.springframework.orm.jpa.JpaTransactionManager;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
+
+import javax.sql.DataSource;
+
+@Configuration
+@EnableJpaRepositories(
+ basePackages = "org.pdxfinder.rdbms.repositories",
+ transactionManagerRef = "h2TransactionManager")
+@EnableTransactionManagement
+public class H2Configuration {
+
+ @Value("${data-dir}")
+ private String dataDir;
+
+ @Bean
+ @ConfigurationProperties("h2.datasource")
+ public DataSource dataSource() {
+ return DataSourceBuilder.create().build();
+ }
+
+ @Bean
+ public PersistenceExceptionTranslationPostProcessor exceptionTranslation() {
+ return new PersistenceExceptionTranslationPostProcessor();
+ }
+
+ @Autowired
+ @Bean
+ public JpaTransactionManager h2TransactionManager(
+ LocalContainerEntityManagerFactoryBean entityManagerFactory
+ ) {
+ return new JpaTransactionManager(entityManagerFactory.getObject());
+ }
+
+ @Autowired
+ @Bean(name = "transactionManager")
+ public PlatformTransactionManager transactionManager(
+ Neo4jTransactionManager neo4jTransactionManager,
+ JpaTransactionManager h2TransactionManager
+ ) {
+ return new ChainedTransactionManager(
+ h2TransactionManager,
+ neo4jTransactionManager
+ );
+ }
+
+
+}
+
+
diff --git a/indexer/src/main/java/org/pdxfinder/configuration/Neo4jConfiguration.java b/indexer/src/main/java/org/pdxfinder/configuration/Neo4jConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..9dbb1293bb60b09fef4f144b58b202dcd0cf3e84
--- /dev/null
+++ b/indexer/src/main/java/org/pdxfinder/configuration/Neo4jConfiguration.java
@@ -0,0 +1,77 @@
+package org.pdxfinder.configuration;
+
+import org.apache.commons.io.FileUtils;
+import org.neo4j.ogm.session.SessionFactory;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
+import org.springframework.data.neo4j.repository.config.EnableNeo4jRepositories;
+import org.springframework.data.neo4j.transaction.Neo4jTransactionManager;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
+
+import java.io.File;
+import java.io.IOException;
+
+@Configuration
+@EnableNeo4jRepositories(
+ basePackages = "org.pdxfinder.graph.repositories",
+ transactionManagerRef = "neo4jTransactionManager")
+@EnableTransactionManagement
+public class Neo4jConfiguration {
+
+ @Value("${spring.data.neo4j.uri}")
+ private String embeddedDataDir;
+
+ @Value("${db-cache-dir}")
+ private String cacheDataDir;
+
+ @Value("${db-refresh}")
+ private boolean embeddedDbRefresh;
+
+ @Value("${data-dir}")
+ private String dataDir;
+
+ @Bean
+ public SessionFactory sessionFactory() throws IOException {
+ refreshEmbeddedDBFromCache();
+ return new SessionFactory(neo4jConfiguration(), "org.pdxfinder.graph");
+ }
+
+ private org.neo4j.ogm.config.Configuration neo4jConfiguration() {
+ return new org.neo4j.ogm.config.Configuration.Builder()
+ .uri(embeddedDataDir)
+ .autoIndex("assert")
+ .build();
+ }
+
+ @Primary
+ @Bean(name = "neo4jTransactionManager")
+ public Neo4jTransactionManager transactionManager() throws IOException {
+ return new Neo4jTransactionManager(sessionFactory());
+ }
+
+
+ private void refreshEmbeddedDBFromCache() throws IOException{
+
+ boolean dataDeleted = false;
+ String dataDir = embeddedDataDir.replace("file://", "");
+
+ if (embeddedDbRefresh) {
+ File data = new File(dataDir);
+ File cache = new File(cacheDataDir);
+
+ if (data.isDirectory()){
+ FileUtils.cleanDirectory(data);
+ dataDeleted = true;
+ }
+
+ if (cache.isDirectory() && dataDeleted){
+ FileUtils.copyDirectory(cache, data);
+ }
+ }
+ }
+
+}
+
+
diff --git a/indexer/src/main/java/org/pdxfinder/dataexport/ExporterTemplates.java b/indexer/src/main/java/org/pdxfinder/dataexport/ExporterTemplates.java
new file mode 100644
index 0000000000000000000000000000000000000000..a0e0452f54813a87b3a59331425bd6fb18cbd28c
--- /dev/null
+++ b/indexer/src/main/java/org/pdxfinder/dataexport/ExporterTemplates.java
@@ -0,0 +1,99 @@
+package org.pdxfinder.dataexport;
+
+import org.apache.poi.ss.usermodel.CellType;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.xssf.usermodel.XSSFSheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.pdxfinder.TSV;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ExporterTemplates {
+
+ private XSSFWorkbook metadataTemplate;
+ private XSSFWorkbook samplePlatformTemplate;
+ private XSSFWorkbook mutationTemplate;
+ private XSSFWorkbook cnaTemplate;
+ private XSSFWorkbook cytoTemplate;
+ private XSSFWorkbook exprTemplate;
+ private XSSFWorkbook drugTemplate;
+ private XSSFWorkbook patientTreatmentTemplate;
+
+ private Map<String, XSSFWorkbook> templatesMap;
+ private String templateDir;
+ private boolean isHarmonized;
+
+
+ public ExporterTemplates(String templateDir, boolean isharmonized) throws IOException {
+ this.templateDir = templateDir;
+ this.templatesMap = new HashMap<>();
+ this.isHarmonized = isharmonized;
+
+ loadTemplates();
+ adjustMetadataTemplateIfHarmonized();
+ addAllSheetsToMap();
+ }
+
+ private void adjustMetadataTemplateIfHarmonized() {
+ if(isHarmonized){
+ XSSFSheet sampleSheet = metadataTemplate.getSheet(TSV.metadataSheetNames.sample.name());
+ for (Row row : sampleSheet) {
+ if (row.getLastCellNum() != -1){
+ row.createCell(row.getLastCellNum(), CellType.STRING);
+ String nextCellValue = row.getCell(8).getStringCellValue();
+ String harmonizedRowMessage = "PDX Finder Harmonized Diagnosis";
+ row.getCell(8).setCellValue(harmonizedRowMessage);
+ for (int i = 9; i < (row.getLastCellNum()); i++) {
+ String previousCellValue = nextCellValue;
+ nextCellValue = row.getCell(i).getStringCellValue();
+ row.getCell(i).setCellValue(previousCellValue);
+ }
+ }
+ }
+ }
+ }
+
+ private XSSFWorkbook getWorkbookFromFS(String templatePath) throws IOException {
+ XSSFWorkbook workbook;
+ File file = new File(templatePath);
+ if (!file.exists()) throw new IOException(String.format("Template %s was not found", templatePath));
+ try (FileInputStream fileInputStream = new FileInputStream(file)) {
+ workbook = new XSSFWorkbook(fileInputStream);
+ } catch (Exception e) {
+ throw new IOException(e);
+ }
+ return workbook;
+ }
+
+ private void loadTemplates() throws IOException {
+ metadataTemplate = getWorkbookFromFS(templateDir+"/" + TSV.templateNames.metadata_template.fileName);
+ samplePlatformTemplate = getWorkbookFromFS(templateDir+"/" + TSV.templateNames.sampleplatform_template.fileName);
+ mutationTemplate = getWorkbookFromFS(templateDir+"/" + TSV.templateNames.mutation_template.fileName);
+ cnaTemplate = getWorkbookFromFS(templateDir+"/" + TSV.templateNames.cna_template.fileName);
+ cytoTemplate = getWorkbookFromFS(templateDir + "/" + TSV.templateNames.cytogenetics_template.fileName);
+ exprTemplate = getWorkbookFromFS(templateDir + "/" + TSV.templateNames.expression_template.fileName);
+ drugTemplate = getWorkbookFromFS(templateDir + "/" + TSV.templateNames.drugdosing_template.fileName);
+ patientTreatmentTemplate = getWorkbookFromFS(templateDir + "/" + TSV.templateNames.patienttreatment_template.fileName);
+ }
+
+ private void addAllSheetsToMap() {
+ templatesMap.put(TSV.templateNames.metadata_template.name(),metadataTemplate);
+ templatesMap.put(TSV.templateNames.sampleplatform_template.name(),samplePlatformTemplate);
+ templatesMap.put(TSV.templateNames.mutation_template.name() ,mutationTemplate);
+ templatesMap.put(TSV.templateNames.cna_template.name() ,cnaTemplate);
+ templatesMap.put(TSV.templateNames.cytogenetics_template.name() ,cytoTemplate);
+ templatesMap.put(TSV.templateNames.expression_template.name() ,exprTemplate);
+ templatesMap.put(TSV.templateNames.drugdosing_template.name(), drugTemplate);
+ templatesMap.put(TSV.templateNames.patienttreatment_template.name(), patientTreatmentTemplate);
+ }
+
+ public XSSFWorkbook getTemplate(String template){
+ return templatesMap.get(template);
+ }
+
+ public boolean isHarmonized(){ return this.isHarmonized; }
+}
diff --git a/indexer/src/main/java/org/pdxfinder/dataexport/MetadataSheets.java b/indexer/src/main/java/org/pdxfinder/dataexport/MetadataSheets.java
new file mode 100644
index 0000000000000000000000000000000000000000..3373cba519e3d595720efc7445cc3b17cafd43b7
--- /dev/null
+++ b/indexer/src/main/java/org/pdxfinder/dataexport/MetadataSheets.java
@@ -0,0 +1,65 @@
+package org.pdxfinder.dataexport;
+
+import org.pdxfinder.TSV;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class MetadataSheets {
+
+ private List<List<String>> checklistDataExport;
+ private List<List<String>> patientSheetDataExport;
+ private List<List<String>> patientSampleSheetDataExport;
+ private List<List<String>> pdxModelSheetDataExport;
+ private List<List<String>> pdxModelValidationSheetDataExport;
+ private List<List<String>> sharingAndContactSheetDataExport;
+ private List<List<String>> loaderRelatedDataSheetDataExport;
+
+ private Map<String, List<List<String>>> exportSheetsMap;
+ private List<List<String>> blankSheet;
+
+ public MetadataSheets() {
+ initDataExportSheets();
+ createExportSheetMap();
+ initBlankSheet();
+ }
+
+ private void initDataExportSheets() {
+ exportSheetsMap = new HashMap<>();
+
+ checklistDataExport = new ArrayList<>();
+ patientSheetDataExport = new ArrayList<>();
+ patientSampleSheetDataExport = new ArrayList<>();
+ pdxModelSheetDataExport = new ArrayList<>();
+ pdxModelValidationSheetDataExport = new ArrayList<>();
+ sharingAndContactSheetDataExport = new ArrayList<>();
+ loaderRelatedDataSheetDataExport = new ArrayList<>();
+ }
+
+ private void createExportSheetMap() {
+ exportSheetsMap.put(TSV.metadataSheetNames.checklist.name(), checklistDataExport);
+ exportSheetsMap.put(TSV.metadataSheetNames.patient.name(),patientSheetDataExport);
+ exportSheetsMap.put(TSV.metadataSheetNames.sample.name(),patientSampleSheetDataExport);
+ exportSheetsMap.put(TSV.metadataSheetNames.model.name(),pdxModelSheetDataExport);
+ exportSheetsMap.put(TSV.metadataSheetNames.model_validation.name(),pdxModelValidationSheetDataExport);
+ exportSheetsMap.put(TSV.metadataSheetNames.sharing.name(),sharingAndContactSheetDataExport);
+ exportSheetsMap.put(TSV.metadataSheetNames.loader.name(),loaderRelatedDataSheetDataExport);
+ }
+
+ private void initBlankSheet() {
+ blankSheet = new ArrayList<>();
+ List<String> blankList = new ArrayList<>();
+ blankSheet.add(blankList);
+ }
+
+ public List<List<String>> get(String exportSheets) {
+ return exportSheetsMap.getOrDefault(exportSheets, blankSheet);
+ }
+
+ public void set(String enumName, List<List<String>> sheetData){
+ exportSheetsMap.put(enumName, sheetData);
+ }
+
+}
diff --git a/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java b/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
index f8edf81dbfe0aaf6dc6a48601d90474248194941..40ba308f0fdaac4077b7ceed28711d8484d8cbd8 100644
--- a/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
+++ b/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
@@ -1,1050 +1,162 @@
package org.pdxfinder.dataexport;
-import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-import org.pdxfinder.graph.dao.*;
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.Group;
+import org.pdxfinder.graph.dao.ModelCreation;
import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
+import org.springframework.stereotype.Component;
-import java.io.*;
-import java.nio.file.Files;
+import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
-
-/*
- * Created by csaba on 02/10/2019.
- */
-@Service
+@Component
public class UniversalDataExporter {
private static final Logger log = LoggerFactory.getLogger(UniversalDataExporter.class);
-
- protected UtilityService utilityService;
- protected DataImportService dataImportService;
-
- protected String templateDir;
-
- private List<List<String>> patientSheetDataExport;
- private List<List<String>> patientTumorSheetDataExport;
- private List<List<String>> patientTreatmentSheetDataExport;
- private List<List<String>> pdxModelSheetDataExport;
- private List<List<String>> pdxModelValidationSheetDataExport;
- private List<List<String>> samplePlatformDescriptionSheetDataExport;
- private List<List<String>> sharingAndContactSheetDataExport;
- private List<List<String>> loaderRelatedDataSheetDataExport;
- private List<List<String>> drugDosingSheetDataExport;
-
- private List<List<String>> mutationSheetDataExport;
- private List<List<String>> cnaSheetDataExport;
- private List<List<String>> cytogeneticsSheetDataExport;
- private List<List<String>> expressionSheetDataExport;
-
- private Group ds;
-
- private static String notSpecified = "Not Specified";
- private static String patientOrigin = "patient";
+ private UniversalDataWriterServices writerUtilities;
+ private UniversalDataExtractionServices extractionServices;
+ private DataImportService dataImportService;
@Autowired
- public UniversalDataExporter(DataImportService dataImportService, UtilityService utilityService) {
-
+ UniversalDataExporter(UniversalDataWriterServices writerUtilities, UniversalDataExtractionServices extractionUtilities, DataImportService dataImportService){
+ this.writerUtilities = writerUtilities;
+ this.extractionServices = extractionUtilities;
this.dataImportService = dataImportService;
- this.utilityService = utilityService;
-
- patientSheetDataExport = new ArrayList<>();
- patientTumorSheetDataExport = new ArrayList<>();
- pdxModelSheetDataExport = new ArrayList<>();
- pdxModelValidationSheetDataExport = new ArrayList<>();
- sharingAndContactSheetDataExport = new ArrayList<>();
- loaderRelatedDataSheetDataExport = new ArrayList<>();
-
- samplePlatformDescriptionSheetDataExport = new ArrayList<>();
-
- mutationSheetDataExport = new ArrayList<>();
- cnaSheetDataExport = new ArrayList<>();
- cytogeneticsSheetDataExport = new ArrayList<>();
- expressionSheetDataExport = new ArrayList<>();
}
- public Group getDs() {
- return ds;
- }
-
- public void setDs(Group ds) {
- this.ds = ds;
- }
-
- public String getTemplateDir() {
- return templateDir;
- }
-
- public void setTemplateDir(String templateDir) {
- this.templateDir = templateDir;
- }
-
- public void init(String templateDir, Group ds){
-
- this.templateDir = templateDir;
- this.ds = ds;
-
- initPatientData();
- initPatientTumorAtCollection();
- initPdxModelDetails();
- initPdxModelValidations();
- initSharingAndContact();
- initLoaderRelatedData();
-
- initSamplePlatformDescription();
-
- initOmicData();
- }
-
- public void export(String exportDir) throws IOException {
-
- XSSFWorkbook metadataTemplate = getWorkbook(templateDir+"/metadata_template.xlsx");
- XSSFWorkbook samplePlatformTemplate = getWorkbook(templateDir+"/sampleplatform_template.xlsx");
- XSSFWorkbook mutationTemplate = getWorkbook(templateDir+"/mutation_template.xlsx");
- XSSFWorkbook cnaTemplate = getWorkbook(templateDir+"/cna_template.xlsx");
- XSSFWorkbook cytoTemplate = getWorkbook(templateDir + "/cytogenetics_template.xlsx");
- XSSFWorkbook exprTemplate = getWorkbook(templateDir + "/expression_template.xlsx");
-
- if (metadataTemplate != null && noMetaDataSheetsAreNull()) {
- updateSheetWithData(metadataTemplate.getSheetAt(1), patientSheetDataExport, 6, 2);
- updateSheetWithData(metadataTemplate.getSheetAt(2), patientTumorSheetDataExport, 6, 2);
- updateSheetWithData(metadataTemplate.getSheetAt(3), pdxModelSheetDataExport, 6, 2);
- updateSheetWithData(metadataTemplate.getSheetAt(4), pdxModelValidationSheetDataExport, 6, 2);
- updateSheetWithData(metadataTemplate.getSheetAt(5), sharingAndContactSheetDataExport, 6, 2);
- updateSheetWithData(metadataTemplate.getSheetAt(6), loaderRelatedDataSheetDataExport, 6, 2);
- }
-
- if (samplePlatformTemplate != null && samplePlatformDescriptionSheetDataExport != null) {
- updateSheetWithData(samplePlatformTemplate.getSheetAt(0), samplePlatformDescriptionSheetDataExport, 6, 1);
- }
-
- Path exportProviderDir = Paths.get(exportDir + "/" + ds.getAbbreviation());
- Files.createDirectories(exportProviderDir);
+ public void exportAllFromGroup(String exportDir, Group dataSource, boolean isHarmonized, String templateDir) throws IOException {
+ String exportProviderDir = Paths.get(String.format("%s/%s/",exportDir ,dataSource.getAbbreviation())).toString();
+ ExporterTemplates templates = new ExporterTemplates(templateDir, isHarmonized);
+ MetadataSheets providerSheets = new MetadataSheets();
+ writerUtilities.createExportDirectories(exportProviderDir);
try {
- if(metadataTemplate != null && noMetaDataSheetsAreNull()) {
- writeFileFromWorkbook(metadataTemplate, exportProviderDir + "/metadata.xlsx");
- }
- if(samplePlatformTemplate != null && samplePlatformDescriptionSheetDataExport != null) {
- writeFileFromWorkbook(samplePlatformTemplate, exportProviderDir + "/sampleplatform.xlsx");
- }
- writeOmicFileFromWorkbook(mutationTemplate, mutationSheetDataExport, exportProviderDir + "/mut/", "_mut.tsv");
- writeOmicFileFromWorkbook(cnaTemplate, cnaSheetDataExport, exportProviderDir + "/cna/", "_cna.tsv" );
- writeOmicFileFromWorkbook(cytoTemplate, cytogeneticsSheetDataExport, exportProviderDir + "/cyto/", "_cyto.tsv" );
- writeOmicFileFromWorkbook(exprTemplate, expressionSheetDataExport, exportProviderDir + "/expr/", "_expr.tsv");
- } catch (Exception e) {
- log.error("error", e);
- }
- }
-
- private boolean noMetaDataSheetsAreNull(){
- return (patientSheetDataExport != null && patientTumorSheetDataExport != null
- && pdxModelSheetDataExport != null && pdxModelValidationSheetDataExport != null
- && sharingAndContactSheetDataExport != null && loaderRelatedDataSheetDataExport != null);
- }
-
- private void writeFileFromWorkbook(XSSFWorkbook dataWorkbook, String fileLocation) throws IOException {
- if (dataWorkbook != null) {
- FileOutputStream fileOut = new FileOutputStream(fileLocation);
- dataWorkbook.write(fileOut);
- fileOut.close();
- }
- }
-
- private void writeOmicFileFromWorkbook(XSSFWorkbook omicWorkbook,List<List<String>> exportSheet, String fileLocation, String suffix ) throws IOException {
- if (omicWorkbook != null && exportSheet != null && !exportSheet.isEmpty()) {
- if (!Paths.get(fileLocation).toFile().exists()) {
- Files.createDirectory(Paths.get(fileLocation));
- }
- String exportURI = fileLocation + ds.getAbbreviation() + suffix;
- readSheetAndWriteOmicTsvFile(omicWorkbook.getSheetAt(0),exportSheet, exportURI);
- }
- }
-
- public void initPatientData() {
-
- if (ds == null) return;
-
- List<Patient> patients = dataImportService.findPatientsByGroup(ds);
-
- for (Patient patient : patients) {
-
- List<String> dataRow = new ArrayList<>();
-
- String patientId = patient.getExternalId();
- String sex = patient.getSex();
- String cancerHistory = patient.getCancerRelevantHistory();
- String ethnicity = patient.getEthnicity();
- String ethnicityAssessment = patient.getEthnicityAssessment();
- String firstDiagnosis = patient.getFirstDiagnosis();
- String ageAtFirstDiagnosis = patient.getAgeAtFirstDiagnosis();
-
- dataRow.add(patientId);
- dataRow.add(sex);
- dataRow.add(cancerHistory);
- dataRow.add(ethnicity);
- dataRow.add(ethnicityAssessment);
- dataRow.add(firstDiagnosis);
- dataRow.add(ageAtFirstDiagnosis);
-
- patientSheetDataExport.add(dataRow);
- }
- }
-
- public void initPatientTumorAtCollection(){
-
- if (ds == null) return;
-
- List<Patient> patients = dataImportService.findPatientTumorAtCollectionDataByDS(ds);
-
- for(Patient patient : patients){
-
- String patientId = patient.getExternalId();
-
- for(PatientSnapshot patientSnapshot : patient.getSnapshots()){
-
- for(Sample sample : patientSnapshot.getSamples()){
-
- List<String> dataRow = new ArrayList<>();
-
- String sampleId = sample.getSourceSampleId();
- String collectionDate = patientSnapshot.getDateAtCollection();
- String collectionEvent = patientSnapshot.getCollectionEvent();
- String elapsedTime = patientSnapshot.getElapsedTime();
- String ageAtCollection = patientSnapshot.getAgeAtCollection();
- String diagnosis = sample.getDiagnosis();
- String tumorType = sample.getType().getName();
- String primarySite = sample.getOriginTissue().getName();
- String collectionSite = sample.getSampleSite().getName();
- String stage = sample.getStage();
- String stageClassification = sample.getStageClassification();
- String grade = sample.getGrade();
- String gradeClassification = sample.getGradeClassification();
- String virologyStatus = patientSnapshot.getVirologyStatus();
- String isPatientTreatmentInfoAvailable = "";
- String treatmentNaive = patientSnapshot.getTreatmentNaive();
- String isPatientTreated = "";
- String wasPatientTreated = "";
- String modelId = "";
- try {
- modelId = dataImportService.findModelBySample(sample).getSourcePdxId();
- }
- catch (Exception e){
- log.error("Error getting model Id from sample: {}", sampleId);
- }
-
- dataRow.add(patientId);
- dataRow.add(sampleId);
- dataRow.add(collectionDate);
- dataRow.add(collectionEvent);
- dataRow.add(elapsedTime);
- dataRow.add(ageAtCollection);
- dataRow.add(diagnosis);
- dataRow.add(tumorType);
- dataRow.add(primarySite);
- dataRow.add(collectionSite);
- dataRow.add(stage);
- dataRow.add(stageClassification);
- dataRow.add(grade);
- dataRow.add(gradeClassification);
- dataRow.add(virologyStatus);
- dataRow.add(isPatientTreatmentInfoAvailable);
- dataRow.add(treatmentNaive);
- dataRow.add(isPatientTreated);
- dataRow.add(wasPatientTreated);
- dataRow.add(modelId);
-
- patientTumorSheetDataExport.add(dataRow);
- }
- }
- }
-
- }
-
- public void initPdxModelDetails(){
-
- if (ds == null) return;
-
- List<ModelCreation> models = dataImportService.findModelsWithSpecimensAndQAByDS(ds.getAbbreviation());
-
- for(ModelCreation model : models){
-
- Map<String, ModelDetails> specimenMap = new HashMap<>();
-
- for(Specimen specimen : model.getSpecimens()){
-
- String passage = specimen.getPassage();
-
- String engraftmentSite = notSpecified;
-
- if(specimen.getEngraftmentSite() != null ){
- engraftmentSite = specimen.getEngraftmentSite().getName();
- }
-
- String engraftmentType = notSpecified;
-
- if(specimen.getEngraftmentType() != null){
- engraftmentType = specimen.getEngraftmentType().getName();
- }
-
- String engraftmentMaterial = notSpecified;
- String engraftmentMaterialStatus = notSpecified;
-
- if(specimen.getEngraftmentMaterial() != null){
- engraftmentMaterial = specimen.getEngraftmentMaterial().getName();
- engraftmentMaterialStatus = specimen.getEngraftmentMaterial().getState();
- }
-
- addEntryToSpecimenMap(
- specimenMap,
- specimen.getHostStrain(),
- engraftmentSite,
- engraftmentType,
- engraftmentMaterial,
- engraftmentMaterialStatus,
- passage);
- }
-
- insertModelSheetDataFromSpecimenMap(specimenMap, model);
-
- }
- }
-
- public void initPdxModelValidations(){
-
- if (ds == null) return;
-
- List<ModelCreation> models = dataImportService.findModelsWithSpecimensAndQAByDS(ds.getAbbreviation());
-
- for(ModelCreation model : models){
-
- if(model != null && model.getQualityAssurance() != null) {
-
- String modelId = model.getSourcePdxId();
-
- for (QualityAssurance qa : model.getQualityAssurance()) {
-
- List<String> dataRow = new ArrayList<>();
-
- String validationTechnique = qa.getTechnology();
- String validationDescription = qa.getDescription();
- String passages = qa.getPassages();
- String nomenclature = qa.getValidationHostStrain();
-
- dataRow.add(modelId);
- dataRow.add(validationTechnique);
- dataRow.add(validationDescription);
- dataRow.add(passages);
- dataRow.add(nomenclature);
-
- pdxModelValidationSheetDataExport.add(dataRow);
- }
- }
- }
- }
-
- public void initSharingAndContact(){
-
- if (ds == null) return;
-
- List<ModelCreation> models = dataImportService.findModelsWithSharingAndContactByDS(ds.getAbbreviation());
-
- for(ModelCreation model : models){
-
- LinkedHashMap<String, String> sharingAndContactRow = new LinkedHashMap<>();
-
- sharingAndContactRow.put("modelId", model.getSourcePdxId());
-
- Group providerGroup = getGroupByType(model, "Provider");
- Group accessGroup = getGroupByType(model, "Accessibility");
- Group projectGroup = getGroupByType(model, "Project");
-
- getGroupData(sharingAndContactRow, providerGroup, accessGroup, projectGroup);
-
- getExternalUrlData(sharingAndContactRow, model.getExternalUrls());
-
- insertSharingAndContactDataForModel(sharingAndContactRow);
-
- }
- }
-
- public void initLoaderRelatedData(){
-
- if (ds == null) return;
-
- List<String> dataRow = new ArrayList<>();
- dataRow.add(ds.getName());
- dataRow.add(ds.getAbbreviation());
- dataRow.add(ds.getUrl());
-
- loaderRelatedDataSheetDataExport.add(dataRow);
-
- }
-
- public void initSamplePlatformDescription(){
-
- if (ds == null) return;
-
- List<ModelCreation> models = dataImportService.findModelXenograftPlatformSampleByDS(ds.getAbbreviation());
-
- for(ModelCreation model : models){
-
- addPatientMolcharDataToSamplePlatform(model);
- addXenoMolcharDataToSamplePlatform(model);
- }
-
- }
-
- public void initOmicData(){
- initGenomicData(mutationSheetDataExport, "mutation");
- initGenomicData(cnaSheetDataExport, "copy number alteration");
- initGenomicData(cytogeneticsSheetDataExport, "cytogenetics");
- initGenomicData(expressionSheetDataExport, "expression");
- }
-
-
- private void initGenomicData(List<List<String>> sheetData, String molcharType){
-
- //TODO, these queries could be optimized to reduce db interactions
- List<ModelCreation> models = dataImportService.findModelsWithSharingAndContactByDS(ds.getAbbreviation());
-
- for(ModelCreation m: models){
- ModelCreation model = dataImportService.findModelWithMolecularDataByDSAndIdAndMolcharType(
- ds.getAbbreviation(),
- m.getSourcePdxId(),
- molcharType);
-
- if(model != null){
-
- String modelId = model.getSourcePdxId();
- log.info("Exporting data for {}", modelId);
-
- initPatientGenomicData(model, sheetData);
- initXenoGenomicData(model, sheetData);
- }
- }
- }
-
- private void insertOmicDataToSheet(
- ModelCreation model,
- String sampleId,
- String sampleOrigin,
- String molcharType,
- Specimen specimen,
- MolecularCharacterization mc,
- List<List<String>> sheetData){
-
- for(MarkerAssociation ma: mc.getMarkerAssociations()){
- List<MolecularData> molecularData;
- try{
- molecularData = ma.decodeMolecularData();
- }
- catch(Exception e){
- log.error("No molecular data in Marker Association on Sample {}", sampleId);
- molecularData = new ArrayList<>();
- }
- for(MolecularData md : molecularData){
- List<String> rowData = new ArrayList<>();
- rowData.add(model.getSourcePdxId());
- rowData.add(sampleId);
- rowData.add(sampleOrigin);
-
- if(sampleOrigin.equals(patientOrigin)){
- //no passage, host strain for patient samples
- rowData.add("");
- rowData.add("");
- }
- else{
-
- rowData.add(specimen.getPassage());
-
- if(specimen.getHostStrain() != null && specimen.getHostStrain().getSymbol() != null){
- rowData.add(specimen.getHostStrain().getSymbol());
- }
- else{
- rowData.add("");
- }
- }
-
- switch (molcharType) {
- case "mutation":
- rowData.add(md.getMarker());
- rowData.add(md.getAminoAcidChange());
- rowData.add(md.getBiotype());
- rowData.add(md.getCodingSequenceChange());
- rowData.add(md.getVariantClass());
- rowData.add(md.getNucleotideChange());
- rowData.add(md.getCodonChange());
- rowData.add(md.getAminoAcidChange());
- rowData.add(md.getConsequence());
- rowData.add(md.getReadDepth());
- rowData.add(md.getAlleleFrequency());
- rowData.add(md.getChromosome());
- rowData.add(md.getSeqStartPosition());
- rowData.add(md.getRefAllele());
- rowData.add(md.getAltAllele());
- rowData.add(md.getUcscGeneId());
- rowData.add(md.getNcbiGeneId());
- rowData.add(md.getNcbiTranscriptId());
- rowData.add(md.getEnsemblGeneId());
- rowData.add(md.getEnsemblTranscriptId());
- rowData.add(md.getExistingVariations());
- rowData.add(md.getGenomeAssembly());
- rowData.add(mc.getPlatform().getName());
- break;
- case "copy number alteration":
- rowData.add(md.getChromosome());
- rowData.add(md.getSeqStartPosition());
- rowData.add(md.getSeqEndPosition());
- rowData.add(md.getMarker());
- rowData.add(md.getUcscGeneId());
- rowData.add(md.getNcbiGeneId());
- rowData.add(md.getEnsemblGeneId());
- rowData.add(md.getCnaLog10RCNA());
- rowData.add(md.getCnaLog2RCNA());
- rowData.add(md.getFold_change());
- rowData.add(md.getCnaCopyNumberStatus());
- rowData.add(md.getCnaGisticValue());
- rowData.add(md.getCnaPicnicValue());
- rowData.add(md.getGenomeAssembly());
- rowData.add(mc.getPlatform().getName());
- break;
- case "cytogenetics":
- rowData.add("");
- rowData.add(md.getMarker());
- rowData.add(md.getCytogeneticsResult());
- rowData.add(md.getMarkerStatusComment());
- rowData.add(mc.getPlatform().getName());
- rowData.add("");
- rowData.add("");
- break;
- case "expression":
- rowData.add(md.getChromosome());
- rowData.add("");
- rowData.add(md.getSeqStartPosition());
- rowData.add(md.getSeqEndPosition());
- rowData.add(md.getMarker());
- rowData.add("");
- rowData.add("");
- rowData.add("");
- rowData.add(md.getRnaSeqCoverage());
- rowData.add(md.getRnaSeqFPKM());
- rowData.add(md.getRnaSeqTPM());
- rowData.add(md.getRnaSeqCount());
- rowData.add(md.getAffyHGEAProbeId());
- rowData.add(md.getAffyHGEAExpressionValue());
- rowData.add(md.getIlluminaHGEAProbeId());
- rowData.add(md.getIlluminaHGEAExpressionValue());
- rowData.add(md.getZscore());
- rowData.add(md.getGenomeAssembly());
- rowData.add(mc.getPlatform().getName());
- break;
- default:
- throw new IllegalArgumentException("Inappropriate Molecular data type passed");
- }
- sheetData.add(rowData);
- }
- }
- }
-
- public void updateSheetWithData(Sheet sheet, List<List<String>> data, int startRow, int startColumn) {
-
- //Workbook rows and cells start at index 0
- if (data != null) {
-
- for (int i = 0; i < data.size(); i++) {
-
- int rowIndex = startRow + i - 1;
- sheet.createRow(rowIndex);
-
- for (int j = 0; j < data.get(i).size(); j++) {
-
-
- int columnIndex = startColumn + j - 1;
- sheet.getRow(rowIndex).createCell(columnIndex);
-
-
- Cell cell;
- try {
- cell = sheet.getRow(rowIndex).getCell(columnIndex);
- cell.setCellValue(data.get(i).get(j));
- } catch (Exception e) {
-
- log.error("Exception in {} {}:{}", sheet.getSheetName(), rowIndex, columnIndex);
- }
- }
- }
- }
- }
-
- public void readSheetAndWriteOmicTsvFile(Sheet xlsxTemplate, List<List<String>> exportSheet, String omicTsvDir) {
-
- try(FileWriter fileWriter = new FileWriter(omicTsvDir)) {
- if (exportSheet != null) {
- copyHeadersFromSheetToTsv(xlsxTemplate,fileWriter);
- writeDataToTsv(xlsxTemplate, exportSheet, fileWriter);
- }
- } catch(Exception e) {
- log.error(String.format("IO Error from reading omic TSV %s",e.toString()));
- }
- }
-
-
- private void copyHeadersFromSheetToTsv(Sheet xlsxTemplate, FileWriter fileWriter) throws IOException {
-
- for (int j = 0; j < xlsxTemplate.getRow(0).getLastCellNum(); j++) {
- Cell cell;
- try {
- cell = xlsxTemplate.getRow(0).getCell(j);
- fileWriter.append(cell.toString());
- fileWriter.append("\t");
- } catch (Exception e) {
- log.error("Exception in loading export headers");
- }
- }
- fileWriter.append("\n");
- }
-
- private void writeDataToTsv(Sheet sheet, List<List<String>> data, FileWriter fileWriter) throws IOException {
- for (int rowIndex = 0; rowIndex < data.size(); rowIndex++) {
- for (int columnIndex = 0; columnIndex < data.get(rowIndex).size(); columnIndex++) {
- try {
- fileWriter.append(data.get(rowIndex).get(columnIndex));
- fileWriter.append("\t");
- } catch (IOException e) {
- log.error("Exception in {} {}:{}", sheet.getSheetName(), rowIndex, columnIndex);
- }
- }
- fileWriter.append("\n");
- }
- }
-
-
- private String getPubmedIDs(ModelCreation model){
-
- StringBuilder pubmedIDs = new StringBuilder();
-
- if(model.getGroups() != null){
-
- for(Group g : model.getGroups()){
-
- if(g.getType().equals("Publication")){
-
- if(pubmedIDs.length() != 0){
- pubmedIDs.append(",");
- }
-
- pubmedIDs.append(g.getPubMedId());
- }
- }
- }
-
- return pubmedIDs.toString();
- }
-
- private void insertModelSheetDataFromSpecimenMap(Map<String, ModelDetails> specimenMap, ModelCreation model){
-
- String modelId = model.getSourcePdxId();
-
- String pubmedIDs = getPubmedIDs(model);
-
- for(Map.Entry<String, ModelDetails> entry : specimenMap.entrySet()){
-
- ModelDetails md = entry.getValue();
- List<String> dataRow = new ArrayList<>();
-
- dataRow.add(modelId);
- dataRow.add(md.getHostStrainName());
- dataRow.add(md.getHostStrainNomenclature());
- dataRow.add(md.getEngraftmentSite());
- dataRow.add(md.getEngraftmentType());
- dataRow.add(md.getEngraftmentMaterial());
- dataRow.add(md.getEngraftmentMaterialStatus());
- dataRow.add(md.getSortedPassages());
- dataRow.add(pubmedIDs);
-
- pdxModelSheetDataExport.add(dataRow);
- }
- }
-
- private void insertSharingAndContactDataForModel(LinkedHashMap<String, String> sharingAndContactRow){
-
- if(sharingAndContactRow != null) {
-
- List<String> dataRow = new ArrayList<>();
-
- dataRow.add(sharingAndContactRow.get("modelId"));
- dataRow.add(sharingAndContactRow.get("providerType"));
- dataRow.add(sharingAndContactRow.get("modelAccessibility"));
- dataRow.add(sharingAndContactRow.get("accessModalities"));
- dataRow.add(sharingAndContactRow.get("contactEmail"));
- dataRow.add(sharingAndContactRow.get("contactName"));
- dataRow.add(sharingAndContactRow.get("contactLink"));
- dataRow.add(sharingAndContactRow.get("modelLink"));
- dataRow.add(sharingAndContactRow.get("providerName"));
- dataRow.add(sharingAndContactRow.get("providerAbbrev"));
- dataRow.add(sharingAndContactRow.get("projectName"));
-
- sharingAndContactSheetDataExport.add(dataRow);
- }
- }
-
- private Group getGroupByType(ModelCreation model, String type){
-
- if(model.getGroups() != null){
-
- for(Group g : model.getGroups()){
-
- if(g.getType().equals(type)){
- return g;
- }
- }
- }
-
- return null;
- }
-
- private void getGroupData(LinkedHashMap<String, String> map, Group providerGroup, Group accessGroup, Group projectGroup){
-
- if(providerGroup != null) {
- map.put("providerType", providerGroup.getProviderType());
- map.put("providerName", providerGroup.getName());
- map.put("providerAbbrev", providerGroup.getAbbreviation());
- }
- else{
- map.put("providerType", "");
- map.put("providerName", "");
- map.put("providerAbbrev", "");
- }
- if(accessGroup != null){
- map.put("modelAccessibility", accessGroup.getAccessibility());
- map.put("accessModalities", accessGroup.getAccessModalities());
- }
- else{
- map.put("modelAccessibility", "");
- map.put("accessModalities", "");
- }
-
- if(projectGroup != null){
- map.put("projectName", projectGroup.getName());
+ exportMetadata(providerSheets,templates, dataSource, isHarmonized, exportProviderDir);
+ exportSamplePlatform(templates, dataSource, exportProviderDir);
+ exportAllOmicSheets(templates, dataSource, exportProviderDir);
+
+ } catch(IOException e) {
+ log.error("IO error while exporting data for {} \n {}",dataSource.getAbbreviation(), e.toString());
+ }
+ }
+
+ public void exportSamplePlatform(ExporterTemplates templates, Group group, String exportProviderDir) throws IOException {
+ List<List<String>> samplePlatform = extractionServices.extractSamplePlatform(group);
+ XSSFWorkbook samplePlatformTemplate = templates.getTemplate(TSV.templateNames.sampleplatform_template.name());
+ String samplePlatformURI = String.format("%s/%s_sampleplatform.xlsx", exportProviderDir, group.getAbbreviation());
+ saveSamplePlatformToXlsx(samplePlatformTemplate, samplePlatform, samplePlatformURI);
+ }
+
+ public void exportMetadata(MetadataSheets providerSheets, ExporterTemplates templates, Group dataSource, boolean isHarmonized, String exportProviderDir) throws IOException {
+ extractionServices.extractMetadata(dataSource, providerSheets, isHarmonized);
+ saveMetadataToXlsx(providerSheets, templates, exportProviderDir, dataSource);
+ }
+
+ private void saveMetadataToXlsx(MetadataSheets providerData, ExporterTemplates templates, String exportProviderDir, Group dataSource) throws IOException {
+ XSSFWorkbook metadataTemplate = templates.getTemplate(TSV.templateNames.metadata_template.name());
+ int sheetNumber = 0;
+ for(TSV.metadataSheetNames sheetName: TSV.metadataSheetNames.values()){
+ writerUtilities.updateXlsxSheetWithData(metadataTemplate.getSheetAt(sheetNumber),
+ providerData.get(sheetName.name()), 6, 2);
+ sheetNumber++;
+ }
+ if(allMetadataSheetsHaveData(providerData)) {
+ String metadataFileURI = String.format("%s/%s_metadata.xlsx", exportProviderDir, dataSource.getAbbreviation());
+ writerUtilities.writXlsxFromWorkbook(metadataTemplate, metadataFileURI);
+ } else { log.error("Empty or Null metadata sheet. Skipping export of Metadata."); }
+ }
+
+ private void saveSamplePlatformToXlsx(XSSFWorkbook samplePlatformTemplate, List<List<String>> samplePlatform, String samplePlatformURI) throws IOException {
+ writerUtilities.updateXlsxSheetWithData(samplePlatformTemplate.getSheetAt(0),
+ samplePlatform, 6, 1);
+ if(!samplePlatform.isEmpty()){
+ writerUtilities.writXlsxFromWorkbook(samplePlatformTemplate, samplePlatformURI);
+ }
+ }
+
+ private void exportAllOmicSheets(ExporterTemplates templates, Group dataSource, String exportProviderDir) throws IOException {
+ XSSFWorkbook mutationTemplate = templates.getTemplate(TSV.templateNames.mutation_template.name());
+ XSSFWorkbook cnaTemplate = templates.getTemplate(TSV.templateNames.cna_template.name());
+ XSSFWorkbook cytoTemplate = templates.getTemplate(TSV.templateNames.cytogenetics_template.name());
+ XSSFWorkbook exprTemplate = templates.getTemplate(TSV.templateNames.expression_template.name());
+ XSSFWorkbook dosingTemplate = templates.getTemplate(TSV.templateNames.drugdosing_template.name());
+ XSSFWorkbook treatmentTemplate = templates.getTemplate(TSV.templateNames.patienttreatment_template.name());
+ String mut = TSV.molecular_characterisation_type.mut.name();
+ String cna = TSV.molecular_characterisation_type.cna.name();
+ String expression = TSV.molecular_characterisation_type.expression.name();
+ String cyto = TSV.molecular_characterisation_type.cyto.name();
+ String dosing = "drug";
+ String treatment = "patientTreatment";
+ Path mutExportURI = Paths.get(String.format("%s/%s/%s_%s.tsv",exportProviderDir, mut, dataSource.getAbbreviation(), mut));
+ Path cnaExportURI = Paths.get(String.format( "%s/%s/%s_%s.tsv",exportProviderDir, cna, dataSource.getAbbreviation(), cna));
+ Path expressionExportURI = Paths.get(String.format("%s/%s/%s_%s.tsv", exportProviderDir, expression, dataSource.getAbbreviation() ,expression));
+ Path cytoExportURI = Paths.get(String.format("%s/%s/%s_%s.tsv",exportProviderDir,cyto, dataSource.getAbbreviation() , cyto));
+ Path dosingExportURI = Paths.get(String.format("%s/%s/%s_%s.tsv", exportProviderDir, dosing, dataSource.getAbbreviation(), dosing));
+ Path treatmentExportURI = Paths.get(String.format("%s/%s/%s_%s.tsv", exportProviderDir, treatment, dataSource.getAbbreviation(), treatment));
+ extractAndSaveOmicByBatch(TSV.molecular_characterisation_type.mut.mcType ,mutationTemplate, mutExportURI,dataSource);
+ extractAndSaveOmicByBatch(TSV.molecular_characterisation_type.cna.mcType ,cnaTemplate, cnaExportURI, dataSource);
+ extractAndSaveOmicByBatch(TSV.molecular_characterisation_type.cyto.mcType ,cytoTemplate, cytoExportURI, dataSource);
+ extractAndSaveOmicByBatch(TSV.molecular_characterisation_type.expression.mcType ,exprTemplate, expressionExportURI,dataSource);
+ extractAndSaveOmicByBatch(dosing, dosingTemplate, dosingExportURI, dataSource);
+ extractAndSaveOmicByBatch(treatment, treatmentTemplate, treatmentExportURI, dataSource);
+ }
+
+ public void extractAndSaveOmicByBatch(String molecularType, XSSFWorkbook template, Path exportURI, Group dataSource) throws IOException {
+ String parentDirectory = exportURI.getParent().toString();
+ String fileURI = exportURI.toString();
+ Sheet templateSheet = template.getSheetAt(0);
+ List<ModelCreation> models;
+ models = getModelsByMolecularTypeAndDataSource(molecularType, dataSource);
+ if(!models.isEmpty()) {
+ writerUtilities.createExportDirectories(parentDirectory);
+ writerUtilities.saveHeadersToTsv(templateSheet, exportURI.toString());
+ List<List<String>> modelsOmicData = new ArrayList<>();
+ int counter = 0;
+ for (ModelCreation model : models) {
+ modelsOmicData.addAll(extractionServices.extractModelsOmicData(model, molecularType));
+ if (counter % 10 == 0) {
+ writerUtilities.appendDataToOmicTsvFile(modelsOmicData, fileURI);
+ modelsOmicData.clear();
+ }
+ counter++;
+ }
+ if (!modelsOmicData.isEmpty()) {
+ writerUtilities.appendDataToOmicTsvFile(modelsOmicData, fileURI);
+ modelsOmicData.clear();
+ }
+ }
+ }
+
+ List<ModelCreation> getModelsByMolecularTypeAndDataSource(String molecularType, Group dataSource) {
+ List<ModelCreation> models;
+ if (molecularType.equals("drug")) {
+ models = dataImportService.findModelsWithTreatmentSummaryByDS(dataSource.getAbbreviation());
+ } else if(molecularType.equals("patientTreatment")) {
+ models = dataImportService.findModelFromPatienSnapshotWithTreatmentSummaryByDS(dataSource.getAbbreviation());
}
else {
- map.put("projectName", "");
- }
- }
-
- private void getExternalUrlData(LinkedHashMap<String, String> map, Collection<ExternalUrl> urls){
-
- map.put("contactEmail", "");
- map.put("contactName", "");
- map.put("contactLink", "");
- map.put("modelLink", "");
-
- if(urls != null){
-
- for(ExternalUrl ex: urls) {
-
- if (ex.getType().equals("contact")) {
-
- if (ex.getUrl() != null && ex.getUrl().contains("@")) {
- map.put("contactEmail", ex.getUrl());
- } else {
- map.put("contactLink", ex.getUrl());
- }
- } else if (ex.getType().equals("source") && ex.getUrl() != null) {
- map.put("modelLink", ex.getUrl());
- }
- }
- }
- }
-
- private void addEntryToSpecimenMap(
- Map<String, ModelDetails> specimenMap,
- HostStrain hostStrain,
- String engraftmentSite,
- String engraftmentType,
- String engraftmentMaterial,
- String engraftmentMaterialStatus,
- String passage){
-
- String specimenMapKey = String.join(
- hostStrain.getName(),
- hostStrain.getSymbol(),
- engraftmentSite,
- engraftmentType,
- engraftmentMaterial,
- engraftmentMaterialStatus);
-
- if(specimenMap.containsKey(specimenMapKey)){
- specimenMap.get(specimenMapKey).getPassages().add(passage);
- }
- else{
-
- ModelDetails md = new ModelDetails(
- hostStrain.getName(),
- hostStrain.getSymbol(),
- engraftmentSite,
- engraftmentType,
- engraftmentMaterial,
- engraftmentMaterialStatus,
- passage);
- specimenMap.put(specimenMapKey, md);
- }
- }
-
- private void addPatientMolcharDataToSamplePlatform(ModelCreation model){
-
- //get the patient sample related molchars first
- if(model.getSample() != null && model.getSample().getMolecularCharacterizations() != null){
-
- for(MolecularCharacterization mc : model.getSample().getMolecularCharacterizations()){
-
- List<String> dataRow = new ArrayList<>();
-
- dataRow.add("");
- dataRow.add(model.getSample().getSourceSampleId());
- dataRow.add(patientOrigin);
- dataRow.add("NA");
- dataRow.add("");
- dataRow.add(model.getSourcePdxId());
- dataRow.add("");
- dataRow.add("");
-
- dataRow.add(mc.getType());
- dataRow.add(mc.getPlatform().getName());
- dataRow.add(mc.getTechnology());
- dataRow.add("");
- dataRow.add("");
- dataRow.add("");
- dataRow.add("");
- dataRow.add("");
- dataRow.add(mc.getPlatform().getUrl());
-
- samplePlatformDescriptionSheetDataExport.add(dataRow);
- }
- }
- }
-
- private void addXenoMolcharDataToSamplePlatform(ModelCreation model){
-
- if(model.getSpecimens() != null){
-
- for(Specimen sp : model.getSpecimens()){
-
- String passage = sp.getPassage();
-
- String hostStrainName = "";
- String hostStrainNomenclature = "";
-
- if(sp.getHostStrain() != null){
- hostStrainName = getHostStrainName(sp);
- hostStrainNomenclature = getHostStrainNomenclature(sp);
- }
-
-
- Sample sample = sp.getSample();
-
- if(sample != null && sample.getMolecularCharacterizations() != null && !sample.getMolecularCharacterizations().isEmpty()){
-
- for(MolecularCharacterization mc : sample.getMolecularCharacterizations()) {
-
- List<String> dataRow = new ArrayList<>();
-
- dataRow.add("");
- dataRow.add(sample.getSourceSampleId());
- dataRow.add("xenograft");
- dataRow.add(passage);
- dataRow.add("");
- dataRow.add(model.getSourcePdxId());
- dataRow.add(hostStrainName);
- dataRow.add(hostStrainNomenclature);
- dataRow.add(mc.getType());
- dataRow.add(mc.getPlatform().getName());
- dataRow.add(mc.getTechnology());
- dataRow.add("");
- dataRow.add("");
- dataRow.add("");
- dataRow.add("");
- dataRow.add("");
- dataRow.add(mc.getPlatform().getUrl());
-
- samplePlatformDescriptionSheetDataExport.add(dataRow);
- }
- }
- }
+ models = dataImportService.findModelsWithMolecularDataByDSAndMolcharType(dataSource.getAbbreviation(), molecularType);
}
-
+ return models;
}
- private void initPatientGenomicData(ModelCreation model, List<List<String>> sheetData){
- if(model.getSample() != null && model.getSample().getMolecularCharacterizations() != null){
-
- String sampleId = model.getSample().getSourceSampleId();
-
- for(MolecularCharacterization mc : model.getSample().getMolecularCharacterizations()){
-
- insertOmicDataToSheet(model, sampleId, patientOrigin, mc.getType(), null, mc, sheetData);
+ private boolean allMetadataSheetsHaveData(MetadataSheets providerData){
+ for(TSV.metadataSheetNames sheetName: TSV.metadataSheetNames.values()){
+ if (providerData.get(sheetName.name()) == null || providerData.get(sheetName.name()).isEmpty() ) {
+ log.error("Metadata sheet {} was not found. Skipping metadata export", sheetName.name());
+ return false;
}
- } else {
- log.error("No molecular data on patient sample found for model {} \n", model.getSourcePdxId());
}
+ return true;
}
- private void initXenoGenomicData(ModelCreation model, List<List<String>> sheetData){
-
- //then look for xenograft molchars
- if(model.getSpecimens()!= null){
-
- for(Specimen sp : model.getSpecimens()){
-
- if(sp.getSample() != null && sp.getSample().getMolecularCharacterizations() != null){
-
- String sampleId = sp.getSample().getSourceSampleId();
-
- for(MolecularCharacterization mc: sp.getSample().getMolecularCharacterizations()){
-
- insertOmicDataToSheet(model, sampleId,"xenograft", mc.getType(), sp, mc, sheetData);
- }
- }
- }
- } else log.error("No specimens found for model {}", model.getId());
- }
-
-
- private XSSFWorkbook getWorkbook(String templatePath) {
-
- File file = new File(templatePath);
- log.debug("Loading template {}", templatePath);
- if (!file.exists()) {
- log.error("Template not found {}", templatePath);
- return null;
- }
-
-
- try (FileInputStream fileInputStream = new FileInputStream(file)) {
-
- return new XSSFWorkbook(fileInputStream);
-
- } catch (IOException e) {
- log.error("There was a problem accessing the file: {}", file, e);
- }
- return null;
- }
-
- private String getHostStrainName(Specimen sp){
-
- return sp.getHostStrain().getName() == null?"":sp.getHostStrain().getName();
- }
-
- private String getHostStrainNomenclature(Specimen sp){
- return sp.getHostStrain().getSymbol() == null?"":sp.getHostStrain().getSymbol();
- }
-
- public List<List<String>> getPatientSheetDataExport() {
- return patientSheetDataExport;
- }
-
- public List<List<String>> getPatientTumorSheetDataExport() {
- return patientTumorSheetDataExport;
- }
-
- public List<List<String>> getPatientTreatmentSheetDataExport() {
- return patientTreatmentSheetDataExport;
- }
-
- public List<List<String>> getPdxModelSheetDataExport() {
- return pdxModelSheetDataExport;
- }
-
- public List<List<String>> getPdxModelValidationSheetDataExport() {
- return pdxModelValidationSheetDataExport;
- }
-
- public List<List<String>> getSamplePlatformDescriptionSheetDataExport() {
- return samplePlatformDescriptionSheetDataExport;
- }
-
- public List<List<String>> getSharingAndContactSheetDataExport() {
- return sharingAndContactSheetDataExport;
- }
-
- public List<List<String>> getCytogeneticsSheetDataExport() {
- return cytogeneticsSheetDataExport;
- }
-
- public List<List<String>> getLoaderRelatedDataSheetDataExport() {
- return loaderRelatedDataSheetDataExport;
- }
-
- public List<List<String>> getDrugDosingSheetDataExport() {
- return drugDosingSheetDataExport;
- }
-
- public void setMutationSheetDataExport(List<List<String>> mutationSheetDataExport) {
- this.mutationSheetDataExport = mutationSheetDataExport;
- }
-
- public List<List<String>> getMutationSheetDataExport() {
- return mutationSheetDataExport;
- }
-
- public List<List<String>> getCnaSheetDataExport() {
- return cnaSheetDataExport;
- }
-
- public void setCnaSheetDataExport(List<List<String>> cnaSheetDataExport) {
- this.cnaSheetDataExport = cnaSheetDataExport;
- }
-
- public void setPatientSheetDataExport(List<List<String>> patientSheetDataExport) {
- this.patientSheetDataExport = patientSheetDataExport;
- }
-
- public void setPatientTumorSheetDataExport(List<List<String>> patientTumorSheetDataExport) {
- this.patientTumorSheetDataExport = patientTumorSheetDataExport;
- }
-
- public void setPatientTreatmentSheetDataExport(List<List<String>> patientTreatmentSheetDataExport) {
- this.patientTreatmentSheetDataExport = patientTreatmentSheetDataExport;
- }
-
- public void setPdxModelSheetDataExport(List<List<String>> pdxModelSheetDataExport) {
- this.pdxModelSheetDataExport = pdxModelSheetDataExport;
- }
-
- public void setPdxModelValidationSheetDataExport(List<List<String>> pdxModelValidationSheetDataExport) {
- this.pdxModelValidationSheetDataExport = pdxModelValidationSheetDataExport;
- }
-
- public void setSamplePlatformDescriptionSheetDataExport(List<List<String>> samplePlatformDescriptionSheetDataExport) {
- this.samplePlatformDescriptionSheetDataExport = samplePlatformDescriptionSheetDataExport;
- }
-
- public void setSharingAndContactSheetDataExport(List<List<String>> sharingAndContactSheetDataExport) {
- this.sharingAndContactSheetDataExport = sharingAndContactSheetDataExport;
- }
-
- public void setCytogeneticsSheetDataExport(List<List<String>> cytogeneticsSheetDataExport) {
- this.cytogeneticsSheetDataExport = cytogeneticsSheetDataExport;
- }
-
- public void setLoaderRelatedDataSheetDataExport(List<List<String>> loaderRelatedDataSheetDataExport) {
- this.loaderRelatedDataSheetDataExport = loaderRelatedDataSheetDataExport;
- }
-
- public void setDrugDosingSheetDataExport(List<List<String>> drugDosingSheetDataExport) {
- this.drugDosingSheetDataExport = drugDosingSheetDataExport;
- }
-
-
}
diff --git a/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExtractionServices.java b/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExtractionServices.java
new file mode 100644
index 0000000000000000000000000000000000000000..fad1c53bc914bc4815c399e0d2f5a69aae0d0a61
--- /dev/null
+++ b/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExtractionServices.java
@@ -0,0 +1,788 @@
+package org.pdxfinder.dataexport;
+
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.*;
+import org.pdxfinder.services.DataImportService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.*;
+import java.util.stream.Collectors;
+
+/*
+ * Created by csaba on 02/10/2019.
+ */
+@Service
+public class UniversalDataExtractionServices {
+
+ private static final Logger log = LoggerFactory.getLogger(UniversalDataExtractionServices.class);
+
+ private DataImportService dataImportService;
+
+ public static final String MODEL_ID = "modelId";
+ public static final String PROVIDER_TYPE = "providerType";
+ public static final String MODEL_ACCESSIBILITY = "modelAccessibility";
+ public static final String ACCESS_MODALITIES = "accessModalities";
+ public static final String CONTACT_EMAIL = "contactEmail";
+ public static final String CONTACT_NAME = "contactName";
+ public static final String CONTACT_LINK = "contactLink";
+ public static final String MODEL_LINK = "modelLink";
+ public static final String PROVIDER_NAME = "providerName";
+ public static final String PROVIDER_ABBREV = "providerAbbrev";
+ public static final String PROJECT_NAME = "projectName";
+ private static final String NOT_SPECIFIED = "Not Specified";
+ private static final String PATIENT_ORIGIN = "patient";
+ private static final String MODEL_ORIGIN = "xenograft";
+
+ static final String EMPTY = "";
+
+ @Autowired
+ public UniversalDataExtractionServices(DataImportService dataImportService) {
+ this.dataImportService = dataImportService;
+ }
+
+ public MetadataSheets extractMetadata(Group group, MetadataSheets sheets, boolean isHarmonized){
+ sheets.set(TSV.metadataSheetNames.checklist.name(), extractChecklist());
+ sheets.set(TSV.metadataSheetNames.patient.name(), extractPatientSheet(group));
+ sheets.set(TSV.metadataSheetNames.sample.name(), extractSampleSheet(group, isHarmonized));
+ sheets.set(TSV.metadataSheetNames.model.name(), extractModelDetails(group));
+ sheets.set(TSV.metadataSheetNames.model_validation.name(), extractModelValidations(group));
+ sheets.set(TSV.metadataSheetNames.sharing.name(), extractSharingAndContact(group));
+ sheets.set(TSV.metadataSheetNames.loader.name(), extractLoaderRelatedData(group));
+ return sheets;
+ }
+
+ public List<List<String>> extractChecklist(){
+ List<List<String>> checklist = new ArrayList<>();
+ List<String> deprecatedMessageRow = new ArrayList<>();
+ deprecatedMessageRow.add(EMPTY);
+ checklist.add(deprecatedMessageRow);
+ return checklist;
+ }
+
+ public List<List<String>> extractPatientSheet(Group group) {
+ List<Patient> patients = dataImportService.findPatientsByGroup(group);
+ List<List<String>> patientSheetDataExport = new ArrayList<>();
+ for (Patient patient : patients) {
+
+ List<String> dataRow = new ArrayList<>();
+
+ String patientId = patient.getExternalId();
+ String sex = patient.getSex();
+ String cancerHistory = patient.getCancerRelevantHistory();
+ String ethnicity = patient.getEthnicity();
+ String ethnicityAssessment = patient.getEthnicityAssessment();
+ String firstDiagnosis = patient.getFirstDiagnosis();
+ String ageAtFirstDiagnosis = patient.getAgeAtFirstDiagnosis();
+
+ dataRow.add(patientId);
+ dataRow.add(sex);
+ dataRow.add(cancerHistory);
+ dataRow.add(ethnicity);
+ dataRow.add(ethnicityAssessment);
+ dataRow.add(firstDiagnosis);
+ dataRow.add(ageAtFirstDiagnosis);
+
+ patientSheetDataExport.add(dataRow);
+ }
+ return patientSheetDataExport;
+ }
+
+ public List<List<String>> extractSampleSheet(Group group, boolean isHarmonized){
+ List<Patient> patients = dataImportService.findPatientTumorAtCollectionDataByDS(group);
+ List<List<String>> sampleSheetDataExport = new ArrayList<>();
+ for(Patient patient : patients){
+ String patientId = patient.getExternalId();
+ for(PatientSnapshot patientSnapshot : patient.getSnapshots()){
+ for(Sample sample : patientSnapshot.getSamples()){
+
+ List<String> dataRow = new ArrayList<>();
+ String sampleId = sample.getSourceSampleId();
+ String collectionDate = patientSnapshot.getDateAtCollection();
+ String collectionEvent = patientSnapshot.getCollectionEvent();
+ String elapsedTime = patientSnapshot.getElapsedTime();
+ String ageAtCollection = patientSnapshot.getAgeAtCollection();
+ String diagnosis = getSampleUnharmonizedDiagnosis(sample);
+ String tumorType = sample.getType().getName();
+ String primarySite = sample.getOriginTissue().getName();
+ String collectionSite = sample.getSampleSite().getName();
+ String stage = sample.getStage();
+ String stageClassification = sample.getStageClassification();
+ String grade = sample.getGrade();
+ String gradeClassification = sample.getGradeClassification();
+ String virologyStatus = patientSnapshot.getVirologyStatus();
+ String isPatientTreatmentInfoAvailable = EMPTY;
+ String treatmentNaive = patientSnapshot.getTreatmentNaive();
+ String isPatientTreated = EMPTY;
+ String wasPatientTreated = EMPTY;
+ String modelId = getModelIdBySample(sample);
+
+ dataRow.add(patientId);
+ dataRow.add(sampleId);
+ dataRow.add(collectionDate);
+ dataRow.add(collectionEvent);
+ dataRow.add(elapsedTime);
+ dataRow.add(ageAtCollection);
+ dataRow.add(diagnosis);
+ addHarmonizedDiagnosis(dataRow, sample, isHarmonized);
+ dataRow.add(tumorType);
+ dataRow.add(primarySite);
+ dataRow.add(collectionSite);
+ dataRow.add(stage);
+ dataRow.add(stageClassification);
+ dataRow.add(grade);
+ dataRow.add(gradeClassification);
+ dataRow.add(virologyStatus);
+ dataRow.add(isPatientTreatmentInfoAvailable);
+ dataRow.add(treatmentNaive);
+ dataRow.add(isPatientTreated);
+ dataRow.add(wasPatientTreated);
+ dataRow.add(modelId);
+ sampleSheetDataExport.add(dataRow);
+ }
+ }
+ }
+ return sampleSheetDataExport;
+ }
+
+ private void addHarmonizedDiagnosis(List<String> dataRow, Sample sample, boolean isHarmonized){
+ if(isHarmonized){
+ String harmonizedDiagnosis = getHarmonizedDiagnosis(sample);
+ dataRow.add(harmonizedDiagnosis);
+ }
+ }
+
+ private String getHarmonizedDiagnosis(Sample sample){
+ String diagnosis = EMPTY;
+ try{
+ diagnosis = sample.getSampleToOntologyRelationship().getOntologyTerm().getLabel();
+ } catch (NullPointerException e){
+ log.warn("Sample {} was not mapped to an ontology term", sample.getSourceSampleId());
+ }
+ return diagnosis;
+ }
+
+ private String getSampleUnharmonizedDiagnosis(Sample sample) {
+ return sample.getDiagnosis();
+ }
+
+ private String getModelIdBySample(Sample sample){
+ String modelId = EMPTY;
+ try {
+ modelId = dataImportService.findModelBySample(sample).getSourcePdxId();
+ }
+ catch (Exception e){
+ log.error("Could not find Model associated with Sample: {} ", sample.getSourceSampleId());
+ }
+ return modelId;
+ }
+
+ public List<List<String>> extractModelDetails(Group group){
+
+ List<ModelCreation> models = dataImportService.findModelsWithSpecimensAndQAByDS(group.getAbbreviation());
+ List<List<String>> modelSheetDataExport = new ArrayList<>();
+ for(ModelCreation model : models){
+ Map<String, ModelDetails> specimenMap = new HashMap<>();
+ for(Specimen specimen : model.getSpecimens()){
+
+ String passage = specimen.getPassage();
+ String engraftmentSite = getEngraftmentSite(specimen);
+ String engraftmentType = getEngraftmentType(specimen);
+ String[] engraftmentMaterialInfo = getEngraftmentMaterialInfo(specimen);
+ String engraftmentMaterial = engraftmentMaterialInfo[0];
+ String engraftmentMaterialStatus = engraftmentMaterialInfo[1];
+
+ addEntryToSpecimenMap(
+ specimenMap,
+ specimen.getHostStrain(),
+ engraftmentSite,
+ engraftmentType,
+ engraftmentMaterial,
+ engraftmentMaterialStatus,
+ passage);
+ }
+ modelSheetDataExport.addAll(insertModelSheetDataFromSpecimenMap(specimenMap, model));
+ }
+ return modelSheetDataExport;
+ }
+
+ private List<List<String>> insertModelSheetDataFromSpecimenMap(Map<String, ModelDetails> specimenMap, ModelCreation model){
+ List<List<String>> modelSheetDataExport = new ArrayList<>();
+ String modelId = model.getSourcePdxId();
+ String pubmedIDs = getPubmedIDs(model);
+
+ for(Map.Entry<String, ModelDetails> entry : specimenMap.entrySet()){
+
+ ModelDetails md = entry.getValue();
+ List<String> dataRow = new ArrayList<>();
+
+ dataRow.add(modelId);
+ dataRow.add(md.getHostStrainName());
+ dataRow.add(md.getHostStrainNomenclature());
+ dataRow.add(md.getEngraftmentSite());
+ dataRow.add(md.getEngraftmentType());
+ dataRow.add(md.getEngraftmentMaterial());
+ dataRow.add(md.getEngraftmentMaterialStatus());
+ dataRow.add(md.getSortedPassages());
+ dataRow.add(pubmedIDs);
+
+ modelSheetDataExport.add(dataRow);
+ }
+ return modelSheetDataExport;
+ }
+
+ private String[] getEngraftmentMaterialInfo(Specimen specimen){
+ String[] engraftmentInfo = {NOT_SPECIFIED, NOT_SPECIFIED};
+ if(Objects.nonNull(specimen.getEngraftmentMaterial())){
+ engraftmentInfo[0] = specimen.getEngraftmentMaterial().getName();
+ engraftmentInfo[1] = specimen.getEngraftmentMaterial().getState();
+ }
+ return engraftmentInfo;
+ }
+
+ private String getEngraftmentSite(Specimen specimen){
+ String engraftmentSite = NOT_SPECIFIED;
+ if (Objects.nonNull(specimen.getEngraftmentSite())){
+ engraftmentSite = specimen.getEngraftmentSite().getName();
+ }
+ return engraftmentSite;
+ }
+
+ private String getEngraftmentType(Specimen specimen){
+ String engraftmentType = NOT_SPECIFIED;
+ if (Objects.nonNull(specimen.getEngraftmentType())){
+ engraftmentType = specimen.getEngraftmentType().getName();
+ }
+ return engraftmentType;
+ }
+
+ public List<List<String>> extractModelValidations(Group group){
+ List<List<String>> modelValidationSheetDataExport = new ArrayList<>();
+ List<ModelCreation> models = dataImportService.findModelsWithSpecimensAndQAByDS(group.getAbbreviation());
+
+ for(ModelCreation model : models){
+
+ if(model != null && model.getQualityAssurance() != null) {
+
+ String modelId = model.getSourcePdxId();
+
+ for (QualityAssurance qa : model.getQualityAssurance()) {
+
+ List<String> dataRow = new ArrayList<>();
+ String validationTechnique = qa.getTechnology();
+ String validationDescription = qa.getDescription();
+ String passages = qa.getPassages();
+ String nomenclature = qa.getValidationHostStrain();
+ dataRow.add(modelId);
+ dataRow.add(validationTechnique);
+ dataRow.add(validationDescription);
+ dataRow.add(passages);
+ dataRow.add(nomenclature);
+ modelValidationSheetDataExport.add(dataRow);
+ }
+ }
+ }
+ return modelValidationSheetDataExport;
+ }
+
+ public List<List<String>> extractSharingAndContact(Group group){
+ List<ModelCreation> models = dataImportService.findModelsWithSharingAndContactByDS(group.getAbbreviation());
+ List<List<String>> sharingAndContactSheetDataExport = new ArrayList<>();
+
+ for(ModelCreation model : models){
+
+ LinkedHashMap<String, String> sharingAndContactRow = new LinkedHashMap<>();
+ sharingAndContactRow.put(MODEL_ID, model.getSourcePdxId());
+ Group providerGroup = getGroupByType(model, "Provider");
+ Group accessGroup = getGroupByType(model, "Accessibility");
+ Group projectGroup = getGroupByType(model, "Project");
+ getGroupData(sharingAndContactRow, providerGroup, accessGroup, projectGroup);
+ getExternalUrlData(sharingAndContactRow, model.getExternalUrls());
+
+ List<String> dataRow = new ArrayList<>();
+ dataRow.add(sharingAndContactRow.get(MODEL_ID));
+ dataRow.add(sharingAndContactRow.get(PROVIDER_TYPE));
+ dataRow.add(sharingAndContactRow.get(MODEL_ACCESSIBILITY));
+ dataRow.add(sharingAndContactRow.get(ACCESS_MODALITIES));
+ dataRow.add(sharingAndContactRow.get(CONTACT_EMAIL));
+ dataRow.add(sharingAndContactRow.get(CONTACT_NAME));
+ dataRow.add(sharingAndContactRow.get(CONTACT_LINK));
+ dataRow.add(sharingAndContactRow.get(MODEL_LINK));
+ dataRow.add(sharingAndContactRow.get(PROVIDER_NAME));
+ dataRow.add(sharingAndContactRow.get(PROVIDER_ABBREV));
+ dataRow.add(sharingAndContactRow.get(PROJECT_NAME));
+ sharingAndContactSheetDataExport.add(dataRow);
+ }
+ return sharingAndContactSheetDataExport;
+ }
+
+ public List<List<String>> extractLoaderRelatedData(Group group){
+ List<List<String>> loaderRelatedDataSheetDataExport = new ArrayList<>();
+ List<String> dataRow = new ArrayList<>();
+ dataRow.add(group.getName());
+ dataRow.add(group.getAbbreviation());
+ dataRow.add(group.getUrl());
+ loaderRelatedDataSheetDataExport.add(dataRow);
+ return loaderRelatedDataSheetDataExport;
+ }
+
+ public List<List<String>> extractSamplePlatform(Group group){
+ List<List<String>> samplePlatformDescriptionSheetDataExport = new ArrayList<>();
+ List<ModelCreation> models = dataImportService.findModelXenograftPlatformSampleByDS(group.getAbbreviation());
+ for(ModelCreation model : models){
+ samplePlatformDescriptionSheetDataExport.addAll(addPatientMolcharDataToSamplePlatform(model));
+ samplePlatformDescriptionSheetDataExport.addAll(addXenoMolcharDataToSamplePlatform(model));
+ }
+ return samplePlatformDescriptionSheetDataExport;
+ }
+
+ public List<List<String>> extractModelsOmicData(ModelCreation model, String molcharType){
+ List<List<String>> modelsOmicExportSheet = new ArrayList<>();
+ if(model != null) {
+ String modelId = model.getSourcePdxId();
+ log.info("ModelId {}: Starting extraction of omic {} data",modelId, molcharType);
+
+ if(molcharType.equals("drug")){
+ modelsOmicExportSheet.addAll(extractDrugDosing(model));
+ }
+ else if(molcharType.equals("patientTreatment")){
+ modelsOmicExportSheet.addAll(extractPatientTreatment(model));
+ }
+ else {
+ modelsOmicExportSheet.addAll(extractPatientSampleOmicData(model, molcharType));
+ modelsOmicExportSheet.addAll(extractXenoSampleOmicDataForEachSpecimen(model, molcharType));
+ }
+ }
+ return modelsOmicExportSheet;
+ }
+
+ private List<List<String>> extractDrugDosing(ModelCreation model){
+ List<List<String>> drugDosingTable =new ArrayList<>();
+ if(model.getTreatmentSummary() != null && model.getTreatmentSummary().getTreatmentProtocols() != null) {
+ String modelId = model.getSourcePdxId();
+ List<TreatmentProtocol> treatmentProtocols = model.getTreatmentSummary().getTreatmentProtocols();
+ for(TreatmentProtocol treatmentProtocol: treatmentProtocols){
+ List<String> drugDosingRow = new ArrayList<>();
+ List<TreatmentComponent> treatmentComponents = treatmentProtocol.getComponents();
+ Response response = treatmentProtocol.getResponse();
+ String description = EMPTY;
+ String classification = EMPTY;
+ if(response != null){
+ description = response.getDescription();
+ classification = response.getDescriptionClassification();
+ }
+ String treatmentName = treatmentComponents.stream()
+ .map(x -> x.getTreatment().getName())
+ .collect(Collectors.joining(" + "));
+ String dose = treatmentComponents.get(0).getDose();
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(modelId);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(treatmentName);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(dose);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(description);
+ drugDosingRow.add(classification);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(EMPTY);
+ drugDosingRow.add(EMPTY);
+ drugDosingTable.add(drugDosingRow);
+ }
+ }
+ return drugDosingTable;
+ }
+
+ private List<List<String>> extractPatientTreatment (ModelCreation model) {
+ List<List<String>> patientTreatmentTable =new ArrayList<>();
+ if (model.getSample() != null && model.getSample().getPatientSnapshot() != null) {
+ PatientSnapshot patientSnapshot = model.getSample().getPatientSnapshot();
+ if (patientSnapshot.getTreatmentSummary() != null && patientSnapshot.getTreatmentSummary().getTreatmentProtocols() != null) {
+ String patientId = patientSnapshot.getPatient().getExternalId();
+ List<TreatmentProtocol> treatmentProtocols = patientSnapshot.getTreatmentSummary().getTreatmentProtocols();
+ for (TreatmentProtocol treatmentProtocol : treatmentProtocols) {
+ List<String> patientTreatmentRow = new ArrayList<>();
+ List<TreatmentComponent> treatmentComponents = treatmentProtocol.getComponents();
+ Response response = treatmentProtocol.getResponse();
+ String treatmentName = treatmentComponents.stream()
+ .map(x -> x.getTreatment().getName())
+ .collect(Collectors.joining(" + "));
+ String dose = treatmentComponents.get(0).getDose();
+ patientTreatmentRow.add(patientId);
+ patientTreatmentRow.add(treatmentName);
+ patientTreatmentRow.add(dose);
+ patientTreatmentRow.add(EMPTY);
+ patientTreatmentRow.add(EMPTY);
+ patientTreatmentRow.add(EMPTY);
+ patientTreatmentRow.add(EMPTY);
+ patientTreatmentRow.add(response.getDescription());
+ patientTreatmentRow.add(response.getDescriptionClassification());
+ patientTreatmentRow.add(EMPTY);
+ patientTreatmentTable.add(patientTreatmentRow);
+ }
+ }
+ }
+ return patientTreatmentTable;
+ }
+ private List<List<String>> parseOmicDataToSheet(
+ ModelCreation model,
+ String sampleId,
+ String sampleOrigin,
+ String molcharType,
+ Specimen specimen,
+ MolecularCharacterization mc){
+
+ List<List<String>> sheetData = new ArrayList<>();
+ for(MarkerAssociation ma: mc.getMarkerAssociations()) {
+ List<MolecularData> molecularData;
+ try {
+ molecularData = ma.decodeMolecularData();
+ } catch (Exception e) {
+ log.error("Error decoding molecular Data on sample Id {} " +
+ "for molecularCharacterization type {}", sampleId, mc.getType());
+ molecularData = new ArrayList<>();
+ }
+ for (MolecularData md : molecularData) {
+ List<String> rowData = new ArrayList<>();
+ rowData.add(model.getSourcePdxId());
+ rowData.add(sampleId);
+ rowData.add(sampleOrigin);
+ rowData.add(getHostStrainNameSymbol(specimen));
+ rowData.add(getPassage(sampleOrigin, specimen));
+ switch (molcharType) {
+ case "mutation":
+ rowData.add(md.getMarker());
+ rowData.add(md.getBiotype());
+ rowData.add(md.getCodingSequenceChange());
+ rowData.add(md.getVariantClass());
+ rowData.add(md.getCodonChange());
+ rowData.add(md.getAminoAcidChange());
+ rowData.add(md.getConsequence());
+ rowData.add(md.getFunctionalPrediction());
+ rowData.add(md.getReadDepth());
+ rowData.add(md.getAlleleFrequency());
+ rowData.add(md.getChromosome());
+ rowData.add(md.getSeqStartPosition());
+ rowData.add(md.getRefAllele());
+ rowData.add(md.getAltAllele());
+ rowData.add(md.getUcscGeneId());
+ rowData.add(md.getNcbiGeneId());
+ rowData.add(md.getNcbiTranscriptId());
+ rowData.add(md.getEnsemblGeneId());
+ rowData.add(md.getEnsemblTranscriptId());
+ rowData.add(md.getExistingVariations());
+ rowData.add(md.getGenomeAssembly());
+ rowData.add(mc.getPlatform().getName());
+ break;
+ case "copy number alteration":
+ rowData.add(md.getChromosome());
+ rowData.add(md.getSeqStartPosition());
+ rowData.add(md.getSeqEndPosition());
+ rowData.add(md.getMarker());
+ rowData.add(md.getUcscGeneId());
+ rowData.add(md.getNcbiGeneId());
+ rowData.add(md.getEnsemblGeneId());
+ rowData.add(md.getCnaLog10RCNA());
+ rowData.add(md.getCnaLog2RCNA());
+ rowData.add(md.getFold_change());
+ rowData.add(md.getCnaCopyNumberStatus());
+ rowData.add(md.getCnaGisticValue());
+ rowData.add(md.getCnaPicnicValue());
+ rowData.add(md.getGenomeAssembly());
+ rowData.add(mc.getPlatform().getName());
+ break;
+ case "cytogenetics":
+ rowData.add(EMPTY);
+ rowData.add(md.getMarker());
+ rowData.add(md.getCytogeneticsResult());
+ rowData.add(md.getMarkerStatusComment());
+ rowData.add(mc.getPlatform().getName());
+ rowData.add(EMPTY);
+ rowData.add(EMPTY);
+ break;
+ case "expression":
+ rowData.add(md.getChromosome());
+ rowData.add(EMPTY);
+ rowData.add(md.getSeqStartPosition());
+ rowData.add(md.getSeqEndPosition());
+ rowData.add(md.getMarker());
+ rowData.add(EMPTY);
+ rowData.add(EMPTY);
+ rowData.add(EMPTY);
+ rowData.add(md.getRnaSeqCoverage());
+ rowData.add(md.getRnaSeqFPKM());
+ rowData.add(md.getRnaSeqTPM());
+ rowData.add(md.getRnaSeqCount());
+ rowData.add(md.getAffyHGEAProbeId());
+ rowData.add(md.getAffyHGEAExpressionValue());
+ rowData.add(md.getIlluminaHGEAProbeId());
+ rowData.add(md.getIlluminaHGEAExpressionValue());
+ rowData.add(md.getZscore());
+ rowData.add(md.getGenomeAssembly());
+ rowData.add(mc.getPlatform().getName());
+ break;
+ default:
+ throw new IllegalArgumentException("Inappropriate molecular data type passed");
+ }
+ sheetData.add(rowData);
+ }
+ }
+ return sheetData;
+ }
+
+ private String getHostStrainNameSymbol(Specimen specimen) {
+ String hostStrainSymbol = EMPTY;
+ if (specimen != null && specimen.getHostStrain() != null && specimen.getHostStrain().getSymbol() != null) {
+ hostStrainSymbol = specimen.getHostStrain().getSymbol();
+ }
+ return hostStrainSymbol;
+ }
+
+ private String getPassage(String sampleOrigin, Specimen specimen) {
+ return (!sampleOrigin.equals(PATIENT_ORIGIN) && specimen != null) ? specimen.getPassage() : EMPTY ;
+ }
+
+ private String getPubmedIDs(ModelCreation model){
+ StringBuilder pubmedIDs = new StringBuilder();
+ if(model.getGroups() != null){
+ for(Group g : model.getGroups()){
+ if(g.getType().equals("Publication")){
+ if(pubmedIDs.length() != 0){
+ pubmedIDs.append(",");
+ }
+ pubmedIDs.append(g.getPubMedId());
+ }
+ }
+ }
+ return pubmedIDs.toString();
+ }
+
+ private Group getGroupByType(ModelCreation model, String type){
+ if(model.getGroups() != null){
+ for(Group g : model.getGroups()){
+ if(g.getType().equals(type)){
+ return g;
+ }
+ }
+ }
+ return null;
+ }
+
+ private void getGroupData(LinkedHashMap<String, String> map, Group providerGroup, Group accessGroup, Group projectGroup){
+
+ if(providerGroup != null) {
+ map.put(PROVIDER_TYPE, providerGroup.getProviderType());
+ map.put(PROVIDER_NAME, providerGroup.getName());
+ map.put(PROVIDER_ABBREV, providerGroup.getAbbreviation());
+ }
+ else{
+ map.put(PROVIDER_TYPE, EMPTY);
+ map.put(PROVIDER_NAME, EMPTY);
+ map.put(PROVIDER_ABBREV, EMPTY);
+ }
+ if(accessGroup != null){
+ map.put(MODEL_ACCESSIBILITY, accessGroup.getAccessibility());
+ map.put(ACCESS_MODALITIES, accessGroup.getAccessModalities());
+ }
+ else{
+ map.put(MODEL_ACCESSIBILITY, EMPTY);
+ map.put(ACCESS_MODALITIES, EMPTY);
+ }
+
+ if(projectGroup != null){
+ map.put(PROJECT_NAME, projectGroup.getName());
+ }
+ else {
+ map.put(PROJECT_NAME, EMPTY);
+ }
+ }
+
+ private void getExternalUrlData(LinkedHashMap<String, String> map, Collection<ExternalUrl> urls){
+ map.put(CONTACT_EMAIL, EMPTY);
+ map.put(CONTACT_NAME, EMPTY);
+ map.put(CONTACT_LINK, EMPTY);
+ map.put(MODEL_LINK, EMPTY);
+
+ if(urls != null){
+ for(ExternalUrl ex: urls) {
+ if (ex.getType().equals("contact")) {
+
+ if (ex.getUrl() != null && ex.getUrl().contains("@")) {
+ map.put(CONTACT_EMAIL, ex.getUrl());
+ } else {
+ map.put(CONTACT_LINK, ex.getUrl());
+ }
+ } else if (ex.getType().equals("source") && ex.getUrl() != null) {
+ map.put(MODEL_LINK, ex.getUrl());
+ }
+ }
+ }
+ }
+
+ private void addEntryToSpecimenMap(
+ Map<String, ModelDetails> specimenMap,
+ HostStrain hostStrain,
+ String engraftmentSite,
+ String engraftmentType,
+ String engraftmentMaterial,
+ String engraftmentMaterialStatus,
+ String passage){
+
+ String specimenMapKey = String.join(
+ hostStrain.getName(),
+ hostStrain.getSymbol(),
+ engraftmentSite,
+ engraftmentType,
+ engraftmentMaterial,
+ engraftmentMaterialStatus);
+
+ if(specimenMap.containsKey(specimenMapKey)){
+ specimenMap.get(specimenMapKey).getPassages().add(passage);
+ }
+ else{
+ ModelDetails md = new ModelDetails(
+ hostStrain.getName(),
+ hostStrain.getSymbol(),
+ engraftmentSite,
+ engraftmentType,
+ engraftmentMaterial,
+ engraftmentMaterialStatus,
+ passage);
+ specimenMap.put(specimenMapKey, md);
+ }
+ }
+
+ private ArrayList<List<String>> addPatientMolcharDataToSamplePlatform(ModelCreation model){
+ ArrayList<List<String>> samplePlatformPatientSheetDataExport = new ArrayList<>();
+ if(model.getSample() != null && model.getSample().getMolecularCharacterizations() != null){
+ for(MolecularCharacterization mc : model.getSample().getMolecularCharacterizations()){
+ List<String> dataRow = new ArrayList<>();
+ dataRow.add(EMPTY);
+ dataRow.add(model.getSample().getSourceSampleId());
+ dataRow.add(PATIENT_ORIGIN);
+ dataRow.add("NA");
+ dataRow.add(EMPTY);
+ dataRow.add(model.getSourcePdxId());
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(mc.getType());
+ dataRow.add(mc.getPlatform().getName());
+ dataRow.add(mc.getTechnology());
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(mc.getPlatform().getUrl());
+
+ samplePlatformPatientSheetDataExport.add(dataRow);
+ }
+ }
+ return samplePlatformPatientSheetDataExport;
+ }
+
+ private List<List<String>> addXenoMolcharDataToSamplePlatform(ModelCreation model){
+ ArrayList<List<String>> samplePlatformXenoDataSheetDataExport = new ArrayList<>();
+ if(Objects.nonNull(model.getSpecimens())){
+ for(Specimen sp : model.getSpecimens()){
+
+ String passage = sp.getPassage();
+ String hostStrainName = getHostStrainName(sp);
+ String hostStrainNomenclature = getHostStrainNomenclature(sp);
+ Sample sample = sp.getSample();
+
+ if(sample != null && sample.getMolecularCharacterizations() != null && !sample.getMolecularCharacterizations().isEmpty()){
+
+ for(MolecularCharacterization mc : sample.getMolecularCharacterizations()) {
+
+ List<String> dataRow = new ArrayList<>();
+
+ dataRow.add(EMPTY);
+ dataRow.add(sample.getSourceSampleId());
+ dataRow.add(MODEL_ORIGIN);
+ dataRow.add(passage);
+ dataRow.add(EMPTY);
+ dataRow.add(model.getSourcePdxId());
+ dataRow.add(hostStrainName);
+ dataRow.add(hostStrainNomenclature);
+ dataRow.add(mc.getType());
+ dataRow.add(mc.getPlatform().getName());
+ dataRow.add(mc.getTechnology());
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(EMPTY);
+ dataRow.add(mc.getPlatform().getUrl());
+
+ samplePlatformXenoDataSheetDataExport.add(dataRow);
+ }
+ }
+ }
+ }
+ return samplePlatformXenoDataSheetDataExport;
+ }
+
+ private List<List<String>> extractPatientSampleOmicData(ModelCreation model, String molcharType){
+ List<List<String>> patientOmic = new ArrayList<>();
+ if(model.getSample() != null && model.getSample().getMolecularCharacterizations() != null){
+ String sampleId = model.getSample().getSourceSampleId();
+
+ for(MolecularCharacterization mc : model.getSample().getMolecularCharacterizations()){
+ if(mc.getType().equals(molcharType)){
+ log.info("ModelId {}: Extracting patient sample {} information",model.getSourcePdxId(), sampleId);
+ patientOmic.addAll(parseOmicDataToSheet(model, sampleId, PATIENT_ORIGIN, mc.getType(), null, mc));
+ }
+ }
+ }
+ return patientOmic;
+ }
+
+ private List<List<String>> extractXenoSampleOmicDataForEachSpecimen(ModelCreation model, String molcharType) {
+ List<List<String>> xenograftOmic = new ArrayList<>();
+ if(model.getSpecimens() != null) {
+ for (Specimen specimen : model.getSpecimens()) {
+ if (specimenHasMolecularCharacterizations(specimen)) {
+ xenograftOmic.addAll(
+ extractXenoSampleOmicDataForEachMolecularCharacterization(specimen, molcharType, model));
+ }
+ }
+ if(xenograftOmic.isEmpty()){
+ log.error("ModelId {}: Error extracting xenograft information", model.getSourcePdxId());
+ }
+ }
+ return xenograftOmic;
+ }
+
+ private List<List<String>> extractXenoSampleOmicDataForEachMolecularCharacterization(Specimen specimen, String molcharType, ModelCreation model){
+ List<List<String>> OmicData = new ArrayList<>();
+ for (MolecularCharacterization mc : specimen.getSample().getMolecularCharacterizations()) {
+ if (mc.getType().equals(molcharType)) {
+ String sampleId = specimen.getSample().getSourceSampleId();
+ log.info("ModelId {}: Extracting sample {} information", model.getSourcePdxId(), sampleId);
+ OmicData.addAll(parseOmicDataToSheet(model, sampleId,
+ MODEL_ORIGIN, mc.getType(), specimen, mc));
+ }
+ }
+ return OmicData;
+ }
+
+ private boolean specimenHasMolecularCharacterizations(Specimen specimen){
+ return (specimen.getSample() != null && specimen.getSample().getMolecularCharacterizations() != null);
+ }
+
+ private String getHostStrainName(Specimen sp){
+ return sp.getHostStrain().getName() == null? EMPTY :sp.getHostStrain().getName();
+ }
+
+ private String getHostStrainNomenclature(Specimen sp){
+ return sp.getHostStrain().getSymbol() == null? EMPTY :sp.getHostStrain().getSymbol();
+ }
+
+}
diff --git a/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataWriterServices.java b/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataWriterServices.java
new file mode 100644
index 0000000000000000000000000000000000000000..b3313bc8482bc40586ebfb7489a29f5a6b993b5b
--- /dev/null
+++ b/indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataWriterServices.java
@@ -0,0 +1,114 @@
+package org.pdxfinder.dataexport;
+
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.List;
+
+import static java.util.Objects.nonNull;
+
+@Component
+public class UniversalDataWriterServices {
+
+ private static final Logger log = LoggerFactory.getLogger(UniversalDataWriterServices.class);
+
+ public void writXlsxFromWorkbook(XSSFWorkbook dataWorkbook, String fileLocation) throws IOException {
+ FileOutputStream fileOut = new FileOutputStream(fileLocation);
+ dataWorkbook.write(fileOut);
+ fileOut.close();
+ }
+
+ public void updateXlsxSheetWithData(Sheet sheet, List<List<String>> data, int startRow, int startColumn) {
+ if (nonNull(data)) {
+ for (int i = 0; i < data.size(); i++) {
+ int rowIndex = startRow + i - 1;
+ sheet.createRow(rowIndex);
+ for (int j = 0; j < data.get(i).size(); j++) {
+ int columnIndex = startColumn + j - 1;
+ sheet.getRow(rowIndex).createCell(columnIndex);
+ Cell cell;
+ try {
+ cell = sheet.getRow(rowIndex).getCell(columnIndex);
+ cell.setCellValue(data.get(i).get(j));
+ } catch (Exception e) {
+ log.error("Exception in {} {}:{}", sheet.getSheetName(), rowIndex, columnIndex);
+ }
+ }
+ }
+ }
+ }
+
+ public void writeSingleOmicFileToTsv(String exportLocation, Sheet template,
+ List<List<String>> exportSheet) throws IOException {
+ createExportDirectories(exportLocation);
+ saveHeadersToTsv(template, exportLocation);
+ appendDataToOmicTsvFile(exportSheet, exportLocation);
+ }
+
+ public void createExportDirectories(String exportFileLocation) throws IOException {
+ Path directory = Paths.get(exportFileLocation);
+ Files.createDirectories(directory);
+ if(!directory.toFile().exists()) {
+ throw new IOException(String.format("Failed to create file directory at %s",
+ directory.toAbsolutePath().toString()));
+ }
+ }
+
+ public void saveHeadersToTsv(Sheet template, String exportFileLocation) {
+ try (FileWriter fileWriter = new FileWriter(exportFileLocation)) {
+ saveHeadersToTsv(template, fileWriter);
+ } catch (IOException e) {
+ log.error("IO Error writing headers from {} to {} \n {}", template.getSheetName(), exportFileLocation, e.toString());
+ }
+ }
+
+ public void appendDataToOmicTsvFile(List<List<String>> exportSheet, String exportFileLocation) {
+ try(FileWriter fileWriter = new FileWriter(exportFileLocation, true)) {
+ if (exportSheet != null) {
+ writeDataToTsv(exportSheet, fileWriter);
+ }
+ } catch(Exception e) {
+ log.error("IO Error from reading omic TSV {}",e.toString());
+ }
+ }
+
+ private void saveHeadersToTsv(Sheet xlsxTemplate, FileWriter fileWriter) throws IOException {
+ for (int j = 0; j < xlsxTemplate.getRow(0).getLastCellNum(); j++) {
+ Cell cell;
+ try {
+ cell = xlsxTemplate.getRow(0).getCell(j);
+ if(cell != null) {
+ fileWriter.append(cell.toString());
+ fileWriter.append("\t");
+ }
+ } catch (IOException e) {
+ log.error("IOException in loading export headers");
+ }
+ }
+ fileWriter.append("\n");
+ }
+
+ private void writeDataToTsv(List<List<String>> data, FileWriter fileWriter) throws IOException {
+ for (int rowIndex = 0; rowIndex < data.size(); rowIndex++) {
+ for (int columnIndex = 0; columnIndex < data.get(rowIndex).size(); columnIndex++) {
+ try {
+ fileWriter.append(data.get(rowIndex).get(columnIndex));
+ fileWriter.append("\t");
+ } catch (IOException e) {
+ log.error("IOException writing data to TSV on {}:{}", rowIndex, columnIndex);
+ }
+ }
+ fileWriter.append("\n");
+ }
+ }
+}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadAdditionalDatasets.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadAdditionalDatasets.java
deleted file mode 100644
index a75d9e0f7b35b6da3c96be3ff11fb1a6bf5ea846..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadAdditionalDatasets.java
+++ /dev/null
@@ -1,278 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.reportmanager.ReportManager;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.dto.NodeSuggestionDTO;
-import org.pdxfinder.services.reporting.MarkerLogEntity;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.BeansException;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.ApplicationContextAware;
-import org.springframework.core.annotation.Order;
-import org.springframework.stereotype.Service;
-
-import java.io.File;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-@Service
-@Order(value = 15)
-public class LoadAdditionalDatasets implements ApplicationContextAware{
-
- @Value("${data-dir}")
- private String finderRootDir;
-
- Logger log = LoggerFactory.getLogger(LoadAdditionalDatasets.class);
-
- private static ApplicationContext context;
- private ReportManager reportManager;
-
- @Autowired
- private DataImportService dataImportService;
-
- @Autowired
- private UtilityService utilityService;
-
-
- public void run() {
-
- reportManager = (ReportManager) context.getBean("ReportManager");
-
- loadAdditionalDatasetForCRL();
- }
-
-
- private void loadAdditionalDatasetForCRL() {
-
- log.info("Loading additional datasets for CRL.");
-
- String templateFileStr = finderRootDir+"/data/UPDOG/CRL/template.xlsx";
- String markerTemplateFileStr = finderRootDir + "/data/UPDOG/CRL/cna_tested_markers/list.csv";
-
- File markerListFile = new File(markerTemplateFileStr);
- File templateFile = new File(templateFileStr);
-
- Set<Marker> markerSet = new HashSet<>();
-
- if(markerListFile.exists() && templateFile.exists()){
-
- List<List<String>> markerList = utilityService.serializeCSVToArrayList(markerTemplateFileStr);
-
- //STEP1: get the marker symbols from the csv file then find the corresponding marker node and add it to a set
- log.info("Found "+markerList.size()+ " markers in the marker file.");
- for(int i = 1; i<markerList.size(); i++){
-
- if(i%500 == 0){
- log.info("Collected "+i+" markers from the repository.");
- }
-
- String markerSymbol = markerList.get(i).get(0);
-
- //skip all symbols with dot in them
- if(markerSymbol.contains(".")){
-
- MarkerLogEntity le = new MarkerLogEntity(this.getClass().getSimpleName(),"CRL", "-", "copy number alteration", "Not Specified", markerSymbol, "","");
- le.setMessage(markerSymbol +" is an unrecognised symbol");
- le.setType("ERROR");
- continue;
-
- }
-
-
- //log.info("Looking up: "+markerSymbol);
- NodeSuggestionDTO nsdto = dataImportService.getSuggestedMarker(this.getClass().getSimpleName(), "CRL", "-", markerSymbol, "copy number alteration", "Not Specified");
-
- if(nsdto.getNode() == null){
-
- //uh oh, we found an unrecognised marker symbol, abort, abort!!!!
- reportManager.addMessage(nsdto.getLogEntity());
-
- continue;
- }
- else{
-
- Marker marker = (Marker) nsdto.getNode();
- markerSet.add(marker);
-
- }
-
- }
-
-
- //STEP2:
-
-
- UniversalLoader updog = new UniversalLoader(reportManager, utilityService, dataImportService);
- updog.setFinderRootDir(finderRootDir);
-
- updog.initTemplates(templateFileStr);
-
- List<List<String>> datasetDerived = updog.getSamplePlatformDescriptionSheetData();
- int row = 6;
-
- for (List<String> derivedDatasetRow : datasetDerived) {
-
- String sampleId = derivedDatasetRow.get(0);
-
- String origin = derivedDatasetRow.get(1);
- String passage = derivedDatasetRow.get(2);
- String nomenclature = derivedDatasetRow.get(3);
- String modelId = derivedDatasetRow.get(4);
- String molCharType = derivedDatasetRow.get(5);
- String platformName = derivedDatasetRow.get(6);
- String platformTechnology = derivedDatasetRow.get(7);
- String platformDescription = derivedDatasetRow.get(8);
- String analysisProtocol = derivedDatasetRow.get(9);
-
- //SKIP everything that is not cna
- if(!molCharType.toLowerCase().equals("copy number alteration")){
-
- row++;
- continue;
- }
-
- platformName = platformName.replaceAll("[^A-Za-z0-9 _-]", "");
-
- ModelCreation model;
- Sample sample = null;
- //patient sample
- if (origin.toLowerCase().equals("patient")) {
-
- sample = dataImportService.findHumanSample(modelId, "CRL");
-
- if (sample != null) {
-
- }
- else {
-
- log.error("Unknown human sample with id: " + sampleId);
- row++;
- continue;
- }
- }
- //xenograft sample
- else if (origin.toLowerCase().equals("engrafted tumor") || origin.toLowerCase().equals("engrafted tumour") || origin.toLowerCase().equals("xenograft") ) {
-
- if (passage == null || passage.isEmpty() || passage.toLowerCase().equals("not specified")) {
-
- log.error("Missing essential value Xenograft Passage in row " + row);
- row++;
- continue;
- }
-
- if (nomenclature == null || nomenclature.isEmpty()) {
-
- log.error("Missing essential value nomenclature in row " + row);
- row++;
- continue;
- }
-
- //need this trick to get rid of 0.0 if there is any
- //if(passage.equals("0.0")) passage = "0";
- int passageInt = (int) Float.parseFloat(passage);
- passage = String.valueOf(passageInt);
-
- model = dataImportService.findModelByIdAndDataSourceWithSpecimensAndHostStrain(modelId, "CRL");
-
- if(model == null){
- log.error("Model "+modelId + " not found, skipping");
- row++;
- continue;
- }
-
- //this specimen should have the appropriate hoststrain, too!
- Specimen specimen = dataImportService.findSpecimenByModelAndPassageAndNomenclature(model, passage, nomenclature);
-
- if(specimen != null) {
-
- sample = specimen.getSample();
-
- }
- else{
- log.error("Specimen not found in row "+row);
- row++;
- continue;
- }
-
- }
-
- //STEP3: find the proper molecular characterization node
- MolecularCharacterization molChar = null;
-
- if(sample != null){
-
- for(MolecularCharacterization mc : sample.getMolecularCharacterizations()){
-
- if(mc.getType().equalsIgnoreCase(molCharType)){
-
- if(mc.getPlatform() != null && mc.getPlatform().getName().equalsIgnoreCase(platformName)){
-
- molChar = mc;
- break;
- }
- }
-
- }
- }
- else{
-
- log.error("Proper sample not found for data in row: "+row);
- row++;
- continue;
- }
-
-
- if(molChar != null){
- //STEP4: link molchar to the markers with a fake MA
- int maCounter = 0;
- MarkerAssociation ma = new MarkerAssociation();
- for(Marker m: markerSet){
-
-
- molChar.addMarkerAssociation(ma);
- maCounter++;
- if(maCounter !=0 && maCounter%500==0){
- dataImportService.saveMolecularCharacterization(molChar);
- log.info("Saved "+maCounter+" associations for "+modelId);
- }
-
- }
-
- //STEP5: save the modified molchar object
- dataImportService.saveMolecularCharacterization(molChar);
- log.info("Saved cna data for model: "+modelId);
-
- }
- else{
- log.error("Proper MolChar object not found for data in row: "+row);
- row++;
- continue;
-
- }
-
-
-
- }
-
-
-
- }
-
-
- }
-
-
-
-
- @Override
- public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
- context = applicationContext;
- }
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadHCI.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadHCI.java
deleted file mode 100644
index e6bf7e9e62466966d6d699159a4e79f62952329b..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadHCI.java
+++ /dev/null
@@ -1,285 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.ds.Standardizer;
-import org.pdxfinder.services.dto.LoaderDTO;
-import org.pdxfinder.services.dto.NodeSuggestionDTO;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.PropertySource;
-import org.springframework.stereotype.Service;
-
-import java.io.*;
-import java.util.*;
-
-
-@Service
-@PropertySource("classpath:loader.properties")
-@ConfigurationProperties(prefix = "hci")
-public class LoadHCI extends LoaderBase {
-
- private final static Logger log = LoggerFactory.getLogger(LoadHCI.class);
-
- @Value("${data-dir}")
- private String finderRootDir;
-
- public LoadHCI(UtilityService utilityService, DataImportService dataImportService) {
- super(utilityService, dataImportService);
- }
-
- public void run() throws Exception {
-
- initMethod();
- globalLoadingOrder();
- }
-
-
- @Override
- protected void initMethod() {
-
- log.info("Loading Huntsman PDX data. ");
-
- dto = new LoaderDTO();
-
- jsonFile = finderRootDir + "/data/" + dataSourceAbbreviation + "/pdx/models.json";
- dataSource = dataSourceAbbreviation;
- filesDirectory = "";
- }
-
-
-
- @Override
- protected void step01GetMetaDataFolder() { }
-
-
-
- // HCI uses common implementation Steps step08GetMetaData,step09LoadPatientData default
-
-
- @Override
- protected void step10LoadExternalURLs() {
-
- loadExternalURLs(dataSourceContact,Standardizer.NOT_SPECIFIED);
- }
-
-
- @Override
- protected void step11LoadBreastMarkers() {
-
- }
-
- // HCI uses common implementation Steps step12CreateModels default
-
-
- @Override
- protected void step13LoadSpecimens() {
-
- dto.getModelCreation().addRelatedSample(dto.getPatientSample());
- dto.getModelCreation().addGroup(providerDS);
-
- dataImportService.saveSample(dto.getPatientSample());
- dataImportService.savePatientSnapshot(dto.getPatientSnapshot());
-
- EngraftmentSite engraftmentSite = dataImportService.getImplantationSite(dto.getImplantationSiteStr());
- EngraftmentType engraftmentType = dataImportService.getImplantationType(dto.getImplantationtypeStr());
-
- // uggh parse strains
- ArrayList<HostStrain> strainList= new ArrayList();
- String strains = dto.getStrain();
- if(strains.contains(" and ")){
- strainList.add(nsgBS);
- strainList.add(nsBS);
- }else if(strains.contains("gamma")){
- strainList.add(nsBS);
- }else{
- strainList.add(nsBS);
- }
-
- int count = 0;
- for(HostStrain strain : strainList){
- count++;
- Specimen specimen = new Specimen();
- specimen.setExternalId(dto.getModelID()+"-"+count);
- specimen.setEngraftmentSite(engraftmentSite);
- specimen.setEngraftmentType(engraftmentType);
- specimen.setHostStrain(strain);
-
- Sample specSample = new Sample();
- specSample.setSourceSampleId(dto.getModelID()+"-"+count);
- specimen.setSample(specSample);
-
- dto.getModelCreation().addSpecimen(specimen);
- dto.getModelCreation().addRelatedSample(specSample);
- dataImportService.saveSpecimen(specimen);
- }
- dataImportService.saveModelCreation(dto.getModelCreation());
- }
-
-
-
-
- @Override
- protected void step14LoadPatientTreatments() {
-
-
- }
-
-
-
-
- @Override
- protected void step15LoadImmunoHistoChemistry() {
-
- String ihcFileStr = String.format("%s/data/%s/ihc/ihc.txt", finderRootDir, dataSourceAbbreviation);
-
- File file = new File(ihcFileStr);
-
- if (file.exists()) {
-
- Platform pl = dataImportService.getPlatform("immunohistochemistry","cytogenetics", providerDS);
-
- String currentLine = "";
- int currentLineCounter = 1;
- String[] row;
-
- Map<String, MolecularCharacterization> molCharMap = new HashMap<>();
-
- try {
- BufferedReader buf = new BufferedReader(new FileReader(ihcFileStr));
-
- while (true) {
- currentLine = buf.readLine();
- if (currentLine == null) {
- break;
- //skip the first two rows
- } else if (currentLineCounter < 3) {
- currentLineCounter++;
- continue;
-
- } else {
- row = currentLine.split("\t");
-
- if (row.length > 0) {
-
- String modelId = row[0];
- String sampleId = row[1];
- String markerSymbol = row[2];
- String result = row[3];
- //System.out.println(modelId);
-
- if (modelId.isEmpty() || sampleId.isEmpty() || markerSymbol.isEmpty() || result.isEmpty())
- continue;
-
- NodeSuggestionDTO nsdto = dataImportService.getSuggestedMarker(this.getClass().getSimpleName(), dataSource, modelId, markerSymbol, "cytogenetics","ImmunoHistoChemistry");
- Marker marker = null;
-
-
- if(nsdto.getNode() == null){
-
- //uh oh, we found an unrecognised marker symbol, abort, abort!!!!
- reportManager.addMessage(nsdto.getLogEntity());
- continue;
- }
- else{
-
- //we have a marker node, check message
-
- marker = (Marker)nsdto.getNode();
-
- if(nsdto.getLogEntity() != null){
- reportManager.addMessage(nsdto.getLogEntity());
- }
-
- MolecularCharacterization mc;
-
- if (molCharMap.containsKey(modelId + "---" + sampleId)) {
-
- mc = molCharMap.get(modelId + "---" + sampleId);
- }
- else {
-
- mc = new MolecularCharacterization();
- mc.setType("cytogenetics");
- mc.setPlatform(pl);
- MarkerAssociation ma = new MarkerAssociation();
- mc.addMarkerAssociation(ma);
-
-
- molCharMap.put(modelId + "---" + sampleId, mc);
- }
-
- MolecularData molecularData = new MolecularData();
- molecularData.setMarker(marker.getHgncSymbol());
- molecularData.setCytogeneticsResult(result);
- mc.getFirstMarkerAssociation().addMolecularData(molecularData);
- mc.addMarker(molecularData.getMarker());
- }
-
-
-
- }
-
-
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- System.out.println(currentLineCounter + " " + currentLine.toString());
- }
-
- //System.out.println(molCharMap.toString());
-
- for (Map.Entry<String, MolecularCharacterization> entry : molCharMap.entrySet()) {
- String key = entry.getKey();
- MolecularCharacterization mc = entry.getValue();
-
- String[] modAndSamp = key.split("---");
- String modelId = modAndSamp[0];
- String sampleId = modAndSamp[1];
-
- //Sample sample = dataImportService.findMouseSampleWithMolcharByModelIdAndDataSourceAndSampleId(modelId, hciDS.getAbbreviation(), sampleId);
- Sample sample = dataImportService.findHumanSampleWithMolcharByModelIdAndDataSource(modelId, providerDS.getAbbreviation());
-
- if (sample == null) {
- log.warn("Missing model or sample: " + modelId + " " + sampleId);
- continue;
- }
-
- sample.addMolecularCharacterization(mc);
- mc.getFirstMarkerAssociation().encodeMolecularData();
- dataImportService.saveSample(sample);
-
- }
-
- } else {
-
- log.warn("Skipping loading IHC for HCI");
- }
-
- }
-
-
-
- @Override
- protected void step16LoadVariationData() { }
-
-
- @Override
- void step17LoadModelDosingStudies() throws Exception {
-
- loadModelDosingStudies();
- }
-
- @Override
- void step18SetAdditionalGroups() {
- throw new UnsupportedOperationException();
- }
-
-
-
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadIRCC.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadIRCC.java
deleted file mode 100644
index cd0d67ab55b2f3cab897c7eb4accbeb64b840572..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadIRCC.java
+++ /dev/null
@@ -1,219 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import joptsimple.OptionParser;
-import joptsimple.OptionSet;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONException;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.ds.Standardizer;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.PropertySource;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
-import java.util.*;
-
-@Service
-@PropertySource("classpath:loader.properties")
-@ConfigurationProperties(prefix = "ircc")
-public class LoadIRCC extends LoaderBase {
- private static final Logger log = LoggerFactory.getLogger(LoadIRCC.class);
-
- // samples -> markerAsssociations
- private HashMap<String, HashSet<MarkerAssociation>> markerAssociations = new HashMap();
- private HashMap<String, HashMap<String, String>> specimenSamples = new HashMap();
- private HashSet<Integer> loadedModelHashes = new HashSet<>();
-
- @Value("${data-dir}")
- private String finderRootDir;
-
- @Value("${irccpdx.variation.max}")
- private int variationMax;
-
- public LoadIRCC(UtilityService utilityService, DataImportService dataImportService) {
- super(utilityService, dataImportService);
- }
-
- public void run() throws Exception {
-
- initMethod();
- irccAlgorithm();
- }
-
-
- public void irccAlgorithm() throws Exception {
-
- step00StartReportManager();
- step02GetMetaDataJSON();
- if (skipThis) return;
- step03CreateProviderGroup();
- step04CreateNSGammaHostStrain();
- step06SetProjectGroup();
- step07GetPDXModels();
-
- for (int i = 0; i < jsonArray.length(); i++) {
- this.jsonData = jsonArray.getJSONObject(i);
-
- if (loadedModelHashes.contains(jsonData.toString().hashCode())) continue;
- loadedModelHashes.add(jsonData.toString().hashCode());
-
- step08GetMetaData();
- step09LoadPatientData();
- step10LoadExternalURLs();
- step12CreateModels();
- step13LoadSpecimens();
- step17LoadModelDosingStudies();
- step16LoadVariationData();
- step18SetAdditionalGroups();
- }
- }
-
- @Override
- protected void initMethod() {
- log.info("Loading IRCC PDX data.");
- finderRootDir = UniversalLoader.stripTrailingSlash(finderRootDir);
- jsonFile = finderRootDir + "/data/" + dataSourceAbbreviation+"/pdx/models.json";
-
- dataSource = dataSourceAbbreviation;
- filesDirectory = "";
-
- platformURL = new HashMap<>();
- platformURL.put("whole exome sequencing_mutation","/platform/whole-exome-sequencing/");
- platformURL.put("TargetedNGS_MUT_mutation","/platform/ircc-gene-panel/");
- platformURL.put("Targeted Next Generation Sequencing_copy number alteration","/platform/ircc-gene-panel/");
-
- }
-
- @Override
- protected void step01GetMetaDataFolder() {
- throw new UnsupportedOperationException();
- }
-
- @Override
- protected void step05CreateNSHostStrain() {
- throw new UnsupportedOperationException();
- }
-
- @Override
- protected void step10LoadExternalURLs() {
- loadExternalURLs(dataSourceContact,Standardizer.NOT_SPECIFIED);
- dataImportService.saveSample(dto.getPatientSample());
- dataImportService.savePatientSnapshot(dto.getPatientSnapshot());
- }
-
- @Override
- protected void step11LoadBreastMarkers() {
- throw new UnsupportedOperationException();
- }
-
- @Override
- protected void step13LoadSpecimens()throws Exception {
-
- dto.getModelCreation().addGroup(providerDS);
-
- JSONArray specimens = dto.getSpecimens();
-
- for (int i = 0; i < specimens.length(); i++) {
- JSONObject specimenJSON = specimens.getJSONObject(i);
-
- String specimenId = specimenJSON.getString("Specimen ID");
- Specimen specimen = dataImportService.getSpecimen(
- dto.getModelCreation(),
- specimenId,
- providerDS.getAbbreviation(),
- specimenJSON.getString("Passage"));
- specimen.setHostStrain(nsgBS);
-
- EngraftmentSite is = dataImportService.getImplantationSite(specimenJSON.getString("Engraftment Site"));
- specimen.setEngraftmentSite(is);
- EngraftmentType it = dataImportService.getImplantationType("Heterotopic");
- specimen.setEngraftmentType(it);
-
- EngraftmentMaterial em = dataImportService.getEngraftmentMaterial(specimenJSON.getString("Engraftment Type"));
- specimen.setEngraftmentMaterial(em);
-
- Sample specSample = new Sample();
- specSample.setSourceSampleId(specimenId);
- specSample.setDataSource(providerDS.getAbbreviation());
-
- specimen.setSample(specSample);
-
- dto.getModelCreation().addSpecimen(specimen);
- dto.getModelCreation().addRelatedSample(specSample);
-
- }
- }
-
- @Override
- protected void step14LoadPatientTreatments() {
- throw new UnsupportedOperationException();
- }
-
- @Override
- protected void step15LoadImmunoHistoChemistry() {
- throw new UnsupportedOperationException();
- }
-
- @Override
- protected void step16LoadVariationData() {
- log.info(String.format("Loading WGS for model %s", dto.getModelCreation().getSourcePdxId()));
- loadOmicData(dto.getModelCreation(), providerDS,"mutation", finderRootDir+"/data/"+dataSource);
- loadOmicData(dto.getModelCreation(), providerDS,"copy number alteration", finderRootDir+"/data/"+dataSource);
- }
-
- @Override
- void step17LoadModelDosingStudies() {
- TreatmentSummary ts;
- if (dto.getModelDosingStudies().length() > 0) {
- ts = new TreatmentSummary();
- ts.setUrl(dosingStudyURL);
-
- for (int t = 0; t < dto.getModelDosingStudies().length(); t++) {
- try {
- JSONObject treatmentObject = dto.getModelDosingStudies().getJSONObject(t);
- TreatmentProtocol treatmentProtocol = dataImportService.getTreatmentProtocol(treatmentObject.getString("Drug"),
- treatmentObject.getString("Dose"),
- treatmentObject.getString("Response Class"), "");
-
- if (treatmentProtocol != null) {
- ts.addTreatmentProtocol(treatmentProtocol);
- }
- } catch (JSONException e) {
- log.error(e.toString());
- }
- ts.setModelCreation(dto.getModelCreation());
- dto.getModelCreation().setTreatmentSummary(ts);
- }
- }
-
- dataImportService.saveModelCreation(dto.getModelCreation());
-
- dataImportService.savePatient(dto.getPatient());
- dataImportService.savePatientSnapshot(dto.getPatientSnapshot());
- dataImportService.saveModelCreation(dto.getModelCreation());
-
- }
-
- @Override
- protected void step18SetAdditionalGroups() {
- Group access = dataImportService.getAccessibilityGroup(
- validateAccessibility(""),
- validateModality("transnational access")
- );
-
- Group project = dataImportService.getProjectGroup("EurOPDX");
-
- dto.getModelCreation().addGroup(access);
- dto.getModelCreation().addGroup(project);
- dataImportService.saveModelCreation(dto.getModelCreation());
- }
-
-
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadJAXData.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadJAXData.java
index 75db36b3536af63edb7b610b8640ddf170ff0be1..cd1ac8daeaac4cd82f335e2d5333998b8f18b178 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadJAXData.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadJAXData.java
@@ -1,8 +1,7 @@
package org.pdxfinder.dataloaders;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.graph.dao.*;
import org.pdxfinder.services.DataImportService;
import org.pdxfinder.services.UtilityService;
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadMDAnderson.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadMDAnderson.java
deleted file mode 100644
index 520ba7f1a4816d29bc4864801c18ceee035097a1..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadMDAnderson.java
+++ /dev/null
@@ -1,151 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import joptsimple.OptionParser;
-import joptsimple.OptionSet;
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
-import org.neo4j.ogm.session.Session;
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.ds.Standardizer;
-import org.pdxfinder.services.dto.LoaderDTO;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.PropertySource;
-import org.springframework.stereotype.Service;
-
-@Service
-@PropertySource("classpath:loader.properties")
-@ConfigurationProperties(prefix = "mda")
-public class LoadMDAnderson extends LoaderBase {
-
- private final static Logger log = LoggerFactory.getLogger(LoadMDAnderson.class);
-
- // private HostStrain nsgBS;
- private Group mdaDS;
- private Group projectGroup;
-
- private Session session;
-
- @Value("${data-dir}")
- private String finderRootDir;
-
- public LoadMDAnderson(UtilityService utilityService, DataImportService dataImportService) {
- super(utilityService, dataImportService);
- }
-
- public void run() throws Exception {
-
- initMethod();
- mdAndersonAlgorithm();
- }
-
-
-
- public void mdAndersonAlgorithm() throws Exception {
-
- step00StartReportManager();
-
- step01GetMetaDataFolder();
-
- if (skipThis) return;
-
- for (int i = 0; i < listOfFiles.length; i++) {
-
- if (listOfFiles[i].isFile()) {
-
- this.jsonFile = rootDataDirectory +"/" + dataSourceAbbreviation + "/pdx/" + listOfFiles[i].getName();
- globalLoadingOrder();
- }
- }
-
- log.info("Finished loading " + dataSourceAbbreviation + " PDX data.");
- }
-
-
-
- @Override
- protected void initMethod() {
-
- log.info("Loading MDAnderson PDX data.");
-
- dto = new LoaderDTO();
- rootDataDirectory = finderRootDir + "/data";
- dataSource = dataSourceAbbreviation;
- filesDirectory = finderRootDir + "/data/" + dataSourceAbbreviation + "/pdx/";
- }
-
- // MD ANDERSON uses default implementation Steps step01GetMetaDataFolder, step02GetMetaDataJSON
-
- @Override
- protected void step04CreateNSGammaHostStrain() {
-
- }
-
- @Override
- protected void step05CreateNSHostStrain() {
-
- }
-
-
- // MD ANDERSON uses default implementation Steps step08GetMetaData, step09LoadPatientData
-
-
- @Override
- protected void step10LoadExternalURLs() {
-
- loadExternalURLs(dataSourceContact,Standardizer.NOT_SPECIFIED);
-
- }
-
-
- @Override
- protected void step11LoadBreastMarkers() {
-
- }
-
-
- // IRCC uses default implementation Steps Step11CreateModels default
-
-
- @Override
- protected void step13LoadSpecimens()throws Exception {
-
- loadSpecimens("mdAnderson");
-
- }
-
-
- @Override
- protected void step14LoadPatientTreatments() {
-
- }
-
-
- @Override
- protected void step15LoadImmunoHistoChemistry() {
-
- }
-
-
- @Override
- protected void step16LoadVariationData() {
-
- }
-
- @Override
- void step17LoadModelDosingStudies() throws Exception {
-
- }
-
- @Override
- void step18SetAdditionalGroups() {
- throw new UnsupportedOperationException();
- }
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadPDMRData.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadPDMRData.java
deleted file mode 100644
index 96d96e81af97cec4db77218508f951bc0b177ffd..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadPDMRData.java
+++ /dev/null
@@ -1,261 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.dto.LoaderDTO;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.PropertySource;
-import org.springframework.stereotype.Service;
-
-import java.util.*;
-
-@Service
-@PropertySource("classpath:loader.properties")
-@ConfigurationProperties(prefix = "pdmr")
-public class LoadPDMRData extends LoaderBase {
-
- private final static Logger log = LoggerFactory.getLogger(LoadPDMRData.class);
-
- @Value("${data-dir}")
- private String finderRootDir;
-
-
- public LoadPDMRData(UtilityService utilityService, DataImportService dataImportService) {
- super(utilityService, dataImportService);
- }
-
-
-
- public void run() throws Exception{
-
- initMethod();
- globalLoadingOrder();
-
- }
-
-
- @Override
- protected void initMethod() {
-
- log.info("Loading PDMR PDX data.");
-
- dto = new LoaderDTO();
-
- jsonFile = finderRootDir +"/data/"+dataSourceAbbreviation+"/pdx/models.json";
- dataSource = dataSourceAbbreviation;
-
- platformURL = new HashMap<>();
- platformURL.put("NCI cancer gene panel_mutation","/platform/pdmr-mut-ts");
- }
-
-
- @Override
- protected void step01GetMetaDataFolder() {
-
- }
-
- // PDMR uses default implementation Steps step02GetMetaDataJSON
-
- @Override
- protected void step05CreateNSHostStrain() {
-
- }
-
-
- @Override
- protected void step06SetProjectGroup() {
-
- }
-
- // PDMR uses default implementation Steps step08GetMetaData
-
- @Override
- protected void step09LoadPatientData() {
-
- if (dataImportService.isExistingModel(providerDS.getAbbreviation(), dto.getModelID())) return;
- super.step09LoadPatientData();
- }
-
-
- @Override
- protected void step10LoadExternalURLs() {
-
- dataImportService.savePatientSnapshot(dto.getPatientSnapshot());
- loadExternalURLs(dataSourceContact, dto.getSourceURL());
- }
-
-
- @Override
- protected void step11LoadBreastMarkers() {
-
- }
-
-
-
- @Override
- protected void step12CreateModels() throws Exception {
-
- List<QualityAssurance> validationList = new ArrayList<>();
- if(dto.getValidationsArr().length() > 0){
-
- for(int k=0; k<dto.getValidationsArr().length(); k++){
-
- JSONObject validationObj = dto.getValidationsArr().getJSONObject(k);
- QualityAssurance qa = new QualityAssurance(validationObj.getString("Technique"), validationObj.getString("Description"), validationObj.getString("Passage"));
- validationList.add(qa);
- }
- }
-
- ModelCreation modelCreation = dataImportService.createModelCreation(dto.getModelID(), providerDS.getAbbreviation(), dto.getPatientSample(), validationList, dto.getExternalUrls());
- modelCreation.addRelatedSample(dto.getPatientSample());
- dto.setModelCreation(modelCreation);
- }
-
-
-
- @Override
- protected void step13LoadSpecimens()throws Exception {
-
- //load specimens
- if(dto.getSamplesArr().length() > 0){
- for(int i=0; i<dto.getSamplesArr().length();i++){
-
- JSONObject sampleObj = dto.getSamplesArr().getJSONObject(i);
- String sampleType = sampleObj.getString("Tumor Type");
-
- if(sampleType.equals("engrafted Tumor")){
-
- String specimenId = sampleObj.getString("Sample ID");
- String passage = sampleObj.getString("Passage");
-
- Specimen specimen = dataImportService.getSpecimen(dto.getModelCreation(),
- specimenId, providerDS.getAbbreviation(), passage);
-
- specimen.setHostStrain(nsgBS);
-
- EngraftmentSite es = dataImportService.getImplantationSite(dto.getImplantationSiteStr());
- specimen.setEngraftmentSite(es);
-
- EngraftmentType et = dataImportService.getImplantationType(dto.getImplantationtypeStr());
- specimen.setEngraftmentType(et);
-
- Sample specSample = new Sample();
-
- specSample.setSourceSampleId(specimenId);
- specSample.setDataSource(providerDS.getAbbreviation());
-
- specimen.setSample(specSample);
-
- dto.getModelCreation().addSpecimen(specimen);
- dto.getModelCreation().addRelatedSample(specSample);
-
- }
-
- }
- }
- }
-
-
-
-
- @Override
- protected void step14LoadPatientTreatments() throws Exception {
-
- TreatmentSummary ts;
-
- //Disable loading treatment temporarily, drug names are not harmonized!
- Boolean loadTreatment = true;
- //don't create two treatmentsummaries for the same snapshot
- if(loadTreatment && dataImportService.findTreatmentSummaryByPatientSnapshot(dto.getPatientSnapshot()) == null){
- ts = new TreatmentSummary();
-
- JSONArray treatmentArr = dto.getPatientTreatments();
-
- for(int k=0; k<treatmentArr.length();k++){
-
- JSONObject treatmentObj = treatmentArr.getJSONObject(k);
- TreatmentProtocol tp = null;
-
- String drugString = "";
- String date = "";
- String duration = treatmentObj.getString("Duration");
- String response = treatmentObj.getString("Response");
- Boolean currentTreatment = false;
-
- try {
- //this is the current treatment
- if (treatmentObj.has("Current Drug")) {
-
- drugString = treatmentObj.getString("Current Drug");
- date = treatmentObj.getString("Starting Date");
- currentTreatment = true;
-
- }
- //not current treatment, create default TreatmentProtocol object
- else {
-
- drugString = treatmentObj.getString("Prior Drug");
- date = treatmentObj.getString("Prior Date");
- currentTreatment = false;
-
- }
-
- if (drugString.equals("Released at Trial Closure") || drugString.equals("No Current Therapy") || drugString.toLowerCase().equals("treatment naive")) continue;
- tp = dataImportService.getTreatmentProtocol(drugString, "", response, currentTreatment);
-
- }
- catch(Exception e){
- e.printStackTrace();
- log.error("Error loading treatment. Model: "+dto.getModelID() +" Drugstring: "+drugString);
- }
- if(tp != null) {
- tp.setTreatmentDate(date);
- tp.addDurationForAllComponents(duration);
- ts.addTreatmentProtocol(tp);
- }
- }
-
- //save summary on snapshot
- if(ts.getTreatmentProtocols() != null && ts.getTreatmentProtocols().size() > 0){
- dto.getPatientSnapshot().setTreatmentSummary(ts);
- dataImportService.savePatientSnapshot(dto.getPatientSnapshot());
- }
-
- }
- dataImportService.saveModelCreation(dto.getModelCreation());
-
- }
-
-
- @Override
- protected void step15LoadImmunoHistoChemistry() {
-
- }
-
-
- @Override
- protected void step16LoadVariationData() {
-
- log.info("Loading NGS for model " + dto.getModelCreation().getSourcePdxId());
-
- loadOmicData(dto.getModelCreation(), providerDS, "mutation",finderRootDir+"/data/"+dataSourceAbbreviation);
- }
-
-
- @Override
- void step17LoadModelDosingStudies() throws Exception {
-
- }
-
- @Override
- void step18SetAdditionalGroups() {
- throw new UnsupportedOperationException();
- }
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadUniversal.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadUniversal.java
deleted file mode 100644
index 24e4c1c88e5536e36f1260111b38b0bcefc39fbc..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadUniversal.java
+++ /dev/null
@@ -1,91 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.ApplicationContextAware;
-import org.pdxfinder.reportmanager.ReportManager;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.context.ApplicationContext;
-import org.springframework.stereotype.Service;
-import java.io.File;
-import java.nio.file.Paths;
-
-
-@Service
-public class LoadUniversal implements ApplicationContextAware {
-
- @Value("${data-dir}")
- private String finderRootDir;
-
- private Logger log = LoggerFactory.getLogger(LoadUniversal.class);
-
- private static ApplicationContext context;
-
- private ReportManager reportManager;
-
- @Autowired
- private DataImportService dataImportService;
-
- @Autowired
- private UtilityService utilityService;
-
-
- public void run(String dataProvider) throws Exception {
-
- finderRootDir = UniversalLoader.stripTrailingSlash(finderRootDir);
-
- String updogDir = String.format("%s/data/UPDOG", finderRootDir);
-
- String providerDir = String.format("%s/%s", updogDir, dataProvider.replace("_","-"));
-
- reportManager = (ReportManager) context.getBean("ReportManager");
-
- File folder = new File(updogDir);
-
- if (folder.exists()) {
-
- File dataDir = Paths.get(providerDir).toFile();
-
- if (dataDir.isDirectory()) {
-
- log.info("******************************************************");
- log.info("* Starting universal loader for {} *", dataProvider);
- log.info("******************************************************");
- log.info("Loading data from {} ", providerDir);
- UniversalLoader updog = new UniversalLoader(reportManager, utilityService, dataImportService);
- updog.setFinderRootDir(finderRootDir);
- updog.initTemplates(providerDir);
- updog.loadTemplateData();
-
- log.info("******************************************************");
- log.info("* Finished running universal loader for {} *", dataProvider);
- log.info("******************************************************");
-
- }
-
- }
- //NO UNIVERSAL TEMPLATES, SKIP
- else {
-
- log.warn("No UPDOG directory found. Who let the dog out?");
- }
-
- }
-
-
- public LoadUniversal(DataImportService dataImportService) {
- this.dataImportService = dataImportService;
- }
-
- public LoadUniversal() {
- }
-
- @Override
- public void setApplicationContext(ApplicationContext applicationContext) {
- this.context = applicationContext;
- }
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadWISTAR.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadWISTAR.java
deleted file mode 100644
index e3111e60f0f83551f0a99dd9c58575768bb2368b..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadWISTAR.java
+++ /dev/null
@@ -1,213 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.ds.Standardizer;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-@Service
-public class LoadWISTAR {
-
- private final static Logger log = LoggerFactory.getLogger(LoadWISTAR.class);
-
- private final static String DATASOURCE_ABBREVIATION = "PDXNet-Wistar-MDAnderson-Penn";
- private final static String DATASOURCE_NAME = "Wistar/MD Anderson/Penn";
- private final static String DATASOURCE_DESCRIPTION = "Wistar-MDAnderson-Penn PDX mouse models for PDXNet.";
- private final static String DATASOURCE_CONTACT = "herlynm@Wistar.org,MDavies@mdanderson.org";
- private final static String SOURCE_URL = null;
-
- private final static String PROVIDER_TYPE = "";
- private final static String ACCESSIBILITY = "";
-
- // for now all samples are of tumor tissue
- private final static Boolean NORMAL_TISSUE_FALSE = false;
-
- private final static String NOT_SPECIFIED = Standardizer.NOT_SPECIFIED;
-
- // private HostStrain nsgBS;
- private Group wistarDS;
- private Group projectGroup;
-
- private DataImportService dataImportService;
- private UtilityService utilityService;
-
- @Value("${data-dir}")
- private String finderRootDir;
-
- public LoadWISTAR(DataImportService dataImportService,
- UtilityService utilityService) {
- this.dataImportService = dataImportService;
- this.utilityService = utilityService;
- }
-
- public void run() throws Exception {
-
- String urlStr = finderRootDir+ "/data/" +DATASOURCE_ABBREVIATION+"/pdx/models.json";
- File file = new File(urlStr);
- if(file.exists()){
-
- log.info("Loading WISTAR PDX data from URL " + urlStr);
- parseJSON(utilityService.parseFile(urlStr));
- }
- else{
-
- log.info("No file found for "+DATASOURCE_ABBREVIATION+", skipping");
- }
-
- }
-
- private void parseJSON(String json) {
-
- wistarDS = dataImportService.getProviderGroup(DATASOURCE_NAME, DATASOURCE_ABBREVIATION,
- DATASOURCE_DESCRIPTION, PROVIDER_TYPE, DATASOURCE_CONTACT, SOURCE_URL);
-
- // nsgBS = loaderUtils.getHostStrain(NSG_BS_SYMBOL, NSG_BS_NAME, NSG_BS_NAME, NSG_BS_URL);
-
- projectGroup = dataImportService.getProjectGroup("PDXNet");
-
- try {
- JSONObject job = new JSONObject(json);
- JSONArray jarray = job.getJSONArray("WISTAR");
-
- for (int i = 0; i < jarray.length(); i++) {
-
- JSONObject j = jarray.getJSONObject(i);
-
- createGraphObjects(j);
- }
-
- } catch (Exception e) {
- log.error("Error getting WISTAR PDX models", e);
-
- }
- }
-
- @Transactional
- void createGraphObjects(JSONObject j) throws Exception {
- String id = j.getString("Model ID").trim();
-
- // the preference is for histology
- String diagnosis = j.getString("Clinical Diagnosis");
- String histology = j.getString("Histology");
-
- if (histology.trim().length() > 0) {
- diagnosis = histology;
- }
-
- if (diagnosis.trim().length() == 0) {
- // no histology no diagnosis -> no model
- return;
- }
-
- String classification = j.getString("Stage") + "/" + j.getString("Grades");
- String stage = j.getString("Stage");
- String grade = j.getString("Grades");
-
- String ethnicity = NOT_SPECIFIED;
- try {
- if (j.getString("Race").trim().length() > 0) {
- ethnicity = j.getString("Race");
- }
- } catch (Exception e) {
- }
-
- try {
- if (j.getString("Ethnicity").trim().length() > 0) {
- ethnicity = j.getString("Ethnicity");
- }
- } catch (Exception e) {
- }
-
- String age = Standardizer.getAge(j.getString("Age"));
-
- String gender = Standardizer.getGender(j.getString("Gender"));
- String patientId = j.getString("Patient ID");
-
- String tumorType = Standardizer.getTumorType(j.getString("Tumor Type"));
- String extractionMethod = j.getString("Sample Type");
-
- Patient patient = dataImportService.getPatientWithSnapshots(patientId, wistarDS);
-
- if(patient == null){
-
- patient = dataImportService.createPatient(patientId, wistarDS, gender, "", Standardizer.getEthnicity(ethnicity));
- }
-
- PatientSnapshot pSnap = dataImportService.getPatientSnapshot(patient, age, "", "", "");
-
-
- //String sourceSampleId, String dataSource, String typeStr, String diagnosis, String originStr,
- //String sampleSiteStr, String extractionMethod, Boolean normalTissue, String stage, String stageClassification,
- // String grade, String gradeClassification
- Sample sample = dataImportService.getSample(id, wistarDS.getAbbreviation(), tumorType, diagnosis, NOT_SPECIFIED,
- NOT_SPECIFIED, extractionMethod, false, stage, "", grade, "");
-
-
-
-
- pSnap.addSample(sample);
-
- dataImportService.saveSample(sample);
- dataImportService.savePatientSnapshot(pSnap);
-
- List<ExternalUrl> externalUrls = new ArrayList<>();
- externalUrls.add(dataImportService.getExternalUrl(ExternalUrl.Type.CONTACT, DATASOURCE_CONTACT));
-
- String qaType = NOT_SPECIFIED;
- try {
- qaType = j.getString("QA") + "on passage " + j.getString("QA Passage");
- } catch (Exception e) {
- // not all groups supplied QA
- }
- String qaPassage = j.has("QA Passage") ? j.getString("QA Passage") : null;
-
- QualityAssurance qa = new QualityAssurance(qaType,
- NOT_SPECIFIED, qaPassage);
- dataImportService.saveQualityAssurance(qa);
-
- String strain = j.getString("Strain");
- HostStrain bs = dataImportService.getHostStrain("", strain, "", "");
-
- String engraftmentSite = Standardizer.getValue("Engraftment Site", j);
-
- String tumorPrep = Standardizer.getValue("Tumor Prep", j);
-
- ModelCreation modelCreation = dataImportService.createModelCreation(id, wistarDS.getAbbreviation(), sample, qa, externalUrls);
- modelCreation.addRelatedSample(sample);
- modelCreation.addGroup(projectGroup);
-
- Specimen specimen = dataImportService.getSpecimen(modelCreation,
- modelCreation.getSourcePdxId(), wistarDS.getAbbreviation(), NOT_SPECIFIED);
-
- specimen.setHostStrain(bs);
-
- EngraftmentSite is = dataImportService.getImplantationSite(engraftmentSite);
- specimen.setEngraftmentSite(is);
-
- EngraftmentType it = dataImportService.getImplantationType(tumorPrep);
- specimen.setEngraftmentType(it);
-
- Sample xenoSample = new Sample();
- xenoSample.setSourceSampleId(modelCreation.getSourcePdxId());
- specimen.setSample(xenoSample);
- modelCreation.addRelatedSample(xenoSample);
- modelCreation.addSpecimen(specimen);
- dataImportService.saveSpecimen(specimen);
-
- dataImportService.saveModelCreation(modelCreation);
-
- }
-
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadWUSTL.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoadWUSTL.java
deleted file mode 100644
index 65af4e2f65a474e86b32697dddee6add4344c127..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoadWUSTL.java
+++ /dev/null
@@ -1,131 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.ds.Standardizer;
-import org.pdxfinder.services.dto.LoaderDTO;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.PropertySource;
-import org.springframework.stereotype.Service;
-
-@Service
-@PropertySource("classpath:loader.properties")
-@ConfigurationProperties(prefix = "wustl")
-public class LoadWUSTL extends LoaderBase {
-
- private final static Logger log = LoggerFactory.getLogger(LoadWUSTL.class);
-
- private Group DS;
- private Group projectGroup;
-
- @Value("${data-dir}")
- private String finderRootDir;
-
- public LoadWUSTL(UtilityService utilityService, DataImportService dataImportService) {
- super(utilityService, dataImportService);
- }
-
- public void run() throws Exception {
- initMethod();
- wustlAlgorithm();
-
- }
-
- public void wustlAlgorithm() throws Exception {
-
- step00StartReportManager();
-
- step01GetMetaDataFolder();
-
- if (skipThis) return;
-
- for (int i = 0; i < listOfFiles.length; i++) {
-
- if (listOfFiles[i].isFile()) {
-
- this.jsonFile = rootDataDirectory + "/data/" + dataSourceAbbreviation + "/pdx/" + listOfFiles[i].getName();
- globalLoadingOrder();
- }
- }
- log.info("Finished loading " + dataSourceAbbreviation + " PDX data.");
- }
-
-
- @Override
- protected void initMethod() {
-
- log.info("Loading WUSTL PDX data.");
-
- dto = new LoaderDTO();
- rootDataDirectory = finderRootDir;
- dataSource = dataSourceAbbreviation;
- filesDirectory = finderRootDir +"/data/" + dataSourceAbbreviation + "/pdx/";
- }
-
- // WUSTL uses default implementation Steps step01GetMetaDataFolder, step02GetMetaDataJSON
-
- @Override
- protected void step04CreateNSGammaHostStrain() {
-
- }
-
- @Override
- protected void step05CreateNSHostStrain() {
-
- }
-
- // WUSTL uses default implementation Steps step08GetMetaData, step09LoadPatientData
-
- @Override
- protected void step10LoadExternalURLs() {
-
- loadExternalURLs(dataSourceContact,Standardizer.NOT_SPECIFIED);
-
- }
-
- @Override
- protected void step11LoadBreastMarkers() {
-
- }
-
- // WUSTL uses default implementation Steps step12CreateModels default
-
- @Override
- protected void step13LoadSpecimens()throws Exception {
-
- loadSpecimens("wustl");
- }
-
-
- @Override
- protected void step14LoadPatientTreatments() {
-
- }
-
-
- @Override
- protected void step15LoadImmunoHistoChemistry() {
-
- }
-
-
- @Override
- protected void step16LoadVariationData() {
-
- }
-
- @Override
- void step17LoadModelDosingStudies() throws Exception {
-
- }
-
- @Override
- void step18SetAdditionalGroups() {
- throw new UnsupportedOperationException();
- }
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/LoaderBase.java b/indexer/src/main/java/org/pdxfinder/dataloaders/LoaderBase.java
index 01b88dd8ef0d4555acffece2b2dd6388d583e93d..06ddccca7a38dd7ce9f9e2d0b650b06cfaf67ca3 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/LoaderBase.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/LoaderBase.java
@@ -1,7 +1,7 @@
package org.pdxfinder.dataloaders;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.JSONArray;
+import com.github.openjson.JSONObject;
import org.pdxfinder.graph.dao.*;
import org.pdxfinder.reportmanager.ReportManager;
import org.pdxfinder.services.DataImportService;
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/UniversalLoader.java b/indexer/src/main/java/org/pdxfinder/dataloaders/UniversalLoader.java
deleted file mode 100644
index 98515024da5d27b8c05a3137725d1dae390540ac..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/UniversalLoader.java
+++ /dev/null
@@ -1,1499 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.ss.usermodel.Sheet;
-import org.apache.poi.ss.usermodel.Workbook;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.reportmanager.ReportManager;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.services.ds.Standardizer;
-import org.pdxfinder.services.dto.NodeSuggestionDTO;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import org.springframework.context.ApplicationContext;
-import org.springframework.stereotype.Component;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.util.*;
-
-/**
- * Univeral Loader, aka UPDOG: Universal PdxData tO Graph
- *
- * "What's UPDOG?"
- * "Nothing much, what's up with you?"
- * Comments may contain egregious dog puns.
- */
-@Component
-public class UniversalLoader extends UniversalLoaderOmic {
-
- private final static Logger log = LoggerFactory.getLogger(UniversalLoader.class);
- static ApplicationContext context;
- ReportManager reportManager;
-
- private String finderRootDir;
- private String dataRootDirectory;
-
- private List<List<String>> patientSheetData;
- private List<List<String>> patientTumorSheetData;
- private List<List<String>> patientTreatmentSheetData;
- private List<List<String>> pdxModelSheetData;
- private List<List<String>> pdxModelValidationSheetData;
- private List<List<String>> samplePlatformDescriptionSheetData;
- private List<List<String>> sharingAndContactSheetData;
- private List<List<String>> cytogeneticsSheetData;
- private List<List<String>> loaderRelatedDataSheetData;
- private List<List<String>> drugDosingSheetData;
-
- private Group ds;
- private Boolean stopLoading;
- private Set<String> modelIDs;
-
- public UniversalLoader(ReportManager reportManager, UtilityService utilityService, DataImportService dataImportService) {
- super(utilityService, dataImportService);
- this.reportManager = reportManager;
- }
-
-
- public void initTemplates(String updogCurrDir) {
-
- log.info("******************************************************");
- log.info("* Initializing Sheet data *");
- log.info("******************************************************");
-
- ds = null;
- stopLoading = false;
-
- patientSheetData = new ArrayList<>();
- patientTumorSheetData = new ArrayList<>();
- pdxModelSheetData = new ArrayList<>();
- pdxModelValidationSheetData = new ArrayList<>();
- sharingAndContactSheetData = new ArrayList<>();
- loaderRelatedDataSheetData = new ArrayList<>();
- Optional<Workbook> metadata = getWorkbook(updogCurrDir, "metadata.xlsx");
- if (metadata.isPresent()) {
- initializeSheetData(metadata.get().getSheetAt(1), patientSheetData);
- initializeSheetData(metadata.get().getSheetAt(2), patientTumorSheetData);
- initializeSheetData(metadata.get().getSheetAt(3), pdxModelSheetData);
- initializeSheetData(metadata.get().getSheetAt(4), pdxModelValidationSheetData);
- initializeSheetData(metadata.get().getSheetAt(5), sharingAndContactSheetData);
- initializeSheetData(metadata.get().getSheetAt(6), loaderRelatedDataSheetData);
- }
-
- samplePlatformDescriptionSheetData = new ArrayList<>();
- Optional<Workbook> samplePlatformDescription = getWorkbook(updogCurrDir, "sampleplatform.xlsx");
- if (samplePlatformDescription.isPresent()) {
- initializeSheetData(samplePlatformDescription.get().getSheetAt(0), samplePlatformDescriptionSheetData);
- }
-
- cytogeneticsSheetData = new ArrayList<>();
- Optional<Workbook> cytogenetics = getWorkbook(updogCurrDir, "cyto/cytogenetics.xlsx");
- if (cytogenetics.isPresent()) {
- initializeSheetData(cytogenetics.get().getSheetAt(0), cytogeneticsSheetData);
- }
-
- patientTreatmentSheetData = new ArrayList<>();
- Optional<Workbook> patientTreatment = getWorkbook(updogCurrDir, "treatment/patienttreatment.xlsx");
- if (patientTreatment.isPresent()) {
- initializeSheetData(patientTreatment.get().getSheetAt(0), patientTreatmentSheetData);
- }
-
- drugDosingSheetData = new ArrayList<>();
- Optional<Workbook> drugDosing = getWorkbook(updogCurrDir, "treatment/drugdosing.xlsx");
- if (drugDosing.isPresent()) {
- initializeSheetData(drugDosing.get().getSheetAt(0), drugDosingSheetData);
- }
- }
-
-
- public void loadTemplateData() {
-
- //:: DON'T CHANGE THE ORDER OF THESE METHODS UNLESS YOU WANT TO RISK THE UNIVERSE TO COLLAPSE!
- createDataSourceGroup();
- createPatients();
- createPatientTumors();
- createPdxModelDetails();
- createPdxModelValidations();
- createSharingAndContacts();
- createDerivedPatientModelDataset();
- createPatientTreatments();
- createOmicData();
- createCytogeneticsData();
-
- }
-
- public Optional<Workbook> getWorkbook(String updogCurrDir, String templatePath) {
- templatePath = String.join("/", updogCurrDir, templatePath);
- File file = new File(templatePath);
- log.debug("Loading template {}", templatePath);
- if (!file.exists()) return Optional.empty();
-
- try (FileInputStream fileInputStream = new FileInputStream(file)) {
- XSSFWorkbook workbook = new XSSFWorkbook(fileInputStream);
- return Optional.of(workbook);
-
- } catch (IOException e) {
- log.error("There was a problem accessing the file: {}", file, e);
- }
- return Optional.empty();
- }
-
- /**
- * Loads the data from a spreadsheet tab into a placeholder
- *
- * @param sheet
- * @param sheetData
- */
- private void initializeSheetData(Sheet sheet, List<List<String>> sheetData) {
-
- Iterator<Row> iterator = sheet.iterator();
- int rowCounter = 0;
- while (iterator.hasNext()) {
-
- Row currentRow = iterator.next();
- rowCounter++;
-
- if (rowCounter < 6) continue;
-
- Iterator<Cell> cellIterator = currentRow.iterator();
- List dataRow = new ArrayList();
- boolean isFirstColumn = true;
- while (cellIterator.hasNext()) {
-
- Cell currentCell = cellIterator.next();
- //skip the first column
- if (isFirstColumn) {
- isFirstColumn = false;
- continue;
- }
-
- //getCellTypeEnum shown as deprecated for version 3.15
- //getCellTypeEnum will be renamed to getCellType starting from version 4.0
-
- String value = null;
- switch (currentCell.getCellType()) {
- case Cell.CELL_TYPE_STRING:
- value = currentCell.getStringCellValue();
- break;
- case Cell.CELL_TYPE_BOOLEAN:
- value = String.valueOf(currentCell.getBooleanCellValue());
- break;
- case Cell.CELL_TYPE_NUMERIC:
- value = String.valueOf(currentCell.getNumericCellValue());
- break;
- }
-
- dataRow.add(value);
- }
- //check if there is some data in the row and they are not all nulls
- if (dataRow.size() > 0 && !isRowOfNulls(dataRow)) {
-
- sheetData.add(dataRow);
-
-
- }
-
- }
- }
-
-
- /**
- * Creates the provider group in the database
- */
- private void createDataSourceGroup() {
-
-
- log.info("******************************************************");
- log.info("* Creating DataSource *");
- log.info("******************************************************");
-
-
- if (loaderRelatedDataSheetData.size() != 1) {
- stopLoading = true;
-
- log.error("Zero or multiple provider definitions! Loading process is terminated.");
- return;
- }
-
- String providerName = loaderRelatedDataSheetData.get(0).get(0);
- String providerAbbreviation = loaderRelatedDataSheetData.get(0).get(1);
- String sourceUrl = loaderRelatedDataSheetData.get(0).get(2);
-
- if (providerName.isEmpty() || providerAbbreviation.isEmpty()) {
- stopLoading = true;
-
- log.error("Missing provider name or abbreviation! Loading process is terminated!");
- return;
- }
-
- ds = dataImportService.getProviderGroup(providerName, providerAbbreviation, "", "", "", sourceUrl);
-
- }
-
- /**
- * Creates the patient nodes
- */
- private void createPatients() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating Patients *");
- log.info("******************************************************");
-
- for (List<String> patientRow : patientSheetData) {
-
- String patientId = patientRow.get(0);
- String sex = patientRow.get(1);
- String cancerHistory = patientRow.get(2);
- String ethnicity = patientRow.get(3);
- String firstDiagnosis = patientRow.get(4);
- String ageAtFirstDiagnosis = patientRow.get(5);
-
- if (patientId != null && ds != null) {
-
- Patient patient = dataImportService.createPatient(patientId, ds, sex, "", Standardizer.getEthnicity(ethnicity));
- patient.setCancerRelevantHistory(cancerHistory);
- patient.setFirstDiagnosis(firstDiagnosis);
- patient.setAgeAtFirstDiagnosis(ageAtFirstDiagnosis);
-
- dataImportService.savePatient(patient);
-
- }
- }
- }
-
- /**
- * Targets an existing patient, creates patient snapshots, patient sample, tumor type and the model
- */
- private void createPatientTumors() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating Patient samples and snapshots *");
- log.info("******************************************************");
-
- int row = 6;
-
- log.info("Tumor row number: " + patientTumorSheetData.size());
- for (List<String> patientTumorRow : patientTumorSheetData) {
-
- String patientId = null;
- String modelId = null;
- String dateOfCollection = null;
- String ageAtCollection = null;
- String collectionEvent = null;
- String elapsedTime = null;
-
- try {
- patientId = patientTumorRow.get(0);
- String sampleId = patientTumorRow.get(1);
- modelId = patientTumorRow.get(19);
-
- //skip rows where patient, model or sample id is null
- if (patientId == null || sampleId == null || modelId == null) continue;
-
- dateOfCollection = patientTumorRow.get(2);
- collectionEvent = patientTumorRow.get(3);
- elapsedTime = patientTumorRow.get(4);
- ageAtCollection = patientTumorRow.get(5);
- String diagnosis = patientTumorRow.get(6);
- String tumorType = patientTumorRow.get(7);
- String originTissue = patientTumorRow.get(8);
- String collectionSite = patientTumorRow.get(9);
- String stage = patientTumorRow.get(10);
- String stageClassification = patientTumorRow.get(11);
- String grade = patientTumorRow.get(12);
- String gradeClassification = patientTumorRow.get(13);
- String virologyStatus = patientTumorRow.get(14);
- String treatmentNaive = patientTumorRow.get(16);
- sampleId = sampleId.trim();
-
- if (modelId == null) {
- log.error("Missing corresponding Model ID in row " + row);
- row++;
- continue;
- }
-
- if (dateOfCollection == null && collectionEvent == null && elapsedTime == null && ageAtCollection == null) {
- log.error("Missing collection info in row " + row);
- row++;
- continue;
- }
-
- //hack to avoid 0.0 values and negative numbers
- if (elapsedTime != null) {
-
- elapsedTime = elapsedTime.replaceAll("[^0-9]", "");
- }
-
-
- Patient patient = dataImportService.getPatientWithSnapshots(patientId, ds);
-
- if (patient == null) {
-
- log.error("Patient does not exist, can not create tumor for " + patientId);
- row++;
- continue;
- }
-
- //need this trick to remove float values, ie: patient age = 30.0
- if (ageAtCollection != null && !ageAtCollection.equals("Not Specified")) {
- int ageAtColl = (int) Float.parseFloat(ageAtCollection);
- ageAtCollection = ageAtColl + "";
- }
-
-
- PatientSnapshot ps = dataImportService.getPatientSnapshot(patient, ageAtCollection, dateOfCollection, collectionEvent, elapsedTime);
- ps.setTreatmentNaive(treatmentNaive);
- ps.setVirologyStatus(virologyStatus);
-
-
- //have the correct snapshot, create a human sample and link it to the snapshot
- tumorType = Standardizer.getTumorType(tumorType);
-
-
- //String sourceSampleId, String dataSource, String typeStr, String diagnosis, String originStr,
- //String sampleSiteStr, String extractionMethod, Boolean normalTissue, String stage, String stageClassification,
- // String grade, String gradeClassification
- Sample sample = dataImportService.getSample(sampleId, ds.getAbbreviation(), tumorType, diagnosis, originTissue,
- collectionSite, "", false, stage, stageClassification, grade, gradeClassification);
-
- ps.addSample(sample);
-
-
- ModelCreation mc = new ModelCreation();
-
- mc.setSourcePdxId(modelId);
- mc.setDataSource(ds.getAbbreviation());
- mc.setSample(sample);
- mc.addRelatedSample(sample);
-
- patient.addSnapshot(ps);
-
- dataImportService.savePatient(patient);
- dataImportService.savePatientSnapshot(ps);
- dataImportService.saveModelCreation(mc);
- row++;
-
- } catch (Exception e) {
- log.error("Exception in row: " + row + " for model: " + modelId);
- log.error("doc:" + dateOfCollection + " ce:" + collectionEvent + " et:" + elapsedTime + " aac:" + ageAtCollection);
- e.printStackTrace();
-
- }
-
- }
-
- }
-
- /**
- * Targets an existing patient and snapshot to create a treatment summary with treatment protocols
- */
- private void createPatientTreatments() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating Patient treatments *");
- log.info("******************************************************");
-
- int row = 6;
- for (List<String> patientTreatmentRow : patientTreatmentSheetData) {
-
- String patientId = patientTreatmentRow.get(0);
- String treatment = patientTreatmentRow.get(1);
- String dose = patientTreatmentRow.get(2);
- String startingDate = patientTreatmentRow.get(3);
- String duration = patientTreatmentRow.get(4);
- String response = patientTreatmentRow.get(7);
- String responseClassification = patientTreatmentRow.get(8);
-
- if (patientId.isEmpty() || treatment.isEmpty()) {
-
- log.error("Empty patient id or treatment in row " + row);
- continue;
- }
-
-
- Patient patient = dataImportService.findPatient(patientId, ds);
-
- if (patient == null) {
-
- log.error("Patient not found: " + patientId);
- continue;
- }
-
- PatientSnapshot ps = dataImportService.findLastPatientSnapshot(patientId, ds);
-
- //at this point a patient should have at least one snapshot, so if ps is null, thats an error
- if (ps == null) {
-
- log.error("No snapshot for patient: " + patientId);
- continue;
- }
-
- String treatmentUrl = loaderRelatedDataSheetData.get(0).get(3);
-
- TreatmentSummary ts = dataImportService.findTreatmentSummaryByPatientSnapshot(ps);
-
- if (ts == null) {
- ts = new TreatmentSummary();
- ts.setUrl(treatmentUrl);
- }
-
- TreatmentProtocol tp = dataImportService.getTreatmentProtocol(treatment, dose, response, responseClassification);
-
- if (tp != null) {
-
- //update treatment component type and duration
- for (TreatmentComponent tc : tp.getComponents()) {
-
- tc.setDuration(duration);
- //never control on humans!
- tc.setType("Drug");
- }
-
- tp.setTreatmentDate(startingDate);
- ts.addTreatmentProtocol(tp);
- }
-
-
- ps.setTreatmentSummary(ts);
- dataImportService.savePatientSnapshot(ps);
- row++;
- }
-
- }
-
- /**
- * Targets an existing model to create specimens with engraftment site, type and material, host strain as well as publication groups
- */
- private void createPdxModelDetails() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating Model details *");
- log.info("******************************************************");
-
- int row = 6;
-
- for (List<String> modelDetailsRow : pdxModelSheetData) {
-
- String modelId = modelDetailsRow.get(0);
- String hostStrainName = modelDetailsRow.get(1);
- String hostStrainNomenclature = modelDetailsRow.get(2);
- String engraftmentSite = modelDetailsRow.get(3);
- String engraftmentType = modelDetailsRow.get(4);
- String engraftmentMaterial = modelDetailsRow.get(5);
- String engraftmentMaterialStatus = modelDetailsRow.get(6);
- String passage = modelDetailsRow.get(7);
- String pubmedIdString = modelDetailsRow.get(8);
-
-
- //check if essential values are not empty
- if (modelId.isEmpty() || hostStrainName.isEmpty() || hostStrainNomenclature.isEmpty() ||
- engraftmentSite.isEmpty() || engraftmentType.isEmpty() || engraftmentMaterial.isEmpty()) {
-
- log.error("Missing essential value in row: " + row);
- row++;
- continue;
-
- }
-
- //at this point the corresponding pdx model node should be created and linked to a human sample
- ModelCreation model = null;
- try {
- model = dataImportService.findModelByIdAndDataSource(modelId, ds.getAbbreviation());
-
- } catch (Exception e) {
- log.error("Error with model: " + modelId + " Probably duplicates?");
- e.printStackTrace();
- }
-
- if (model == null) {
-
- log.error("Missing model, cannot add details: " + modelId);
- row++;
- continue;
- }
-
- //CREATING SPECIMENS: engraftment site, type and material
-
- EngraftmentSite es = dataImportService.getImplantationSite(engraftmentSite);
- EngraftmentType et = dataImportService.getImplantationType(engraftmentType);
- EngraftmentMaterial em = dataImportService.createEngraftmentMaterial(engraftmentMaterial, engraftmentMaterialStatus);
-
- HostStrain hostStrain = null;
- try {
- hostStrain = dataImportService.getHostStrain(hostStrainName, hostStrainNomenclature, "", "");
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- // passage = 1,3,5
- if (passage.contains(",")) {
-
- String[] passageArr = passage.split(",");
-
- for (int i = 0; i < passageArr.length; i++) {
-
- //create specimens with engraftment data
- Specimen specimen = new Specimen();
- specimen.setPassage(passageArr[i].trim());
- specimen.setEngraftmentSite(es);
- specimen.setEngraftmentType(et);
- specimen.setEngraftmentMaterial(em);
- specimen.setHostStrain(hostStrain);
-
- model.addSpecimen(specimen);
- }
- }
- //the passage is a single number
- else if (passage.matches("\\d+")) {
-
- //need this trick to get rid of fractures if there is any
- int passageInt = Integer.parseInt(passage);
- passage = String.valueOf(passageInt);
-
- //create specimens with engraftment data
- Specimen specimen = new Specimen();
- specimen.setPassage(passage);
- specimen.setEngraftmentSite(es);
- specimen.setEngraftmentType(et);
- specimen.setEngraftmentMaterial(em);
- specimen.setHostStrain(hostStrain);
-
- model.addSpecimen(specimen);
-
- } else if (passage.matches("[+-]?([0-9]*[.])?[0-9]+")) {
-
- //need this trick to get rid of fractures if there is any
- double passageDouble = Double.parseDouble(passage);
- passage = String.valueOf((int)passageDouble);
-
- //create specimens with engraftment data
- Specimen specimen = new Specimen();
- specimen.setPassage(passage);
- specimen.setEngraftmentSite(es);
- specimen.setEngraftmentType(et);
- specimen.setEngraftmentMaterial(em);
- specimen.setHostStrain(hostStrain);
-
- model.addSpecimen(specimen);
- } else {
-
- log.error("Not supported value(" + passage + ") for passage at row " + row);
- }
-
- //CREATE PUBLICATION GROUPS
-
- //check if pubmed id is in the right format, ie id starts with PMID
- if (pubmedIdString != null && !pubmedIdString.isEmpty() && pubmedIdString.toLowerCase().contains("pmid")) {
-
- // pubmed ids separated with a comma, create multiple groups
- if (pubmedIdString.contains(",")) {
-
- String[] pubmedArr = pubmedIdString.split(",");
-
- for (int i = 0; i < pubmedArr.length; i++) {
-
- Group g = dataImportService.getPublicationGroup(pubmedArr[i].trim());
- model.addGroup(g);
- }
- }
- //single publication, create one group only
- else {
-
- Group g = dataImportService.getPublicationGroup(pubmedIdString.trim());
- model.addGroup(g);
- }
-
- }
-
- dataImportService.saveModelCreation(model);
- row++;
- }
- }
-
- /**
- * Targets existing model to add validation (QA) nodes
- */
- private void createPdxModelValidations() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating Model validations *");
- log.info("******************************************************");
-
- int row = 6;
-
- for (List<String> pdxModelValidationRow : pdxModelValidationSheetData) {
-
- String modelId = "";
- String validationTechnique = "";
- String validationDescription = "";
- String passages = "";
- String validationHostStrain = "";
-
- try {
- modelId = pdxModelValidationRow.get(0);
- validationTechnique = pdxModelValidationRow.get(1);
- validationDescription = pdxModelValidationRow.get(2);
- passages = pdxModelValidationRow.get(3);
- validationHostStrain = pdxModelValidationRow.get(4);
- } catch (Exception e) {
-
- log.error("Error in row: " + row);
- e.printStackTrace();
- }
-
- if (modelId.isEmpty() || validationTechnique.isEmpty()) {
-
- log.error("Empty essential value in row: " + row);
- row++;
- continue;
- }
-
-
- //at this point the corresponding pdx model node should be created and available for lookup
- ModelCreation model = dataImportService.findModelByIdAndDataSource(modelId, ds.getAbbreviation());
-
- if (model == null) {
-
- log.error("Missing model, cannot add validation: " + modelId);
- row++;
- continue;
- }
-
- //need this trick to get rid of 0.0 if there is any
- String[] passageArr = passages.split(",");
- passages = "";
-
- for (int i = 0; i < passageArr.length; i++) {
-
- String pass;
- try {
- int passageInt = (int) Float.parseFloat(passageArr[i]);
- pass = String.valueOf(passageInt);
- } catch (NumberFormatException | NullPointerException nfe) {
-
- pass = passageArr[i];
- }
-
- passages += pass + ",";
- }
- //remove that last comma
- passages = passages.substring(0, passages.length() - 1);
-
- QualityAssurance qa = new QualityAssurance();
- qa.setTechnology(validationTechnique);
- qa.setDescription(validationDescription);
- qa.setPassages(passages);
-
- model.addQualityAssurance(qa);
- dataImportService.saveModelCreation(model);
-
- }
- }
-
- /**
- * Requirements:
- * <p>
- * PATIENT
- * existing patient sample
- * <p>
- * XENOGRAFT
- * existing model, specimen, creates xeno sample if not present
- * <p>
- * Creates a molecular characterization with a platform and links it to the appropriate sample
- */
- private void createDerivedPatientModelDataset() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating dataset derived from patients and models *");
- log.info("******************************************************");
-
- int row = 6;
- this.modelIDs = new HashSet<>();
-
- for (List<String> derivedDatasetRow : samplePlatformDescriptionSheetData) {
-
- String sampleId = derivedDatasetRow.get(0);
-
- String origin = derivedDatasetRow.get(1);
- String passage = derivedDatasetRow.get(2);
- String engraftedTumorCollectionSite = derivedDatasetRow.get(3);
- String modelId = derivedDatasetRow.get(4);
- String hostStrainName = derivedDatasetRow.get(5);
-
- String nomenclature = derivedDatasetRow.get(6);
-
- String molCharType = derivedDatasetRow.get(7);
- String platformName = derivedDatasetRow.get(8);
- String platformTechnology = derivedDatasetRow.get(9);
- String platformDescription = derivedDatasetRow.get(10);
- String analysisProtocol = derivedDatasetRow.get(11);
-
- String platformUrl = derivedDatasetRow.get(15);
-
-
- if (platformUrl != null) {
- platformUrl = platformUrl.replaceAll("[^A-Za-z0-9 /_-]", "");
- }
-
-
- //TODO: get additional fields from the sheet
-
- //check essential values
-
- if (sampleId == null || origin == null || modelId == null
- || molCharType == null || platformName == null || platformTechnology == null || platformDescription == null
- ) {
-
- log.error("Missing essential value in row " + row);
- row++;
- continue;
- }
-
- sampleId = sampleId.trim();
- ModelCreation model;
- Sample sample;
- Platform platform;
-
- String platformTag = "";
-
- switch(molCharType) {
- case "mutation" :
- platformTag = "_mut";
- break;
- case "copy number alteration" :
- platformTag = "_cna";
- break;
- case "expression" :
- platformTag = "_expr";
- break;
- default:
- break;
- }
-
-
- //patient sample
- if (origin.toLowerCase().equals("patient")) {
-
- sample = dataImportService.findHumanSample(modelId, ds.getAbbreviation());
-
- if (sample != null) {
-
- platform = dataImportService.getPlatform(platformName, molCharType, ds);
-
- if ((platform.getUrl() == null || platform.getUrl().isEmpty()) && platformUrl != null && platformUrl.length() > 3) {
- log.info("Saved platform:" + platform.getName() + " Url: " + (platform.getUrl() == null ? "null" : platform.getUrl()) + " Url in file: " + platformUrl);
- platform.setUrl(platformUrl);
- dataImportService.savePlatform(platform);
- log.info("Updating platform url");
- } else {
-
- log.warn("Platform " + platform.getName()+platformTag + " was not updated. ");
- }
-
- MolecularCharacterization mc = new MolecularCharacterization();
- mc.setPlatform(platform);
- mc.setType(molCharType.toLowerCase());
- mc.setTechnology(platformTechnology);
- sample.addMolecularCharacterization(mc);
- sample.setSourceSampleId(sampleId);
- dataImportService.saveSample(sample);
-
- } else {
-
- log.error("Unknown human sample with id: " + sampleId);
- row++;
- continue;
- }
-
-
- }
-
-
- //xenograft sample
- //specimen should have been created before
- else if (origin.toLowerCase().equals("engrafted tumor") || origin.toLowerCase().equals("engrafted tumour") || origin.toLowerCase().equals("xenograft")) {
-
- if (passage == null || passage.isEmpty() || passage.toLowerCase().equals("not specified")) {
-
- log.error("Missing essential value Xenograft Passage in row " + row);
- row++;
- continue;
- }
-
- if (nomenclature == null || nomenclature.isEmpty()) {
-
- log.error("Missing essential value nomenclature in row " + row);
- row++;
- continue;
- }
-
- //need this trick to get rid of 0.0 if there is any
- //if(passage.equals("0.0")) passage = "0";
- int passageInt = (int) Float.parseFloat(passage);
- passage = String.valueOf(passageInt);
-
- model = dataImportService.findModelByIdAndDataSourceWithSpecimensAndHostStrain(modelId, ds.getAbbreviation());
-
- if (model == null) {
- log.error("Model " + modelId + " not found, skipping");
- row++;
- continue;
- }
-
- //check if targeted specimen is present, if not, create it
- Specimen specimen = null;
-
- for (Specimen sp : model.getSpecimens()) {
- //specimen passage and host strain nomenclature are the same
- if (sp.getPassage().equals(passage) && sp.getHostStrain().getSymbol().equals(nomenclature)) {
-
- specimen = sp;
- break;
- }
- }
-
- //this is a new specimen
- if (specimen == null) {
-
- HostStrain hostStrain = null;
-
- try {
- hostStrain = dataImportService.getHostStrain(hostStrainName, nomenclature, null, null);
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- specimen = new Specimen();
- specimen.setPassage(passage);
- specimen.setHostStrain(hostStrain);
-
- Sample s = new Sample();
- s.setSourceSampleId(sampleId);
- specimen.setSample(s);
- model.addSpecimen(specimen);
-
- }
-
-
- sample = specimen.getSample();
-
- if (sample == null) {
-
- sample = new Sample();
- sample.setSourceSampleId(sampleId);
-
- }
-
-
- platform = dataImportService.getPlatform(platformName, molCharType, ds);
-
- if ((platform.getUrl() == null || platform.getUrl().isEmpty()) && platformUrl != null && platformUrl.length() > 3) {
- log.info("Saved platform:" + platform.getName() + " Url: " + (platform.getUrl() == null ? "null" : platform.getUrl()) + " Url in file: " + platformUrl);
- platform.setUrl(platformUrl);
- dataImportService.savePlatform(platform);
- log.info("Updating platform url");
- }
-
- MolecularCharacterization mc = new MolecularCharacterization();
- mc.setPlatform(platform);
- mc.setType(molCharType.toLowerCase());
- mc.setTechnology(platformTechnology);
- sample.addMolecularCharacterization(mc);
- model.addRelatedSample(sample);
-
- specimen.setSample(sample);
-
- model.addSpecimen(specimen);
- model.addRelatedSample(sample);
- dataImportService.saveModelCreation(model);
- dataImportService.saveSpecimen(specimen);
- dataImportService.saveSample(sample);
-
- //log.info(" Specimen with the following details was created: "+modelId+" "+passage+" "+nomenclature+ " in row: "+row);
-
-
- } else {
- //origin is not patient nor xenograft
- log.error("Unknown sample origin in row " + row);
- }
-
- this.modelIDs.add(modelId);
- row++;
- }
-
- }
-
-
- private void createOmicData() {
-
- log.info("******************************************************");
- log.info("* Loading Omic Data *");
- log.info("******************************************************");
- log.info(this.modelIDs.toString());
-
- omicDataSource = ds.getAbbreviation();
- dataSourceAbbreviation = loaderRelatedDataSheetData.get(0).get(1);
- finderRootDir = stripTrailingSlash(finderRootDir);
- dataRootDirectory = finderRootDir + "/data/UPDOG";
-
- omicModelID = "Model_ID";
- omicSampleID = "Sample_ID";
- omicSampleOrigin = "sample_origin";
- omicPassage = "Passage";
- omicHostStrainName = "host_strain_name";
- omicHgncSymbol = "hgnc_symbol";
- omicAminoAcidChange = "amino_acid_change";
- omicNucleotideChange = "nucleotide_change";
- omicConsequence = "consequence";
- omicReadDepth = "read_depth";
- omicAlleleFrequency = "Allele_frequency";
- omicChromosome = "chromosome";
- omicSeqStartPosition = "seq_start_position";
- omicRefAllele = "ref_allele";
- omicAltAllele = "alt_allele";
- omicUcscGeneId = "ucsc_gene_id";
- omicNcbiGeneId = "ncbi_gene_id";
- omicEnsemblGeneId = "ensembl_gene_id";
- omicEnsemblTranscriptId = "ensembl_transcript_id";
- omicRsIdVariants = "rs_id_Variant";
- omicGenomeAssembly = "genome_assembly";
- omicPlatform = "Platform";
-
- omicSeqEndPosition = "seq_end_position";
- omicCnaLog10RCNA = "log10R_cna";
- omicCnaLog2RCNA = "log2R_cna";
- omicCnaCopyNumberStatus = "copy_number_status";
- omicCnaGisticvalue = "gistic_value_cna";
- omicCnaPicnicValue = "picnic_value";
- rnaSeqCoverage = "RNAseq_coverage";
- rnaSeqFPKM = "RNAseq_FPKM";
- rnaSeqTPM = "RNAseq_TPM";
- rnaSeqCount = "RNAseq_count";
- affyHGEAProbeId = "affy_HGEA_probeID";
- affyHGEAExpressionValue = "Affy_HGEA_expressionValue";
- illuminaHGEAProbeId = "Illumina_HGEA_probeID";
- illuminaHGEAExpressionValue = "Illumina_HGEA_expressionValue";
-
-
-
- platformURL = new HashMap<>();
-
- if (dataSourceAbbreviation.equals("CRL")) {
- omicDataFilesType = "ONE_FILE_PER_MODEL";
- omicFileExtension = "csv";
- }
- else if(dataSourceAbbreviation.equals("UOM-BC")){
- omicDataFilesType = "ONE_FILE_PER_MODEL";
- omicFileExtension = "xlsx";
- }
- else {
- omicDataFilesType = "ALL_MODELS_IN_ONE_FILE";
- omicFileExtension = "xlsx";
- }
-
-
- String providerDataRootDir = dataRootDirectory + "/" +dataSourceAbbreviation;
-
- String mutationDataDir = dataRootDirectory + "/" + dataSourceAbbreviation + "/mut/";
- String cnaDataDir = dataRootDirectory + "/" + dataSourceAbbreviation + "/cna/";
- String transcriptomicDataDir = dataRootDirectory + "/" + dataSourceAbbreviation + "/trans/";
-
- File mutationData = new File(mutationDataDir);
- File cnaData = new File(cnaDataDir);
- File transcriptomicData = new File(transcriptomicDataDir);
-
-
- log.info("Provider data root dir: "+providerDataRootDir);
- for (String modelId : this.modelIDs) {
-
- ModelCreation modelCreation = dataImportService.findBySourcePdxIdAndDataSourceWithSamplesAndSpecimensAndHostStrain(modelId, ds.getAbbreviation());
-
- if (modelCreation != null) {
-
- // Mutation Data Load
- if (mutationData.exists()) {
- log.info("Loading mutation for " + modelId);
- loadOmicData(modelCreation, ds, "mutation", providerDataRootDir);
- }
-
- // Copy Number Alteration Data Load
- if (cnaData.exists()) {
- log.info("Loading cna for " + modelId);
- loadOmicData(modelCreation, ds, "copy number alteration", providerDataRootDir);
- }
-
- // Transcriptomics
- if(transcriptomicData.exists()){
- log.info("Loading expression for {}",modelId);
- loadOmicData(modelCreation, ds, "expression", providerDataRootDir);
- }
-
-
- } else {
-
- log.error("Cannot load omic data for missing model: " + modelId);
- }
-
- }
-
-
- }
-
-
- /**
- * Targets existing model, creates external urls, updates provider type
- */
- private void createSharingAndContacts() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating Sharing and contact info *");
- log.info("******************************************************");
-
- int row = 6;
-
- for (List<String> sharingAndContactRow : sharingAndContactSheetData) {
-
- String modelId = sharingAndContactRow.get(0);
- String dataProviderType = sharingAndContactRow.get(1);
- String modelAccessibility = sharingAndContactRow.get(2);
- String accessModalities = sharingAndContactRow.get(3);
- String contactEmail = sharingAndContactRow.get(4);
- String contactFormLink = sharingAndContactRow.get(6);
- String modelLinkToDB = sharingAndContactRow.get(7);
- String providerAbbreviation = sharingAndContactRow.get(9);
- String projectName = sharingAndContactRow.get(10);
-
- if (modelId.isEmpty()) {
-
- log.error("Model id is empty in row: " + row);
- row++;
- continue;
- }
-
- if (accessModalities == null) accessModalities = "";
- if (modelAccessibility == null) modelAccessibility = "";
-
- //at this point the corresponding pdx model node should be created
-
- ModelCreation model = dataImportService.findModelByIdAndDataSource(modelId, ds.getAbbreviation());
-
- if (model == null) {
-
- log.error("Missing model, cannot add sharing and contact info: " + modelId);
- row++;
- continue;
- }
-
- //Add contact provider and view data
- List<ExternalUrl> externalUrls = new ArrayList<>();
- if(contactEmail != null && !contactEmail.isEmpty()){
- externalUrls.add(dataImportService.getExternalUrl(ExternalUrl.Type.CONTACT, contactEmail));
- }
-
- if(contactFormLink != null && !contactFormLink.isEmpty()){
- externalUrls.add(dataImportService.getExternalUrl(ExternalUrl.Type.CONTACT, contactFormLink));
- }
-
- externalUrls.add(dataImportService.getExternalUrl(ExternalUrl.Type.SOURCE, modelLinkToDB));
- model.setExternalUrls(externalUrls);
-
-
- if (projectName != null && !projectName.isEmpty()) {
-
- Group project = dataImportService.getProjectGroup(projectName);
- model.addGroup(project);
- }
-
- if (modelAccessibility != "" || accessModalities != "") {
-
- Group access = dataImportService.getAccessibilityGroup(modelAccessibility, accessModalities);
- model.addGroup(access);
- }
- dataImportService.saveModelCreation(model);
-
- //Update datasource
- ds.setProviderType(dataProviderType);
- ds.setContact(contactEmail);
-
-
- }
-
- dataImportService.saveGroup(ds);
-
- }
-
-
- private void createCytogeneticsData() {
-
- if (stopLoading) return;
-
- log.info("******************************************************");
- log.info("* Creating breast and or colorectal markers *");
- log.info("******************************************************");
-
- int row = 6;
-
- Map<String, MolecularCharacterization> existingMolcharNodes = new HashMap<>();
- Map<String, MolecularCharacterization> toBeCreatedMolcharNodes = new HashMap<>();
-
- for (List<String> dataRow : cytogeneticsSheetData) {
-
- String passage = dataRow.get(2);
- String modelId = dataRow.get(4);
- String origin = dataRow.get(1);
-
-
- if(origin.toLowerCase().equals("xenograft")) {
- String pass = passage;
-
-
- try {
- int passageInt = (int) Float.parseFloat(pass);
- passage = String.valueOf(passageInt);
- } catch (NumberFormatException | NullPointerException nfe) {
-
- log.error("Invalid passage " + passage + " for model:" + modelId);
- }
- }
- else{
- passage = "NA";
- }
-
- ModelCreation modelCreation = dataImportService.findBySourcePdxIdAndDataSourceWithSamplesAndSpecimensAndHostStrain(modelId, ds.getAbbreviation());
-
- if(modelCreation == null){
- log.error("Missing model +"+modelId + " in row "+row);
- row++;
- continue;
- }
-
- //get all molchars related to patient sample
- if(modelCreation.getSample().getMolecularCharacterizations() != null){
-
- for(MolecularCharacterization mc : modelCreation.getSample().getMolecularCharacterizations()){
-
- if (mc != null && mc.getPlatform() != null){
-
- String molcharKey = modelCreation.getSourcePdxId()+ "__"+modelCreation.getSample().getSourceSampleId() + "__" + passage + "__" + mc.getPlatform().getName()+ "__patient__"+mc.getType();
- existingMolcharNodes.put(molcharKey, mc);
- }
- }
- }
-
-
- //then all molchars related to xenograft samples
-
- if(modelCreation.getSpecimens()!= null){
-
- for(Specimen sp: modelCreation.getSpecimens()){
-
- Sample sample = sp.getSample();
-
- if(sample != null && sample.getMolecularCharacterizations() != null){
-
- for(MolecularCharacterization mc: sample.getMolecularCharacterizations()){
-
- if(sample.getSourceSampleId() == null ) log.error("Missing sampleid for "+modelId);
- if(sp.getPassage() == null) log.error("Missing passage for "+modelId);
- if(mc.getPlatform() == null) log.error("Missing platform for "+modelId);
-
- if(mc.getPlatform().getName() == null) log.error("Missing platform name for "+modelId);
-
- String molcharKey = modelCreation.getSourcePdxId()+ "__"+ sample.getSourceSampleId() + "__" + sp.getPassage() + "__" + mc.getPlatform().getName()+ "__xenograft__"+mc.getType();
- existingMolcharNodes.put(molcharKey, mc);
- }
- }
- }
- }
-
- row++;
- }
-
-
-
- //TODO: At some point deal with micro-satelite instability. Currently those rows are skipped. We don't want instability in our lives just yet.
-
- //first get all markers for the individual molchar objects
- MarkerAssociation ma = new MarkerAssociation();
- for (List<String> dataRow : cytogeneticsSheetData) {
-
- String sampleId = dataRow.get(0);
- String origin = dataRow.get(1);
- String passage = dataRow.get(2);
- String nomenclature = dataRow.get(3);
- String modelId = dataRow.get(4);
- String markerSymbol = dataRow.get(5);
- String markerStatus = dataRow.get(6);
- String technique = dataRow.get(8);
- String platform = dataRow.get(9);
- String characterizationType = "Unknown";
-
-
-
- if (origin == null || modelId == null || markerSymbol == null || markerStatus == null || technique == null) {
- log.error("Missing essential value in row " + row);
- row++;
- continue;
- }
-
- if(origin.toLowerCase().equals("xenograft")) {
- String pass = passage;
-
- try {
- int passageInt = (int) Float.parseFloat(pass);
- passage = String.valueOf(passageInt);
- } catch (NumberFormatException | NullPointerException nfe) {
-
- log.error("Invalid passage "+passage +" for model:"+modelId);
- }
- }
- else{
-
- passage = "NA";
- }
-
-
- MolecularCharacterization mc;
- Platform pl;
- Marker marker = null;
-
- if (technique.toLowerCase().equals("immunohistochemistry") || technique.toLowerCase().equals("fish")) {
- characterizationType = "cytogenetics";
- }
-
- NodeSuggestionDTO nsdto = dataImportService.getSuggestedMarker(this.getClass().getSimpleName(), ds.getAbbreviation(), modelId, markerSymbol, characterizationType, technique);
-
- if (nsdto.getNode() == null) {
-
- //uh oh, we found an unrecognised marker symbol, abort, abort!!!!
- reportManager.addMessage(nsdto.getLogEntity());
- continue;
- } else {
-
- marker = (Marker) nsdto.getNode();
-
- MolecularCharacterization molecularCharacterization;
-
- String molcharKey = modelId + "__"+ sampleId + "__" + passage + "__" + technique + "__" +origin.toLowerCase() + "__cytogenetics";
-
- if(existingMolcharNodes.containsKey(molcharKey)){
- molecularCharacterization = existingMolcharNodes.get(molcharKey);
- }
- else if(toBeCreatedMolcharNodes.containsKey(molcharKey)){
- molecularCharacterization = toBeCreatedMolcharNodes.get(molcharKey);
- }
- else{
- log.info("Looking at molchar "+molcharKey);
- //log.info("Existing keys: ");
- //log.info(existingMolcharNodes.keySet().toString());
- molecularCharacterization = new MolecularCharacterization();
- molecularCharacterization.setType("cytogenetics");
- molecularCharacterization.setPlatform(dataImportService.getPlatform(technique,"cytogenetics", ds));
- toBeCreatedMolcharNodes.put(molcharKey, molecularCharacterization);
- }
-
- MolecularData md = new MolecularData();
- md.setMarker(marker.getHgncSymbol());
-
-
- if (technique.toLowerCase().equals("immunohistochemistry") || technique.toLowerCase().equals("fish")) {
-
- md.setCytogeneticsResult(markerStatus);
- }
- //what if it is not ihc?
-
- molecularCharacterization.addMarkerAssociation(ma);
-
- }
-
-
- row++;
- }
-
-
- //get the corresponding samples for the molchar objects, link them and save them.
- for(Map.Entry<String, MolecularCharacterization> mcEntry : existingMolcharNodes.entrySet()){
-
- dataImportService.saveMolecularCharacterization(mcEntry.getValue());
- }
-
-
- //PHASE 3: get objects from cache and persist them
- for(Map.Entry<String, MolecularCharacterization> mcEntry : toBeCreatedMolcharNodes.entrySet()){
-
- String mcKey = mcEntry.getKey();
- MolecularCharacterization mc = mcEntry.getValue();
-
- String[] mcKeyArr = mcKey.split("__");
- //String molcharKey = modelId + "__"+ sampleId + "__" + passage + "__" + technique + "__" +origin.toLowerCase() + "__cytogenetics";
- String modelId = mcKeyArr[0];
- String sampleId = mcKeyArr[1];
- String pass = getPassage(mcKeyArr[2]);
- String sampleOrigin = mcKeyArr[4];
-
- ModelCreation modelCreation = dataImportService.findBySourcePdxIdAndDataSourceWithSamplesAndSpecimensAndHostStrain(modelId, ds.getAbbreviation());
-
- if(modelCreation == null){
- log.error("Missing model: "+modelId);
- continue;
- }
-
- boolean foundSpecimen = false;
-
- if(sampleOrigin.toLowerCase().equals("patient")){
-
- Sample patientSample = modelCreation.getSample();
- patientSample.setSourceSampleId(sampleId);
- patientSample.addMolecularCharacterization(mc);
-
- }
- //xenograft
- else if(sampleOrigin.toLowerCase().equals("xenograft")){
-
- if(modelCreation.getSpecimens() != null){
-
- for(Specimen specimen : modelCreation.getSpecimens()){
-
- if(specimen.getPassage().equals(pass)){
-
- if(specimen.getSample() != null && specimen.getSample().getSourceSampleId().equals(sampleId)){
-
- Sample xenograftSample = specimen.getSample();
- xenograftSample.addMolecularCharacterization(mc);
-
- foundSpecimen = true;
- }
- }
- }
- }
-
-
- //this passage is either not present yet or the linked sample has a different ID, create a specimen with sample and link mc
- if(!foundSpecimen){
- log.info("Creating new specimen for "+mcKey);
-
- Sample xenograftSample = new Sample();
- xenograftSample.setSourceSampleId(sampleId);
- xenograftSample.addMolecularCharacterization(mc);
-
- Specimen specimen = new Specimen();
- specimen.setPassage(pass);
- specimen.setSample(xenograftSample);
-
-
- modelCreation.addRelatedSample(xenograftSample);
- modelCreation.addSpecimen(specimen);
- }
-
-
- }
-
-
-
- dataImportService.saveModelCreation(modelCreation);
-
-
-
- }
-
- log.info("******************************************************");
- log.info("* Finished creating breast and or colorectal markers *");
- log.info("******************************************************");
-
- }
-
- /**
- * Checks if a list consists of nulls only
- *
- * @param list
- */
- boolean isRowOfNulls(List list) {
- for (Object o : list)
- if (!(o == null))
- return false;
- return true;
- }
-
-
- private String getMolcharType(String technique) {
-
- if (technique.toLowerCase().equals("immunohistochemistry")) {
- return "cytogenetics";
- } else if (technique.toLowerCase().equals("fish")) {
- return "cytogenetics";
- }
-
- return null;
- }
-
- public static String stripTrailingSlash(String filePath) {
- return filePath.endsWith("/") ?
- filePath.replaceFirst("/$", "") :
- filePath;
- }
-
-
- public List<List<String>> getPatientSheetData() {
- return patientSheetData;
- }
-
- public List<List<String>> getPatientTumorSheetData() {
- return patientTumorSheetData;
- }
-
- public List<List<String>> getPatientTreatmentSheetData() {
- return patientTreatmentSheetData;
- }
-
- public List<List<String>> getPdxModelSheetData() {
- return pdxModelSheetData;
- }
-
- public List<List<String>> getPdxModelValidationSheetData() {
- return pdxModelValidationSheetData;
- }
-
- public List<List<String>> getSamplePlatformDescriptionSheetData() {
- return samplePlatformDescriptionSheetData;
- }
-
- public List<List<String>> getSharingAndContactSheetData() {
- return sharingAndContactSheetData;
- }
-
- public List<List<String>> getCytogeneticsSheetData() {
- return cytogeneticsSheetData;
- }
-
- public List<List<String>> getLoaderRelatedDataSheetData() {
- return loaderRelatedDataSheetData;
- }
-
- public String getFinderRootDir() {
- return finderRootDir;
- }
-
- public void setFinderRootDir(String finderRootDir) {
- this.finderRootDir = finderRootDir;
- }
-}
\ No newline at end of file
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Reader.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Reader.java
index 060b050eeefd6d4af8b62a9df34ddeed75e0d20e..f474fc2d7727a06fd9922947c9478db0ea7f0feb 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Reader.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Reader.java
@@ -1,13 +1,15 @@
package org.pdxfinder.dataloaders.updog;
-import org.springframework.stereotype.Component;
-
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
import tech.tablesaw.api.Table;
import java.io.IOException;
-import java.nio.file.*;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.PathMatcher;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@@ -21,7 +23,6 @@ public class Reader {
Map<String, Table> readAllTsvFilesIn(Path targetDirectory, PathMatcher filter) {
HashMap<String, Table> tables = new HashMap<>();
-
try (final Stream<Path> stream = Files.list(targetDirectory)) {
stream
.filter(filter::matches)
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableSetUtilities.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableSetUtilities.java
index 6ca0e1a772b7bb47ff95f68126ff11f79154255f..433a86df2c330b952350953134e2680ef4d5f8c8 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableSetUtilities.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableSetUtilities.java
@@ -1,16 +1,10 @@
package org.pdxfinder.dataloaders.updog;
import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.tuple.Pair;
-import org.apache.poi.util.StringUtil;
import tech.tablesaw.api.Table;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
+import java.util.*;
+import java.util.stream.*;
public class TableSetUtilities {
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableUtilities.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableUtilities.java
index 5e3d711a9daecfe17c93a71eb66d354ea733fe8f..4f1027fa9daaaf91e3e3e77101852693077440d8 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableUtilities.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableUtilities.java
@@ -8,7 +8,8 @@ import tech.tablesaw.api.Table;
import tech.tablesaw.io.csv.CsvReadOptions;
import tech.tablesaw.selection.Selection;
-import java.io.*;
+import java.io.File;
+import java.io.IOException;
public final class TableUtilities {
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
index 03b0aff79de585c9fea19a00cf0a7d1ff21d9814..2c98e1570806759c5227b2b198c4e891526a012d 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
@@ -3,14 +3,18 @@ package org.pdxfinder.dataloaders.updog;
import org.pdxfinder.dataloaders.updog.domainobjectcreation.DomainObjectCreator;
import org.pdxfinder.dataloaders.updog.tablevalidation.*;
import org.pdxfinder.dataloaders.updog.tablevalidation.error.ValidationError;
-import org.slf4j.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Component;
import tech.tablesaw.api.Table;
import java.nio.file.FileSystems;
import java.nio.file.Path;
import java.nio.file.PathMatcher;
-import java.util.*;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
@Component
public class Updog {
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/DomainObjectCreator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/DomainObjectCreator.java
index eb82f5a06bc4029c8d6978c903f308de55745384..8afb5b9727526a1b79515c7bdc367a8a7247c6c9 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/DomainObjectCreator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/DomainObjectCreator.java
@@ -1,8 +1,8 @@
package org.pdxfinder.dataloaders.updog.domainobjectcreation;
import org.apache.commons.lang3.StringUtils;
+import org.pdxfinder.TSV;
import org.pdxfinder.dataloaders.updog.Reader;
-import org.pdxfinder.dataloaders.updog.TSV;
import org.pdxfinder.dataloaders.updog.TableSetCleaner;
import org.pdxfinder.graph.dao.*;
import org.pdxfinder.services.DataImportService;
@@ -977,12 +977,6 @@ public class DomainObjectCreator {
log.error("Exception with key "+sampleKey);
}
}
- private void encodeMolecularDataFor(MolecularCharacterization mc) {
- if (mc.hasMarkerAssociations()) {
- mc.setMarkers(getMarkers(mc.getFirstMarkerAssociation()));
- mc.getFirstMarkerAssociation().encodeMolecularData();
- }
- }
private void encodeMolecularDataFor(MolecularCharacterization mc, String sampleKey) {
if (mc.hasMarkerAssociations()) {
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/GroupCreator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/GroupCreator.java
index 41ba0ea1c8c20d34a8e265840a5d2095132974c4..bd9fac5457ae624180c7160becf078731a84ebcd 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/GroupCreator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/GroupCreator.java
@@ -1,6 +1,6 @@
package org.pdxfinder.dataloaders.updog.domainobjectcreation;
-import org.pdxfinder.dataloaders.updog.TSV;
+import org.pdxfinder.TSV;
import org.pdxfinder.graph.dao.Group;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreator.java
index d523ce6ddc7ae47a39f0b91ee9bf156d1689110c..149fe7012cce08a3c0744198fd200916a61711e5 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreator.java
@@ -1,6 +1,6 @@
package org.pdxfinder.dataloaders.updog.domainobjectcreation;
-import org.pdxfinder.dataloaders.updog.TSV;
+import org.pdxfinder.TSV;
import org.pdxfinder.graph.dao.Group;
import org.pdxfinder.graph.dao.ModelCreation;
import org.pdxfinder.graph.dao.Sample;
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/PatientCreator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/PatientCreator.java
index 86bfd0e5abe6b34a10fe3ece95f1a5e072f3ff34..bd62c310adcc8cf38dd4ab467bea85bff2845fc7 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/PatientCreator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/PatientCreator.java
@@ -1,6 +1,6 @@
package org.pdxfinder.dataloaders.updog.domainobjectcreation;
-import org.pdxfinder.dataloaders.updog.TSV;
+import org.pdxfinder.TSV;
import org.pdxfinder.graph.dao.Group;
import org.pdxfinder.graph.dao.Patient;
import org.slf4j.Logger;
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreator.java
index 9bf98778e60917ff8220259e1bfbf6bd4ecf48a3..3e907f6d3e191728d9ffad599dd27d1b23fb9ae8 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreator.java
@@ -1,6 +1,6 @@
package org.pdxfinder.dataloaders.updog.domainobjectcreation;
-import org.pdxfinder.dataloaders.updog.TSV;
+import org.pdxfinder.TSV;
import org.pdxfinder.graph.dao.Sample;
import org.pdxfinder.graph.dao.Tissue;
import org.pdxfinder.graph.dao.TumorType;
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreator.java
index 8b0b664d9e6f087f9b4306f5e79d8ae29c244844..00fc22e67529aeecc8a9b666b246e9438e14ffd2 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreator.java
@@ -1,12 +1,7 @@
package org.pdxfinder.dataloaders.updog.domainobjectcreation;
-import org.pdxfinder.dataloaders.updog.TSV;
-import org.pdxfinder.graph.dao.EngraftmentMaterial;
-import org.pdxfinder.graph.dao.EngraftmentSite;
-import org.pdxfinder.graph.dao.EngraftmentType;
-import org.pdxfinder.graph.dao.HostStrain;
-import org.pdxfinder.graph.dao.Sample;
-import org.pdxfinder.graph.dao.Specimen;
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporter.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporter.java
index 1e016d1a47578fc6e99d0a38b7dacf5744c1edfc..d5938f16539f8948cde39c1019592c79fcee42bc 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporter.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporter.java
@@ -2,9 +2,10 @@ package org.pdxfinder.dataloaders.updog.tablevalidation;
import org.apache.commons.collections4.CollectionUtils;
import org.pdxfinder.dataloaders.updog.tablevalidation.error.ValidationError;
-import org.slf4j.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
-import java.util.*;
+import java.util.List;
public class ErrorReporter {
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/Validator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/Validator.java
index 4225a06fdfc61b70e38eded906847dfd81b6a4a1..c341bbcf2f5c1122a1f6a84757cc45a727335ec3 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/Validator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/Validator.java
@@ -2,11 +2,14 @@ package org.pdxfinder.dataloaders.updog.tablevalidation;
import org.apache.commons.collections4.CollectionUtils;
import org.pdxfinder.dataloaders.updog.tablevalidation.error.*;
-import org.slf4j.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Component;
import tech.tablesaw.api.Table;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
@Component
public class Validator {
@@ -27,14 +30,7 @@ public class Validator {
TableSetSpecification tableSetSpecification
) {
checkRequiredTablesPresent(tableSet, tableSetSpecification);
- if (CollectionUtils.isNotEmpty(validationErrors)) {
- log.error(
- "Not all required tables where present for {}. Aborting further validation",
- tableSetSpecification.getProvider());
- return validationErrors;
- }
performColumnValidations(tableSet, tableSetSpecification);
-
return validationErrors;
}
@@ -42,12 +38,25 @@ public class Validator {
Map<String, Table> tableSet,
TableSetSpecification tableSetSpecification
) {
+ if (thereAreErrors(validationErrors, tableSetSpecification)) return;
checkRequiredColumnsPresent(tableSet, tableSetSpecification);
checkAllNonEmptyValuesPresent(tableSet, tableSetSpecification);
checkAllUniqueColumnsForDuplicates(tableSet, tableSetSpecification);
checkRelationsValid(tableSet, tableSetSpecification);
}
+ private boolean thereAreErrors(
+ List<ValidationError> validationErrors,
+ TableSetSpecification tableSetSpecification
+ ) {
+ if (CollectionUtils.isNotEmpty(validationErrors)) {
+ log.error(
+ "Not all required tables where present for {}. Aborting further validation",
+ tableSetSpecification.getProvider());
+ }
+ return CollectionUtils.isNotEmpty(validationErrors);
+ }
+
private void checkRequiredTablesPresent(
Map<String, Table> tableSet,
TableSetSpecification tableSetSpecification
@@ -96,4 +105,13 @@ public class Validator {
return this.validationErrors;
}
+ public static void reportAnyErrors(List<ValidationError> validationErrors) {
+ if (CollectionUtils.isNotEmpty(validationErrors))
+ for (ValidationError error : validationErrors) {
+ log.error(error.message());
+ }
+ else
+ log.info("There were no validation errors raised, great!");
+ }
+
}
diff --git a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreator.java b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreator.java
index 1d0e833df47f796495547f8375ca5be6f3ef4d46..8d553db41ab3c2d682470268eef1afe60e8cfa61 100644
--- a/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreator.java
+++ b/indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreator.java
@@ -113,20 +113,20 @@ public class BrokenRelationErrorCreator extends ErrorCreator {
private boolean missingLeftColumn(Map<String, Table> tableSet, Relation relation) {
return tableMissingColumn(
tableSet.get(relation.leftTable()),
- relation.leftColumn());
+ relation.leftColumn(), relation.leftTable());
}
private boolean missingRightColumn(Map<String, Table> tableSet, Relation relation) {
return tableMissingColumn(
tableSet.get(relation.rightTable()),
- relation.rightColumn());
+ relation.rightColumn(), relation.rightTable());
}
- private boolean tableMissingColumn(Table table, String columnName) {
+ private boolean tableMissingColumn(Table table, String columnName, String tableName) {
try {
return !table.columnNames().contains(columnName);
} catch (NullPointerException e) {
- log.error("Couldn't access table {} {}", e, table);
+ log.error("Couldn't access table {} because of {}",tableName, e.toString());
return true;
}
}
diff --git a/indexer/src/main/java/org/pdxfinder/mapping/LinkSamplesToNCITTerms.java b/indexer/src/main/java/org/pdxfinder/mapping/LinkSamplesToNCITTerms.java
index 833dcef72e8aed30b8c756e36d770f0209b2a8c7..21eb599e45cf60ce34222c10ae05b3b5b9a83851 100644
--- a/indexer/src/main/java/org/pdxfinder/mapping/LinkSamplesToNCITTerms.java
+++ b/indexer/src/main/java/org/pdxfinder/mapping/LinkSamplesToNCITTerms.java
@@ -119,9 +119,7 @@ public class LinkSamplesToNCITTerms {
//log.info("Mapping "+diagnosis+" to "+mappingRule.getOntologyTerm());
}
}
-
}
-
startNode += batchSize;
}
diff --git a/indexer/src/main/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTerms.java b/indexer/src/main/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTerms.java
index 6ea833f0c3ae0a13ed8c3f11f58b9e7a624ce085..57c587697401a3b8dfddd749d467f28aa1e565d8 100644
--- a/indexer/src/main/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTerms.java
+++ b/indexer/src/main/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTerms.java
@@ -11,8 +11,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
/*
* Created by csaba on 05/06/2019.
@@ -109,43 +108,32 @@ public class LinkTreatmentsToNCITTerms {
}
- private void addRelationshipToTreatments(Collection<Treatment> treatments, String dataSource){
+ public void addRelationshipToTreatments(Collection<Treatment> treatments, String dataSource){
+ List<String> missingOntologyTerms = new ArrayList<>();
for(Treatment treatment : treatments){
-
MappingEntity me = mappingService.getTreatmentMapping(dataSource, treatment.getName());
-
if(me == null){
-
//TODO: deal with missing mapping rules here
log.warn("No mapping rule found for "+dataSource+" "+treatment.getName());
-
mappingService.saveUnmappedTreatment(dataSource, treatment.getName());
}
else{
-
-
- OntologyTerm ot = dataImportService.findOntologyTermByUrl(me.getMappedTermUrl());
-
- if(ot == null){
-
-
- log.error("Ontology term not found "+me.getMappedTermUrl());
- }
- else{
-
+ OntologyTerm ontologyTerm = dataImportService.findOntologyTermByUrl(me.getMappedTermUrl());
+ if (Objects.isNull(ontologyTerm)) {
+ missingOntologyTerms.add(me.getMappedTermLabel());
+ } else {
TreatmentToOntologyRelationship r = new TreatmentToOntologyRelationship();
r.setType(me.getMapType());
r.setJustification(me.getJustification());
- r.setOntologyTerm(ot);
+ r.setOntologyTerm(ontologyTerm);
r.setTreatment(treatment);
-
-
treatment.setTreatmentToOntologyRelationship(r);
dataImportService.saveTreatment(treatment);
}
}
}
+ log.error("Failed to find {} ontology terms: {}", missingOntologyTerms.size(), missingOntologyTerms);
}
diff --git a/indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java b/indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
index 3cf183501198140787b770e0a265d5a4a293fb4c..4ed52aa836a4aaf922339aa9703f1f8474b71229 100644
--- a/indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
+++ b/indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
@@ -1,18 +1,13 @@
package org.pdxfinder.postload;
-import com.google.gson.Gson;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.dataloaders.UniversalLoader;
+import com.github.openjson.*;
import org.pdxfinder.graph.dao.*;
import org.pdxfinder.graph.queryresults.MutatedMarkerData;
import org.pdxfinder.reportmanager.ReportManager;
import org.pdxfinder.services.DataImportService;
import org.pdxfinder.services.DrugService;
-import org.pdxfinder.services.UtilityService;
import org.pdxfinder.services.ds.ModelForQuery;
import org.pdxfinder.services.dto.DataAvailableDTO;
-import org.pdxfinder.services.dto.NodeSuggestionDTO;
-import org.pdxfinder.services.reporting.MarkerLogEntity;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.BeansException;
@@ -21,13 +16,7 @@ import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.core.annotation.Order;
-
import org.springframework.stereotype.Service;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
import java.util.*;
import java.util.stream.Collectors;
@@ -42,8 +31,6 @@ public class CreateDataProjections implements ApplicationContextAware{
private DataImportService dataImportService;
private DrugService drugService;
- private UtilityService utilityService;
-
@Value("${user.home}")
String homeDir;
@@ -60,9 +47,6 @@ public class CreateDataProjections implements ApplicationContextAware{
private List<ModelForQuery> modelForQueryDP = new ArrayList<>();
- //"platform"=>"marker"=>"set of model ids"
- private Map<String, Map<String, Set<Long>>> wtMarkersDataProjection = new HashMap<>();
-
//"drugname"=>"response"=>"set of model ids"
private Map<String, Map<String, Set<Long>>> modelDrugResponseDP = new HashMap<>();
@@ -92,11 +76,10 @@ public class CreateDataProjections implements ApplicationContextAware{
protected static ApplicationContext context;
@Autowired
- public CreateDataProjections(DataImportService dataImportService, DrugService drugService, UtilityService utilityService) {
+ public CreateDataProjections(DataImportService dataImportService, DrugService drugService) {
this.dataImportService = dataImportService;
this.drugService = drugService;
- this.utilityService = utilityService;
}
public void run() {
@@ -524,133 +507,6 @@ public class CreateDataProjections implements ApplicationContextAware{
}
- private void addCharlesRiverCNA() throws Exception {
-
- log.info("Loading additional datasets for CRL.");
-
- String templateFileStr = finderRootDir + "/data/UPDOG/CRL/metadata.xlsx";
- String markerTemplateFileStr = finderRootDir + "/data/UPDOG/CRL/cna_tested_markers/list.csv";
-
- File markerListFile = new File(markerTemplateFileStr);
- File templateFile = new File(templateFileStr);
-
- Set<Marker> markerSet = new HashSet<>();
-
- if (markerListFile.exists() && templateFile.exists()) {
-
- List<List<String>> markerList = utilityService.serializeCSVToArrayList(markerTemplateFileStr);
-
- //STEP1: get the marker symbols from the csv file then find the corresponding marker node and add it to a set
- log.info("Found " + markerList.size() + " markers in the marker file.");
- for (int i = 1; i < markerList.size(); i++) {
-
- if (i % 500 == 0) {
- log.info("Collected " + i + " markers from the repository.");
- }
-
- String markerSymbol = markerList.get(i).get(0);
-
- //skip all symbols with dot in them
- if (markerSymbol.contains(".")) {
-
- MarkerLogEntity le = new MarkerLogEntity(this.getClass().getSimpleName(), "CRL", "-", "copy number alteration", "Not Specified", markerSymbol, "", "");
- le.setMessage(markerSymbol + " is an unrecognised symbol");
- le.setType("ERROR");
- continue;
-
- }
-
-
- //log.info("Looking up: "+markerSymbol);
- NodeSuggestionDTO nsdto = dataImportService.getSuggestedMarker(this.getClass().getSimpleName(), "CRL", "-", markerSymbol, "copy number alteration", "Not Specified");
-
- if (nsdto.getNode() == null) {
-
- //uh oh, we found an unrecognised marker symbol, abort, abort!!!!
- reportManager.addMessage(nsdto.getLogEntity());
-
- continue;
- } else {
-
- Marker marker = (Marker) nsdto.getNode();
- markerSet.add(marker);
-
- }
-
- }
-
-
- //STEP2:
-
- Set<Long> modelIdSet = new HashSet<>();
-
- UniversalLoader updog = new UniversalLoader(reportManager, utilityService, dataImportService);
- updog.setFinderRootDir(finderRootDir);
-
- updog.initTemplates(templateFileStr);
-
- List<List<String>> datasetDerived = updog.getSamplePlatformDescriptionSheetData();
- int row = 6;
-
- for (List<String> derivedDatasetRow : datasetDerived) {
-
- String sampleId = derivedDatasetRow.get(0);
-
- String origin = derivedDatasetRow.get(1);
- String passage = derivedDatasetRow.get(2);
- String nomenclature = derivedDatasetRow.get(3);
- String modelId = derivedDatasetRow.get(4);
- String molCharType = derivedDatasetRow.get(5);
- String platformName = derivedDatasetRow.get(6);
- String platformTechnology = derivedDatasetRow.get(7);
- String platformDescription = derivedDatasetRow.get(8);
- String analysisProtocol = derivedDatasetRow.get(9);
-
- //SKIP everything that is not cna
- if (!molCharType.toLowerCase().equals("copy number alteration")) {
-
- row++;
- continue;
- }
-
-
- ModelCreation modelCreation = dataImportService.findModelByIdAndDataSource(modelId, "CRL");
-
- if(modelCreation != null){
-
- modelIdSet.add(modelCreation.getId());
- }
- else{
- log.error("Not found model: "+modelId);
- }
-
-
- }
-
-
- //STEP3: save the same markers for all models
-
- for(Marker m: markerSet){
- if(copyNumberAlterationDP.containsKey(m.getHgncSymbol())){
-
- copyNumberAlterationDP.get(m.getHgncSymbol()).addAll(modelIdSet);
- }
- else{
-
- copyNumberAlterationDP.put(m.getHgncSymbol(), modelIdSet);
- }
-
- }
-
-
- log.info("DONE faking CNA data for CRL.");
-
- }
- else{
- log.error("Missing files for creating CRL CNA projection.");
- }
- }
-
private void addToOneParamDP(Map<String, Set<Long>> collection, String key, Long modelId){
if(key == null || key.isEmpty()) return;
@@ -659,7 +515,6 @@ public class CreateDataProjections implements ApplicationContextAware{
collection.get(key).add(modelId);
}
else{
-
Set<Long> s = new HashSet();
s.add(modelId);
collection.put(key, s);
@@ -670,138 +525,51 @@ public class CreateDataProjections implements ApplicationContextAware{
private void addToTwoParamDP(Map<String, Map<String, Set<Long>>> collection, String key1, String key2, Long modelId){
if(collection.containsKey(key1)){
-
if(collection.get(key1).containsKey(key2)){
collection.get(key1).get(key2).add(modelId);
-
}
else{
-
Set<Long> set = new HashSet<>();
set.add(modelId);
collection.get(key1).put(key2, set);
}
}
else{
-
Set<Long> set = new HashSet<>();
set.add(modelId);
-
Map<String, Set<Long>> map = new HashMap<>();
map.put(key2, set);
-
collection.put(key1, map);
}
-
}
private void addToThreeParamDP(Map<String, Map<String, Map<String, Set<Long>>>> collection, String key1, String key2, String key3, Long modelId){
if(collection.containsKey(key1)){
-
if(collection.get(key1).containsKey(key2)){
-
if(collection.get(key1).get(key2).containsKey(key3)){
-
collection.get(key1).get(key2).get(key3).add(modelId);
}
else{
-
Set<Long> models = new HashSet<>(Arrays.asList(modelId));
collection.get(key1).get(key2).put(key3,models);
}
-
}
else{
-
Set<Long> models = new HashSet<>(Arrays.asList(modelId));
-
Map<String, Set<Long>> map3 = new HashMap();
map3.put(key3,models);
-
collection.get(key1).put(key2, map3);
-
}
-
-
-
}
else{
Set<Long> models = new HashSet<>(Arrays.asList(modelId));
-
Map<String, Set<Long>> map3 = new HashMap();
map3.put(key3,models);
-
- Map map2 = new HashMap();
- map2.put(key2, map3);
-
- collection.put(key1, map2);
- }
-
-
- }
-
- private void addToFourParamDP(Map<String, Map<String, Map<String, Map<String, Set<Long>>>>> collection, String key1, String key2, String key3, String key4, Long modelId){
-
- if(collection.containsKey(key1)){
-
- if(collection.get(key1).containsKey(key2)){
-
- if(collection.get(key1).get(key2).containsKey(key3)){
-
- if(collection.get(key1).get(key2).get(key3).containsKey(key4)){
-
- collection.get(key1).get(key2).get(key3).get(key4).add(modelId);
- }
- else{
-
- Set<Long> models = new HashSet<>(Arrays.asList(modelId));
-
- collection.get(key1).get(key2).get(key3).put(key4, models);
- }
-
- }
- else{
-
- Set<Long> models = new HashSet<>(Arrays.asList(modelId));
-
- Map<String, Set<Long>> map4 = new HashMap();
- map4.put(key4, models);
-
- collection.get(key1).get(key2).put(key3, map4);
- }
-
- }
- else{
-
- Set<Long> models = new HashSet<>(Arrays.asList(modelId));
-
- Map<String, Set<Long>> map4 = new HashMap();
- map4.put(key4, models);
-
- Map map3 = new HashMap();
- map3.put(key3, map4);
-
- collection.get(key1).put(key2, map3);
- }
-
-
- }
- else{
-
- Set<Long> models = new HashSet<>(Arrays.asList(modelId));
-
- Map<String, Set<Long>> map4 = new HashMap();
- map4.put(key4, models);
-
- Map map3 = new HashMap();
- map3.put(key3, map4);
-
Map map2 = new HashMap();
map2.put(key2, map3);
-
collection.put(key1, map2);
}
@@ -917,30 +685,6 @@ public class CreateDataProjections implements ApplicationContextAware{
}
-
- /*
- if (!mutationPlatformsByModel.containsKey(mc.getId())) {
- mutationPlatformsByModel.put(mc.getId(), new ArrayList<>());
- }
- // Are there any molecular characterizations associated to this model?
- if (mc.getRelatedSamples().stream().map(Sample::getMolecularCharacterizations).mapToLong(Collection::size).sum() > 0) {
- // Get all molecular characterizations platforms into a list
- mutationPlatformsByModel.get(mc.getId()).addAll(
- mc.getRelatedSamples().stream()
- .map(Sample::getMolecularCharacterizations)
- .flatMap(Collection::stream)
- .map(x -> {
- if (dataImportService.countMarkerAssociationBySourcePdxId(mc.getSourcePdxId(), x.getPlatform().getName()) != 0) {
- return x.getPlatform().getName();
- } else {
- return " ";
- }
- })
- .distinct()
- .collect(Collectors.toList()));
- }
- */
-
}
Map<String, String> cancerSystemMap = new HashMap<>();
@@ -1097,7 +841,7 @@ public class CreateDataProjections implements ApplicationContextAware{
// Add all top level systems (translated) to the Model
for (String s : allOntologyTerms.stream().map(OntologyTerm::getLabel).collect(Collectors.toSet())) {
- if (cancerSystemMap.keySet().contains(s)) {
+ if (cancerSystemMap.containsKey(s)) {
if (mfq.getCancerSystem() == null) {
mfq.setCancerSystem(new ArrayList<>());
@@ -1168,11 +912,8 @@ public class CreateDataProjections implements ApplicationContextAware{
mfqDP.setLabel("ModelForQuery");
}
- //log.info("MFQ value toString:"+modelForQueryDP.toString());
- Gson gson = new Gson();
- String jsonMfqDP = gson.toJson(this.modelForQueryDP);
+ String jsonMfqDP = JSONObject.wrap(modelForQueryDP).toString();
mfqDP.setValue(jsonMfqDP);
- //log.info("MFQ value:"+jsonMfqDP);
dataImportService.saveDataProjection(mfqDP);
@@ -1210,65 +951,56 @@ public class CreateDataProjections implements ApplicationContextAware{
private void createModelDrugResponseDataProjection(){
- log.info("Creating Model Drug Response DP");
+ log.info("Creating Model Drug Response Data Projection");
List<TreatmentSummary> treatmentSummaries = drugService.getModelTreatmentSummariesWithDrugAndResponse();
for(TreatmentSummary ts : treatmentSummaries){
-
ModelCreation model = dataImportService.findModelByTreatmentSummary(ts);
-
//check if treatment is linked to a model
if(model != null){
-
Long modelId = model.getId();
+ processModelDrugs(modelId, ts);
+ }
+ }
+ }
- for(TreatmentProtocol tp : ts.getTreatmentProtocols()){
-
- //this bit adds the drugA + drugB + drugC etc to the options
- String drugName = tp.getTreatmentString(true);
- String response = tp.getResponse().getDescription();
- addToModelDrugResponseDP(modelId, drugName, response);
-
-
- //we also need to deal with regimens
- List<String> regimenDrugs = new ArrayList<>();
- for(TreatmentComponent tc: tp.getComponents()){
-
- Treatment t = tc.getTreatment();
- OntologyTerm ot = t.getTreatmentToOntologyRelationship().getOntologyTerm();
-
- if(ot.getType().equals("treatment regimen") && ot.getSubclassOf() != null && !ot.getSubclassOf().isEmpty()){
-
-
-
- for(OntologyTerm ot2: ot.getSubclassOf()){
+ public void processModelDrugs(Long modelId, TreatmentSummary ts){
- regimenDrugs.add(ot2.getLabel());
+ for(TreatmentProtocol tp : ts.getTreatmentProtocols()){
+ //this bit adds the drugA + drugB + drugC etc to the options
+ String drugName = tp.getTreatmentString(true);
+ String response = tp.getResponse().getDescription();
+ addToModelDrugResponseDP(modelId, drugName, response);
- }
-
- }
- }
+ processModelRegimens(modelId, tp, response);
+ }
+ }
- //sort them alphabetically
- if(regimenDrugs.size() != 0){
- Collections.sort(regimenDrugs);
- drugName = String.join(" and ", regimenDrugs);
- addToModelDrugResponseDP(modelId, drugName, response);
- }
+ public void processModelRegimens(Long modelId, TreatmentProtocol tp, String response){
+ List<String> regimenDrugs = new ArrayList<>();
+ for(TreatmentComponent tc: tp.getComponents()){
+ Treatment t = tc.getTreatment();
+ OntologyTerm ot = t.getTreatmentToOntologyRelationship().getOntologyTerm();
+ if(ot.getType().equals("treatment regimen") && ot.getSubclassOf() != null && !ot.getSubclassOf().isEmpty()){
+ for(OntologyTerm ot2: ot.getSubclassOf()){
+ regimenDrugs.add(ot2.getLabel());
}
}
}
- System.out.println();
+ //sort them alphabetically
+ if(regimenDrugs.size() != 0){
+ Collections.sort(regimenDrugs);
+ String drugName = String.join(" and ", regimenDrugs);
+ addToModelDrugResponseDP(modelId, drugName, response);
+ }
}
-
private void createPatientTreatmentDataProjection(){
- log.info("Creating patient treatment DP");
+ log.info("Creating patient treatment data projection");
List<TreatmentSummary> treatmentSummaries = drugService.getPatientTreatmentSummariesWithDrug();
@@ -1346,7 +1078,7 @@ public class CreateDataProjections implements ApplicationContextAware{
private void createFrequentlyMutatedGenesDataProjection(){
- log.info("Creating Frequently Mutated Genes DP");
+ log.info("Creating Frequently Mutated Genes data projection");
for(Map.Entry<String, Set<Long>> entry : frequentlyMutatedMarkers.entrySet() ){
@@ -1423,251 +1155,147 @@ public class CreateDataProjections implements ApplicationContextAware{
drugDosingDP.get(drug).add(modelId);
}
- private void saveDataProjections(){
+ public void saveDataProjections(){
log.info("Saving DataProjections");
- DataProjection pmvmDP = dataImportService.findDataProjectionByLabel("PlatformMarkerVariantModel");
-
- if (pmvmDP == null){
-
- pmvmDP = new DataProjection();
- pmvmDP.setLabel("PlatformMarkerVariantModel");
- }
-
- DataProjection mvDP = dataImportService.findDataProjectionByLabel("MarkerVariant");
-
- if(mvDP == null){
-
- mvDP = new DataProjection();
- mvDP.setLabel("MarkerVariant");
- }
-
- DataProjection drugDP = dataImportService.findDataProjectionByLabel("ModelDrugData");
-
- if(drugDP == null){
-
- drugDP = new DataProjection();
- drugDP.setLabel("ModelDrugData");
- }
-
- DataProjection ihcDP = dataImportService.findDataProjectionByLabel("breast cancer markers");
-
- if(ihcDP == null){
- ihcDP = new DataProjection();
- ihcDP.setLabel("breast cancer markers");
- }
-
- DataProjection cytoDP = dataImportService.findDataProjectionByLabel("cytogenetics");
-
- if(cytoDP == null){
- cytoDP = new DataProjection();
- cytoDP.setLabel("cytogenetics");
- }
-
- DataProjection cnaDP = dataImportService.findDataProjectionByLabel("copy number alteration");
-
-
- if(cnaDP == null){
- cnaDP = new DataProjection();
- cnaDP.setLabel("copy number alteration");
- }
-
-
- DataProjection expDP = dataImportService.findDataProjectionByLabel("expression");
-
-
- if(expDP == null){
- expDP = new DataProjection();
- expDP.setLabel("expression");
- }
-
-
- DataProjection daDP = dataImportService.findDataProjectionByLabel("data available");
-
- if(daDP == null){
- daDP = new DataProjection();
- daDP.setLabel("data available");
- }
-
- DataProjection fmgDP = dataImportService.findDataProjectionByLabel("frequently mutated genes");
-
- if(fmgDP == null){
- fmgDP = new DataProjection();
- fmgDP.setLabel("frequently mutated genes");
- }
-
- DataProjection ptDP = dataImportService.findDataProjectionByLabel("patient treatment");
-
- if(ptDP == null){
- ptDP = new DataProjection();
- ptDP.setLabel("patient treatment");
- }
-
- DataProjection ddDP = dataImportService.findDataProjectionByLabel("drug dosing counter");
-
- if(ddDP == null){
- ddDP = new DataProjection();
- ddDP.setLabel("drug dosing counter");
- }
+ saveDP("PlatformMarkerVariantModel", mutatedPlatformMarkerVariantModelDP);
+ saveDP("MarkerVariant", mutatedMarkerVariantDP);
+ saveDP("ModelDrugData", modelDrugResponseDP);
+ saveDP("breast cancer markers", immunoHistoChemistryDP);
+ saveDP("cytogenetics", cytogeneticsDP);
+ saveDP("copy number alteration", copyNumberAlterationDP);
+ saveDP("expression", expressionDP);
+ saveDP("data available", dataAvailableDP);
+ saveDP("frequently mutated genes", frequentlyMutatedMarkersDP);
+ saveDP("patient treatment", patientTreatmentDP);
+ saveDP("drug dosing counter", drugDosingDP);
- JSONObject json;
+ }
+ public DataProjection saveDP(String dpName, Object values){
- try{
- json = new JSONObject(mutatedPlatformMarkerVariantModelDP.toString());
- pmvmDP.setValue(json.toString());
- }
- catch(Exception e){
+ DataProjection dataProjection = dataImportService.findDataProjectionByLabel(dpName);
- e.printStackTrace();
- log.error(mutatedPlatformMarkerVariantModelDP.toString());
+ if(dataProjection== null){
+ dataProjection = new DataProjection();
+ dataProjection.setLabel(dpName);
}
- try{
- json = new JSONObject(mutatedMarkerVariantDP.toString());
- mvDP.setValue(json.toString());
- }
- catch(Exception e){
- e.printStackTrace();
- log.error(mutatedMarkerVariantDP.toString());
- }
- try{
- json = new JSONObject(modelDrugResponseDP.toString());
- drugDP.setValue(json.toString());
- }
- catch(Exception e){
- e.printStackTrace();
- log.error(modelDrugResponseDP.toString());
- }
+ dataProjection.setValue(createJsonString(values));
+ return dataImportService.saveDataProjection(dataProjection);
+ }
- try{
- json = new JSONObject(immunoHistoChemistryDP.toString());
- ihcDP.setValue(json.toString());
+ public String createJsonString(Object jstring){
+ try {
+ return JSONObject.wrap(jstring).toString();
}
catch(Exception e){
- e.printStackTrace();
- log.error(immunoHistoChemistryDP.toString());
+ log.error("There was an error serializing the map object to JSON");
}
+ return "";
+ }
- try{
- json = new JSONObject(copyNumberAlterationDP.toString());
- cnaDP.setValue(json.toString());
- }
- catch(Exception e){
- e.printStackTrace();
- log.error(copyNumberAlterationDP.toString());
- }
- try{
- json = new JSONObject(dataAvailableDP.toString());
- daDP.setValue(json.toString());
- }
- catch(Exception e){
+ @Override
+ public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
+ context = applicationContext;
+ }
- e.printStackTrace();
- log.error(dataAvailableDP.toString());
- }
-
- try{
- json = new JSONObject(patientTreatmentDP.toString());
- ptDP.setValue(json.toString());
- System.out.println();
- }
- catch(Exception e){
- e.printStackTrace();
- log.error(patientTreatmentDP.toString());
- }
+ public void setMutatedPlatformMarkerVariantModelDP(Map<String, Map<String, Map<String, Set<Long>>>> mutatedPlatformMarkerVariantModelDP) {
+ this.mutatedPlatformMarkerVariantModelDP = mutatedPlatformMarkerVariantModelDP;
+ }
- try{
- fmgDP.setValue(frequentlyMutatedMarkersDP.toString());
- }
- catch(Exception e){
+ public void setMutatedMarkerVariantDP(Map<String, Set<String>> mutatedMarkerVariantDP) {
+ this.mutatedMarkerVariantDP = mutatedMarkerVariantDP;
+ }
- e.printStackTrace();
- log.error(frequentlyMutatedMarkersDP.toString());
- }
+ public void setModelForQueryDP(List<ModelForQuery> modelForQueryDP) {
+ this.modelForQueryDP = modelForQueryDP;
+ }
- try{
- json = new JSONObject(cytogeneticsDP.toString());
- cytoDP.setValue(json.toString());
+ public void setModelDrugResponseDP(Map<String, Map<String, Set<Long>>> modelDrugResponseDP) {
+ this.modelDrugResponseDP = modelDrugResponseDP;
+ }
- }
- catch(Exception e){
- e.printStackTrace();
- log.error(cytogeneticsDP.toString());
- }
+ public void setImmunoHistoChemistryDP(Map<String, Map<String, Set<Long>>> immunoHistoChemistryDP) {
+ this.immunoHistoChemistryDP = immunoHistoChemistryDP;
+ }
- try{
- json = new JSONObject(expressionDP.toString());
- expDP.setValue(json.toString());
+ public void setCytogeneticsDP(Map<String, Map<String, Set<Long>>> cytogeneticsDP) {
+ this.cytogeneticsDP = cytogeneticsDP;
+ }
- }
- catch(Exception e){
- e.printStackTrace();
- log.error(expressionDP.toString());
- }
+ public void setCopyNumberAlterationDP(Map<String, Set<Long>> copyNumberAlterationDP) {
+ this.copyNumberAlterationDP = copyNumberAlterationDP;
+ }
- try{
- json = new JSONObject(drugDosingDP.toString());
- ddDP.setValue(json.toString());
+ public void setExpressionDP(Map<String, Map<String, Set<Long>>> expressionDP) {
+ this.expressionDP = expressionDP;
+ }
- }
- catch(Exception e){
- e.printStackTrace();
- log.error(drugDosingDP.toString());
- }
+ public void setDataAvailableDP(Map<String, List<DataAvailableDTO>> dataAvailableDP) {
+ this.dataAvailableDP = dataAvailableDP;
+ }
+ public void setFrequentlyMutatedMarkersDP(List<MutatedMarkerData> frequentlyMutatedMarkersDP) {
+ this.frequentlyMutatedMarkersDP = frequentlyMutatedMarkersDP;
+ }
- dataImportService.saveDataProjection(pmvmDP);
- dataImportService.saveDataProjection(mvDP);
- dataImportService.saveDataProjection(drugDP);
- dataImportService.saveDataProjection(ihcDP);
- dataImportService.saveDataProjection(cnaDP);
- dataImportService.saveDataProjection(daDP);
- dataImportService.saveDataProjection(fmgDP);
- dataImportService.saveDataProjection(ptDP);
- dataImportService.saveDataProjection(cytoDP);
- dataImportService.saveDataProjection(expDP);
- dataImportService.saveDataProjection(ddDP);
+ public void setDrugDosingDP(Map<String, Set<Long>> drugDosingDP) {
+ this.drugDosingDP = drugDosingDP;
+ }
+ public void setPatientTreatmentDP(Map<String, Set<Long>> patientTreatmentDP) {
+ this.patientTreatmentDP = patientTreatmentDP;
}
+ public Map<String, Map<String, Map<String, Set<Long>>>> getMutatedPlatformMarkerVariantModelDP() {
+ return mutatedPlatformMarkerVariantModelDP;
+ }
+ public Map<String, Set<String>> getMutatedMarkerVariantDP() {
+ return mutatedMarkerVariantDP;
+ }
- private String createJsonString(Object jstring){
+ public List<ModelForQuery> getModelForQueryDP() {
+ return modelForQueryDP;
+ }
- try{
+ public Map<String, Map<String, Set<Long>>> getModelDrugResponseDP() {
+ return modelDrugResponseDP;
+ }
- JSONObject json = new JSONObject(jstring);
- return json.toString();
- }
- catch(Exception e){
+ public Map<String, Map<String, Set<Long>>> getImmunoHistoChemistryDP() {
+ return immunoHistoChemistryDP;
+ }
- e.printStackTrace();
- }
+ public Map<String, Map<String, Set<Long>>> getCytogeneticsDP() {
+ return cytogeneticsDP;
+ }
- return "";
+ public Map<String, Set<Long>> getCopyNumberAlterationDP() {
+ return copyNumberAlterationDP;
}
- private void dumpDataToFile(){
- log.info("Dumping data to file");
- String fileName = "/Users/csaba/Documents/pdxFinderDump.txt";
- try {
- BufferedWriter writer = new BufferedWriter(new FileWriter(fileName, false));
+ public Map<String, Map<String, Set<Long>>> getExpressionDP() {
+ return expressionDP;
+ }
- writer.append(immunoHistoChemistryDP.toString());
- writer.close();
+ public Map<String, List<DataAvailableDTO>> getDataAvailableDP() {
+ return dataAvailableDP;
+ }
- } catch (IOException e) {
- e.printStackTrace();
- }
+ public List<MutatedMarkerData> getFrequentlyMutatedMarkersDP() {
+ return frequentlyMutatedMarkersDP;
+ }
+ public Map<String, Set<Long>> getDrugDosingDP() {
+ return drugDosingDP;
}
- @Override
- public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
- context = applicationContext;
+ public Map<String, Set<Long>> getPatientTreatmentDP() {
+ return patientTreatmentDP;
}
}
diff --git a/indexer/src/main/java/org/pdxfinder/postload/MolcharAPITest.java b/indexer/src/main/java/org/pdxfinder/postload/MolcharAPITest.java
index 9542e2d5f12540b156853d80f8d8fd936b6910cf..81f17764e2852e93e5095ca9a8678fe3208070b4 100644
--- a/indexer/src/main/java/org/pdxfinder/postload/MolcharAPITest.java
+++ b/indexer/src/main/java/org/pdxfinder/postload/MolcharAPITest.java
@@ -67,7 +67,7 @@ public class MolcharAPITest implements CommandLineRunner{
long startTime = System.currentTimeMillis();
- MolecularDataTableDTO dto = detailsService.getMolecularDataTable(id.toString());
+ MolecularDataTableDTO dto = detailsService.getMolecularDataTable(id.toString(), false);
long endTime = System.currentTimeMillis();
long totalTime = endTime - startTime;
diff --git a/indexer/src/main/java/org/pdxfinder/postload/SetDataVisibility.java b/indexer/src/main/java/org/pdxfinder/postload/SetDataVisibility.java
index 671ef458752923cbc899eae2f8abb2051a1e03a6..5fd19c7dfc5b3a8dc7d7529be0374347a6b87629 100644
--- a/indexer/src/main/java/org/pdxfinder/postload/SetDataVisibility.java
+++ b/indexer/src/main/java/org/pdxfinder/postload/SetDataVisibility.java
@@ -30,6 +30,8 @@ public class SetDataVisibility {
log.info("Applying data visibility rules");
applyDataVisibilityRules("CRL");
+ applyDataVisibilityRules("Curie-LC");
+ applyDataVisibilityRules("Curie-BC");
long endTime = System.currentTimeMillis();
long totalTime = endTime - startTime;
@@ -42,26 +44,24 @@ public class SetDataVisibility {
}
- private void applyDataVisibilityRules(String datasourceAbbrev){
+ public void applyDataVisibilityRules(String datasourceAbbrev){
log.info("Disabling data visibility for "+datasourceAbbrev);
int molcharCounter = dataImportService.findMolcharNumberByDataSource(datasourceAbbrev);
for(int i=0; i < molcharCounter; i+=50){
-
List<MolecularCharacterization> molChars = dataImportService.findMolcharByDataSourceSkipLimit(datasourceAbbrev, i, 50);
-
- for(MolecularCharacterization mc:molChars){
-
- mc.setVisible(false);
- dataImportService.saveMolecularCharacterization(mc);
- }
-
+ disableVisibility(molChars);
+ dataImportService.saveMolecularCharacterizations(molChars);
}
+ }
+ public void disableVisibility(List<MolecularCharacterization> molChars){
+ for(MolecularCharacterization mc:molChars){
+ mc.setVisible(false);
+ }
}
-
}
diff --git a/indexer/src/main/java/org/pdxfinder/postload/ValidateDB.java b/indexer/src/main/java/org/pdxfinder/postload/ValidateDB.java
deleted file mode 100644
index 0c315d3a7824a82a11a752d0b5ae281a6206dafd..0000000000000000000000000000000000000000
--- a/indexer/src/main/java/org/pdxfinder/postload/ValidateDB.java
+++ /dev/null
@@ -1,152 +0,0 @@
-package org.pdxfinder.postload;
-
-/*
- * Created by csaba on 15/11/2018.
- */
-
-import joptsimple.OptionParser;
-import joptsimple.OptionSet;
-import org.pdxfinder.graph.dao.DataProjection;
-import org.pdxfinder.graph.dao.Marker;
-import org.pdxfinder.graph.dao.OntologyTerm;
-import org.pdxfinder.services.DataImportService;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.CommandLineRunner;
-import org.springframework.core.annotation.Order;
-import org.springframework.stereotype.Component;
-import org.springframework.stereotype.Service;
-
-import java.util.HashSet;
-import java.util.Set;
-
-@Service
-@Order(value = 92)
-public class ValidateDB {
-
- private static Logger log = LoggerFactory.getLogger(ValidateDB.class);
-
- private DataImportService dataImportService;
-
-
- public ValidateDB(DataImportService dataImportService) {
- this.dataImportService = dataImportService;
- }
-
- public void run() {
-
- log.info("******************************************************");
- log.info("* Starting validation checks *");
- log.info("******************************************************");
-
- runValidationChecks();
-
- }
-
-
- private void runValidationChecks(){
-
-
- /*
- Scenarios when DB is invalid:
- - Missing DataProjection nodes
- - Patients with multiple treatmentsummaries
-
- Scenarios when DB is valid with warnings:
- - Found nodes without relationships and they are not DataProjections
- - Platforms without url attribute value
- */
-
-
-
-
- boolean isDBValid = true;
- boolean noWarnings = true;
-
- //check if there is any unlinked nodes that are not dataprojections
-
-
- log.info("Looking for sad nodes (nodes without a relationship)");
- Set<String> unlinkedNodeTypeSet = new HashSet<>();
- /*
- //this is disabled now, needs to be batched
-
- Set<Object> unlinkedNodes = dataImportService.findUnlinkedNodes();
-
- if(unlinkedNodes.size() == 0){
- log.error("DataProjection nodes not found - invalid database!");
- isDBValid = false;
- }
- else{
-
- for(Object node : unlinkedNodes){
-
- if(!(node instanceof DataProjection || node instanceof Marker || node instanceof OntologyTerm) ){
- //Uh-oh! We found a lonely node that is not DataProjection or Marker!!!
- unlinkedNodeTypeSet.add(node.getClass().getSimpleName());
- }
- }
- }
-
- */
-
-
- //check if there is any patient with multiple treatment summaries
- log.info("Looking for patients with multiple treatment summaries");
- Set<Object> patientsWithMultipleSummaries = dataImportService.findPatientsWithMultipleSummaries();
-
- if(patientsWithMultipleSummaries.size() > 0){
- isDBValid = false;
-
- log.error("Found patients with multiple treatment summaries!");
- }
-
- //check if there is any platform without url
- log.info("Validating platforms");
- Set<Object> platformsWithoutUrl = dataImportService.findPlatformsWithoutUrl();
-
- if(platformsWithoutUrl.size() > 0){
-
- noWarnings = false;
- log.warn("Found Platforms without url: "+ platformsWithoutUrl.toString());
- }
-
-
-
- //TODO: Check if DataProjection nodes are there
- //TODO: Define additional db checks!
-
-
-
- //list errors
- if(unlinkedNodeTypeSet.size() > 0){
- noWarnings = false;
- log.warn("Node types found without a relationship: "+unlinkedNodeTypeSet.toString());
- log.warn("Get those nodes a relationship!");
- }
-
-
- //inform user
- if(noWarnings && isDBValid){
-
- log.info("*******************************************************");
- log.info("* Finished DB validation: VALID DATABASE, NO WARNINGS *");
- log.info("*******************************************************");
- }
- else if(!noWarnings){
- log.warn("********************************************************");
- log.warn("* Finished DB validation: VALID DATABASE WITH WARNINGS *");
- log.warn("********************************************************");
- }
- else if(!isDBValid){
-
- log.error("*******************************************************");
- log.error("* Finished DB validation: INVALID DATABASE *");
- log.error("*******************************************************");
- }
-
-
-
- }
-
-}
diff --git a/indexer/src/main/java/org/pdxfinder/reportmanager/ReportManager.java b/indexer/src/main/java/org/pdxfinder/reportmanager/ReportManager.java
index d0ac01d3b736b2a5b99905d7b5ff72f90f398af2..4d6d9bf1953a786643b8caf6b0f546aa4569c201 100644
--- a/indexer/src/main/java/org/pdxfinder/reportmanager/ReportManager.java
+++ b/indexer/src/main/java/org/pdxfinder/reportmanager/ReportManager.java
@@ -6,6 +6,8 @@ package org.pdxfinder.reportmanager;
import org.pdxfinder.services.reporting.LogEntity;
import org.pdxfinder.services.reporting.MarkerLogEntity;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.springframework.core.annotation.Order;
import org.springframework.stereotype.Component;
@@ -16,6 +18,8 @@ import java.util.List;
@Order(value = -80)
public class ReportManager {
+ private final static Logger log = LoggerFactory.getLogger(ReportManager.class);
+
private List<LogEntity> messages;
public ReportManager() {
@@ -32,18 +36,14 @@ public class ReportManager {
public void printMessages(String level){
- if(messages.size() == 0){
- System.out.println("There are no message entries in the Report Manager.");
+ if (messages.size() == 0) {
+ log.info("There are no message entries in the Report Manager.");
}
- else{
-
+ else {
for(LogEntity le: messages){
-
if(le.getType().equals(level) || level.equals("ALL")){
- System.out.println(le);
+ log.info(le.toString());
}
-
-
}
}
}
diff --git a/indexer/src/main/java/org/pdxfinder/utils/CbpTransformer.java b/indexer/src/main/java/org/pdxfinder/utils/CbpTransformer.java
index 6d05049b538eb4405248c014ff5b7db995960873..cae7d0c2ab94af2089203c7257395eb3743fb269 100644
--- a/indexer/src/main/java/org/pdxfinder/utils/CbpTransformer.java
+++ b/indexer/src/main/java/org/pdxfinder/utils/CbpTransformer.java
@@ -1,7 +1,10 @@
package org.pdxfinder.utils;
-import org.pdxfinder.dataexport.UniversalDataExporter;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.pdxfinder.TSV;
+import org.pdxfinder.dataexport.ExporterTemplates;
+import org.pdxfinder.dataexport.UniversalDataWriterServices;
import org.pdxfinder.graph.dao.Group;
import org.pdxfinder.services.OmicTransformationService;
import org.pdxfinder.services.UtilityService;
@@ -13,10 +16,7 @@ import java.io.File;
import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import java.util.concurrent.atomic.AtomicInteger;
@Service
@@ -26,56 +26,62 @@ public class CbpTransformer {
private UtilityService utilityService;
private OmicTransformationService omicTransformationService;
- private UniversalDataExporter universalDataExporter;
+ private UniversalDataWriterServices universalDataWriterUtilities;
- CbpTransformer(UtilityService utilityService, OmicTransformationService omicTransformationService, UniversalDataExporter universalDataExporter){
+ CbpTransformer(UtilityService utilityService, OmicTransformationService omicTransformationService,
+ UniversalDataWriterServices universalDataWriterUtilities){
this.utilityService = utilityService;
this.omicTransformationService = omicTransformationService;
- this.universalDataExporter = universalDataExporter;
+ this.universalDataWriterUtilities = universalDataWriterUtilities;
}
-
private static String notSpecified = "Not Specified";
private static String patientId = "patientId";
private static String sampleId = "sampleId";
- private static String entrezGeneId = "EntrezGeneId";
-
+ private static String entrezGeneId = "entrezGeneId";
+ private static String mutFileId = TSV.molecular_characterisation_type.mut.name();
+ private static String cnaFileId = TSV.molecular_characterisation_type.cna.name();
public enum cbioType {
MUT,
GISTIC
}
public void exportCBP(File exportDir,File templateDir, File pathToJson, cbioType dataType) throws IOException {
-
if (doesFileNotExist(exportDir) || doesFileNotExist(templateDir) || doesFileNotExist(pathToJson)) {
throw new IOException(String.format("A string argument passed to the exportCBP does not point to an existing file." +
"%s %n %s %n %s %n", exportDir, templateDir, pathToJson));
}
+ ExporterTemplates templates = new ExporterTemplates(templateDir.toString(), false);
Group jsonGroup = createGroupWithJsonsFilename(pathToJson.getAbsolutePath());
-
List<Map<String, Object>> listMapTable = utilityService.serializeJSONToMaps(pathToJson.getAbsolutePath());
- cbpMapsToSheetsByDataType(listMapTable, dataType);
-
- universalDataExporter.setDs(jsonGroup);
- universalDataExporter.setTemplateDir(templateDir.getAbsolutePath());
- universalDataExporter.export(exportDir.getAbsolutePath());
+ List<List<String>> cbioParsedData = cbpMapsToSheetsByDataType(listMapTable, dataType);
+
+ Path providerDir = Paths.get(exportDir + "/" + jsonGroup.getAbbreviation());
+ String exportUri = "";
+ if(dataType.equals(cbioType.MUT)) {
+ exportUri = String.format("%s/%s/%s_%s", providerDir,mutFileId,jsonGroup.getAbbreviation(),mutFileId);
+ Sheet mutationTemplate = templates.getTemplate(TSV.templateNames.mutation_template.name()).getSheetAt(0);
+ universalDataWriterUtilities.writeSingleOmicFileToTsv(exportUri,mutationTemplate, cbioParsedData);
+ } else if(dataType.equals(cbioType.GISTIC)){
+ exportUri = String.format("%s/%s/%s_%s", providerDir,cnaFileId,jsonGroup.getAbbreviation(),cnaFileId);
+ Sheet cnaTemplate = templates.getTemplate(TSV.templateNames.cna_template.name()).getSheetAt(0);
+ universalDataWriterUtilities.writeSingleOmicFileToTsv(exportUri,cnaTemplate, cbioParsedData);
+ }
}
- private void cbpMapsToSheetsByDataType(List<Map<String, Object>> listMapTable, cbioType dataType){
-
- List<List<String>> sheet;
+ private List<List<String>> cbpMapsToSheetsByDataType(List<Map<String, Object>> listMapTable, cbioType dataType){
+ List<List<String>> parsedCbioData = new ArrayList<>();
if(dataType.equals(cbioType.MUT)){
- sheet = cbpMutJsonMapsToSheet(listMapTable);
- universalDataExporter.setMutationSheetDataExport(sheet);
+ parsedCbioData = cbpMutJsonMapsToSheet(listMapTable);
}
- else if(dataType.equals(cbioType.GISTIC)) {
- sheet = cbpGisticsonMapsToSheet(listMapTable);
- universalDataExporter.setCnaSheetDataExport(sheet);
+ else if(dataType.equals(cbioType.GISTIC)) {
+ parsedCbioData = cbpGisticsonMapsToSheet(listMapTable);
}
+ return parsedCbioData;
}
private List<List<String>> cbpMutJsonMapsToSheet(List<Map<String, Object>> jsonMap){
AtomicInteger rowCount = new AtomicInteger();
- List<List<String>> sheet = new ArrayList<>();
+ List<List<String>> cbioData = new ArrayList<>();
jsonMap.forEach(f -> {
try {
rowCount.incrementAndGet();
@@ -85,28 +91,30 @@ public class CbpTransformer {
row.add(notSpecified);
row.add(notSpecified);
row.add(notSpecified);
- row.add(omicTransformationService.ncbiGeneIdToHgncSymbol(String.valueOf(f.get(entrezGeneId))));
- addBlanksToList(row, 9);
+ row.add(parseHugoGeneDetails((LinkedHashMap<Object, Object>) f.get("gene")));
+ addBlanksToList(row, 7);
+ row.add(String.valueOf(f.getOrDefault("tumorAltCount", "")));
+ row.add("");
row.add(f.get("chr").toString());
row.add(f.get("startPosition").toString());
row.add(f.get("referenceAllele").toString());
row.add(f.get("variantAllele").toString());
addBlanksToList(row, 6);
row.add(f.get("ncbiBuild").toString());
- row.add("");
- sheet.add(row);
+ cbioData.add(row);
}catch(NullPointerException e){
log.error(String.format("Missing value in Json Mut map. Skipping Json Map %d", rowCount.get()));
}
});
- return sheet;
+ return cbioData;
}
private List<List<String>> cbpGisticsonMapsToSheet(List<Map<String,Object>> jsonMap){
+ List<List<String>> cbioData = new ArrayList<>();
- List<List<String>> sheet = new ArrayList<>();
jsonMap.forEach(f -> {
+ try {
List<String> row = new LinkedList<>();
row.add(f.get(patientId).toString());
row.add(f.get(sampleId).toString());
@@ -114,15 +122,27 @@ public class CbpTransformer {
row.add(notSpecified);
row.add(notSpecified);
addBlanksToList(row,3);
- row.add(omicTransformationService.ncbiGeneIdToHgncSymbol(String.valueOf(f.get(entrezGeneId))));
- row.add(f.get(entrezGeneId).toString());
- addBlanksToList(row, 6);
+ row.add(parseHugoGeneDetails((LinkedHashMap<Object, Object>) f.get("gene")));
+ row.add("");
+ row.add(f.getOrDefault(entrezGeneId, "").toString());
+ addBlanksToList(row, 5);
row.add(f.get("alteration").toString());
addBlanksToList(row, 3);
-
- sheet.add(row);
+ cbioData.add(row);
+ }catch(NullPointerException e){
+ log.error("Missing value in Json gistic map. Skipping Json Map row");
+ }
});
- return sheet;
+ return cbioData;
+ }
+
+ private String parseHugoGeneDetails(LinkedHashMap<Object, Object> geneDetails){
+ String hugoGene = (String) geneDetails.getOrDefault("hugoGeneSymbol", "");
+ if (hugoGene.isEmpty()) {
+ hugoGene = omicTransformationService
+ .ncbiGeneIdToHgncSymbol((String) geneDetails.getOrDefault(entrezGeneId,""));
+ }
+ return hugoGene;
}
private Group createGroupWithJsonsFilename(String pathToJson) {
diff --git a/indexer/src/main/java/org/pdxfinder/utils/CreateLocalFeeds.java b/indexer/src/main/java/org/pdxfinder/utils/CreateLocalFeeds.java
index bf800d821709611909b36297bd5e5913c17b0108..f71e7d7640405e97dba2ed683497b9755478f84e 100644
--- a/indexer/src/main/java/org/pdxfinder/utils/CreateLocalFeeds.java
+++ b/indexer/src/main/java/org/pdxfinder/utils/CreateLocalFeeds.java
@@ -1,11 +1,8 @@
package org.pdxfinder.utils;
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
import joptsimple.OptionParser;
import joptsimple.OptionSet;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
+import com.github.openjson.*;
import org.pdxfinder.services.TransformerService;
import org.pdxfinder.services.UtilityService;
import org.slf4j.Logger;
@@ -13,14 +10,12 @@ import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.CommandLineRunner;
+import org.springframework.context.annotation.PropertySource;
import org.springframework.core.annotation.Order;
import org.springframework.stereotype.Component;
import java.io.*;
-import java.nio.charset.Charset;
-import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
/**
@@ -44,6 +39,7 @@ import java.util.Map;
* Created by csaba on 08/10/2018.
*/
@Component
+@PropertySource("classpath:datafeed.properties")
@Order(value = 0)
public class CreateLocalFeeds implements CommandLineRunner {
diff --git a/indexer/src/main/resources/application.properties b/indexer/src/main/resources/application.properties
index 370a66a47a869dfef50e51b3741288505af2de81..a080aa66c838c2c5a9f0dfcc18dfa7fe515212bb 100644
--- a/indexer/src/main/resources/application.properties
+++ b/indexer/src/main/resources/application.properties
@@ -1,108 +1,30 @@
-cd # Disable spring web components from loading
-spring.main.web-environment=false
-
-# Default logging level to INFO
-logging.level.=INFO
-
-# Tone down Spring extra-chatty components
-logging.level.org.springframework.boot.autoconfigure.logging=ERROR
-logging.level.org.springframework.data.neo4j.mapping.Neo4jPersistentProperty=ERROR
-logging.level.org.neo4j.ogm.drivers.http.request.HttpRequest=ERROR
-logging.level.org.neo4j.ogm.drivers.embedded.request.EmbeddedRequest=ERROR
-#spring.data.neo4j.username=neo4j
-#spring.data.neo4j.password=neo5j
-spring.data.neo4j.embedded.enabled=true
-spring.data.neo4j.uri=file://${user.home}/Documents/pdx.graphdb
-
+# Logging
+logging.path=log/
+logging.group.graphdb=org.neo4j, org.springframework.data.neo4j
+logging.level.root=info
+logging.level.graphdb=error
+logging.pattern.console=%d{HH:mm:ss::SSS} %highlight(%-5level) %clr(%-40.40C){cyan} : %m%n%wEx
+
+# Local data location defaults
+data-dir=
+pdxfinder.root.dir=
db-cache-dir=${user.home}/Documents/cache
db-refresh=false
-
-# NON-GRAPH Datasource Config properties
-spring.datasource.url=jdbc:h2:${data-dir}/h2-db/data;AUTO_SERVER=true;DB_CLOSE_ON_EXIT=FALSE
-spring.datasource.username=neo4j
-spring.datasource.password=neo5j
-spring.datasource.driver-class-name=org.h2.Driver
-spring.h2.console.settings.trace=true
-spring.jpa.hibernate.ddl-auto=update
-
-
-jaxpdx.file=
-jaxpdx.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?allModels=gimme
-jaxpdx.variation.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelVariation=
-jaxpdx.histology.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelHistology=
-jaxpdx.cna.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelCNV=
-jaxpdx.rnaseq.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelExpression=
-# quit after loading this many variants for a model (one model has ~63000)
-# -1 will load all, 0 will load none
-jaxpdx.variation.max=-1
-
-# This is unlikely to change for years, but we might want to look at patch numbers?
-jaxpdx.ref.assembly=GRCh38
-
-
-pdmrpdx.file=pdxinfo.json
-pdmrpdx.url=
-pdmrpdx.variation.url=
-pdmrpdx.histology.url=
-pdmrpdx.variation.max=-1
-pdmrpdx.ref.assembly=
-pdmrpdx.mutations.file
-
-#For MD Anderson
-mdapdx.url=
-mda.urls=
-
-#For Huntsman Cancer Institute
-hcipdx.url=
-hci.ihc.file=
-
-
-#For WISTAR
-wistarpdx.url=
-
-#WUSTL
-wustl.urls=
-
-
-#New IRCC
-irccpdx.url=
-irccpdx.variation.url=
-irccpdx.variation.max =-1
-
-
ncitpredef.file=
-
-
-
-#mappings file containing diagnosis to NCIT links
+data.directory=
+provider=
mappings.diagnosis.file=file.json
-
-#mappings file containing diagnosis to NCIT links
mappings.diagnosis.file2=file.json
-
-#a list of template file uri separated with a comma
-universal.template.files=
-
-# root directory for local data feeds
-data-dir=
-pdxfinder.root.dir=
-
-# local directory for log files
-pdxfinder.log.dir=${data-dir}
-
mappings.mappedTermUrl=http://localhost/data/mappings.json
-data.directory=
+# Graph database config
+spring.data.neo4j.uri=file://${user.home}/Documents/pdx.graphdb
-provider=
+# Relational database config
+h2.datasource.jdbc-url=jdbc:h2:${data-dir}/h2-db/data;AUTO_SERVER=true;DB_CLOSE_ON_EXIT=FALSE
+h2.datasource.username=neo4j
+h2.datasource.password=neo5j
+h2.datasource.driver-class-name=org.h2.Driver
+spring.h2.console.settings.trace=true
+spring.jpa.hibernate.ddl-auto=update
-# Email Notification Configurations
-#spring.mail.default-encoding = UTF-8
-#spring.mail.host = mail.pdxinder.org
-#spring.mail.username =
-#spring.mail.password =
-#spring.mail.port: 26
-#spring.mail.properties.mail.smtp.auth = true
-#spring.mail.properties.mail.smtp.auth.starttls.enable = true
-#spring.mail.protocol = smtp
-#spring.mail.test-connection = false
\ No newline at end of file
diff --git a/indexer/src/main/resources/datafeed.properties b/indexer/src/main/resources/datafeed.properties
new file mode 100644
index 0000000000000000000000000000000000000000..b36adaefc84464014db8680fad2355b854850b76
--- /dev/null
+++ b/indexer/src/main/resources/datafeed.properties
@@ -0,0 +1,33 @@
+# Local feed constants
+
+jaxpdx.ref.assembly=GRCh38
+jaxpdx.file=
+jaxpdx.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?allModels=gimme
+jaxpdx.variation.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelVariation=
+jaxpdx.histology.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelHistology=
+jaxpdx.cna.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelCNV=
+jaxpdx.rnaseq.url=http://tumor.informatics.jax.org/PDXInfo/JSONData.do?modelExpression=
+# -1 will load all, 0 will load none
+jaxpdx.variation.max=-1
+
+pdmrpdx.file=pdxinfo.json
+pdmrpdx.url=
+pdmrpdx.variation.url=
+pdmrpdx.histology.url=
+pdmrpdx.variation.max=-1
+pdmrpdx.ref.assembly=
+pdmrpdx.mutations.file
+
+mdapdx.url=
+mda.urls=
+
+hcipdx.url=
+hci.ihc.file=
+
+wistarpdx.url=
+
+wustl.urls=
+
+irccpdx.url=
+irccpdx.variation.url=
+irccpdx.variation.max =-1
\ No newline at end of file
diff --git a/indexer/src/main/resources/loader.properties b/indexer/src/main/resources/loader.properties
index 5aa6ddc0066615a2a82e96190550f30b50fd1f2c..a5705949b452945407af232b916b017b6e88a896 100644
--- a/indexer/src/main/resources/loader.properties
+++ b/indexer/src/main/resources/loader.properties
@@ -15,7 +15,7 @@ hci.projectGroup = PDXNet
hci.nsgBsName = NOD scid gamma
hci.nsgBsSymbol = NOD.Cg-Prkdc<sup>scid</sup> Il2rg<sup>tm1Wjl</sup>/SzJ
-hci.nsgBsDesc
+hci.nsgBsDesc =
hci.nsgbsURL = http://jax.org/strain/005557
hci.nsBsName = NOD scid
@@ -117,7 +117,7 @@ ircc.projectGroup = EurOPDX
ircc.nsgBsName = NOD scid gamma
ircc.nsgBsSymbol = NOD.Cg-Prkdc<sup>scid</sup> Il2rg<sup>tm1Wjl</sup>/SzJ
-ircc.nsgBsDesc
+ircc.nsgBsDesc =
ircc.nsgbsURL = http://jax.org/strain/005557
ircc.nsBsName =
ircc.nsBsSymbol =
diff --git a/indexer/src/main/resources/logback.xml b/indexer/src/main/resources/logback.xml
new file mode 100644
index 0000000000000000000000000000000000000000..92a6d2c5916efc5d7bdf10306157388d2920ad66
--- /dev/null
+++ b/indexer/src/main/resources/logback.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration scan="true">
+
+ <!--include configuration from spring boot's application properties-->
+ <include resource="org/springframework/boot/logging/logback/base.xml"/>
+ <!--suppress logback config logging-->
+ <statusListener class="ch.qos.logback.core.status.NopStatusListener" />
+
+ <appender name="Validator" class="ch.qos.logback.core.FileAppender">
+ <file>log/validation_errors.html</file>
+ <encoder class="ch.qos.logback.core.encoder.LayoutWrappingEncoder">
+ <layout class="ch.qos.logback.classic.html.HTMLLayout">
+ <pattern>%level%msg</pattern>
+ <cssBuilder class="ch.qos.logback.classic.html.UrlCssBuilder">
+ <url>../web/src/main/resources/static/css/validationLog.css</url>
+ </cssBuilder>
+ </layout>
+ </encoder>
+ </appender>
+
+ <appender name="RollingLog" class="ch.qos.logback.core.rolling.RollingFileAppender">
+ <file>log/debug.log</file>
+ <encoder class="ch.qos.logback.classic.encoder.PatternLayoutEncoder">
+ <Pattern>%d{dd-MM-yyyy HH:mm:ss.SSS} [%thread] %-5level %logger{36}.%M - %msg%n</Pattern>
+ </encoder>
+ <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+ <fileNamePattern>log/archived/log_%d{dd-MM-yyyy}.log</fileNamePattern>
+ <totalSizeCap>100MB</totalSizeCap>
+ </rollingPolicy>
+ </appender>
+
+ <root level="debug">
+ <appender-ref ref="RollingLog" />
+ </root>
+
+ <logger name="org.pdxfinder.dataloaders.updog.tablevalidation.Validator" level="ERROR">
+ <appender-ref ref="Validator" />
+ </logger>
+
+
+</configuration>
diff --git a/indexer/src/test/java/org/pdxfinder/BaseTest.java b/indexer/src/test/java/org/pdxfinder/BaseTest.java
index 3934a36986a655a36f424a6178f53cda2ab2f44b..684a08a842f6afe0fa80bdd87574754f36492378 100644
--- a/indexer/src/test/java/org/pdxfinder/BaseTest.java
+++ b/indexer/src/test/java/org/pdxfinder/BaseTest.java
@@ -15,7 +15,7 @@ import org.springframework.transaction.annotation.Transactional;
@RunWith(SpringRunner.class)
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.NONE)
@ContextConfiguration(classes = {TestConfig.class})
-@TestPropertySource(locations = {"classpath:ogm.properties"})
+@TestPropertySource(locations = {"classpath:application.properties"})
@Transactional
@Ignore
public class BaseTest {
diff --git a/indexer/src/test/java/org/pdxfinder/TestConfig.java b/indexer/src/test/java/org/pdxfinder/TestConfig.java
index fa46ff413bcef433dcebe5372f381376e33b123c..15b78f7bc8004ee83df9020fa887d855547872b7 100755
--- a/indexer/src/test/java/org/pdxfinder/TestConfig.java
+++ b/indexer/src/test/java/org/pdxfinder/TestConfig.java
@@ -9,12 +9,23 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
-@EnableNeo4jRepositories("org.pdxfinder.graph.repositories")
+@EnableNeo4jRepositories(value = "org.pdxfinder.graph.repositories")
public class TestConfig {
+/*
+ @Bean
+ public SessionFactory sessionFactory() {
+ return new SessionFactory("org.pdxfinder");
+ }
+
+*/
+ @Bean
+ public org.neo4j.ogm.config.Configuration getConfiguration() {
+ return new org.neo4j.ogm.config.Configuration.Builder().build();
+ }
@Bean
public SessionFactory sessionFactory() {
- return new SessionFactory("org.pdxfinder.*");
+ return new SessionFactory(getConfiguration(), "org.pdxfinder.*");
}
@Bean
@@ -23,3 +34,4 @@ public class TestConfig {
}
}
+
diff --git a/indexer/src/test/java/org/pdxfinder/commandline/FinderCommandLineTest.java b/indexer/src/test/java/org/pdxfinder/commandline/FinderCommandLineTest.java
index e09e256dbb7335b0559d440e06227bb9e6c79f5d..a56fb8bbd3908a3436ccf13c2cb1da6d300e0355 100644
--- a/indexer/src/test/java/org/pdxfinder/commandline/FinderCommandLineTest.java
+++ b/indexer/src/test/java/org/pdxfinder/commandline/FinderCommandLineTest.java
@@ -25,57 +25,38 @@ public class FinderCommandLineTest extends BaseTest {
@Mock private FinderTransformer finderTransformer;
@InjectMocks private FinderCommandLine.Transform transform;
- @Mock private FinderExporter finderExporter;
- @InjectMocks private FinderCommandLine.Export export;
-
@Before
public void setUp() {
MockitoAnnotations.initMocks(this);
doNothing().when(this.finderLoader).run(
- anyListOf(DataProvider.class),
- any(File.class),
- anyBoolean(), anyBoolean(), anyBoolean(), anyBoolean()
+ anyListOf(DataProvider.class),
+ any(File.class),
+ anyBoolean(), anyBoolean(), anyBoolean(), anyBoolean()
);
}
- /*
@Test public void givenLoadOnlyMinimal_LoaderIsCalled() {
- String[] args = {"--only=Test_Minimal", "--data-dir=path/", "--keep-db"};
+ String[] args = {"--only=Test_Minimal", "--data-dir=path/"};
int exitCode = new CommandLine(load).execute(args);
assertEquals(0, exitCode);
verify(this.finderLoader).run(
- anyListOf(DataProvider.class),
- any(File.class),
- anyBoolean(), anyBoolean(), anyBoolean(), anyBoolean()
+ anyList(),
+ any(File.class),
+ anyBoolean(), anyBoolean(), anyBoolean(), anyBoolean()
);
verifyNoMoreInteractions(this.finderLoader);
}
@Test public void givenLoadAll_callsLoader() {
- String[] args = {"--group=All", "--data-dir=path/", "--keep-db"};
+ String[] args = {"--group=All", "--data-dir=path/"};
int exitCode = new CommandLine(load).execute(args);
assertEquals(0, exitCode);
verify(this.finderLoader).run(
- anyListOf(DataProvider.class),
- any(File.class),
- anyBoolean(), anyBoolean(), anyBoolean(), anyBoolean()
- );
- verifyNoMoreInteractions(this.finderLoader);
- }
-*/
- @Test public void givenTransform_When_exportAllisCalled_Then_callsTransformer() throws IOException {
- String[] args = {"--data-dir=path/", "-c=MUT"};
- int exitCode = new CommandLine(transform).execute(args);
- assertEquals(0, exitCode);
- verify(this.finderTransformer).run(
+ anyList(),
any(File.class),
- any(),
- any(),
- any(File.class),
- any(),
- any()
+ anyBoolean(), anyBoolean(), anyBoolean(), anyBoolean()
);
- verifyNoMoreInteractions(this.finderTransformer);
+ verifyNoMoreInteractions(this.finderLoader);
}
@Test public void givenTransform_When_cbioPortalIsCalled_Then_callsTransformer() throws IOException {
@@ -93,7 +74,6 @@ public class FinderCommandLineTest extends BaseTest {
verifyNoMoreInteractions(this.finderTransformer);
}
-
@Test public void givenTransform_WhenTwoExclusiveArgumentsArepassed_Then_ReturnNonZeroExit() {
String[] args = {"--data-dir=path/", "--export=test", "--all"};
int exitCode = new CommandLine(transform).execute(args);
diff --git a/indexer/src/test/java/org/pdxfinder/commandline/FinderExporterTest.java b/indexer/src/test/java/org/pdxfinder/commandline/FinderExporterTest.java
index 2cf9d73944dd4f82704af9fda4e04910a3f9281e..75fd924f4f4f0a31d17c6dfc19f00b767dbb97b8 100644
--- a/indexer/src/test/java/org/pdxfinder/commandline/FinderExporterTest.java
+++ b/indexer/src/test/java/org/pdxfinder/commandline/FinderExporterTest.java
@@ -4,11 +4,12 @@ import org.junit.Before;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TemporaryFolder;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.Spy;
import org.pdxfinder.BaseTest;
+import org.pdxfinder.dataexport.UniversalDataExtractionServices;
import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.springframework.boot.test.mock.mockito.MockBean;
-import org.springframework.boot.test.mock.mockito.SpyBean;
import java.io.File;
import java.io.IOException;
@@ -23,33 +24,47 @@ public class FinderExporterTest extends BaseTest {
public TemporaryFolder folder = new TemporaryFolder();
private File tempFile;
- @MockBean
- private UtilityService utilityService;
- @MockBean
+ @Mock
private DataImportService dataImportService;
+ @Mock
+ private UniversalDataExtractionServices universalDataExtractionUtilities;
- @SpyBean
- FinderExporter finderExporter;
+ @Spy
+ @InjectMocks
+ private FinderExporter finderExporter;
@Before public void init() throws IOException {
tempFile = folder.newFile();
}
@Test
- public void Given_loadAllisTrue_When_runIsCalled_Then_CallExportAll() throws IOException {
+ public void given_loadAllisTrue_When_runIsCalled_Then_CallExportAll() throws IOException {
finderExporter.setDefaultDirectory(tempFile.getAbsolutePath());
- finderExporter.run(null, null, true);
- verify(finderExporter).exportAllGroups(any(File.class)) ;
+ finderExporter.run(null, null, true,false );
+ verify(finderExporter).exportAllGroups(any(File.class), eq(false)) ;
}
@Test
- public void Given_provider_when_runIsCalled_Then_CallExport() throws IOException {
+ public void given_provider_when_runIsCalled_Then_CallExport() throws IOException {
finderExporter.setDefaultDirectory(tempFile.getAbsolutePath());
- finderExporter.run(null, "test", false);
+ finderExporter.run(null, "test", false,false);
verify(finderExporter).export(
eq(tempFile.getAbsoluteFile()),
- eq("test")
+ eq("test"),
+ eq(false)
);
}
+ @Test
+ public void given_WithSingleProviderAndharmonizedIsTrue_when_runisCalled_Then_CallExport() throws IOException {
+ finderExporter.setDefaultDirectory(tempFile.getAbsolutePath());
+ finderExporter.run(null, "test", false, true);
+ verify(finderExporter).export(
+ eq(tempFile.getAbsoluteFile()),
+ eq("test"),
+ eq(true)
+ );
+
+ }
+
}
diff --git a/indexer/src/test/java/org/pdxfinder/commandline/FinderLoaderTest.java b/indexer/src/test/java/org/pdxfinder/commandline/FinderLoaderTest.java
index b08241f560643e7e297182db82bdc6483f228410..397e46cc6fe175c91d0cd6227a55c5cc8c5fa1b2 100644
--- a/indexer/src/test/java/org/pdxfinder/commandline/FinderLoaderTest.java
+++ b/indexer/src/test/java/org/pdxfinder/commandline/FinderLoaderTest.java
@@ -10,27 +10,24 @@ import org.pdxfinder.BaseTest;
import org.pdxfinder.LoadDiseaseOntology;
import org.pdxfinder.dataloaders.LoadJAXData;
import org.pdxfinder.dataloaders.updog.Updog;
-import org.pdxfinder.services.constants.DataProvider;
-import org.pdxfinder.dataloaders.LoadAdditionalDatasets;
import org.pdxfinder.mapping.LinkSamplesToNCITTerms;
import org.pdxfinder.mapping.LinkTreatmentsToNCITTerms;
import org.pdxfinder.postload.CreateDataProjections;
import org.pdxfinder.postload.SetDataVisibility;
-import org.pdxfinder.postload.ValidateDB;
import org.pdxfinder.services.DataImportService;
+import org.pdxfinder.services.constants.DataProvider;
import org.pdxfinder.services.constants.DataUrl;
import org.pdxfinder.services.loader.envload.LoadMarkers;
import org.pdxfinder.services.loader.envload.LoadNCIT;
import org.pdxfinder.services.loader.envload.LoadNCITDrugs;
-import java.nio.file.Path;
import java.io.File;
+import java.nio.file.Path;
import java.util.Arrays;
import java.util.Collections;
import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.*;
-import static org.mockito.Mockito.verifyNoMoreInteractions;
public class FinderLoaderTest extends BaseTest {
@@ -46,12 +43,10 @@ public class FinderLoaderTest extends BaseTest {
private DataProvider updogDataProvider;
private static boolean NO_VALIDATION_ONLY = false;
- @Mock private LoadAdditionalDatasets loadAdditionalDatasets;
@Mock private LinkSamplesToNCITTerms linkSamplesToNCITTerms;
@Mock private LinkTreatmentsToNCITTerms linkTreatmentsToNCITTerms;
@Mock private CreateDataProjections createDataProjections;
@Mock private SetDataVisibility setDataVisibility;
- @Mock private ValidateDB validateDB;
@Mock private File dataDirectory;
@Spy
@@ -68,12 +63,10 @@ public class FinderLoaderTest extends BaseTest {
doNothing().when(this.loadMarkers).loadGenes(anyString());
doNothing().when(this.loadNCIT).loadOntology(anyString());
doNothing().when(this.loadNCITDrugs).loadRegimens();
- doNothing().when(this.loadAdditionalDatasets).run();
doNothing().when(this.linkSamplesToNCITTerms).run();
doNothing().when(this.linkTreatmentsToNCITTerms).run();
doNothing().when(this.createDataProjections).run();
doNothing().when(this.setDataVisibility).run();
- doNothing().when(this.validateDB).run();
doNothing().when(this.updog).run(any(Path.class), anyString(), anyBoolean());
this.dataProvider = DataProvider.JAX;
diff --git a/indexer/src/test/java/org/pdxfinder/commandline/FinderTransformerTest.java b/indexer/src/test/java/org/pdxfinder/commandline/FinderTransformerTest.java
index 269cd22820e4fb4a9bdc119bea5a8891ed1c7803..6da7986fd0dc8dc4c498686a6346d8340867aa8b 100644
--- a/indexer/src/test/java/org/pdxfinder/commandline/FinderTransformerTest.java
+++ b/indexer/src/test/java/org/pdxfinder/commandline/FinderTransformerTest.java
@@ -1,9 +1,6 @@
package org.pdxfinder.commandline;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Rule;
-import org.junit.Test;
+import org.junit.*;
import org.junit.rules.TemporaryFolder;
import org.mockito.*;
import org.pdxfinder.BaseTest;
@@ -14,7 +11,6 @@ import org.springframework.boot.test.mock.mockito.MockBean;
import java.io.File;
import java.io.IOException;
-import static org.mockito.Matchers.*;
import static org.mockito.Mockito.*;
public class FinderTransformerTest extends BaseTest {
diff --git a/indexer/src/test/java/org/pdxfinder/dataexport/CbpTransformerTests.java b/indexer/src/test/java/org/pdxfinder/dataexport/CbpTransformerTests.java
index 6be033b079209d67b44c602936368a3dd469716d..6710fbd2dcf29870806e3992cf19419ea21af9af 100644
--- a/indexer/src/test/java/org/pdxfinder/dataexport/CbpTransformerTests.java
+++ b/indexer/src/test/java/org/pdxfinder/dataexport/CbpTransformerTests.java
@@ -1,27 +1,33 @@
package org.pdxfinder.dataexport;
-import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-import org.junit.*;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
import org.junit.rules.TemporaryFolder;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
import org.mockito.InjectMocks;
import org.mockito.Mock;
-import org.mockito.Mockito;
import org.pdxfinder.BaseTest;
+import org.pdxfinder.TSV;
import org.pdxfinder.services.OmicTransformationService;
import org.pdxfinder.services.UtilityService;
import org.pdxfinder.utils.CbpTransformer;
import org.pdxfinder.utils.CbpTransformer.cbioType;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.when;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Paths;
+import java.util.*;
-import java.io.*;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import static org.mockito.Matchers.*;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
public class CbpTransformerTests extends BaseTest {
@@ -34,16 +40,18 @@ public class CbpTransformerTests extends BaseTest {
@Mock
private OmicTransformationService omicTransformationService;
@Mock
- private UniversalDataExporter universalDataExporter;
+ private UniversalDataWriterServices universalDataWriterUtilities;
+ @Captor
+ private ArgumentCaptor<ArrayList<List<String>>> captor;
@InjectMocks
private CbpTransformer cbpTransformer;
private File jsonDummy;
private File exportFolder;
- private File templatesFolder;
private cbioType mutDataType;
private cbioType gisticDataType;
+ private String templatesFolder;
@Before
public void init() throws IOException {
@@ -54,30 +62,33 @@ public class CbpTransformerTests extends BaseTest {
TemporaryFolder rootFolder = new TemporaryFolder();
rootFolder.create();
exportFolder = rootFolder.newFolder();
- templatesFolder = rootFolder.newFolder();
- createMockTemplate();
+
+ TemporaryFolder templateRoot = new TemporaryFolder();
+ templateRoot.create();
+ templatesFolder = templateRoot.getRoot().getAbsolutePath();
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.metadata_template.fileName, 7);
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.sampleplatform_template.fileName, 2);
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.mutation_template.fileName, 2);
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.cna_template.fileName, 2);
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.cytogenetics_template.fileName, 2);
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.expression_template.fileName, 2);
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.drugdosing_template.fileName, 2);
+ writeWorkbook(templatesFolder + "/" + TSV.templateNames.patienttreatment_template.fileName, 2);
}
- public void createMockTemplate() throws IOException {
+ private void writeWorkbook(String directory, int sheetCount) throws IOException {
+ OutputStream out = new FileOutputStream(directory);
XSSFWorkbook workbook = new XSSFWorkbook();
- Sheet omic = workbook.createSheet("Test");
- Row headers = omic.createRow(0);
- for(int i = 0; i < 25; i++){
- headers.createCell(i).setCellValue(i );
+ for (int i = 0; i < sheetCount; i++) {
+ workbook.createSheet();
}
-
- FileOutputStream out = new FileOutputStream(new File(templatesFolder.getAbsoluteFile() + "/mutation_template.xlsx"));
workbook.write(out);
- out.close();
-
- FileOutputStream cnaOut = new FileOutputStream(new File(templatesFolder.getAbsoluteFile() + "/cna_template.xlsx"));
- workbook.write(cnaOut);
- out.close();
}
+
@Test(expected = IOException.class)
public void Given_nonExistentJsonFilesArePassed_WhenExportCBPisCalled_Then_throwIOexception() throws IOException {
- cbpTransformer.exportCBP(exportFolder, templatesFolder, new File("/tmp/not/existing"), mutDataType);
+ cbpTransformer.exportCBP(exportFolder, new File(templatesFolder), new File("/tmp/not/existing"), mutDataType);
}
@Test(expected = IOException.class)
@@ -87,9 +98,11 @@ public class CbpTransformerTests extends BaseTest {
@Test
public void Give_JsonArrayAndValidImportDirectory_When_exportsIsCalled__ThenNewMutDirExists() throws IOException {
+ String mut = TSV.molecular_characterisation_type.mut.mcType;
+ String mutFileId = TSV.molecular_characterisation_type.mut.name();
String ns = "Not Specified";
- List<Map<String, Object>> dummyListMap = new ArrayList<Map<String,Object >>();
+ List<Map<String, Object>> dummyListMap = new ArrayList<>();
Map<String, Object> dummyMap= new HashMap<>();
dummyMap.put("patientId","1");
dummyMap.put("sampleId","2");
@@ -104,10 +117,47 @@ public class CbpTransformerTests extends BaseTest {
when(utilityService.serializeJSONToMaps(jsonDummy.getAbsolutePath()))
.thenReturn(dummyListMap);
+ cbpTransformer.exportCBP(exportFolder, new File(templatesFolder), jsonDummy, mutDataType);
+
+ String filename = Paths.get(jsonDummy.getAbsolutePath()).getFileName().toString();
+ String expectedExportURI = String.format("%s/%s/%s/%s_%s",exportFolder, filename,"mut",filename, mutFileId);
+ verify(universalDataWriterUtilities).writeSingleOmicFileToTsv(eq(expectedExportURI), any(Sheet.class), anyList());
+ }
+
+ @Test
+ public void Give_nestedGeneInformationInJason_When_cbioportalExporterIsCalled_ThenFileContainsGeneInformation() throws IOException {
+ String cnaFileId = TSV.molecular_characterisation_type.cna.name();
+ String geneSymbol = "CELSR1";
+
+ Map<String, Object> geneMap = new LinkedHashMap<>();
+ geneMap.put("entrezGeneId",9620);
+ geneMap.put("hugoGeneSymbol", geneSymbol);
+ geneMap.put("type", "protien_coding");
+
+ List<Map<String, Object>> dummyListMap = new ArrayList<>();
+ Map<String, Object> dummyMap= new HashMap<>();
+ dummyMap.put("patientId","1");
+ dummyMap.put("sampleId","2");
+ dummyMap.put("entrezGeneId","00001");
+ dummyMap.put("chr","3");
+ dummyMap.put("gene", geneMap);
+ dummyMap.put("startPosition","4");
+ dummyMap.put("referenceAllele","5");
+ dummyMap.put("alteration","2");
+ dummyMap.put("ncbiBuild","7");
+ dummyListMap.add(dummyMap);
+
+ when(utilityService.serializeJSONToMaps(jsonDummy.getAbsolutePath()))
+ .thenReturn(dummyListMap);
+
+ cbpTransformer.exportCBP(exportFolder, new File(templatesFolder), jsonDummy, gisticDataType);
- cbpTransformer.exportCBP(exportFolder, templatesFolder, jsonDummy, mutDataType);
+ String filename = Paths.get(jsonDummy.getAbsolutePath()).getFileName().toString();
+ String expectedExportURI = String.format("%s/%s/%s/%s_%s",exportFolder, filename,"cna",filename, cnaFileId);
+ verify(universalDataWriterUtilities).writeSingleOmicFileToTsv(eq(expectedExportURI), any(Sheet.class), captor.capture());
- Mockito.verify(universalDataExporter, times(1)).export(exportFolder.getAbsolutePath());
+ String geneName = captor.getValue().get(0).get(8);
+ Assert.assertEquals(geneName, geneSymbol);
}
}
diff --git a/indexer/src/test/java/org/pdxfinder/dataexport/DataExportTest.java b/indexer/src/test/java/org/pdxfinder/dataexport/DataExportTest.java
deleted file mode 100644
index a9d11baa4426ae637703a9e343e8aa003e228f86..0000000000000000000000000000000000000000
--- a/indexer/src/test/java/org/pdxfinder/dataexport/DataExportTest.java
+++ /dev/null
@@ -1,368 +0,0 @@
-package org.pdxfinder.dataexport;
-
-import org.apache.poi.ss.usermodel.*;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.InjectMocks;
-import org.mockito.Mock;
-import org.pdxfinder.BaseTest;
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.services.DataImportService;;
-
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-import static org.mockito.Mockito.when;
-
-public class DataExportTest extends BaseTest {
-
- @Mock
- private DataImportService dataImportService;
-
- @InjectMocks
- protected UniversalDataExporter universalDataExporter;
-
- Group providerGroup;
-
- private static final String ncbiId = "XR_929159.2";
- private static final String biotype = "protien_coding";
- private static final String codingSequenceChange = "3154G>A";
- private static final String variantClass = "SNV";
-
- @Before
- public void setUp() {
- providerGroup = Group.createProviderGroup("TestGroup", "TG", "", "Academia", "Bob", "Bob's page");
- }
-
- @Test
- public void Given_PatientAndProvider_When_GetPatientSheetIsCalled_Then_PatientDataIsInRowOne() {
-
- when(dataImportService.findPatientsByGroup(providerGroup))
- .thenReturn(getPatientListForTest());
-
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initPatientData();
- List<List<String>> patientData = universalDataExporter.getPatientSheetDataExport();
-
- Assert.assertEquals("p123", patientData.get(0).get(0));
- }
-
- @Test
- public void Given_PatientAndModelAndSample_When_PatientTumorSheetIsCalled_Then_PatientDataIsInRowOne(){
-
- Patient patient = new Patient("p123", "male", "", "", providerGroup);
- PatientSnapshot patientSnapshot = new PatientSnapshot();
- patientSnapshot.setAgeAtCollection("65");
- Sample sample = new Sample();
- sample.setSourceSampleId("s123");
-
- TumorType tt = new TumorType("Metastatic");
- Tissue ot = new Tissue("Brain");
- Tissue ss = new Tissue("Brain");
-
- sample.setType(tt);
- sample.setOriginTissue(ot);
- sample.setSampleSite(ss);
-
- patientSnapshot.addSample(sample);
- patient.addSnapshot(patientSnapshot);
-
- List<Patient> patientList = new ArrayList<>();
- patientList.add(patient);
-
- ModelCreation modelCreation = new ModelCreation();
- modelCreation.setSourcePdxId("m123");
-
- when(dataImportService.findPatientTumorAtCollectionDataByDS(providerGroup))
- .thenReturn(patientList);
- when(dataImportService.findModelBySample(sample))
- .thenReturn(modelCreation);
-
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initPatientTumorAtCollection();
-
- List<List<String>> patientTumorAtCollection = universalDataExporter.getPatientTumorSheetDataExport();
- Assert.assertEquals("p123", patientTumorAtCollection.get(0).get(0));
- }
-
- @Test
- public void Given_ModelWithDetails_When_GetModelDetailsIsCalled_Then_ModelDataIsInRowOne(){
-
- when( dataImportService.findModelsWithSpecimensAndQAByDS(providerGroup.getAbbreviation()))
- .thenReturn(getModelListForTest());
-
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initPdxModelDetails();
- universalDataExporter.initPdxModelValidations();
-
- List<List<String>> pdxModelDetails = universalDataExporter.getPdxModelSheetDataExport();
- List<List<String>> pdxModelValidations = universalDataExporter.getPdxModelValidationSheetDataExport();
-
- Assert.assertEquals("m123", pdxModelDetails.get(0).get(0));
- Assert.assertEquals("hsname", pdxModelDetails.get(0).get(1));
-
- Assert.assertEquals("m123", pdxModelValidations.get(0).get(0));
- Assert.assertEquals("technology", pdxModelValidations.get(0).get(1));
-
- }
-
- @Test
- public void Given_Provider_When_GetSharingAndContactSheetIsCalled_Then_SharingAndContactDataIsInRowOne(){
-
- when(dataImportService.findModelsWithSharingAndContactByDS(providerGroup.getAbbreviation()))
- .thenReturn(getModelListForTest());
-
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initSharingAndContact();
-
- List<List<String>> sharingAndContact = universalDataExporter.getSharingAndContactSheetDataExport();
-
- Assert.assertEquals("m123", sharingAndContact.get(0).get(0));
- Assert.assertEquals("Academia", sharingAndContact.get(0).get(1));
-
- }
-
- @Test
- public void Given_Provider_When_GetLoaderRelatedSheetIsCalled_Then_DataIsInRowOne(){
-
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initLoaderRelatedData();
-
- List<List<String>> loaderRelatedData = universalDataExporter.getLoaderRelatedDataSheetDataExport();
-
- Assert.assertEquals("TG", loaderRelatedData.get(0).get(1));
-
-
- }
-
- @Test
- public void Given_ModelWithMolecularData_When_GetSamplePlatformSheetIsCalled_Then_SamplePlatformDataIsInRowOne(){
-
- when(dataImportService.findModelXenograftPlatformSampleByDS(providerGroup.getAbbreviation()))
- .thenReturn(getModelListForTest());
-
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initSamplePlatformDescription();
-
- List<List<String>> samplePlatformDescription = universalDataExporter.getSamplePlatformDescriptionSheetDataExport();
-
- Assert.assertEquals("s123", samplePlatformDescription.get(0).get(1));
- Assert.assertEquals("xs123", samplePlatformDescription.get(1).get(1));
-
- }
-
- @Test
- public void Given_ModelwithMutationData_When_initGenomicDataIsCalled_Then_MutationDataIsInRowOne(){
-
- List<ModelCreation> modelList = getModelListForTest();
-
- when(dataImportService.findModelsWithSharingAndContactByDS((providerGroup.getAbbreviation())))
- .thenReturn(modelList);
-
- when(dataImportService.findModelWithMolecularDataByDSAndIdAndMolcharType(
- providerGroup.getAbbreviation(),"m123", "mutation"))
- .thenReturn(modelList.get(0));
-
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initOmicData();
- List<List<String>> mutationData = universalDataExporter.getMutationSheetDataExport();
-
- Assert.assertTrue(mutationData.get(0).contains(ncbiId));
- Assert.assertTrue(mutationData.get(0).contains(biotype));
- Assert.assertTrue(mutationData.get(0).contains(codingSequenceChange));
- Assert.assertTrue(mutationData.get(0).contains(variantClass));
-
- }
-
-
- @Test
- public void Given_SheetRowData_When_UpdateSheetIsCalled_Then_SheetIsUpdated(){
-
- Workbook wb = new XSSFWorkbook();
- Sheet sheet1 = wb.createSheet("Sheet1");
-
- List<String> rowData = new ArrayList<>(Arrays.asList("1","2","3","4"));
- List<List<String>> data = new ArrayList<>();
- data.add(rowData);
-
- universalDataExporter.updateSheetWithData(sheet1, data, 1, 1);
-
- Assert.assertEquals("2", sheet1.getRow(0).getCell(1).getStringCellValue());
- }
-
- @Test
- public void Given_dataIsReadyToExport_When_exportIsCalled_Then_createCorrectFileStructure() throws IOException {
-
- Path metaData = Paths.get( "/tmp/metadata_template.xlsx");
- Path samplePlatform = Paths.get("/tmp/sampleplatform_template.xlsx" );
- Path mutation = Paths.get("/tmp/mutation_template.xlsx");
- Path cnaTemplate = Paths.get("/tmp/cna_template.xlsx");
-
- List<List<String>> genericSheet = new ArrayList<>();
- List<String> genericColumn = new ArrayList<>();
- genericSheet.add(genericColumn);
-
- universalDataExporter.setPatientSheetDataExport(genericSheet);
- universalDataExporter.setPatientTumorSheetDataExport(genericSheet);
- universalDataExporter.setPatientTreatmentSheetDataExport(genericSheet);
- universalDataExporter.setPdxModelSheetDataExport(genericSheet);
- universalDataExporter.setPdxModelValidationSheetDataExport(genericSheet);
- universalDataExporter.setSamplePlatformDescriptionSheetDataExport(genericSheet);
- universalDataExporter.setSharingAndContactSheetDataExport(genericSheet);
- universalDataExporter.setCytogeneticsSheetDataExport(genericSheet);
- universalDataExporter.setLoaderRelatedDataSheetDataExport(genericSheet);
- universalDataExporter.setDrugDosingSheetDataExport(genericSheet);
- universalDataExporter.setCnaSheetDataExport(genericSheet);
- universalDataExporter.setMutationSheetDataExport(genericSheet);
-
-
- Workbook metaDataXlsx = new XSSFWorkbook();
- Workbook samplePlatformXlsx = new XSSFWorkbook();
- Workbook mutationXlsx = new XSSFWorkbook();
- Workbook cnaTemplateXlsx = new XSSFWorkbook();
-
- for(int i = 0; i < 7; i++) {
- metaDataXlsx.createSheet(String.format("%s", i));
- }
-
- samplePlatformXlsx.createSheet("0");
- mutationXlsx.createSheet("0");
- cnaTemplateXlsx.createSheet("0");
-
- metaDataXlsx.write(new FileOutputStream(metaData.toFile()));
- samplePlatformXlsx.write(new FileOutputStream(samplePlatform.toFile()));
- mutationXlsx.write(new FileOutputStream(mutation.toFile()));
- cnaTemplateXlsx.write(new FileOutputStream(cnaTemplate.toFile()));
-
- try {
- universalDataExporter.setTemplateDir("/tmp");
- universalDataExporter.setDs(providerGroup);
- universalDataExporter.initPatientData();
- universalDataExporter.export("/tmp");
- } finally {
-
- Files.delete(metaData);
- Files.delete(samplePlatform);
- Files.delete(mutation);
- Files.delete(cnaTemplate);
- }
-
- Path expectedProviderDir = Paths.get("/tmp/TG");
- Path expectedCnaDir = Paths.get("/tmp/TG/cna");
- Path expectedMutDir = Paths.get("/tmp/TG/mut");
- Path expectedMetaData = Paths.get("/tmp/TG/metadata.xlsx");
-
- Assert.assertTrue(expectedProviderDir.toFile().exists());
- Assert.assertTrue(expectedCnaDir.toFile().exists());
- Assert.assertTrue(expectedMutDir.toFile().exists());
- Assert.assertTrue(expectedMetaData.toFile().exists());
-
- }
-
-
-
-
- private List<ModelCreation> getModelListForTest(){
-
- List<ModelCreation> modelCreationList = new ArrayList<>();
-
- ModelCreation model = new ModelCreation();
- model.setSourcePdxId("m123");
-
- Group accessGroup = Group.createAccessibilityGroup("Academia", "transnational");
- Group project = new Group("project1", "p1", "Project");
-
- Group publicationGroup = new Group();
- publicationGroup.setType("Publication");
- publicationGroup.setPubMedId("12345");
-
- model.addGroup(publicationGroup);
- model.addGroup(providerGroup);
- model.addGroup(accessGroup);
- model.addGroup(project);
-
- ExternalUrl url = new ExternalUrl(ExternalUrl.Type.CONTACT,"email@address.com");
- List<ExternalUrl> urlList = new ArrayList<>();
- urlList.add(url);
- model.setExternalUrls(urlList);
-
- QualityAssurance qualityAssurance = new QualityAssurance("technology", "description", "1,2");
- model.addQualityAssurance(qualityAssurance);
-
- Sample patientSample = new Sample();
- patientSample.setSourceSampleId("s123");
-
- model.setSample(patientSample);
-
- MolecularCharacterization molecularCharacterization = new MolecularCharacterization();
- molecularCharacterization.setType("mutation");
- molecularCharacterization.setTechnology("techtest");
-
- MarkerAssociation ma = new MarkerAssociation();
- ma.setMolecularDataString("[{\"biotype\": \"" + biotype + "\",\"codingSequenceChange\":\"" + codingSequenceChange + "\"," +
- "\"variantClass\":\""+ variantClass + "\",\"codonChange\"" +
- ":\"Gtt/Att\",\"aminoAcidChange\":\"E763*\",\"consequence\":\"\",\"functionalPrediction\":\"Nonsense_Mutation\"," +
- "\"readDepth\":\"403\",\"alleleFrequency\":\"0.464\",\"chromosome\":\"5\",\"seqStartPosition\":\"112173578\"," +
- "\"refAllele\":\"G\",\"altAllele\":\"T\",\"ucscGeneId\":\"\",\"ncbiGeneId\":\"" + ncbiId + "\",\"ncbiTranscriptId\":" +
- "\"XR_929159.2\",\"existingVariations\":\"CM106354,COSM5010432\",\"genomeAssembly\":\"hg19\",\"nucleotideChange\"" +
- ":\"\",\"marker\":\"APC\"}]");
-
- molecularCharacterization.setMarkerAssociations(Collections.singletonList(ma));
- Platform platform = new Platform();
- platform.setName("platform");
- platform.setUrl("platformurl");
-
- molecularCharacterization.setPlatform(platform);
- patientSample.addMolecularCharacterization(molecularCharacterization);
-
- //setting up the xeno sample
- Specimen specimen = new Specimen();
- specimen.setPassage("1");
- specimen.setHostStrain(new HostStrain("hssymbol", "hsname"));
-
- Sample xenoSample = new Sample();
- xenoSample.setSourceSampleId("xs123");
- specimen.setSample(xenoSample);
- xenoSample.addMolecularCharacterization(molecularCharacterization);
- model.addSpecimen(specimen);
-
-
- modelCreationList.add(model);
-
- //setting up cna data
- MolecularCharacterization molecularCharacterization2 = new MolecularCharacterization();
- molecularCharacterization2.setType("copy number alteration");
- molecularCharacterization2.setPlatform(platform);
- MolecularData md2 = new MolecularData();
- md2.setCnaCopyNumberStatus("cnaStatus");
- xenoSample.addMolecularCharacterization(molecularCharacterization2);
-
- return modelCreationList;
- }
-
- private List<Patient> getPatientListForTest(){
-
- Patient patient = new Patient("p123", "male", "", "", providerGroup);
- patient.setCancerRelevantHistory("");
- patient.setFirstDiagnosis("");
- patient.setAgeAtFirstDiagnosis("60");
-
- List<Patient> patientList = new ArrayList<>();
- patientList.add(patient);
-
-
-
- return patientList;
- }
-
-
-}
diff --git a/indexer/src/test/java/org/pdxfinder/dataexport/ExportTemplatesTest.java b/indexer/src/test/java/org/pdxfinder/dataexport/ExportTemplatesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..b87e057f56a0389a7a2484d0eea1281353d307df
--- /dev/null
+++ b/indexer/src/test/java/org/pdxfinder/dataexport/ExportTemplatesTest.java
@@ -0,0 +1,74 @@
+package org.pdxfinder.dataexport;
+
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.junit.Assert;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.Group;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+
+public class ExportTemplatesTest extends BaseTest {
+
+ private String templateDir;
+ private Group group;
+
+
+ private void writeWorkbook(String directory, int sheetCount) throws IOException {
+ OutputStream out = new FileOutputStream(directory);
+ XSSFWorkbook workbook = new XSSFWorkbook();
+ for (int i = 0; i < sheetCount; i++) {
+ workbook.createSheet();
+ }
+ workbook.write(out);
+ }
+
+ @Test
+ public void Give_dataIsHarmonized_When_exportTemplatesAreInitialized_Then_adjustedTemplatesIsMade() throws IOException {
+ TemporaryFolder templateRoot = new TemporaryFolder();
+ templateRoot.create();
+ templateDir = templateRoot.getRoot().getAbsolutePath();
+
+ OutputStream out = new FileOutputStream(templateDir + "/" + TSV.templateNames.metadata_template.fileName);
+ XSSFWorkbook workbook = new XSSFWorkbook();
+ Sheet sheet = workbook.createSheet(TSV.metadataSheetNames.sample.name());
+ Row row = sheet.createRow(0);
+
+ for (int i = 0; i < 24; i++){
+ row.createCell(i).setCellValue(String.valueOf(i));
+ }
+
+ for (int i = 1; i < 7; i++) {
+ workbook.createSheet();
+ }
+ workbook.write(out);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.sampleplatform_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.mutation_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.cna_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.cytogenetics_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.expression_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.drugdosing_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.patienttreatment_template.fileName, 2);
+ group = new Group("test", "test", "test");
+
+ ExporterTemplates templates = new ExporterTemplates(templateDir, true);
+ XSSFWorkbook actualMetadataTemplate = templates.getTemplate(TSV.templateNames.metadata_template.name());
+ Sheet actualSheet = actualMetadataTemplate.getSheet(TSV.metadataSheetNames.sample.name());
+ Row actualRow = actualSheet.getRow(0);
+
+ Assert.assertEquals(actualRow.getCell(8).getStringCellValue(), "PDX Finder Harmonized Diagnosis");
+ for(int i = 10; i < 25; i++){
+ Assert.assertEquals(String.valueOf(i-1), actualRow.getCell(i).getStringCellValue());
+ }
+ }
+
+
+
+}
diff --git a/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExportTests.java b/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExportTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..af00c41b0cd37aeb0543cd50bc28a67071e8729f
--- /dev/null
+++ b/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExportTests.java
@@ -0,0 +1,165 @@
+package org.pdxfinder.dataexport;
+
+
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.Group;
+import org.pdxfinder.graph.dao.ModelCreation;
+import org.pdxfinder.services.DataImportService;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import static org.mockito.Mockito.*;
+
+public class UniversalDataExportTests extends BaseTest {
+
+ @Mock
+ private UniversalDataWriterServices writerUtilities;
+
+ @Mock
+ private UniversalDataExtractionServices extractionUtilities;
+
+ @Mock
+ private DataImportService dataImportService;
+
+ @InjectMocks
+ private UniversalDataExporter universalDataExporter;
+
+ private String templateDir;
+ private Group group;
+ private ExporterTemplates templates;
+ private List<List<String>> testSheet;
+
+
+ @Before
+ public void init() throws IOException {
+ TemporaryFolder templateRoot = new TemporaryFolder();
+ templateRoot.create();
+ templateDir = templateRoot.getRoot().getAbsolutePath();
+ writeWorkbook(templateDir + "/" + TSV.templateNames.metadata_template.fileName, 7);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.sampleplatform_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.mutation_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.cna_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.cytogenetics_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.expression_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.drugdosing_template.fileName, 2);
+ writeWorkbook(templateDir + "/" + TSV.templateNames.patienttreatment_template.fileName, 2);
+
+ templateDir = templateRoot.getRoot().getAbsolutePath();
+ templates = new ExporterTemplates(templateDir, false);
+ group = new Group("test", "test", "test");
+
+ testSheet = new ArrayList<>();
+ ArrayList<String> testRow = new ArrayList<>();
+ testSheet.add(testRow);
+ }
+
+ private void writeWorkbook(String directory, int sheetCount) throws IOException {
+ OutputStream out = new FileOutputStream(directory);
+ XSSFWorkbook workbook = new XSSFWorkbook();
+ for (int i = 0; i < sheetCount; i++) {
+ workbook.createSheet();
+ }
+ workbook.write(out);
+ }
+
+ @Test
+ public void Given_dummyTemplatesAndNoData_ExportSamplePlatform_ExtractionUtilitesAreCalledWithoutWrite() throws IOException {
+ universalDataExporter.exportSamplePlatform(templates, group, templateDir);
+
+ verify(extractionUtilities, times(1)).extractSamplePlatform(group);
+ verify(writerUtilities, times(1)).updateXlsxSheetWithData(any(Sheet.class),
+ any(List.class), anyInt(), anyInt());
+
+ verify(writerUtilities, never()).writXlsxFromWorkbook(any(XSSFWorkbook.class), anyString());
+ }
+
+ @Test
+ public void Given_dummyTemplatesWithData_ExportSamplePlatform_ExtractionUtilitesAreCalledWithWrite() throws IOException {
+ when(extractionUtilities.extractSamplePlatform(group)).thenReturn(testSheet);
+
+ XSSFWorkbook samplePlatformTemplate = templates.getTemplate(TSV.templateNames.sampleplatform_template.name());
+ universalDataExporter.exportSamplePlatform(templates, group, templateDir);
+
+ verify(writerUtilities).updateXlsxSheetWithData(eq(samplePlatformTemplate.getSheetAt(0)),
+ any(ArrayList.class), anyInt(), anyInt());
+ verify(writerUtilities).writXlsxFromWorkbook(eq(samplePlatformTemplate), anyString());
+ }
+
+ @Test
+ public void Given_dummyTemplatesAndNoData_ExportMetadata_ExtractionUtilitesAreCalledWithoutWriting() throws IOException {
+ MetadataSheets metadataSheets = new MetadataSheets();
+ when(extractionUtilities.extractMetadata(group, metadataSheets, false)).thenReturn(metadataSheets);
+
+ universalDataExporter.exportMetadata(metadataSheets, templates, group, false, templateDir);
+ verify(writerUtilities, times(7)).updateXlsxSheetWithData(any(Sheet.class),
+ any(List.class), anyInt(), anyInt());
+
+ verify(writerUtilities, never()).writXlsxFromWorkbook(any(XSSFWorkbook.class), anyString());
+ }
+
+ @Test
+ public void Given_NoModels_When_callToExtractAndSaveOmicsByBatch_Then_doNotRun() throws IOException {
+ String molecularType = "Mutation";
+ Path testExportURI = Paths.get("/path/to/export");
+ when(universalDataExporter.getModelsByMolecularTypeAndDataSource(molecularType, group))
+ .thenReturn(new ArrayList<>());
+
+ universalDataExporter.extractAndSaveOmicByBatch(molecularType,
+ templates.getTemplate(TSV.templateNames.mutation_template.name()),testExportURI, group);
+
+ verify(writerUtilities, never()).saveHeadersToTsv(any(Sheet.class),anyString());
+ verify(extractionUtilities, never()).extractModelsOmicData(any(ModelCreation.class), anyString());
+ }
+
+ @Test
+ public void Given_aSingleModel_When_callToExtractAndSaveOmicsByBatch_Then_runOnce() throws IOException {
+ String molecularType = "Mutation";
+ Path testExportURI = Paths.get("/path/to/export");
+ ModelCreation testModel = new ModelCreation();
+ when(universalDataExporter.getModelsByMolecularTypeAndDataSource(molecularType, group))
+ .thenReturn(Collections.singletonList(testModel));
+
+ universalDataExporter.extractAndSaveOmicByBatch(molecularType,
+ templates.getTemplate(TSV.templateNames.mutation_template.name()),testExportURI, group);
+
+ verify(writerUtilities).saveHeadersToTsv(any(Sheet.class),eq(testExportURI.toString()));
+ verify(extractionUtilities).extractModelsOmicData(eq(testModel), eq(molecularType));
+ verify(writerUtilities).appendDataToOmicTsvFile(anyList(), eq(testExportURI.toString()));
+ }
+
+ @Test
+ public void Given_elevenModel_When_callToExtractAndSaveOmicsByBatch_Then_runOnceInBatchThenAgain() throws IOException {
+ String molecularType = "Mutation";
+ Path testExportURI = Paths.get("/path/to/export");
+ ModelCreation[] testModelList = new ModelCreation[11];
+ for(int i = 0; i < 11; i++){
+ testModelList[i] = new ModelCreation();
+ }
+
+ when(universalDataExporter.getModelsByMolecularTypeAndDataSource(molecularType, group))
+ .thenReturn(Arrays.asList(testModelList));
+
+ universalDataExporter.extractAndSaveOmicByBatch(molecularType,
+ templates.getTemplate(TSV.templateNames.mutation_template.name()),testExportURI, group);
+
+ verify(writerUtilities).saveHeadersToTsv(any(Sheet.class),eq(testExportURI.toString()));
+ verify(extractionUtilities, times(11)).extractModelsOmicData(any(ModelCreation.class), eq(molecularType));
+ verify(writerUtilities, times(2)).appendDataToOmicTsvFile(anyList(), eq(testExportURI.toString()));
+ }
+}
diff --git a/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExtractorUtilitiesTest.java b/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExtractorUtilitiesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..30f9224621428e446b74067074590abd92189e1f
--- /dev/null
+++ b/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExtractorUtilitiesTest.java
@@ -0,0 +1,329 @@
+package org.pdxfinder.dataexport;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.*;
+import org.pdxfinder.services.DataImportService;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import static org.mockito.Mockito.when;
+
+public class UniversalDataExtractorUtilitiesTest extends BaseTest {
+
+ @Mock
+ private DataImportService dataImportService;
+
+ @InjectMocks
+ protected UniversalDataExtractionServices extractor;
+
+ Group providerGroup;
+
+ private static final String ncbiId = "XR_929159.2";
+ private static final String biotype = "protien_coding";
+ private static final String codingSequenceChange = "3154G>A";
+ private static final String variantClass = "SNV";
+ private static final String cnaLog2RCNA = "-0.01234";
+ private static final String marker = "SMAD3";
+ private static final String patientSampleId = "s123";
+ private static final String xenoSampleId = "xs123";
+ private static final String mutMolType = TSV.molecular_characterisation_type.mut.mcType;
+ private static final String cnaMolType = TSV.molecular_characterisation_type.cna.mcType;
+
+ private String TEST_DRUG = "TEST_DRUG";
+ private String TEST_DOSE = "TEST_DOSE";
+ private String TEST_RESPONSE = "TEST_RESPONSE";
+ private String MODEL_ID = "m123";
+ private String PATIENT_ID = "PATIETNID";
+
+ @Before
+ public void setUp() {
+ providerGroup = Group.createProviderGroup("TestGroup", "TG", "", "Academia", "Bob", "Bob's page");
+ }
+
+ @Test
+ public void Given_PatientAndProvider_When_GetPatientSheetIsCalled_Then_PatientDataIsInRowOne() {
+ when(dataImportService.findPatientsByGroup(providerGroup))
+ .thenReturn(getPatientListForTest());
+
+ List<List<String>> patientData = extractor.extractPatientSheet(providerGroup);
+ Assert.assertEquals("p123", patientData.get(0).get(0));
+ }
+
+ @Test
+ public void Given_PatientAndModelAndSample_When_PatientSampleSheetIsCalled_Then_PatientDataIsInRowOne(){
+ Patient patient = new Patient("p123", "male", "", "", providerGroup);
+ PatientSnapshot patientSnapshot = new PatientSnapshot();
+ patientSnapshot.setAgeAtCollection("65");
+ Sample sample = new Sample();
+ sample.setSourceSampleId("s123");
+
+ TumorType tt = new TumorType("Metastatic");
+ Tissue ot = new Tissue("Brain");
+ Tissue ss = new Tissue("Brain");
+
+ sample.setType(tt);
+ sample.setOriginTissue(ot);
+ sample.setSampleSite(ss);
+
+ patientSnapshot.addSample(sample);
+ patient.addSnapshot(patientSnapshot);
+
+ List<Patient> patientList = new ArrayList<>();
+ patientList.add(patient);
+
+ ModelCreation modelCreation = new ModelCreation();
+ modelCreation.setSourcePdxId(MODEL_ID);
+
+ when(dataImportService.findPatientTumorAtCollectionDataByDS(providerGroup))
+ .thenReturn(patientList);
+ when(dataImportService.findModelBySample(sample))
+ .thenReturn(modelCreation);
+
+ extractor.extractSampleSheet(providerGroup, false);
+
+ List<List<String>> patientSampleSheet = extractor.extractSampleSheet(providerGroup, false);
+ Assert.assertEquals("p123", patientSampleSheet.get(0).get(0));
+ }
+
+ @Test
+ public void Given_ModelWithDetails_When_GetModelDetailsIsCalled_Then_ModelDataIsInRowOne(){
+
+ when( dataImportService.findModelsWithSpecimensAndQAByDS(providerGroup.getAbbreviation()))
+ .thenReturn(getModelListForTest());
+
+ extractor.extractModelDetails(providerGroup);
+ extractor.extractModelValidations(providerGroup);
+
+ List<List<String>> pdxModelDetails = extractor.extractModelDetails(providerGroup);
+ List<List<String>> pdxModelValidations = extractor.extractModelValidations(providerGroup);
+
+ Assert.assertEquals(MODEL_ID, pdxModelDetails.get(0).get(0));
+ Assert.assertEquals("hsname", pdxModelDetails.get(0).get(1));
+
+ Assert.assertEquals(MODEL_ID, pdxModelValidations.get(0).get(0));
+ Assert.assertEquals("technology", pdxModelValidations.get(0).get(1));
+
+ }
+
+ @Test
+ public void Given_Provider_When_GetSharingAndContactSheetIsCalled_Then_SharingAndContactDataIsInRowOne(){
+ when(dataImportService.findModelsWithSharingAndContactByDS(providerGroup.getAbbreviation()))
+ .thenReturn(getModelListForTest());
+
+ List<List<String>> sharingAndContact = extractor.extractSharingAndContact(providerGroup);
+
+ Assert.assertEquals(MODEL_ID, sharingAndContact.get(0).get(0));
+ Assert.assertEquals("Academia", sharingAndContact.get(0).get(1));
+ }
+
+ @Test
+ public void Given_Provider_When_GetLoaderRelatedSheetIsCalled_Then_DataIsInRowOne(){
+ List<List<String>> loaderRelatedData = extractor.extractLoaderRelatedData(providerGroup);
+ Assert.assertEquals("TG", loaderRelatedData.get(0).get(1));
+ }
+
+ @Test
+ public void Given_ModelWithMolecularData_When_GetSamplePlatformSheetIsCalled_Then_SamplePlatformDataIsInRowOne(){
+
+ when(dataImportService.findModelXenograftPlatformSampleByDS(providerGroup.getAbbreviation()))
+ .thenReturn(getModelListForTest());
+
+ List<List<String>> samplePlatformDescription = extractor.extractSamplePlatform(providerGroup);
+
+ Assert.assertEquals(patientSampleId, samplePlatformDescription.get(0).get(1));
+ Assert.assertEquals(xenoSampleId, samplePlatformDescription.get(2).get(1));
+ }
+
+ @Test
+ public void Given_XenograftSamplewithMutationAndCna_When_extractGroupOmicDataIsCalled_Then_returnAppropriateDataForEach(){
+ List<ModelCreation> modelList = getModelListForTest();
+ ModelCreation testModel = modelList.get(0);
+
+ List<List<String>> mutationData = extractor.extractModelsOmicData(modelList.get(0),mutMolType);
+ List<List<String>> cnaData = extractor.extractModelsOmicData(testModel,cnaMolType);
+ Assert.assertTrue(mutationData.get(0).contains(ncbiId));
+ Assert.assertTrue(mutationData.get(0).contains(biotype));
+ Assert.assertTrue(mutationData.get(0).contains(codingSequenceChange));
+ Assert.assertTrue(mutationData.get(0).contains(variantClass));
+ Assert.assertFalse(mutationData.get(0).contains(cnaLog2RCNA));
+ Assert.assertFalse(mutationData.get(0).contains(marker));
+
+ Assert.assertTrue(cnaData.get(0).contains(cnaLog2RCNA));
+ Assert.assertTrue(cnaData.get(0).contains(marker));
+ Assert.assertFalse(cnaData.get(0).contains(biotype));
+ Assert.assertFalse(cnaData.get(0).contains(variantClass));
+ }
+
+ @Test
+ public void Given_PatientSamplewithMutationAndCna_When_extractGroupOmicDataIsCalled_Then_returnAppropriateDataForEach(){
+ List<ModelCreation> modelList = getModelListForTest();
+ ModelCreation testModel = modelList.get(0);
+ List<List<String>> mutationData = extractor.extractModelsOmicData(testModel, mutMolType);
+ List<List<String>> cnaData = extractor.extractModelsOmicData(testModel, cnaMolType);
+ Assert.assertTrue(mutationData.get(0).contains(ncbiId));
+ Assert.assertFalse(mutationData.get(0).contains(marker));
+ Assert.assertTrue(cnaData.get(0).contains(marker));
+ Assert.assertFalse(cnaData.get(0).contains(biotype));
+ }
+
+
+ @Test
+ public void Given_ModelwithMutationData_When_extractModelDataIsCalledwithDifferentMolcType_Then_NoDataIsRetrieved(){
+ List<ModelCreation> modelList = getModelListForTest();
+ ModelCreation testModel = modelList.get(0);
+ List<List<String>> expressionData = extractor.extractModelsOmicData(testModel,"expression");
+ Assert.assertEquals(0, expressionData.size());
+ }
+
+ @Test
+ public void Given_ModelwithDosingData_When_extractModelIsCalled_Then_DrugDosingIsRetrieved(){
+ List<ModelCreation> modelList = getModelListForTest();
+ ModelCreation testModel = modelList.get(0);
+ testModel.setTreatmentSummary(buildTreatmentSummaryTreeToModel());
+ List<List<String>> dosingData = extractor.extractModelsOmicData(testModel,"drug");
+ Assert.assertEquals(1, dosingData.size());
+ Assert.assertEquals(MODEL_ID, dosingData.get(0).get(2));
+ Assert.assertEquals(TEST_DRUG, dosingData.get(0).get(4));
+ Assert.assertEquals(TEST_DOSE, dosingData.get(0).get(6));
+ Assert.assertEquals(TEST_RESPONSE, dosingData.get(0).get(10));
+ }
+
+ @Test
+ public void Given_ModelwithPatientData_When_extractModelIsCalled_Then_PatientTreatmentIsRetrieved(){
+ List<ModelCreation> modelList = getModelListForTest();
+ ModelCreation testModel = modelList.get(0);
+ testModel.getSample().getPatientSnapshot().setTreatmentSummary(buildTreatmentSummaryTreeToModel());
+ List<List<String>> dosingData = extractor.extractModelsOmicData(testModel,"patientTreatment");
+ Assert.assertEquals(1, dosingData.size());
+ Assert.assertEquals(PATIENT_ID, dosingData.get(0).get(0));
+ Assert.assertEquals(TEST_DRUG, dosingData.get(0).get(1));
+ Assert.assertEquals(TEST_DOSE, dosingData.get(0).get(2));
+ Assert.assertEquals(TEST_RESPONSE, dosingData.get(0).get(7));
+ }
+
+
+
+ private List<ModelCreation> getModelListForTest(){
+ List<ModelCreation> modelCreationList = new ArrayList<>();
+
+ ModelCreation model = new ModelCreation();
+ model.setSourcePdxId(MODEL_ID);
+
+ setModelGroups(model);
+ setExternalUrl(model);
+
+ QualityAssurance qualityAssurance = new QualityAssurance("technology", "description", "1,2");
+ model.addQualityAssurance(qualityAssurance);
+
+ Patient patient = new Patient(PATIENT_ID, new Group());
+ PatientSnapshot patientSnapshot = new PatientSnapshot(patient, "0");
+
+ Sample patientSample = new Sample();
+ patientSample.setSourceSampleId(patientSampleId);
+ patientSample.setPatientSnapshot(patientSnapshot);
+
+ model.setSample(patientSample);
+
+ Specimen specimen = new Specimen();
+ specimen.setPassage("1");
+ specimen.setHostStrain(new HostStrain("hssymbol", "hsname"));
+
+ Sample xenoSample = new Sample();
+ xenoSample.setSourceSampleId(xenoSampleId);
+ specimen.setSample(xenoSample);
+ model.addSpecimen(specimen);
+
+ String mutJson = "[{\"biotype\": \"" + biotype + "\",\"codingSequenceChange\":\"" + codingSequenceChange + "\"," +
+ "\"variantClass\":\""+ variantClass + "\",\"codonChange\"" +
+ ":\"Gtt/Att\",\"aminoAcidChange\":\"E763*\",\"consequence\":\"\",\"functionalPrediction\":\"Nonsense_Mutation\"," +
+ "\"readDepth\":\"403\",\"alleleFrequency\":\"0.464\",\"chromosome\":\"5\",\"seqStartPosition\":\"112173578\"," +
+ "\"refAllele\":\"G\",\"altAllele\":\"T\",\"ucscGeneId\":\"\",\"ncbiGeneId\":\"" + ncbiId + "\",\"ncbiTranscriptId\":" +
+ "\"XR_929159.2\",\"existingVariations\":\"CM106354,COSM5010432\",\"genomeAssembly\":\"hg19\",\"nucleotideChange\"" +
+ ":\"\",\"marker\":\"APC\"}]";
+
+ String cnaJson = "[{\"chromosome\":\"\",\"seqStartPosition\":\"\",\"genomeAssembly\":\"\"," +
+ "\"seqEndPosition\":\"\",\"cnaLog10RCNA\":\"\",\"cnaLog2RCNA\":\"" + cnaLog2RCNA + "\"," +
+ "\"cnaCopyNumberStatus\":\"Normal\",\"cnaGisticValue\":\"\"" +
+ ",\"cnaPicnicValue\":\"\",\"marker\":\"" + marker + "\"}]";
+
+ Platform platform = new Platform();
+ platform.setName("platform");
+ platform.setUrl("platformurl");
+
+ MolecularCharacterization mutMc = createMolecularDataStructure(mutMolType, mutJson, platform);
+ MolecularCharacterization cnaMc = createMolecularDataStructure(cnaMolType, cnaJson, platform);
+ xenoSample.addMolecularCharacterization(mutMc);
+ xenoSample.addMolecularCharacterization(cnaMc);
+ patientSample.addMolecularCharacterization(mutMc);
+ patientSample.addMolecularCharacterization(cnaMc);
+
+ modelCreationList.add(model);
+ return modelCreationList;
+ }
+
+ private void setModelGroups(ModelCreation model){
+ Group accessGroup = Group.createAccessibilityGroup("Academia", "transnational");
+ Group project = new Group("project1", "p1", "Project");
+
+ Group publicationGroup = new Group();
+ publicationGroup.setType("Publication");
+ publicationGroup.setPubMedId("12345");
+
+ model.addGroup(publicationGroup);
+ model.addGroup(providerGroup);
+ model.addGroup(accessGroup);
+ model.addGroup(project);
+ }
+
+ private void setExternalUrl(ModelCreation model){
+ ExternalUrl url = new ExternalUrl(ExternalUrl.Type.CONTACT,"email@address.com");
+ List<ExternalUrl> urlList = new ArrayList<>();
+ urlList.add(url);
+ model.setExternalUrls(urlList);
+ }
+
+ private List<Patient> getPatientListForTest(){
+
+ Patient patient = new Patient("p123", "male", "", "", providerGroup);
+ patient.setCancerRelevantHistory("");
+ patient.setFirstDiagnosis("");
+ patient.setAgeAtFirstDiagnosis("60");
+
+ List<Patient> patientList = new ArrayList<>();
+ patientList.add(patient);
+
+ return patientList;
+ }
+
+ private MolecularCharacterization createMolecularDataStructure(String molType, String markerAssociation, Platform platform){
+ MolecularCharacterization molecularCharacterization = new MolecularCharacterization();
+ molecularCharacterization.setType(molType);
+ molecularCharacterization.setTechnology("techtest");
+
+ MarkerAssociation ma = new MarkerAssociation();
+ ma.setMolecularDataString(markerAssociation);
+
+ molecularCharacterization.setMarkerAssociations(Collections.singletonList(ma));
+ molecularCharacterization.setPlatform(platform);
+ return molecularCharacterization;
+ }
+
+ private TreatmentSummary buildTreatmentSummaryTreeToModel(){
+ Treatment treatment = new Treatment(TEST_DRUG);
+ TreatmentComponent treatmentComponent = new TreatmentComponent(TEST_DOSE, treatment);
+ TreatmentProtocol treatmentProtocol = new TreatmentProtocol();
+ treatmentProtocol.setComponents(Collections.singletonList(treatmentComponent));
+ treatmentProtocol.setResponse(new Response(TEST_RESPONSE, treatmentProtocol));
+ TreatmentSummary treatmentSummary = new TreatmentSummary();
+ treatmentSummary.setTreatmentProtocols(Collections.singletonList(treatmentProtocol));
+ return treatmentSummary;
+ }
+}
\ No newline at end of file
diff --git a/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataWriterUtilitiesTests.java b/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataWriterUtilitiesTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..6e8158a47e35de8aac1cd25abc38c1c6bd0d9518
--- /dev/null
+++ b/indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataWriterUtilitiesTests.java
@@ -0,0 +1,112 @@
+package org.pdxfinder.dataexport;
+
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.junit.Assert;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.services.DataImportService;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+public class UniversalDataWriterUtilitiesTests extends BaseTest {
+
+ @Mock
+ private DataImportService dataImportService;
+
+ @InjectMocks
+ protected UniversalDataWriterServices universalDataWriterUtilities;
+
+
+ @Test
+ public void Given_SheetRowData_When_UpdateSheetIsCalled_Then_SheetIsUpdated(){
+ Workbook wb = new XSSFWorkbook();
+ Sheet sheet1 = wb.createSheet("Sheet1");
+
+ List<String> rowData = new ArrayList<>(Arrays.asList("1","2","3","4"));
+ List<List<String>> data = new ArrayList<>();
+ data.add(rowData);
+
+ universalDataWriterUtilities.updateXlsxSheetWithData(sheet1, data, 1, 1);
+ Assert.assertEquals("2", sheet1.getRow(0).getCell(1).getStringCellValue());
+ }
+
+ @Test
+ public void Given_nonExistingDirectoryStructureURI_CreateExportDirectiesIsCalled_createFullStructure() throws IOException {
+ TemporaryFolder rootFolder = new TemporaryFolder();
+ rootFolder.create();
+ String rootFolderURI = rootFolder.getRoot().getAbsolutePath();
+ String testExportURI = String.format("%s/%s/%s/data_mut.tsv", rootFolderURI, "testProvider", "mut");
+ universalDataWriterUtilities.createExportDirectories(testExportURI);
+ Assert.assertTrue(Paths.get(testExportURI).getParent().toFile().exists());
+
+ }
+
+ @Test
+ public void Given_templatesAndexportLocation_WhenCopyHeaderIsCalled_WriteHeadersToTsvThenEOF() throws IOException {
+ TemporaryFolder rootFolder = new TemporaryFolder();
+ rootFolder.create();
+ String tsvURI = String.format("%s/test_mut.tsv", rootFolder.getRoot().getAbsoluteFile());
+ XSSFWorkbook templateWB = new XSSFWorkbook();
+ templateWB.createSheet();
+ Sheet sheet = templateWB.getSheetAt(0);
+ sheet.createRow(0);
+ Row row = sheet.getRow(0);
+ for(int i=0; i < 23; i++) {
+ row.createCell(i).setCellValue(i);
+ }
+ universalDataWriterUtilities.saveHeadersToTsv(sheet, tsvURI);
+ File actualFile = Paths.get(tsvURI).toFile();
+ Assert.assertTrue(actualFile.exists());
+ BufferedReader reader = new BufferedReader(new FileReader(tsvURI));
+ String[] delimitedHeaders = reader.readLine().split("\t");
+ float index = 0;
+ for(String header: delimitedHeaders){
+ Assert.assertEquals(String.format("%.1f", index), header);
+ index++;
+ }
+ Assert.assertEquals( null, reader.readLine());
+ }
+
+ @Test
+ public void Given_dataTableWithOneRow_WhenAppendedDataIsCalled_WriteToFirstLineThenToSecond() throws IOException{
+ TemporaryFolder rootFolder = new TemporaryFolder();
+ rootFolder.create();
+ String tsvURI = String.format("%s/test_mut.tsv", rootFolder.getRoot().getAbsoluteFile());
+ List<List<String>> testProviderData = new ArrayList<>();
+ List<String> testRow = new ArrayList<>();
+ for(int i = 0; i < 23; i++){
+ testRow.add(String.valueOf(i));
+ }
+ testProviderData.add(testRow);
+ universalDataWriterUtilities.appendDataToOmicTsvFile(testProviderData, tsvURI);
+ universalDataWriterUtilities.appendDataToOmicTsvFile(testProviderData, tsvURI);
+ BufferedReader reader = new BufferedReader(new FileReader(tsvURI));
+ String[] actualDelimitedCellValues1 = reader.readLine().split("\t");
+ String[] actualDelimitedCellValues2 = reader.readLine().split("\t");
+
+ testForSequentialCellValues(actualDelimitedCellValues1);
+ testForSequentialCellValues(actualDelimitedCellValues2);
+ Assert.assertEquals( null, reader.readLine());
+ }
+
+ private void testForSequentialCellValues(String[] delimitedCellValues){
+ int index = 0;
+ for(String cellData: delimitedCellValues){
+ Assert.assertEquals(String.valueOf(index), cellData);
+ index++;
+ }
+ }
+}
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/LoadIRCCTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/LoadIRCCTest.java
deleted file mode 100644
index 5395cbbff30f5258978d2488519915a01395edc4..0000000000000000000000000000000000000000
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/LoadIRCCTest.java
+++ /dev/null
@@ -1,99 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.InjectMocks;
-import org.mockito.MockitoAnnotations;
-import org.neo4j.ogm.json.JSONArray;
-import org.neo4j.ogm.json.JSONObject;
-import org.pdxfinder.BaseTest;
-import org.pdxfinder.graph.dao.*;
-import org.pdxfinder.graph.repositories.SpecimenRepository;
-import org.pdxfinder.services.DataImportService;
-import org.pdxfinder.services.UtilityService;
-import org.springframework.boot.test.mock.mockito.MockBean;
-
-import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertThat;
-import static org.mockito.Mockito.when;
-
-public class LoadIRCCTest extends BaseTest {
-
- private Group transnationalAccess;
- private Group badAccess;
-
-
-
- @Before public void init() {
- MockitoAnnotations.initMocks(this);
- transnationalAccess = new Group();
- transnationalAccess.setName("transnational access");
- badAccess = new Group();
- badAccess.setName("another group");
-
- loader.providerDS = Group.createProviderGroup(
- "Test IRCC Provider",
- "IRCC-CRC",
- "Test provider description",
- "Academia",
- "Joe Bloggs",
- "ircc.example.com");
- }
-
- @MockBean UtilityService utilityService;
- @MockBean DataImportService dataImportService;
- @MockBean SpecimenRepository specimenRepository;
- @InjectMocks private LoadIRCC loader;
-
- @Test
- public void Given_ValidSpecimen_WhenLoadSpecimen_Then_SpecimenAddedToModel() throws Exception {
- ModelCreation modelCreation = new ModelCreation("1");
- JSONArray specimens = new JSONArray(
- "[{" +
- "\"Specimen ID\":\"CRCTEST\"," +
- "\"Engraftment Type\":\"tissue fragment\"," +
- "\"Engraftment Site\":\"subcutis right\"," +
- "\"Strain\":\"NOD SCID\"," +
- "\"Passage\":\"1\"," +
- "\"Platforms\":[ " +
- "{\"Platform\":\"RealTimePCR_GCN\"}" +
- "]" +
- "}]"
- );
- JSONObject json = specimens.getJSONObject(0);
- Specimen specimen = new Specimen();
- specimen.setExternalId(json.getString("Specimen ID"));
- specimen.setPassage(json.getString("Passage"));
-
- loader.dto.setModelCreation(modelCreation);
- loader.dto.setSpecimens(specimens);
-
-
- when(dataImportService.getSpecimen(
- modelCreation,
- json.getString("Specimen ID"),
- loader.providerDS.getAbbreviation(),
- json.getString("Passage"))
- ).thenReturn(specimen);
-
- loader.step13LoadSpecimens();
-
- assertEquals( "CRCTEST", loader.dto.getSpecimens().getJSONObject(0).getString("Specimen ID"));
- assertThat(loader.dto.getModelCreation().getSpecimens().contains(specimen), is(true));
- }
-
- @Test
- public void Given_IRCCCRCModel_When_AddAccessModality_Then_AddToTransnationalAccessGroup() {
- when(dataImportService.getAccessibilityGroup("", "transnational access"))
- .thenReturn(transnationalAccess);
-
- ModelCreation mc = new ModelCreation();
- loader.dto.setModelCreation(mc);
- loader.step18SetAdditionalGroups();
-
- assertThat(loader.dto.getModelCreation().getGroups().contains(transnationalAccess), is(true));
- assertThat(loader.dto.getModelCreation().getGroups().contains(badAccess), is(false));
- }
-
-}
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/UniversalLoaderTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/UniversalLoaderTest.java
deleted file mode 100644
index f72dbd8a153a5b2390918a62afe683f95eb96d25..0000000000000000000000000000000000000000
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/UniversalLoaderTest.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package org.pdxfinder.dataloaders;
-
-import org.apache.poi.ss.usermodel.Workbook;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.InjectMocks;
-import org.mockito.MockitoAnnotations;
-import org.pdxfinder.BaseTest;
-
-import java.util.Optional;
-
-import static org.junit.Assert.assertEquals;
-
-public class UniversalLoaderTest extends BaseTest {
-
- @Before
- public void setUp() {
- MockitoAnnotations.initMocks(this);
- }
-
- @InjectMocks private UniversalLoader loader;
-
- @Test
- public void Given_BaseFilePathContainsTrailingSlash_WhenLoading_PathIsCleaned() {
- assertEquals("file/path", UniversalLoader.stripTrailingSlash("file/path/"));
- }
-
- @Test
- public void Given_BaseFilePathDoesNotContainTrailingSlash_WhenLoading_PathIsClean() {
- assertEquals("file/path", UniversalLoader.stripTrailingSlash("file/path"));
- }
-
- @Test
- public void Given_NonExistingExcelTemplate_WhenLoading_ReturnOptionalEmpty() {
- Optional<Workbook> workbook = loader.getWorkbook(".", "does/not/exist/test.xlsx");
- assertEquals(Optional.empty(), workbook);
- }
-
-}
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/UpdogTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/UpdogTest.java
index 701a6b0a245229007b341ffd0cd9ef59884ae26c..3a0d2a504a3cb4d30ac425193d0c926732f64ca8 100644
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/UpdogTest.java
+++ b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/UpdogTest.java
@@ -181,4 +181,4 @@ public class UpdogTest {
);
}
-}
\ No newline at end of file
+}
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreatorTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreatorTest.java
index 695ab79a9a2669ee433722b1d9e01f576cb77646..95da74b0e25076781446726c0a5afb36b08683d1 100644
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreatorTest.java
+++ b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreatorTest.java
@@ -1,17 +1,12 @@
package org.pdxfinder.dataloaders.updog.domainobjectcreation;
-import org.apache.catalina.Host;
import org.junit.Before;
import org.junit.Test;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
-import org.pdxfinder.dataloaders.updog.TSV;
-import org.pdxfinder.graph.dao.Group;
-import org.pdxfinder.graph.dao.HostStrain;
-import org.pdxfinder.graph.dao.ModelCreation;
-import org.pdxfinder.graph.dao.Sample;
-import org.pdxfinder.graph.dao.Specimen;
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.*;
import tech.tablesaw.api.Row;
import tech.tablesaw.api.Table;
@@ -20,7 +15,7 @@ import java.util.Map;
import java.util.Set;
import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertThat;
public class ModelCreationCreatorTest {
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreatorTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreatorTest.java
index d679c65e472ee3207cd00dd36018d3a90fff1fe5..1b7888fea56d0e9d2f94e2b1ad5bd8e45634d2ab 100644
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreatorTest.java
+++ b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreatorTest.java
@@ -5,7 +5,7 @@ import org.junit.Test;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
-import org.pdxfinder.dataloaders.updog.TSV;
+import org.pdxfinder.TSV;
import org.pdxfinder.graph.dao.Sample;
import org.pdxfinder.graph.dao.Tissue;
import org.pdxfinder.graph.dao.TumorType;
@@ -15,8 +15,7 @@ import tech.tablesaw.api.Table;
import java.util.Map;
import java.util.Set;
-import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
public class SampleCreatorTest {
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreatorTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreatorTest.java
index acc62f8e7b46273343e626b9391d463f7649ca39..431d34e81de63b8bf4c8517df062138ec4be54ed 100644
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreatorTest.java
+++ b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreatorTest.java
@@ -5,19 +5,15 @@ import org.junit.Test;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
-import org.pdxfinder.dataloaders.updog.TSV;
-import org.pdxfinder.graph.dao.EngraftmentMaterial;
-import org.pdxfinder.graph.dao.EngraftmentSite;
-import org.pdxfinder.graph.dao.EngraftmentType;
-import org.pdxfinder.graph.dao.HostStrain;
-import org.pdxfinder.graph.dao.Specimen;
+import org.pdxfinder.TSV;
+import org.pdxfinder.graph.dao.*;
import tech.tablesaw.api.Row;
import tech.tablesaw.api.Table;
import java.util.Map;
import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertThat;
public class SpecimenCreatorTest {
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporterTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporterTest.java
index ec9dda43b7312e681da5845d8f28d01734eddf33..d7969489312f92c06627f17fb59a676cdb3e0ab9 100644
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporterTest.java
+++ b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporterTest.java
@@ -1,15 +1,15 @@
package org.pdxfinder.dataloaders.updog.tablevalidation;
import org.junit.Test;
-import org.mockito.Mock;
-import org.pdxfinder.dataloaders.updog.tablevalidation.error.*;
-import org.slf4j.Logger;
+import org.pdxfinder.dataloaders.updog.tablevalidation.error.EmptyValueError;
+import org.pdxfinder.dataloaders.updog.tablevalidation.error.EmptyValueErrorCreator;
+import org.pdxfinder.dataloaders.updog.tablevalidation.error.ValidationError;
import tech.tablesaw.api.Table;
import java.util.ArrayList;
import java.util.List;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
public class ErrorReporterTest {
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreatorTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreatorTest.java
index 7dbddf5ea21d48af218d2c113efb7dc6000cd6cd..9ae52913ab60e45798c7e6c974723078f713565d 100644
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreatorTest.java
+++ b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreatorTest.java
@@ -7,14 +7,11 @@ import org.pdxfinder.dataloaders.updog.tablevalidation.TableSetSpecification;
import tech.tablesaw.api.StringColumn;
import tech.tablesaw.api.Table;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
public class BrokenRelationErrorCreatorTest {
diff --git a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/EmptyValueErrorCreatorTest.java b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/EmptyValueErrorCreatorTest.java
index 753c7b2394a691591cc08ec964fe7c05db5ecb09..79b00b1740e88c4aa9a52f89661b88ab7d2323bc 100644
--- a/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/EmptyValueErrorCreatorTest.java
+++ b/indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/EmptyValueErrorCreatorTest.java
@@ -10,16 +10,12 @@ import org.pdxfinder.dataloaders.updog.tablevalidation.TableSetSpecification;
import tech.tablesaw.api.StringColumn;
import tech.tablesaw.api.Table;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
public class EmptyValueErrorCreatorTest {
diff --git a/indexer/src/test/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTermsTest.java b/indexer/src/test/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTermsTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..d78efb3d2faac5a734b7256cc12c99d3e6436619
--- /dev/null
+++ b/indexer/src/test/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTermsTest.java
@@ -0,0 +1,74 @@
+package org.pdxfinder.mapping;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.OntologyTerm;
+import org.pdxfinder.graph.dao.Treatment;
+import org.pdxfinder.rdbms.dao.MappingEntity;
+import org.pdxfinder.services.DataImportService;
+import org.pdxfinder.services.MappingService;
+import org.springframework.boot.test.mock.mockito.MockBean;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.mockito.Mockito.*;
+
+public class LinkTreatmentsToNCITTermsTest extends BaseTest {
+
+ @MockBean
+ private MappingService mappingService;
+ @MockBean
+ private DataImportService dataImportService;
+
+ LinkTreatmentsToNCITTerms linkTreatmentsToNCITTerms;
+
+
+ @Before
+ public void init(){
+ linkTreatmentsToNCITTerms = new LinkTreatmentsToNCITTerms(mappingService, dataImportService);
+ }
+
+
+ @Test
+ public void Given_Treatments_When_AddRelationshipToTreatments_Then_NewRelationshipIsPresent(){
+ when(mappingService.getTreatmentMapping(any(), any())).thenReturn(getMappingEntity());
+ when(dataImportService.findOntologyTermByUrl(any())).thenReturn(getOntologyTerm());
+
+ List<Treatment> treatments = getTreatments();
+ linkTreatmentsToNCITTerms.addRelationshipToTreatments(treatments, "DS");
+ Assert.assertEquals("otlabel1",treatments.get(0).getTreatmentToOntologyRelationship().getOntologyTerm().getLabel());
+
+ }
+
+
+
+ private MappingEntity getMappingEntity(){
+
+ MappingEntity me = new MappingEntity();
+ me.setJustification("");
+ me.setMapType("direct");
+ me.setMappedTermLabel("label1");
+
+ return me;
+ }
+
+ private OntologyTerm getOntologyTerm(){
+ OntologyTerm ot = new OntologyTerm();
+ ot.setLabel("otlabel1");
+ ot.setUrl("url1");
+ return ot;
+ }
+
+ private List<Treatment> getTreatments(){
+
+ List<Treatment> treatments = new ArrayList<>();
+
+ Treatment t1 = new Treatment("drug1");
+ treatments.add(t1);
+
+ return treatments;
+ }
+}
diff --git a/indexer/src/test/java/org/pdxfinder/postload/DataProjectionTest.java b/indexer/src/test/java/org/pdxfinder/postload/DataProjectionTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..697841d2d5d7bb5819e2f3b8eaa3abb76718ab53
--- /dev/null
+++ b/indexer/src/test/java/org/pdxfinder/postload/DataProjectionTest.java
@@ -0,0 +1,178 @@
+package org.pdxfinder.postload;
+
+import org.apache.commons.collections4.map.HashedMap;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.*;
+import org.pdxfinder.services.DataImportService;
+import org.pdxfinder.services.DrugService;
+
+import org.springframework.boot.test.mock.mockito.MockBean;
+import static org.mockito.Mockito.*;
+
+import java.util.*;
+
+
+public class DataProjectionTest extends BaseTest {
+
+
+ CreateDataProjections createDataProjections;
+
+ @MockBean
+ DataImportService dataImportService;
+
+ @MockBean
+ DrugService drugService;
+
+
+ @Before
+ public void init() {
+
+ createDataProjections = new CreateDataProjections(dataImportService, drugService);
+
+
+ }
+
+ @Test
+ public void given_HashMapDP_when_saveDP_then_Saved(){
+ createDataProjections.setCytogeneticsDP(getTwoKeyData());
+ createDataProjections.setMutatedPlatformMarkerVariantModelDP(getThreeKeyData());
+ createDataProjections.setModelDrugResponseDP(getTwoKeyData());
+ createDataProjections.setImmunoHistoChemistryDP(getTwoKeyData());
+ createDataProjections.setCopyNumberAlterationDP(getOneKeyData());
+ createDataProjections.setExpressionDP(getTwoKeyData());
+ createDataProjections.setDrugDosingDP(getOneKeyData());
+ createDataProjections.setPatientTreatmentDP(getOneKeyData());
+ createDataProjections.setFrequentlyMutatedMarkersDP(new ArrayList<>());
+ createDataProjections.setExpressionDP(getTwoKeyData());
+ createDataProjections.setDataAvailableDP(new HashedMap<>());
+ createDataProjections.setFrequentlyMutatedMarkersDP(new ArrayList<>());
+
+ when(dataImportService.saveDataProjection(any())).thenAnswer(i -> i.getArguments()[0]);
+ when(dataImportService.findDataProjectionByLabel(any())).thenReturn(null);
+
+ createDataProjections.saveDataProjections();
+
+ Assert.assertEquals("cytogenetics", createDataProjections.saveDP("cytogenetics",
+ createDataProjections.getCytogeneticsDP()).getLabel());
+ Assert.assertEquals("copy number alteration", createDataProjections.saveDP("copy number alteration",
+ createDataProjections.getCopyNumberAlterationDP()).getLabel());
+ Assert.assertEquals("expression", createDataProjections.saveDP("expression",
+ createDataProjections.getExpressionDP()).getLabel());
+ Assert.assertEquals("PlatformMarkerVariantModel", createDataProjections.saveDP("PlatformMarkerVariantModel",
+ createDataProjections.getMutatedPlatformMarkerVariantModelDP()).getLabel());
+ Assert.assertEquals("ModelDrugData", createDataProjections.saveDP("ModelDrugData",
+ createDataProjections.getModelDrugResponseDP()).getLabel());
+ Assert.assertEquals("breast cancer markers", createDataProjections.saveDP("breast cancer markers",
+ createDataProjections.getImmunoHistoChemistryDP()).getLabel());
+ Assert.assertEquals("drug dosing counter", createDataProjections.saveDP("drug dosing counter",
+ createDataProjections.getDrugDosingDP()).getLabel());
+ Assert.assertEquals("patient treatment", createDataProjections.saveDP("patient treatment",
+ createDataProjections.getPatientTreatmentDP()).getLabel());
+ Assert.assertEquals("MarkerVariant", createDataProjections.saveDP("MarkerVariant",
+ createDataProjections.getMutatedMarkerVariantDP()).getLabel());
+ Assert.assertEquals("data available", createDataProjections.saveDP("data available",
+ createDataProjections.getDataAvailableDP()).getLabel());
+ Assert.assertEquals("frequently mutated genes", createDataProjections.saveDP("frequently mutated genes",
+ createDataProjections.getFrequentlyMutatedMarkersDP()).getLabel());
+ }
+
+ @Test
+ public void given_Json_when_jsonKeyIsNull_then_ExceptionIsThrown(){
+ Map<String, Long> map = new HashedMap<>();
+ map.put(null, new Long(1));
+ Assert.assertEquals("", createDataProjections.createJsonString(map));
+
+ }
+
+ @Test
+ public void given_TreatmentSummary_when_Process_then_MapIsPopulated(){
+ TreatmentSummary ts = getTreatmentSummary();
+ createDataProjections.processModelDrugs(new Long(1), ts);
+ Assert.assertEquals(true,createDataProjections.getModelDrugResponseDP().containsKey("label5regimen"));
+ Assert.assertEquals(true,createDataProjections.getModelDrugResponseDP().containsKey("label1 and label2"));
+ }
+
+ private Map<String, Set<Long>> getOneKeyData(){
+
+ Set<Long> modelIds = new HashSet<>();
+ modelIds.add(new Long(1));
+ Map<String, Set<Long>> map1 = new HashMap<>();
+ map1.put("key1", modelIds);
+ return map1;
+ }
+
+ private Map<String, Map<String, Set<Long>>> getTwoKeyData(){
+
+ Set<Long> modelIds = new HashSet<>();
+ modelIds.add(new Long(1));
+ Map<String, Set<Long>> map2 = new HashMap<>();
+ Map<String, Map<String, Set<Long>>> map1 = new HashMap<>();
+ map2.put("key2", modelIds);
+ map1.put("key1", map2);
+ return map1;
+ }
+
+ private Map<String, Map<String, Map<String, Set<Long>>>> getThreeKeyData(){
+
+ Set<Long> modelIds = new HashSet<>();
+ modelIds.add(new Long(1));
+ Map<String, Set<Long>> map3 = new HashMap<>();
+ Map<String, Map<String, Set<Long>>> map2 = new HashMap<>();
+ Map<String, Map<String, Map<String, Set<Long>>>> map1 = new HashMap<>();
+ map3.put("key3",modelIds);
+ map2.put("key2", map3);
+ map1.put("key1", map2);
+ return map1;
+ }
+
+
+ private TreatmentSummary getTreatmentSummary(){
+ TreatmentSummary ts = new TreatmentSummary();
+ TreatmentProtocol tp1 = new TreatmentProtocol();
+ TreatmentProtocol tp2 = new TreatmentProtocol();
+ Response response = new Response();
+ response.setDescription("description");
+ tp1.setResponse(response);
+ tp2.setResponse(response);
+ TreatmentComponent tc1 = new TreatmentComponent();
+ TreatmentComponent tc2 = new TreatmentComponent();
+ TreatmentComponent tc3 = new TreatmentComponent();
+ Treatment t1 = new Treatment("regimendrug1");
+ Treatment t2 = new Treatment("drug2");
+ Treatment t3 = new Treatment("drug3");
+ TreatmentToOntologyRelationship ttor1 = new TreatmentToOntologyRelationship();
+ TreatmentToOntologyRelationship ttor2 = new TreatmentToOntologyRelationship();
+ TreatmentToOntologyRelationship ttor3 = new TreatmentToOntologyRelationship();
+ OntologyTerm ot1 = new OntologyTerm("url1", "label1");
+ OntologyTerm ot2 = new OntologyTerm("url2", "label2");
+ OntologyTerm ot3 = new OntologyTerm("url3", "label3");
+ OntologyTerm ot4 = new OntologyTerm("url4", "label4");
+ ot1.setType("Drug");
+ ot2.setType("Drug");
+ ot3.setType("Drug");
+ ot4.setType("Drug");
+ OntologyTerm regimen = new OntologyTerm("url5", "label5regimen");
+ regimen.setType("treatment regimen");
+ regimen.addSubclass(ot3);
+ regimen.addSubclass(ot4);
+ t1.setTreatmentToOntologyRelationship(ttor1);
+ ttor1.setOntologyTerm(regimen);
+ tc1.setTreatment(t1);
+ tp1.addTreatmentComponent(tc1);
+ ts.addTreatmentProtocol(tp1);
+ tc2.setTreatment(t2);
+ tc3.setTreatment(t3);
+ t2.setTreatmentToOntologyRelationship(ttor2);
+ t3.setTreatmentToOntologyRelationship(ttor3);
+ ttor2.setOntologyTerm(ot1);
+ ttor3.setOntologyTerm(ot2);
+ tp2.addTreatmentComponent(tc2);
+ tp2.addTreatmentComponent(tc3);
+ ts.addTreatmentProtocol(tp2);
+ return ts;
+ }
+
+}
diff --git a/indexer/src/test/java/org/pdxfinder/postload/SetDataVisibilityTest.java b/indexer/src/test/java/org/pdxfinder/postload/SetDataVisibilityTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..9e4f5055c745882e970b1c8321e4bd7b760f6c45
--- /dev/null
+++ b/indexer/src/test/java/org/pdxfinder/postload/SetDataVisibilityTest.java
@@ -0,0 +1,60 @@
+package org.pdxfinder.postload;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.pdxfinder.BaseTest;
+import org.pdxfinder.graph.dao.MolecularCharacterization;
+import org.pdxfinder.services.DataImportService;
+import org.springframework.boot.test.mock.mockito.MockBean;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.mockito.Mockito.*;
+
+public class SetDataVisibilityTest extends BaseTest {
+
+ @MockBean
+ DataImportService dataImportService;
+
+ SetDataVisibility setDataVisibility;
+
+ @Before
+ public void init(){
+
+ setDataVisibility = new SetDataVisibility(dataImportService);
+ }
+
+ @Test
+ public void Given_MolecularCharacterizations_When_DisablingVisibility_Then_VisibilityDisabled(){
+
+ List<MolecularCharacterization> molchars = getMolchars();
+ setDataVisibility.disableVisibility(molchars);
+ Assert.assertEquals(false, molchars.get(0).isVisible());
+ }
+
+ @Test
+ public void Given_DataSource_When_ApplyRules_Then_RulesApplied(){
+
+ when(dataImportService.findMolcharNumberByDataSource("TEST")).thenReturn(2);
+ when(dataImportService.findMolcharByDataSourceSkipLimit("TEST", 0, 50)).thenReturn(getMolchars());
+
+ setDataVisibility.applyDataVisibilityRules("TEST");
+ List<MolecularCharacterization> molcharList = getMolchars();
+ verify(dataImportService, times(1)).saveMolecularCharacterizations(any());
+ }
+
+
+ private List<MolecularCharacterization> getMolchars(){
+
+ MolecularCharacterization mc1 = new MolecularCharacterization();
+ MolecularCharacterization mc2 = new MolecularCharacterization();
+ List<MolecularCharacterization> list = new ArrayList<>();
+
+ list.add(mc1);
+ list.add(mc2);
+ return list;
+ }
+
+}
diff --git a/package-list b/package-list
deleted file mode 100644
index 937c43e86aeefdba2791207655a608f51ff026d0..0000000000000000000000000000000000000000
--- a/package-list
+++ /dev/null
@@ -1 +0,0 @@
-org.sprintell
diff --git a/web/pom.xml b/web/pom.xml
index 4c79da9c6bff4911f24f65a263e6a50fda8faca9..21c72bcae63c5769cb3db73990f40d033bd57aaa 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -25,11 +25,6 @@
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
- <dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-thymeleaf</artifactId>
- </dependency>
-
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
@@ -46,6 +41,17 @@
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j-ogm-bolt-driver</artifactId>
+ <version>3.1.20</version>
+ </dependency>
+ <dependency>
+ <!-- WARNING, do not update db engine (stable: 1.4.197) cause compatibility issues, see https://github.com/h2database/h2database/issues/2078 -->
+ <groupId>com.h2database</groupId>
+ <artifactId>h2</artifactId>
+ <version>1.4.197</version>
+ </dependency>
</dependencies>
<build>
diff --git a/web/src/main/java/org/pdxfinder/web/controllers/AjaxController.java b/web/src/main/java/org/pdxfinder/web/controllers/AjaxController.java
index 3a8e39fb690a40c8ab05ee03310c656e3d643ca9..ee82a1daccba8f1467041c9c6abf89a65ac23d32 100644
--- a/web/src/main/java/org/pdxfinder/web/controllers/AjaxController.java
+++ b/web/src/main/java/org/pdxfinder/web/controllers/AjaxController.java
@@ -10,14 +10,13 @@ import org.pdxfinder.services.pdf.Label;
import org.pdxfinder.services.pdf.PdfHelper;
import org.pdxfinder.services.pdf.Report;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.web.bind.annotation.*;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
import javax.servlet.http.HttpServletRequest;
-import java.util.HashMap;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Arrays;
+import java.util.*;
/*
* Created by csaba on 03/05/2018.
@@ -178,7 +177,7 @@ public class AjaxController {
@GetMapping("/getmoleculardata/{molcharId}")
public MolecularDataTableDTO getMolecularTableData(@PathVariable String molcharId){
- return detailsService.getMolecularDataTable(molcharId);
+ return detailsService.getMolecularDataTable(molcharId, false);
}
diff --git a/web/src/main/java/org/pdxfinder/web/controllers/CBioController.java b/web/src/main/java/org/pdxfinder/web/controllers/CBioController.java
index 3358354ce3094b5ec2e5c6edccb20b2176ab45f3..2dcb670839d78a45084e3feb30dd8a89a82c2611 100644
--- a/web/src/main/java/org/pdxfinder/web/controllers/CBioController.java
+++ b/web/src/main/java/org/pdxfinder/web/controllers/CBioController.java
@@ -60,10 +60,11 @@ public class CBioController {
@RequestParam("project") Optional<List<String>> project,
@RequestParam("data_available") Optional<List<String>> data_available,
@RequestParam("breast_cancer_markers") Optional<List<String>> breast_cancer_markers,
- @RequestParam( "access_modalities" ) Optional<List<String>> access_modalities,
+ @RequestParam("access_modalities") Optional<List<String>> access_modalities,
@RequestParam("copy_number_alteration") Optional<List<String>> copy_number_alteration,
@RequestParam("gene_expression") Optional<List<String>> gene_expression,
@RequestParam("cytogenetics") Optional<List<String>> cytogenetics,
+ @RequestParam("model_id") Optional<List<String>> model_id,
Login login
) {
@@ -86,11 +87,12 @@ public class CBioController {
logger.info("copy_number_alteration" + copy_number_alteration.toString());
logger.info("gene_expression" + gene_expression.toString());
logger.info("cytogenetics" + cytogenetics.toString());
+ logger.info("model_id" + cytogenetics.toString());
List<String> ids = captureIDs(query, datasource, diagnosis, patient_age, patient_treatment, patient_treatment_status,
patient_gender, sample_origin_tissue, cancer_system, sample_tumor_type, mutation, drug, project,
- data_available, breast_cancer_markers, access_modalities, copy_number_alteration, gene_expression, cytogenetics);
+ data_available, breast_cancer_markers, access_modalities, copy_number_alteration, gene_expression, cytogenetics, model_id);
String tmp_list = createTmpList(ids);
@@ -246,7 +248,8 @@ public class CBioController {
Optional<List<String>> access_modalities,
Optional<List<String>> copy_number_alteration,
Optional<List<String>> gene_expressions,
- Optional<List<String>> cytogenetics) {
+ Optional<List<String>> cytogenetics,
+ Optional<List<String>> model_id) {
/* DS: old
ExportDTO eDTO = searchService.export(query, datasource,
@@ -265,7 +268,7 @@ public class CBioController {
ExportDTO eDTO = searchService.export(query, datasource,
diagnosis, patient_age, patient_treatment, patient_treatment_status, patient_gender, sample_origin_tissue, cancer_system,
sample_tumor_type, mutation, drug, project, data_available, breast_cancer_markers, access_modalities,
- copy_number_alteration, gene_expressions, cytogenetics);
+ copy_number_alteration, gene_expressions, cytogenetics, model_id);
return eDTO.getResults().stream().map(ModelForQuery::getExternalId).collect(Collectors.toList());
}
diff --git a/web/src/main/java/org/pdxfinder/web/controllers/DetailsController.java b/web/src/main/java/org/pdxfinder/web/controllers/DetailsController.java
index 2db52c89563a0a9e8812633ef7bec128b2dff133..ad2928fac8601f3f06be4804ded006bb0cb49a3c 100644
--- a/web/src/main/java/org/pdxfinder/web/controllers/DetailsController.java
+++ b/web/src/main/java/org/pdxfinder/web/controllers/DetailsController.java
@@ -9,12 +9,16 @@ import org.pdxfinder.services.pdf.PdfHelper;
import org.pdxfinder.services.pdf.Report;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
-import org.springframework.web.bind.annotation.*;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.ResponseBody;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
-import java.util.*;
+import java.util.List;
+import java.util.Map;
@Controller
@@ -51,11 +55,11 @@ public class DetailsController {
@PathVariable String molcharType,
@PathVariable String molcharId) throws IOException {
- List<Map<String, Object>> molecularDataRowDTOS = detailsService.getMolecularDataTable(molcharId).getMolecularDataCsv();
+ List<Map<String, Object>> molecularDataRowDTOS = detailsService.getMolecularDataTable(molcharId, true).getMolecularDataCsv();
String output = utilityService.serializeToCsvWithIncludeNonEmpty(molecularDataRowDTOS);
response.setContentType("application/octet-stream");
- response.setHeader("Content-Disposition", String.format("attachment; filename=dataportal.europdx.eu_%s_%s_%s.csv",dataSrc, modelId, molcharType));
+ response.setHeader("Content-Disposition", String.format("attachment; filename=pdxfinder.org_%s_%s_%s.csv",dataSrc, modelId, molcharType));
response.getOutputStream().flush();
return output;
}
diff --git a/web/src/main/java/org/pdxfinder/web/controllers/SearchController.java b/web/src/main/java/org/pdxfinder/web/controllers/SearchController.java
index 43f63eb39d589792a0a5667ee0a8b3846ad005eb..11fe1453c5db5992f240b10b8f1102a66e650aae 100644
--- a/web/src/main/java/org/pdxfinder/web/controllers/SearchController.java
+++ b/web/src/main/java/org/pdxfinder/web/controllers/SearchController.java
@@ -8,8 +8,6 @@ import org.pdxfinder.services.ds.ModelForQueryExport;
import org.pdxfinder.services.dto.ExportDTO;
import org.pdxfinder.web.model.Identity;
import org.pdxfinder.web.model.Login;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -29,7 +27,6 @@ import java.util.stream.Collectors;
public class SearchController {
private SearchService searchService;
- private Logger logger = LoggerFactory.getLogger(SearchController.class);
public SearchController(SearchService searchService) {
@@ -54,16 +51,19 @@ public class SearchController {
@RequestParam("project") Optional<List<String>> project,
@RequestParam("data_available") Optional<List<String>> data_available,
@RequestParam("breast_cancer_markers") Optional<List<String>> breast_cancer_markers,
- @RequestParam("breast_cancer_markers") Optional<List<String>> access_modalities,
+ @RequestParam("access_modalities") Optional<List<String>> access_modalities,
@RequestParam("copy_number_alteration") Optional<List<String>> copy_number_alteration,
@RequestParam("gene_expression") Optional<List<String>> gene_expression,
- @RequestParam("cytogenetics") Optional<List<String>> cytogenetics
- ) {
+ @RequestParam("cytogenetics") Optional<List<String>> cytogenetics,
+ @RequestParam("model_id") Optional<List<String>> model_id
+
+ ) {
+
ExportDTO eDTO = searchService.export(query, datasource,
diagnosis, patient_age, patient_treatment, patient_treatment_status, patient_gender, sample_origin_tissue, cancer_system,
sample_tumor_type, mutation, drug, project, data_available, breast_cancer_markers, access_modalities, copy_number_alteration,
- gene_expression, cytogenetics);
+ gene_expression, cytogenetics, model_id);
Set<ModelForQueryExport> exportResults = eDTO.getResults().stream().map(ModelForQueryExport::new).collect(Collectors.toSet());
@@ -107,21 +107,21 @@ public class SearchController {
@RequestParam("project") Optional<List<String>> project,
@RequestParam("data_available") Optional<List<String>> data_available,
@RequestParam("breast_cancer_markers") Optional<List<String>> breast_cancer_markers,
- @RequestParam( "access_modalities" ) Optional<List<String>> access_modalities,
+ @RequestParam("access_modalities") Optional<List<String>> access_modalities,
@RequestParam("copy_number_alteration") Optional<List<String>> copy_number_alteration,
@RequestParam("gene_expression") Optional<List<String>> gene_expression,
@RequestParam("cytogenetics") Optional<List<String>> cytogenetics,
+ @RequestParam("model_id") Optional<List<String>> model_id,
+
@RequestParam(value = "page", defaultValue = "1") Integer page,
@RequestParam(value = "size", defaultValue = "10") Integer size,
Login login, Identity identity){
- logger.info(login.toString());
-
String authPass = System.getenv("AUTH_PASS");
if (authPass == null) authPass = "";
if (!login.isAuthorized() && !authPass.equals("1")) {
- model.addAttribute("returnTo", "/search");
+ model.addAttribute("returnTo", "/search");
model.addAttribute("identityName", null);
return "authentication";
}
@@ -134,16 +134,8 @@ public class SearchController {
model.addAttribute("websearch", searchService.webSearch(query, datasource,
diagnosis, patient_age, patient_treatment, patient_treatment_status, patient_gender, sample_origin_tissue, cancer_system,
sample_tumor_type, mutation, drug, project, data_available, breast_cancer_markers, access_modalities, copy_number_alteration, gene_expression,
- cytogenetics, page, size));
-
- // model.addAttribute("websearch", searchService.webSearch(query, datasource,
- // diagnosis, patient_age, patient_treatment, patient_treatment_status, patient_gender, sample_origin_tissue, cancer_system,
- // sample_tumor_type, mutation, drug, project, data_available, breast_cancer_markers, copy_number_alteration, page, size));
-
+ cytogenetics, model_id, page, size));
- // model.addAttribute("websearch", searchService.webSearch(query, datasource,
- // diagnosis, patient_age, patient_treatment, patient_treatment_status, patient_gender, sample_origin_tissue, cancer_system,
- // sample_tumor_type, mutation, drug, project, data_available, breast_cancer_markers, access_modalities, copy_number_alteration, page, size));
return "search";
}
diff --git a/web/src/main/resources/application.properties b/web/src/main/resources/application.properties
index b3ff60513fb9a4edef6dbeb11a1505db8d408a0a..b7985c1bd178ebe2a7610227fc0176960bffe5d4 100644
--- a/web/src/main/resources/application.properties
+++ b/web/src/main/resources/application.properties
@@ -1,28 +1,28 @@
-management.security.enabled=false
-#spring.data.rest.base-path=/api
spring.jackson.serialization.indent_output=true
# Enable certain actuator endpoints
-endpoints.env.enabled=true
-endpoints.env.sensitive=false
+management.endpoint.env.enabled=true
+management.endpoints.web.base-path=/manage
+management.endpoints.web.exposure.include=env
# Default logging level to INFO
logging.level.=INFO
# Tone down Spring extra-chatty components
logging.level.org.springframework.boot.autoconfigure.logging=ERROR
-logging.level.org.springframework.data.neo4j.mapping.Neo4jPersistentProperty=ERROR
+logging.level.org.springframework.data.neo4j.mapping.Neo4jPersistentProperty=ERROR
spring.data.neo4j.username=neo4j
spring.data.neo4j.password=neo5j
-spring.data.neo4j.uri=http://neo4j:7474
-#spring.data.neo4j.uri=http://dataportal-beta.edirex.ics.muni.cz:7474
-
+spring.data.neo4j.uri=bolt://neo4j
+#spring.data.neo4j.uri=bolt://dataportal-beta.edirex.ics.muni.cz
server.error.whitelabel.enabled=false
spring.thymeleaf.cache=false
-server.context-path=/data
+server.servlet.context-path=/data
+
#mappings file containing diagnosis to NCIT links
mappings.diagnosis.file=file.json
+mappings.mappedTermUrl=
edirex.datahubapi=GITLAB-CI
edirex.k8sapi=GITLAB-CI
@@ -33,12 +33,9 @@ edirex.debugmode=false
#edirex.debugmode=true
-mappings.mappedTermUrl=
-
-pdxfinder.root.dir=
-
-management.health.mail.enabled=false
data-dir=
+pdxfinder.root.dir=
data.directory=
+management.health.mail.enabled=false
diff --git a/web/src/main/resources/static/css/validationLog.css b/web/src/main/resources/static/css/validationLog.css
new file mode 100644
index 0000000000000000000000000000000000000000..ca5381c6c208b8831be40593b79e1904f42f3bae
--- /dev/null
+++ b/web/src/main/resources/static/css/validationLog.css
@@ -0,0 +1,19 @@
+@import url("app.css");
+
+body {
+ background: #fff;
+ padding: 2em;
+}
+
+.header {
+ font-weight: bold;
+ text-transform: uppercase;
+}
+
+.error > .Level{
+ color: darkred;
+}
+
+.info {
+ color: #3b5999;
+}
\ No newline at end of file
diff --git a/web/src/main/resources/static/js/chart.bundle.js b/web/src/main/resources/static/js/chart.bundle.js
deleted file mode 100644
index bf6ee755c4a3683e7056e051c98034ab2c582cd1..0000000000000000000000000000000000000000
--- a/web/src/main/resources/static/js/chart.bundle.js
+++ /dev/null
@@ -1,18962 +0,0 @@
-/*!
- * Chart.js
- * http://chartjs.org/
- * Version: 2.7.3
- *
- * Copyright 2018 Chart.js Contributors
- * Released under the MIT license
- * https://github.com/chartjs/Chart.js/blob/master/LICENSE.md
- */
-(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.Chart = f()}})(function(){var define,module,exports;return (function(){function r(e,n,t){function o(i,f){if(!n[i]){if(!e[i]){var c="function"==typeof require&&require;if(!f&&c)return c(i,!0);if(u)return u(i,!0);var a=new Error("Cannot find module '"+i+"'");throw a.code="MODULE_NOT_FOUND",a}var p=n[i]={exports:{}};e[i][0].call(p.exports,function(r){var n=e[i][1][r];return o(n||r)},p,p.exports,r,e,n,t)}return n[i].exports}for(var u="function"==typeof require&&require,i=0;i<t.length;i++)o(t[i]);return o}return r})()({1:[function(require,module,exports){
-/* MIT license */
-var colorNames = require(5);
-
-module.exports = {
- getRgba: getRgba,
- getHsla: getHsla,
- getRgb: getRgb,
- getHsl: getHsl,
- getHwb: getHwb,
- getAlpha: getAlpha,
-
- hexString: hexString,
- rgbString: rgbString,
- rgbaString: rgbaString,
- percentString: percentString,
- percentaString: percentaString,
- hslString: hslString,
- hslaString: hslaString,
- hwbString: hwbString,
- keyword: keyword
-}
-
-function getRgba(string) {
- if (!string) {
- return;
- }
- var abbr = /^#([a-fA-F0-9]{3})$/i,
- hex = /^#([a-fA-F0-9]{6})$/i,
- rgba = /^rgba?\(\s*([+-]?\d+)\s*,\s*([+-]?\d+)\s*,\s*([+-]?\d+)\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/i,
- per = /^rgba?\(\s*([+-]?[\d\.]+)\%\s*,\s*([+-]?[\d\.]+)\%\s*,\s*([+-]?[\d\.]+)\%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/i,
- keyword = /(\w+)/;
-
- var rgb = [0, 0, 0],
- a = 1,
- match = string.match(abbr);
- if (match) {
- match = match[1];
- for (var i = 0; i < rgb.length; i++) {
- rgb[i] = parseInt(match[i] + match[i], 16);
- }
- }
- else if (match = string.match(hex)) {
- match = match[1];
- for (var i = 0; i < rgb.length; i++) {
- rgb[i] = parseInt(match.slice(i * 2, i * 2 + 2), 16);
- }
- }
- else if (match = string.match(rgba)) {
- for (var i = 0; i < rgb.length; i++) {
- rgb[i] = parseInt(match[i + 1]);
- }
- a = parseFloat(match[4]);
- }
- else if (match = string.match(per)) {
- for (var i = 0; i < rgb.length; i++) {
- rgb[i] = Math.round(parseFloat(match[i + 1]) * 2.55);
- }
- a = parseFloat(match[4]);
- }
- else if (match = string.match(keyword)) {
- if (match[1] == "transparent") {
- return [0, 0, 0, 0];
- }
- rgb = colorNames[match[1]];
- if (!rgb) {
- return;
- }
- }
-
- for (var i = 0; i < rgb.length; i++) {
- rgb[i] = scale(rgb[i], 0, 255);
- }
- if (!a && a != 0) {
- a = 1;
- }
- else {
- a = scale(a, 0, 1);
- }
- rgb[3] = a;
- return rgb;
-}
-
-function getHsla(string) {
- if (!string) {
- return;
- }
- var hsl = /^hsla?\(\s*([+-]?\d+)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)/;
- var match = string.match(hsl);
- if (match) {
- var alpha = parseFloat(match[4]);
- var h = scale(parseInt(match[1]), 0, 360),
- s = scale(parseFloat(match[2]), 0, 100),
- l = scale(parseFloat(match[3]), 0, 100),
- a = scale(isNaN(alpha) ? 1 : alpha, 0, 1);
- return [h, s, l, a];
- }
-}
-
-function getHwb(string) {
- if (!string) {
- return;
- }
- var hwb = /^hwb\(\s*([+-]?\d+)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)/;
- var match = string.match(hwb);
- if (match) {
- var alpha = parseFloat(match[4]);
- var h = scale(parseInt(match[1]), 0, 360),
- w = scale(parseFloat(match[2]), 0, 100),
- b = scale(parseFloat(match[3]), 0, 100),
- a = scale(isNaN(alpha) ? 1 : alpha, 0, 1);
- return [h, w, b, a];
- }
-}
-
-function getRgb(string) {
- var rgba = getRgba(string);
- return rgba && rgba.slice(0, 3);
-}
-
-function getHsl(string) {
- var hsla = getHsla(string);
- return hsla && hsla.slice(0, 3);
-}
-
-function getAlpha(string) {
- var vals = getRgba(string);
- if (vals) {
- return vals[3];
- }
- else if (vals = getHsla(string)) {
- return vals[3];
- }
- else if (vals = getHwb(string)) {
- return vals[3];
- }
-}
-
-// generators
-function hexString(rgb) {
- return "#" + hexDouble(rgb[0]) + hexDouble(rgb[1])
- + hexDouble(rgb[2]);
-}
-
-function rgbString(rgba, alpha) {
- if (alpha < 1 || (rgba[3] && rgba[3] < 1)) {
- return rgbaString(rgba, alpha);
- }
- return "rgb(" + rgba[0] + ", " + rgba[1] + ", " + rgba[2] + ")";
-}
-
-function rgbaString(rgba, alpha) {
- if (alpha === undefined) {
- alpha = (rgba[3] !== undefined ? rgba[3] : 1);
- }
- return "rgba(" + rgba[0] + ", " + rgba[1] + ", " + rgba[2]
- + ", " + alpha + ")";
-}
-
-function percentString(rgba, alpha) {
- if (alpha < 1 || (rgba[3] && rgba[3] < 1)) {
- return percentaString(rgba, alpha);
- }
- var r = Math.round(rgba[0]/255 * 100),
- g = Math.round(rgba[1]/255 * 100),
- b = Math.round(rgba[2]/255 * 100);
-
- return "rgb(" + r + "%, " + g + "%, " + b + "%)";
-}
-
-function percentaString(rgba, alpha) {
- var r = Math.round(rgba[0]/255 * 100),
- g = Math.round(rgba[1]/255 * 100),
- b = Math.round(rgba[2]/255 * 100);
- return "rgba(" + r + "%, " + g + "%, " + b + "%, " + (alpha || rgba[3] || 1) + ")";
-}
-
-function hslString(hsla, alpha) {
- if (alpha < 1 || (hsla[3] && hsla[3] < 1)) {
- return hslaString(hsla, alpha);
- }
- return "hsl(" + hsla[0] + ", " + hsla[1] + "%, " + hsla[2] + "%)";
-}
-
-function hslaString(hsla, alpha) {
- if (alpha === undefined) {
- alpha = (hsla[3] !== undefined ? hsla[3] : 1);
- }
- return "hsla(" + hsla[0] + ", " + hsla[1] + "%, " + hsla[2] + "%, "
- + alpha + ")";
-}
-
-// hwb is a bit different than rgb(a) & hsl(a) since there is no alpha specific syntax
-// (hwb have alpha optional & 1 is default value)
-function hwbString(hwb, alpha) {
- if (alpha === undefined) {
- alpha = (hwb[3] !== undefined ? hwb[3] : 1);
- }
- return "hwb(" + hwb[0] + ", " + hwb[1] + "%, " + hwb[2] + "%"
- + (alpha !== undefined && alpha !== 1 ? ", " + alpha : "") + ")";
-}
-
-function keyword(rgb) {
- return reverseNames[rgb.slice(0, 3)];
-}
-
-// helpers
-function scale(num, min, max) {
- return Math.min(Math.max(min, num), max);
-}
-
-function hexDouble(num) {
- var str = num.toString(16).toUpperCase();
- return (str.length < 2) ? "0" + str : str;
-}
-
-
-//create a list of reverse color names
-var reverseNames = {};
-for (var name in colorNames) {
- reverseNames[colorNames[name]] = name;
-}
-
-},{"5":5}],2:[function(require,module,exports){
-/* MIT license */
-var convert = require(4);
-var string = require(1);
-
-var Color = function (obj) {
- if (obj instanceof Color) {
- return obj;
- }
- if (!(this instanceof Color)) {
- return new Color(obj);
- }
-
- this.valid = false;
- this.values = {
- rgb: [0, 0, 0],
- hsl: [0, 0, 0],
- hsv: [0, 0, 0],
- hwb: [0, 0, 0],
- cmyk: [0, 0, 0, 0],
- alpha: 1
- };
-
- // parse Color() argument
- var vals;
- if (typeof obj === 'string') {
- vals = string.getRgba(obj);
- if (vals) {
- this.setValues('rgb', vals);
- } else if (vals = string.getHsla(obj)) {
- this.setValues('hsl', vals);
- } else if (vals = string.getHwb(obj)) {
- this.setValues('hwb', vals);
- }
- } else if (typeof obj === 'object') {
- vals = obj;
- if (vals.r !== undefined || vals.red !== undefined) {
- this.setValues('rgb', vals);
- } else if (vals.l !== undefined || vals.lightness !== undefined) {
- this.setValues('hsl', vals);
- } else if (vals.v !== undefined || vals.value !== undefined) {
- this.setValues('hsv', vals);
- } else if (vals.w !== undefined || vals.whiteness !== undefined) {
- this.setValues('hwb', vals);
- } else if (vals.c !== undefined || vals.cyan !== undefined) {
- this.setValues('cmyk', vals);
- }
- }
-};
-
-Color.prototype = {
- isValid: function () {
- return this.valid;
- },
- rgb: function () {
- return this.setSpace('rgb', arguments);
- },
- hsl: function () {
- return this.setSpace('hsl', arguments);
- },
- hsv: function () {
- return this.setSpace('hsv', arguments);
- },
- hwb: function () {
- return this.setSpace('hwb', arguments);
- },
- cmyk: function () {
- return this.setSpace('cmyk', arguments);
- },
-
- rgbArray: function () {
- return this.values.rgb;
- },
- hslArray: function () {
- return this.values.hsl;
- },
- hsvArray: function () {
- return this.values.hsv;
- },
- hwbArray: function () {
- var values = this.values;
- if (values.alpha !== 1) {
- return values.hwb.concat([values.alpha]);
- }
- return values.hwb;
- },
- cmykArray: function () {
- return this.values.cmyk;
- },
- rgbaArray: function () {
- var values = this.values;
- return values.rgb.concat([values.alpha]);
- },
- hslaArray: function () {
- var values = this.values;
- return values.hsl.concat([values.alpha]);
- },
- alpha: function (val) {
- if (val === undefined) {
- return this.values.alpha;
- }
- this.setValues('alpha', val);
- return this;
- },
-
- red: function (val) {
- return this.setChannel('rgb', 0, val);
- },
- green: function (val) {
- return this.setChannel('rgb', 1, val);
- },
- blue: function (val) {
- return this.setChannel('rgb', 2, val);
- },
- hue: function (val) {
- if (val) {
- val %= 360;
- val = val < 0 ? 360 + val : val;
- }
- return this.setChannel('hsl', 0, val);
- },
- saturation: function (val) {
- return this.setChannel('hsl', 1, val);
- },
- lightness: function (val) {
- return this.setChannel('hsl', 2, val);
- },
- saturationv: function (val) {
- return this.setChannel('hsv', 1, val);
- },
- whiteness: function (val) {
- return this.setChannel('hwb', 1, val);
- },
- blackness: function (val) {
- return this.setChannel('hwb', 2, val);
- },
- value: function (val) {
- return this.setChannel('hsv', 2, val);
- },
- cyan: function (val) {
- return this.setChannel('cmyk', 0, val);
- },
- magenta: function (val) {
- return this.setChannel('cmyk', 1, val);
- },
- yellow: function (val) {
- return this.setChannel('cmyk', 2, val);
- },
- black: function (val) {
- return this.setChannel('cmyk', 3, val);
- },
-
- hexString: function () {
- return string.hexString(this.values.rgb);
- },
- rgbString: function () {
- return string.rgbString(this.values.rgb, this.values.alpha);
- },
- rgbaString: function () {
- return string.rgbaString(this.values.rgb, this.values.alpha);
- },
- percentString: function () {
- return string.percentString(this.values.rgb, this.values.alpha);
- },
- hslString: function () {
- return string.hslString(this.values.hsl, this.values.alpha);
- },
- hslaString: function () {
- return string.hslaString(this.values.hsl, this.values.alpha);
- },
- hwbString: function () {
- return string.hwbString(this.values.hwb, this.values.alpha);
- },
- keyword: function () {
- return string.keyword(this.values.rgb, this.values.alpha);
- },
-
- rgbNumber: function () {
- var rgb = this.values.rgb;
- return (rgb[0] << 16) | (rgb[1] << 8) | rgb[2];
- },
-
- luminosity: function () {
- // http://www.w3.org/TR/WCAG20/#relativeluminancedef
- var rgb = this.values.rgb;
- var lum = [];
- for (var i = 0; i < rgb.length; i++) {
- var chan = rgb[i] / 255;
- lum[i] = (chan <= 0.03928) ? chan / 12.92 : Math.pow(((chan + 0.055) / 1.055), 2.4);
- }
- return 0.2126 * lum[0] + 0.7152 * lum[1] + 0.0722 * lum[2];
- },
-
- contrast: function (color2) {
- // http://www.w3.org/TR/WCAG20/#contrast-ratiodef
- var lum1 = this.luminosity();
- var lum2 = color2.luminosity();
- if (lum1 > lum2) {
- return (lum1 + 0.05) / (lum2 + 0.05);
- }
- return (lum2 + 0.05) / (lum1 + 0.05);
- },
-
- level: function (color2) {
- var contrastRatio = this.contrast(color2);
- if (contrastRatio >= 7.1) {
- return 'AAA';
- }
-
- return (contrastRatio >= 4.5) ? 'AA' : '';
- },
-
- dark: function () {
- // YIQ equation from http://24ways.org/2010/calculating-color-contrast
- var rgb = this.values.rgb;
- var yiq = (rgb[0] * 299 + rgb[1] * 587 + rgb[2] * 114) / 1000;
- return yiq < 128;
- },
-
- light: function () {
- return !this.dark();
- },
-
- negate: function () {
- var rgb = [];
- for (var i = 0; i < 3; i++) {
- rgb[i] = 255 - this.values.rgb[i];
- }
- this.setValues('rgb', rgb);
- return this;
- },
-
- lighten: function (ratio) {
- var hsl = this.values.hsl;
- hsl[2] += hsl[2] * ratio;
- this.setValues('hsl', hsl);
- return this;
- },
-
- darken: function (ratio) {
- var hsl = this.values.hsl;
- hsl[2] -= hsl[2] * ratio;
- this.setValues('hsl', hsl);
- return this;
- },
-
- saturate: function (ratio) {
- var hsl = this.values.hsl;
- hsl[1] += hsl[1] * ratio;
- this.setValues('hsl', hsl);
- return this;
- },
-
- desaturate: function (ratio) {
- var hsl = this.values.hsl;
- hsl[1] -= hsl[1] * ratio;
- this.setValues('hsl', hsl);
- return this;
- },
-
- whiten: function (ratio) {
- var hwb = this.values.hwb;
- hwb[1] += hwb[1] * ratio;
- this.setValues('hwb', hwb);
- return this;
- },
-
- blacken: function (ratio) {
- var hwb = this.values.hwb;
- hwb[2] += hwb[2] * ratio;
- this.setValues('hwb', hwb);
- return this;
- },
-
- greyscale: function () {
- var rgb = this.values.rgb;
- // http://en.wikipedia.org/wiki/Grayscale#Converting_color_to_grayscale
- var val = rgb[0] * 0.3 + rgb[1] * 0.59 + rgb[2] * 0.11;
- this.setValues('rgb', [val, val, val]);
- return this;
- },
-
- clearer: function (ratio) {
- var alpha = this.values.alpha;
- this.setValues('alpha', alpha - (alpha * ratio));
- return this;
- },
-
- opaquer: function (ratio) {
- var alpha = this.values.alpha;
- this.setValues('alpha', alpha + (alpha * ratio));
- return this;
- },
-
- rotate: function (degrees) {
- var hsl = this.values.hsl;
- var hue = (hsl[0] + degrees) % 360;
- hsl[0] = hue < 0 ? 360 + hue : hue;
- this.setValues('hsl', hsl);
- return this;
- },
-
- /**
- * Ported from sass implementation in C
- * https://github.com/sass/libsass/blob/0e6b4a2850092356aa3ece07c6b249f0221caced/functions.cpp#L209
- */
- mix: function (mixinColor, weight) {
- var color1 = this;
- var color2 = mixinColor;
- var p = weight === undefined ? 0.5 : weight;
-
- var w = 2 * p - 1;
- var a = color1.alpha() - color2.alpha();
-
- var w1 = (((w * a === -1) ? w : (w + a) / (1 + w * a)) + 1) / 2.0;
- var w2 = 1 - w1;
-
- return this
- .rgb(
- w1 * color1.red() + w2 * color2.red(),
- w1 * color1.green() + w2 * color2.green(),
- w1 * color1.blue() + w2 * color2.blue()
- )
- .alpha(color1.alpha() * p + color2.alpha() * (1 - p));
- },
-
- toJSON: function () {
- return this.rgb();
- },
-
- clone: function () {
- // NOTE(SB): using node-clone creates a dependency to Buffer when using browserify,
- // making the final build way to big to embed in Chart.js. So let's do it manually,
- // assuming that values to clone are 1 dimension arrays containing only numbers,
- // except 'alpha' which is a number.
- var result = new Color();
- var source = this.values;
- var target = result.values;
- var value, type;
-
- for (var prop in source) {
- if (source.hasOwnProperty(prop)) {
- value = source[prop];
- type = ({}).toString.call(value);
- if (type === '[object Array]') {
- target[prop] = value.slice(0);
- } else if (type === '[object Number]') {
- target[prop] = value;
- } else {
- console.error('unexpected color value:', value);
- }
- }
- }
-
- return result;
- }
-};
-
-Color.prototype.spaces = {
- rgb: ['red', 'green', 'blue'],
- hsl: ['hue', 'saturation', 'lightness'],
- hsv: ['hue', 'saturation', 'value'],
- hwb: ['hue', 'whiteness', 'blackness'],
- cmyk: ['cyan', 'magenta', 'yellow', 'black']
-};
-
-Color.prototype.maxes = {
- rgb: [255, 255, 255],
- hsl: [360, 100, 100],
- hsv: [360, 100, 100],
- hwb: [360, 100, 100],
- cmyk: [100, 100, 100, 100]
-};
-
-Color.prototype.getValues = function (space) {
- var values = this.values;
- var vals = {};
-
- for (var i = 0; i < space.length; i++) {
- vals[space.charAt(i)] = values[space][i];
- }
-
- if (values.alpha !== 1) {
- vals.a = values.alpha;
- }
-
- // {r: 255, g: 255, b: 255, a: 0.4}
- return vals;
-};
-
-Color.prototype.setValues = function (space, vals) {
- var values = this.values;
- var spaces = this.spaces;
- var maxes = this.maxes;
- var alpha = 1;
- var i;
-
- this.valid = true;
-
- if (space === 'alpha') {
- alpha = vals;
- } else if (vals.length) {
- // [10, 10, 10]
- values[space] = vals.slice(0, space.length);
- alpha = vals[space.length];
- } else if (vals[space.charAt(0)] !== undefined) {
- // {r: 10, g: 10, b: 10}
- for (i = 0; i < space.length; i++) {
- values[space][i] = vals[space.charAt(i)];
- }
-
- alpha = vals.a;
- } else if (vals[spaces[space][0]] !== undefined) {
- // {red: 10, green: 10, blue: 10}
- var chans = spaces[space];
-
- for (i = 0; i < space.length; i++) {
- values[space][i] = vals[chans[i]];
- }
-
- alpha = vals.alpha;
- }
-
- values.alpha = Math.max(0, Math.min(1, (alpha === undefined ? values.alpha : alpha)));
-
- if (space === 'alpha') {
- return false;
- }
-
- var capped;
-
- // cap values of the space prior converting all values
- for (i = 0; i < space.length; i++) {
- capped = Math.max(0, Math.min(maxes[space][i], values[space][i]));
- values[space][i] = Math.round(capped);
- }
-
- // convert to all the other color spaces
- for (var sname in spaces) {
- if (sname !== space) {
- values[sname] = convert[space][sname](values[space]);
- }
- }
-
- return true;
-};
-
-Color.prototype.setSpace = function (space, args) {
- var vals = args[0];
-
- if (vals === undefined) {
- // color.rgb()
- return this.getValues(space);
- }
-
- // color.rgb(10, 10, 10)
- if (typeof vals === 'number') {
- vals = Array.prototype.slice.call(args);
- }
-
- this.setValues(space, vals);
- return this;
-};
-
-Color.prototype.setChannel = function (space, index, val) {
- var svalues = this.values[space];
- if (val === undefined) {
- // color.red()
- return svalues[index];
- } else if (val === svalues[index]) {
- // color.red(color.red())
- return this;
- }
-
- // color.red(100)
- svalues[index] = val;
- this.setValues(space, svalues);
-
- return this;
-};
-
-if (typeof window !== 'undefined') {
- window.Color = Color;
-}
-
-module.exports = Color;
-
-},{"1":1,"4":4}],3:[function(require,module,exports){
-/* MIT license */
-
-module.exports = {
- rgb2hsl: rgb2hsl,
- rgb2hsv: rgb2hsv,
- rgb2hwb: rgb2hwb,
- rgb2cmyk: rgb2cmyk,
- rgb2keyword: rgb2keyword,
- rgb2xyz: rgb2xyz,
- rgb2lab: rgb2lab,
- rgb2lch: rgb2lch,
-
- hsl2rgb: hsl2rgb,
- hsl2hsv: hsl2hsv,
- hsl2hwb: hsl2hwb,
- hsl2cmyk: hsl2cmyk,
- hsl2keyword: hsl2keyword,
-
- hsv2rgb: hsv2rgb,
- hsv2hsl: hsv2hsl,
- hsv2hwb: hsv2hwb,
- hsv2cmyk: hsv2cmyk,
- hsv2keyword: hsv2keyword,
-
- hwb2rgb: hwb2rgb,
- hwb2hsl: hwb2hsl,
- hwb2hsv: hwb2hsv,
- hwb2cmyk: hwb2cmyk,
- hwb2keyword: hwb2keyword,
-
- cmyk2rgb: cmyk2rgb,
- cmyk2hsl: cmyk2hsl,
- cmyk2hsv: cmyk2hsv,
- cmyk2hwb: cmyk2hwb,
- cmyk2keyword: cmyk2keyword,
-
- keyword2rgb: keyword2rgb,
- keyword2hsl: keyword2hsl,
- keyword2hsv: keyword2hsv,
- keyword2hwb: keyword2hwb,
- keyword2cmyk: keyword2cmyk,
- keyword2lab: keyword2lab,
- keyword2xyz: keyword2xyz,
-
- xyz2rgb: xyz2rgb,
- xyz2lab: xyz2lab,
- xyz2lch: xyz2lch,
-
- lab2xyz: lab2xyz,
- lab2rgb: lab2rgb,
- lab2lch: lab2lch,
-
- lch2lab: lch2lab,
- lch2xyz: lch2xyz,
- lch2rgb: lch2rgb
-}
-
-
-function rgb2hsl(rgb) {
- var r = rgb[0]/255,
- g = rgb[1]/255,
- b = rgb[2]/255,
- min = Math.min(r, g, b),
- max = Math.max(r, g, b),
- delta = max - min,
- h, s, l;
-
- if (max == min)
- h = 0;
- else if (r == max)
- h = (g - b) / delta;
- else if (g == max)
- h = 2 + (b - r) / delta;
- else if (b == max)
- h = 4 + (r - g)/ delta;
-
- h = Math.min(h * 60, 360);
-
- if (h < 0)
- h += 360;
-
- l = (min + max) / 2;
-
- if (max == min)
- s = 0;
- else if (l <= 0.5)
- s = delta / (max + min);
- else
- s = delta / (2 - max - min);
-
- return [h, s * 100, l * 100];
-}
-
-function rgb2hsv(rgb) {
- var r = rgb[0],
- g = rgb[1],
- b = rgb[2],
- min = Math.min(r, g, b),
- max = Math.max(r, g, b),
- delta = max - min,
- h, s, v;
-
- if (max == 0)
- s = 0;
- else
- s = (delta/max * 1000)/10;
-
- if (max == min)
- h = 0;
- else if (r == max)
- h = (g - b) / delta;
- else if (g == max)
- h = 2 + (b - r) / delta;
- else if (b == max)
- h = 4 + (r - g) / delta;
-
- h = Math.min(h * 60, 360);
-
- if (h < 0)
- h += 360;
-
- v = ((max / 255) * 1000) / 10;
-
- return [h, s, v];
-}
-
-function rgb2hwb(rgb) {
- var r = rgb[0],
- g = rgb[1],
- b = rgb[2],
- h = rgb2hsl(rgb)[0],
- w = 1/255 * Math.min(r, Math.min(g, b)),
- b = 1 - 1/255 * Math.max(r, Math.max(g, b));
-
- return [h, w * 100, b * 100];
-}
-
-function rgb2cmyk(rgb) {
- var r = rgb[0] / 255,
- g = rgb[1] / 255,
- b = rgb[2] / 255,
- c, m, y, k;
-
- k = Math.min(1 - r, 1 - g, 1 - b);
- c = (1 - r - k) / (1 - k) || 0;
- m = (1 - g - k) / (1 - k) || 0;
- y = (1 - b - k) / (1 - k) || 0;
- return [c * 100, m * 100, y * 100, k * 100];
-}
-
-function rgb2keyword(rgb) {
- return reverseKeywords[JSON.stringify(rgb)];
-}
-
-function rgb2xyz(rgb) {
- var r = rgb[0] / 255,
- g = rgb[1] / 255,
- b = rgb[2] / 255;
-
- // assume sRGB
- r = r > 0.04045 ? Math.pow(((r + 0.055) / 1.055), 2.4) : (r / 12.92);
- g = g > 0.04045 ? Math.pow(((g + 0.055) / 1.055), 2.4) : (g / 12.92);
- b = b > 0.04045 ? Math.pow(((b + 0.055) / 1.055), 2.4) : (b / 12.92);
-
- var x = (r * 0.4124) + (g * 0.3576) + (b * 0.1805);
- var y = (r * 0.2126) + (g * 0.7152) + (b * 0.0722);
- var z = (r * 0.0193) + (g * 0.1192) + (b * 0.9505);
-
- return [x * 100, y *100, z * 100];
-}
-
-function rgb2lab(rgb) {
- var xyz = rgb2xyz(rgb),
- x = xyz[0],
- y = xyz[1],
- z = xyz[2],
- l, a, b;
-
- x /= 95.047;
- y /= 100;
- z /= 108.883;
-
- x = x > 0.008856 ? Math.pow(x, 1/3) : (7.787 * x) + (16 / 116);
- y = y > 0.008856 ? Math.pow(y, 1/3) : (7.787 * y) + (16 / 116);
- z = z > 0.008856 ? Math.pow(z, 1/3) : (7.787 * z) + (16 / 116);
-
- l = (116 * y) - 16;
- a = 500 * (x - y);
- b = 200 * (y - z);
-
- return [l, a, b];
-}
-
-function rgb2lch(args) {
- return lab2lch(rgb2lab(args));
-}
-
-function hsl2rgb(hsl) {
- var h = hsl[0] / 360,
- s = hsl[1] / 100,
- l = hsl[2] / 100,
- t1, t2, t3, rgb, val;
-
- if (s == 0) {
- val = l * 255;
- return [val, val, val];
- }
-
- if (l < 0.5)
- t2 = l * (1 + s);
- else
- t2 = l + s - l * s;
- t1 = 2 * l - t2;
-
- rgb = [0, 0, 0];
- for (var i = 0; i < 3; i++) {
- t3 = h + 1 / 3 * - (i - 1);
- t3 < 0 && t3++;
- t3 > 1 && t3--;
-
- if (6 * t3 < 1)
- val = t1 + (t2 - t1) * 6 * t3;
- else if (2 * t3 < 1)
- val = t2;
- else if (3 * t3 < 2)
- val = t1 + (t2 - t1) * (2 / 3 - t3) * 6;
- else
- val = t1;
-
- rgb[i] = val * 255;
- }
-
- return rgb;
-}
-
-function hsl2hsv(hsl) {
- var h = hsl[0],
- s = hsl[1] / 100,
- l = hsl[2] / 100,
- sv, v;
-
- if(l === 0) {
- // no need to do calc on black
- // also avoids divide by 0 error
- return [0, 0, 0];
- }
-
- l *= 2;
- s *= (l <= 1) ? l : 2 - l;
- v = (l + s) / 2;
- sv = (2 * s) / (l + s);
- return [h, sv * 100, v * 100];
-}
-
-function hsl2hwb(args) {
- return rgb2hwb(hsl2rgb(args));
-}
-
-function hsl2cmyk(args) {
- return rgb2cmyk(hsl2rgb(args));
-}
-
-function hsl2keyword(args) {
- return rgb2keyword(hsl2rgb(args));
-}
-
-
-function hsv2rgb(hsv) {
- var h = hsv[0] / 60,
- s = hsv[1] / 100,
- v = hsv[2] / 100,
- hi = Math.floor(h) % 6;
-
- var f = h - Math.floor(h),
- p = 255 * v * (1 - s),
- q = 255 * v * (1 - (s * f)),
- t = 255 * v * (1 - (s * (1 - f))),
- v = 255 * v;
-
- switch(hi) {
- case 0:
- return [v, t, p];
- case 1:
- return [q, v, p];
- case 2:
- return [p, v, t];
- case 3:
- return [p, q, v];
- case 4:
- return [t, p, v];
- case 5:
- return [v, p, q];
- }
-}
-
-function hsv2hsl(hsv) {
- var h = hsv[0],
- s = hsv[1] / 100,
- v = hsv[2] / 100,
- sl, l;
-
- l = (2 - s) * v;
- sl = s * v;
- sl /= (l <= 1) ? l : 2 - l;
- sl = sl || 0;
- l /= 2;
- return [h, sl * 100, l * 100];
-}
-
-function hsv2hwb(args) {
- return rgb2hwb(hsv2rgb(args))
-}
-
-function hsv2cmyk(args) {
- return rgb2cmyk(hsv2rgb(args));
-}
-
-function hsv2keyword(args) {
- return rgb2keyword(hsv2rgb(args));
-}
-
-// http://dev.w3.org/csswg/css-color/#hwb-to-rgb
-function hwb2rgb(hwb) {
- var h = hwb[0] / 360,
- wh = hwb[1] / 100,
- bl = hwb[2] / 100,
- ratio = wh + bl,
- i, v, f, n;
-
- // wh + bl cant be > 1
- if (ratio > 1) {
- wh /= ratio;
- bl /= ratio;
- }
-
- i = Math.floor(6 * h);
- v = 1 - bl;
- f = 6 * h - i;
- if ((i & 0x01) != 0) {
- f = 1 - f;
- }
- n = wh + f * (v - wh); // linear interpolation
-
- switch (i) {
- default:
- case 6:
- case 0: r = v; g = n; b = wh; break;
- case 1: r = n; g = v; b = wh; break;
- case 2: r = wh; g = v; b = n; break;
- case 3: r = wh; g = n; b = v; break;
- case 4: r = n; g = wh; b = v; break;
- case 5: r = v; g = wh; b = n; break;
- }
-
- return [r * 255, g * 255, b * 255];
-}
-
-function hwb2hsl(args) {
- return rgb2hsl(hwb2rgb(args));
-}
-
-function hwb2hsv(args) {
- return rgb2hsv(hwb2rgb(args));
-}
-
-function hwb2cmyk(args) {
- return rgb2cmyk(hwb2rgb(args));
-}
-
-function hwb2keyword(args) {
- return rgb2keyword(hwb2rgb(args));
-}
-
-function cmyk2rgb(cmyk) {
- var c = cmyk[0] / 100,
- m = cmyk[1] / 100,
- y = cmyk[2] / 100,
- k = cmyk[3] / 100,
- r, g, b;
-
- r = 1 - Math.min(1, c * (1 - k) + k);
- g = 1 - Math.min(1, m * (1 - k) + k);
- b = 1 - Math.min(1, y * (1 - k) + k);
- return [r * 255, g * 255, b * 255];
-}
-
-function cmyk2hsl(args) {
- return rgb2hsl(cmyk2rgb(args));
-}
-
-function cmyk2hsv(args) {
- return rgb2hsv(cmyk2rgb(args));
-}
-
-function cmyk2hwb(args) {
- return rgb2hwb(cmyk2rgb(args));
-}
-
-function cmyk2keyword(args) {
- return rgb2keyword(cmyk2rgb(args));
-}
-
-
-function xyz2rgb(xyz) {
- var x = xyz[0] / 100,
- y = xyz[1] / 100,
- z = xyz[2] / 100,
- r, g, b;
-
- r = (x * 3.2406) + (y * -1.5372) + (z * -0.4986);
- g = (x * -0.9689) + (y * 1.8758) + (z * 0.0415);
- b = (x * 0.0557) + (y * -0.2040) + (z * 1.0570);
-
- // assume sRGB
- r = r > 0.0031308 ? ((1.055 * Math.pow(r, 1.0 / 2.4)) - 0.055)
- : r = (r * 12.92);
-
- g = g > 0.0031308 ? ((1.055 * Math.pow(g, 1.0 / 2.4)) - 0.055)
- : g = (g * 12.92);
-
- b = b > 0.0031308 ? ((1.055 * Math.pow(b, 1.0 / 2.4)) - 0.055)
- : b = (b * 12.92);
-
- r = Math.min(Math.max(0, r), 1);
- g = Math.min(Math.max(0, g), 1);
- b = Math.min(Math.max(0, b), 1);
-
- return [r * 255, g * 255, b * 255];
-}
-
-function xyz2lab(xyz) {
- var x = xyz[0],
- y = xyz[1],
- z = xyz[2],
- l, a, b;
-
- x /= 95.047;
- y /= 100;
- z /= 108.883;
-
- x = x > 0.008856 ? Math.pow(x, 1/3) : (7.787 * x) + (16 / 116);
- y = y > 0.008856 ? Math.pow(y, 1/3) : (7.787 * y) + (16 / 116);
- z = z > 0.008856 ? Math.pow(z, 1/3) : (7.787 * z) + (16 / 116);
-
- l = (116 * y) - 16;
- a = 500 * (x - y);
- b = 200 * (y - z);
-
- return [l, a, b];
-}
-
-function xyz2lch(args) {
- return lab2lch(xyz2lab(args));
-}
-
-function lab2xyz(lab) {
- var l = lab[0],
- a = lab[1],
- b = lab[2],
- x, y, z, y2;
-
- if (l <= 8) {
- y = (l * 100) / 903.3;
- y2 = (7.787 * (y / 100)) + (16 / 116);
- } else {
- y = 100 * Math.pow((l + 16) / 116, 3);
- y2 = Math.pow(y / 100, 1/3);
- }
-
- x = x / 95.047 <= 0.008856 ? x = (95.047 * ((a / 500) + y2 - (16 / 116))) / 7.787 : 95.047 * Math.pow((a / 500) + y2, 3);
-
- z = z / 108.883 <= 0.008859 ? z = (108.883 * (y2 - (b / 200) - (16 / 116))) / 7.787 : 108.883 * Math.pow(y2 - (b / 200), 3);
-
- return [x, y, z];
-}
-
-function lab2lch(lab) {
- var l = lab[0],
- a = lab[1],
- b = lab[2],
- hr, h, c;
-
- hr = Math.atan2(b, a);
- h = hr * 360 / 2 / Math.PI;
- if (h < 0) {
- h += 360;
- }
- c = Math.sqrt(a * a + b * b);
- return [l, c, h];
-}
-
-function lab2rgb(args) {
- return xyz2rgb(lab2xyz(args));
-}
-
-function lch2lab(lch) {
- var l = lch[0],
- c = lch[1],
- h = lch[2],
- a, b, hr;
-
- hr = h / 360 * 2 * Math.PI;
- a = c * Math.cos(hr);
- b = c * Math.sin(hr);
- return [l, a, b];
-}
-
-function lch2xyz(args) {
- return lab2xyz(lch2lab(args));
-}
-
-function lch2rgb(args) {
- return lab2rgb(lch2lab(args));
-}
-
-function keyword2rgb(keyword) {
- return cssKeywords[keyword];
-}
-
-function keyword2hsl(args) {
- return rgb2hsl(keyword2rgb(args));
-}
-
-function keyword2hsv(args) {
- return rgb2hsv(keyword2rgb(args));
-}
-
-function keyword2hwb(args) {
- return rgb2hwb(keyword2rgb(args));
-}
-
-function keyword2cmyk(args) {
- return rgb2cmyk(keyword2rgb(args));
-}
-
-function keyword2lab(args) {
- return rgb2lab(keyword2rgb(args));
-}
-
-function keyword2xyz(args) {
- return rgb2xyz(keyword2rgb(args));
-}
-
-var cssKeywords = {
- aliceblue: [240,248,255],
- antiquewhite: [250,235,215],
- aqua: [0,255,255],
- aquamarine: [127,255,212],
- azure: [240,255,255],
- beige: [245,245,220],
- bisque: [255,228,196],
- black: [0,0,0],
- blanchedalmond: [255,235,205],
- blue: [0,0,255],
- blueviolet: [138,43,226],
- brown: [165,42,42],
- burlywood: [222,184,135],
- cadetblue: [95,158,160],
- chartreuse: [127,255,0],
- chocolate: [210,105,30],
- coral: [255,127,80],
- cornflowerblue: [100,149,237],
- cornsilk: [255,248,220],
- crimson: [220,20,60],
- cyan: [0,255,255],
- darkblue: [0,0,139],
- darkcyan: [0,139,139],
- darkgoldenrod: [184,134,11],
- darkgray: [169,169,169],
- darkgreen: [0,100,0],
- darkgrey: [169,169,169],
- darkkhaki: [189,183,107],
- darkmagenta: [139,0,139],
- darkolivegreen: [85,107,47],
- darkorange: [255,140,0],
- darkorchid: [153,50,204],
- darkred: [139,0,0],
- darksalmon: [233,150,122],
- darkseagreen: [143,188,143],
- darkslateblue: [72,61,139],
- darkslategray: [47,79,79],
- darkslategrey: [47,79,79],
- darkturquoise: [0,206,209],
- darkviolet: [148,0,211],
- deeppink: [255,20,147],
- deepskyblue: [0,191,255],
- dimgray: [105,105,105],
- dimgrey: [105,105,105],
- dodgerblue: [30,144,255],
- firebrick: [178,34,34],
- floralwhite: [255,250,240],
- forestgreen: [34,139,34],
- fuchsia: [255,0,255],
- gainsboro: [220,220,220],
- ghostwhite: [248,248,255],
- gold: [255,215,0],
- goldenrod: [218,165,32],
- gray: [128,128,128],
- green: [0,128,0],
- greenyellow: [173,255,47],
- grey: [128,128,128],
- honeydew: [240,255,240],
- hotpink: [255,105,180],
- indianred: [205,92,92],
- indigo: [75,0,130],
- ivory: [255,255,240],
- khaki: [240,230,140],
- lavender: [230,230,250],
- lavenderblush: [255,240,245],
- lawngreen: [124,252,0],
- lemonchiffon: [255,250,205],
- lightblue: [173,216,230],
- lightcoral: [240,128,128],
- lightcyan: [224,255,255],
- lightgoldenrodyellow: [250,250,210],
- lightgray: [211,211,211],
- lightgreen: [144,238,144],
- lightgrey: [211,211,211],
- lightpink: [255,182,193],
- lightsalmon: [255,160,122],
- lightseagreen: [32,178,170],
- lightskyblue: [135,206,250],
- lightslategray: [119,136,153],
- lightslategrey: [119,136,153],
- lightsteelblue: [176,196,222],
- lightyellow: [255,255,224],
- lime: [0,255,0],
- limegreen: [50,205,50],
- linen: [250,240,230],
- magenta: [255,0,255],
- maroon: [128,0,0],
- mediumaquamarine: [102,205,170],
- mediumblue: [0,0,205],
- mediumorchid: [186,85,211],
- mediumpurple: [147,112,219],
- mediumseagreen: [60,179,113],
- mediumslateblue: [123,104,238],
- mediumspringgreen: [0,250,154],
- mediumturquoise: [72,209,204],
- mediumvioletred: [199,21,133],
- midnightblue: [25,25,112],
- mintcream: [245,255,250],
- mistyrose: [255,228,225],
- moccasin: [255,228,181],
- navajowhite: [255,222,173],
- navy: [0,0,128],
- oldlace: [253,245,230],
- olive: [128,128,0],
- olivedrab: [107,142,35],
- orange: [255,165,0],
- orangered: [255,69,0],
- orchid: [218,112,214],
- palegoldenrod: [238,232,170],
- palegreen: [152,251,152],
- paleturquoise: [175,238,238],
- palevioletred: [219,112,147],
- papayawhip: [255,239,213],
- peachpuff: [255,218,185],
- peru: [205,133,63],
- pink: [255,192,203],
- plum: [221,160,221],
- powderblue: [176,224,230],
- purple: [128,0,128],
- rebeccapurple: [102, 51, 153],
- red: [255,0,0],
- rosybrown: [188,143,143],
- royalblue: [65,105,225],
- saddlebrown: [139,69,19],
- salmon: [250,128,114],
- sandybrown: [244,164,96],
- seagreen: [46,139,87],
- seashell: [255,245,238],
- sienna: [160,82,45],
- silver: [192,192,192],
- skyblue: [135,206,235],
- slateblue: [106,90,205],
- slategray: [112,128,144],
- slategrey: [112,128,144],
- snow: [255,250,250],
- springgreen: [0,255,127],
- steelblue: [70,130,180],
- tan: [210,180,140],
- teal: [0,128,128],
- thistle: [216,191,216],
- tomato: [255,99,71],
- turquoise: [64,224,208],
- violet: [238,130,238],
- wheat: [245,222,179],
- white: [255,255,255],
- whitesmoke: [245,245,245],
- yellow: [255,255,0],
- yellowgreen: [154,205,50]
-};
-
-var reverseKeywords = {};
-for (var key in cssKeywords) {
- reverseKeywords[JSON.stringify(cssKeywords[key])] = key;
-}
-
-},{}],4:[function(require,module,exports){
-var conversions = require(3);
-
-var convert = function() {
- return new Converter();
-}
-
-for (var func in conversions) {
- // export Raw versions
- convert[func + "Raw"] = (function(func) {
- // accept array or plain args
- return function(arg) {
- if (typeof arg == "number")
- arg = Array.prototype.slice.call(arguments);
- return conversions[func](arg);
- }
- })(func);
-
- var pair = /(\w+)2(\w+)/.exec(func),
- from = pair[1],
- to = pair[2];
-
- // export rgb2hsl and ["rgb"]["hsl"]
- convert[from] = convert[from] || {};
-
- convert[from][to] = convert[func] = (function(func) {
- return function(arg) {
- if (typeof arg == "number")
- arg = Array.prototype.slice.call(arguments);
-
- var val = conversions[func](arg);
- if (typeof val == "string" || val === undefined)
- return val; // keyword
-
- for (var i = 0; i < val.length; i++)
- val[i] = Math.round(val[i]);
- return val;
- }
- })(func);
-}
-
-
-/* Converter does lazy conversion and caching */
-var Converter = function() {
- this.convs = {};
-};
-
-/* Either get the values for a space or
- set the values for a space, depending on args */
-Converter.prototype.routeSpace = function(space, args) {
- var values = args[0];
- if (values === undefined) {
- // color.rgb()
- return this.getValues(space);
- }
- // color.rgb(10, 10, 10)
- if (typeof values == "number") {
- values = Array.prototype.slice.call(args);
- }
-
- return this.setValues(space, values);
-};
-
-/* Set the values for a space, invalidating cache */
-Converter.prototype.setValues = function(space, values) {
- this.space = space;
- this.convs = {};
- this.convs[space] = values;
- return this;
-};
-
-/* Get the values for a space. If there's already
- a conversion for the space, fetch it, otherwise
- compute it */
-Converter.prototype.getValues = function(space) {
- var vals = this.convs[space];
- if (!vals) {
- var fspace = this.space,
- from = this.convs[fspace];
- vals = convert[fspace][space](from);
-
- this.convs[space] = vals;
- }
- return vals;
-};
-
-["rgb", "hsl", "hsv", "cmyk", "keyword"].forEach(function(space) {
- Converter.prototype[space] = function(vals) {
- return this.routeSpace(space, arguments);
- }
-});
-
-module.exports = convert;
-},{"3":3}],5:[function(require,module,exports){
-'use strict'
-
-module.exports = {
- "aliceblue": [240, 248, 255],
- "antiquewhite": [250, 235, 215],
- "aqua": [0, 255, 255],
- "aquamarine": [127, 255, 212],
- "azure": [240, 255, 255],
- "beige": [245, 245, 220],
- "bisque": [255, 228, 196],
- "black": [0, 0, 0],
- "blanchedalmond": [255, 235, 205],
- "blue": [0, 0, 255],
- "blueviolet": [138, 43, 226],
- "brown": [165, 42, 42],
- "burlywood": [222, 184, 135],
- "cadetblue": [95, 158, 160],
- "chartreuse": [127, 255, 0],
- "chocolate": [210, 105, 30],
- "coral": [255, 127, 80],
- "cornflowerblue": [100, 149, 237],
- "cornsilk": [255, 248, 220],
- "crimson": [220, 20, 60],
- "cyan": [0, 255, 255],
- "darkblue": [0, 0, 139],
- "darkcyan": [0, 139, 139],
- "darkgoldenrod": [184, 134, 11],
- "darkgray": [169, 169, 169],
- "darkgreen": [0, 100, 0],
- "darkgrey": [169, 169, 169],
- "darkkhaki": [189, 183, 107],
- "darkmagenta": [139, 0, 139],
- "darkolivegreen": [85, 107, 47],
- "darkorange": [255, 140, 0],
- "darkorchid": [153, 50, 204],
- "darkred": [139, 0, 0],
- "darksalmon": [233, 150, 122],
- "darkseagreen": [143, 188, 143],
- "darkslateblue": [72, 61, 139],
- "darkslategray": [47, 79, 79],
- "darkslategrey": [47, 79, 79],
- "darkturquoise": [0, 206, 209],
- "darkviolet": [148, 0, 211],
- "deeppink": [255, 20, 147],
- "deepskyblue": [0, 191, 255],
- "dimgray": [105, 105, 105],
- "dimgrey": [105, 105, 105],
- "dodgerblue": [30, 144, 255],
- "firebrick": [178, 34, 34],
- "floralwhite": [255, 250, 240],
- "forestgreen": [34, 139, 34],
- "fuchsia": [255, 0, 255],
- "gainsboro": [220, 220, 220],
- "ghostwhite": [248, 248, 255],
- "gold": [255, 215, 0],
- "goldenrod": [218, 165, 32],
- "gray": [128, 128, 128],
- "green": [0, 128, 0],
- "greenyellow": [173, 255, 47],
- "grey": [128, 128, 128],
- "honeydew": [240, 255, 240],
- "hotpink": [255, 105, 180],
- "indianred": [205, 92, 92],
- "indigo": [75, 0, 130],
- "ivory": [255, 255, 240],
- "khaki": [240, 230, 140],
- "lavender": [230, 230, 250],
- "lavenderblush": [255, 240, 245],
- "lawngreen": [124, 252, 0],
- "lemonchiffon": [255, 250, 205],
- "lightblue": [173, 216, 230],
- "lightcoral": [240, 128, 128],
- "lightcyan": [224, 255, 255],
- "lightgoldenrodyellow": [250, 250, 210],
- "lightgray": [211, 211, 211],
- "lightgreen": [144, 238, 144],
- "lightgrey": [211, 211, 211],
- "lightpink": [255, 182, 193],
- "lightsalmon": [255, 160, 122],
- "lightseagreen": [32, 178, 170],
- "lightskyblue": [135, 206, 250],
- "lightslategray": [119, 136, 153],
- "lightslategrey": [119, 136, 153],
- "lightsteelblue": [176, 196, 222],
- "lightyellow": [255, 255, 224],
- "lime": [0, 255, 0],
- "limegreen": [50, 205, 50],
- "linen": [250, 240, 230],
- "magenta": [255, 0, 255],
- "maroon": [128, 0, 0],
- "mediumaquamarine": [102, 205, 170],
- "mediumblue": [0, 0, 205],
- "mediumorchid": [186, 85, 211],
- "mediumpurple": [147, 112, 219],
- "mediumseagreen": [60, 179, 113],
- "mediumslateblue": [123, 104, 238],
- "mediumspringgreen": [0, 250, 154],
- "mediumturquoise": [72, 209, 204],
- "mediumvioletred": [199, 21, 133],
- "midnightblue": [25, 25, 112],
- "mintcream": [245, 255, 250],
- "mistyrose": [255, 228, 225],
- "moccasin": [255, 228, 181],
- "navajowhite": [255, 222, 173],
- "navy": [0, 0, 128],
- "oldlace": [253, 245, 230],
- "olive": [128, 128, 0],
- "olivedrab": [107, 142, 35],
- "orange": [255, 165, 0],
- "orangered": [255, 69, 0],
- "orchid": [218, 112, 214],
- "palegoldenrod": [238, 232, 170],
- "palegreen": [152, 251, 152],
- "paleturquoise": [175, 238, 238],
- "palevioletred": [219, 112, 147],
- "papayawhip": [255, 239, 213],
- "peachpuff": [255, 218, 185],
- "peru": [205, 133, 63],
- "pink": [255, 192, 203],
- "plum": [221, 160, 221],
- "powderblue": [176, 224, 230],
- "purple": [128, 0, 128],
- "rebeccapurple": [102, 51, 153],
- "red": [255, 0, 0],
- "rosybrown": [188, 143, 143],
- "royalblue": [65, 105, 225],
- "saddlebrown": [139, 69, 19],
- "salmon": [250, 128, 114],
- "sandybrown": [244, 164, 96],
- "seagreen": [46, 139, 87],
- "seashell": [255, 245, 238],
- "sienna": [160, 82, 45],
- "silver": [192, 192, 192],
- "skyblue": [135, 206, 235],
- "slateblue": [106, 90, 205],
- "slategray": [112, 128, 144],
- "slategrey": [112, 128, 144],
- "snow": [255, 250, 250],
- "springgreen": [0, 255, 127],
- "steelblue": [70, 130, 180],
- "tan": [210, 180, 140],
- "teal": [0, 128, 128],
- "thistle": [216, 191, 216],
- "tomato": [255, 99, 71],
- "turquoise": [64, 224, 208],
- "violet": [238, 130, 238],
- "wheat": [245, 222, 179],
- "white": [255, 255, 255],
- "whitesmoke": [245, 245, 245],
- "yellow": [255, 255, 0],
- "yellowgreen": [154, 205, 50]
-};
-
-},{}],6:[function(require,module,exports){
-//! moment.js
-
-;(function (global, factory) {
- typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() :
- typeof define === 'function' && define.amd ? define(factory) :
- global.moment = factory()
-}(this, (function () { 'use strict';
-
- var hookCallback;
-
- function hooks () {
- return hookCallback.apply(null, arguments);
- }
-
- // This is done to register the method called with moment()
- // without creating circular dependencies.
- function setHookCallback (callback) {
- hookCallback = callback;
- }
-
- function isArray(input) {
- return input instanceof Array || Object.prototype.toString.call(input) === '[object Array]';
- }
-
- function isObject(input) {
- // IE8 will treat undefined and null as object if it wasn't for
- // input != null
- return input != null && Object.prototype.toString.call(input) === '[object Object]';
- }
-
- function isObjectEmpty(obj) {
- if (Object.getOwnPropertyNames) {
- return (Object.getOwnPropertyNames(obj).length === 0);
- } else {
- var k;
- for (k in obj) {
- if (obj.hasOwnProperty(k)) {
- return false;
- }
- }
- return true;
- }
- }
-
- function isUndefined(input) {
- return input === void 0;
- }
-
- function isNumber(input) {
- return typeof input === 'number' || Object.prototype.toString.call(input) === '[object Number]';
- }
-
- function isDate(input) {
- return input instanceof Date || Object.prototype.toString.call(input) === '[object Date]';
- }
-
- function map(arr, fn) {
- var res = [], i;
- for (i = 0; i < arr.length; ++i) {
- res.push(fn(arr[i], i));
- }
- return res;
- }
-
- function hasOwnProp(a, b) {
- return Object.prototype.hasOwnProperty.call(a, b);
- }
-
- function extend(a, b) {
- for (var i in b) {
- if (hasOwnProp(b, i)) {
- a[i] = b[i];
- }
- }
-
- if (hasOwnProp(b, 'toString')) {
- a.toString = b.toString;
- }
-
- if (hasOwnProp(b, 'valueOf')) {
- a.valueOf = b.valueOf;
- }
-
- return a;
- }
-
- function createUTC (input, format, locale, strict) {
- return createLocalOrUTC(input, format, locale, strict, true).utc();
- }
-
- function defaultParsingFlags() {
- // We need to deep clone this object.
- return {
- empty : false,
- unusedTokens : [],
- unusedInput : [],
- overflow : -2,
- charsLeftOver : 0,
- nullInput : false,
- invalidMonth : null,
- invalidFormat : false,
- userInvalidated : false,
- iso : false,
- parsedDateParts : [],
- meridiem : null,
- rfc2822 : false,
- weekdayMismatch : false
- };
- }
-
- function getParsingFlags(m) {
- if (m._pf == null) {
- m._pf = defaultParsingFlags();
- }
- return m._pf;
- }
-
- var some;
- if (Array.prototype.some) {
- some = Array.prototype.some;
- } else {
- some = function (fun) {
- var t = Object(this);
- var len = t.length >>> 0;
-
- for (var i = 0; i < len; i++) {
- if (i in t && fun.call(this, t[i], i, t)) {
- return true;
- }
- }
-
- return false;
- };
- }
-
- function isValid(m) {
- if (m._isValid == null) {
- var flags = getParsingFlags(m);
- var parsedParts = some.call(flags.parsedDateParts, function (i) {
- return i != null;
- });
- var isNowValid = !isNaN(m._d.getTime()) &&
- flags.overflow < 0 &&
- !flags.empty &&
- !flags.invalidMonth &&
- !flags.invalidWeekday &&
- !flags.weekdayMismatch &&
- !flags.nullInput &&
- !flags.invalidFormat &&
- !flags.userInvalidated &&
- (!flags.meridiem || (flags.meridiem && parsedParts));
-
- if (m._strict) {
- isNowValid = isNowValid &&
- flags.charsLeftOver === 0 &&
- flags.unusedTokens.length === 0 &&
- flags.bigHour === undefined;
- }
-
- if (Object.isFrozen == null || !Object.isFrozen(m)) {
- m._isValid = isNowValid;
- }
- else {
- return isNowValid;
- }
- }
- return m._isValid;
- }
-
- function createInvalid (flags) {
- var m = createUTC(NaN);
- if (flags != null) {
- extend(getParsingFlags(m), flags);
- }
- else {
- getParsingFlags(m).userInvalidated = true;
- }
-
- return m;
- }
-
- // Plugins that add properties should also add the key here (null value),
- // so we can properly clone ourselves.
- var momentProperties = hooks.momentProperties = [];
-
- function copyConfig(to, from) {
- var i, prop, val;
-
- if (!isUndefined(from._isAMomentObject)) {
- to._isAMomentObject = from._isAMomentObject;
- }
- if (!isUndefined(from._i)) {
- to._i = from._i;
- }
- if (!isUndefined(from._f)) {
- to._f = from._f;
- }
- if (!isUndefined(from._l)) {
- to._l = from._l;
- }
- if (!isUndefined(from._strict)) {
- to._strict = from._strict;
- }
- if (!isUndefined(from._tzm)) {
- to._tzm = from._tzm;
- }
- if (!isUndefined(from._isUTC)) {
- to._isUTC = from._isUTC;
- }
- if (!isUndefined(from._offset)) {
- to._offset = from._offset;
- }
- if (!isUndefined(from._pf)) {
- to._pf = getParsingFlags(from);
- }
- if (!isUndefined(from._locale)) {
- to._locale = from._locale;
- }
-
- if (momentProperties.length > 0) {
- for (i = 0; i < momentProperties.length; i++) {
- prop = momentProperties[i];
- val = from[prop];
- if (!isUndefined(val)) {
- to[prop] = val;
- }
- }
- }
-
- return to;
- }
-
- var updateInProgress = false;
-
- // Moment prototype object
- function Moment(config) {
- copyConfig(this, config);
- this._d = new Date(config._d != null ? config._d.getTime() : NaN);
- if (!this.isValid()) {
- this._d = new Date(NaN);
- }
- // Prevent infinite loop in case updateOffset creates new moment
- // objects.
- if (updateInProgress === false) {
- updateInProgress = true;
- hooks.updateOffset(this);
- updateInProgress = false;
- }
- }
-
- function isMoment (obj) {
- return obj instanceof Moment || (obj != null && obj._isAMomentObject != null);
- }
-
- function absFloor (number) {
- if (number < 0) {
- // -0 -> 0
- return Math.ceil(number) || 0;
- } else {
- return Math.floor(number);
- }
- }
-
- function toInt(argumentForCoercion) {
- var coercedNumber = +argumentForCoercion,
- value = 0;
-
- if (coercedNumber !== 0 && isFinite(coercedNumber)) {
- value = absFloor(coercedNumber);
- }
-
- return value;
- }
-
- // compare two arrays, return the number of differences
- function compareArrays(array1, array2, dontConvert) {
- var len = Math.min(array1.length, array2.length),
- lengthDiff = Math.abs(array1.length - array2.length),
- diffs = 0,
- i;
- for (i = 0; i < len; i++) {
- if ((dontConvert && array1[i] !== array2[i]) ||
- (!dontConvert && toInt(array1[i]) !== toInt(array2[i]))) {
- diffs++;
- }
- }
- return diffs + lengthDiff;
- }
-
- function warn(msg) {
- if (hooks.suppressDeprecationWarnings === false &&
- (typeof console !== 'undefined') && console.warn) {
- console.warn('Deprecation warning: ' + msg);
- }
- }
-
- function deprecate(msg, fn) {
- var firstTime = true;
-
- return extend(function () {
- if (hooks.deprecationHandler != null) {
- hooks.deprecationHandler(null, msg);
- }
- if (firstTime) {
- var args = [];
- var arg;
- for (var i = 0; i < arguments.length; i++) {
- arg = '';
- if (typeof arguments[i] === 'object') {
- arg += '\n[' + i + '] ';
- for (var key in arguments[0]) {
- arg += key + ': ' + arguments[0][key] + ', ';
- }
- arg = arg.slice(0, -2); // Remove trailing comma and space
- } else {
- arg = arguments[i];
- }
- args.push(arg);
- }
- warn(msg + '\nArguments: ' + Array.prototype.slice.call(args).join('') + '\n' + (new Error()).stack);
- firstTime = false;
- }
- return fn.apply(this, arguments);
- }, fn);
- }
-
- var deprecations = {};
-
- function deprecateSimple(name, msg) {
- if (hooks.deprecationHandler != null) {
- hooks.deprecationHandler(name, msg);
- }
- if (!deprecations[name]) {
- warn(msg);
- deprecations[name] = true;
- }
- }
-
- hooks.suppressDeprecationWarnings = false;
- hooks.deprecationHandler = null;
-
- function isFunction(input) {
- return input instanceof Function || Object.prototype.toString.call(input) === '[object Function]';
- }
-
- function set (config) {
- var prop, i;
- for (i in config) {
- prop = config[i];
- if (isFunction(prop)) {
- this[i] = prop;
- } else {
- this['_' + i] = prop;
- }
- }
- this._config = config;
- // Lenient ordinal parsing accepts just a number in addition to
- // number + (possibly) stuff coming from _dayOfMonthOrdinalParse.
- // TODO: Remove "ordinalParse" fallback in next major release.
- this._dayOfMonthOrdinalParseLenient = new RegExp(
- (this._dayOfMonthOrdinalParse.source || this._ordinalParse.source) +
- '|' + (/\d{1,2}/).source);
- }
-
- function mergeConfigs(parentConfig, childConfig) {
- var res = extend({}, parentConfig), prop;
- for (prop in childConfig) {
- if (hasOwnProp(childConfig, prop)) {
- if (isObject(parentConfig[prop]) && isObject(childConfig[prop])) {
- res[prop] = {};
- extend(res[prop], parentConfig[prop]);
- extend(res[prop], childConfig[prop]);
- } else if (childConfig[prop] != null) {
- res[prop] = childConfig[prop];
- } else {
- delete res[prop];
- }
- }
- }
- for (prop in parentConfig) {
- if (hasOwnProp(parentConfig, prop) &&
- !hasOwnProp(childConfig, prop) &&
- isObject(parentConfig[prop])) {
- // make sure changes to properties don't modify parent config
- res[prop] = extend({}, res[prop]);
- }
- }
- return res;
- }
-
- function Locale(config) {
- if (config != null) {
- this.set(config);
- }
- }
-
- var keys;
-
- if (Object.keys) {
- keys = Object.keys;
- } else {
- keys = function (obj) {
- var i, res = [];
- for (i in obj) {
- if (hasOwnProp(obj, i)) {
- res.push(i);
- }
- }
- return res;
- };
- }
-
- var defaultCalendar = {
- sameDay : '[Today at] LT',
- nextDay : '[Tomorrow at] LT',
- nextWeek : 'dddd [at] LT',
- lastDay : '[Yesterday at] LT',
- lastWeek : '[Last] dddd [at] LT',
- sameElse : 'L'
- };
-
- function calendar (key, mom, now) {
- var output = this._calendar[key] || this._calendar['sameElse'];
- return isFunction(output) ? output.call(mom, now) : output;
- }
-
- var defaultLongDateFormat = {
- LTS : 'h:mm:ss A',
- LT : 'h:mm A',
- L : 'MM/DD/YYYY',
- LL : 'MMMM D, YYYY',
- LLL : 'MMMM D, YYYY h:mm A',
- LLLL : 'dddd, MMMM D, YYYY h:mm A'
- };
-
- function longDateFormat (key) {
- var format = this._longDateFormat[key],
- formatUpper = this._longDateFormat[key.toUpperCase()];
-
- if (format || !formatUpper) {
- return format;
- }
-
- this._longDateFormat[key] = formatUpper.replace(/MMMM|MM|DD|dddd/g, function (val) {
- return val.slice(1);
- });
-
- return this._longDateFormat[key];
- }
-
- var defaultInvalidDate = 'Invalid date';
-
- function invalidDate () {
- return this._invalidDate;
- }
-
- var defaultOrdinal = '%d';
- var defaultDayOfMonthOrdinalParse = /\d{1,2}/;
-
- function ordinal (number) {
- return this._ordinal.replace('%d', number);
- }
-
- var defaultRelativeTime = {
- future : 'in %s',
- past : '%s ago',
- s : 'a few seconds',
- ss : '%d seconds',
- m : 'a minute',
- mm : '%d minutes',
- h : 'an hour',
- hh : '%d hours',
- d : 'a day',
- dd : '%d days',
- M : 'a month',
- MM : '%d months',
- y : 'a year',
- yy : '%d years'
- };
-
- function relativeTime (number, withoutSuffix, string, isFuture) {
- var output = this._relativeTime[string];
- return (isFunction(output)) ?
- output(number, withoutSuffix, string, isFuture) :
- output.replace(/%d/i, number);
- }
-
- function pastFuture (diff, output) {
- var format = this._relativeTime[diff > 0 ? 'future' : 'past'];
- return isFunction(format) ? format(output) : format.replace(/%s/i, output);
- }
-
- var aliases = {};
-
- function addUnitAlias (unit, shorthand) {
- var lowerCase = unit.toLowerCase();
- aliases[lowerCase] = aliases[lowerCase + 's'] = aliases[shorthand] = unit;
- }
-
- function normalizeUnits(units) {
- return typeof units === 'string' ? aliases[units] || aliases[units.toLowerCase()] : undefined;
- }
-
- function normalizeObjectUnits(inputObject) {
- var normalizedInput = {},
- normalizedProp,
- prop;
-
- for (prop in inputObject) {
- if (hasOwnProp(inputObject, prop)) {
- normalizedProp = normalizeUnits(prop);
- if (normalizedProp) {
- normalizedInput[normalizedProp] = inputObject[prop];
- }
- }
- }
-
- return normalizedInput;
- }
-
- var priorities = {};
-
- function addUnitPriority(unit, priority) {
- priorities[unit] = priority;
- }
-
- function getPrioritizedUnits(unitsObj) {
- var units = [];
- for (var u in unitsObj) {
- units.push({unit: u, priority: priorities[u]});
- }
- units.sort(function (a, b) {
- return a.priority - b.priority;
- });
- return units;
- }
-
- function zeroFill(number, targetLength, forceSign) {
- var absNumber = '' + Math.abs(number),
- zerosToFill = targetLength - absNumber.length,
- sign = number >= 0;
- return (sign ? (forceSign ? '+' : '') : '-') +
- Math.pow(10, Math.max(0, zerosToFill)).toString().substr(1) + absNumber;
- }
-
- var formattingTokens = /(\[[^\[]*\])|(\\)?([Hh]mm(ss)?|Mo|MM?M?M?|Do|DDDo|DD?D?D?|ddd?d?|do?|w[o|w]?|W[o|W]?|Qo?|YYYYYY|YYYYY|YYYY|YY|gg(ggg?)?|GG(GGG?)?|e|E|a|A|hh?|HH?|kk?|mm?|ss?|S{1,9}|x|X|zz?|ZZ?|.)/g;
-
- var localFormattingTokens = /(\[[^\[]*\])|(\\)?(LTS|LT|LL?L?L?|l{1,4})/g;
-
- var formatFunctions = {};
-
- var formatTokenFunctions = {};
-
- // token: 'M'
- // padded: ['MM', 2]
- // ordinal: 'Mo'
- // callback: function () { this.month() + 1 }
- function addFormatToken (token, padded, ordinal, callback) {
- var func = callback;
- if (typeof callback === 'string') {
- func = function () {
- return this[callback]();
- };
- }
- if (token) {
- formatTokenFunctions[token] = func;
- }
- if (padded) {
- formatTokenFunctions[padded[0]] = function () {
- return zeroFill(func.apply(this, arguments), padded[1], padded[2]);
- };
- }
- if (ordinal) {
- formatTokenFunctions[ordinal] = function () {
- return this.localeData().ordinal(func.apply(this, arguments), token);
- };
- }
- }
-
- function removeFormattingTokens(input) {
- if (input.match(/\[[\s\S]/)) {
- return input.replace(/^\[|\]$/g, '');
- }
- return input.replace(/\\/g, '');
- }
-
- function makeFormatFunction(format) {
- var array = format.match(formattingTokens), i, length;
-
- for (i = 0, length = array.length; i < length; i++) {
- if (formatTokenFunctions[array[i]]) {
- array[i] = formatTokenFunctions[array[i]];
- } else {
- array[i] = removeFormattingTokens(array[i]);
- }
- }
-
- return function (mom) {
- var output = '', i;
- for (i = 0; i < length; i++) {
- output += isFunction(array[i]) ? array[i].call(mom, format) : array[i];
- }
- return output;
- };
- }
-
- // format date using native date object
- function formatMoment(m, format) {
- if (!m.isValid()) {
- return m.localeData().invalidDate();
- }
-
- format = expandFormat(format, m.localeData());
- formatFunctions[format] = formatFunctions[format] || makeFormatFunction(format);
-
- return formatFunctions[format](m);
- }
-
- function expandFormat(format, locale) {
- var i = 5;
-
- function replaceLongDateFormatTokens(input) {
- return locale.longDateFormat(input) || input;
- }
-
- localFormattingTokens.lastIndex = 0;
- while (i >= 0 && localFormattingTokens.test(format)) {
- format = format.replace(localFormattingTokens, replaceLongDateFormatTokens);
- localFormattingTokens.lastIndex = 0;
- i -= 1;
- }
-
- return format;
- }
-
- var match1 = /\d/; // 0 - 9
- var match2 = /\d\d/; // 00 - 99
- var match3 = /\d{3}/; // 000 - 999
- var match4 = /\d{4}/; // 0000 - 9999
- var match6 = /[+-]?\d{6}/; // -999999 - 999999
- var match1to2 = /\d\d?/; // 0 - 99
- var match3to4 = /\d\d\d\d?/; // 999 - 9999
- var match5to6 = /\d\d\d\d\d\d?/; // 99999 - 999999
- var match1to3 = /\d{1,3}/; // 0 - 999
- var match1to4 = /\d{1,4}/; // 0 - 9999
- var match1to6 = /[+-]?\d{1,6}/; // -999999 - 999999
-
- var matchUnsigned = /\d+/; // 0 - inf
- var matchSigned = /[+-]?\d+/; // -inf - inf
-
- var matchOffset = /Z|[+-]\d\d:?\d\d/gi; // +00:00 -00:00 +0000 -0000 or Z
- var matchShortOffset = /Z|[+-]\d\d(?::?\d\d)?/gi; // +00 -00 +00:00 -00:00 +0000 -0000 or Z
-
- var matchTimestamp = /[+-]?\d+(\.\d{1,3})?/; // 123456789 123456789.123
-
- // any word (or two) characters or numbers including two/three word month in arabic.
- // includes scottish gaelic two word and hyphenated months
- var matchWord = /[0-9]{0,256}['a-z\u00A0-\u05FF\u0700-\uD7FF\uF900-\uFDCF\uFDF0-\uFF07\uFF10-\uFFEF]{1,256}|[\u0600-\u06FF\/]{1,256}(\s*?[\u0600-\u06FF]{1,256}){1,2}/i;
-
- var regexes = {};
-
- function addRegexToken (token, regex, strictRegex) {
- regexes[token] = isFunction(regex) ? regex : function (isStrict, localeData) {
- return (isStrict && strictRegex) ? strictRegex : regex;
- };
- }
-
- function getParseRegexForToken (token, config) {
- if (!hasOwnProp(regexes, token)) {
- return new RegExp(unescapeFormat(token));
- }
-
- return regexes[token](config._strict, config._locale);
- }
-
- // Code from http://stackoverflow.com/questions/3561493/is-there-a-regexp-escape-function-in-javascript
- function unescapeFormat(s) {
- return regexEscape(s.replace('\\', '').replace(/\\(\[)|\\(\])|\[([^\]\[]*)\]|\\(.)/g, function (matched, p1, p2, p3, p4) {
- return p1 || p2 || p3 || p4;
- }));
- }
-
- function regexEscape(s) {
- return s.replace(/[-\/\\^$*+?.()|[\]{}]/g, '\\$&');
- }
-
- var tokens = {};
-
- function addParseToken (token, callback) {
- var i, func = callback;
- if (typeof token === 'string') {
- token = [token];
- }
- if (isNumber(callback)) {
- func = function (input, array) {
- array[callback] = toInt(input);
- };
- }
- for (i = 0; i < token.length; i++) {
- tokens[token[i]] = func;
- }
- }
-
- function addWeekParseToken (token, callback) {
- addParseToken(token, function (input, array, config, token) {
- config._w = config._w || {};
- callback(input, config._w, config, token);
- });
- }
-
- function addTimeToArrayFromToken(token, input, config) {
- if (input != null && hasOwnProp(tokens, token)) {
- tokens[token](input, config._a, config, token);
- }
- }
-
- var YEAR = 0;
- var MONTH = 1;
- var DATE = 2;
- var HOUR = 3;
- var MINUTE = 4;
- var SECOND = 5;
- var MILLISECOND = 6;
- var WEEK = 7;
- var WEEKDAY = 8;
-
- // FORMATTING
-
- addFormatToken('Y', 0, 0, function () {
- var y = this.year();
- return y <= 9999 ? '' + y : '+' + y;
- });
-
- addFormatToken(0, ['YY', 2], 0, function () {
- return this.year() % 100;
- });
-
- addFormatToken(0, ['YYYY', 4], 0, 'year');
- addFormatToken(0, ['YYYYY', 5], 0, 'year');
- addFormatToken(0, ['YYYYYY', 6, true], 0, 'year');
-
- // ALIASES
-
- addUnitAlias('year', 'y');
-
- // PRIORITIES
-
- addUnitPriority('year', 1);
-
- // PARSING
-
- addRegexToken('Y', matchSigned);
- addRegexToken('YY', match1to2, match2);
- addRegexToken('YYYY', match1to4, match4);
- addRegexToken('YYYYY', match1to6, match6);
- addRegexToken('YYYYYY', match1to6, match6);
-
- addParseToken(['YYYYY', 'YYYYYY'], YEAR);
- addParseToken('YYYY', function (input, array) {
- array[YEAR] = input.length === 2 ? hooks.parseTwoDigitYear(input) : toInt(input);
- });
- addParseToken('YY', function (input, array) {
- array[YEAR] = hooks.parseTwoDigitYear(input);
- });
- addParseToken('Y', function (input, array) {
- array[YEAR] = parseInt(input, 10);
- });
-
- // HELPERS
-
- function daysInYear(year) {
- return isLeapYear(year) ? 366 : 365;
- }
-
- function isLeapYear(year) {
- return (year % 4 === 0 && year % 100 !== 0) || year % 400 === 0;
- }
-
- // HOOKS
-
- hooks.parseTwoDigitYear = function (input) {
- return toInt(input) + (toInt(input) > 68 ? 1900 : 2000);
- };
-
- // MOMENTS
-
- var getSetYear = makeGetSet('FullYear', true);
-
- function getIsLeapYear () {
- return isLeapYear(this.year());
- }
-
- function makeGetSet (unit, keepTime) {
- return function (value) {
- if (value != null) {
- set$1(this, unit, value);
- hooks.updateOffset(this, keepTime);
- return this;
- } else {
- return get(this, unit);
- }
- };
- }
-
- function get (mom, unit) {
- return mom.isValid() ?
- mom._d['get' + (mom._isUTC ? 'UTC' : '') + unit]() : NaN;
- }
-
- function set$1 (mom, unit, value) {
- if (mom.isValid() && !isNaN(value)) {
- if (unit === 'FullYear' && isLeapYear(mom.year()) && mom.month() === 1 && mom.date() === 29) {
- mom._d['set' + (mom._isUTC ? 'UTC' : '') + unit](value, mom.month(), daysInMonth(value, mom.month()));
- }
- else {
- mom._d['set' + (mom._isUTC ? 'UTC' : '') + unit](value);
- }
- }
- }
-
- // MOMENTS
-
- function stringGet (units) {
- units = normalizeUnits(units);
- if (isFunction(this[units])) {
- return this[units]();
- }
- return this;
- }
-
-
- function stringSet (units, value) {
- if (typeof units === 'object') {
- units = normalizeObjectUnits(units);
- var prioritized = getPrioritizedUnits(units);
- for (var i = 0; i < prioritized.length; i++) {
- this[prioritized[i].unit](units[prioritized[i].unit]);
- }
- } else {
- units = normalizeUnits(units);
- if (isFunction(this[units])) {
- return this[units](value);
- }
- }
- return this;
- }
-
- function mod(n, x) {
- return ((n % x) + x) % x;
- }
-
- var indexOf;
-
- if (Array.prototype.indexOf) {
- indexOf = Array.prototype.indexOf;
- } else {
- indexOf = function (o) {
- // I know
- var i;
- for (i = 0; i < this.length; ++i) {
- if (this[i] === o) {
- return i;
- }
- }
- return -1;
- };
- }
-
- function daysInMonth(year, month) {
- if (isNaN(year) || isNaN(month)) {
- return NaN;
- }
- var modMonth = mod(month, 12);
- year += (month - modMonth) / 12;
- return modMonth === 1 ? (isLeapYear(year) ? 29 : 28) : (31 - modMonth % 7 % 2);
- }
-
- // FORMATTING
-
- addFormatToken('M', ['MM', 2], 'Mo', function () {
- return this.month() + 1;
- });
-
- addFormatToken('MMM', 0, 0, function (format) {
- return this.localeData().monthsShort(this, format);
- });
-
- addFormatToken('MMMM', 0, 0, function (format) {
- return this.localeData().months(this, format);
- });
-
- // ALIASES
-
- addUnitAlias('month', 'M');
-
- // PRIORITY
-
- addUnitPriority('month', 8);
-
- // PARSING
-
- addRegexToken('M', match1to2);
- addRegexToken('MM', match1to2, match2);
- addRegexToken('MMM', function (isStrict, locale) {
- return locale.monthsShortRegex(isStrict);
- });
- addRegexToken('MMMM', function (isStrict, locale) {
- return locale.monthsRegex(isStrict);
- });
-
- addParseToken(['M', 'MM'], function (input, array) {
- array[MONTH] = toInt(input) - 1;
- });
-
- addParseToken(['MMM', 'MMMM'], function (input, array, config, token) {
- var month = config._locale.monthsParse(input, token, config._strict);
- // if we didn't find a month name, mark the date as invalid.
- if (month != null) {
- array[MONTH] = month;
- } else {
- getParsingFlags(config).invalidMonth = input;
- }
- });
-
- // LOCALES
-
- var MONTHS_IN_FORMAT = /D[oD]?(\[[^\[\]]*\]|\s)+MMMM?/;
- var defaultLocaleMonths = 'January_February_March_April_May_June_July_August_September_October_November_December'.split('_');
- function localeMonths (m, format) {
- if (!m) {
- return isArray(this._months) ? this._months :
- this._months['standalone'];
- }
- return isArray(this._months) ? this._months[m.month()] :
- this._months[(this._months.isFormat || MONTHS_IN_FORMAT).test(format) ? 'format' : 'standalone'][m.month()];
- }
-
- var defaultLocaleMonthsShort = 'Jan_Feb_Mar_Apr_May_Jun_Jul_Aug_Sep_Oct_Nov_Dec'.split('_');
- function localeMonthsShort (m, format) {
- if (!m) {
- return isArray(this._monthsShort) ? this._monthsShort :
- this._monthsShort['standalone'];
- }
- return isArray(this._monthsShort) ? this._monthsShort[m.month()] :
- this._monthsShort[MONTHS_IN_FORMAT.test(format) ? 'format' : 'standalone'][m.month()];
- }
-
- function handleStrictParse(monthName, format, strict) {
- var i, ii, mom, llc = monthName.toLocaleLowerCase();
- if (!this._monthsParse) {
- // this is not used
- this._monthsParse = [];
- this._longMonthsParse = [];
- this._shortMonthsParse = [];
- for (i = 0; i < 12; ++i) {
- mom = createUTC([2000, i]);
- this._shortMonthsParse[i] = this.monthsShort(mom, '').toLocaleLowerCase();
- this._longMonthsParse[i] = this.months(mom, '').toLocaleLowerCase();
- }
- }
-
- if (strict) {
- if (format === 'MMM') {
- ii = indexOf.call(this._shortMonthsParse, llc);
- return ii !== -1 ? ii : null;
- } else {
- ii = indexOf.call(this._longMonthsParse, llc);
- return ii !== -1 ? ii : null;
- }
- } else {
- if (format === 'MMM') {
- ii = indexOf.call(this._shortMonthsParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._longMonthsParse, llc);
- return ii !== -1 ? ii : null;
- } else {
- ii = indexOf.call(this._longMonthsParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._shortMonthsParse, llc);
- return ii !== -1 ? ii : null;
- }
- }
- }
-
- function localeMonthsParse (monthName, format, strict) {
- var i, mom, regex;
-
- if (this._monthsParseExact) {
- return handleStrictParse.call(this, monthName, format, strict);
- }
-
- if (!this._monthsParse) {
- this._monthsParse = [];
- this._longMonthsParse = [];
- this._shortMonthsParse = [];
- }
-
- // TODO: add sorting
- // Sorting makes sure if one month (or abbr) is a prefix of another
- // see sorting in computeMonthsParse
- for (i = 0; i < 12; i++) {
- // make the regex if we don't have it already
- mom = createUTC([2000, i]);
- if (strict && !this._longMonthsParse[i]) {
- this._longMonthsParse[i] = new RegExp('^' + this.months(mom, '').replace('.', '') + '$', 'i');
- this._shortMonthsParse[i] = new RegExp('^' + this.monthsShort(mom, '').replace('.', '') + '$', 'i');
- }
- if (!strict && !this._monthsParse[i]) {
- regex = '^' + this.months(mom, '') + '|^' + this.monthsShort(mom, '');
- this._monthsParse[i] = new RegExp(regex.replace('.', ''), 'i');
- }
- // test the regex
- if (strict && format === 'MMMM' && this._longMonthsParse[i].test(monthName)) {
- return i;
- } else if (strict && format === 'MMM' && this._shortMonthsParse[i].test(monthName)) {
- return i;
- } else if (!strict && this._monthsParse[i].test(monthName)) {
- return i;
- }
- }
- }
-
- // MOMENTS
-
- function setMonth (mom, value) {
- var dayOfMonth;
-
- if (!mom.isValid()) {
- // No op
- return mom;
- }
-
- if (typeof value === 'string') {
- if (/^\d+$/.test(value)) {
- value = toInt(value);
- } else {
- value = mom.localeData().monthsParse(value);
- // TODO: Another silent failure?
- if (!isNumber(value)) {
- return mom;
- }
- }
- }
-
- dayOfMonth = Math.min(mom.date(), daysInMonth(mom.year(), value));
- mom._d['set' + (mom._isUTC ? 'UTC' : '') + 'Month'](value, dayOfMonth);
- return mom;
- }
-
- function getSetMonth (value) {
- if (value != null) {
- setMonth(this, value);
- hooks.updateOffset(this, true);
- return this;
- } else {
- return get(this, 'Month');
- }
- }
-
- function getDaysInMonth () {
- return daysInMonth(this.year(), this.month());
- }
-
- var defaultMonthsShortRegex = matchWord;
- function monthsShortRegex (isStrict) {
- if (this._monthsParseExact) {
- if (!hasOwnProp(this, '_monthsRegex')) {
- computeMonthsParse.call(this);
- }
- if (isStrict) {
- return this._monthsShortStrictRegex;
- } else {
- return this._monthsShortRegex;
- }
- } else {
- if (!hasOwnProp(this, '_monthsShortRegex')) {
- this._monthsShortRegex = defaultMonthsShortRegex;
- }
- return this._monthsShortStrictRegex && isStrict ?
- this._monthsShortStrictRegex : this._monthsShortRegex;
- }
- }
-
- var defaultMonthsRegex = matchWord;
- function monthsRegex (isStrict) {
- if (this._monthsParseExact) {
- if (!hasOwnProp(this, '_monthsRegex')) {
- computeMonthsParse.call(this);
- }
- if (isStrict) {
- return this._monthsStrictRegex;
- } else {
- return this._monthsRegex;
- }
- } else {
- if (!hasOwnProp(this, '_monthsRegex')) {
- this._monthsRegex = defaultMonthsRegex;
- }
- return this._monthsStrictRegex && isStrict ?
- this._monthsStrictRegex : this._monthsRegex;
- }
- }
-
- function computeMonthsParse () {
- function cmpLenRev(a, b) {
- return b.length - a.length;
- }
-
- var shortPieces = [], longPieces = [], mixedPieces = [],
- i, mom;
- for (i = 0; i < 12; i++) {
- // make the regex if we don't have it already
- mom = createUTC([2000, i]);
- shortPieces.push(this.monthsShort(mom, ''));
- longPieces.push(this.months(mom, ''));
- mixedPieces.push(this.months(mom, ''));
- mixedPieces.push(this.monthsShort(mom, ''));
- }
- // Sorting makes sure if one month (or abbr) is a prefix of another it
- // will match the longer piece.
- shortPieces.sort(cmpLenRev);
- longPieces.sort(cmpLenRev);
- mixedPieces.sort(cmpLenRev);
- for (i = 0; i < 12; i++) {
- shortPieces[i] = regexEscape(shortPieces[i]);
- longPieces[i] = regexEscape(longPieces[i]);
- }
- for (i = 0; i < 24; i++) {
- mixedPieces[i] = regexEscape(mixedPieces[i]);
- }
-
- this._monthsRegex = new RegExp('^(' + mixedPieces.join('|') + ')', 'i');
- this._monthsShortRegex = this._monthsRegex;
- this._monthsStrictRegex = new RegExp('^(' + longPieces.join('|') + ')', 'i');
- this._monthsShortStrictRegex = new RegExp('^(' + shortPieces.join('|') + ')', 'i');
- }
-
- function createDate (y, m, d, h, M, s, ms) {
- // can't just apply() to create a date:
- // https://stackoverflow.com/q/181348
- var date = new Date(y, m, d, h, M, s, ms);
-
- // the date constructor remaps years 0-99 to 1900-1999
- if (y < 100 && y >= 0 && isFinite(date.getFullYear())) {
- date.setFullYear(y);
- }
- return date;
- }
-
- function createUTCDate (y) {
- var date = new Date(Date.UTC.apply(null, arguments));
-
- // the Date.UTC function remaps years 0-99 to 1900-1999
- if (y < 100 && y >= 0 && isFinite(date.getUTCFullYear())) {
- date.setUTCFullYear(y);
- }
- return date;
- }
-
- // start-of-first-week - start-of-year
- function firstWeekOffset(year, dow, doy) {
- var // first-week day -- which january is always in the first week (4 for iso, 1 for other)
- fwd = 7 + dow - doy,
- // first-week day local weekday -- which local weekday is fwd
- fwdlw = (7 + createUTCDate(year, 0, fwd).getUTCDay() - dow) % 7;
-
- return -fwdlw + fwd - 1;
- }
-
- // https://en.wikipedia.org/wiki/ISO_week_date#Calculating_a_date_given_the_year.2C_week_number_and_weekday
- function dayOfYearFromWeeks(year, week, weekday, dow, doy) {
- var localWeekday = (7 + weekday - dow) % 7,
- weekOffset = firstWeekOffset(year, dow, doy),
- dayOfYear = 1 + 7 * (week - 1) + localWeekday + weekOffset,
- resYear, resDayOfYear;
-
- if (dayOfYear <= 0) {
- resYear = year - 1;
- resDayOfYear = daysInYear(resYear) + dayOfYear;
- } else if (dayOfYear > daysInYear(year)) {
- resYear = year + 1;
- resDayOfYear = dayOfYear - daysInYear(year);
- } else {
- resYear = year;
- resDayOfYear = dayOfYear;
- }
-
- return {
- year: resYear,
- dayOfYear: resDayOfYear
- };
- }
-
- function weekOfYear(mom, dow, doy) {
- var weekOffset = firstWeekOffset(mom.year(), dow, doy),
- week = Math.floor((mom.dayOfYear() - weekOffset - 1) / 7) + 1,
- resWeek, resYear;
-
- if (week < 1) {
- resYear = mom.year() - 1;
- resWeek = week + weeksInYear(resYear, dow, doy);
- } else if (week > weeksInYear(mom.year(), dow, doy)) {
- resWeek = week - weeksInYear(mom.year(), dow, doy);
- resYear = mom.year() + 1;
- } else {
- resYear = mom.year();
- resWeek = week;
- }
-
- return {
- week: resWeek,
- year: resYear
- };
- }
-
- function weeksInYear(year, dow, doy) {
- var weekOffset = firstWeekOffset(year, dow, doy),
- weekOffsetNext = firstWeekOffset(year + 1, dow, doy);
- return (daysInYear(year) - weekOffset + weekOffsetNext) / 7;
- }
-
- // FORMATTING
-
- addFormatToken('w', ['ww', 2], 'wo', 'week');
- addFormatToken('W', ['WW', 2], 'Wo', 'isoWeek');
-
- // ALIASES
-
- addUnitAlias('week', 'w');
- addUnitAlias('isoWeek', 'W');
-
- // PRIORITIES
-
- addUnitPriority('week', 5);
- addUnitPriority('isoWeek', 5);
-
- // PARSING
-
- addRegexToken('w', match1to2);
- addRegexToken('ww', match1to2, match2);
- addRegexToken('W', match1to2);
- addRegexToken('WW', match1to2, match2);
-
- addWeekParseToken(['w', 'ww', 'W', 'WW'], function (input, week, config, token) {
- week[token.substr(0, 1)] = toInt(input);
- });
-
- // HELPERS
-
- // LOCALES
-
- function localeWeek (mom) {
- return weekOfYear(mom, this._week.dow, this._week.doy).week;
- }
-
- var defaultLocaleWeek = {
- dow : 0, // Sunday is the first day of the week.
- doy : 6 // The week that contains Jan 1st is the first week of the year.
- };
-
- function localeFirstDayOfWeek () {
- return this._week.dow;
- }
-
- function localeFirstDayOfYear () {
- return this._week.doy;
- }
-
- // MOMENTS
-
- function getSetWeek (input) {
- var week = this.localeData().week(this);
- return input == null ? week : this.add((input - week) * 7, 'd');
- }
-
- function getSetISOWeek (input) {
- var week = weekOfYear(this, 1, 4).week;
- return input == null ? week : this.add((input - week) * 7, 'd');
- }
-
- // FORMATTING
-
- addFormatToken('d', 0, 'do', 'day');
-
- addFormatToken('dd', 0, 0, function (format) {
- return this.localeData().weekdaysMin(this, format);
- });
-
- addFormatToken('ddd', 0, 0, function (format) {
- return this.localeData().weekdaysShort(this, format);
- });
-
- addFormatToken('dddd', 0, 0, function (format) {
- return this.localeData().weekdays(this, format);
- });
-
- addFormatToken('e', 0, 0, 'weekday');
- addFormatToken('E', 0, 0, 'isoWeekday');
-
- // ALIASES
-
- addUnitAlias('day', 'd');
- addUnitAlias('weekday', 'e');
- addUnitAlias('isoWeekday', 'E');
-
- // PRIORITY
- addUnitPriority('day', 11);
- addUnitPriority('weekday', 11);
- addUnitPriority('isoWeekday', 11);
-
- // PARSING
-
- addRegexToken('d', match1to2);
- addRegexToken('e', match1to2);
- addRegexToken('E', match1to2);
- addRegexToken('dd', function (isStrict, locale) {
- return locale.weekdaysMinRegex(isStrict);
- });
- addRegexToken('ddd', function (isStrict, locale) {
- return locale.weekdaysShortRegex(isStrict);
- });
- addRegexToken('dddd', function (isStrict, locale) {
- return locale.weekdaysRegex(isStrict);
- });
-
- addWeekParseToken(['dd', 'ddd', 'dddd'], function (input, week, config, token) {
- var weekday = config._locale.weekdaysParse(input, token, config._strict);
- // if we didn't get a weekday name, mark the date as invalid
- if (weekday != null) {
- week.d = weekday;
- } else {
- getParsingFlags(config).invalidWeekday = input;
- }
- });
-
- addWeekParseToken(['d', 'e', 'E'], function (input, week, config, token) {
- week[token] = toInt(input);
- });
-
- // HELPERS
-
- function parseWeekday(input, locale) {
- if (typeof input !== 'string') {
- return input;
- }
-
- if (!isNaN(input)) {
- return parseInt(input, 10);
- }
-
- input = locale.weekdaysParse(input);
- if (typeof input === 'number') {
- return input;
- }
-
- return null;
- }
-
- function parseIsoWeekday(input, locale) {
- if (typeof input === 'string') {
- return locale.weekdaysParse(input) % 7 || 7;
- }
- return isNaN(input) ? null : input;
- }
-
- // LOCALES
-
- var defaultLocaleWeekdays = 'Sunday_Monday_Tuesday_Wednesday_Thursday_Friday_Saturday'.split('_');
- function localeWeekdays (m, format) {
- if (!m) {
- return isArray(this._weekdays) ? this._weekdays :
- this._weekdays['standalone'];
- }
- return isArray(this._weekdays) ? this._weekdays[m.day()] :
- this._weekdays[this._weekdays.isFormat.test(format) ? 'format' : 'standalone'][m.day()];
- }
-
- var defaultLocaleWeekdaysShort = 'Sun_Mon_Tue_Wed_Thu_Fri_Sat'.split('_');
- function localeWeekdaysShort (m) {
- return (m) ? this._weekdaysShort[m.day()] : this._weekdaysShort;
- }
-
- var defaultLocaleWeekdaysMin = 'Su_Mo_Tu_We_Th_Fr_Sa'.split('_');
- function localeWeekdaysMin (m) {
- return (m) ? this._weekdaysMin[m.day()] : this._weekdaysMin;
- }
-
- function handleStrictParse$1(weekdayName, format, strict) {
- var i, ii, mom, llc = weekdayName.toLocaleLowerCase();
- if (!this._weekdaysParse) {
- this._weekdaysParse = [];
- this._shortWeekdaysParse = [];
- this._minWeekdaysParse = [];
-
- for (i = 0; i < 7; ++i) {
- mom = createUTC([2000, 1]).day(i);
- this._minWeekdaysParse[i] = this.weekdaysMin(mom, '').toLocaleLowerCase();
- this._shortWeekdaysParse[i] = this.weekdaysShort(mom, '').toLocaleLowerCase();
- this._weekdaysParse[i] = this.weekdays(mom, '').toLocaleLowerCase();
- }
- }
-
- if (strict) {
- if (format === 'dddd') {
- ii = indexOf.call(this._weekdaysParse, llc);
- return ii !== -1 ? ii : null;
- } else if (format === 'ddd') {
- ii = indexOf.call(this._shortWeekdaysParse, llc);
- return ii !== -1 ? ii : null;
- } else {
- ii = indexOf.call(this._minWeekdaysParse, llc);
- return ii !== -1 ? ii : null;
- }
- } else {
- if (format === 'dddd') {
- ii = indexOf.call(this._weekdaysParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._shortWeekdaysParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._minWeekdaysParse, llc);
- return ii !== -1 ? ii : null;
- } else if (format === 'ddd') {
- ii = indexOf.call(this._shortWeekdaysParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._weekdaysParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._minWeekdaysParse, llc);
- return ii !== -1 ? ii : null;
- } else {
- ii = indexOf.call(this._minWeekdaysParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._weekdaysParse, llc);
- if (ii !== -1) {
- return ii;
- }
- ii = indexOf.call(this._shortWeekdaysParse, llc);
- return ii !== -1 ? ii : null;
- }
- }
- }
-
- function localeWeekdaysParse (weekdayName, format, strict) {
- var i, mom, regex;
-
- if (this._weekdaysParseExact) {
- return handleStrictParse$1.call(this, weekdayName, format, strict);
- }
-
- if (!this._weekdaysParse) {
- this._weekdaysParse = [];
- this._minWeekdaysParse = [];
- this._shortWeekdaysParse = [];
- this._fullWeekdaysParse = [];
- }
-
- for (i = 0; i < 7; i++) {
- // make the regex if we don't have it already
-
- mom = createUTC([2000, 1]).day(i);
- if (strict && !this._fullWeekdaysParse[i]) {
- this._fullWeekdaysParse[i] = new RegExp('^' + this.weekdays(mom, '').replace('.', '\\.?') + '$', 'i');
- this._shortWeekdaysParse[i] = new RegExp('^' + this.weekdaysShort(mom, '').replace('.', '\\.?') + '$', 'i');
- this._minWeekdaysParse[i] = new RegExp('^' + this.weekdaysMin(mom, '').replace('.', '\\.?') + '$', 'i');
- }
- if (!this._weekdaysParse[i]) {
- regex = '^' + this.weekdays(mom, '') + '|^' + this.weekdaysShort(mom, '') + '|^' + this.weekdaysMin(mom, '');
- this._weekdaysParse[i] = new RegExp(regex.replace('.', ''), 'i');
- }
- // test the regex
- if (strict && format === 'dddd' && this._fullWeekdaysParse[i].test(weekdayName)) {
- return i;
- } else if (strict && format === 'ddd' && this._shortWeekdaysParse[i].test(weekdayName)) {
- return i;
- } else if (strict && format === 'dd' && this._minWeekdaysParse[i].test(weekdayName)) {
- return i;
- } else if (!strict && this._weekdaysParse[i].test(weekdayName)) {
- return i;
- }
- }
- }
-
- // MOMENTS
-
- function getSetDayOfWeek (input) {
- if (!this.isValid()) {
- return input != null ? this : NaN;
- }
- var day = this._isUTC ? this._d.getUTCDay() : this._d.getDay();
- if (input != null) {
- input = parseWeekday(input, this.localeData());
- return this.add(input - day, 'd');
- } else {
- return day;
- }
- }
-
- function getSetLocaleDayOfWeek (input) {
- if (!this.isValid()) {
- return input != null ? this : NaN;
- }
- var weekday = (this.day() + 7 - this.localeData()._week.dow) % 7;
- return input == null ? weekday : this.add(input - weekday, 'd');
- }
-
- function getSetISODayOfWeek (input) {
- if (!this.isValid()) {
- return input != null ? this : NaN;
- }
-
- // behaves the same as moment#day except
- // as a getter, returns 7 instead of 0 (1-7 range instead of 0-6)
- // as a setter, sunday should belong to the previous week.
-
- if (input != null) {
- var weekday = parseIsoWeekday(input, this.localeData());
- return this.day(this.day() % 7 ? weekday : weekday - 7);
- } else {
- return this.day() || 7;
- }
- }
-
- var defaultWeekdaysRegex = matchWord;
- function weekdaysRegex (isStrict) {
- if (this._weekdaysParseExact) {
- if (!hasOwnProp(this, '_weekdaysRegex')) {
- computeWeekdaysParse.call(this);
- }
- if (isStrict) {
- return this._weekdaysStrictRegex;
- } else {
- return this._weekdaysRegex;
- }
- } else {
- if (!hasOwnProp(this, '_weekdaysRegex')) {
- this._weekdaysRegex = defaultWeekdaysRegex;
- }
- return this._weekdaysStrictRegex && isStrict ?
- this._weekdaysStrictRegex : this._weekdaysRegex;
- }
- }
-
- var defaultWeekdaysShortRegex = matchWord;
- function weekdaysShortRegex (isStrict) {
- if (this._weekdaysParseExact) {
- if (!hasOwnProp(this, '_weekdaysRegex')) {
- computeWeekdaysParse.call(this);
- }
- if (isStrict) {
- return this._weekdaysShortStrictRegex;
- } else {
- return this._weekdaysShortRegex;
- }
- } else {
- if (!hasOwnProp(this, '_weekdaysShortRegex')) {
- this._weekdaysShortRegex = defaultWeekdaysShortRegex;
- }
- return this._weekdaysShortStrictRegex && isStrict ?
- this._weekdaysShortStrictRegex : this._weekdaysShortRegex;
- }
- }
-
- var defaultWeekdaysMinRegex = matchWord;
- function weekdaysMinRegex (isStrict) {
- if (this._weekdaysParseExact) {
- if (!hasOwnProp(this, '_weekdaysRegex')) {
- computeWeekdaysParse.call(this);
- }
- if (isStrict) {
- return this._weekdaysMinStrictRegex;
- } else {
- return this._weekdaysMinRegex;
- }
- } else {
- if (!hasOwnProp(this, '_weekdaysMinRegex')) {
- this._weekdaysMinRegex = defaultWeekdaysMinRegex;
- }
- return this._weekdaysMinStrictRegex && isStrict ?
- this._weekdaysMinStrictRegex : this._weekdaysMinRegex;
- }
- }
-
-
- function computeWeekdaysParse () {
- function cmpLenRev(a, b) {
- return b.length - a.length;
- }
-
- var minPieces = [], shortPieces = [], longPieces = [], mixedPieces = [],
- i, mom, minp, shortp, longp;
- for (i = 0; i < 7; i++) {
- // make the regex if we don't have it already
- mom = createUTC([2000, 1]).day(i);
- minp = this.weekdaysMin(mom, '');
- shortp = this.weekdaysShort(mom, '');
- longp = this.weekdays(mom, '');
- minPieces.push(minp);
- shortPieces.push(shortp);
- longPieces.push(longp);
- mixedPieces.push(minp);
- mixedPieces.push(shortp);
- mixedPieces.push(longp);
- }
- // Sorting makes sure if one weekday (or abbr) is a prefix of another it
- // will match the longer piece.
- minPieces.sort(cmpLenRev);
- shortPieces.sort(cmpLenRev);
- longPieces.sort(cmpLenRev);
- mixedPieces.sort(cmpLenRev);
- for (i = 0; i < 7; i++) {
- shortPieces[i] = regexEscape(shortPieces[i]);
- longPieces[i] = regexEscape(longPieces[i]);
- mixedPieces[i] = regexEscape(mixedPieces[i]);
- }
-
- this._weekdaysRegex = new RegExp('^(' + mixedPieces.join('|') + ')', 'i');
- this._weekdaysShortRegex = this._weekdaysRegex;
- this._weekdaysMinRegex = this._weekdaysRegex;
-
- this._weekdaysStrictRegex = new RegExp('^(' + longPieces.join('|') + ')', 'i');
- this._weekdaysShortStrictRegex = new RegExp('^(' + shortPieces.join('|') + ')', 'i');
- this._weekdaysMinStrictRegex = new RegExp('^(' + minPieces.join('|') + ')', 'i');
- }
-
- // FORMATTING
-
- function hFormat() {
- return this.hours() % 12 || 12;
- }
-
- function kFormat() {
- return this.hours() || 24;
- }
-
- addFormatToken('H', ['HH', 2], 0, 'hour');
- addFormatToken('h', ['hh', 2], 0, hFormat);
- addFormatToken('k', ['kk', 2], 0, kFormat);
-
- addFormatToken('hmm', 0, 0, function () {
- return '' + hFormat.apply(this) + zeroFill(this.minutes(), 2);
- });
-
- addFormatToken('hmmss', 0, 0, function () {
- return '' + hFormat.apply(this) + zeroFill(this.minutes(), 2) +
- zeroFill(this.seconds(), 2);
- });
-
- addFormatToken('Hmm', 0, 0, function () {
- return '' + this.hours() + zeroFill(this.minutes(), 2);
- });
-
- addFormatToken('Hmmss', 0, 0, function () {
- return '' + this.hours() + zeroFill(this.minutes(), 2) +
- zeroFill(this.seconds(), 2);
- });
-
- function meridiem (token, lowercase) {
- addFormatToken(token, 0, 0, function () {
- return this.localeData().meridiem(this.hours(), this.minutes(), lowercase);
- });
- }
-
- meridiem('a', true);
- meridiem('A', false);
-
- // ALIASES
-
- addUnitAlias('hour', 'h');
-
- // PRIORITY
- addUnitPriority('hour', 13);
-
- // PARSING
-
- function matchMeridiem (isStrict, locale) {
- return locale._meridiemParse;
- }
-
- addRegexToken('a', matchMeridiem);
- addRegexToken('A', matchMeridiem);
- addRegexToken('H', match1to2);
- addRegexToken('h', match1to2);
- addRegexToken('k', match1to2);
- addRegexToken('HH', match1to2, match2);
- addRegexToken('hh', match1to2, match2);
- addRegexToken('kk', match1to2, match2);
-
- addRegexToken('hmm', match3to4);
- addRegexToken('hmmss', match5to6);
- addRegexToken('Hmm', match3to4);
- addRegexToken('Hmmss', match5to6);
-
- addParseToken(['H', 'HH'], HOUR);
- addParseToken(['k', 'kk'], function (input, array, config) {
- var kInput = toInt(input);
- array[HOUR] = kInput === 24 ? 0 : kInput;
- });
- addParseToken(['a', 'A'], function (input, array, config) {
- config._isPm = config._locale.isPM(input);
- config._meridiem = input;
- });
- addParseToken(['h', 'hh'], function (input, array, config) {
- array[HOUR] = toInt(input);
- getParsingFlags(config).bigHour = true;
- });
- addParseToken('hmm', function (input, array, config) {
- var pos = input.length - 2;
- array[HOUR] = toInt(input.substr(0, pos));
- array[MINUTE] = toInt(input.substr(pos));
- getParsingFlags(config).bigHour = true;
- });
- addParseToken('hmmss', function (input, array, config) {
- var pos1 = input.length - 4;
- var pos2 = input.length - 2;
- array[HOUR] = toInt(input.substr(0, pos1));
- array[MINUTE] = toInt(input.substr(pos1, 2));
- array[SECOND] = toInt(input.substr(pos2));
- getParsingFlags(config).bigHour = true;
- });
- addParseToken('Hmm', function (input, array, config) {
- var pos = input.length - 2;
- array[HOUR] = toInt(input.substr(0, pos));
- array[MINUTE] = toInt(input.substr(pos));
- });
- addParseToken('Hmmss', function (input, array, config) {
- var pos1 = input.length - 4;
- var pos2 = input.length - 2;
- array[HOUR] = toInt(input.substr(0, pos1));
- array[MINUTE] = toInt(input.substr(pos1, 2));
- array[SECOND] = toInt(input.substr(pos2));
- });
-
- // LOCALES
-
- function localeIsPM (input) {
- // IE8 Quirks Mode & IE7 Standards Mode do not allow accessing strings like arrays
- // Using charAt should be more compatible.
- return ((input + '').toLowerCase().charAt(0) === 'p');
- }
-
- var defaultLocaleMeridiemParse = /[ap]\.?m?\.?/i;
- function localeMeridiem (hours, minutes, isLower) {
- if (hours > 11) {
- return isLower ? 'pm' : 'PM';
- } else {
- return isLower ? 'am' : 'AM';
- }
- }
-
-
- // MOMENTS
-
- // Setting the hour should keep the time, because the user explicitly
- // specified which hour they want. So trying to maintain the same hour (in
- // a new timezone) makes sense. Adding/subtracting hours does not follow
- // this rule.
- var getSetHour = makeGetSet('Hours', true);
-
- var baseConfig = {
- calendar: defaultCalendar,
- longDateFormat: defaultLongDateFormat,
- invalidDate: defaultInvalidDate,
- ordinal: defaultOrdinal,
- dayOfMonthOrdinalParse: defaultDayOfMonthOrdinalParse,
- relativeTime: defaultRelativeTime,
-
- months: defaultLocaleMonths,
- monthsShort: defaultLocaleMonthsShort,
-
- week: defaultLocaleWeek,
-
- weekdays: defaultLocaleWeekdays,
- weekdaysMin: defaultLocaleWeekdaysMin,
- weekdaysShort: defaultLocaleWeekdaysShort,
-
- meridiemParse: defaultLocaleMeridiemParse
- };
-
- // internal storage for locale config files
- var locales = {};
- var localeFamilies = {};
- var globalLocale;
-
- function normalizeLocale(key) {
- return key ? key.toLowerCase().replace('_', '-') : key;
- }
-
- // pick the locale from the array
- // try ['en-au', 'en-gb'] as 'en-au', 'en-gb', 'en', as in move through the list trying each
- // substring from most specific to least, but move to the next array item if it's a more specific variant than the current root
- function chooseLocale(names) {
- var i = 0, j, next, locale, split;
-
- while (i < names.length) {
- split = normalizeLocale(names[i]).split('-');
- j = split.length;
- next = normalizeLocale(names[i + 1]);
- next = next ? next.split('-') : null;
- while (j > 0) {
- locale = loadLocale(split.slice(0, j).join('-'));
- if (locale) {
- return locale;
- }
- if (next && next.length >= j && compareArrays(split, next, true) >= j - 1) {
- //the next array item is better than a shallower substring of this one
- break;
- }
- j--;
- }
- i++;
- }
- return globalLocale;
- }
-
- function loadLocale(name) {
- var oldLocale = null;
- // TODO: Find a better way to register and load all the locales in Node
- if (!locales[name] && (typeof module !== 'undefined') &&
- module && module.exports) {
- try {
- oldLocale = globalLocale._abbr;
- var aliasedRequire = require;
- aliasedRequire('./locale/' + name);
- getSetGlobalLocale(oldLocale);
- } catch (e) {}
- }
- return locales[name];
- }
-
- // This function will load locale and then set the global locale. If
- // no arguments are passed in, it will simply return the current global
- // locale key.
- function getSetGlobalLocale (key, values) {
- var data;
- if (key) {
- if (isUndefined(values)) {
- data = getLocale(key);
- }
- else {
- data = defineLocale(key, values);
- }
-
- if (data) {
- // moment.duration._locale = moment._locale = data;
- globalLocale = data;
- }
- else {
- if ((typeof console !== 'undefined') && console.warn) {
- //warn user if arguments are passed but the locale could not be set
- console.warn('Locale ' + key + ' not found. Did you forget to load it?');
- }
- }
- }
-
- return globalLocale._abbr;
- }
-
- function defineLocale (name, config) {
- if (config !== null) {
- var locale, parentConfig = baseConfig;
- config.abbr = name;
- if (locales[name] != null) {
- deprecateSimple('defineLocaleOverride',
- 'use moment.updateLocale(localeName, config) to change ' +
- 'an existing locale. moment.defineLocale(localeName, ' +
- 'config) should only be used for creating a new locale ' +
- 'See http://momentjs.com/guides/#/warnings/define-locale/ for more info.');
- parentConfig = locales[name]._config;
- } else if (config.parentLocale != null) {
- if (locales[config.parentLocale] != null) {
- parentConfig = locales[config.parentLocale]._config;
- } else {
- locale = loadLocale(config.parentLocale);
- if (locale != null) {
- parentConfig = locale._config;
- } else {
- if (!localeFamilies[config.parentLocale]) {
- localeFamilies[config.parentLocale] = [];
- }
- localeFamilies[config.parentLocale].push({
- name: name,
- config: config
- });
- return null;
- }
- }
- }
- locales[name] = new Locale(mergeConfigs(parentConfig, config));
-
- if (localeFamilies[name]) {
- localeFamilies[name].forEach(function (x) {
- defineLocale(x.name, x.config);
- });
- }
-
- // backwards compat for now: also set the locale
- // make sure we set the locale AFTER all child locales have been
- // created, so we won't end up with the child locale set.
- getSetGlobalLocale(name);
-
-
- return locales[name];
- } else {
- // useful for testing
- delete locales[name];
- return null;
- }
- }
-
- function updateLocale(name, config) {
- if (config != null) {
- var locale, tmpLocale, parentConfig = baseConfig;
- // MERGE
- tmpLocale = loadLocale(name);
- if (tmpLocale != null) {
- parentConfig = tmpLocale._config;
- }
- config = mergeConfigs(parentConfig, config);
- locale = new Locale(config);
- locale.parentLocale = locales[name];
- locales[name] = locale;
-
- // backwards compat for now: also set the locale
- getSetGlobalLocale(name);
- } else {
- // pass null for config to unupdate, useful for tests
- if (locales[name] != null) {
- if (locales[name].parentLocale != null) {
- locales[name] = locales[name].parentLocale;
- } else if (locales[name] != null) {
- delete locales[name];
- }
- }
- }
- return locales[name];
- }
-
- // returns locale data
- function getLocale (key) {
- var locale;
-
- if (key && key._locale && key._locale._abbr) {
- key = key._locale._abbr;
- }
-
- if (!key) {
- return globalLocale;
- }
-
- if (!isArray(key)) {
- //short-circuit everything else
- locale = loadLocale(key);
- if (locale) {
- return locale;
- }
- key = [key];
- }
-
- return chooseLocale(key);
- }
-
- function listLocales() {
- return keys(locales);
- }
-
- function checkOverflow (m) {
- var overflow;
- var a = m._a;
-
- if (a && getParsingFlags(m).overflow === -2) {
- overflow =
- a[MONTH] < 0 || a[MONTH] > 11 ? MONTH :
- a[DATE] < 1 || a[DATE] > daysInMonth(a[YEAR], a[MONTH]) ? DATE :
- a[HOUR] < 0 || a[HOUR] > 24 || (a[HOUR] === 24 && (a[MINUTE] !== 0 || a[SECOND] !== 0 || a[MILLISECOND] !== 0)) ? HOUR :
- a[MINUTE] < 0 || a[MINUTE] > 59 ? MINUTE :
- a[SECOND] < 0 || a[SECOND] > 59 ? SECOND :
- a[MILLISECOND] < 0 || a[MILLISECOND] > 999 ? MILLISECOND :
- -1;
-
- if (getParsingFlags(m)._overflowDayOfYear && (overflow < YEAR || overflow > DATE)) {
- overflow = DATE;
- }
- if (getParsingFlags(m)._overflowWeeks && overflow === -1) {
- overflow = WEEK;
- }
- if (getParsingFlags(m)._overflowWeekday && overflow === -1) {
- overflow = WEEKDAY;
- }
-
- getParsingFlags(m).overflow = overflow;
- }
-
- return m;
- }
-
- // Pick the first defined of two or three arguments.
- function defaults(a, b, c) {
- if (a != null) {
- return a;
- }
- if (b != null) {
- return b;
- }
- return c;
- }
-
- function currentDateArray(config) {
- // hooks is actually the exported moment object
- var nowValue = new Date(hooks.now());
- if (config._useUTC) {
- return [nowValue.getUTCFullYear(), nowValue.getUTCMonth(), nowValue.getUTCDate()];
- }
- return [nowValue.getFullYear(), nowValue.getMonth(), nowValue.getDate()];
- }
-
- // convert an array to a date.
- // the array should mirror the parameters below
- // note: all values past the year are optional and will default to the lowest possible value.
- // [year, month, day , hour, minute, second, millisecond]
- function configFromArray (config) {
- var i, date, input = [], currentDate, expectedWeekday, yearToUse;
-
- if (config._d) {
- return;
- }
-
- currentDate = currentDateArray(config);
-
- //compute day of the year from weeks and weekdays
- if (config._w && config._a[DATE] == null && config._a[MONTH] == null) {
- dayOfYearFromWeekInfo(config);
- }
-
- //if the day of the year is set, figure out what it is
- if (config._dayOfYear != null) {
- yearToUse = defaults(config._a[YEAR], currentDate[YEAR]);
-
- if (config._dayOfYear > daysInYear(yearToUse) || config._dayOfYear === 0) {
- getParsingFlags(config)._overflowDayOfYear = true;
- }
-
- date = createUTCDate(yearToUse, 0, config._dayOfYear);
- config._a[MONTH] = date.getUTCMonth();
- config._a[DATE] = date.getUTCDate();
- }
-
- // Default to current date.
- // * if no year, month, day of month are given, default to today
- // * if day of month is given, default month and year
- // * if month is given, default only year
- // * if year is given, don't default anything
- for (i = 0; i < 3 && config._a[i] == null; ++i) {
- config._a[i] = input[i] = currentDate[i];
- }
-
- // Zero out whatever was not defaulted, including time
- for (; i < 7; i++) {
- config._a[i] = input[i] = (config._a[i] == null) ? (i === 2 ? 1 : 0) : config._a[i];
- }
-
- // Check for 24:00:00.000
- if (config._a[HOUR] === 24 &&
- config._a[MINUTE] === 0 &&
- config._a[SECOND] === 0 &&
- config._a[MILLISECOND] === 0) {
- config._nextDay = true;
- config._a[HOUR] = 0;
- }
-
- config._d = (config._useUTC ? createUTCDate : createDate).apply(null, input);
- expectedWeekday = config._useUTC ? config._d.getUTCDay() : config._d.getDay();
-
- // Apply timezone offset from input. The actual utcOffset can be changed
- // with parseZone.
- if (config._tzm != null) {
- config._d.setUTCMinutes(config._d.getUTCMinutes() - config._tzm);
- }
-
- if (config._nextDay) {
- config._a[HOUR] = 24;
- }
-
- // check for mismatching day of week
- if (config._w && typeof config._w.d !== 'undefined' && config._w.d !== expectedWeekday) {
- getParsingFlags(config).weekdayMismatch = true;
- }
- }
-
- function dayOfYearFromWeekInfo(config) {
- var w, weekYear, week, weekday, dow, doy, temp, weekdayOverflow;
-
- w = config._w;
- if (w.GG != null || w.W != null || w.E != null) {
- dow = 1;
- doy = 4;
-
- // TODO: We need to take the current isoWeekYear, but that depends on
- // how we interpret now (local, utc, fixed offset). So create
- // a now version of current config (take local/utc/offset flags, and
- // create now).
- weekYear = defaults(w.GG, config._a[YEAR], weekOfYear(createLocal(), 1, 4).year);
- week = defaults(w.W, 1);
- weekday = defaults(w.E, 1);
- if (weekday < 1 || weekday > 7) {
- weekdayOverflow = true;
- }
- } else {
- dow = config._locale._week.dow;
- doy = config._locale._week.doy;
-
- var curWeek = weekOfYear(createLocal(), dow, doy);
-
- weekYear = defaults(w.gg, config._a[YEAR], curWeek.year);
-
- // Default to current week.
- week = defaults(w.w, curWeek.week);
-
- if (w.d != null) {
- // weekday -- low day numbers are considered next week
- weekday = w.d;
- if (weekday < 0 || weekday > 6) {
- weekdayOverflow = true;
- }
- } else if (w.e != null) {
- // local weekday -- counting starts from begining of week
- weekday = w.e + dow;
- if (w.e < 0 || w.e > 6) {
- weekdayOverflow = true;
- }
- } else {
- // default to begining of week
- weekday = dow;
- }
- }
- if (week < 1 || week > weeksInYear(weekYear, dow, doy)) {
- getParsingFlags(config)._overflowWeeks = true;
- } else if (weekdayOverflow != null) {
- getParsingFlags(config)._overflowWeekday = true;
- } else {
- temp = dayOfYearFromWeeks(weekYear, week, weekday, dow, doy);
- config._a[YEAR] = temp.year;
- config._dayOfYear = temp.dayOfYear;
- }
- }
-
- // iso 8601 regex
- // 0000-00-00 0000-W00 or 0000-W00-0 + T + 00 or 00:00 or 00:00:00 or 00:00:00.000 + +00:00 or +0000 or +00)
- var extendedIsoRegex = /^\s*((?:[+-]\d{6}|\d{4})-(?:\d\d-\d\d|W\d\d-\d|W\d\d|\d\d\d|\d\d))(?:(T| )(\d\d(?::\d\d(?::\d\d(?:[.,]\d+)?)?)?)([\+\-]\d\d(?::?\d\d)?|\s*Z)?)?$/;
- var basicIsoRegex = /^\s*((?:[+-]\d{6}|\d{4})(?:\d\d\d\d|W\d\d\d|W\d\d|\d\d\d|\d\d))(?:(T| )(\d\d(?:\d\d(?:\d\d(?:[.,]\d+)?)?)?)([\+\-]\d\d(?::?\d\d)?|\s*Z)?)?$/;
-
- var tzRegex = /Z|[+-]\d\d(?::?\d\d)?/;
-
- var isoDates = [
- ['YYYYYY-MM-DD', /[+-]\d{6}-\d\d-\d\d/],
- ['YYYY-MM-DD', /\d{4}-\d\d-\d\d/],
- ['GGGG-[W]WW-E', /\d{4}-W\d\d-\d/],
- ['GGGG-[W]WW', /\d{4}-W\d\d/, false],
- ['YYYY-DDD', /\d{4}-\d{3}/],
- ['YYYY-MM', /\d{4}-\d\d/, false],
- ['YYYYYYMMDD', /[+-]\d{10}/],
- ['YYYYMMDD', /\d{8}/],
- // YYYYMM is NOT allowed by the standard
- ['GGGG[W]WWE', /\d{4}W\d{3}/],
- ['GGGG[W]WW', /\d{4}W\d{2}/, false],
- ['YYYYDDD', /\d{7}/]
- ];
-
- // iso time formats and regexes
- var isoTimes = [
- ['HH:mm:ss.SSSS', /\d\d:\d\d:\d\d\.\d+/],
- ['HH:mm:ss,SSSS', /\d\d:\d\d:\d\d,\d+/],
- ['HH:mm:ss', /\d\d:\d\d:\d\d/],
- ['HH:mm', /\d\d:\d\d/],
- ['HHmmss.SSSS', /\d\d\d\d\d\d\.\d+/],
- ['HHmmss,SSSS', /\d\d\d\d\d\d,\d+/],
- ['HHmmss', /\d\d\d\d\d\d/],
- ['HHmm', /\d\d\d\d/],
- ['HH', /\d\d/]
- ];
-
- var aspNetJsonRegex = /^\/?Date\((\-?\d+)/i;
-
- // date from iso format
- function configFromISO(config) {
- var i, l,
- string = config._i,
- match = extendedIsoRegex.exec(string) || basicIsoRegex.exec(string),
- allowTime, dateFormat, timeFormat, tzFormat;
-
- if (match) {
- getParsingFlags(config).iso = true;
-
- for (i = 0, l = isoDates.length; i < l; i++) {
- if (isoDates[i][1].exec(match[1])) {
- dateFormat = isoDates[i][0];
- allowTime = isoDates[i][2] !== false;
- break;
- }
- }
- if (dateFormat == null) {
- config._isValid = false;
- return;
- }
- if (match[3]) {
- for (i = 0, l = isoTimes.length; i < l; i++) {
- if (isoTimes[i][1].exec(match[3])) {
- // match[2] should be 'T' or space
- timeFormat = (match[2] || ' ') + isoTimes[i][0];
- break;
- }
- }
- if (timeFormat == null) {
- config._isValid = false;
- return;
- }
- }
- if (!allowTime && timeFormat != null) {
- config._isValid = false;
- return;
- }
- if (match[4]) {
- if (tzRegex.exec(match[4])) {
- tzFormat = 'Z';
- } else {
- config._isValid = false;
- return;
- }
- }
- config._f = dateFormat + (timeFormat || '') + (tzFormat || '');
- configFromStringAndFormat(config);
- } else {
- config._isValid = false;
- }
- }
-
- // RFC 2822 regex: For details see https://tools.ietf.org/html/rfc2822#section-3.3
- var rfc2822 = /^(?:(Mon|Tue|Wed|Thu|Fri|Sat|Sun),?\s)?(\d{1,2})\s(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)\s(\d{2,4})\s(\d\d):(\d\d)(?::(\d\d))?\s(?:(UT|GMT|[ECMP][SD]T)|([Zz])|([+-]\d{4}))$/;
-
- function extractFromRFC2822Strings(yearStr, monthStr, dayStr, hourStr, minuteStr, secondStr) {
- var result = [
- untruncateYear(yearStr),
- defaultLocaleMonthsShort.indexOf(monthStr),
- parseInt(dayStr, 10),
- parseInt(hourStr, 10),
- parseInt(minuteStr, 10)
- ];
-
- if (secondStr) {
- result.push(parseInt(secondStr, 10));
- }
-
- return result;
- }
-
- function untruncateYear(yearStr) {
- var year = parseInt(yearStr, 10);
- if (year <= 49) {
- return 2000 + year;
- } else if (year <= 999) {
- return 1900 + year;
- }
- return year;
- }
-
- function preprocessRFC2822(s) {
- // Remove comments and folding whitespace and replace multiple-spaces with a single space
- return s.replace(/\([^)]*\)|[\n\t]/g, ' ').replace(/(\s\s+)/g, ' ').replace(/^\s\s*/, '').replace(/\s\s*$/, '');
- }
-
- function checkWeekday(weekdayStr, parsedInput, config) {
- if (weekdayStr) {
- // TODO: Replace the vanilla JS Date object with an indepentent day-of-week check.
- var weekdayProvided = defaultLocaleWeekdaysShort.indexOf(weekdayStr),
- weekdayActual = new Date(parsedInput[0], parsedInput[1], parsedInput[2]).getDay();
- if (weekdayProvided !== weekdayActual) {
- getParsingFlags(config).weekdayMismatch = true;
- config._isValid = false;
- return false;
- }
- }
- return true;
- }
-
- var obsOffsets = {
- UT: 0,
- GMT: 0,
- EDT: -4 * 60,
- EST: -5 * 60,
- CDT: -5 * 60,
- CST: -6 * 60,
- MDT: -6 * 60,
- MST: -7 * 60,
- PDT: -7 * 60,
- PST: -8 * 60
- };
-
- function calculateOffset(obsOffset, militaryOffset, numOffset) {
- if (obsOffset) {
- return obsOffsets[obsOffset];
- } else if (militaryOffset) {
- // the only allowed military tz is Z
- return 0;
- } else {
- var hm = parseInt(numOffset, 10);
- var m = hm % 100, h = (hm - m) / 100;
- return h * 60 + m;
- }
- }
-
- // date and time from ref 2822 format
- function configFromRFC2822(config) {
- var match = rfc2822.exec(preprocessRFC2822(config._i));
- if (match) {
- var parsedArray = extractFromRFC2822Strings(match[4], match[3], match[2], match[5], match[6], match[7]);
- if (!checkWeekday(match[1], parsedArray, config)) {
- return;
- }
-
- config._a = parsedArray;
- config._tzm = calculateOffset(match[8], match[9], match[10]);
-
- config._d = createUTCDate.apply(null, config._a);
- config._d.setUTCMinutes(config._d.getUTCMinutes() - config._tzm);
-
- getParsingFlags(config).rfc2822 = true;
- } else {
- config._isValid = false;
- }
- }
-
- // date from iso format or fallback
- function configFromString(config) {
- var matched = aspNetJsonRegex.exec(config._i);
-
- if (matched !== null) {
- config._d = new Date(+matched[1]);
- return;
- }
-
- configFromISO(config);
- if (config._isValid === false) {
- delete config._isValid;
- } else {
- return;
- }
-
- configFromRFC2822(config);
- if (config._isValid === false) {
- delete config._isValid;
- } else {
- return;
- }
-
- // Final attempt, use Input Fallback
- hooks.createFromInputFallback(config);
- }
-
- hooks.createFromInputFallback = deprecate(
- 'value provided is not in a recognized RFC2822 or ISO format. moment construction falls back to js Date(), ' +
- 'which is not reliable across all browsers and versions. Non RFC2822/ISO date formats are ' +
- 'discouraged and will be removed in an upcoming major release. Please refer to ' +
- 'http://momentjs.com/guides/#/warnings/js-date/ for more info.',
- function (config) {
- config._d = new Date(config._i + (config._useUTC ? ' UTC' : ''));
- }
- );
-
- // constant that refers to the ISO standard
- hooks.ISO_8601 = function () {};
-
- // constant that refers to the RFC 2822 form
- hooks.RFC_2822 = function () {};
-
- // date from string and format string
- function configFromStringAndFormat(config) {
- // TODO: Move this to another part of the creation flow to prevent circular deps
- if (config._f === hooks.ISO_8601) {
- configFromISO(config);
- return;
- }
- if (config._f === hooks.RFC_2822) {
- configFromRFC2822(config);
- return;
- }
- config._a = [];
- getParsingFlags(config).empty = true;
-
- // This array is used to make a Date, either with `new Date` or `Date.UTC`
- var string = '' + config._i,
- i, parsedInput, tokens, token, skipped,
- stringLength = string.length,
- totalParsedInputLength = 0;
-
- tokens = expandFormat(config._f, config._locale).match(formattingTokens) || [];
-
- for (i = 0; i < tokens.length; i++) {
- token = tokens[i];
- parsedInput = (string.match(getParseRegexForToken(token, config)) || [])[0];
- // console.log('token', token, 'parsedInput', parsedInput,
- // 'regex', getParseRegexForToken(token, config));
- if (parsedInput) {
- skipped = string.substr(0, string.indexOf(parsedInput));
- if (skipped.length > 0) {
- getParsingFlags(config).unusedInput.push(skipped);
- }
- string = string.slice(string.indexOf(parsedInput) + parsedInput.length);
- totalParsedInputLength += parsedInput.length;
- }
- // don't parse if it's not a known token
- if (formatTokenFunctions[token]) {
- if (parsedInput) {
- getParsingFlags(config).empty = false;
- }
- else {
- getParsingFlags(config).unusedTokens.push(token);
- }
- addTimeToArrayFromToken(token, parsedInput, config);
- }
- else if (config._strict && !parsedInput) {
- getParsingFlags(config).unusedTokens.push(token);
- }
- }
-
- // add remaining unparsed input length to the string
- getParsingFlags(config).charsLeftOver = stringLength - totalParsedInputLength;
- if (string.length > 0) {
- getParsingFlags(config).unusedInput.push(string);
- }
-
- // clear _12h flag if hour is <= 12
- if (config._a[HOUR] <= 12 &&
- getParsingFlags(config).bigHour === true &&
- config._a[HOUR] > 0) {
- getParsingFlags(config).bigHour = undefined;
- }
-
- getParsingFlags(config).parsedDateParts = config._a.slice(0);
- getParsingFlags(config).meridiem = config._meridiem;
- // handle meridiem
- config._a[HOUR] = meridiemFixWrap(config._locale, config._a[HOUR], config._meridiem);
-
- configFromArray(config);
- checkOverflow(config);
- }
-
-
- function meridiemFixWrap (locale, hour, meridiem) {
- var isPm;
-
- if (meridiem == null) {
- // nothing to do
- return hour;
- }
- if (locale.meridiemHour != null) {
- return locale.meridiemHour(hour, meridiem);
- } else if (locale.isPM != null) {
- // Fallback
- isPm = locale.isPM(meridiem);
- if (isPm && hour < 12) {
- hour += 12;
- }
- if (!isPm && hour === 12) {
- hour = 0;
- }
- return hour;
- } else {
- // this is not supposed to happen
- return hour;
- }
- }
-
- // date from string and array of format strings
- function configFromStringAndArray(config) {
- var tempConfig,
- bestMoment,
-
- scoreToBeat,
- i,
- currentScore;
-
- if (config._f.length === 0) {
- getParsingFlags(config).invalidFormat = true;
- config._d = new Date(NaN);
- return;
- }
-
- for (i = 0; i < config._f.length; i++) {
- currentScore = 0;
- tempConfig = copyConfig({}, config);
- if (config._useUTC != null) {
- tempConfig._useUTC = config._useUTC;
- }
- tempConfig._f = config._f[i];
- configFromStringAndFormat(tempConfig);
-
- if (!isValid(tempConfig)) {
- continue;
- }
-
- // if there is any input that was not parsed add a penalty for that format
- currentScore += getParsingFlags(tempConfig).charsLeftOver;
-
- //or tokens
- currentScore += getParsingFlags(tempConfig).unusedTokens.length * 10;
-
- getParsingFlags(tempConfig).score = currentScore;
-
- if (scoreToBeat == null || currentScore < scoreToBeat) {
- scoreToBeat = currentScore;
- bestMoment = tempConfig;
- }
- }
-
- extend(config, bestMoment || tempConfig);
- }
-
- function configFromObject(config) {
- if (config._d) {
- return;
- }
-
- var i = normalizeObjectUnits(config._i);
- config._a = map([i.year, i.month, i.day || i.date, i.hour, i.minute, i.second, i.millisecond], function (obj) {
- return obj && parseInt(obj, 10);
- });
-
- configFromArray(config);
- }
-
- function createFromConfig (config) {
- var res = new Moment(checkOverflow(prepareConfig(config)));
- if (res._nextDay) {
- // Adding is smart enough around DST
- res.add(1, 'd');
- res._nextDay = undefined;
- }
-
- return res;
- }
-
- function prepareConfig (config) {
- var input = config._i,
- format = config._f;
-
- config._locale = config._locale || getLocale(config._l);
-
- if (input === null || (format === undefined && input === '')) {
- return createInvalid({nullInput: true});
- }
-
- if (typeof input === 'string') {
- config._i = input = config._locale.preparse(input);
- }
-
- if (isMoment(input)) {
- return new Moment(checkOverflow(input));
- } else if (isDate(input)) {
- config._d = input;
- } else if (isArray(format)) {
- configFromStringAndArray(config);
- } else if (format) {
- configFromStringAndFormat(config);
- } else {
- configFromInput(config);
- }
-
- if (!isValid(config)) {
- config._d = null;
- }
-
- return config;
- }
-
- function configFromInput(config) {
- var input = config._i;
- if (isUndefined(input)) {
- config._d = new Date(hooks.now());
- } else if (isDate(input)) {
- config._d = new Date(input.valueOf());
- } else if (typeof input === 'string') {
- configFromString(config);
- } else if (isArray(input)) {
- config._a = map(input.slice(0), function (obj) {
- return parseInt(obj, 10);
- });
- configFromArray(config);
- } else if (isObject(input)) {
- configFromObject(config);
- } else if (isNumber(input)) {
- // from milliseconds
- config._d = new Date(input);
- } else {
- hooks.createFromInputFallback(config);
- }
- }
-
- function createLocalOrUTC (input, format, locale, strict, isUTC) {
- var c = {};
-
- if (locale === true || locale === false) {
- strict = locale;
- locale = undefined;
- }
-
- if ((isObject(input) && isObjectEmpty(input)) ||
- (isArray(input) && input.length === 0)) {
- input = undefined;
- }
- // object construction must be done this way.
- // https://github.com/moment/moment/issues/1423
- c._isAMomentObject = true;
- c._useUTC = c._isUTC = isUTC;
- c._l = locale;
- c._i = input;
- c._f = format;
- c._strict = strict;
-
- return createFromConfig(c);
- }
-
- function createLocal (input, format, locale, strict) {
- return createLocalOrUTC(input, format, locale, strict, false);
- }
-
- var prototypeMin = deprecate(
- 'moment().min is deprecated, use moment.max instead. http://momentjs.com/guides/#/warnings/min-max/',
- function () {
- var other = createLocal.apply(null, arguments);
- if (this.isValid() && other.isValid()) {
- return other < this ? this : other;
- } else {
- return createInvalid();
- }
- }
- );
-
- var prototypeMax = deprecate(
- 'moment().max is deprecated, use moment.min instead. http://momentjs.com/guides/#/warnings/min-max/',
- function () {
- var other = createLocal.apply(null, arguments);
- if (this.isValid() && other.isValid()) {
- return other > this ? this : other;
- } else {
- return createInvalid();
- }
- }
- );
-
- // Pick a moment m from moments so that m[fn](other) is true for all
- // other. This relies on the function fn to be transitive.
- //
- // moments should either be an array of moment objects or an array, whose
- // first element is an array of moment objects.
- function pickBy(fn, moments) {
- var res, i;
- if (moments.length === 1 && isArray(moments[0])) {
- moments = moments[0];
- }
- if (!moments.length) {
- return createLocal();
- }
- res = moments[0];
- for (i = 1; i < moments.length; ++i) {
- if (!moments[i].isValid() || moments[i][fn](res)) {
- res = moments[i];
- }
- }
- return res;
- }
-
- // TODO: Use [].sort instead?
- function min () {
- var args = [].slice.call(arguments, 0);
-
- return pickBy('isBefore', args);
- }
-
- function max () {
- var args = [].slice.call(arguments, 0);
-
- return pickBy('isAfter', args);
- }
-
- var now = function () {
- return Date.now ? Date.now() : +(new Date());
- };
-
- var ordering = ['year', 'quarter', 'month', 'week', 'day', 'hour', 'minute', 'second', 'millisecond'];
-
- function isDurationValid(m) {
- for (var key in m) {
- if (!(indexOf.call(ordering, key) !== -1 && (m[key] == null || !isNaN(m[key])))) {
- return false;
- }
- }
-
- var unitHasDecimal = false;
- for (var i = 0; i < ordering.length; ++i) {
- if (m[ordering[i]]) {
- if (unitHasDecimal) {
- return false; // only allow non-integers for smallest unit
- }
- if (parseFloat(m[ordering[i]]) !== toInt(m[ordering[i]])) {
- unitHasDecimal = true;
- }
- }
- }
-
- return true;
- }
-
- function isValid$1() {
- return this._isValid;
- }
-
- function createInvalid$1() {
- return createDuration(NaN);
- }
-
- function Duration (duration) {
- var normalizedInput = normalizeObjectUnits(duration),
- years = normalizedInput.year || 0,
- quarters = normalizedInput.quarter || 0,
- months = normalizedInput.month || 0,
- weeks = normalizedInput.week || 0,
- days = normalizedInput.day || 0,
- hours = normalizedInput.hour || 0,
- minutes = normalizedInput.minute || 0,
- seconds = normalizedInput.second || 0,
- milliseconds = normalizedInput.millisecond || 0;
-
- this._isValid = isDurationValid(normalizedInput);
-
- // representation for dateAddRemove
- this._milliseconds = +milliseconds +
- seconds * 1e3 + // 1000
- minutes * 6e4 + // 1000 * 60
- hours * 1000 * 60 * 60; //using 1000 * 60 * 60 instead of 36e5 to avoid floating point rounding errors https://github.com/moment/moment/issues/2978
- // Because of dateAddRemove treats 24 hours as different from a
- // day when working around DST, we need to store them separately
- this._days = +days +
- weeks * 7;
- // It is impossible to translate months into days without knowing
- // which months you are are talking about, so we have to store
- // it separately.
- this._months = +months +
- quarters * 3 +
- years * 12;
-
- this._data = {};
-
- this._locale = getLocale();
-
- this._bubble();
- }
-
- function isDuration (obj) {
- return obj instanceof Duration;
- }
-
- function absRound (number) {
- if (number < 0) {
- return Math.round(-1 * number) * -1;
- } else {
- return Math.round(number);
- }
- }
-
- // FORMATTING
-
- function offset (token, separator) {
- addFormatToken(token, 0, 0, function () {
- var offset = this.utcOffset();
- var sign = '+';
- if (offset < 0) {
- offset = -offset;
- sign = '-';
- }
- return sign + zeroFill(~~(offset / 60), 2) + separator + zeroFill(~~(offset) % 60, 2);
- });
- }
-
- offset('Z', ':');
- offset('ZZ', '');
-
- // PARSING
-
- addRegexToken('Z', matchShortOffset);
- addRegexToken('ZZ', matchShortOffset);
- addParseToken(['Z', 'ZZ'], function (input, array, config) {
- config._useUTC = true;
- config._tzm = offsetFromString(matchShortOffset, input);
- });
-
- // HELPERS
-
- // timezone chunker
- // '+10:00' > ['10', '00']
- // '-1530' > ['-15', '30']
- var chunkOffset = /([\+\-]|\d\d)/gi;
-
- function offsetFromString(matcher, string) {
- var matches = (string || '').match(matcher);
-
- if (matches === null) {
- return null;
- }
-
- var chunk = matches[matches.length - 1] || [];
- var parts = (chunk + '').match(chunkOffset) || ['-', 0, 0];
- var minutes = +(parts[1] * 60) + toInt(parts[2]);
-
- return minutes === 0 ?
- 0 :
- parts[0] === '+' ? minutes : -minutes;
- }
-
- // Return a moment from input, that is local/utc/zone equivalent to model.
- function cloneWithOffset(input, model) {
- var res, diff;
- if (model._isUTC) {
- res = model.clone();
- diff = (isMoment(input) || isDate(input) ? input.valueOf() : createLocal(input).valueOf()) - res.valueOf();
- // Use low-level api, because this fn is low-level api.
- res._d.setTime(res._d.valueOf() + diff);
- hooks.updateOffset(res, false);
- return res;
- } else {
- return createLocal(input).local();
- }
- }
-
- function getDateOffset (m) {
- // On Firefox.24 Date#getTimezoneOffset returns a floating point.
- // https://github.com/moment/moment/pull/1871
- return -Math.round(m._d.getTimezoneOffset() / 15) * 15;
- }
-
- // HOOKS
-
- // This function will be called whenever a moment is mutated.
- // It is intended to keep the offset in sync with the timezone.
- hooks.updateOffset = function () {};
-
- // MOMENTS
-
- // keepLocalTime = true means only change the timezone, without
- // affecting the local hour. So 5:31:26 +0300 --[utcOffset(2, true)]-->
- // 5:31:26 +0200 It is possible that 5:31:26 doesn't exist with offset
- // +0200, so we adjust the time as needed, to be valid.
- //
- // Keeping the time actually adds/subtracts (one hour)
- // from the actual represented time. That is why we call updateOffset
- // a second time. In case it wants us to change the offset again
- // _changeInProgress == true case, then we have to adjust, because
- // there is no such time in the given timezone.
- function getSetOffset (input, keepLocalTime, keepMinutes) {
- var offset = this._offset || 0,
- localAdjust;
- if (!this.isValid()) {
- return input != null ? this : NaN;
- }
- if (input != null) {
- if (typeof input === 'string') {
- input = offsetFromString(matchShortOffset, input);
- if (input === null) {
- return this;
- }
- } else if (Math.abs(input) < 16 && !keepMinutes) {
- input = input * 60;
- }
- if (!this._isUTC && keepLocalTime) {
- localAdjust = getDateOffset(this);
- }
- this._offset = input;
- this._isUTC = true;
- if (localAdjust != null) {
- this.add(localAdjust, 'm');
- }
- if (offset !== input) {
- if (!keepLocalTime || this._changeInProgress) {
- addSubtract(this, createDuration(input - offset, 'm'), 1, false);
- } else if (!this._changeInProgress) {
- this._changeInProgress = true;
- hooks.updateOffset(this, true);
- this._changeInProgress = null;
- }
- }
- return this;
- } else {
- return this._isUTC ? offset : getDateOffset(this);
- }
- }
-
- function getSetZone (input, keepLocalTime) {
- if (input != null) {
- if (typeof input !== 'string') {
- input = -input;
- }
-
- this.utcOffset(input, keepLocalTime);
-
- return this;
- } else {
- return -this.utcOffset();
- }
- }
-
- function setOffsetToUTC (keepLocalTime) {
- return this.utcOffset(0, keepLocalTime);
- }
-
- function setOffsetToLocal (keepLocalTime) {
- if (this._isUTC) {
- this.utcOffset(0, keepLocalTime);
- this._isUTC = false;
-
- if (keepLocalTime) {
- this.subtract(getDateOffset(this), 'm');
- }
- }
- return this;
- }
-
- function setOffsetToParsedOffset () {
- if (this._tzm != null) {
- this.utcOffset(this._tzm, false, true);
- } else if (typeof this._i === 'string') {
- var tZone = offsetFromString(matchOffset, this._i);
- if (tZone != null) {
- this.utcOffset(tZone);
- }
- else {
- this.utcOffset(0, true);
- }
- }
- return this;
- }
-
- function hasAlignedHourOffset (input) {
- if (!this.isValid()) {
- return false;
- }
- input = input ? createLocal(input).utcOffset() : 0;
-
- return (this.utcOffset() - input) % 60 === 0;
- }
-
- function isDaylightSavingTime () {
- return (
- this.utcOffset() > this.clone().month(0).utcOffset() ||
- this.utcOffset() > this.clone().month(5).utcOffset()
- );
- }
-
- function isDaylightSavingTimeShifted () {
- if (!isUndefined(this._isDSTShifted)) {
- return this._isDSTShifted;
- }
-
- var c = {};
-
- copyConfig(c, this);
- c = prepareConfig(c);
-
- if (c._a) {
- var other = c._isUTC ? createUTC(c._a) : createLocal(c._a);
- this._isDSTShifted = this.isValid() &&
- compareArrays(c._a, other.toArray()) > 0;
- } else {
- this._isDSTShifted = false;
- }
-
- return this._isDSTShifted;
- }
-
- function isLocal () {
- return this.isValid() ? !this._isUTC : false;
- }
-
- function isUtcOffset () {
- return this.isValid() ? this._isUTC : false;
- }
-
- function isUtc () {
- return this.isValid() ? this._isUTC && this._offset === 0 : false;
- }
-
- // ASP.NET json date format regex
- var aspNetRegex = /^(\-|\+)?(?:(\d*)[. ])?(\d+)\:(\d+)(?:\:(\d+)(\.\d*)?)?$/;
-
- // from http://docs.closure-library.googlecode.com/git/closure_goog_date_date.js.source.html
- // somewhat more in line with 4.4.3.2 2004 spec, but allows decimal anywhere
- // and further modified to allow for strings containing both week and day
- var isoRegex = /^(-|\+)?P(?:([-+]?[0-9,.]*)Y)?(?:([-+]?[0-9,.]*)M)?(?:([-+]?[0-9,.]*)W)?(?:([-+]?[0-9,.]*)D)?(?:T(?:([-+]?[0-9,.]*)H)?(?:([-+]?[0-9,.]*)M)?(?:([-+]?[0-9,.]*)S)?)?$/;
-
- function createDuration (input, key) {
- var duration = input,
- // matching against regexp is expensive, do it on demand
- match = null,
- sign,
- ret,
- diffRes;
-
- if (isDuration(input)) {
- duration = {
- ms : input._milliseconds,
- d : input._days,
- M : input._months
- };
- } else if (isNumber(input)) {
- duration = {};
- if (key) {
- duration[key] = input;
- } else {
- duration.milliseconds = input;
- }
- } else if (!!(match = aspNetRegex.exec(input))) {
- sign = (match[1] === '-') ? -1 : 1;
- duration = {
- y : 0,
- d : toInt(match[DATE]) * sign,
- h : toInt(match[HOUR]) * sign,
- m : toInt(match[MINUTE]) * sign,
- s : toInt(match[SECOND]) * sign,
- ms : toInt(absRound(match[MILLISECOND] * 1000)) * sign // the millisecond decimal point is included in the match
- };
- } else if (!!(match = isoRegex.exec(input))) {
- sign = (match[1] === '-') ? -1 : (match[1] === '+') ? 1 : 1;
- duration = {
- y : parseIso(match[2], sign),
- M : parseIso(match[3], sign),
- w : parseIso(match[4], sign),
- d : parseIso(match[5], sign),
- h : parseIso(match[6], sign),
- m : parseIso(match[7], sign),
- s : parseIso(match[8], sign)
- };
- } else if (duration == null) {// checks for null or undefined
- duration = {};
- } else if (typeof duration === 'object' && ('from' in duration || 'to' in duration)) {
- diffRes = momentsDifference(createLocal(duration.from), createLocal(duration.to));
-
- duration = {};
- duration.ms = diffRes.milliseconds;
- duration.M = diffRes.months;
- }
-
- ret = new Duration(duration);
-
- if (isDuration(input) && hasOwnProp(input, '_locale')) {
- ret._locale = input._locale;
- }
-
- return ret;
- }
-
- createDuration.fn = Duration.prototype;
- createDuration.invalid = createInvalid$1;
-
- function parseIso (inp, sign) {
- // We'd normally use ~~inp for this, but unfortunately it also
- // converts floats to ints.
- // inp may be undefined, so careful calling replace on it.
- var res = inp && parseFloat(inp.replace(',', '.'));
- // apply sign while we're at it
- return (isNaN(res) ? 0 : res) * sign;
- }
-
- function positiveMomentsDifference(base, other) {
- var res = {milliseconds: 0, months: 0};
-
- res.months = other.month() - base.month() +
- (other.year() - base.year()) * 12;
- if (base.clone().add(res.months, 'M').isAfter(other)) {
- --res.months;
- }
-
- res.milliseconds = +other - +(base.clone().add(res.months, 'M'));
-
- return res;
- }
-
- function momentsDifference(base, other) {
- var res;
- if (!(base.isValid() && other.isValid())) {
- return {milliseconds: 0, months: 0};
- }
-
- other = cloneWithOffset(other, base);
- if (base.isBefore(other)) {
- res = positiveMomentsDifference(base, other);
- } else {
- res = positiveMomentsDifference(other, base);
- res.milliseconds = -res.milliseconds;
- res.months = -res.months;
- }
-
- return res;
- }
-
- // TODO: remove 'name' arg after deprecation is removed
- function createAdder(direction, name) {
- return function (val, period) {
- var dur, tmp;
- //invert the arguments, but complain about it
- if (period !== null && !isNaN(+period)) {
- deprecateSimple(name, 'moment().' + name + '(period, number) is deprecated. Please use moment().' + name + '(number, period). ' +
- 'See http://momentjs.com/guides/#/warnings/add-inverted-param/ for more info.');
- tmp = val; val = period; period = tmp;
- }
-
- val = typeof val === 'string' ? +val : val;
- dur = createDuration(val, period);
- addSubtract(this, dur, direction);
- return this;
- };
- }
-
- function addSubtract (mom, duration, isAdding, updateOffset) {
- var milliseconds = duration._milliseconds,
- days = absRound(duration._days),
- months = absRound(duration._months);
-
- if (!mom.isValid()) {
- // No op
- return;
- }
-
- updateOffset = updateOffset == null ? true : updateOffset;
-
- if (months) {
- setMonth(mom, get(mom, 'Month') + months * isAdding);
- }
- if (days) {
- set$1(mom, 'Date', get(mom, 'Date') + days * isAdding);
- }
- if (milliseconds) {
- mom._d.setTime(mom._d.valueOf() + milliseconds * isAdding);
- }
- if (updateOffset) {
- hooks.updateOffset(mom, days || months);
- }
- }
-
- var add = createAdder(1, 'add');
- var subtract = createAdder(-1, 'subtract');
-
- function getCalendarFormat(myMoment, now) {
- var diff = myMoment.diff(now, 'days', true);
- return diff < -6 ? 'sameElse' :
- diff < -1 ? 'lastWeek' :
- diff < 0 ? 'lastDay' :
- diff < 1 ? 'sameDay' :
- diff < 2 ? 'nextDay' :
- diff < 7 ? 'nextWeek' : 'sameElse';
- }
-
- function calendar$1 (time, formats) {
- // We want to compare the start of today, vs this.
- // Getting start-of-today depends on whether we're local/utc/offset or not.
- var now = time || createLocal(),
- sod = cloneWithOffset(now, this).startOf('day'),
- format = hooks.calendarFormat(this, sod) || 'sameElse';
-
- var output = formats && (isFunction(formats[format]) ? formats[format].call(this, now) : formats[format]);
-
- return this.format(output || this.localeData().calendar(format, this, createLocal(now)));
- }
-
- function clone () {
- return new Moment(this);
- }
-
- function isAfter (input, units) {
- var localInput = isMoment(input) ? input : createLocal(input);
- if (!(this.isValid() && localInput.isValid())) {
- return false;
- }
- units = normalizeUnits(!isUndefined(units) ? units : 'millisecond');
- if (units === 'millisecond') {
- return this.valueOf() > localInput.valueOf();
- } else {
- return localInput.valueOf() < this.clone().startOf(units).valueOf();
- }
- }
-
- function isBefore (input, units) {
- var localInput = isMoment(input) ? input : createLocal(input);
- if (!(this.isValid() && localInput.isValid())) {
- return false;
- }
- units = normalizeUnits(!isUndefined(units) ? units : 'millisecond');
- if (units === 'millisecond') {
- return this.valueOf() < localInput.valueOf();
- } else {
- return this.clone().endOf(units).valueOf() < localInput.valueOf();
- }
- }
-
- function isBetween (from, to, units, inclusivity) {
- inclusivity = inclusivity || '()';
- return (inclusivity[0] === '(' ? this.isAfter(from, units) : !this.isBefore(from, units)) &&
- (inclusivity[1] === ')' ? this.isBefore(to, units) : !this.isAfter(to, units));
- }
-
- function isSame (input, units) {
- var localInput = isMoment(input) ? input : createLocal(input),
- inputMs;
- if (!(this.isValid() && localInput.isValid())) {
- return false;
- }
- units = normalizeUnits(units || 'millisecond');
- if (units === 'millisecond') {
- return this.valueOf() === localInput.valueOf();
- } else {
- inputMs = localInput.valueOf();
- return this.clone().startOf(units).valueOf() <= inputMs && inputMs <= this.clone().endOf(units).valueOf();
- }
- }
-
- function isSameOrAfter (input, units) {
- return this.isSame(input, units) || this.isAfter(input,units);
- }
-
- function isSameOrBefore (input, units) {
- return this.isSame(input, units) || this.isBefore(input,units);
- }
-
- function diff (input, units, asFloat) {
- var that,
- zoneDelta,
- output;
-
- if (!this.isValid()) {
- return NaN;
- }
-
- that = cloneWithOffset(input, this);
-
- if (!that.isValid()) {
- return NaN;
- }
-
- zoneDelta = (that.utcOffset() - this.utcOffset()) * 6e4;
-
- units = normalizeUnits(units);
-
- switch (units) {
- case 'year': output = monthDiff(this, that) / 12; break;
- case 'month': output = monthDiff(this, that); break;
- case 'quarter': output = monthDiff(this, that) / 3; break;
- case 'second': output = (this - that) / 1e3; break; // 1000
- case 'minute': output = (this - that) / 6e4; break; // 1000 * 60
- case 'hour': output = (this - that) / 36e5; break; // 1000 * 60 * 60
- case 'day': output = (this - that - zoneDelta) / 864e5; break; // 1000 * 60 * 60 * 24, negate dst
- case 'week': output = (this - that - zoneDelta) / 6048e5; break; // 1000 * 60 * 60 * 24 * 7, negate dst
- default: output = this - that;
- }
-
- return asFloat ? output : absFloor(output);
- }
-
- function monthDiff (a, b) {
- // difference in months
- var wholeMonthDiff = ((b.year() - a.year()) * 12) + (b.month() - a.month()),
- // b is in (anchor - 1 month, anchor + 1 month)
- anchor = a.clone().add(wholeMonthDiff, 'months'),
- anchor2, adjust;
-
- if (b - anchor < 0) {
- anchor2 = a.clone().add(wholeMonthDiff - 1, 'months');
- // linear across the month
- adjust = (b - anchor) / (anchor - anchor2);
- } else {
- anchor2 = a.clone().add(wholeMonthDiff + 1, 'months');
- // linear across the month
- adjust = (b - anchor) / (anchor2 - anchor);
- }
-
- //check for negative zero, return zero if negative zero
- return -(wholeMonthDiff + adjust) || 0;
- }
-
- hooks.defaultFormat = 'YYYY-MM-DDTHH:mm:ssZ';
- hooks.defaultFormatUtc = 'YYYY-MM-DDTHH:mm:ss[Z]';
-
- function toString () {
- return this.clone().locale('en').format('ddd MMM DD YYYY HH:mm:ss [GMT]ZZ');
- }
-
- function toISOString(keepOffset) {
- if (!this.isValid()) {
- return null;
- }
- var utc = keepOffset !== true;
- var m = utc ? this.clone().utc() : this;
- if (m.year() < 0 || m.year() > 9999) {
- return formatMoment(m, utc ? 'YYYYYY-MM-DD[T]HH:mm:ss.SSS[Z]' : 'YYYYYY-MM-DD[T]HH:mm:ss.SSSZ');
- }
- if (isFunction(Date.prototype.toISOString)) {
- // native implementation is ~50x faster, use it when we can
- if (utc) {
- return this.toDate().toISOString();
- } else {
- return new Date(this.valueOf() + this.utcOffset() * 60 * 1000).toISOString().replace('Z', formatMoment(m, 'Z'));
- }
- }
- return formatMoment(m, utc ? 'YYYY-MM-DD[T]HH:mm:ss.SSS[Z]' : 'YYYY-MM-DD[T]HH:mm:ss.SSSZ');
- }
-
- /**
- * Return a human readable representation of a moment that can
- * also be evaluated to get a new moment which is the same
- *
- * @link https://nodejs.org/dist/latest/docs/api/util.html#util_custom_inspect_function_on_objects
- */
- function inspect () {
- if (!this.isValid()) {
- return 'moment.invalid(/* ' + this._i + ' */)';
- }
- var func = 'moment';
- var zone = '';
- if (!this.isLocal()) {
- func = this.utcOffset() === 0 ? 'moment.utc' : 'moment.parseZone';
- zone = 'Z';
- }
- var prefix = '[' + func + '("]';
- var year = (0 <= this.year() && this.year() <= 9999) ? 'YYYY' : 'YYYYYY';
- var datetime = '-MM-DD[T]HH:mm:ss.SSS';
- var suffix = zone + '[")]';
-
- return this.format(prefix + year + datetime + suffix);
- }
-
- function format (inputString) {
- if (!inputString) {
- inputString = this.isUtc() ? hooks.defaultFormatUtc : hooks.defaultFormat;
- }
- var output = formatMoment(this, inputString);
- return this.localeData().postformat(output);
- }
-
- function from (time, withoutSuffix) {
- if (this.isValid() &&
- ((isMoment(time) && time.isValid()) ||
- createLocal(time).isValid())) {
- return createDuration({to: this, from: time}).locale(this.locale()).humanize(!withoutSuffix);
- } else {
- return this.localeData().invalidDate();
- }
- }
-
- function fromNow (withoutSuffix) {
- return this.from(createLocal(), withoutSuffix);
- }
-
- function to (time, withoutSuffix) {
- if (this.isValid() &&
- ((isMoment(time) && time.isValid()) ||
- createLocal(time).isValid())) {
- return createDuration({from: this, to: time}).locale(this.locale()).humanize(!withoutSuffix);
- } else {
- return this.localeData().invalidDate();
- }
- }
-
- function toNow (withoutSuffix) {
- return this.to(createLocal(), withoutSuffix);
- }
-
- // If passed a locale key, it will set the locale for this
- // instance. Otherwise, it will return the locale configuration
- // variables for this instance.
- function locale (key) {
- var newLocaleData;
-
- if (key === undefined) {
- return this._locale._abbr;
- } else {
- newLocaleData = getLocale(key);
- if (newLocaleData != null) {
- this._locale = newLocaleData;
- }
- return this;
- }
- }
-
- var lang = deprecate(
- 'moment().lang() is deprecated. Instead, use moment().localeData() to get the language configuration. Use moment().locale() to change languages.',
- function (key) {
- if (key === undefined) {
- return this.localeData();
- } else {
- return this.locale(key);
- }
- }
- );
-
- function localeData () {
- return this._locale;
- }
-
- function startOf (units) {
- units = normalizeUnits(units);
- // the following switch intentionally omits break keywords
- // to utilize falling through the cases.
- switch (units) {
- case 'year':
- this.month(0);
- /* falls through */
- case 'quarter':
- case 'month':
- this.date(1);
- /* falls through */
- case 'week':
- case 'isoWeek':
- case 'day':
- case 'date':
- this.hours(0);
- /* falls through */
- case 'hour':
- this.minutes(0);
- /* falls through */
- case 'minute':
- this.seconds(0);
- /* falls through */
- case 'second':
- this.milliseconds(0);
- }
-
- // weeks are a special case
- if (units === 'week') {
- this.weekday(0);
- }
- if (units === 'isoWeek') {
- this.isoWeekday(1);
- }
-
- // quarters are also special
- if (units === 'quarter') {
- this.month(Math.floor(this.month() / 3) * 3);
- }
-
- return this;
- }
-
- function endOf (units) {
- units = normalizeUnits(units);
- if (units === undefined || units === 'millisecond') {
- return this;
- }
-
- // 'date' is an alias for 'day', so it should be considered as such.
- if (units === 'date') {
- units = 'day';
- }
-
- return this.startOf(units).add(1, (units === 'isoWeek' ? 'week' : units)).subtract(1, 'ms');
- }
-
- function valueOf () {
- return this._d.valueOf() - ((this._offset || 0) * 60000);
- }
-
- function unix () {
- return Math.floor(this.valueOf() / 1000);
- }
-
- function toDate () {
- return new Date(this.valueOf());
- }
-
- function toArray () {
- var m = this;
- return [m.year(), m.month(), m.date(), m.hour(), m.minute(), m.second(), m.millisecond()];
- }
-
- function toObject () {
- var m = this;
- return {
- years: m.year(),
- months: m.month(),
- date: m.date(),
- hours: m.hours(),
- minutes: m.minutes(),
- seconds: m.seconds(),
- milliseconds: m.milliseconds()
- };
- }
-
- function toJSON () {
- // new Date(NaN).toJSON() === null
- return this.isValid() ? this.toISOString() : null;
- }
-
- function isValid$2 () {
- return isValid(this);
- }
-
- function parsingFlags () {
- return extend({}, getParsingFlags(this));
- }
-
- function invalidAt () {
- return getParsingFlags(this).overflow;
- }
-
- function creationData() {
- return {
- input: this._i,
- format: this._f,
- locale: this._locale,
- isUTC: this._isUTC,
- strict: this._strict
- };
- }
-
- // FORMATTING
-
- addFormatToken(0, ['gg', 2], 0, function () {
- return this.weekYear() % 100;
- });
-
- addFormatToken(0, ['GG', 2], 0, function () {
- return this.isoWeekYear() % 100;
- });
-
- function addWeekYearFormatToken (token, getter) {
- addFormatToken(0, [token, token.length], 0, getter);
- }
-
- addWeekYearFormatToken('gggg', 'weekYear');
- addWeekYearFormatToken('ggggg', 'weekYear');
- addWeekYearFormatToken('GGGG', 'isoWeekYear');
- addWeekYearFormatToken('GGGGG', 'isoWeekYear');
-
- // ALIASES
-
- addUnitAlias('weekYear', 'gg');
- addUnitAlias('isoWeekYear', 'GG');
-
- // PRIORITY
-
- addUnitPriority('weekYear', 1);
- addUnitPriority('isoWeekYear', 1);
-
-
- // PARSING
-
- addRegexToken('G', matchSigned);
- addRegexToken('g', matchSigned);
- addRegexToken('GG', match1to2, match2);
- addRegexToken('gg', match1to2, match2);
- addRegexToken('GGGG', match1to4, match4);
- addRegexToken('gggg', match1to4, match4);
- addRegexToken('GGGGG', match1to6, match6);
- addRegexToken('ggggg', match1to6, match6);
-
- addWeekParseToken(['gggg', 'ggggg', 'GGGG', 'GGGGG'], function (input, week, config, token) {
- week[token.substr(0, 2)] = toInt(input);
- });
-
- addWeekParseToken(['gg', 'GG'], function (input, week, config, token) {
- week[token] = hooks.parseTwoDigitYear(input);
- });
-
- // MOMENTS
-
- function getSetWeekYear (input) {
- return getSetWeekYearHelper.call(this,
- input,
- this.week(),
- this.weekday(),
- this.localeData()._week.dow,
- this.localeData()._week.doy);
- }
-
- function getSetISOWeekYear (input) {
- return getSetWeekYearHelper.call(this,
- input, this.isoWeek(), this.isoWeekday(), 1, 4);
- }
-
- function getISOWeeksInYear () {
- return weeksInYear(this.year(), 1, 4);
- }
-
- function getWeeksInYear () {
- var weekInfo = this.localeData()._week;
- return weeksInYear(this.year(), weekInfo.dow, weekInfo.doy);
- }
-
- function getSetWeekYearHelper(input, week, weekday, dow, doy) {
- var weeksTarget;
- if (input == null) {
- return weekOfYear(this, dow, doy).year;
- } else {
- weeksTarget = weeksInYear(input, dow, doy);
- if (week > weeksTarget) {
- week = weeksTarget;
- }
- return setWeekAll.call(this, input, week, weekday, dow, doy);
- }
- }
-
- function setWeekAll(weekYear, week, weekday, dow, doy) {
- var dayOfYearData = dayOfYearFromWeeks(weekYear, week, weekday, dow, doy),
- date = createUTCDate(dayOfYearData.year, 0, dayOfYearData.dayOfYear);
-
- this.year(date.getUTCFullYear());
- this.month(date.getUTCMonth());
- this.date(date.getUTCDate());
- return this;
- }
-
- // FORMATTING
-
- addFormatToken('Q', 0, 'Qo', 'quarter');
-
- // ALIASES
-
- addUnitAlias('quarter', 'Q');
-
- // PRIORITY
-
- addUnitPriority('quarter', 7);
-
- // PARSING
-
- addRegexToken('Q', match1);
- addParseToken('Q', function (input, array) {
- array[MONTH] = (toInt(input) - 1) * 3;
- });
-
- // MOMENTS
-
- function getSetQuarter (input) {
- return input == null ? Math.ceil((this.month() + 1) / 3) : this.month((input - 1) * 3 + this.month() % 3);
- }
-
- // FORMATTING
-
- addFormatToken('D', ['DD', 2], 'Do', 'date');
-
- // ALIASES
-
- addUnitAlias('date', 'D');
-
- // PRIORITY
- addUnitPriority('date', 9);
-
- // PARSING
-
- addRegexToken('D', match1to2);
- addRegexToken('DD', match1to2, match2);
- addRegexToken('Do', function (isStrict, locale) {
- // TODO: Remove "ordinalParse" fallback in next major release.
- return isStrict ?
- (locale._dayOfMonthOrdinalParse || locale._ordinalParse) :
- locale._dayOfMonthOrdinalParseLenient;
- });
-
- addParseToken(['D', 'DD'], DATE);
- addParseToken('Do', function (input, array) {
- array[DATE] = toInt(input.match(match1to2)[0]);
- });
-
- // MOMENTS
-
- var getSetDayOfMonth = makeGetSet('Date', true);
-
- // FORMATTING
-
- addFormatToken('DDD', ['DDDD', 3], 'DDDo', 'dayOfYear');
-
- // ALIASES
-
- addUnitAlias('dayOfYear', 'DDD');
-
- // PRIORITY
- addUnitPriority('dayOfYear', 4);
-
- // PARSING
-
- addRegexToken('DDD', match1to3);
- addRegexToken('DDDD', match3);
- addParseToken(['DDD', 'DDDD'], function (input, array, config) {
- config._dayOfYear = toInt(input);
- });
-
- // HELPERS
-
- // MOMENTS
-
- function getSetDayOfYear (input) {
- var dayOfYear = Math.round((this.clone().startOf('day') - this.clone().startOf('year')) / 864e5) + 1;
- return input == null ? dayOfYear : this.add((input - dayOfYear), 'd');
- }
-
- // FORMATTING
-
- addFormatToken('m', ['mm', 2], 0, 'minute');
-
- // ALIASES
-
- addUnitAlias('minute', 'm');
-
- // PRIORITY
-
- addUnitPriority('minute', 14);
-
- // PARSING
-
- addRegexToken('m', match1to2);
- addRegexToken('mm', match1to2, match2);
- addParseToken(['m', 'mm'], MINUTE);
-
- // MOMENTS
-
- var getSetMinute = makeGetSet('Minutes', false);
-
- // FORMATTING
-
- addFormatToken('s', ['ss', 2], 0, 'second');
-
- // ALIASES
-
- addUnitAlias('second', 's');
-
- // PRIORITY
-
- addUnitPriority('second', 15);
-
- // PARSING
-
- addRegexToken('s', match1to2);
- addRegexToken('ss', match1to2, match2);
- addParseToken(['s', 'ss'], SECOND);
-
- // MOMENTS
-
- var getSetSecond = makeGetSet('Seconds', false);
-
- // FORMATTING
-
- addFormatToken('S', 0, 0, function () {
- return ~~(this.millisecond() / 100);
- });
-
- addFormatToken(0, ['SS', 2], 0, function () {
- return ~~(this.millisecond() / 10);
- });
-
- addFormatToken(0, ['SSS', 3], 0, 'millisecond');
- addFormatToken(0, ['SSSS', 4], 0, function () {
- return this.millisecond() * 10;
- });
- addFormatToken(0, ['SSSSS', 5], 0, function () {
- return this.millisecond() * 100;
- });
- addFormatToken(0, ['SSSSSS', 6], 0, function () {
- return this.millisecond() * 1000;
- });
- addFormatToken(0, ['SSSSSSS', 7], 0, function () {
- return this.millisecond() * 10000;
- });
- addFormatToken(0, ['SSSSSSSS', 8], 0, function () {
- return this.millisecond() * 100000;
- });
- addFormatToken(0, ['SSSSSSSSS', 9], 0, function () {
- return this.millisecond() * 1000000;
- });
-
-
- // ALIASES
-
- addUnitAlias('millisecond', 'ms');
-
- // PRIORITY
-
- addUnitPriority('millisecond', 16);
-
- // PARSING
-
- addRegexToken('S', match1to3, match1);
- addRegexToken('SS', match1to3, match2);
- addRegexToken('SSS', match1to3, match3);
-
- var token;
- for (token = 'SSSS'; token.length <= 9; token += 'S') {
- addRegexToken(token, matchUnsigned);
- }
-
- function parseMs(input, array) {
- array[MILLISECOND] = toInt(('0.' + input) * 1000);
- }
-
- for (token = 'S'; token.length <= 9; token += 'S') {
- addParseToken(token, parseMs);
- }
- // MOMENTS
-
- var getSetMillisecond = makeGetSet('Milliseconds', false);
-
- // FORMATTING
-
- addFormatToken('z', 0, 0, 'zoneAbbr');
- addFormatToken('zz', 0, 0, 'zoneName');
-
- // MOMENTS
-
- function getZoneAbbr () {
- return this._isUTC ? 'UTC' : '';
- }
-
- function getZoneName () {
- return this._isUTC ? 'Coordinated Universal Time' : '';
- }
-
- var proto = Moment.prototype;
-
- proto.add = add;
- proto.calendar = calendar$1;
- proto.clone = clone;
- proto.diff = diff;
- proto.endOf = endOf;
- proto.format = format;
- proto.from = from;
- proto.fromNow = fromNow;
- proto.to = to;
- proto.toNow = toNow;
- proto.get = stringGet;
- proto.invalidAt = invalidAt;
- proto.isAfter = isAfter;
- proto.isBefore = isBefore;
- proto.isBetween = isBetween;
- proto.isSame = isSame;
- proto.isSameOrAfter = isSameOrAfter;
- proto.isSameOrBefore = isSameOrBefore;
- proto.isValid = isValid$2;
- proto.lang = lang;
- proto.locale = locale;
- proto.localeData = localeData;
- proto.max = prototypeMax;
- proto.min = prototypeMin;
- proto.parsingFlags = parsingFlags;
- proto.set = stringSet;
- proto.startOf = startOf;
- proto.subtract = subtract;
- proto.toArray = toArray;
- proto.toObject = toObject;
- proto.toDate = toDate;
- proto.toISOString = toISOString;
- proto.inspect = inspect;
- proto.toJSON = toJSON;
- proto.toString = toString;
- proto.unix = unix;
- proto.valueOf = valueOf;
- proto.creationData = creationData;
- proto.year = getSetYear;
- proto.isLeapYear = getIsLeapYear;
- proto.weekYear = getSetWeekYear;
- proto.isoWeekYear = getSetISOWeekYear;
- proto.quarter = proto.quarters = getSetQuarter;
- proto.month = getSetMonth;
- proto.daysInMonth = getDaysInMonth;
- proto.week = proto.weeks = getSetWeek;
- proto.isoWeek = proto.isoWeeks = getSetISOWeek;
- proto.weeksInYear = getWeeksInYear;
- proto.isoWeeksInYear = getISOWeeksInYear;
- proto.date = getSetDayOfMonth;
- proto.day = proto.days = getSetDayOfWeek;
- proto.weekday = getSetLocaleDayOfWeek;
- proto.isoWeekday = getSetISODayOfWeek;
- proto.dayOfYear = getSetDayOfYear;
- proto.hour = proto.hours = getSetHour;
- proto.minute = proto.minutes = getSetMinute;
- proto.second = proto.seconds = getSetSecond;
- proto.millisecond = proto.milliseconds = getSetMillisecond;
- proto.utcOffset = getSetOffset;
- proto.utc = setOffsetToUTC;
- proto.local = setOffsetToLocal;
- proto.parseZone = setOffsetToParsedOffset;
- proto.hasAlignedHourOffset = hasAlignedHourOffset;
- proto.isDST = isDaylightSavingTime;
- proto.isLocal = isLocal;
- proto.isUtcOffset = isUtcOffset;
- proto.isUtc = isUtc;
- proto.isUTC = isUtc;
- proto.zoneAbbr = getZoneAbbr;
- proto.zoneName = getZoneName;
- proto.dates = deprecate('dates accessor is deprecated. Use date instead.', getSetDayOfMonth);
- proto.months = deprecate('months accessor is deprecated. Use month instead', getSetMonth);
- proto.years = deprecate('years accessor is deprecated. Use year instead', getSetYear);
- proto.zone = deprecate('moment().zone is deprecated, use moment().utcOffset instead. http://momentjs.com/guides/#/warnings/zone/', getSetZone);
- proto.isDSTShifted = deprecate('isDSTShifted is deprecated. See http://momentjs.com/guides/#/warnings/dst-shifted/ for more information', isDaylightSavingTimeShifted);
-
- function createUnix (input) {
- return createLocal(input * 1000);
- }
-
- function createInZone () {
- return createLocal.apply(null, arguments).parseZone();
- }
-
- function preParsePostFormat (string) {
- return string;
- }
-
- var proto$1 = Locale.prototype;
-
- proto$1.calendar = calendar;
- proto$1.longDateFormat = longDateFormat;
- proto$1.invalidDate = invalidDate;
- proto$1.ordinal = ordinal;
- proto$1.preparse = preParsePostFormat;
- proto$1.postformat = preParsePostFormat;
- proto$1.relativeTime = relativeTime;
- proto$1.pastFuture = pastFuture;
- proto$1.set = set;
-
- proto$1.months = localeMonths;
- proto$1.monthsShort = localeMonthsShort;
- proto$1.monthsParse = localeMonthsParse;
- proto$1.monthsRegex = monthsRegex;
- proto$1.monthsShortRegex = monthsShortRegex;
- proto$1.week = localeWeek;
- proto$1.firstDayOfYear = localeFirstDayOfYear;
- proto$1.firstDayOfWeek = localeFirstDayOfWeek;
-
- proto$1.weekdays = localeWeekdays;
- proto$1.weekdaysMin = localeWeekdaysMin;
- proto$1.weekdaysShort = localeWeekdaysShort;
- proto$1.weekdaysParse = localeWeekdaysParse;
-
- proto$1.weekdaysRegex = weekdaysRegex;
- proto$1.weekdaysShortRegex = weekdaysShortRegex;
- proto$1.weekdaysMinRegex = weekdaysMinRegex;
-
- proto$1.isPM = localeIsPM;
- proto$1.meridiem = localeMeridiem;
-
- function get$1 (format, index, field, setter) {
- var locale = getLocale();
- var utc = createUTC().set(setter, index);
- return locale[field](utc, format);
- }
-
- function listMonthsImpl (format, index, field) {
- if (isNumber(format)) {
- index = format;
- format = undefined;
- }
-
- format = format || '';
-
- if (index != null) {
- return get$1(format, index, field, 'month');
- }
-
- var i;
- var out = [];
- for (i = 0; i < 12; i++) {
- out[i] = get$1(format, i, field, 'month');
- }
- return out;
- }
-
- // ()
- // (5)
- // (fmt, 5)
- // (fmt)
- // (true)
- // (true, 5)
- // (true, fmt, 5)
- // (true, fmt)
- function listWeekdaysImpl (localeSorted, format, index, field) {
- if (typeof localeSorted === 'boolean') {
- if (isNumber(format)) {
- index = format;
- format = undefined;
- }
-
- format = format || '';
- } else {
- format = localeSorted;
- index = format;
- localeSorted = false;
-
- if (isNumber(format)) {
- index = format;
- format = undefined;
- }
-
- format = format || '';
- }
-
- var locale = getLocale(),
- shift = localeSorted ? locale._week.dow : 0;
-
- if (index != null) {
- return get$1(format, (index + shift) % 7, field, 'day');
- }
-
- var i;
- var out = [];
- for (i = 0; i < 7; i++) {
- out[i] = get$1(format, (i + shift) % 7, field, 'day');
- }
- return out;
- }
-
- function listMonths (format, index) {
- return listMonthsImpl(format, index, 'months');
- }
-
- function listMonthsShort (format, index) {
- return listMonthsImpl(format, index, 'monthsShort');
- }
-
- function listWeekdays (localeSorted, format, index) {
- return listWeekdaysImpl(localeSorted, format, index, 'weekdays');
- }
-
- function listWeekdaysShort (localeSorted, format, index) {
- return listWeekdaysImpl(localeSorted, format, index, 'weekdaysShort');
- }
-
- function listWeekdaysMin (localeSorted, format, index) {
- return listWeekdaysImpl(localeSorted, format, index, 'weekdaysMin');
- }
-
- getSetGlobalLocale('en', {
- dayOfMonthOrdinalParse: /\d{1,2}(th|st|nd|rd)/,
- ordinal : function (number) {
- var b = number % 10,
- output = (toInt(number % 100 / 10) === 1) ? 'th' :
- (b === 1) ? 'st' :
- (b === 2) ? 'nd' :
- (b === 3) ? 'rd' : 'th';
- return number + output;
- }
- });
-
- // Side effect imports
-
- hooks.lang = deprecate('moment.lang is deprecated. Use moment.locale instead.', getSetGlobalLocale);
- hooks.langData = deprecate('moment.langData is deprecated. Use moment.localeData instead.', getLocale);
-
- var mathAbs = Math.abs;
-
- function abs () {
- var data = this._data;
-
- this._milliseconds = mathAbs(this._milliseconds);
- this._days = mathAbs(this._days);
- this._months = mathAbs(this._months);
-
- data.milliseconds = mathAbs(data.milliseconds);
- data.seconds = mathAbs(data.seconds);
- data.minutes = mathAbs(data.minutes);
- data.hours = mathAbs(data.hours);
- data.months = mathAbs(data.months);
- data.years = mathAbs(data.years);
-
- return this;
- }
-
- function addSubtract$1 (duration, input, value, direction) {
- var other = createDuration(input, value);
-
- duration._milliseconds += direction * other._milliseconds;
- duration._days += direction * other._days;
- duration._months += direction * other._months;
-
- return duration._bubble();
- }
-
- // supports only 2.0-style add(1, 's') or add(duration)
- function add$1 (input, value) {
- return addSubtract$1(this, input, value, 1);
- }
-
- // supports only 2.0-style subtract(1, 's') or subtract(duration)
- function subtract$1 (input, value) {
- return addSubtract$1(this, input, value, -1);
- }
-
- function absCeil (number) {
- if (number < 0) {
- return Math.floor(number);
- } else {
- return Math.ceil(number);
- }
- }
-
- function bubble () {
- var milliseconds = this._milliseconds;
- var days = this._days;
- var months = this._months;
- var data = this._data;
- var seconds, minutes, hours, years, monthsFromDays;
-
- // if we have a mix of positive and negative values, bubble down first
- // check: https://github.com/moment/moment/issues/2166
- if (!((milliseconds >= 0 && days >= 0 && months >= 0) ||
- (milliseconds <= 0 && days <= 0 && months <= 0))) {
- milliseconds += absCeil(monthsToDays(months) + days) * 864e5;
- days = 0;
- months = 0;
- }
-
- // The following code bubbles up values, see the tests for
- // examples of what that means.
- data.milliseconds = milliseconds % 1000;
-
- seconds = absFloor(milliseconds / 1000);
- data.seconds = seconds % 60;
-
- minutes = absFloor(seconds / 60);
- data.minutes = minutes % 60;
-
- hours = absFloor(minutes / 60);
- data.hours = hours % 24;
-
- days += absFloor(hours / 24);
-
- // convert days to months
- monthsFromDays = absFloor(daysToMonths(days));
- months += monthsFromDays;
- days -= absCeil(monthsToDays(monthsFromDays));
-
- // 12 months -> 1 year
- years = absFloor(months / 12);
- months %= 12;
-
- data.days = days;
- data.months = months;
- data.years = years;
-
- return this;
- }
-
- function daysToMonths (days) {
- // 400 years have 146097 days (taking into account leap year rules)
- // 400 years have 12 months === 4800
- return days * 4800 / 146097;
- }
-
- function monthsToDays (months) {
- // the reverse of daysToMonths
- return months * 146097 / 4800;
- }
-
- function as (units) {
- if (!this.isValid()) {
- return NaN;
- }
- var days;
- var months;
- var milliseconds = this._milliseconds;
-
- units = normalizeUnits(units);
-
- if (units === 'month' || units === 'year') {
- days = this._days + milliseconds / 864e5;
- months = this._months + daysToMonths(days);
- return units === 'month' ? months : months / 12;
- } else {
- // handle milliseconds separately because of floating point math errors (issue #1867)
- days = this._days + Math.round(monthsToDays(this._months));
- switch (units) {
- case 'week' : return days / 7 + milliseconds / 6048e5;
- case 'day' : return days + milliseconds / 864e5;
- case 'hour' : return days * 24 + milliseconds / 36e5;
- case 'minute' : return days * 1440 + milliseconds / 6e4;
- case 'second' : return days * 86400 + milliseconds / 1000;
- // Math.floor prevents floating point math errors here
- case 'millisecond': return Math.floor(days * 864e5) + milliseconds;
- default: throw new Error('Unknown unit ' + units);
- }
- }
- }
-
- // TODO: Use this.as('ms')?
- function valueOf$1 () {
- if (!this.isValid()) {
- return NaN;
- }
- return (
- this._milliseconds +
- this._days * 864e5 +
- (this._months % 12) * 2592e6 +
- toInt(this._months / 12) * 31536e6
- );
- }
-
- function makeAs (alias) {
- return function () {
- return this.as(alias);
- };
- }
-
- var asMilliseconds = makeAs('ms');
- var asSeconds = makeAs('s');
- var asMinutes = makeAs('m');
- var asHours = makeAs('h');
- var asDays = makeAs('d');
- var asWeeks = makeAs('w');
- var asMonths = makeAs('M');
- var asYears = makeAs('y');
-
- function clone$1 () {
- return createDuration(this);
- }
-
- function get$2 (units) {
- units = normalizeUnits(units);
- return this.isValid() ? this[units + 's']() : NaN;
- }
-
- function makeGetter(name) {
- return function () {
- return this.isValid() ? this._data[name] : NaN;
- };
- }
-
- var milliseconds = makeGetter('milliseconds');
- var seconds = makeGetter('seconds');
- var minutes = makeGetter('minutes');
- var hours = makeGetter('hours');
- var days = makeGetter('days');
- var months = makeGetter('months');
- var years = makeGetter('years');
-
- function weeks () {
- return absFloor(this.days() / 7);
- }
-
- var round = Math.round;
- var thresholds = {
- ss: 44, // a few seconds to seconds
- s : 45, // seconds to minute
- m : 45, // minutes to hour
- h : 22, // hours to day
- d : 26, // days to month
- M : 11 // months to year
- };
-
- // helper function for moment.fn.from, moment.fn.fromNow, and moment.duration.fn.humanize
- function substituteTimeAgo(string, number, withoutSuffix, isFuture, locale) {
- return locale.relativeTime(number || 1, !!withoutSuffix, string, isFuture);
- }
-
- function relativeTime$1 (posNegDuration, withoutSuffix, locale) {
- var duration = createDuration(posNegDuration).abs();
- var seconds = round(duration.as('s'));
- var minutes = round(duration.as('m'));
- var hours = round(duration.as('h'));
- var days = round(duration.as('d'));
- var months = round(duration.as('M'));
- var years = round(duration.as('y'));
-
- var a = seconds <= thresholds.ss && ['s', seconds] ||
- seconds < thresholds.s && ['ss', seconds] ||
- minutes <= 1 && ['m'] ||
- minutes < thresholds.m && ['mm', minutes] ||
- hours <= 1 && ['h'] ||
- hours < thresholds.h && ['hh', hours] ||
- days <= 1 && ['d'] ||
- days < thresholds.d && ['dd', days] ||
- months <= 1 && ['M'] ||
- months < thresholds.M && ['MM', months] ||
- years <= 1 && ['y'] || ['yy', years];
-
- a[2] = withoutSuffix;
- a[3] = +posNegDuration > 0;
- a[4] = locale;
- return substituteTimeAgo.apply(null, a);
- }
-
- // This function allows you to set the rounding function for relative time strings
- function getSetRelativeTimeRounding (roundingFunction) {
- if (roundingFunction === undefined) {
- return round;
- }
- if (typeof(roundingFunction) === 'function') {
- round = roundingFunction;
- return true;
- }
- return false;
- }
-
- // This function allows you to set a threshold for relative time strings
- function getSetRelativeTimeThreshold (threshold, limit) {
- if (thresholds[threshold] === undefined) {
- return false;
- }
- if (limit === undefined) {
- return thresholds[threshold];
- }
- thresholds[threshold] = limit;
- if (threshold === 's') {
- thresholds.ss = limit - 1;
- }
- return true;
- }
-
- function humanize (withSuffix) {
- if (!this.isValid()) {
- return this.localeData().invalidDate();
- }
-
- var locale = this.localeData();
- var output = relativeTime$1(this, !withSuffix, locale);
-
- if (withSuffix) {
- output = locale.pastFuture(+this, output);
- }
-
- return locale.postformat(output);
- }
-
- var abs$1 = Math.abs;
-
- function sign(x) {
- return ((x > 0) - (x < 0)) || +x;
- }
-
- function toISOString$1() {
- // for ISO strings we do not use the normal bubbling rules:
- // * milliseconds bubble up until they become hours
- // * days do not bubble at all
- // * months bubble up until they become years
- // This is because there is no context-free conversion between hours and days
- // (think of clock changes)
- // and also not between days and months (28-31 days per month)
- if (!this.isValid()) {
- return this.localeData().invalidDate();
- }
-
- var seconds = abs$1(this._milliseconds) / 1000;
- var days = abs$1(this._days);
- var months = abs$1(this._months);
- var minutes, hours, years;
-
- // 3600 seconds -> 60 minutes -> 1 hour
- minutes = absFloor(seconds / 60);
- hours = absFloor(minutes / 60);
- seconds %= 60;
- minutes %= 60;
-
- // 12 months -> 1 year
- years = absFloor(months / 12);
- months %= 12;
-
-
- // inspired by https://github.com/dordille/moment-isoduration/blob/master/moment.isoduration.js
- var Y = years;
- var M = months;
- var D = days;
- var h = hours;
- var m = minutes;
- var s = seconds ? seconds.toFixed(3).replace(/\.?0+$/, '') : '';
- var total = this.asSeconds();
-
- if (!total) {
- // this is the same as C#'s (Noda) and python (isodate)...
- // but not other JS (goog.date)
- return 'P0D';
- }
-
- var totalSign = total < 0 ? '-' : '';
- var ymSign = sign(this._months) !== sign(total) ? '-' : '';
- var daysSign = sign(this._days) !== sign(total) ? '-' : '';
- var hmsSign = sign(this._milliseconds) !== sign(total) ? '-' : '';
-
- return totalSign + 'P' +
- (Y ? ymSign + Y + 'Y' : '') +
- (M ? ymSign + M + 'M' : '') +
- (D ? daysSign + D + 'D' : '') +
- ((h || m || s) ? 'T' : '') +
- (h ? hmsSign + h + 'H' : '') +
- (m ? hmsSign + m + 'M' : '') +
- (s ? hmsSign + s + 'S' : '');
- }
-
- var proto$2 = Duration.prototype;
-
- proto$2.isValid = isValid$1;
- proto$2.abs = abs;
- proto$2.add = add$1;
- proto$2.subtract = subtract$1;
- proto$2.as = as;
- proto$2.asMilliseconds = asMilliseconds;
- proto$2.asSeconds = asSeconds;
- proto$2.asMinutes = asMinutes;
- proto$2.asHours = asHours;
- proto$2.asDays = asDays;
- proto$2.asWeeks = asWeeks;
- proto$2.asMonths = asMonths;
- proto$2.asYears = asYears;
- proto$2.valueOf = valueOf$1;
- proto$2._bubble = bubble;
- proto$2.clone = clone$1;
- proto$2.get = get$2;
- proto$2.milliseconds = milliseconds;
- proto$2.seconds = seconds;
- proto$2.minutes = minutes;
- proto$2.hours = hours;
- proto$2.days = days;
- proto$2.weeks = weeks;
- proto$2.months = months;
- proto$2.years = years;
- proto$2.humanize = humanize;
- proto$2.toISOString = toISOString$1;
- proto$2.toString = toISOString$1;
- proto$2.toJSON = toISOString$1;
- proto$2.locale = locale;
- proto$2.localeData = localeData;
-
- proto$2.toIsoString = deprecate('toIsoString() is deprecated. Please use toISOString() instead (notice the capitals)', toISOString$1);
- proto$2.lang = lang;
-
- // Side effect imports
-
- // FORMATTING
-
- addFormatToken('X', 0, 0, 'unix');
- addFormatToken('x', 0, 0, 'valueOf');
-
- // PARSING
-
- addRegexToken('x', matchSigned);
- addRegexToken('X', matchTimestamp);
- addParseToken('X', function (input, array, config) {
- config._d = new Date(parseFloat(input, 10) * 1000);
- });
- addParseToken('x', function (input, array, config) {
- config._d = new Date(toInt(input));
- });
-
- // Side effect imports
-
-
- hooks.version = '2.22.2';
-
- setHookCallback(createLocal);
-
- hooks.fn = proto;
- hooks.min = min;
- hooks.max = max;
- hooks.now = now;
- hooks.utc = createUTC;
- hooks.unix = createUnix;
- hooks.months = listMonths;
- hooks.isDate = isDate;
- hooks.locale = getSetGlobalLocale;
- hooks.invalid = createInvalid;
- hooks.duration = createDuration;
- hooks.isMoment = isMoment;
- hooks.weekdays = listWeekdays;
- hooks.parseZone = createInZone;
- hooks.localeData = getLocale;
- hooks.isDuration = isDuration;
- hooks.monthsShort = listMonthsShort;
- hooks.weekdaysMin = listWeekdaysMin;
- hooks.defineLocale = defineLocale;
- hooks.updateLocale = updateLocale;
- hooks.locales = listLocales;
- hooks.weekdaysShort = listWeekdaysShort;
- hooks.normalizeUnits = normalizeUnits;
- hooks.relativeTimeRounding = getSetRelativeTimeRounding;
- hooks.relativeTimeThreshold = getSetRelativeTimeThreshold;
- hooks.calendarFormat = getCalendarFormat;
- hooks.prototype = proto;
-
- // currently HTML5 input type only supports 24-hour formats
- hooks.HTML5_FMT = {
- DATETIME_LOCAL: 'YYYY-MM-DDTHH:mm', // <input type="datetime-local" />
- DATETIME_LOCAL_SECONDS: 'YYYY-MM-DDTHH:mm:ss', // <input type="datetime-local" step="1" />
- DATETIME_LOCAL_MS: 'YYYY-MM-DDTHH:mm:ss.SSS', // <input type="datetime-local" step="0.001" />
- DATE: 'YYYY-MM-DD', // <input type="date" />
- TIME: 'HH:mm', // <input type="time" />
- TIME_SECONDS: 'HH:mm:ss', // <input type="time" step="1" />
- TIME_MS: 'HH:mm:ss.SSS', // <input type="time" step="0.001" />
- WEEK: 'YYYY-[W]WW', // <input type="week" />
- MONTH: 'YYYY-MM' // <input type="month" />
- };
-
- return hooks;
-
-})));
-
-},{}],7:[function(require,module,exports){
-/**
- * @namespace Chart
- */
-var Chart = require(30)();
-
-Chart.helpers = require(46);
-
-// @todo dispatch these helpers into appropriated helpers/helpers.* file and write unit tests!
-require(28)(Chart);
-
-Chart.Animation = require(22);
-Chart.animationService = require(23);
-Chart.defaults = require(26);
-Chart.Element = require(27);
-Chart.elements = require(41);
-Chart.Interaction = require(29);
-Chart.layouts = require(31);
-Chart.platform = require(49);
-Chart.plugins = require(32);
-Chart.Scale = require(33);
-Chart.scaleService = require(34);
-Chart.Ticks = require(35);
-Chart.Tooltip = require(36);
-
-require(24)(Chart);
-require(25)(Chart);
-
-require(56)(Chart);
-require(54)(Chart);
-require(55)(Chart);
-require(57)(Chart);
-require(58)(Chart);
-require(59)(Chart);
-
-// Controllers must be loaded after elements
-// See Chart.core.datasetController.dataElementType
-require(15)(Chart);
-require(16)(Chart);
-require(17)(Chart);
-require(18)(Chart);
-require(19)(Chart);
-require(20)(Chart);
-require(21)(Chart);
-
-require(8)(Chart);
-require(9)(Chart);
-require(10)(Chart);
-require(11)(Chart);
-require(12)(Chart);
-require(13)(Chart);
-require(14)(Chart);
-
-// Loading built-in plugins
-var plugins = require(50);
-for (var k in plugins) {
- if (plugins.hasOwnProperty(k)) {
- Chart.plugins.register(plugins[k]);
- }
-}
-
-Chart.platform.initialize();
-
-module.exports = Chart;
-if (typeof window !== 'undefined') {
- window.Chart = Chart;
-}
-
-// DEPRECATIONS
-
-/**
- * Provided for backward compatibility, not available anymore
- * @namespace Chart.Legend
- * @deprecated since version 2.1.5
- * @todo remove at version 3
- * @private
- */
-Chart.Legend = plugins.legend._element;
-
-/**
- * Provided for backward compatibility, not available anymore
- * @namespace Chart.Title
- * @deprecated since version 2.1.5
- * @todo remove at version 3
- * @private
- */
-Chart.Title = plugins.title._element;
-
-/**
- * Provided for backward compatibility, use Chart.plugins instead
- * @namespace Chart.pluginService
- * @deprecated since version 2.1.5
- * @todo remove at version 3
- * @private
- */
-Chart.pluginService = Chart.plugins;
-
-/**
- * Provided for backward compatibility, inheriting from Chart.PlugingBase has no
- * effect, instead simply create/register plugins via plain JavaScript objects.
- * @interface Chart.PluginBase
- * @deprecated since version 2.5.0
- * @todo remove at version 3
- * @private
- */
-Chart.PluginBase = Chart.Element.extend({});
-
-/**
- * Provided for backward compatibility, use Chart.helpers.canvas instead.
- * @namespace Chart.canvasHelpers
- * @deprecated since version 2.6.0
- * @todo remove at version 3
- * @private
- */
-Chart.canvasHelpers = Chart.helpers.canvas;
-
-/**
- * Provided for backward compatibility, use Chart.layouts instead.
- * @namespace Chart.layoutService
- * @deprecated since version 2.8.0
- * @todo remove at version 3
- * @private
- */
-Chart.layoutService = Chart.layouts;
-
-},{"10":10,"11":11,"12":12,"13":13,"14":14,"15":15,"16":16,"17":17,"18":18,"19":19,"20":20,"21":21,"22":22,"23":23,"24":24,"25":25,"26":26,"27":27,"28":28,"29":29,"30":30,"31":31,"32":32,"33":33,"34":34,"35":35,"36":36,"41":41,"46":46,"49":49,"50":50,"54":54,"55":55,"56":56,"57":57,"58":58,"59":59,"8":8,"9":9}],8:[function(require,module,exports){
-'use strict';
-
-module.exports = function(Chart) {
-
- Chart.Bar = function(context, config) {
- config.type = 'bar';
-
- return new Chart(context, config);
- };
-
-};
-
-},{}],9:[function(require,module,exports){
-'use strict';
-
-module.exports = function(Chart) {
-
- Chart.Bubble = function(context, config) {
- config.type = 'bubble';
- return new Chart(context, config);
- };
-
-};
-
-},{}],10:[function(require,module,exports){
-'use strict';
-
-module.exports = function(Chart) {
-
- Chart.Doughnut = function(context, config) {
- config.type = 'doughnut';
-
- return new Chart(context, config);
- };
-
-};
-
-},{}],11:[function(require,module,exports){
-'use strict';
-
-module.exports = function(Chart) {
-
- Chart.Line = function(context, config) {
- config.type = 'line';
-
- return new Chart(context, config);
- };
-
-};
-
-},{}],12:[function(require,module,exports){
-'use strict';
-
-module.exports = function(Chart) {
-
- Chart.PolarArea = function(context, config) {
- config.type = 'polarArea';
-
- return new Chart(context, config);
- };
-
-};
-
-},{}],13:[function(require,module,exports){
-'use strict';
-
-module.exports = function(Chart) {
-
- Chart.Radar = function(context, config) {
- config.type = 'radar';
-
- return new Chart(context, config);
- };
-
-};
-
-},{}],14:[function(require,module,exports){
-'use strict';
-
-module.exports = function(Chart) {
- Chart.Scatter = function(context, config) {
- config.type = 'scatter';
- return new Chart(context, config);
- };
-};
-
-},{}],15:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var elements = require(41);
-var helpers = require(46);
-
-defaults._set('bar', {
- hover: {
- mode: 'label'
- },
-
- scales: {
- xAxes: [{
- type: 'category',
-
- // Specific to Bar Controller
- categoryPercentage: 0.8,
- barPercentage: 0.9,
-
- // offset settings
- offset: true,
-
- // grid line settings
- gridLines: {
- offsetGridLines: true
- }
- }],
-
- yAxes: [{
- type: 'linear'
- }]
- }
-});
-
-defaults._set('horizontalBar', {
- hover: {
- mode: 'index',
- axis: 'y'
- },
-
- scales: {
- xAxes: [{
- type: 'linear',
- position: 'bottom'
- }],
-
- yAxes: [{
- position: 'left',
- type: 'category',
-
- // Specific to Horizontal Bar Controller
- categoryPercentage: 0.8,
- barPercentage: 0.9,
-
- // offset settings
- offset: true,
-
- // grid line settings
- gridLines: {
- offsetGridLines: true
- }
- }]
- },
-
- elements: {
- rectangle: {
- borderSkipped: 'left'
- }
- },
-
- tooltips: {
- callbacks: {
- title: function(item, data) {
- // Pick first xLabel for now
- var title = '';
-
- if (item.length > 0) {
- if (item[0].yLabel) {
- title = item[0].yLabel;
- } else if (data.labels.length > 0 && item[0].index < data.labels.length) {
- title = data.labels[item[0].index];
- }
- }
-
- return title;
- },
-
- label: function(item, data) {
- var datasetLabel = data.datasets[item.datasetIndex].label || '';
- return datasetLabel + ': ' + item.xLabel;
- }
- },
- mode: 'index',
- axis: 'y'
- }
-});
-
-/**
- * Computes the "optimal" sample size to maintain bars equally sized while preventing overlap.
- * @private
- */
-function computeMinSampleSize(scale, pixels) {
- var min = scale.isHorizontal() ? scale.width : scale.height;
- var ticks = scale.getTicks();
- var prev, curr, i, ilen;
-
- for (i = 1, ilen = pixels.length; i < ilen; ++i) {
- min = Math.min(min, pixels[i] - pixels[i - 1]);
- }
-
- for (i = 0, ilen = ticks.length; i < ilen; ++i) {
- curr = scale.getPixelForTick(i);
- min = i > 0 ? Math.min(min, curr - prev) : min;
- prev = curr;
- }
-
- return min;
-}
-
-/**
- * Computes an "ideal" category based on the absolute bar thickness or, if undefined or null,
- * uses the smallest interval (see computeMinSampleSize) that prevents bar overlapping. This
- * mode currently always generates bars equally sized (until we introduce scriptable options?).
- * @private
- */
-function computeFitCategoryTraits(index, ruler, options) {
- var thickness = options.barThickness;
- var count = ruler.stackCount;
- var curr = ruler.pixels[index];
- var size, ratio;
-
- if (helpers.isNullOrUndef(thickness)) {
- size = ruler.min * options.categoryPercentage;
- ratio = options.barPercentage;
- } else {
- // When bar thickness is enforced, category and bar percentages are ignored.
- // Note(SB): we could add support for relative bar thickness (e.g. barThickness: '50%')
- // and deprecate barPercentage since this value is ignored when thickness is absolute.
- size = thickness * count;
- ratio = 1;
- }
-
- return {
- chunk: size / count,
- ratio: ratio,
- start: curr - (size / 2)
- };
-}
-
-/**
- * Computes an "optimal" category that globally arranges bars side by side (no gap when
- * percentage options are 1), based on the previous and following categories. This mode
- * generates bars with different widths when data are not evenly spaced.
- * @private
- */
-function computeFlexCategoryTraits(index, ruler, options) {
- var pixels = ruler.pixels;
- var curr = pixels[index];
- var prev = index > 0 ? pixels[index - 1] : null;
- var next = index < pixels.length - 1 ? pixels[index + 1] : null;
- var percent = options.categoryPercentage;
- var start, size;
-
- if (prev === null) {
- // first data: its size is double based on the next point or,
- // if it's also the last data, we use the scale end extremity.
- prev = curr - (next === null ? ruler.end - curr : next - curr);
- }
-
- if (next === null) {
- // last data: its size is also double based on the previous point.
- next = curr + curr - prev;
- }
-
- start = curr - ((curr - prev) / 2) * percent;
- size = ((next - prev) / 2) * percent;
-
- return {
- chunk: size / ruler.stackCount,
- ratio: options.barPercentage,
- start: start
- };
-}
-
-module.exports = function(Chart) {
-
- Chart.controllers.bar = Chart.DatasetController.extend({
-
- dataElementType: elements.Rectangle,
-
- initialize: function() {
- var me = this;
- var meta;
-
- Chart.DatasetController.prototype.initialize.apply(me, arguments);
-
- meta = me.getMeta();
- meta.stack = me.getDataset().stack;
- meta.bar = true;
- },
-
- update: function(reset) {
- var me = this;
- var rects = me.getMeta().data;
- var i, ilen;
-
- me._ruler = me.getRuler();
-
- for (i = 0, ilen = rects.length; i < ilen; ++i) {
- me.updateElement(rects[i], i, reset);
- }
- },
-
- updateElement: function(rectangle, index, reset) {
- var me = this;
- var chart = me.chart;
- var meta = me.getMeta();
- var dataset = me.getDataset();
- var custom = rectangle.custom || {};
- var rectangleOptions = chart.options.elements.rectangle;
-
- rectangle._xScale = me.getScaleForId(meta.xAxisID);
- rectangle._yScale = me.getScaleForId(meta.yAxisID);
- rectangle._datasetIndex = me.index;
- rectangle._index = index;
-
- rectangle._model = {
- datasetLabel: dataset.label,
- label: chart.data.labels[index],
- borderSkipped: custom.borderSkipped ? custom.borderSkipped : rectangleOptions.borderSkipped,
- backgroundColor: custom.backgroundColor ? custom.backgroundColor : helpers.valueAtIndexOrDefault(dataset.backgroundColor, index, rectangleOptions.backgroundColor),
- borderColor: custom.borderColor ? custom.borderColor : helpers.valueAtIndexOrDefault(dataset.borderColor, index, rectangleOptions.borderColor),
- borderWidth: custom.borderWidth ? custom.borderWidth : helpers.valueAtIndexOrDefault(dataset.borderWidth, index, rectangleOptions.borderWidth)
- };
-
- me.updateElementGeometry(rectangle, index, reset);
-
- rectangle.pivot();
- },
-
- /**
- * @private
- */
- updateElementGeometry: function(rectangle, index, reset) {
- var me = this;
- var model = rectangle._model;
- var vscale = me.getValueScale();
- var base = vscale.getBasePixel();
- var horizontal = vscale.isHorizontal();
- var ruler = me._ruler || me.getRuler();
- var vpixels = me.calculateBarValuePixels(me.index, index);
- var ipixels = me.calculateBarIndexPixels(me.index, index, ruler);
-
- model.horizontal = horizontal;
- model.base = reset ? base : vpixels.base;
- model.x = horizontal ? reset ? base : vpixels.head : ipixels.center;
- model.y = horizontal ? ipixels.center : reset ? base : vpixels.head;
- model.height = horizontal ? ipixels.size : undefined;
- model.width = horizontal ? undefined : ipixels.size;
- },
-
- /**
- * @private
- */
- getValueScaleId: function() {
- return this.getMeta().yAxisID;
- },
-
- /**
- * @private
- */
- getIndexScaleId: function() {
- return this.getMeta().xAxisID;
- },
-
- /**
- * @private
- */
- getValueScale: function() {
- return this.getScaleForId(this.getValueScaleId());
- },
-
- /**
- * @private
- */
- getIndexScale: function() {
- return this.getScaleForId(this.getIndexScaleId());
- },
-
- /**
- * Returns the stacks based on groups and bar visibility.
- * @param {Number} [last] - The dataset index
- * @returns {Array} The stack list
- * @private
- */
- _getStacks: function(last) {
- var me = this;
- var chart = me.chart;
- var scale = me.getIndexScale();
- var stacked = scale.options.stacked;
- var ilen = last === undefined ? chart.data.datasets.length : last + 1;
- var stacks = [];
- var i, meta;
-
- for (i = 0; i < ilen; ++i) {
- meta = chart.getDatasetMeta(i);
- if (meta.bar && chart.isDatasetVisible(i) &&
- (stacked === false ||
- (stacked === true && stacks.indexOf(meta.stack) === -1) ||
- (stacked === undefined && (meta.stack === undefined || stacks.indexOf(meta.stack) === -1)))) {
- stacks.push(meta.stack);
- }
- }
-
- return stacks;
- },
-
- /**
- * Returns the effective number of stacks based on groups and bar visibility.
- * @private
- */
- getStackCount: function() {
- return this._getStacks().length;
- },
-
- /**
- * Returns the stack index for the given dataset based on groups and bar visibility.
- * @param {Number} [datasetIndex] - The dataset index
- * @param {String} [name] - The stack name to find
- * @returns {Number} The stack index
- * @private
- */
- getStackIndex: function(datasetIndex, name) {
- var stacks = this._getStacks(datasetIndex);
- var index = (name !== undefined)
- ? stacks.indexOf(name)
- : -1; // indexOf returns -1 if element is not present
-
- return (index === -1)
- ? stacks.length - 1
- : index;
- },
-
- /**
- * @private
- */
- getRuler: function() {
- var me = this;
- var scale = me.getIndexScale();
- var stackCount = me.getStackCount();
- var datasetIndex = me.index;
- var isHorizontal = scale.isHorizontal();
- var start = isHorizontal ? scale.left : scale.top;
- var end = start + (isHorizontal ? scale.width : scale.height);
- var pixels = [];
- var i, ilen, min;
-
- for (i = 0, ilen = me.getMeta().data.length; i < ilen; ++i) {
- pixels.push(scale.getPixelForValue(null, i, datasetIndex));
- }
-
- min = helpers.isNullOrUndef(scale.options.barThickness)
- ? computeMinSampleSize(scale, pixels)
- : -1;
-
- return {
- min: min,
- pixels: pixels,
- start: start,
- end: end,
- stackCount: stackCount,
- scale: scale
- };
- },
-
- /**
- * Note: pixel values are not clamped to the scale area.
- * @private
- */
- calculateBarValuePixels: function(datasetIndex, index) {
- var me = this;
- var chart = me.chart;
- var meta = me.getMeta();
- var scale = me.getValueScale();
- var datasets = chart.data.datasets;
- var value = scale.getRightValue(datasets[datasetIndex].data[index]);
- var stacked = scale.options.stacked;
- var stack = meta.stack;
- var start = 0;
- var i, imeta, ivalue, base, head, size;
-
- if (stacked || (stacked === undefined && stack !== undefined)) {
- for (i = 0; i < datasetIndex; ++i) {
- imeta = chart.getDatasetMeta(i);
-
- if (imeta.bar &&
- imeta.stack === stack &&
- imeta.controller.getValueScaleId() === scale.id &&
- chart.isDatasetVisible(i)) {
-
- ivalue = scale.getRightValue(datasets[i].data[index]);
- if ((value < 0 && ivalue < 0) || (value >= 0 && ivalue > 0)) {
- start += ivalue;
- }
- }
- }
- }
-
- base = scale.getPixelForValue(start);
- head = scale.getPixelForValue(start + value);
- size = (head - base) / 2;
-
- return {
- size: size,
- base: base,
- head: head,
- center: head + size / 2
- };
- },
-
- /**
- * @private
- */
- calculateBarIndexPixels: function(datasetIndex, index, ruler) {
- var me = this;
- var options = ruler.scale.options;
- var range = options.barThickness === 'flex'
- ? computeFlexCategoryTraits(index, ruler, options)
- : computeFitCategoryTraits(index, ruler, options);
-
- var stackIndex = me.getStackIndex(datasetIndex, me.getMeta().stack);
- var center = range.start + (range.chunk * stackIndex) + (range.chunk / 2);
- var size = Math.min(
- helpers.valueOrDefault(options.maxBarThickness, Infinity),
- range.chunk * range.ratio);
-
- return {
- base: center - size / 2,
- head: center + size / 2,
- center: center,
- size: size
- };
- },
-
- draw: function() {
- var me = this;
- var chart = me.chart;
- var scale = me.getValueScale();
- var rects = me.getMeta().data;
- var dataset = me.getDataset();
- var ilen = rects.length;
- var i = 0;
-
- helpers.canvas.clipArea(chart.ctx, chart.chartArea);
-
- for (; i < ilen; ++i) {
- if (!isNaN(scale.getRightValue(dataset.data[i]))) {
- rects[i].draw();
- }
- }
-
- helpers.canvas.unclipArea(chart.ctx);
- },
- });
-
- Chart.controllers.horizontalBar = Chart.controllers.bar.extend({
- /**
- * @private
- */
- getValueScaleId: function() {
- return this.getMeta().xAxisID;
- },
-
- /**
- * @private
- */
- getIndexScaleId: function() {
- return this.getMeta().yAxisID;
- }
- });
-};
-
-},{"26":26,"41":41,"46":46}],16:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var elements = require(41);
-var helpers = require(46);
-
-defaults._set('bubble', {
- hover: {
- mode: 'single'
- },
-
- scales: {
- xAxes: [{
- type: 'linear', // bubble should probably use a linear scale by default
- position: 'bottom',
- id: 'x-axis-0' // need an ID so datasets can reference the scale
- }],
- yAxes: [{
- type: 'linear',
- position: 'left',
- id: 'y-axis-0'
- }]
- },
-
- tooltips: {
- callbacks: {
- title: function() {
- // Title doesn't make sense for scatter since we format the data as a point
- return '';
- },
- label: function(item, data) {
- var datasetLabel = data.datasets[item.datasetIndex].label || '';
- var dataPoint = data.datasets[item.datasetIndex].data[item.index];
- return datasetLabel + ': (' + item.xLabel + ', ' + item.yLabel + ', ' + dataPoint.r + ')';
- }
- }
- }
-});
-
-
-module.exports = function(Chart) {
-
- Chart.controllers.bubble = Chart.DatasetController.extend({
- /**
- * @protected
- */
- dataElementType: elements.Point,
-
- /**
- * @protected
- */
- update: function(reset) {
- var me = this;
- var meta = me.getMeta();
- var points = meta.data;
-
- // Update Points
- helpers.each(points, function(point, index) {
- me.updateElement(point, index, reset);
- });
- },
-
- /**
- * @protected
- */
- updateElement: function(point, index, reset) {
- var me = this;
- var meta = me.getMeta();
- var custom = point.custom || {};
- var xScale = me.getScaleForId(meta.xAxisID);
- var yScale = me.getScaleForId(meta.yAxisID);
- var options = me._resolveElementOptions(point, index);
- var data = me.getDataset().data[index];
- var dsIndex = me.index;
-
- var x = reset ? xScale.getPixelForDecimal(0.5) : xScale.getPixelForValue(typeof data === 'object' ? data : NaN, index, dsIndex);
- var y = reset ? yScale.getBasePixel() : yScale.getPixelForValue(data, index, dsIndex);
-
- point._xScale = xScale;
- point._yScale = yScale;
- point._options = options;
- point._datasetIndex = dsIndex;
- point._index = index;
- point._model = {
- backgroundColor: options.backgroundColor,
- borderColor: options.borderColor,
- borderWidth: options.borderWidth,
- hitRadius: options.hitRadius,
- pointStyle: options.pointStyle,
- rotation: options.rotation,
- radius: reset ? 0 : options.radius,
- skip: custom.skip || isNaN(x) || isNaN(y),
- x: x,
- y: y,
- };
-
- point.pivot();
- },
-
- /**
- * @protected
- */
- setHoverStyle: function(point) {
- var model = point._model;
- var options = point._options;
- point.$previousStyle = {
- backgroundColor: model.backgroundColor,
- borderColor: model.borderColor,
- borderWidth: model.borderWidth,
- radius: model.radius
- };
- model.backgroundColor = helpers.valueOrDefault(options.hoverBackgroundColor, helpers.getHoverColor(options.backgroundColor));
- model.borderColor = helpers.valueOrDefault(options.hoverBorderColor, helpers.getHoverColor(options.borderColor));
- model.borderWidth = helpers.valueOrDefault(options.hoverBorderWidth, options.borderWidth);
- model.radius = options.radius + options.hoverRadius;
- },
-
- /**
- * @private
- */
- _resolveElementOptions: function(point, index) {
- var me = this;
- var chart = me.chart;
- var datasets = chart.data.datasets;
- var dataset = datasets[me.index];
- var custom = point.custom || {};
- var options = chart.options.elements.point;
- var resolve = helpers.options.resolve;
- var data = dataset.data[index];
- var values = {};
- var i, ilen, key;
-
- // Scriptable options
- var context = {
- chart: chart,
- dataIndex: index,
- dataset: dataset,
- datasetIndex: me.index
- };
-
- var keys = [
- 'backgroundColor',
- 'borderColor',
- 'borderWidth',
- 'hoverBackgroundColor',
- 'hoverBorderColor',
- 'hoverBorderWidth',
- 'hoverRadius',
- 'hitRadius',
- 'pointStyle',
- 'rotation'
- ];
-
- for (i = 0, ilen = keys.length; i < ilen; ++i) {
- key = keys[i];
- values[key] = resolve([
- custom[key],
- dataset[key],
- options[key]
- ], context, index);
- }
-
- // Custom radius resolution
- values.radius = resolve([
- custom.radius,
- data ? data.r : undefined,
- dataset.radius,
- options.radius
- ], context, index);
- return values;
- }
- });
-};
-
-},{"26":26,"41":41,"46":46}],17:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var elements = require(41);
-var helpers = require(46);
-
-defaults._set('doughnut', {
- animation: {
- // Boolean - Whether we animate the rotation of the Doughnut
- animateRotate: true,
- // Boolean - Whether we animate scaling the Doughnut from the centre
- animateScale: false
- },
- hover: {
- mode: 'single'
- },
- legendCallback: function(chart) {
- var text = [];
- text.push('<ul class="' + chart.id + '-legend">');
-
- var data = chart.data;
- var datasets = data.datasets;
- var labels = data.labels;
-
- if (datasets.length) {
- for (var i = 0; i < datasets[0].data.length; ++i) {
- text.push('<li><span style="background-color:' + datasets[0].backgroundColor[i] + '"></span>');
- if (labels[i]) {
- text.push(labels[i]);
- }
- text.push('</li>');
- }
- }
-
- text.push('</ul>');
- return text.join('');
- },
- legend: {
- labels: {
- generateLabels: function(chart) {
- var data = chart.data;
- if (data.labels.length && data.datasets.length) {
- return data.labels.map(function(label, i) {
- var meta = chart.getDatasetMeta(0);
- var ds = data.datasets[0];
- var arc = meta.data[i];
- var custom = arc && arc.custom || {};
- var valueAtIndexOrDefault = helpers.valueAtIndexOrDefault;
- var arcOpts = chart.options.elements.arc;
- var fill = custom.backgroundColor ? custom.backgroundColor : valueAtIndexOrDefault(ds.backgroundColor, i, arcOpts.backgroundColor);
- var stroke = custom.borderColor ? custom.borderColor : valueAtIndexOrDefault(ds.borderColor, i, arcOpts.borderColor);
- var bw = custom.borderWidth ? custom.borderWidth : valueAtIndexOrDefault(ds.borderWidth, i, arcOpts.borderWidth);
-
- return {
- text: label,
- fillStyle: fill,
- strokeStyle: stroke,
- lineWidth: bw,
- hidden: isNaN(ds.data[i]) || meta.data[i].hidden,
-
- // Extra data used for toggling the correct item
- index: i
- };
- });
- }
- return [];
- }
- },
-
- onClick: function(e, legendItem) {
- var index = legendItem.index;
- var chart = this.chart;
- var i, ilen, meta;
-
- for (i = 0, ilen = (chart.data.datasets || []).length; i < ilen; ++i) {
- meta = chart.getDatasetMeta(i);
- // toggle visibility of index if exists
- if (meta.data[index]) {
- meta.data[index].hidden = !meta.data[index].hidden;
- }
- }
-
- chart.update();
- }
- },
-
- // The percentage of the chart that we cut out of the middle.
- cutoutPercentage: 50,
-
- // The rotation of the chart, where the first data arc begins.
- rotation: Math.PI * -0.5,
-
- // The total circumference of the chart.
- circumference: Math.PI * 2.0,
-
- // Need to override these to give a nice default
- tooltips: {
- callbacks: {
- title: function() {
- return '';
- },
- label: function(tooltipItem, data) {
- var dataLabel = data.labels[tooltipItem.index];
- var value = ': ' + data.datasets[tooltipItem.datasetIndex].data[tooltipItem.index];
-
- if (helpers.isArray(dataLabel)) {
- // show value on first line of multiline label
- // need to clone because we are changing the value
- dataLabel = dataLabel.slice();
- dataLabel[0] += value;
- } else {
- dataLabel += value;
- }
-
- return dataLabel;
- }
- }
- }
-});
-
-defaults._set('pie', helpers.clone(defaults.doughnut));
-defaults._set('pie', {
- cutoutPercentage: 0
-});
-
-module.exports = function(Chart) {
-
- Chart.controllers.doughnut = Chart.controllers.pie = Chart.DatasetController.extend({
-
- dataElementType: elements.Arc,
-
- linkScales: helpers.noop,
-
- // Get index of the dataset in relation to the visible datasets. This allows determining the inner and outer radius correctly
- getRingIndex: function(datasetIndex) {
- var ringIndex = 0;
-
- for (var j = 0; j < datasetIndex; ++j) {
- if (this.chart.isDatasetVisible(j)) {
- ++ringIndex;
- }
- }
-
- return ringIndex;
- },
-
- update: function(reset) {
- var me = this;
- var chart = me.chart;
- var chartArea = chart.chartArea;
- var opts = chart.options;
- var arcOpts = opts.elements.arc;
- var availableWidth = chartArea.right - chartArea.left - arcOpts.borderWidth;
- var availableHeight = chartArea.bottom - chartArea.top - arcOpts.borderWidth;
- var minSize = Math.min(availableWidth, availableHeight);
- var offset = {x: 0, y: 0};
- var meta = me.getMeta();
- var cutoutPercentage = opts.cutoutPercentage;
- var circumference = opts.circumference;
-
- // If the chart's circumference isn't a full circle, calculate minSize as a ratio of the width/height of the arc
- if (circumference < Math.PI * 2.0) {
- var startAngle = opts.rotation % (Math.PI * 2.0);
- startAngle += Math.PI * 2.0 * (startAngle >= Math.PI ? -1 : startAngle < -Math.PI ? 1 : 0);
- var endAngle = startAngle + circumference;
- var start = {x: Math.cos(startAngle), y: Math.sin(startAngle)};
- var end = {x: Math.cos(endAngle), y: Math.sin(endAngle)};
- var contains0 = (startAngle <= 0 && endAngle >= 0) || (startAngle <= Math.PI * 2.0 && Math.PI * 2.0 <= endAngle);
- var contains90 = (startAngle <= Math.PI * 0.5 && Math.PI * 0.5 <= endAngle) || (startAngle <= Math.PI * 2.5 && Math.PI * 2.5 <= endAngle);
- var contains180 = (startAngle <= -Math.PI && -Math.PI <= endAngle) || (startAngle <= Math.PI && Math.PI <= endAngle);
- var contains270 = (startAngle <= -Math.PI * 0.5 && -Math.PI * 0.5 <= endAngle) || (startAngle <= Math.PI * 1.5 && Math.PI * 1.5 <= endAngle);
- var cutout = cutoutPercentage / 100.0;
- var min = {x: contains180 ? -1 : Math.min(start.x * (start.x < 0 ? 1 : cutout), end.x * (end.x < 0 ? 1 : cutout)), y: contains270 ? -1 : Math.min(start.y * (start.y < 0 ? 1 : cutout), end.y * (end.y < 0 ? 1 : cutout))};
- var max = {x: contains0 ? 1 : Math.max(start.x * (start.x > 0 ? 1 : cutout), end.x * (end.x > 0 ? 1 : cutout)), y: contains90 ? 1 : Math.max(start.y * (start.y > 0 ? 1 : cutout), end.y * (end.y > 0 ? 1 : cutout))};
- var size = {width: (max.x - min.x) * 0.5, height: (max.y - min.y) * 0.5};
- minSize = Math.min(availableWidth / size.width, availableHeight / size.height);
- offset = {x: (max.x + min.x) * -0.5, y: (max.y + min.y) * -0.5};
- }
-
- chart.borderWidth = me.getMaxBorderWidth(meta.data);
- chart.outerRadius = Math.max((minSize - chart.borderWidth) / 2, 0);
- chart.innerRadius = Math.max(cutoutPercentage ? (chart.outerRadius / 100) * (cutoutPercentage) : 0, 0);
- chart.radiusLength = (chart.outerRadius - chart.innerRadius) / chart.getVisibleDatasetCount();
- chart.offsetX = offset.x * chart.outerRadius;
- chart.offsetY = offset.y * chart.outerRadius;
-
- meta.total = me.calculateTotal();
-
- me.outerRadius = chart.outerRadius - (chart.radiusLength * me.getRingIndex(me.index));
- me.innerRadius = Math.max(me.outerRadius - chart.radiusLength, 0);
-
- helpers.each(meta.data, function(arc, index) {
- me.updateElement(arc, index, reset);
- });
- },
-
- updateElement: function(arc, index, reset) {
- var me = this;
- var chart = me.chart;
- var chartArea = chart.chartArea;
- var opts = chart.options;
- var animationOpts = opts.animation;
- var centerX = (chartArea.left + chartArea.right) / 2;
- var centerY = (chartArea.top + chartArea.bottom) / 2;
- var startAngle = opts.rotation; // non reset case handled later
- var endAngle = opts.rotation; // non reset case handled later
- var dataset = me.getDataset();
- var circumference = reset && animationOpts.animateRotate ? 0 : arc.hidden ? 0 : me.calculateCircumference(dataset.data[index]) * (opts.circumference / (2.0 * Math.PI));
- var innerRadius = reset && animationOpts.animateScale ? 0 : me.innerRadius;
- var outerRadius = reset && animationOpts.animateScale ? 0 : me.outerRadius;
- var valueAtIndexOrDefault = helpers.valueAtIndexOrDefault;
-
- helpers.extend(arc, {
- // Utility
- _datasetIndex: me.index,
- _index: index,
-
- // Desired view properties
- _model: {
- x: centerX + chart.offsetX,
- y: centerY + chart.offsetY,
- startAngle: startAngle,
- endAngle: endAngle,
- circumference: circumference,
- outerRadius: outerRadius,
- innerRadius: innerRadius,
- label: valueAtIndexOrDefault(dataset.label, index, chart.data.labels[index])
- }
- });
-
- var model = arc._model;
-
- // Resets the visual styles
- var custom = arc.custom || {};
- var valueOrDefault = helpers.valueAtIndexOrDefault;
- var elementOpts = this.chart.options.elements.arc;
- model.backgroundColor = custom.backgroundColor ? custom.backgroundColor : valueOrDefault(dataset.backgroundColor, index, elementOpts.backgroundColor);
- model.borderColor = custom.borderColor ? custom.borderColor : valueOrDefault(dataset.borderColor, index, elementOpts.borderColor);
- model.borderWidth = custom.borderWidth ? custom.borderWidth : valueOrDefault(dataset.borderWidth, index, elementOpts.borderWidth);
-
- // Set correct angles if not resetting
- if (!reset || !animationOpts.animateRotate) {
- if (index === 0) {
- model.startAngle = opts.rotation;
- } else {
- model.startAngle = me.getMeta().data[index - 1]._model.endAngle;
- }
-
- model.endAngle = model.startAngle + model.circumference;
- }
-
- arc.pivot();
- },
-
- calculateTotal: function() {
- var dataset = this.getDataset();
- var meta = this.getMeta();
- var total = 0;
- var value;
-
- helpers.each(meta.data, function(element, index) {
- value = dataset.data[index];
- if (!isNaN(value) && !element.hidden) {
- total += Math.abs(value);
- }
- });
-
- /* if (total === 0) {
- total = NaN;
- }*/
-
- return total;
- },
-
- calculateCircumference: function(value) {
- var total = this.getMeta().total;
- if (total > 0 && !isNaN(value)) {
- return (Math.PI * 2.0) * (Math.abs(value) / total);
- }
- return 0;
- },
-
- // gets the max border or hover width to properly scale pie charts
- getMaxBorderWidth: function(arcs) {
- var max = 0;
- var index = this.index;
- var length = arcs.length;
- var borderWidth;
- var hoverWidth;
-
- for (var i = 0; i < length; i++) {
- borderWidth = arcs[i]._model ? arcs[i]._model.borderWidth : 0;
- hoverWidth = arcs[i]._chart ? arcs[i]._chart.config.data.datasets[index].hoverBorderWidth : 0;
-
- max = borderWidth > max ? borderWidth : max;
- max = hoverWidth > max ? hoverWidth : max;
- }
- return max;
- }
- });
-};
-
-},{"26":26,"41":41,"46":46}],18:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var elements = require(41);
-var helpers = require(46);
-
-defaults._set('line', {
- showLines: true,
- spanGaps: false,
-
- hover: {
- mode: 'label'
- },
-
- scales: {
- xAxes: [{
- type: 'category',
- id: 'x-axis-0'
- }],
- yAxes: [{
- type: 'linear',
- id: 'y-axis-0'
- }]
- }
-});
-
-module.exports = function(Chart) {
-
- function lineEnabled(dataset, options) {
- return helpers.valueOrDefault(dataset.showLine, options.showLines);
- }
-
- Chart.controllers.line = Chart.DatasetController.extend({
-
- datasetElementType: elements.Line,
-
- dataElementType: elements.Point,
-
- update: function(reset) {
- var me = this;
- var meta = me.getMeta();
- var line = meta.dataset;
- var points = meta.data || [];
- var options = me.chart.options;
- var lineElementOptions = options.elements.line;
- var scale = me.getScaleForId(meta.yAxisID);
- var i, ilen, custom;
- var dataset = me.getDataset();
- var showLine = lineEnabled(dataset, options);
-
- // Update Line
- if (showLine) {
- custom = line.custom || {};
-
- // Compatibility: If the properties are defined with only the old name, use those values
- if ((dataset.tension !== undefined) && (dataset.lineTension === undefined)) {
- dataset.lineTension = dataset.tension;
- }
-
- // Utility
- line._scale = scale;
- line._datasetIndex = me.index;
- // Data
- line._children = points;
- // Model
- line._model = {
- // Appearance
- // The default behavior of lines is to break at null values, according
- // to https://github.com/chartjs/Chart.js/issues/2435#issuecomment-216718158
- // This option gives lines the ability to span gaps
- spanGaps: dataset.spanGaps ? dataset.spanGaps : options.spanGaps,
- tension: custom.tension ? custom.tension : helpers.valueOrDefault(dataset.lineTension, lineElementOptions.tension),
- backgroundColor: custom.backgroundColor ? custom.backgroundColor : (dataset.backgroundColor || lineElementOptions.backgroundColor),
- borderWidth: custom.borderWidth ? custom.borderWidth : (dataset.borderWidth || lineElementOptions.borderWidth),
- borderColor: custom.borderColor ? custom.borderColor : (dataset.borderColor || lineElementOptions.borderColor),
- borderCapStyle: custom.borderCapStyle ? custom.borderCapStyle : (dataset.borderCapStyle || lineElementOptions.borderCapStyle),
- borderDash: custom.borderDash ? custom.borderDash : (dataset.borderDash || lineElementOptions.borderDash),
- borderDashOffset: custom.borderDashOffset ? custom.borderDashOffset : (dataset.borderDashOffset || lineElementOptions.borderDashOffset),
- borderJoinStyle: custom.borderJoinStyle ? custom.borderJoinStyle : (dataset.borderJoinStyle || lineElementOptions.borderJoinStyle),
- fill: custom.fill ? custom.fill : (dataset.fill !== undefined ? dataset.fill : lineElementOptions.fill),
- steppedLine: custom.steppedLine ? custom.steppedLine : helpers.valueOrDefault(dataset.steppedLine, lineElementOptions.stepped),
- cubicInterpolationMode: custom.cubicInterpolationMode ? custom.cubicInterpolationMode : helpers.valueOrDefault(dataset.cubicInterpolationMode, lineElementOptions.cubicInterpolationMode),
- };
-
- line.pivot();
- }
-
- // Update Points
- for (i = 0, ilen = points.length; i < ilen; ++i) {
- me.updateElement(points[i], i, reset);
- }
-
- if (showLine && line._model.tension !== 0) {
- me.updateBezierControlPoints();
- }
-
- // Now pivot the point for animation
- for (i = 0, ilen = points.length; i < ilen; ++i) {
- points[i].pivot();
- }
- },
-
- getPointBackgroundColor: function(point, index) {
- var backgroundColor = this.chart.options.elements.point.backgroundColor;
- var dataset = this.getDataset();
- var custom = point.custom || {};
-
- if (custom.backgroundColor) {
- backgroundColor = custom.backgroundColor;
- } else if (dataset.pointBackgroundColor) {
- backgroundColor = helpers.valueAtIndexOrDefault(dataset.pointBackgroundColor, index, backgroundColor);
- } else if (dataset.backgroundColor) {
- backgroundColor = dataset.backgroundColor;
- }
-
- return backgroundColor;
- },
-
- getPointBorderColor: function(point, index) {
- var borderColor = this.chart.options.elements.point.borderColor;
- var dataset = this.getDataset();
- var custom = point.custom || {};
-
- if (custom.borderColor) {
- borderColor = custom.borderColor;
- } else if (dataset.pointBorderColor) {
- borderColor = helpers.valueAtIndexOrDefault(dataset.pointBorderColor, index, borderColor);
- } else if (dataset.borderColor) {
- borderColor = dataset.borderColor;
- }
-
- return borderColor;
- },
-
- getPointBorderWidth: function(point, index) {
- var borderWidth = this.chart.options.elements.point.borderWidth;
- var dataset = this.getDataset();
- var custom = point.custom || {};
-
- if (!isNaN(custom.borderWidth)) {
- borderWidth = custom.borderWidth;
- } else if (!isNaN(dataset.pointBorderWidth) || helpers.isArray(dataset.pointBorderWidth)) {
- borderWidth = helpers.valueAtIndexOrDefault(dataset.pointBorderWidth, index, borderWidth);
- } else if (!isNaN(dataset.borderWidth)) {
- borderWidth = dataset.borderWidth;
- }
-
- return borderWidth;
- },
-
- getPointRotation: function(point, index) {
- var pointRotation = this.chart.options.elements.point.rotation;
- var dataset = this.getDataset();
- var custom = point.custom || {};
-
- if (!isNaN(custom.rotation)) {
- pointRotation = custom.rotation;
- } else if (!isNaN(dataset.pointRotation) || helpers.isArray(dataset.pointRotation)) {
- pointRotation = helpers.valueAtIndexOrDefault(dataset.pointRotation, index, pointRotation);
- }
- return pointRotation;
- },
-
- updateElement: function(point, index, reset) {
- var me = this;
- var meta = me.getMeta();
- var custom = point.custom || {};
- var dataset = me.getDataset();
- var datasetIndex = me.index;
- var value = dataset.data[index];
- var yScale = me.getScaleForId(meta.yAxisID);
- var xScale = me.getScaleForId(meta.xAxisID);
- var pointOptions = me.chart.options.elements.point;
- var x, y;
-
- // Compatibility: If the properties are defined with only the old name, use those values
- if ((dataset.radius !== undefined) && (dataset.pointRadius === undefined)) {
- dataset.pointRadius = dataset.radius;
- }
- if ((dataset.hitRadius !== undefined) && (dataset.pointHitRadius === undefined)) {
- dataset.pointHitRadius = dataset.hitRadius;
- }
-
- x = xScale.getPixelForValue(typeof value === 'object' ? value : NaN, index, datasetIndex);
- y = reset ? yScale.getBasePixel() : me.calculatePointY(value, index, datasetIndex);
-
- // Utility
- point._xScale = xScale;
- point._yScale = yScale;
- point._datasetIndex = datasetIndex;
- point._index = index;
-
- // Desired view properties
- point._model = {
- x: x,
- y: y,
- skip: custom.skip || isNaN(x) || isNaN(y),
- // Appearance
- radius: custom.radius || helpers.valueAtIndexOrDefault(dataset.pointRadius, index, pointOptions.radius),
- pointStyle: custom.pointStyle || helpers.valueAtIndexOrDefault(dataset.pointStyle, index, pointOptions.pointStyle),
- rotation: me.getPointRotation(point, index),
- backgroundColor: me.getPointBackgroundColor(point, index),
- borderColor: me.getPointBorderColor(point, index),
- borderWidth: me.getPointBorderWidth(point, index),
- tension: meta.dataset._model ? meta.dataset._model.tension : 0,
- steppedLine: meta.dataset._model ? meta.dataset._model.steppedLine : false,
- // Tooltip
- hitRadius: custom.hitRadius || helpers.valueAtIndexOrDefault(dataset.pointHitRadius, index, pointOptions.hitRadius)
- };
- },
-
- calculatePointY: function(value, index, datasetIndex) {
- var me = this;
- var chart = me.chart;
- var meta = me.getMeta();
- var yScale = me.getScaleForId(meta.yAxisID);
- var sumPos = 0;
- var sumNeg = 0;
- var i, ds, dsMeta;
-
- if (yScale.options.stacked) {
- for (i = 0; i < datasetIndex; i++) {
- ds = chart.data.datasets[i];
- dsMeta = chart.getDatasetMeta(i);
- if (dsMeta.type === 'line' && dsMeta.yAxisID === yScale.id && chart.isDatasetVisible(i)) {
- var stackedRightValue = Number(yScale.getRightValue(ds.data[index]));
- if (stackedRightValue < 0) {
- sumNeg += stackedRightValue || 0;
- } else {
- sumPos += stackedRightValue || 0;
- }
- }
- }
-
- var rightValue = Number(yScale.getRightValue(value));
- if (rightValue < 0) {
- return yScale.getPixelForValue(sumNeg + rightValue);
- }
- return yScale.getPixelForValue(sumPos + rightValue);
- }
-
- return yScale.getPixelForValue(value);
- },
-
- updateBezierControlPoints: function() {
- var me = this;
- var meta = me.getMeta();
- var area = me.chart.chartArea;
- var points = (meta.data || []);
- var i, ilen, point, model, controlPoints;
-
- // Only consider points that are drawn in case the spanGaps option is used
- if (meta.dataset._model.spanGaps) {
- points = points.filter(function(pt) {
- return !pt._model.skip;
- });
- }
-
- function capControlPoint(pt, min, max) {
- return Math.max(Math.min(pt, max), min);
- }
-
- if (meta.dataset._model.cubicInterpolationMode === 'monotone') {
- helpers.splineCurveMonotone(points);
- } else {
- for (i = 0, ilen = points.length; i < ilen; ++i) {
- point = points[i];
- model = point._model;
- controlPoints = helpers.splineCurve(
- helpers.previousItem(points, i)._model,
- model,
- helpers.nextItem(points, i)._model,
- meta.dataset._model.tension
- );
- model.controlPointPreviousX = controlPoints.previous.x;
- model.controlPointPreviousY = controlPoints.previous.y;
- model.controlPointNextX = controlPoints.next.x;
- model.controlPointNextY = controlPoints.next.y;
- }
- }
-
- if (me.chart.options.elements.line.capBezierPoints) {
- for (i = 0, ilen = points.length; i < ilen; ++i) {
- model = points[i]._model;
- model.controlPointPreviousX = capControlPoint(model.controlPointPreviousX, area.left, area.right);
- model.controlPointPreviousY = capControlPoint(model.controlPointPreviousY, area.top, area.bottom);
- model.controlPointNextX = capControlPoint(model.controlPointNextX, area.left, area.right);
- model.controlPointNextY = capControlPoint(model.controlPointNextY, area.top, area.bottom);
- }
- }
- },
-
- draw: function() {
- var me = this;
- var chart = me.chart;
- var meta = me.getMeta();
- var points = meta.data || [];
- var area = chart.chartArea;
- var ilen = points.length;
- var halfBorderWidth;
- var i = 0;
-
- if (lineEnabled(me.getDataset(), chart.options)) {
- halfBorderWidth = (meta.dataset._model.borderWidth || 0) / 2;
-
- helpers.canvas.clipArea(chart.ctx, {
- left: area.left,
- right: area.right,
- top: area.top - halfBorderWidth,
- bottom: area.bottom + halfBorderWidth
- });
-
- meta.dataset.draw();
-
- helpers.canvas.unclipArea(chart.ctx);
- }
-
- // Draw the points
- for (; i < ilen; ++i) {
- points[i].draw(area);
- }
- },
-
- setHoverStyle: function(element) {
- // Point
- var dataset = this.chart.data.datasets[element._datasetIndex];
- var index = element._index;
- var custom = element.custom || {};
- var model = element._model;
-
- element.$previousStyle = {
- backgroundColor: model.backgroundColor,
- borderColor: model.borderColor,
- borderWidth: model.borderWidth,
- radius: model.radius
- };
-
- model.backgroundColor = custom.hoverBackgroundColor || helpers.valueAtIndexOrDefault(dataset.pointHoverBackgroundColor, index, helpers.getHoverColor(model.backgroundColor));
- model.borderColor = custom.hoverBorderColor || helpers.valueAtIndexOrDefault(dataset.pointHoverBorderColor, index, helpers.getHoverColor(model.borderColor));
- model.borderWidth = custom.hoverBorderWidth || helpers.valueAtIndexOrDefault(dataset.pointHoverBorderWidth, index, model.borderWidth);
- model.radius = custom.hoverRadius || helpers.valueAtIndexOrDefault(dataset.pointHoverRadius, index, this.chart.options.elements.point.hoverRadius);
- },
- });
-};
-
-},{"26":26,"41":41,"46":46}],19:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var elements = require(41);
-var helpers = require(46);
-
-defaults._set('polarArea', {
- scale: {
- type: 'radialLinear',
- angleLines: {
- display: false
- },
- gridLines: {
- circular: true
- },
- pointLabels: {
- display: false
- },
- ticks: {
- beginAtZero: true
- }
- },
-
- // Boolean - Whether to animate the rotation of the chart
- animation: {
- animateRotate: true,
- animateScale: true
- },
-
- startAngle: -0.5 * Math.PI,
- legendCallback: function(chart) {
- var text = [];
- text.push('<ul class="' + chart.id + '-legend">');
-
- var data = chart.data;
- var datasets = data.datasets;
- var labels = data.labels;
-
- if (datasets.length) {
- for (var i = 0; i < datasets[0].data.length; ++i) {
- text.push('<li><span style="background-color:' + datasets[0].backgroundColor[i] + '"></span>');
- if (labels[i]) {
- text.push(labels[i]);
- }
- text.push('</li>');
- }
- }
-
- text.push('</ul>');
- return text.join('');
- },
- legend: {
- labels: {
- generateLabels: function(chart) {
- var data = chart.data;
- if (data.labels.length && data.datasets.length) {
- return data.labels.map(function(label, i) {
- var meta = chart.getDatasetMeta(0);
- var ds = data.datasets[0];
- var arc = meta.data[i];
- var custom = arc.custom || {};
- var valueAtIndexOrDefault = helpers.valueAtIndexOrDefault;
- var arcOpts = chart.options.elements.arc;
- var fill = custom.backgroundColor ? custom.backgroundColor : valueAtIndexOrDefault(ds.backgroundColor, i, arcOpts.backgroundColor);
- var stroke = custom.borderColor ? custom.borderColor : valueAtIndexOrDefault(ds.borderColor, i, arcOpts.borderColor);
- var bw = custom.borderWidth ? custom.borderWidth : valueAtIndexOrDefault(ds.borderWidth, i, arcOpts.borderWidth);
-
- return {
- text: label,
- fillStyle: fill,
- strokeStyle: stroke,
- lineWidth: bw,
- hidden: isNaN(ds.data[i]) || meta.data[i].hidden,
-
- // Extra data used for toggling the correct item
- index: i
- };
- });
- }
- return [];
- }
- },
-
- onClick: function(e, legendItem) {
- var index = legendItem.index;
- var chart = this.chart;
- var i, ilen, meta;
-
- for (i = 0, ilen = (chart.data.datasets || []).length; i < ilen; ++i) {
- meta = chart.getDatasetMeta(i);
- meta.data[index].hidden = !meta.data[index].hidden;
- }
-
- chart.update();
- }
- },
-
- // Need to override these to give a nice default
- tooltips: {
- callbacks: {
- title: function() {
- return '';
- },
- label: function(item, data) {
- return data.labels[item.index] + ': ' + item.yLabel;
- }
- }
- }
-});
-
-module.exports = function(Chart) {
-
- Chart.controllers.polarArea = Chart.DatasetController.extend({
-
- dataElementType: elements.Arc,
-
- linkScales: helpers.noop,
-
- update: function(reset) {
- var me = this;
- var dataset = me.getDataset();
- var meta = me.getMeta();
- var start = me.chart.options.startAngle || 0;
- var starts = me._starts = [];
- var angles = me._angles = [];
- var i, ilen, angle;
-
- me._updateRadius();
-
- meta.count = me.countVisibleElements();
-
- for (i = 0, ilen = dataset.data.length; i < ilen; i++) {
- starts[i] = start;
- angle = me._computeAngle(i);
- angles[i] = angle;
- start += angle;
- }
-
- helpers.each(meta.data, function(arc, index) {
- me.updateElement(arc, index, reset);
- });
- },
-
- /**
- * @private
- */
- _updateRadius: function() {
- var me = this;
- var chart = me.chart;
- var chartArea = chart.chartArea;
- var opts = chart.options;
- var arcOpts = opts.elements.arc;
- var minSize = Math.min(chartArea.right - chartArea.left, chartArea.bottom - chartArea.top);
-
- chart.outerRadius = Math.max((minSize - arcOpts.borderWidth / 2) / 2, 0);
- chart.innerRadius = Math.max(opts.cutoutPercentage ? (chart.outerRadius / 100) * (opts.cutoutPercentage) : 1, 0);
- chart.radiusLength = (chart.outerRadius - chart.innerRadius) / chart.getVisibleDatasetCount();
-
- me.outerRadius = chart.outerRadius - (chart.radiusLength * me.index);
- me.innerRadius = me.outerRadius - chart.radiusLength;
- },
-
- updateElement: function(arc, index, reset) {
- var me = this;
- var chart = me.chart;
- var dataset = me.getDataset();
- var opts = chart.options;
- var animationOpts = opts.animation;
- var scale = chart.scale;
- var labels = chart.data.labels;
-
- var centerX = scale.xCenter;
- var centerY = scale.yCenter;
-
- // var negHalfPI = -0.5 * Math.PI;
- var datasetStartAngle = opts.startAngle;
- var distance = arc.hidden ? 0 : scale.getDistanceFromCenterForValue(dataset.data[index]);
- var startAngle = me._starts[index];
- var endAngle = startAngle + (arc.hidden ? 0 : me._angles[index]);
-
- var resetRadius = animationOpts.animateScale ? 0 : scale.getDistanceFromCenterForValue(dataset.data[index]);
-
- helpers.extend(arc, {
- // Utility
- _datasetIndex: me.index,
- _index: index,
- _scale: scale,
-
- // Desired view properties
- _model: {
- x: centerX,
- y: centerY,
- innerRadius: 0,
- outerRadius: reset ? resetRadius : distance,
- startAngle: reset && animationOpts.animateRotate ? datasetStartAngle : startAngle,
- endAngle: reset && animationOpts.animateRotate ? datasetStartAngle : endAngle,
- label: helpers.valueAtIndexOrDefault(labels, index, labels[index])
- }
- });
-
- // Apply border and fill style
- var elementOpts = this.chart.options.elements.arc;
- var custom = arc.custom || {};
- var valueOrDefault = helpers.valueAtIndexOrDefault;
- var model = arc._model;
-
- model.backgroundColor = custom.backgroundColor ? custom.backgroundColor : valueOrDefault(dataset.backgroundColor, index, elementOpts.backgroundColor);
- model.borderColor = custom.borderColor ? custom.borderColor : valueOrDefault(dataset.borderColor, index, elementOpts.borderColor);
- model.borderWidth = custom.borderWidth ? custom.borderWidth : valueOrDefault(dataset.borderWidth, index, elementOpts.borderWidth);
-
- arc.pivot();
- },
-
- countVisibleElements: function() {
- var dataset = this.getDataset();
- var meta = this.getMeta();
- var count = 0;
-
- helpers.each(meta.data, function(element, index) {
- if (!isNaN(dataset.data[index]) && !element.hidden) {
- count++;
- }
- });
-
- return count;
- },
-
- /**
- * @private
- */
- _computeAngle: function(index) {
- var me = this;
- var count = this.getMeta().count;
- var dataset = me.getDataset();
- var meta = me.getMeta();
-
- if (isNaN(dataset.data[index]) || meta.data[index].hidden) {
- return 0;
- }
-
- // Scriptable options
- var context = {
- chart: me.chart,
- dataIndex: index,
- dataset: dataset,
- datasetIndex: me.index
- };
-
- return helpers.options.resolve([
- me.chart.options.elements.arc.angle,
- (2 * Math.PI) / count
- ], context, index);
- }
- });
-};
-
-},{"26":26,"41":41,"46":46}],20:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var elements = require(41);
-var helpers = require(46);
-
-defaults._set('radar', {
- scale: {
- type: 'radialLinear'
- },
- elements: {
- line: {
- tension: 0 // no bezier in radar
- }
- }
-});
-
-module.exports = function(Chart) {
-
- Chart.controllers.radar = Chart.DatasetController.extend({
-
- datasetElementType: elements.Line,
-
- dataElementType: elements.Point,
-
- linkScales: helpers.noop,
-
- update: function(reset) {
- var me = this;
- var meta = me.getMeta();
- var line = meta.dataset;
- var points = meta.data;
- var custom = line.custom || {};
- var dataset = me.getDataset();
- var lineElementOptions = me.chart.options.elements.line;
- var scale = me.chart.scale;
-
- // Compatibility: If the properties are defined with only the old name, use those values
- if ((dataset.tension !== undefined) && (dataset.lineTension === undefined)) {
- dataset.lineTension = dataset.tension;
- }
-
- helpers.extend(meta.dataset, {
- // Utility
- _datasetIndex: me.index,
- _scale: scale,
- // Data
- _children: points,
- _loop: true,
- // Model
- _model: {
- // Appearance
- tension: custom.tension ? custom.tension : helpers.valueOrDefault(dataset.lineTension, lineElementOptions.tension),
- backgroundColor: custom.backgroundColor ? custom.backgroundColor : (dataset.backgroundColor || lineElementOptions.backgroundColor),
- borderWidth: custom.borderWidth ? custom.borderWidth : (dataset.borderWidth || lineElementOptions.borderWidth),
- borderColor: custom.borderColor ? custom.borderColor : (dataset.borderColor || lineElementOptions.borderColor),
- fill: custom.fill ? custom.fill : (dataset.fill !== undefined ? dataset.fill : lineElementOptions.fill),
- borderCapStyle: custom.borderCapStyle ? custom.borderCapStyle : (dataset.borderCapStyle || lineElementOptions.borderCapStyle),
- borderDash: custom.borderDash ? custom.borderDash : (dataset.borderDash || lineElementOptions.borderDash),
- borderDashOffset: custom.borderDashOffset ? custom.borderDashOffset : (dataset.borderDashOffset || lineElementOptions.borderDashOffset),
- borderJoinStyle: custom.borderJoinStyle ? custom.borderJoinStyle : (dataset.borderJoinStyle || lineElementOptions.borderJoinStyle),
- }
- });
-
- meta.dataset.pivot();
-
- // Update Points
- helpers.each(points, function(point, index) {
- me.updateElement(point, index, reset);
- }, me);
-
- // Update bezier control points
- me.updateBezierControlPoints();
- },
- updateElement: function(point, index, reset) {
- var me = this;
- var custom = point.custom || {};
- var dataset = me.getDataset();
- var scale = me.chart.scale;
- var pointElementOptions = me.chart.options.elements.point;
- var pointPosition = scale.getPointPositionForValue(index, dataset.data[index]);
-
- // Compatibility: If the properties are defined with only the old name, use those values
- if ((dataset.radius !== undefined) && (dataset.pointRadius === undefined)) {
- dataset.pointRadius = dataset.radius;
- }
- if ((dataset.hitRadius !== undefined) && (dataset.pointHitRadius === undefined)) {
- dataset.pointHitRadius = dataset.hitRadius;
- }
-
- helpers.extend(point, {
- // Utility
- _datasetIndex: me.index,
- _index: index,
- _scale: scale,
-
- // Desired view properties
- _model: {
- x: reset ? scale.xCenter : pointPosition.x, // value not used in dataset scale, but we want a consistent API between scales
- y: reset ? scale.yCenter : pointPosition.y,
-
- // Appearance
- tension: custom.tension ? custom.tension : helpers.valueOrDefault(dataset.lineTension, me.chart.options.elements.line.tension),
- radius: custom.radius ? custom.radius : helpers.valueAtIndexOrDefault(dataset.pointRadius, index, pointElementOptions.radius),
- backgroundColor: custom.backgroundColor ? custom.backgroundColor : helpers.valueAtIndexOrDefault(dataset.pointBackgroundColor, index, pointElementOptions.backgroundColor),
- borderColor: custom.borderColor ? custom.borderColor : helpers.valueAtIndexOrDefault(dataset.pointBorderColor, index, pointElementOptions.borderColor),
- borderWidth: custom.borderWidth ? custom.borderWidth : helpers.valueAtIndexOrDefault(dataset.pointBorderWidth, index, pointElementOptions.borderWidth),
- pointStyle: custom.pointStyle ? custom.pointStyle : helpers.valueAtIndexOrDefault(dataset.pointStyle, index, pointElementOptions.pointStyle),
- rotation: custom.rotation ? custom.rotation : helpers.valueAtIndexOrDefault(dataset.pointRotation, index, pointElementOptions.rotation),
-
- // Tooltip
- hitRadius: custom.hitRadius ? custom.hitRadius : helpers.valueAtIndexOrDefault(dataset.pointHitRadius, index, pointElementOptions.hitRadius)
- }
- });
-
- point._model.skip = custom.skip ? custom.skip : (isNaN(point._model.x) || isNaN(point._model.y));
- },
- updateBezierControlPoints: function() {
- var chartArea = this.chart.chartArea;
- var meta = this.getMeta();
-
- helpers.each(meta.data, function(point, index) {
- var model = point._model;
- var controlPoints = helpers.splineCurve(
- helpers.previousItem(meta.data, index, true)._model,
- model,
- helpers.nextItem(meta.data, index, true)._model,
- model.tension
- );
-
- // Prevent the bezier going outside of the bounds of the graph
- model.controlPointPreviousX = Math.max(Math.min(controlPoints.previous.x, chartArea.right), chartArea.left);
- model.controlPointPreviousY = Math.max(Math.min(controlPoints.previous.y, chartArea.bottom), chartArea.top);
-
- model.controlPointNextX = Math.max(Math.min(controlPoints.next.x, chartArea.right), chartArea.left);
- model.controlPointNextY = Math.max(Math.min(controlPoints.next.y, chartArea.bottom), chartArea.top);
-
- // Now pivot the point for animation
- point.pivot();
- });
- },
-
- setHoverStyle: function(point) {
- // Point
- var dataset = this.chart.data.datasets[point._datasetIndex];
- var custom = point.custom || {};
- var index = point._index;
- var model = point._model;
-
- point.$previousStyle = {
- backgroundColor: model.backgroundColor,
- borderColor: model.borderColor,
- borderWidth: model.borderWidth,
- radius: model.radius
- };
-
- model.radius = custom.hoverRadius ? custom.hoverRadius : helpers.valueAtIndexOrDefault(dataset.pointHoverRadius, index, this.chart.options.elements.point.hoverRadius);
- model.backgroundColor = custom.hoverBackgroundColor ? custom.hoverBackgroundColor : helpers.valueAtIndexOrDefault(dataset.pointHoverBackgroundColor, index, helpers.getHoverColor(model.backgroundColor));
- model.borderColor = custom.hoverBorderColor ? custom.hoverBorderColor : helpers.valueAtIndexOrDefault(dataset.pointHoverBorderColor, index, helpers.getHoverColor(model.borderColor));
- model.borderWidth = custom.hoverBorderWidth ? custom.hoverBorderWidth : helpers.valueAtIndexOrDefault(dataset.pointHoverBorderWidth, index, model.borderWidth);
- },
- });
-};
-
-},{"26":26,"41":41,"46":46}],21:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-
-defaults._set('scatter', {
- hover: {
- mode: 'single'
- },
-
- scales: {
- xAxes: [{
- id: 'x-axis-1', // need an ID so datasets can reference the scale
- type: 'linear', // scatter should not use a category axis
- position: 'bottom'
- }],
- yAxes: [{
- id: 'y-axis-1',
- type: 'linear',
- position: 'left'
- }]
- },
-
- showLines: false,
-
- tooltips: {
- callbacks: {
- title: function() {
- return ''; // doesn't make sense for scatter since data are formatted as a point
- },
- label: function(item) {
- return '(' + item.xLabel + ', ' + item.yLabel + ')';
- }
- }
- }
-});
-
-module.exports = function(Chart) {
-
- // Scatter charts use line controllers
- Chart.controllers.scatter = Chart.controllers.line;
-
-};
-
-},{"26":26}],22:[function(require,module,exports){
-'use strict';
-
-var Element = require(27);
-
-var exports = module.exports = Element.extend({
- chart: null, // the animation associated chart instance
- currentStep: 0, // the current animation step
- numSteps: 60, // default number of steps
- easing: '', // the easing to use for this animation
- render: null, // render function used by the animation service
-
- onAnimationProgress: null, // user specified callback to fire on each step of the animation
- onAnimationComplete: null, // user specified callback to fire when the animation finishes
-});
-
-// DEPRECATIONS
-
-/**
- * Provided for backward compatibility, use Chart.Animation instead
- * @prop Chart.Animation#animationObject
- * @deprecated since version 2.6.0
- * @todo remove at version 3
- */
-Object.defineProperty(exports.prototype, 'animationObject', {
- get: function() {
- return this;
- }
-});
-
-/**
- * Provided for backward compatibility, use Chart.Animation#chart instead
- * @prop Chart.Animation#chartInstance
- * @deprecated since version 2.6.0
- * @todo remove at version 3
- */
-Object.defineProperty(exports.prototype, 'chartInstance', {
- get: function() {
- return this.chart;
- },
- set: function(value) {
- this.chart = value;
- }
-});
-
-},{"27":27}],23:[function(require,module,exports){
-/* global window: false */
-'use strict';
-
-var defaults = require(26);
-var helpers = require(46);
-
-defaults._set('global', {
- animation: {
- duration: 1000,
- easing: 'easeOutQuart',
- onProgress: helpers.noop,
- onComplete: helpers.noop
- }
-});
-
-module.exports = {
- frameDuration: 17,
- animations: [],
- dropFrames: 0,
- request: null,
-
- /**
- * @param {Chart} chart - The chart to animate.
- * @param {Chart.Animation} animation - The animation that we will animate.
- * @param {Number} duration - The animation duration in ms.
- * @param {Boolean} lazy - if true, the chart is not marked as animating to enable more responsive interactions
- */
- addAnimation: function(chart, animation, duration, lazy) {
- var animations = this.animations;
- var i, ilen;
-
- animation.chart = chart;
-
- if (!lazy) {
- chart.animating = true;
- }
-
- for (i = 0, ilen = animations.length; i < ilen; ++i) {
- if (animations[i].chart === chart) {
- animations[i] = animation;
- return;
- }
- }
-
- animations.push(animation);
-
- // If there are no animations queued, manually kickstart a digest, for lack of a better word
- if (animations.length === 1) {
- this.requestAnimationFrame();
- }
- },
-
- cancelAnimation: function(chart) {
- var index = helpers.findIndex(this.animations, function(animation) {
- return animation.chart === chart;
- });
-
- if (index !== -1) {
- this.animations.splice(index, 1);
- chart.animating = false;
- }
- },
-
- requestAnimationFrame: function() {
- var me = this;
- if (me.request === null) {
- // Skip animation frame requests until the active one is executed.
- // This can happen when processing mouse events, e.g. 'mousemove'
- // and 'mouseout' events will trigger multiple renders.
- me.request = helpers.requestAnimFrame.call(window, function() {
- me.request = null;
- me.startDigest();
- });
- }
- },
-
- /**
- * @private
- */
- startDigest: function() {
- var me = this;
- var startTime = Date.now();
- var framesToDrop = 0;
-
- if (me.dropFrames > 1) {
- framesToDrop = Math.floor(me.dropFrames);
- me.dropFrames = me.dropFrames % 1;
- }
-
- me.advance(1 + framesToDrop);
-
- var endTime = Date.now();
-
- me.dropFrames += (endTime - startTime) / me.frameDuration;
-
- // Do we have more stuff to animate?
- if (me.animations.length > 0) {
- me.requestAnimationFrame();
- }
- },
-
- /**
- * @private
- */
- advance: function(count) {
- var animations = this.animations;
- var animation, chart;
- var i = 0;
-
- while (i < animations.length) {
- animation = animations[i];
- chart = animation.chart;
-
- animation.currentStep = (animation.currentStep || 0) + count;
- animation.currentStep = Math.min(animation.currentStep, animation.numSteps);
-
- helpers.callback(animation.render, [chart, animation], chart);
- helpers.callback(animation.onAnimationProgress, [animation], chart);
-
- if (animation.currentStep >= animation.numSteps) {
- helpers.callback(animation.onAnimationComplete, [animation], chart);
- chart.animating = false;
- animations.splice(i, 1);
- } else {
- ++i;
- }
- }
- }
-};
-
-},{"26":26,"46":46}],24:[function(require,module,exports){
-'use strict';
-
-var Animation = require(22);
-var animations = require(23);
-var defaults = require(26);
-var helpers = require(46);
-var Interaction = require(29);
-var layouts = require(31);
-var platform = require(49);
-var plugins = require(32);
-var scaleService = require(34);
-var Tooltip = require(36);
-
-module.exports = function(Chart) {
-
- // Create a dictionary of chart types, to allow for extension of existing types
- Chart.types = {};
-
- // Store a reference to each instance - allowing us to globally resize chart instances on window resize.
- // Destroy method on the chart will remove the instance of the chart from this reference.
- Chart.instances = {};
-
- // Controllers available for dataset visualization eg. bar, line, slice, etc.
- Chart.controllers = {};
-
- /**
- * Initializes the given config with global and chart default values.
- */
- function initConfig(config) {
- config = config || {};
-
- // Do NOT use configMerge() for the data object because this method merges arrays
- // and so would change references to labels and datasets, preventing data updates.
- var data = config.data = config.data || {};
- data.datasets = data.datasets || [];
- data.labels = data.labels || [];
-
- config.options = helpers.configMerge(
- defaults.global,
- defaults[config.type],
- config.options || {});
-
- return config;
- }
-
- /**
- * Updates the config of the chart
- * @param chart {Chart} chart to update the options for
- */
- function updateConfig(chart) {
- var newOptions = chart.options;
-
- helpers.each(chart.scales, function(scale) {
- layouts.removeBox(chart, scale);
- });
-
- newOptions = helpers.configMerge(
- Chart.defaults.global,
- Chart.defaults[chart.config.type],
- newOptions);
-
- chart.options = chart.config.options = newOptions;
- chart.ensureScalesHaveIDs();
- chart.buildOrUpdateScales();
- // Tooltip
- chart.tooltip._options = newOptions.tooltips;
- chart.tooltip.initialize();
- }
-
- function positionIsHorizontal(position) {
- return position === 'top' || position === 'bottom';
- }
-
- helpers.extend(Chart.prototype, /** @lends Chart */ {
- /**
- * @private
- */
- construct: function(item, config) {
- var me = this;
-
- config = initConfig(config);
-
- var context = platform.acquireContext(item, config);
- var canvas = context && context.canvas;
- var height = canvas && canvas.height;
- var width = canvas && canvas.width;
-
- me.id = helpers.uid();
- me.ctx = context;
- me.canvas = canvas;
- me.config = config;
- me.width = width;
- me.height = height;
- me.aspectRatio = height ? width / height : null;
- me.options = config.options;
- me._bufferedRender = false;
-
- /**
- * Provided for backward compatibility, Chart and Chart.Controller have been merged,
- * the "instance" still need to be defined since it might be called from plugins.
- * @prop Chart#chart
- * @deprecated since version 2.6.0
- * @todo remove at version 3
- * @private
- */
- me.chart = me;
- me.controller = me; // chart.chart.controller #inception
-
- // Add the chart instance to the global namespace
- Chart.instances[me.id] = me;
-
- // Define alias to the config data: `chart.data === chart.config.data`
- Object.defineProperty(me, 'data', {
- get: function() {
- return me.config.data;
- },
- set: function(value) {
- me.config.data = value;
- }
- });
-
- if (!context || !canvas) {
- // The given item is not a compatible context2d element, let's return before finalizing
- // the chart initialization but after setting basic chart / controller properties that
- // can help to figure out that the chart is not valid (e.g chart.canvas !== null);
- // https://github.com/chartjs/Chart.js/issues/2807
- console.error("Failed to create chart: can't acquire context from the given item");
- return;
- }
-
- me.initialize();
- me.update();
- },
-
- /**
- * @private
- */
- initialize: function() {
- var me = this;
-
- // Before init plugin notification
- plugins.notify(me, 'beforeInit');
-
- helpers.retinaScale(me, me.options.devicePixelRatio);
-
- me.bindEvents();
-
- if (me.options.responsive) {
- // Initial resize before chart draws (must be silent to preserve initial animations).
- me.resize(true);
- }
-
- // Make sure scales have IDs and are built before we build any controllers.
- me.ensureScalesHaveIDs();
- me.buildOrUpdateScales();
- me.initToolTip();
-
- // After init plugin notification
- plugins.notify(me, 'afterInit');
-
- return me;
- },
-
- clear: function() {
- helpers.canvas.clear(this);
- return this;
- },
-
- stop: function() {
- // Stops any current animation loop occurring
- animations.cancelAnimation(this);
- return this;
- },
-
- resize: function(silent) {
- var me = this;
- var options = me.options;
- var canvas = me.canvas;
- var aspectRatio = (options.maintainAspectRatio && me.aspectRatio) || null;
-
- // the canvas render width and height will be casted to integers so make sure that
- // the canvas display style uses the same integer values to avoid blurring effect.
-
- // Set to 0 instead of canvas.size because the size defaults to 300x150 if the element is collapsed
- var newWidth = Math.max(0, Math.floor(helpers.getMaximumWidth(canvas)));
- var newHeight = Math.max(0, Math.floor(aspectRatio ? newWidth / aspectRatio : helpers.getMaximumHeight(canvas)));
-
- if (me.width === newWidth && me.height === newHeight) {
- return;
- }
-
- canvas.width = me.width = newWidth;
- canvas.height = me.height = newHeight;
- canvas.style.width = newWidth + 'px';
- canvas.style.height = newHeight + 'px';
-
- helpers.retinaScale(me, options.devicePixelRatio);
-
- if (!silent) {
- // Notify any plugins about the resize
- var newSize = {width: newWidth, height: newHeight};
- plugins.notify(me, 'resize', [newSize]);
-
- // Notify of resize
- if (me.options.onResize) {
- me.options.onResize(me, newSize);
- }
-
- me.stop();
- me.update({
- duration: me.options.responsiveAnimationDuration
- });
- }
- },
-
- ensureScalesHaveIDs: function() {
- var options = this.options;
- var scalesOptions = options.scales || {};
- var scaleOptions = options.scale;
-
- helpers.each(scalesOptions.xAxes, function(xAxisOptions, index) {
- xAxisOptions.id = xAxisOptions.id || ('x-axis-' + index);
- });
-
- helpers.each(scalesOptions.yAxes, function(yAxisOptions, index) {
- yAxisOptions.id = yAxisOptions.id || ('y-axis-' + index);
- });
-
- if (scaleOptions) {
- scaleOptions.id = scaleOptions.id || 'scale';
- }
- },
-
- /**
- * Builds a map of scale ID to scale object for future lookup.
- */
- buildOrUpdateScales: function() {
- var me = this;
- var options = me.options;
- var scales = me.scales || {};
- var items = [];
- var updated = Object.keys(scales).reduce(function(obj, id) {
- obj[id] = false;
- return obj;
- }, {});
-
- if (options.scales) {
- items = items.concat(
- (options.scales.xAxes || []).map(function(xAxisOptions) {
- return {options: xAxisOptions, dtype: 'category', dposition: 'bottom'};
- }),
- (options.scales.yAxes || []).map(function(yAxisOptions) {
- return {options: yAxisOptions, dtype: 'linear', dposition: 'left'};
- })
- );
- }
-
- if (options.scale) {
- items.push({
- options: options.scale,
- dtype: 'radialLinear',
- isDefault: true,
- dposition: 'chartArea'
- });
- }
-
- helpers.each(items, function(item) {
- var scaleOptions = item.options;
- var id = scaleOptions.id;
- var scaleType = helpers.valueOrDefault(scaleOptions.type, item.dtype);
-
- if (positionIsHorizontal(scaleOptions.position) !== positionIsHorizontal(item.dposition)) {
- scaleOptions.position = item.dposition;
- }
-
- updated[id] = true;
- var scale = null;
- if (id in scales && scales[id].type === scaleType) {
- scale = scales[id];
- scale.options = scaleOptions;
- scale.ctx = me.ctx;
- scale.chart = me;
- } else {
- var scaleClass = scaleService.getScaleConstructor(scaleType);
- if (!scaleClass) {
- return;
- }
- scale = new scaleClass({
- id: id,
- type: scaleType,
- options: scaleOptions,
- ctx: me.ctx,
- chart: me
- });
- scales[scale.id] = scale;
- }
-
- scale.mergeTicksOptions();
-
- // TODO(SB): I think we should be able to remove this custom case (options.scale)
- // and consider it as a regular scale part of the "scales"" map only! This would
- // make the logic easier and remove some useless? custom code.
- if (item.isDefault) {
- me.scale = scale;
- }
- });
- // clear up discarded scales
- helpers.each(updated, function(hasUpdated, id) {
- if (!hasUpdated) {
- delete scales[id];
- }
- });
-
- me.scales = scales;
-
- scaleService.addScalesToLayout(this);
- },
-
- buildOrUpdateControllers: function() {
- var me = this;
- var types = [];
- var newControllers = [];
-
- helpers.each(me.data.datasets, function(dataset, datasetIndex) {
- var meta = me.getDatasetMeta(datasetIndex);
- var type = dataset.type || me.config.type;
-
- if (meta.type && meta.type !== type) {
- me.destroyDatasetMeta(datasetIndex);
- meta = me.getDatasetMeta(datasetIndex);
- }
- meta.type = type;
-
- types.push(meta.type);
-
- if (meta.controller) {
- meta.controller.updateIndex(datasetIndex);
- meta.controller.linkScales();
- } else {
- var ControllerClass = Chart.controllers[meta.type];
- if (ControllerClass === undefined) {
- throw new Error('"' + meta.type + '" is not a chart type.');
- }
-
- meta.controller = new ControllerClass(me, datasetIndex);
- newControllers.push(meta.controller);
- }
- }, me);
-
- return newControllers;
- },
-
- /**
- * Reset the elements of all datasets
- * @private
- */
- resetElements: function() {
- var me = this;
- helpers.each(me.data.datasets, function(dataset, datasetIndex) {
- me.getDatasetMeta(datasetIndex).controller.reset();
- }, me);
- },
-
- /**
- * Resets the chart back to it's state before the initial animation
- */
- reset: function() {
- this.resetElements();
- this.tooltip.initialize();
- },
-
- update: function(config) {
- var me = this;
-
- if (!config || typeof config !== 'object') {
- // backwards compatibility
- config = {
- duration: config,
- lazy: arguments[1]
- };
- }
-
- updateConfig(me);
-
- // plugins options references might have change, let's invalidate the cache
- // https://github.com/chartjs/Chart.js/issues/5111#issuecomment-355934167
- plugins._invalidate(me);
-
- if (plugins.notify(me, 'beforeUpdate') === false) {
- return;
- }
-
- // In case the entire data object changed
- me.tooltip._data = me.data;
-
- // Make sure dataset controllers are updated and new controllers are reset
- var newControllers = me.buildOrUpdateControllers();
-
- // Make sure all dataset controllers have correct meta data counts
- helpers.each(me.data.datasets, function(dataset, datasetIndex) {
- me.getDatasetMeta(datasetIndex).controller.buildOrUpdateElements();
- }, me);
-
- me.updateLayout();
-
- // Can only reset the new controllers after the scales have been updated
- if (me.options.animation && me.options.animation.duration) {
- helpers.each(newControllers, function(controller) {
- controller.reset();
- });
- }
-
- me.updateDatasets();
-
- // Need to reset tooltip in case it is displayed with elements that are removed
- // after update.
- me.tooltip.initialize();
-
- // Last active contains items that were previously in the tooltip.
- // When we reset the tooltip, we need to clear it
- me.lastActive = [];
-
- // Do this before render so that any plugins that need final scale updates can use it
- plugins.notify(me, 'afterUpdate');
-
- if (me._bufferedRender) {
- me._bufferedRequest = {
- duration: config.duration,
- easing: config.easing,
- lazy: config.lazy
- };
- } else {
- me.render(config);
- }
- },
-
- /**
- * Updates the chart layout unless a plugin returns `false` to the `beforeLayout`
- * hook, in which case, plugins will not be called on `afterLayout`.
- * @private
- */
- updateLayout: function() {
- var me = this;
-
- if (plugins.notify(me, 'beforeLayout') === false) {
- return;
- }
-
- layouts.update(this, this.width, this.height);
-
- /**
- * Provided for backward compatibility, use `afterLayout` instead.
- * @method IPlugin#afterScaleUpdate
- * @deprecated since version 2.5.0
- * @todo remove at version 3
- * @private
- */
- plugins.notify(me, 'afterScaleUpdate');
- plugins.notify(me, 'afterLayout');
- },
-
- /**
- * Updates all datasets unless a plugin returns `false` to the `beforeDatasetsUpdate`
- * hook, in which case, plugins will not be called on `afterDatasetsUpdate`.
- * @private
- */
- updateDatasets: function() {
- var me = this;
-
- if (plugins.notify(me, 'beforeDatasetsUpdate') === false) {
- return;
- }
-
- for (var i = 0, ilen = me.data.datasets.length; i < ilen; ++i) {
- me.updateDataset(i);
- }
-
- plugins.notify(me, 'afterDatasetsUpdate');
- },
-
- /**
- * Updates dataset at index unless a plugin returns `false` to the `beforeDatasetUpdate`
- * hook, in which case, plugins will not be called on `afterDatasetUpdate`.
- * @private
- */
- updateDataset: function(index) {
- var me = this;
- var meta = me.getDatasetMeta(index);
- var args = {
- meta: meta,
- index: index
- };
-
- if (plugins.notify(me, 'beforeDatasetUpdate', [args]) === false) {
- return;
- }
-
- meta.controller.update();
-
- plugins.notify(me, 'afterDatasetUpdate', [args]);
- },
-
- render: function(config) {
- var me = this;
-
- if (!config || typeof config !== 'object') {
- // backwards compatibility
- config = {
- duration: config,
- lazy: arguments[1]
- };
- }
-
- var duration = config.duration;
- var lazy = config.lazy;
-
- if (plugins.notify(me, 'beforeRender') === false) {
- return;
- }
-
- var animationOptions = me.options.animation;
- var onComplete = function(animation) {
- plugins.notify(me, 'afterRender');
- helpers.callback(animationOptions && animationOptions.onComplete, [animation], me);
- };
-
- if (animationOptions && ((typeof duration !== 'undefined' && duration !== 0) || (typeof duration === 'undefined' && animationOptions.duration !== 0))) {
- var animation = new Animation({
- numSteps: (duration || animationOptions.duration) / 16.66, // 60 fps
- easing: config.easing || animationOptions.easing,
-
- render: function(chart, animationObject) {
- var easingFunction = helpers.easing.effects[animationObject.easing];
- var currentStep = animationObject.currentStep;
- var stepDecimal = currentStep / animationObject.numSteps;
-
- chart.draw(easingFunction(stepDecimal), stepDecimal, currentStep);
- },
-
- onAnimationProgress: animationOptions.onProgress,
- onAnimationComplete: onComplete
- });
-
- animations.addAnimation(me, animation, duration, lazy);
- } else {
- me.draw();
-
- // See https://github.com/chartjs/Chart.js/issues/3781
- onComplete(new Animation({numSteps: 0, chart: me}));
- }
-
- return me;
- },
-
- draw: function(easingValue) {
- var me = this;
-
- me.clear();
-
- if (helpers.isNullOrUndef(easingValue)) {
- easingValue = 1;
- }
-
- me.transition(easingValue);
-
- if (me.width <= 0 || me.height <= 0) {
- return;
- }
-
- if (plugins.notify(me, 'beforeDraw', [easingValue]) === false) {
- return;
- }
-
- // Draw all the scales
- helpers.each(me.boxes, function(box) {
- box.draw(me.chartArea);
- }, me);
-
- if (me.scale) {
- me.scale.draw();
- }
-
- me.drawDatasets(easingValue);
- me._drawTooltip(easingValue);
-
- plugins.notify(me, 'afterDraw', [easingValue]);
- },
-
- /**
- * @private
- */
- transition: function(easingValue) {
- var me = this;
-
- for (var i = 0, ilen = (me.data.datasets || []).length; i < ilen; ++i) {
- if (me.isDatasetVisible(i)) {
- me.getDatasetMeta(i).controller.transition(easingValue);
- }
- }
-
- me.tooltip.transition(easingValue);
- },
-
- /**
- * Draws all datasets unless a plugin returns `false` to the `beforeDatasetsDraw`
- * hook, in which case, plugins will not be called on `afterDatasetsDraw`.
- * @private
- */
- drawDatasets: function(easingValue) {
- var me = this;
-
- if (plugins.notify(me, 'beforeDatasetsDraw', [easingValue]) === false) {
- return;
- }
-
- // Draw datasets reversed to support proper line stacking
- for (var i = (me.data.datasets || []).length - 1; i >= 0; --i) {
- if (me.isDatasetVisible(i)) {
- me.drawDataset(i, easingValue);
- }
- }
-
- plugins.notify(me, 'afterDatasetsDraw', [easingValue]);
- },
-
- /**
- * Draws dataset at index unless a plugin returns `false` to the `beforeDatasetDraw`
- * hook, in which case, plugins will not be called on `afterDatasetDraw`.
- * @private
- */
- drawDataset: function(index, easingValue) {
- var me = this;
- var meta = me.getDatasetMeta(index);
- var args = {
- meta: meta,
- index: index,
- easingValue: easingValue
- };
-
- if (plugins.notify(me, 'beforeDatasetDraw', [args]) === false) {
- return;
- }
-
- meta.controller.draw(easingValue);
-
- plugins.notify(me, 'afterDatasetDraw', [args]);
- },
-
- /**
- * Draws tooltip unless a plugin returns `false` to the `beforeTooltipDraw`
- * hook, in which case, plugins will not be called on `afterTooltipDraw`.
- * @private
- */
- _drawTooltip: function(easingValue) {
- var me = this;
- var tooltip = me.tooltip;
- var args = {
- tooltip: tooltip,
- easingValue: easingValue
- };
-
- if (plugins.notify(me, 'beforeTooltipDraw', [args]) === false) {
- return;
- }
-
- tooltip.draw();
-
- plugins.notify(me, 'afterTooltipDraw', [args]);
- },
-
- // Get the single element that was clicked on
- // @return : An object containing the dataset index and element index of the matching element. Also contains the rectangle that was draw
- getElementAtEvent: function(e) {
- return Interaction.modes.single(this, e);
- },
-
- getElementsAtEvent: function(e) {
- return Interaction.modes.label(this, e, {intersect: true});
- },
-
- getElementsAtXAxis: function(e) {
- return Interaction.modes['x-axis'](this, e, {intersect: true});
- },
-
- getElementsAtEventForMode: function(e, mode, options) {
- var method = Interaction.modes[mode];
- if (typeof method === 'function') {
- return method(this, e, options);
- }
-
- return [];
- },
-
- getDatasetAtEvent: function(e) {
- return Interaction.modes.dataset(this, e, {intersect: true});
- },
-
- getDatasetMeta: function(datasetIndex) {
- var me = this;
- var dataset = me.data.datasets[datasetIndex];
- if (!dataset._meta) {
- dataset._meta = {};
- }
-
- var meta = dataset._meta[me.id];
- if (!meta) {
- meta = dataset._meta[me.id] = {
- type: null,
- data: [],
- dataset: null,
- controller: null,
- hidden: null, // See isDatasetVisible() comment
- xAxisID: null,
- yAxisID: null
- };
- }
-
- return meta;
- },
-
- getVisibleDatasetCount: function() {
- var count = 0;
- for (var i = 0, ilen = this.data.datasets.length; i < ilen; ++i) {
- if (this.isDatasetVisible(i)) {
- count++;
- }
- }
- return count;
- },
-
- isDatasetVisible: function(datasetIndex) {
- var meta = this.getDatasetMeta(datasetIndex);
-
- // meta.hidden is a per chart dataset hidden flag override with 3 states: if true or false,
- // the dataset.hidden value is ignored, else if null, the dataset hidden state is returned.
- return typeof meta.hidden === 'boolean' ? !meta.hidden : !this.data.datasets[datasetIndex].hidden;
- },
-
- generateLegend: function() {
- return this.options.legendCallback(this);
- },
-
- /**
- * @private
- */
- destroyDatasetMeta: function(datasetIndex) {
- var id = this.id;
- var dataset = this.data.datasets[datasetIndex];
- var meta = dataset._meta && dataset._meta[id];
-
- if (meta) {
- meta.controller.destroy();
- delete dataset._meta[id];
- }
- },
-
- destroy: function() {
- var me = this;
- var canvas = me.canvas;
- var i, ilen;
-
- me.stop();
-
- // dataset controllers need to cleanup associated data
- for (i = 0, ilen = me.data.datasets.length; i < ilen; ++i) {
- me.destroyDatasetMeta(i);
- }
-
- if (canvas) {
- me.unbindEvents();
- helpers.canvas.clear(me);
- platform.releaseContext(me.ctx);
- me.canvas = null;
- me.ctx = null;
- }
-
- plugins.notify(me, 'destroy');
-
- delete Chart.instances[me.id];
- },
-
- toBase64Image: function() {
- return this.canvas.toDataURL.apply(this.canvas, arguments);
- },
-
- initToolTip: function() {
- var me = this;
- me.tooltip = new Tooltip({
- _chart: me,
- _chartInstance: me, // deprecated, backward compatibility
- _data: me.data,
- _options: me.options.tooltips
- }, me);
- },
-
- /**
- * @private
- */
- bindEvents: function() {
- var me = this;
- var listeners = me._listeners = {};
- var listener = function() {
- me.eventHandler.apply(me, arguments);
- };
-
- helpers.each(me.options.events, function(type) {
- platform.addEventListener(me, type, listener);
- listeners[type] = listener;
- });
-
- // Elements used to detect size change should not be injected for non responsive charts.
- // See https://github.com/chartjs/Chart.js/issues/2210
- if (me.options.responsive) {
- listener = function() {
- me.resize();
- };
-
- platform.addEventListener(me, 'resize', listener);
- listeners.resize = listener;
- }
- },
-
- /**
- * @private
- */
- unbindEvents: function() {
- var me = this;
- var listeners = me._listeners;
- if (!listeners) {
- return;
- }
-
- delete me._listeners;
- helpers.each(listeners, function(listener, type) {
- platform.removeEventListener(me, type, listener);
- });
- },
-
- updateHoverStyle: function(elements, mode, enabled) {
- var method = enabled ? 'setHoverStyle' : 'removeHoverStyle';
- var element, i, ilen;
-
- for (i = 0, ilen = elements.length; i < ilen; ++i) {
- element = elements[i];
- if (element) {
- this.getDatasetMeta(element._datasetIndex).controller[method](element);
- }
- }
- },
-
- /**
- * @private
- */
- eventHandler: function(e) {
- var me = this;
- var tooltip = me.tooltip;
-
- if (plugins.notify(me, 'beforeEvent', [e]) === false) {
- return;
- }
-
- // Buffer any update calls so that renders do not occur
- me._bufferedRender = true;
- me._bufferedRequest = null;
-
- var changed = me.handleEvent(e);
- // for smooth tooltip animations issue #4989
- // the tooltip should be the source of change
- // Animation check workaround:
- // tooltip._start will be null when tooltip isn't animating
- if (tooltip) {
- changed = tooltip._start
- ? tooltip.handleEvent(e)
- : changed | tooltip.handleEvent(e);
- }
-
- plugins.notify(me, 'afterEvent', [e]);
-
- var bufferedRequest = me._bufferedRequest;
- if (bufferedRequest) {
- // If we have an update that was triggered, we need to do a normal render
- me.render(bufferedRequest);
- } else if (changed && !me.animating) {
- // If entering, leaving, or changing elements, animate the change via pivot
- me.stop();
-
- // We only need to render at this point. Updating will cause scales to be
- // recomputed generating flicker & using more memory than necessary.
- me.render({
- duration: me.options.hover.animationDuration,
- lazy: true
- });
- }
-
- me._bufferedRender = false;
- me._bufferedRequest = null;
-
- return me;
- },
-
- /**
- * Handle an event
- * @private
- * @param {IEvent} event the event to handle
- * @return {Boolean} true if the chart needs to re-render
- */
- handleEvent: function(e) {
- var me = this;
- var options = me.options || {};
- var hoverOptions = options.hover;
- var changed = false;
-
- me.lastActive = me.lastActive || [];
-
- // Find Active Elements for hover and tooltips
- if (e.type === 'mouseout') {
- me.active = [];
- } else {
- me.active = me.getElementsAtEventForMode(e, hoverOptions.mode, hoverOptions);
- }
-
- // Invoke onHover hook
- // Need to call with native event here to not break backwards compatibility
- helpers.callback(options.onHover || options.hover.onHover, [e.native, me.active], me);
-
- if (e.type === 'mouseup' || e.type === 'click') {
- if (options.onClick) {
- // Use e.native here for backwards compatibility
- options.onClick.call(me, e.native, me.active);
- }
- }
-
- // Remove styling for last active (even if it may still be active)
- if (me.lastActive.length) {
- me.updateHoverStyle(me.lastActive, hoverOptions.mode, false);
- }
-
- // Built in hover styling
- if (me.active.length && hoverOptions.mode) {
- me.updateHoverStyle(me.active, hoverOptions.mode, true);
- }
-
- changed = !helpers.arrayEquals(me.active, me.lastActive);
-
- // Remember Last Actives
- me.lastActive = me.active;
-
- return changed;
- }
- });
-
- /**
- * Provided for backward compatibility, use Chart instead.
- * @class Chart.Controller
- * @deprecated since version 2.6.0
- * @todo remove at version 3
- * @private
- */
- Chart.Controller = Chart;
-};
-
-},{"22":22,"23":23,"26":26,"29":29,"31":31,"32":32,"34":34,"36":36,"46":46,"49":49}],25:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-
-module.exports = function(Chart) {
-
- var arrayEvents = ['push', 'pop', 'shift', 'splice', 'unshift'];
-
- /**
- * Hooks the array methods that add or remove values ('push', pop', 'shift', 'splice',
- * 'unshift') and notify the listener AFTER the array has been altered. Listeners are
- * called on the 'onData*' callbacks (e.g. onDataPush, etc.) with same arguments.
- */
- function listenArrayEvents(array, listener) {
- if (array._chartjs) {
- array._chartjs.listeners.push(listener);
- return;
- }
-
- Object.defineProperty(array, '_chartjs', {
- configurable: true,
- enumerable: false,
- value: {
- listeners: [listener]
- }
- });
-
- arrayEvents.forEach(function(key) {
- var method = 'onData' + key.charAt(0).toUpperCase() + key.slice(1);
- var base = array[key];
-
- Object.defineProperty(array, key, {
- configurable: true,
- enumerable: false,
- value: function() {
- var args = Array.prototype.slice.call(arguments);
- var res = base.apply(this, args);
-
- helpers.each(array._chartjs.listeners, function(object) {
- if (typeof object[method] === 'function') {
- object[method].apply(object, args);
- }
- });
-
- return res;
- }
- });
- });
- }
-
- /**
- * Removes the given array event listener and cleanup extra attached properties (such as
- * the _chartjs stub and overridden methods) if array doesn't have any more listeners.
- */
- function unlistenArrayEvents(array, listener) {
- var stub = array._chartjs;
- if (!stub) {
- return;
- }
-
- var listeners = stub.listeners;
- var index = listeners.indexOf(listener);
- if (index !== -1) {
- listeners.splice(index, 1);
- }
-
- if (listeners.length > 0) {
- return;
- }
-
- arrayEvents.forEach(function(key) {
- delete array[key];
- });
-
- delete array._chartjs;
- }
-
- // Base class for all dataset controllers (line, bar, etc)
- Chart.DatasetController = function(chart, datasetIndex) {
- this.initialize(chart, datasetIndex);
- };
-
- helpers.extend(Chart.DatasetController.prototype, {
-
- /**
- * Element type used to generate a meta dataset (e.g. Chart.element.Line).
- * @type {Chart.core.element}
- */
- datasetElementType: null,
-
- /**
- * Element type used to generate a meta data (e.g. Chart.element.Point).
- * @type {Chart.core.element}
- */
- dataElementType: null,
-
- initialize: function(chart, datasetIndex) {
- var me = this;
- me.chart = chart;
- me.index = datasetIndex;
- me.linkScales();
- me.addElements();
- },
-
- updateIndex: function(datasetIndex) {
- this.index = datasetIndex;
- },
-
- linkScales: function() {
- var me = this;
- var meta = me.getMeta();
- var dataset = me.getDataset();
-
- if (meta.xAxisID === null || !(meta.xAxisID in me.chart.scales)) {
- meta.xAxisID = dataset.xAxisID || me.chart.options.scales.xAxes[0].id;
- }
- if (meta.yAxisID === null || !(meta.yAxisID in me.chart.scales)) {
- meta.yAxisID = dataset.yAxisID || me.chart.options.scales.yAxes[0].id;
- }
- },
-
- getDataset: function() {
- return this.chart.data.datasets[this.index];
- },
-
- getMeta: function() {
- return this.chart.getDatasetMeta(this.index);
- },
-
- getScaleForId: function(scaleID) {
- return this.chart.scales[scaleID];
- },
-
- reset: function() {
- this.update(true);
- },
-
- /**
- * @private
- */
- destroy: function() {
- if (this._data) {
- unlistenArrayEvents(this._data, this);
- }
- },
-
- createMetaDataset: function() {
- var me = this;
- var type = me.datasetElementType;
- return type && new type({
- _chart: me.chart,
- _datasetIndex: me.index
- });
- },
-
- createMetaData: function(index) {
- var me = this;
- var type = me.dataElementType;
- return type && new type({
- _chart: me.chart,
- _datasetIndex: me.index,
- _index: index
- });
- },
-
- addElements: function() {
- var me = this;
- var meta = me.getMeta();
- var data = me.getDataset().data || [];
- var metaData = meta.data;
- var i, ilen;
-
- for (i = 0, ilen = data.length; i < ilen; ++i) {
- metaData[i] = metaData[i] || me.createMetaData(i);
- }
-
- meta.dataset = meta.dataset || me.createMetaDataset();
- },
-
- addElementAndReset: function(index) {
- var element = this.createMetaData(index);
- this.getMeta().data.splice(index, 0, element);
- this.updateElement(element, index, true);
- },
-
- buildOrUpdateElements: function() {
- var me = this;
- var dataset = me.getDataset();
- var data = dataset.data || (dataset.data = []);
-
- // In order to correctly handle data addition/deletion animation (an thus simulate
- // real-time charts), we need to monitor these data modifications and synchronize
- // the internal meta data accordingly.
- if (me._data !== data) {
- if (me._data) {
- // This case happens when the user replaced the data array instance.
- unlistenArrayEvents(me._data, me);
- }
-
- listenArrayEvents(data, me);
- me._data = data;
- }
-
- // Re-sync meta data in case the user replaced the data array or if we missed
- // any updates and so make sure that we handle number of datapoints changing.
- me.resyncElements();
- },
-
- update: helpers.noop,
-
- transition: function(easingValue) {
- var meta = this.getMeta();
- var elements = meta.data || [];
- var ilen = elements.length;
- var i = 0;
-
- for (; i < ilen; ++i) {
- elements[i].transition(easingValue);
- }
-
- if (meta.dataset) {
- meta.dataset.transition(easingValue);
- }
- },
-
- draw: function() {
- var meta = this.getMeta();
- var elements = meta.data || [];
- var ilen = elements.length;
- var i = 0;
-
- if (meta.dataset) {
- meta.dataset.draw();
- }
-
- for (; i < ilen; ++i) {
- elements[i].draw();
- }
- },
-
- removeHoverStyle: function(element) {
- helpers.merge(element._model, element.$previousStyle || {});
- delete element.$previousStyle;
- },
-
- setHoverStyle: function(element) {
- var dataset = this.chart.data.datasets[element._datasetIndex];
- var index = element._index;
- var custom = element.custom || {};
- var valueOrDefault = helpers.valueAtIndexOrDefault;
- var getHoverColor = helpers.getHoverColor;
- var model = element._model;
-
- element.$previousStyle = {
- backgroundColor: model.backgroundColor,
- borderColor: model.borderColor,
- borderWidth: model.borderWidth
- };
-
- model.backgroundColor = custom.hoverBackgroundColor ? custom.hoverBackgroundColor : valueOrDefault(dataset.hoverBackgroundColor, index, getHoverColor(model.backgroundColor));
- model.borderColor = custom.hoverBorderColor ? custom.hoverBorderColor : valueOrDefault(dataset.hoverBorderColor, index, getHoverColor(model.borderColor));
- model.borderWidth = custom.hoverBorderWidth ? custom.hoverBorderWidth : valueOrDefault(dataset.hoverBorderWidth, index, model.borderWidth);
- },
-
- /**
- * @private
- */
- resyncElements: function() {
- var me = this;
- var meta = me.getMeta();
- var data = me.getDataset().data;
- var numMeta = meta.data.length;
- var numData = data.length;
-
- if (numData < numMeta) {
- meta.data.splice(numData, numMeta - numData);
- } else if (numData > numMeta) {
- me.insertElements(numMeta, numData - numMeta);
- }
- },
-
- /**
- * @private
- */
- insertElements: function(start, count) {
- for (var i = 0; i < count; ++i) {
- this.addElementAndReset(start + i);
- }
- },
-
- /**
- * @private
- */
- onDataPush: function() {
- this.insertElements(this.getDataset().data.length - 1, arguments.length);
- },
-
- /**
- * @private
- */
- onDataPop: function() {
- this.getMeta().data.pop();
- },
-
- /**
- * @private
- */
- onDataShift: function() {
- this.getMeta().data.shift();
- },
-
- /**
- * @private
- */
- onDataSplice: function(start, count) {
- this.getMeta().data.splice(start, count);
- this.insertElements(start, arguments.length - 2);
- },
-
- /**
- * @private
- */
- onDataUnshift: function() {
- this.insertElements(0, arguments.length);
- }
- });
-
- Chart.DatasetController.extend = helpers.inherits;
-};
-
-},{"46":46}],26:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-
-module.exports = {
- /**
- * @private
- */
- _set: function(scope, values) {
- return helpers.merge(this[scope] || (this[scope] = {}), values);
- }
-};
-
-},{"46":46}],27:[function(require,module,exports){
-'use strict';
-
-var color = require(2);
-var helpers = require(46);
-
-function interpolate(start, view, model, ease) {
- var keys = Object.keys(model);
- var i, ilen, key, actual, origin, target, type, c0, c1;
-
- for (i = 0, ilen = keys.length; i < ilen; ++i) {
- key = keys[i];
-
- target = model[key];
-
- // if a value is added to the model after pivot() has been called, the view
- // doesn't contain it, so let's initialize the view to the target value.
- if (!view.hasOwnProperty(key)) {
- view[key] = target;
- }
-
- actual = view[key];
-
- if (actual === target || key[0] === '_') {
- continue;
- }
-
- if (!start.hasOwnProperty(key)) {
- start[key] = actual;
- }
-
- origin = start[key];
-
- type = typeof target;
-
- if (type === typeof origin) {
- if (type === 'string') {
- c0 = color(origin);
- if (c0.valid) {
- c1 = color(target);
- if (c1.valid) {
- view[key] = c1.mix(c0, ease).rgbString();
- continue;
- }
- }
- } else if (type === 'number' && isFinite(origin) && isFinite(target)) {
- view[key] = origin + (target - origin) * ease;
- continue;
- }
- }
-
- view[key] = target;
- }
-}
-
-var Element = function(configuration) {
- helpers.extend(this, configuration);
- this.initialize.apply(this, arguments);
-};
-
-helpers.extend(Element.prototype, {
-
- initialize: function() {
- this.hidden = false;
- },
-
- pivot: function() {
- var me = this;
- if (!me._view) {
- me._view = helpers.clone(me._model);
- }
- me._start = {};
- return me;
- },
-
- transition: function(ease) {
- var me = this;
- var model = me._model;
- var start = me._start;
- var view = me._view;
-
- // No animation -> No Transition
- if (!model || ease === 1) {
- me._view = model;
- me._start = null;
- return me;
- }
-
- if (!view) {
- view = me._view = {};
- }
-
- if (!start) {
- start = me._start = {};
- }
-
- interpolate(start, view, model, ease);
-
- return me;
- },
-
- tooltipPosition: function() {
- return {
- x: this._model.x,
- y: this._model.y
- };
- },
-
- hasValue: function() {
- return helpers.isNumber(this._model.x) && helpers.isNumber(this._model.y);
- }
-});
-
-Element.extend = helpers.inherits;
-
-module.exports = Element;
-
-},{"2":2,"46":46}],28:[function(require,module,exports){
-/* global window: false */
-/* global document: false */
-'use strict';
-
-var color = require(2);
-var defaults = require(26);
-var helpers = require(46);
-var scaleService = require(34);
-
-module.exports = function() {
-
- // -- Basic js utility methods
-
- helpers.configMerge = function(/* objects ... */) {
- return helpers.merge(helpers.clone(arguments[0]), [].slice.call(arguments, 1), {
- merger: function(key, target, source, options) {
- var tval = target[key] || {};
- var sval = source[key];
-
- if (key === 'scales') {
- // scale config merging is complex. Add our own function here for that
- target[key] = helpers.scaleMerge(tval, sval);
- } else if (key === 'scale') {
- // used in polar area & radar charts since there is only one scale
- target[key] = helpers.merge(tval, [scaleService.getScaleDefaults(sval.type), sval]);
- } else {
- helpers._merger(key, target, source, options);
- }
- }
- });
- };
-
- helpers.scaleMerge = function(/* objects ... */) {
- return helpers.merge(helpers.clone(arguments[0]), [].slice.call(arguments, 1), {
- merger: function(key, target, source, options) {
- if (key === 'xAxes' || key === 'yAxes') {
- var slen = source[key].length;
- var i, type, scale;
-
- if (!target[key]) {
- target[key] = [];
- }
-
- for (i = 0; i < slen; ++i) {
- scale = source[key][i];
- type = helpers.valueOrDefault(scale.type, key === 'xAxes' ? 'category' : 'linear');
-
- if (i >= target[key].length) {
- target[key].push({});
- }
-
- if (!target[key][i].type || (scale.type && scale.type !== target[key][i].type)) {
- // new/untyped scale or type changed: let's apply the new defaults
- // then merge source scale to correctly overwrite the defaults.
- helpers.merge(target[key][i], [scaleService.getScaleDefaults(type), scale]);
- } else {
- // scales type are the same
- helpers.merge(target[key][i], scale);
- }
- }
- } else {
- helpers._merger(key, target, source, options);
- }
- }
- });
- };
-
- helpers.where = function(collection, filterCallback) {
- if (helpers.isArray(collection) && Array.prototype.filter) {
- return collection.filter(filterCallback);
- }
- var filtered = [];
-
- helpers.each(collection, function(item) {
- if (filterCallback(item)) {
- filtered.push(item);
- }
- });
-
- return filtered;
- };
- helpers.findIndex = Array.prototype.findIndex ?
- function(array, callback, scope) {
- return array.findIndex(callback, scope);
- } :
- function(array, callback, scope) {
- scope = scope === undefined ? array : scope;
- for (var i = 0, ilen = array.length; i < ilen; ++i) {
- if (callback.call(scope, array[i], i, array)) {
- return i;
- }
- }
- return -1;
- };
- helpers.findNextWhere = function(arrayToSearch, filterCallback, startIndex) {
- // Default to start of the array
- if (helpers.isNullOrUndef(startIndex)) {
- startIndex = -1;
- }
- for (var i = startIndex + 1; i < arrayToSearch.length; i++) {
- var currentItem = arrayToSearch[i];
- if (filterCallback(currentItem)) {
- return currentItem;
- }
- }
- };
- helpers.findPreviousWhere = function(arrayToSearch, filterCallback, startIndex) {
- // Default to end of the array
- if (helpers.isNullOrUndef(startIndex)) {
- startIndex = arrayToSearch.length;
- }
- for (var i = startIndex - 1; i >= 0; i--) {
- var currentItem = arrayToSearch[i];
- if (filterCallback(currentItem)) {
- return currentItem;
- }
- }
- };
-
- // -- Math methods
- helpers.isNumber = function(n) {
- return !isNaN(parseFloat(n)) && isFinite(n);
- };
- helpers.almostEquals = function(x, y, epsilon) {
- return Math.abs(x - y) < epsilon;
- };
- helpers.almostWhole = function(x, epsilon) {
- var rounded = Math.round(x);
- return (((rounded - epsilon) < x) && ((rounded + epsilon) > x));
- };
- helpers.max = function(array) {
- return array.reduce(function(max, value) {
- if (!isNaN(value)) {
- return Math.max(max, value);
- }
- return max;
- }, Number.NEGATIVE_INFINITY);
- };
- helpers.min = function(array) {
- return array.reduce(function(min, value) {
- if (!isNaN(value)) {
- return Math.min(min, value);
- }
- return min;
- }, Number.POSITIVE_INFINITY);
- };
- helpers.sign = Math.sign ?
- function(x) {
- return Math.sign(x);
- } :
- function(x) {
- x = +x; // convert to a number
- if (x === 0 || isNaN(x)) {
- return x;
- }
- return x > 0 ? 1 : -1;
- };
- helpers.log10 = Math.log10 ?
- function(x) {
- return Math.log10(x);
- } :
- function(x) {
- var exponent = Math.log(x) * Math.LOG10E; // Math.LOG10E = 1 / Math.LN10.
- // Check for whole powers of 10,
- // which due to floating point rounding error should be corrected.
- var powerOf10 = Math.round(exponent);
- var isPowerOf10 = x === Math.pow(10, powerOf10);
-
- return isPowerOf10 ? powerOf10 : exponent;
- };
- helpers.toRadians = function(degrees) {
- return degrees * (Math.PI / 180);
- };
- helpers.toDegrees = function(radians) {
- return radians * (180 / Math.PI);
- };
- // Gets the angle from vertical upright to the point about a centre.
- helpers.getAngleFromPoint = function(centrePoint, anglePoint) {
- var distanceFromXCenter = anglePoint.x - centrePoint.x;
- var distanceFromYCenter = anglePoint.y - centrePoint.y;
- var radialDistanceFromCenter = Math.sqrt(distanceFromXCenter * distanceFromXCenter + distanceFromYCenter * distanceFromYCenter);
-
- var angle = Math.atan2(distanceFromYCenter, distanceFromXCenter);
-
- if (angle < (-0.5 * Math.PI)) {
- angle += 2.0 * Math.PI; // make sure the returned angle is in the range of (-PI/2, 3PI/2]
- }
-
- return {
- angle: angle,
- distance: radialDistanceFromCenter
- };
- };
- helpers.distanceBetweenPoints = function(pt1, pt2) {
- return Math.sqrt(Math.pow(pt2.x - pt1.x, 2) + Math.pow(pt2.y - pt1.y, 2));
- };
- helpers.aliasPixel = function(pixelWidth) {
- return (pixelWidth % 2 === 0) ? 0 : 0.5;
- };
- helpers.splineCurve = function(firstPoint, middlePoint, afterPoint, t) {
- // Props to Rob Spencer at scaled innovation for his post on splining between points
- // http://scaledinnovation.com/analytics/splines/aboutSplines.html
-
- // This function must also respect "skipped" points
-
- var previous = firstPoint.skip ? middlePoint : firstPoint;
- var current = middlePoint;
- var next = afterPoint.skip ? middlePoint : afterPoint;
-
- var d01 = Math.sqrt(Math.pow(current.x - previous.x, 2) + Math.pow(current.y - previous.y, 2));
- var d12 = Math.sqrt(Math.pow(next.x - current.x, 2) + Math.pow(next.y - current.y, 2));
-
- var s01 = d01 / (d01 + d12);
- var s12 = d12 / (d01 + d12);
-
- // If all points are the same, s01 & s02 will be inf
- s01 = isNaN(s01) ? 0 : s01;
- s12 = isNaN(s12) ? 0 : s12;
-
- var fa = t * s01; // scaling factor for triangle Ta
- var fb = t * s12;
-
- return {
- previous: {
- x: current.x - fa * (next.x - previous.x),
- y: current.y - fa * (next.y - previous.y)
- },
- next: {
- x: current.x + fb * (next.x - previous.x),
- y: current.y + fb * (next.y - previous.y)
- }
- };
- };
- helpers.EPSILON = Number.EPSILON || 1e-14;
- helpers.splineCurveMonotone = function(points) {
- // This function calculates BĂ©zier control points in a similar way than |splineCurve|,
- // but preserves monotonicity of the provided data and ensures no local extremums are added
- // between the dataset discrete points due to the interpolation.
- // See : https://en.wikipedia.org/wiki/Monotone_cubic_interpolation
-
- var pointsWithTangents = (points || []).map(function(point) {
- return {
- model: point._model,
- deltaK: 0,
- mK: 0
- };
- });
-
- // Calculate slopes (deltaK) and initialize tangents (mK)
- var pointsLen = pointsWithTangents.length;
- var i, pointBefore, pointCurrent, pointAfter;
- for (i = 0; i < pointsLen; ++i) {
- pointCurrent = pointsWithTangents[i];
- if (pointCurrent.model.skip) {
- continue;
- }
-
- pointBefore = i > 0 ? pointsWithTangents[i - 1] : null;
- pointAfter = i < pointsLen - 1 ? pointsWithTangents[i + 1] : null;
- if (pointAfter && !pointAfter.model.skip) {
- var slopeDeltaX = (pointAfter.model.x - pointCurrent.model.x);
-
- // In the case of two points that appear at the same x pixel, slopeDeltaX is 0
- pointCurrent.deltaK = slopeDeltaX !== 0 ? (pointAfter.model.y - pointCurrent.model.y) / slopeDeltaX : 0;
- }
-
- if (!pointBefore || pointBefore.model.skip) {
- pointCurrent.mK = pointCurrent.deltaK;
- } else if (!pointAfter || pointAfter.model.skip) {
- pointCurrent.mK = pointBefore.deltaK;
- } else if (this.sign(pointBefore.deltaK) !== this.sign(pointCurrent.deltaK)) {
- pointCurrent.mK = 0;
- } else {
- pointCurrent.mK = (pointBefore.deltaK + pointCurrent.deltaK) / 2;
- }
- }
-
- // Adjust tangents to ensure monotonic properties
- var alphaK, betaK, tauK, squaredMagnitude;
- for (i = 0; i < pointsLen - 1; ++i) {
- pointCurrent = pointsWithTangents[i];
- pointAfter = pointsWithTangents[i + 1];
- if (pointCurrent.model.skip || pointAfter.model.skip) {
- continue;
- }
-
- if (helpers.almostEquals(pointCurrent.deltaK, 0, this.EPSILON)) {
- pointCurrent.mK = pointAfter.mK = 0;
- continue;
- }
-
- alphaK = pointCurrent.mK / pointCurrent.deltaK;
- betaK = pointAfter.mK / pointCurrent.deltaK;
- squaredMagnitude = Math.pow(alphaK, 2) + Math.pow(betaK, 2);
- if (squaredMagnitude <= 9) {
- continue;
- }
-
- tauK = 3 / Math.sqrt(squaredMagnitude);
- pointCurrent.mK = alphaK * tauK * pointCurrent.deltaK;
- pointAfter.mK = betaK * tauK * pointCurrent.deltaK;
- }
-
- // Compute control points
- var deltaX;
- for (i = 0; i < pointsLen; ++i) {
- pointCurrent = pointsWithTangents[i];
- if (pointCurrent.model.skip) {
- continue;
- }
-
- pointBefore = i > 0 ? pointsWithTangents[i - 1] : null;
- pointAfter = i < pointsLen - 1 ? pointsWithTangents[i + 1] : null;
- if (pointBefore && !pointBefore.model.skip) {
- deltaX = (pointCurrent.model.x - pointBefore.model.x) / 3;
- pointCurrent.model.controlPointPreviousX = pointCurrent.model.x - deltaX;
- pointCurrent.model.controlPointPreviousY = pointCurrent.model.y - deltaX * pointCurrent.mK;
- }
- if (pointAfter && !pointAfter.model.skip) {
- deltaX = (pointAfter.model.x - pointCurrent.model.x) / 3;
- pointCurrent.model.controlPointNextX = pointCurrent.model.x + deltaX;
- pointCurrent.model.controlPointNextY = pointCurrent.model.y + deltaX * pointCurrent.mK;
- }
- }
- };
- helpers.nextItem = function(collection, index, loop) {
- if (loop) {
- return index >= collection.length - 1 ? collection[0] : collection[index + 1];
- }
- return index >= collection.length - 1 ? collection[collection.length - 1] : collection[index + 1];
- };
- helpers.previousItem = function(collection, index, loop) {
- if (loop) {
- return index <= 0 ? collection[collection.length - 1] : collection[index - 1];
- }
- return index <= 0 ? collection[0] : collection[index - 1];
- };
- // Implementation of the nice number algorithm used in determining where axis labels will go
- helpers.niceNum = function(range, round) {
- var exponent = Math.floor(helpers.log10(range));
- var fraction = range / Math.pow(10, exponent);
- var niceFraction;
-
- if (round) {
- if (fraction < 1.5) {
- niceFraction = 1;
- } else if (fraction < 3) {
- niceFraction = 2;
- } else if (fraction < 7) {
- niceFraction = 5;
- } else {
- niceFraction = 10;
- }
- } else if (fraction <= 1.0) {
- niceFraction = 1;
- } else if (fraction <= 2) {
- niceFraction = 2;
- } else if (fraction <= 5) {
- niceFraction = 5;
- } else {
- niceFraction = 10;
- }
-
- return niceFraction * Math.pow(10, exponent);
- };
- // Request animation polyfill - http://www.paulirish.com/2011/requestanimationframe-for-smart-animating/
- helpers.requestAnimFrame = (function() {
- if (typeof window === 'undefined') {
- return function(callback) {
- callback();
- };
- }
- return window.requestAnimationFrame ||
- window.webkitRequestAnimationFrame ||
- window.mozRequestAnimationFrame ||
- window.oRequestAnimationFrame ||
- window.msRequestAnimationFrame ||
- function(callback) {
- return window.setTimeout(callback, 1000 / 60);
- };
- }());
- // -- DOM methods
- helpers.getRelativePosition = function(evt, chart) {
- var mouseX, mouseY;
- var e = evt.originalEvent || evt;
- var canvas = evt.target || evt.srcElement;
- var boundingRect = canvas.getBoundingClientRect();
-
- var touches = e.touches;
- if (touches && touches.length > 0) {
- mouseX = touches[0].clientX;
- mouseY = touches[0].clientY;
-
- } else {
- mouseX = e.clientX;
- mouseY = e.clientY;
- }
-
- // Scale mouse coordinates into canvas coordinates
- // by following the pattern laid out by 'jerryj' in the comments of
- // http://www.html5canvastutorials.com/advanced/html5-canvas-mouse-coordinates/
- var paddingLeft = parseFloat(helpers.getStyle(canvas, 'padding-left'));
- var paddingTop = parseFloat(helpers.getStyle(canvas, 'padding-top'));
- var paddingRight = parseFloat(helpers.getStyle(canvas, 'padding-right'));
- var paddingBottom = parseFloat(helpers.getStyle(canvas, 'padding-bottom'));
- var width = boundingRect.right - boundingRect.left - paddingLeft - paddingRight;
- var height = boundingRect.bottom - boundingRect.top - paddingTop - paddingBottom;
-
- // We divide by the current device pixel ratio, because the canvas is scaled up by that amount in each direction. However
- // the backend model is in unscaled coordinates. Since we are going to deal with our model coordinates, we go back here
- mouseX = Math.round((mouseX - boundingRect.left - paddingLeft) / (width) * canvas.width / chart.currentDevicePixelRatio);
- mouseY = Math.round((mouseY - boundingRect.top - paddingTop) / (height) * canvas.height / chart.currentDevicePixelRatio);
-
- return {
- x: mouseX,
- y: mouseY
- };
-
- };
-
- // Private helper function to convert max-width/max-height values that may be percentages into a number
- function parseMaxStyle(styleValue, node, parentProperty) {
- var valueInPixels;
- if (typeof styleValue === 'string') {
- valueInPixels = parseInt(styleValue, 10);
-
- if (styleValue.indexOf('%') !== -1) {
- // percentage * size in dimension
- valueInPixels = valueInPixels / 100 * node.parentNode[parentProperty];
- }
- } else {
- valueInPixels = styleValue;
- }
-
- return valueInPixels;
- }
-
- /**
- * Returns if the given value contains an effective constraint.
- * @private
- */
- function isConstrainedValue(value) {
- return value !== undefined && value !== null && value !== 'none';
- }
-
- // Private helper to get a constraint dimension
- // @param domNode : the node to check the constraint on
- // @param maxStyle : the style that defines the maximum for the direction we are using (maxWidth / maxHeight)
- // @param percentageProperty : property of parent to use when calculating width as a percentage
- // @see http://www.nathanaeljones.com/blog/2013/reading-max-width-cross-browser
- function getConstraintDimension(domNode, maxStyle, percentageProperty) {
- var view = document.defaultView;
- var parentNode = helpers._getParentNode(domNode);
- var constrainedNode = view.getComputedStyle(domNode)[maxStyle];
- var constrainedContainer = view.getComputedStyle(parentNode)[maxStyle];
- var hasCNode = isConstrainedValue(constrainedNode);
- var hasCContainer = isConstrainedValue(constrainedContainer);
- var infinity = Number.POSITIVE_INFINITY;
-
- if (hasCNode || hasCContainer) {
- return Math.min(
- hasCNode ? parseMaxStyle(constrainedNode, domNode, percentageProperty) : infinity,
- hasCContainer ? parseMaxStyle(constrainedContainer, parentNode, percentageProperty) : infinity);
- }
-
- return 'none';
- }
- // returns Number or undefined if no constraint
- helpers.getConstraintWidth = function(domNode) {
- return getConstraintDimension(domNode, 'max-width', 'clientWidth');
- };
- // returns Number or undefined if no constraint
- helpers.getConstraintHeight = function(domNode) {
- return getConstraintDimension(domNode, 'max-height', 'clientHeight');
- };
- /**
- * @private
- */
- helpers._calculatePadding = function(container, padding, parentDimension) {
- padding = helpers.getStyle(container, padding);
-
- return padding.indexOf('%') > -1 ? parentDimension / parseInt(padding, 10) : parseInt(padding, 10);
- };
- /**
- * @private
- */
- helpers._getParentNode = function(domNode) {
- var parent = domNode.parentNode;
- if (parent && parent.host) {
- parent = parent.host;
- }
- return parent;
- };
- helpers.getMaximumWidth = function(domNode) {
- var container = helpers._getParentNode(domNode);
- if (!container) {
- return domNode.clientWidth;
- }
-
- var clientWidth = container.clientWidth;
- var paddingLeft = helpers._calculatePadding(container, 'padding-left', clientWidth);
- var paddingRight = helpers._calculatePadding(container, 'padding-right', clientWidth);
-
- var w = clientWidth - paddingLeft - paddingRight;
- var cw = helpers.getConstraintWidth(domNode);
- return isNaN(cw) ? w : Math.min(w, cw);
- };
- helpers.getMaximumHeight = function(domNode) {
- var container = helpers._getParentNode(domNode);
- if (!container) {
- return domNode.clientHeight;
- }
-
- var clientHeight = container.clientHeight;
- var paddingTop = helpers._calculatePadding(container, 'padding-top', clientHeight);
- var paddingBottom = helpers._calculatePadding(container, 'padding-bottom', clientHeight);
-
- var h = clientHeight - paddingTop - paddingBottom;
- var ch = helpers.getConstraintHeight(domNode);
- return isNaN(ch) ? h : Math.min(h, ch);
- };
- helpers.getStyle = function(el, property) {
- return el.currentStyle ?
- el.currentStyle[property] :
- document.defaultView.getComputedStyle(el, null).getPropertyValue(property);
- };
- helpers.retinaScale = function(chart, forceRatio) {
- var pixelRatio = chart.currentDevicePixelRatio = forceRatio || (typeof window !== 'undefined' && window.devicePixelRatio) || 1;
- if (pixelRatio === 1) {
- return;
- }
-
- var canvas = chart.canvas;
- var height = chart.height;
- var width = chart.width;
-
- canvas.height = height * pixelRatio;
- canvas.width = width * pixelRatio;
- chart.ctx.scale(pixelRatio, pixelRatio);
-
- // If no style has been set on the canvas, the render size is used as display size,
- // making the chart visually bigger, so let's enforce it to the "correct" values.
- // See https://github.com/chartjs/Chart.js/issues/3575
- if (!canvas.style.height && !canvas.style.width) {
- canvas.style.height = height + 'px';
- canvas.style.width = width + 'px';
- }
- };
- // -- Canvas methods
- helpers.fontString = function(pixelSize, fontStyle, fontFamily) {
- return fontStyle + ' ' + pixelSize + 'px ' + fontFamily;
- };
- helpers.longestText = function(ctx, font, arrayOfThings, cache) {
- cache = cache || {};
- var data = cache.data = cache.data || {};
- var gc = cache.garbageCollect = cache.garbageCollect || [];
-
- if (cache.font !== font) {
- data = cache.data = {};
- gc = cache.garbageCollect = [];
- cache.font = font;
- }
-
- ctx.font = font;
- var longest = 0;
- helpers.each(arrayOfThings, function(thing) {
- // Undefined strings and arrays should not be measured
- if (thing !== undefined && thing !== null && helpers.isArray(thing) !== true) {
- longest = helpers.measureText(ctx, data, gc, longest, thing);
- } else if (helpers.isArray(thing)) {
- // if it is an array lets measure each element
- // to do maybe simplify this function a bit so we can do this more recursively?
- helpers.each(thing, function(nestedThing) {
- // Undefined strings and arrays should not be measured
- if (nestedThing !== undefined && nestedThing !== null && !helpers.isArray(nestedThing)) {
- longest = helpers.measureText(ctx, data, gc, longest, nestedThing);
- }
- });
- }
- });
-
- var gcLen = gc.length / 2;
- if (gcLen > arrayOfThings.length) {
- for (var i = 0; i < gcLen; i++) {
- delete data[gc[i]];
- }
- gc.splice(0, gcLen);
- }
- return longest;
- };
- helpers.measureText = function(ctx, data, gc, longest, string) {
- var textWidth = data[string];
- if (!textWidth) {
- textWidth = data[string] = ctx.measureText(string).width;
- gc.push(string);
- }
- if (textWidth > longest) {
- longest = textWidth;
- }
- return longest;
- };
- helpers.numberOfLabelLines = function(arrayOfThings) {
- var numberOfLines = 1;
- helpers.each(arrayOfThings, function(thing) {
- if (helpers.isArray(thing)) {
- if (thing.length > numberOfLines) {
- numberOfLines = thing.length;
- }
- }
- });
- return numberOfLines;
- };
-
- helpers.color = !color ?
- function(value) {
- console.error('Color.js not found!');
- return value;
- } :
- function(value) {
- /* global CanvasGradient */
- if (value instanceof CanvasGradient) {
- value = defaults.global.defaultColor;
- }
-
- return color(value);
- };
-
- helpers.getHoverColor = function(colorValue) {
- /* global CanvasPattern */
- return (colorValue instanceof CanvasPattern) ?
- colorValue :
- helpers.color(colorValue).saturate(0.5).darken(0.1).rgbString();
- };
-};
-
-},{"2":2,"26":26,"34":34,"46":46}],29:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-
-/**
- * Helper function to get relative position for an event
- * @param {Event|IEvent} event - The event to get the position for
- * @param {Chart} chart - The chart
- * @returns {Point} the event position
- */
-function getRelativePosition(e, chart) {
- if (e.native) {
- return {
- x: e.x,
- y: e.y
- };
- }
-
- return helpers.getRelativePosition(e, chart);
-}
-
-/**
- * Helper function to traverse all of the visible elements in the chart
- * @param chart {chart} the chart
- * @param handler {Function} the callback to execute for each visible item
- */
-function parseVisibleItems(chart, handler) {
- var datasets = chart.data.datasets;
- var meta, i, j, ilen, jlen;
-
- for (i = 0, ilen = datasets.length; i < ilen; ++i) {
- if (!chart.isDatasetVisible(i)) {
- continue;
- }
-
- meta = chart.getDatasetMeta(i);
- for (j = 0, jlen = meta.data.length; j < jlen; ++j) {
- var element = meta.data[j];
- if (!element._view.skip) {
- handler(element);
- }
- }
- }
-}
-
-/**
- * Helper function to get the items that intersect the event position
- * @param items {ChartElement[]} elements to filter
- * @param position {Point} the point to be nearest to
- * @return {ChartElement[]} the nearest items
- */
-function getIntersectItems(chart, position) {
- var elements = [];
-
- parseVisibleItems(chart, function(element) {
- if (element.inRange(position.x, position.y)) {
- elements.push(element);
- }
- });
-
- return elements;
-}
-
-/**
- * Helper function to get the items nearest to the event position considering all visible items in teh chart
- * @param chart {Chart} the chart to look at elements from
- * @param position {Point} the point to be nearest to
- * @param intersect {Boolean} if true, only consider items that intersect the position
- * @param distanceMetric {Function} function to provide the distance between points
- * @return {ChartElement[]} the nearest items
- */
-function getNearestItems(chart, position, intersect, distanceMetric) {
- var minDistance = Number.POSITIVE_INFINITY;
- var nearestItems = [];
-
- parseVisibleItems(chart, function(element) {
- if (intersect && !element.inRange(position.x, position.y)) {
- return;
- }
-
- var center = element.getCenterPoint();
- var distance = distanceMetric(position, center);
-
- if (distance < minDistance) {
- nearestItems = [element];
- minDistance = distance;
- } else if (distance === minDistance) {
- // Can have multiple items at the same distance in which case we sort by size
- nearestItems.push(element);
- }
- });
-
- return nearestItems;
-}
-
-/**
- * Get a distance metric function for two points based on the
- * axis mode setting
- * @param {String} axis the axis mode. x|y|xy
- */
-function getDistanceMetricForAxis(axis) {
- var useX = axis.indexOf('x') !== -1;
- var useY = axis.indexOf('y') !== -1;
-
- return function(pt1, pt2) {
- var deltaX = useX ? Math.abs(pt1.x - pt2.x) : 0;
- var deltaY = useY ? Math.abs(pt1.y - pt2.y) : 0;
- return Math.sqrt(Math.pow(deltaX, 2) + Math.pow(deltaY, 2));
- };
-}
-
-function indexMode(chart, e, options) {
- var position = getRelativePosition(e, chart);
- // Default axis for index mode is 'x' to match old behaviour
- options.axis = options.axis || 'x';
- var distanceMetric = getDistanceMetricForAxis(options.axis);
- var items = options.intersect ? getIntersectItems(chart, position) : getNearestItems(chart, position, false, distanceMetric);
- var elements = [];
-
- if (!items.length) {
- return [];
- }
-
- chart.data.datasets.forEach(function(dataset, datasetIndex) {
- if (chart.isDatasetVisible(datasetIndex)) {
- var meta = chart.getDatasetMeta(datasetIndex);
- var element = meta.data[items[0]._index];
-
- // don't count items that are skipped (null data)
- if (element && !element._view.skip) {
- elements.push(element);
- }
- }
- });
-
- return elements;
-}
-
-/**
- * @interface IInteractionOptions
- */
-/**
- * If true, only consider items that intersect the point
- * @name IInterfaceOptions#boolean
- * @type Boolean
- */
-
-/**
- * Contains interaction related functions
- * @namespace Chart.Interaction
- */
-module.exports = {
- // Helper function for different modes
- modes: {
- single: function(chart, e) {
- var position = getRelativePosition(e, chart);
- var elements = [];
-
- parseVisibleItems(chart, function(element) {
- if (element.inRange(position.x, position.y)) {
- elements.push(element);
- return elements;
- }
- });
-
- return elements.slice(0, 1);
- },
-
- /**
- * @function Chart.Interaction.modes.label
- * @deprecated since version 2.4.0
- * @todo remove at version 3
- * @private
- */
- label: indexMode,
-
- /**
- * Returns items at the same index. If the options.intersect parameter is true, we only return items if we intersect something
- * If the options.intersect mode is false, we find the nearest item and return the items at the same index as that item
- * @function Chart.Interaction.modes.index
- * @since v2.4.0
- * @param chart {chart} the chart we are returning items from
- * @param e {Event} the event we are find things at
- * @param options {IInteractionOptions} options to use during interaction
- * @return {Chart.Element[]} Array of elements that are under the point. If none are found, an empty array is returned
- */
- index: indexMode,
-
- /**
- * Returns items in the same dataset. If the options.intersect parameter is true, we only return items if we intersect something
- * If the options.intersect is false, we find the nearest item and return the items in that dataset
- * @function Chart.Interaction.modes.dataset
- * @param chart {chart} the chart we are returning items from
- * @param e {Event} the event we are find things at
- * @param options {IInteractionOptions} options to use during interaction
- * @return {Chart.Element[]} Array of elements that are under the point. If none are found, an empty array is returned
- */
- dataset: function(chart, e, options) {
- var position = getRelativePosition(e, chart);
- options.axis = options.axis || 'xy';
- var distanceMetric = getDistanceMetricForAxis(options.axis);
- var items = options.intersect ? getIntersectItems(chart, position) : getNearestItems(chart, position, false, distanceMetric);
-
- if (items.length > 0) {
- items = chart.getDatasetMeta(items[0]._datasetIndex).data;
- }
-
- return items;
- },
-
- /**
- * @function Chart.Interaction.modes.x-axis
- * @deprecated since version 2.4.0. Use index mode and intersect == true
- * @todo remove at version 3
- * @private
- */
- 'x-axis': function(chart, e) {
- return indexMode(chart, e, {intersect: false});
- },
-
- /**
- * Point mode returns all elements that hit test based on the event position
- * of the event
- * @function Chart.Interaction.modes.intersect
- * @param chart {chart} the chart we are returning items from
- * @param e {Event} the event we are find things at
- * @return {Chart.Element[]} Array of elements that are under the point. If none are found, an empty array is returned
- */
- point: function(chart, e) {
- var position = getRelativePosition(e, chart);
- return getIntersectItems(chart, position);
- },
-
- /**
- * nearest mode returns the element closest to the point
- * @function Chart.Interaction.modes.intersect
- * @param chart {chart} the chart we are returning items from
- * @param e {Event} the event we are find things at
- * @param options {IInteractionOptions} options to use
- * @return {Chart.Element[]} Array of elements that are under the point. If none are found, an empty array is returned
- */
- nearest: function(chart, e, options) {
- var position = getRelativePosition(e, chart);
- options.axis = options.axis || 'xy';
- var distanceMetric = getDistanceMetricForAxis(options.axis);
- var nearestItems = getNearestItems(chart, position, options.intersect, distanceMetric);
-
- // We have multiple items at the same distance from the event. Now sort by smallest
- if (nearestItems.length > 1) {
- nearestItems.sort(function(a, b) {
- var sizeA = a.getArea();
- var sizeB = b.getArea();
- var ret = sizeA - sizeB;
-
- if (ret === 0) {
- // if equal sort by dataset index
- ret = a._datasetIndex - b._datasetIndex;
- }
-
- return ret;
- });
- }
-
- // Return only 1 item
- return nearestItems.slice(0, 1);
- },
-
- /**
- * x mode returns the elements that hit-test at the current x coordinate
- * @function Chart.Interaction.modes.x
- * @param chart {chart} the chart we are returning items from
- * @param e {Event} the event we are find things at
- * @param options {IInteractionOptions} options to use
- * @return {Chart.Element[]} Array of elements that are under the point. If none are found, an empty array is returned
- */
- x: function(chart, e, options) {
- var position = getRelativePosition(e, chart);
- var items = [];
- var intersectsItem = false;
-
- parseVisibleItems(chart, function(element) {
- if (element.inXRange(position.x)) {
- items.push(element);
- }
-
- if (element.inRange(position.x, position.y)) {
- intersectsItem = true;
- }
- });
-
- // If we want to trigger on an intersect and we don't have any items
- // that intersect the position, return nothing
- if (options.intersect && !intersectsItem) {
- items = [];
- }
- return items;
- },
-
- /**
- * y mode returns the elements that hit-test at the current y coordinate
- * @function Chart.Interaction.modes.y
- * @param chart {chart} the chart we are returning items from
- * @param e {Event} the event we are find things at
- * @param options {IInteractionOptions} options to use
- * @return {Chart.Element[]} Array of elements that are under the point. If none are found, an empty array is returned
- */
- y: function(chart, e, options) {
- var position = getRelativePosition(e, chart);
- var items = [];
- var intersectsItem = false;
-
- parseVisibleItems(chart, function(element) {
- if (element.inYRange(position.y)) {
- items.push(element);
- }
-
- if (element.inRange(position.x, position.y)) {
- intersectsItem = true;
- }
- });
-
- // If we want to trigger on an intersect and we don't have any items
- // that intersect the position, return nothing
- if (options.intersect && !intersectsItem) {
- items = [];
- }
- return items;
- }
- }
-};
-
-},{"46":46}],30:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-
-defaults._set('global', {
- responsive: true,
- responsiveAnimationDuration: 0,
- maintainAspectRatio: true,
- events: ['mousemove', 'mouseout', 'click', 'touchstart', 'touchmove'],
- hover: {
- onHover: null,
- mode: 'nearest',
- intersect: true,
- animationDuration: 400
- },
- onClick: null,
- defaultColor: 'rgba(0,0,0,0.1)',
- defaultFontColor: '#666',
- defaultFontFamily: "'Helvetica Neue', 'Helvetica', 'Arial', sans-serif",
- defaultFontSize: 12,
- defaultFontStyle: 'normal',
- showLines: true,
-
- // Element defaults defined in element extensions
- elements: {},
-
- // Layout options such as padding
- layout: {
- padding: {
- top: 0,
- right: 0,
- bottom: 0,
- left: 0
- }
- }
-});
-
-module.exports = function() {
-
- // Occupy the global variable of Chart, and create a simple base class
- var Chart = function(item, config) {
- this.construct(item, config);
- return this;
- };
-
- Chart.Chart = Chart;
-
- return Chart;
-};
-
-},{"26":26}],31:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-
-function filterByPosition(array, position) {
- return helpers.where(array, function(v) {
- return v.position === position;
- });
-}
-
-function sortByWeight(array, reverse) {
- array.forEach(function(v, i) {
- v._tmpIndex_ = i;
- return v;
- });
- array.sort(function(a, b) {
- var v0 = reverse ? b : a;
- var v1 = reverse ? a : b;
- return v0.weight === v1.weight ?
- v0._tmpIndex_ - v1._tmpIndex_ :
- v0.weight - v1.weight;
- });
- array.forEach(function(v) {
- delete v._tmpIndex_;
- });
-}
-
-/**
- * @interface ILayoutItem
- * @prop {String} position - The position of the item in the chart layout. Possible values are
- * 'left', 'top', 'right', 'bottom', and 'chartArea'
- * @prop {Number} weight - The weight used to sort the item. Higher weights are further away from the chart area
- * @prop {Boolean} fullWidth - if true, and the item is horizontal, then push vertical boxes down
- * @prop {Function} isHorizontal - returns true if the layout item is horizontal (ie. top or bottom)
- * @prop {Function} update - Takes two parameters: width and height. Returns size of item
- * @prop {Function} getPadding - Returns an object with padding on the edges
- * @prop {Number} width - Width of item. Must be valid after update()
- * @prop {Number} height - Height of item. Must be valid after update()
- * @prop {Number} left - Left edge of the item. Set by layout system and cannot be used in update
- * @prop {Number} top - Top edge of the item. Set by layout system and cannot be used in update
- * @prop {Number} right - Right edge of the item. Set by layout system and cannot be used in update
- * @prop {Number} bottom - Bottom edge of the item. Set by layout system and cannot be used in update
- */
-
-// The layout service is very self explanatory. It's responsible for the layout within a chart.
-// Scales, Legends and Plugins all rely on the layout service and can easily register to be placed anywhere they need
-// It is this service's responsibility of carrying out that layout.
-module.exports = {
- defaults: {},
-
- /**
- * Register a box to a chart.
- * A box is simply a reference to an object that requires layout. eg. Scales, Legend, Title.
- * @param {Chart} chart - the chart to use
- * @param {ILayoutItem} item - the item to add to be layed out
- */
- addBox: function(chart, item) {
- if (!chart.boxes) {
- chart.boxes = [];
- }
-
- // initialize item with default values
- item.fullWidth = item.fullWidth || false;
- item.position = item.position || 'top';
- item.weight = item.weight || 0;
-
- chart.boxes.push(item);
- },
-
- /**
- * Remove a layoutItem from a chart
- * @param {Chart} chart - the chart to remove the box from
- * @param {Object} layoutItem - the item to remove from the layout
- */
- removeBox: function(chart, layoutItem) {
- var index = chart.boxes ? chart.boxes.indexOf(layoutItem) : -1;
- if (index !== -1) {
- chart.boxes.splice(index, 1);
- }
- },
-
- /**
- * Sets (or updates) options on the given `item`.
- * @param {Chart} chart - the chart in which the item lives (or will be added to)
- * @param {Object} item - the item to configure with the given options
- * @param {Object} options - the new item options.
- */
- configure: function(chart, item, options) {
- var props = ['fullWidth', 'position', 'weight'];
- var ilen = props.length;
- var i = 0;
- var prop;
-
- for (; i < ilen; ++i) {
- prop = props[i];
- if (options.hasOwnProperty(prop)) {
- item[prop] = options[prop];
- }
- }
- },
-
- /**
- * Fits boxes of the given chart into the given size by having each box measure itself
- * then running a fitting algorithm
- * @param {Chart} chart - the chart
- * @param {Number} width - the width to fit into
- * @param {Number} height - the height to fit into
- */
- update: function(chart, width, height) {
- if (!chart) {
- return;
- }
-
- var layoutOptions = chart.options.layout || {};
- var padding = helpers.options.toPadding(layoutOptions.padding);
- var leftPadding = padding.left;
- var rightPadding = padding.right;
- var topPadding = padding.top;
- var bottomPadding = padding.bottom;
-
- var leftBoxes = filterByPosition(chart.boxes, 'left');
- var rightBoxes = filterByPosition(chart.boxes, 'right');
- var topBoxes = filterByPosition(chart.boxes, 'top');
- var bottomBoxes = filterByPosition(chart.boxes, 'bottom');
- var chartAreaBoxes = filterByPosition(chart.boxes, 'chartArea');
-
- // Sort boxes by weight. A higher weight is further away from the chart area
- sortByWeight(leftBoxes, true);
- sortByWeight(rightBoxes, false);
- sortByWeight(topBoxes, true);
- sortByWeight(bottomBoxes, false);
-
- // Essentially we now have any number of boxes on each of the 4 sides.
- // Our canvas looks like the following.
- // The areas L1 and L2 are the left axes. R1 is the right axis, T1 is the top axis and
- // B1 is the bottom axis
- // There are also 4 quadrant-like locations (left to right instead of clockwise) reserved for chart overlays
- // These locations are single-box locations only, when trying to register a chartArea location that is already taken,
- // an error will be thrown.
- //
- // |----------------------------------------------------|
- // | T1 (Full Width) |
- // |----------------------------------------------------|
- // | | | T2 | |
- // | |----|-------------------------------------|----|
- // | | | C1 | | C2 | |
- // | | |----| |----| |
- // | | | | |
- // | L1 | L2 | ChartArea (C0) | R1 |
- // | | | | |
- // | | |----| |----| |
- // | | | C3 | | C4 | |
- // | |----|-------------------------------------|----|
- // | | | B1 | |
- // |----------------------------------------------------|
- // | B2 (Full Width) |
- // |----------------------------------------------------|
- //
- // What we do to find the best sizing, we do the following
- // 1. Determine the minimum size of the chart area.
- // 2. Split the remaining width equally between each vertical axis
- // 3. Split the remaining height equally between each horizontal axis
- // 4. Give each layout the maximum size it can be. The layout will return it's minimum size
- // 5. Adjust the sizes of each axis based on it's minimum reported size.
- // 6. Refit each axis
- // 7. Position each axis in the final location
- // 8. Tell the chart the final location of the chart area
- // 9. Tell any axes that overlay the chart area the positions of the chart area
-
- // Step 1
- var chartWidth = width - leftPadding - rightPadding;
- var chartHeight = height - topPadding - bottomPadding;
- var chartAreaWidth = chartWidth / 2; // min 50%
- var chartAreaHeight = chartHeight / 2; // min 50%
-
- // Step 2
- var verticalBoxWidth = (width - chartAreaWidth) / (leftBoxes.length + rightBoxes.length);
-
- // Step 3
- var horizontalBoxHeight = (height - chartAreaHeight) / (topBoxes.length + bottomBoxes.length);
-
- // Step 4
- var maxChartAreaWidth = chartWidth;
- var maxChartAreaHeight = chartHeight;
- var minBoxSizes = [];
-
- function getMinimumBoxSize(box) {
- var minSize;
- var isHorizontal = box.isHorizontal();
-
- if (isHorizontal) {
- minSize = box.update(box.fullWidth ? chartWidth : maxChartAreaWidth, horizontalBoxHeight);
- maxChartAreaHeight -= minSize.height;
- } else {
- minSize = box.update(verticalBoxWidth, maxChartAreaHeight);
- maxChartAreaWidth -= minSize.width;
- }
-
- minBoxSizes.push({
- horizontal: isHorizontal,
- minSize: minSize,
- box: box,
- });
- }
-
- helpers.each(leftBoxes.concat(rightBoxes, topBoxes, bottomBoxes), getMinimumBoxSize);
-
- // If a horizontal box has padding, we move the left boxes over to avoid ugly charts (see issue #2478)
- var maxHorizontalLeftPadding = 0;
- var maxHorizontalRightPadding = 0;
- var maxVerticalTopPadding = 0;
- var maxVerticalBottomPadding = 0;
-
- helpers.each(topBoxes.concat(bottomBoxes), function(horizontalBox) {
- if (horizontalBox.getPadding) {
- var boxPadding = horizontalBox.getPadding();
- maxHorizontalLeftPadding = Math.max(maxHorizontalLeftPadding, boxPadding.left);
- maxHorizontalRightPadding = Math.max(maxHorizontalRightPadding, boxPadding.right);
- }
- });
-
- helpers.each(leftBoxes.concat(rightBoxes), function(verticalBox) {
- if (verticalBox.getPadding) {
- var boxPadding = verticalBox.getPadding();
- maxVerticalTopPadding = Math.max(maxVerticalTopPadding, boxPadding.top);
- maxVerticalBottomPadding = Math.max(maxVerticalBottomPadding, boxPadding.bottom);
- }
- });
-
- // At this point, maxChartAreaHeight and maxChartAreaWidth are the size the chart area could
- // be if the axes are drawn at their minimum sizes.
- // Steps 5 & 6
- var totalLeftBoxesWidth = leftPadding;
- var totalRightBoxesWidth = rightPadding;
- var totalTopBoxesHeight = topPadding;
- var totalBottomBoxesHeight = bottomPadding;
-
- // Function to fit a box
- function fitBox(box) {
- var minBoxSize = helpers.findNextWhere(minBoxSizes, function(minBox) {
- return minBox.box === box;
- });
-
- if (minBoxSize) {
- if (box.isHorizontal()) {
- var scaleMargin = {
- left: Math.max(totalLeftBoxesWidth, maxHorizontalLeftPadding),
- right: Math.max(totalRightBoxesWidth, maxHorizontalRightPadding),
- top: 0,
- bottom: 0
- };
-
- // Don't use min size here because of label rotation. When the labels are rotated, their rotation highly depends
- // on the margin. Sometimes they need to increase in size slightly
- box.update(box.fullWidth ? chartWidth : maxChartAreaWidth, chartHeight / 2, scaleMargin);
- } else {
- box.update(minBoxSize.minSize.width, maxChartAreaHeight);
- }
- }
- }
-
- // Update, and calculate the left and right margins for the horizontal boxes
- helpers.each(leftBoxes.concat(rightBoxes), fitBox);
-
- helpers.each(leftBoxes, function(box) {
- totalLeftBoxesWidth += box.width;
- });
-
- helpers.each(rightBoxes, function(box) {
- totalRightBoxesWidth += box.width;
- });
-
- // Set the Left and Right margins for the horizontal boxes
- helpers.each(topBoxes.concat(bottomBoxes), fitBox);
-
- // Figure out how much margin is on the top and bottom of the vertical boxes
- helpers.each(topBoxes, function(box) {
- totalTopBoxesHeight += box.height;
- });
-
- helpers.each(bottomBoxes, function(box) {
- totalBottomBoxesHeight += box.height;
- });
-
- function finalFitVerticalBox(box) {
- var minBoxSize = helpers.findNextWhere(minBoxSizes, function(minSize) {
- return minSize.box === box;
- });
-
- var scaleMargin = {
- left: 0,
- right: 0,
- top: totalTopBoxesHeight,
- bottom: totalBottomBoxesHeight
- };
-
- if (minBoxSize) {
- box.update(minBoxSize.minSize.width, maxChartAreaHeight, scaleMargin);
- }
- }
-
- // Let the left layout know the final margin
- helpers.each(leftBoxes.concat(rightBoxes), finalFitVerticalBox);
-
- // Recalculate because the size of each layout might have changed slightly due to the margins (label rotation for instance)
- totalLeftBoxesWidth = leftPadding;
- totalRightBoxesWidth = rightPadding;
- totalTopBoxesHeight = topPadding;
- totalBottomBoxesHeight = bottomPadding;
-
- helpers.each(leftBoxes, function(box) {
- totalLeftBoxesWidth += box.width;
- });
-
- helpers.each(rightBoxes, function(box) {
- totalRightBoxesWidth += box.width;
- });
-
- helpers.each(topBoxes, function(box) {
- totalTopBoxesHeight += box.height;
- });
- helpers.each(bottomBoxes, function(box) {
- totalBottomBoxesHeight += box.height;
- });
-
- // We may be adding some padding to account for rotated x axis labels
- var leftPaddingAddition = Math.max(maxHorizontalLeftPadding - totalLeftBoxesWidth, 0);
- totalLeftBoxesWidth += leftPaddingAddition;
- totalRightBoxesWidth += Math.max(maxHorizontalRightPadding - totalRightBoxesWidth, 0);
-
- var topPaddingAddition = Math.max(maxVerticalTopPadding - totalTopBoxesHeight, 0);
- totalTopBoxesHeight += topPaddingAddition;
- totalBottomBoxesHeight += Math.max(maxVerticalBottomPadding - totalBottomBoxesHeight, 0);
-
- // Figure out if our chart area changed. This would occur if the dataset layout label rotation
- // changed due to the application of the margins in step 6. Since we can only get bigger, this is safe to do
- // without calling `fit` again
- var newMaxChartAreaHeight = height - totalTopBoxesHeight - totalBottomBoxesHeight;
- var newMaxChartAreaWidth = width - totalLeftBoxesWidth - totalRightBoxesWidth;
-
- if (newMaxChartAreaWidth !== maxChartAreaWidth || newMaxChartAreaHeight !== maxChartAreaHeight) {
- helpers.each(leftBoxes, function(box) {
- box.height = newMaxChartAreaHeight;
- });
-
- helpers.each(rightBoxes, function(box) {
- box.height = newMaxChartAreaHeight;
- });
-
- helpers.each(topBoxes, function(box) {
- if (!box.fullWidth) {
- box.width = newMaxChartAreaWidth;
- }
- });
-
- helpers.each(bottomBoxes, function(box) {
- if (!box.fullWidth) {
- box.width = newMaxChartAreaWidth;
- }
- });
-
- maxChartAreaHeight = newMaxChartAreaHeight;
- maxChartAreaWidth = newMaxChartAreaWidth;
- }
-
- // Step 7 - Position the boxes
- var left = leftPadding + leftPaddingAddition;
- var top = topPadding + topPaddingAddition;
-
- function placeBox(box) {
- if (box.isHorizontal()) {
- box.left = box.fullWidth ? leftPadding : totalLeftBoxesWidth;
- box.right = box.fullWidth ? width - rightPadding : totalLeftBoxesWidth + maxChartAreaWidth;
- box.top = top;
- box.bottom = top + box.height;
-
- // Move to next point
- top = box.bottom;
-
- } else {
-
- box.left = left;
- box.right = left + box.width;
- box.top = totalTopBoxesHeight;
- box.bottom = totalTopBoxesHeight + maxChartAreaHeight;
-
- // Move to next point
- left = box.right;
- }
- }
-
- helpers.each(leftBoxes.concat(topBoxes), placeBox);
-
- // Account for chart width and height
- left += maxChartAreaWidth;
- top += maxChartAreaHeight;
-
- helpers.each(rightBoxes, placeBox);
- helpers.each(bottomBoxes, placeBox);
-
- // Step 8
- chart.chartArea = {
- left: totalLeftBoxesWidth,
- top: totalTopBoxesHeight,
- right: totalLeftBoxesWidth + maxChartAreaWidth,
- bottom: totalTopBoxesHeight + maxChartAreaHeight
- };
-
- // Step 9
- helpers.each(chartAreaBoxes, function(box) {
- box.left = chart.chartArea.left;
- box.top = chart.chartArea.top;
- box.right = chart.chartArea.right;
- box.bottom = chart.chartArea.bottom;
-
- box.update(maxChartAreaWidth, maxChartAreaHeight);
- });
- }
-};
-
-},{"46":46}],32:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var helpers = require(46);
-
-defaults._set('global', {
- plugins: {}
-});
-
-/**
- * The plugin service singleton
- * @namespace Chart.plugins
- * @since 2.1.0
- */
-module.exports = {
- /**
- * Globally registered plugins.
- * @private
- */
- _plugins: [],
-
- /**
- * This identifier is used to invalidate the descriptors cache attached to each chart
- * when a global plugin is registered or unregistered. In this case, the cache ID is
- * incremented and descriptors are regenerated during following API calls.
- * @private
- */
- _cacheId: 0,
-
- /**
- * Registers the given plugin(s) if not already registered.
- * @param {Array|Object} plugins plugin instance(s).
- */
- register: function(plugins) {
- var p = this._plugins;
- ([]).concat(plugins).forEach(function(plugin) {
- if (p.indexOf(plugin) === -1) {
- p.push(plugin);
- }
- });
-
- this._cacheId++;
- },
-
- /**
- * Unregisters the given plugin(s) only if registered.
- * @param {Array|Object} plugins plugin instance(s).
- */
- unregister: function(plugins) {
- var p = this._plugins;
- ([]).concat(plugins).forEach(function(plugin) {
- var idx = p.indexOf(plugin);
- if (idx !== -1) {
- p.splice(idx, 1);
- }
- });
-
- this._cacheId++;
- },
-
- /**
- * Remove all registered plugins.
- * @since 2.1.5
- */
- clear: function() {
- this._plugins = [];
- this._cacheId++;
- },
-
- /**
- * Returns the number of registered plugins?
- * @returns {Number}
- * @since 2.1.5
- */
- count: function() {
- return this._plugins.length;
- },
-
- /**
- * Returns all registered plugin instances.
- * @returns {Array} array of plugin objects.
- * @since 2.1.5
- */
- getAll: function() {
- return this._plugins;
- },
-
- /**
- * Calls enabled plugins for `chart` on the specified hook and with the given args.
- * This method immediately returns as soon as a plugin explicitly returns false. The
- * returned value can be used, for instance, to interrupt the current action.
- * @param {Object} chart - The chart instance for which plugins should be called.
- * @param {String} hook - The name of the plugin method to call (e.g. 'beforeUpdate').
- * @param {Array} [args] - Extra arguments to apply to the hook call.
- * @returns {Boolean} false if any of the plugins return false, else returns true.
- */
- notify: function(chart, hook, args) {
- var descriptors = this.descriptors(chart);
- var ilen = descriptors.length;
- var i, descriptor, plugin, params, method;
-
- for (i = 0; i < ilen; ++i) {
- descriptor = descriptors[i];
- plugin = descriptor.plugin;
- method = plugin[hook];
- if (typeof method === 'function') {
- params = [chart].concat(args || []);
- params.push(descriptor.options);
- if (method.apply(plugin, params) === false) {
- return false;
- }
- }
- }
-
- return true;
- },
-
- /**
- * Returns descriptors of enabled plugins for the given chart.
- * @returns {Array} [{ plugin, options }]
- * @private
- */
- descriptors: function(chart) {
- var cache = chart.$plugins || (chart.$plugins = {});
- if (cache.id === this._cacheId) {
- return cache.descriptors;
- }
-
- var plugins = [];
- var descriptors = [];
- var config = (chart && chart.config) || {};
- var options = (config.options && config.options.plugins) || {};
-
- this._plugins.concat(config.plugins || []).forEach(function(plugin) {
- var idx = plugins.indexOf(plugin);
- if (idx !== -1) {
- return;
- }
-
- var id = plugin.id;
- var opts = options[id];
- if (opts === false) {
- return;
- }
-
- if (opts === true) {
- opts = helpers.clone(defaults.global.plugins[id]);
- }
-
- plugins.push(plugin);
- descriptors.push({
- plugin: plugin,
- options: opts || {}
- });
- });
-
- cache.descriptors = descriptors;
- cache.id = this._cacheId;
- return descriptors;
- },
-
- /**
- * Invalidates cache for the given chart: descriptors hold a reference on plugin option,
- * but in some cases, this reference can be changed by the user when updating options.
- * https://github.com/chartjs/Chart.js/issues/5111#issuecomment-355934167
- * @private
- */
- _invalidate: function(chart) {
- delete chart.$plugins;
- }
-};
-
-/**
- * Plugin extension hooks.
- * @interface IPlugin
- * @since 2.1.0
- */
-/**
- * @method IPlugin#beforeInit
- * @desc Called before initializing `chart`.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#afterInit
- * @desc Called after `chart` has been initialized and before the first update.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeUpdate
- * @desc Called before updating `chart`. If any plugin returns `false`, the update
- * is cancelled (and thus subsequent render(s)) until another `update` is triggered.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart update.
- */
-/**
- * @method IPlugin#afterUpdate
- * @desc Called after `chart` has been updated and before rendering. Note that this
- * hook will not be called if the chart update has been previously cancelled.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeDatasetsUpdate
- * @desc Called before updating the `chart` datasets. If any plugin returns `false`,
- * the datasets update is cancelled until another `update` is triggered.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} false to cancel the datasets update.
- * @since version 2.1.5
-*/
-/**
- * @method IPlugin#afterDatasetsUpdate
- * @desc Called after the `chart` datasets have been updated. Note that this hook
- * will not be called if the datasets update has been previously cancelled.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- * @since version 2.1.5
- */
-/**
- * @method IPlugin#beforeDatasetUpdate
- * @desc Called before updating the `chart` dataset at the given `args.index`. If any plugin
- * returns `false`, the datasets update is cancelled until another `update` is triggered.
- * @param {Chart} chart - The chart instance.
- * @param {Object} args - The call arguments.
- * @param {Number} args.index - The dataset index.
- * @param {Object} args.meta - The dataset metadata.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart datasets drawing.
- */
-/**
- * @method IPlugin#afterDatasetUpdate
- * @desc Called after the `chart` datasets at the given `args.index` has been updated. Note
- * that this hook will not be called if the datasets update has been previously cancelled.
- * @param {Chart} chart - The chart instance.
- * @param {Object} args - The call arguments.
- * @param {Number} args.index - The dataset index.
- * @param {Object} args.meta - The dataset metadata.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeLayout
- * @desc Called before laying out `chart`. If any plugin returns `false`,
- * the layout update is cancelled until another `update` is triggered.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart layout.
- */
-/**
- * @method IPlugin#afterLayout
- * @desc Called after the `chart` has been layed out. Note that this hook will not
- * be called if the layout update has been previously cancelled.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeRender
- * @desc Called before rendering `chart`. If any plugin returns `false`,
- * the rendering is cancelled until another `render` is triggered.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart rendering.
- */
-/**
- * @method IPlugin#afterRender
- * @desc Called after the `chart` has been fully rendered (and animation completed). Note
- * that this hook will not be called if the rendering has been previously cancelled.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeDraw
- * @desc Called before drawing `chart` at every animation frame specified by the given
- * easing value. If any plugin returns `false`, the frame drawing is cancelled until
- * another `render` is triggered.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Number} easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart drawing.
- */
-/**
- * @method IPlugin#afterDraw
- * @desc Called after the `chart` has been drawn for the specific easing value. Note
- * that this hook will not be called if the drawing has been previously cancelled.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Number} easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeDatasetsDraw
- * @desc Called before drawing the `chart` datasets. If any plugin returns `false`,
- * the datasets drawing is cancelled until another `render` is triggered.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Number} easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart datasets drawing.
- */
-/**
- * @method IPlugin#afterDatasetsDraw
- * @desc Called after the `chart` datasets have been drawn. Note that this hook
- * will not be called if the datasets drawing has been previously cancelled.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Number} easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeDatasetDraw
- * @desc Called before drawing the `chart` dataset at the given `args.index` (datasets
- * are drawn in the reverse order). If any plugin returns `false`, the datasets drawing
- * is cancelled until another `render` is triggered.
- * @param {Chart} chart - The chart instance.
- * @param {Object} args - The call arguments.
- * @param {Number} args.index - The dataset index.
- * @param {Object} args.meta - The dataset metadata.
- * @param {Number} args.easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart datasets drawing.
- */
-/**
- * @method IPlugin#afterDatasetDraw
- * @desc Called after the `chart` datasets at the given `args.index` have been drawn
- * (datasets are drawn in the reverse order). Note that this hook will not be called
- * if the datasets drawing has been previously cancelled.
- * @param {Chart} chart - The chart instance.
- * @param {Object} args - The call arguments.
- * @param {Number} args.index - The dataset index.
- * @param {Object} args.meta - The dataset metadata.
- * @param {Number} args.easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeTooltipDraw
- * @desc Called before drawing the `tooltip`. If any plugin returns `false`,
- * the tooltip drawing is cancelled until another `render` is triggered.
- * @param {Chart} chart - The chart instance.
- * @param {Object} args - The call arguments.
- * @param {Object} args.tooltip - The tooltip.
- * @param {Number} args.easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- * @returns {Boolean} `false` to cancel the chart tooltip drawing.
- */
-/**
- * @method IPlugin#afterTooltipDraw
- * @desc Called after drawing the `tooltip`. Note that this hook will not
- * be called if the tooltip drawing has been previously cancelled.
- * @param {Chart} chart - The chart instance.
- * @param {Object} args - The call arguments.
- * @param {Object} args.tooltip - The tooltip.
- * @param {Number} args.easingValue - The current animation value, between 0.0 and 1.0.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#beforeEvent
- * @desc Called before processing the specified `event`. If any plugin returns `false`,
- * the event will be discarded.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {IEvent} event - The event object.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#afterEvent
- * @desc Called after the `event` has been consumed. Note that this hook
- * will not be called if the `event` has been previously discarded.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {IEvent} event - The event object.
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#resize
- * @desc Called after the chart as been resized.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Number} size - The new canvas display size (eq. canvas.style width & height).
- * @param {Object} options - The plugin options.
- */
-/**
- * @method IPlugin#destroy
- * @desc Called after the chart as been destroyed.
- * @param {Chart.Controller} chart - The chart instance.
- * @param {Object} options - The plugin options.
- */
-
-},{"26":26,"46":46}],33:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-var helpers = require(46);
-var Ticks = require(35);
-
-defaults._set('scale', {
- display: true,
- position: 'left',
- offset: false,
-
- // grid line settings
- gridLines: {
- display: true,
- color: 'rgba(0, 0, 0, 0.1)',
- lineWidth: 1,
- drawBorder: true,
- drawOnChartArea: true,
- drawTicks: true,
- tickMarkLength: 10,
- zeroLineWidth: 1,
- zeroLineColor: 'rgba(0,0,0,0.25)',
- zeroLineBorderDash: [],
- zeroLineBorderDashOffset: 0.0,
- offsetGridLines: false,
- borderDash: [],
- borderDashOffset: 0.0
- },
-
- // scale label
- scaleLabel: {
- // display property
- display: false,
-
- // actual label
- labelString: '',
-
- // line height
- lineHeight: 1.2,
-
- // top/bottom padding
- padding: {
- top: 4,
- bottom: 4
- }
- },
-
- // label settings
- ticks: {
- beginAtZero: false,
- minRotation: 0,
- maxRotation: 50,
- mirror: false,
- padding: 0,
- reverse: false,
- display: true,
- autoSkip: true,
- autoSkipPadding: 0,
- labelOffset: 0,
- // We pass through arrays to be rendered as multiline labels, we convert Others to strings here.
- callback: Ticks.formatters.values,
- minor: {},
- major: {}
- }
-});
-
-function labelsFromTicks(ticks) {
- var labels = [];
- var i, ilen;
-
- for (i = 0, ilen = ticks.length; i < ilen; ++i) {
- labels.push(ticks[i].label);
- }
-
- return labels;
-}
-
-function getLineValue(scale, index, offsetGridLines) {
- var lineValue = scale.getPixelForTick(index);
-
- if (offsetGridLines) {
- if (index === 0) {
- lineValue -= (scale.getPixelForTick(1) - lineValue) / 2;
- } else {
- lineValue -= (lineValue - scale.getPixelForTick(index - 1)) / 2;
- }
- }
- return lineValue;
-}
-
-function computeTextSize(context, tick, font) {
- return helpers.isArray(tick) ?
- helpers.longestText(context, font, tick) :
- context.measureText(tick).width;
-}
-
-function parseFontOptions(options) {
- var valueOrDefault = helpers.valueOrDefault;
- var globalDefaults = defaults.global;
- var size = valueOrDefault(options.fontSize, globalDefaults.defaultFontSize);
- var style = valueOrDefault(options.fontStyle, globalDefaults.defaultFontStyle);
- var family = valueOrDefault(options.fontFamily, globalDefaults.defaultFontFamily);
-
- return {
- size: size,
- style: style,
- family: family,
- font: helpers.fontString(size, style, family)
- };
-}
-
-function parseLineHeight(options) {
- return helpers.options.toLineHeight(
- helpers.valueOrDefault(options.lineHeight, 1.2),
- helpers.valueOrDefault(options.fontSize, defaults.global.defaultFontSize));
-}
-
-module.exports = Element.extend({
- /**
- * Get the padding needed for the scale
- * @method getPadding
- * @private
- * @returns {Padding} the necessary padding
- */
- getPadding: function() {
- var me = this;
- return {
- left: me.paddingLeft || 0,
- top: me.paddingTop || 0,
- right: me.paddingRight || 0,
- bottom: me.paddingBottom || 0
- };
- },
-
- /**
- * Returns the scale tick objects ({label, major})
- * @since 2.7
- */
- getTicks: function() {
- return this._ticks;
- },
-
- // These methods are ordered by lifecyle. Utilities then follow.
- // Any function defined here is inherited by all scale types.
- // Any function can be extended by the scale type
-
- mergeTicksOptions: function() {
- var ticks = this.options.ticks;
- if (ticks.minor === false) {
- ticks.minor = {
- display: false
- };
- }
- if (ticks.major === false) {
- ticks.major = {
- display: false
- };
- }
- for (var key in ticks) {
- if (key !== 'major' && key !== 'minor') {
- if (typeof ticks.minor[key] === 'undefined') {
- ticks.minor[key] = ticks[key];
- }
- if (typeof ticks.major[key] === 'undefined') {
- ticks.major[key] = ticks[key];
- }
- }
- }
- },
- beforeUpdate: function() {
- helpers.callback(this.options.beforeUpdate, [this]);
- },
-
- update: function(maxWidth, maxHeight, margins) {
- var me = this;
- var i, ilen, labels, label, ticks, tick;
-
- // Update Lifecycle - Probably don't want to ever extend or overwrite this function ;)
- me.beforeUpdate();
-
- // Absorb the master measurements
- me.maxWidth = maxWidth;
- me.maxHeight = maxHeight;
- me.margins = helpers.extend({
- left: 0,
- right: 0,
- top: 0,
- bottom: 0
- }, margins);
- me.longestTextCache = me.longestTextCache || {};
-
- // Dimensions
- me.beforeSetDimensions();
- me.setDimensions();
- me.afterSetDimensions();
-
- // Data min/max
- me.beforeDataLimits();
- me.determineDataLimits();
- me.afterDataLimits();
-
- // Ticks - `this.ticks` is now DEPRECATED!
- // Internal ticks are now stored as objects in the PRIVATE `this._ticks` member
- // and must not be accessed directly from outside this class. `this.ticks` being
- // around for long time and not marked as private, we can't change its structure
- // without unexpected breaking changes. If you need to access the scale ticks,
- // use scale.getTicks() instead.
-
- me.beforeBuildTicks();
-
- // New implementations should return an array of objects but for BACKWARD COMPAT,
- // we still support no return (`this.ticks` internally set by calling this method).
- ticks = me.buildTicks() || [];
-
- me.afterBuildTicks();
-
- me.beforeTickToLabelConversion();
-
- // New implementations should return the formatted tick labels but for BACKWARD
- // COMPAT, we still support no return (`this.ticks` internally changed by calling
- // this method and supposed to contain only string values).
- labels = me.convertTicksToLabels(ticks) || me.ticks;
-
- me.afterTickToLabelConversion();
-
- me.ticks = labels; // BACKWARD COMPATIBILITY
-
- // IMPORTANT: from this point, we consider that `this.ticks` will NEVER change!
-
- // BACKWARD COMPAT: synchronize `_ticks` with labels (so potentially `this.ticks`)
- for (i = 0, ilen = labels.length; i < ilen; ++i) {
- label = labels[i];
- tick = ticks[i];
- if (!tick) {
- ticks.push(tick = {
- label: label,
- major: false
- });
- } else {
- tick.label = label;
- }
- }
-
- me._ticks = ticks;
-
- // Tick Rotation
- me.beforeCalculateTickRotation();
- me.calculateTickRotation();
- me.afterCalculateTickRotation();
- // Fit
- me.beforeFit();
- me.fit();
- me.afterFit();
- //
- me.afterUpdate();
-
- return me.minSize;
-
- },
- afterUpdate: function() {
- helpers.callback(this.options.afterUpdate, [this]);
- },
-
- //
-
- beforeSetDimensions: function() {
- helpers.callback(this.options.beforeSetDimensions, [this]);
- },
- setDimensions: function() {
- var me = this;
- // Set the unconstrained dimension before label rotation
- if (me.isHorizontal()) {
- // Reset position before calculating rotation
- me.width = me.maxWidth;
- me.left = 0;
- me.right = me.width;
- } else {
- me.height = me.maxHeight;
-
- // Reset position before calculating rotation
- me.top = 0;
- me.bottom = me.height;
- }
-
- // Reset padding
- me.paddingLeft = 0;
- me.paddingTop = 0;
- me.paddingRight = 0;
- me.paddingBottom = 0;
- },
- afterSetDimensions: function() {
- helpers.callback(this.options.afterSetDimensions, [this]);
- },
-
- // Data limits
- beforeDataLimits: function() {
- helpers.callback(this.options.beforeDataLimits, [this]);
- },
- determineDataLimits: helpers.noop,
- afterDataLimits: function() {
- helpers.callback(this.options.afterDataLimits, [this]);
- },
-
- //
- beforeBuildTicks: function() {
- helpers.callback(this.options.beforeBuildTicks, [this]);
- },
- buildTicks: helpers.noop,
- afterBuildTicks: function() {
- helpers.callback(this.options.afterBuildTicks, [this]);
- },
-
- beforeTickToLabelConversion: function() {
- helpers.callback(this.options.beforeTickToLabelConversion, [this]);
- },
- convertTicksToLabels: function() {
- var me = this;
- // Convert ticks to strings
- var tickOpts = me.options.ticks;
- me.ticks = me.ticks.map(tickOpts.userCallback || tickOpts.callback, this);
- },
- afterTickToLabelConversion: function() {
- helpers.callback(this.options.afterTickToLabelConversion, [this]);
- },
-
- //
-
- beforeCalculateTickRotation: function() {
- helpers.callback(this.options.beforeCalculateTickRotation, [this]);
- },
- calculateTickRotation: function() {
- var me = this;
- var context = me.ctx;
- var tickOpts = me.options.ticks;
- var labels = labelsFromTicks(me._ticks);
-
- // Get the width of each grid by calculating the difference
- // between x offsets between 0 and 1.
- var tickFont = parseFontOptions(tickOpts);
- context.font = tickFont.font;
-
- var labelRotation = tickOpts.minRotation || 0;
-
- if (labels.length && me.options.display && me.isHorizontal()) {
- var originalLabelWidth = helpers.longestText(context, tickFont.font, labels, me.longestTextCache);
- var labelWidth = originalLabelWidth;
- var cosRotation, sinRotation;
-
- // Allow 3 pixels x2 padding either side for label readability
- var tickWidth = me.getPixelForTick(1) - me.getPixelForTick(0) - 6;
-
- // Max label rotation can be set or default to 90 - also act as a loop counter
- while (labelWidth > tickWidth && labelRotation < tickOpts.maxRotation) {
- var angleRadians = helpers.toRadians(labelRotation);
- cosRotation = Math.cos(angleRadians);
- sinRotation = Math.sin(angleRadians);
-
- if (sinRotation * originalLabelWidth > me.maxHeight) {
- // go back one step
- labelRotation--;
- break;
- }
-
- labelRotation++;
- labelWidth = cosRotation * originalLabelWidth;
- }
- }
-
- me.labelRotation = labelRotation;
- },
- afterCalculateTickRotation: function() {
- helpers.callback(this.options.afterCalculateTickRotation, [this]);
- },
-
- //
-
- beforeFit: function() {
- helpers.callback(this.options.beforeFit, [this]);
- },
- fit: function() {
- var me = this;
- // Reset
- var minSize = me.minSize = {
- width: 0,
- height: 0
- };
-
- var labels = labelsFromTicks(me._ticks);
-
- var opts = me.options;
- var tickOpts = opts.ticks;
- var scaleLabelOpts = opts.scaleLabel;
- var gridLineOpts = opts.gridLines;
- var display = opts.display;
- var isHorizontal = me.isHorizontal();
-
- var tickFont = parseFontOptions(tickOpts);
- var tickMarkLength = opts.gridLines.tickMarkLength;
-
- // Width
- if (isHorizontal) {
- // subtract the margins to line up with the chartArea if we are a full width scale
- minSize.width = me.isFullWidth() ? me.maxWidth - me.margins.left - me.margins.right : me.maxWidth;
- } else {
- minSize.width = display && gridLineOpts.drawTicks ? tickMarkLength : 0;
- }
-
- // height
- if (isHorizontal) {
- minSize.height = display && gridLineOpts.drawTicks ? tickMarkLength : 0;
- } else {
- minSize.height = me.maxHeight; // fill all the height
- }
-
- // Are we showing a title for the scale?
- if (scaleLabelOpts.display && display) {
- var scaleLabelLineHeight = parseLineHeight(scaleLabelOpts);
- var scaleLabelPadding = helpers.options.toPadding(scaleLabelOpts.padding);
- var deltaHeight = scaleLabelLineHeight + scaleLabelPadding.height;
-
- if (isHorizontal) {
- minSize.height += deltaHeight;
- } else {
- minSize.width += deltaHeight;
- }
- }
-
- // Don't bother fitting the ticks if we are not showing them
- if (tickOpts.display && display) {
- var largestTextWidth = helpers.longestText(me.ctx, tickFont.font, labels, me.longestTextCache);
- var tallestLabelHeightInLines = helpers.numberOfLabelLines(labels);
- var lineSpace = tickFont.size * 0.5;
- var tickPadding = me.options.ticks.padding;
-
- if (isHorizontal) {
- // A horizontal axis is more constrained by the height.
- me.longestLabelWidth = largestTextWidth;
-
- var angleRadians = helpers.toRadians(me.labelRotation);
- var cosRotation = Math.cos(angleRadians);
- var sinRotation = Math.sin(angleRadians);
-
- // TODO - improve this calculation
- var labelHeight = (sinRotation * largestTextWidth)
- + (tickFont.size * tallestLabelHeightInLines)
- + (lineSpace * (tallestLabelHeightInLines - 1))
- + lineSpace; // padding
-
- minSize.height = Math.min(me.maxHeight, minSize.height + labelHeight + tickPadding);
-
- me.ctx.font = tickFont.font;
- var firstLabelWidth = computeTextSize(me.ctx, labels[0], tickFont.font);
- var lastLabelWidth = computeTextSize(me.ctx, labels[labels.length - 1], tickFont.font);
-
- // Ensure that our ticks are always inside the canvas. When rotated, ticks are right aligned
- // which means that the right padding is dominated by the font height
- if (me.labelRotation !== 0) {
- me.paddingLeft = opts.position === 'bottom' ? (cosRotation * firstLabelWidth) + 3 : (cosRotation * lineSpace) + 3; // add 3 px to move away from canvas edges
- me.paddingRight = opts.position === 'bottom' ? (cosRotation * lineSpace) + 3 : (cosRotation * lastLabelWidth) + 3;
- } else {
- me.paddingLeft = firstLabelWidth / 2 + 3; // add 3 px to move away from canvas edges
- me.paddingRight = lastLabelWidth / 2 + 3;
- }
- } else {
- // A vertical axis is more constrained by the width. Labels are the
- // dominant factor here, so get that length first and account for padding
- if (tickOpts.mirror) {
- largestTextWidth = 0;
- } else {
- // use lineSpace for consistency with horizontal axis
- // tickPadding is not implemented for horizontal
- largestTextWidth += tickPadding + lineSpace;
- }
-
- minSize.width = Math.min(me.maxWidth, minSize.width + largestTextWidth);
-
- me.paddingTop = tickFont.size / 2;
- me.paddingBottom = tickFont.size / 2;
- }
- }
-
- me.handleMargins();
-
- me.width = minSize.width;
- me.height = minSize.height;
- },
-
- /**
- * Handle margins and padding interactions
- * @private
- */
- handleMargins: function() {
- var me = this;
- if (me.margins) {
- me.paddingLeft = Math.max(me.paddingLeft - me.margins.left, 0);
- me.paddingTop = Math.max(me.paddingTop - me.margins.top, 0);
- me.paddingRight = Math.max(me.paddingRight - me.margins.right, 0);
- me.paddingBottom = Math.max(me.paddingBottom - me.margins.bottom, 0);
- }
- },
-
- afterFit: function() {
- helpers.callback(this.options.afterFit, [this]);
- },
-
- // Shared Methods
- isHorizontal: function() {
- return this.options.position === 'top' || this.options.position === 'bottom';
- },
- isFullWidth: function() {
- return (this.options.fullWidth);
- },
-
- // Get the correct value. NaN bad inputs, If the value type is object get the x or y based on whether we are horizontal or not
- getRightValue: function(rawValue) {
- // Null and undefined values first
- if (helpers.isNullOrUndef(rawValue)) {
- return NaN;
- }
- // isNaN(object) returns true, so make sure NaN is checking for a number; Discard Infinite values
- if (typeof rawValue === 'number' && !isFinite(rawValue)) {
- return NaN;
- }
- // If it is in fact an object, dive in one more level
- if (rawValue) {
- if (this.isHorizontal()) {
- if (rawValue.x !== undefined) {
- return this.getRightValue(rawValue.x);
- }
- } else if (rawValue.y !== undefined) {
- return this.getRightValue(rawValue.y);
- }
- }
-
- // Value is good, return it
- return rawValue;
- },
-
- /**
- * Used to get the value to display in the tooltip for the data at the given index
- * @param index
- * @param datasetIndex
- */
- getLabelForIndex: helpers.noop,
-
- /**
- * Returns the location of the given data point. Value can either be an index or a numerical value
- * The coordinate (0, 0) is at the upper-left corner of the canvas
- * @param value
- * @param index
- * @param datasetIndex
- */
- getPixelForValue: helpers.noop,
-
- /**
- * Used to get the data value from a given pixel. This is the inverse of getPixelForValue
- * The coordinate (0, 0) is at the upper-left corner of the canvas
- * @param pixel
- */
- getValueForPixel: helpers.noop,
-
- /**
- * Returns the location of the tick at the given index
- * The coordinate (0, 0) is at the upper-left corner of the canvas
- */
- getPixelForTick: function(index) {
- var me = this;
- var offset = me.options.offset;
- if (me.isHorizontal()) {
- var innerWidth = me.width - (me.paddingLeft + me.paddingRight);
- var tickWidth = innerWidth / Math.max((me._ticks.length - (offset ? 0 : 1)), 1);
- var pixel = (tickWidth * index) + me.paddingLeft;
-
- if (offset) {
- pixel += tickWidth / 2;
- }
-
- var finalVal = me.left + Math.round(pixel);
- finalVal += me.isFullWidth() ? me.margins.left : 0;
- return finalVal;
- }
- var innerHeight = me.height - (me.paddingTop + me.paddingBottom);
- return me.top + (index * (innerHeight / (me._ticks.length - 1)));
- },
-
- /**
- * Utility for getting the pixel location of a percentage of scale
- * The coordinate (0, 0) is at the upper-left corner of the canvas
- */
- getPixelForDecimal: function(decimal) {
- var me = this;
- if (me.isHorizontal()) {
- var innerWidth = me.width - (me.paddingLeft + me.paddingRight);
- var valueOffset = (innerWidth * decimal) + me.paddingLeft;
-
- var finalVal = me.left + Math.round(valueOffset);
- finalVal += me.isFullWidth() ? me.margins.left : 0;
- return finalVal;
- }
- return me.top + (decimal * me.height);
- },
-
- /**
- * Returns the pixel for the minimum chart value
- * The coordinate (0, 0) is at the upper-left corner of the canvas
- */
- getBasePixel: function() {
- return this.getPixelForValue(this.getBaseValue());
- },
-
- getBaseValue: function() {
- var me = this;
- var min = me.min;
- var max = me.max;
-
- return me.beginAtZero ? 0 :
- min < 0 && max < 0 ? max :
- min > 0 && max > 0 ? min :
- 0;
- },
-
- /**
- * Returns a subset of ticks to be plotted to avoid overlapping labels.
- * @private
- */
- _autoSkip: function(ticks) {
- var skipRatio;
- var me = this;
- var isHorizontal = me.isHorizontal();
- var optionTicks = me.options.ticks.minor;
- var tickCount = ticks.length;
- var labelRotationRadians = helpers.toRadians(me.labelRotation);
- var cosRotation = Math.cos(labelRotationRadians);
- var longestRotatedLabel = me.longestLabelWidth * cosRotation;
- var result = [];
- var i, tick, shouldSkip;
-
- // figure out the maximum number of gridlines to show
- var maxTicks;
- if (optionTicks.maxTicksLimit) {
- maxTicks = optionTicks.maxTicksLimit;
- }
-
- if (isHorizontal) {
- skipRatio = false;
-
- if ((longestRotatedLabel + optionTicks.autoSkipPadding) * tickCount > (me.width - (me.paddingLeft + me.paddingRight))) {
- skipRatio = 1 + Math.floor(((longestRotatedLabel + optionTicks.autoSkipPadding) * tickCount) / (me.width - (me.paddingLeft + me.paddingRight)));
- }
-
- // if they defined a max number of optionTicks,
- // increase skipRatio until that number is met
- if (maxTicks && tickCount > maxTicks) {
- skipRatio = Math.max(skipRatio, Math.floor(tickCount / maxTicks));
- }
- }
-
- for (i = 0; i < tickCount; i++) {
- tick = ticks[i];
-
- // Since we always show the last tick,we need may need to hide the last shown one before
- shouldSkip = (skipRatio > 1 && i % skipRatio > 0) || (i % skipRatio === 0 && i + skipRatio >= tickCount);
- if (shouldSkip && i !== tickCount - 1) {
- // leave tick in place but make sure it's not displayed (#4635)
- delete tick.label;
- }
- result.push(tick);
- }
- return result;
- },
-
- // Actually draw the scale on the canvas
- // @param {rectangle} chartArea : the area of the chart to draw full grid lines on
- draw: function(chartArea) {
- var me = this;
- var options = me.options;
- if (!options.display) {
- return;
- }
-
- var context = me.ctx;
- var globalDefaults = defaults.global;
- var optionTicks = options.ticks.minor;
- var optionMajorTicks = options.ticks.major || optionTicks;
- var gridLines = options.gridLines;
- var scaleLabel = options.scaleLabel;
-
- var isRotated = me.labelRotation !== 0;
- var isHorizontal = me.isHorizontal();
-
- var ticks = optionTicks.autoSkip ? me._autoSkip(me.getTicks()) : me.getTicks();
- var tickFontColor = helpers.valueOrDefault(optionTicks.fontColor, globalDefaults.defaultFontColor);
- var tickFont = parseFontOptions(optionTicks);
- var majorTickFontColor = helpers.valueOrDefault(optionMajorTicks.fontColor, globalDefaults.defaultFontColor);
- var majorTickFont = parseFontOptions(optionMajorTicks);
-
- var tl = gridLines.drawTicks ? gridLines.tickMarkLength : 0;
-
- var scaleLabelFontColor = helpers.valueOrDefault(scaleLabel.fontColor, globalDefaults.defaultFontColor);
- var scaleLabelFont = parseFontOptions(scaleLabel);
- var scaleLabelPadding = helpers.options.toPadding(scaleLabel.padding);
- var labelRotationRadians = helpers.toRadians(me.labelRotation);
-
- var itemsToDraw = [];
-
- var axisWidth = me.options.gridLines.lineWidth;
- var xTickStart = options.position === 'right' ? me.left : me.right - axisWidth - tl;
- var xTickEnd = options.position === 'right' ? me.left + tl : me.right;
- var yTickStart = options.position === 'bottom' ? me.top + axisWidth : me.bottom - tl - axisWidth;
- var yTickEnd = options.position === 'bottom' ? me.top + axisWidth + tl : me.bottom + axisWidth;
-
- helpers.each(ticks, function(tick, index) {
- // autoskipper skipped this tick (#4635)
- if (helpers.isNullOrUndef(tick.label)) {
- return;
- }
-
- var label = tick.label;
- var lineWidth, lineColor, borderDash, borderDashOffset;
- if (index === me.zeroLineIndex && options.offset === gridLines.offsetGridLines) {
- // Draw the first index specially
- lineWidth = gridLines.zeroLineWidth;
- lineColor = gridLines.zeroLineColor;
- borderDash = gridLines.zeroLineBorderDash;
- borderDashOffset = gridLines.zeroLineBorderDashOffset;
- } else {
- lineWidth = helpers.valueAtIndexOrDefault(gridLines.lineWidth, index);
- lineColor = helpers.valueAtIndexOrDefault(gridLines.color, index);
- borderDash = helpers.valueOrDefault(gridLines.borderDash, globalDefaults.borderDash);
- borderDashOffset = helpers.valueOrDefault(gridLines.borderDashOffset, globalDefaults.borderDashOffset);
- }
-
- // Common properties
- var tx1, ty1, tx2, ty2, x1, y1, x2, y2, labelX, labelY;
- var textAlign = 'middle';
- var textBaseline = 'middle';
- var tickPadding = optionTicks.padding;
-
- if (isHorizontal) {
- var labelYOffset = tl + tickPadding;
-
- if (options.position === 'bottom') {
- // bottom
- textBaseline = !isRotated ? 'top' : 'middle';
- textAlign = !isRotated ? 'center' : 'right';
- labelY = me.top + labelYOffset;
- } else {
- // top
- textBaseline = !isRotated ? 'bottom' : 'middle';
- textAlign = !isRotated ? 'center' : 'left';
- labelY = me.bottom - labelYOffset;
- }
-
- var xLineValue = getLineValue(me, index, gridLines.offsetGridLines && ticks.length > 1);
- if (xLineValue < me.left) {
- lineColor = 'rgba(0,0,0,0)';
- }
- xLineValue += helpers.aliasPixel(lineWidth);
-
- labelX = me.getPixelForTick(index) + optionTicks.labelOffset; // x values for optionTicks (need to consider offsetLabel option)
-
- tx1 = tx2 = x1 = x2 = xLineValue;
- ty1 = yTickStart;
- ty2 = yTickEnd;
- y1 = chartArea.top;
- y2 = chartArea.bottom + axisWidth;
- } else {
- var isLeft = options.position === 'left';
- var labelXOffset;
-
- if (optionTicks.mirror) {
- textAlign = isLeft ? 'left' : 'right';
- labelXOffset = tickPadding;
- } else {
- textAlign = isLeft ? 'right' : 'left';
- labelXOffset = tl + tickPadding;
- }
-
- labelX = isLeft ? me.right - labelXOffset : me.left + labelXOffset;
-
- var yLineValue = getLineValue(me, index, gridLines.offsetGridLines && ticks.length > 1);
- if (yLineValue < me.top) {
- lineColor = 'rgba(0,0,0,0)';
- }
- yLineValue += helpers.aliasPixel(lineWidth);
-
- labelY = me.getPixelForTick(index) + optionTicks.labelOffset;
-
- tx1 = xTickStart;
- tx2 = xTickEnd;
- x1 = chartArea.left;
- x2 = chartArea.right + axisWidth;
- ty1 = ty2 = y1 = y2 = yLineValue;
- }
-
- itemsToDraw.push({
- tx1: tx1,
- ty1: ty1,
- tx2: tx2,
- ty2: ty2,
- x1: x1,
- y1: y1,
- x2: x2,
- y2: y2,
- labelX: labelX,
- labelY: labelY,
- glWidth: lineWidth,
- glColor: lineColor,
- glBorderDash: borderDash,
- glBorderDashOffset: borderDashOffset,
- rotation: -1 * labelRotationRadians,
- label: label,
- major: tick.major,
- textBaseline: textBaseline,
- textAlign: textAlign
- });
- });
-
- // Draw all of the tick labels, tick marks, and grid lines at the correct places
- helpers.each(itemsToDraw, function(itemToDraw) {
- if (gridLines.display) {
- context.save();
- context.lineWidth = itemToDraw.glWidth;
- context.strokeStyle = itemToDraw.glColor;
- if (context.setLineDash) {
- context.setLineDash(itemToDraw.glBorderDash);
- context.lineDashOffset = itemToDraw.glBorderDashOffset;
- }
-
- context.beginPath();
-
- if (gridLines.drawTicks) {
- context.moveTo(itemToDraw.tx1, itemToDraw.ty1);
- context.lineTo(itemToDraw.tx2, itemToDraw.ty2);
- }
-
- if (gridLines.drawOnChartArea) {
- context.moveTo(itemToDraw.x1, itemToDraw.y1);
- context.lineTo(itemToDraw.x2, itemToDraw.y2);
- }
-
- context.stroke();
- context.restore();
- }
-
- if (optionTicks.display) {
- // Make sure we draw text in the correct color and font
- context.save();
- context.translate(itemToDraw.labelX, itemToDraw.labelY);
- context.rotate(itemToDraw.rotation);
- context.font = itemToDraw.major ? majorTickFont.font : tickFont.font;
- context.fillStyle = itemToDraw.major ? majorTickFontColor : tickFontColor;
- context.textBaseline = itemToDraw.textBaseline;
- context.textAlign = itemToDraw.textAlign;
-
- var label = itemToDraw.label;
- if (helpers.isArray(label)) {
- var lineCount = label.length;
- var lineHeight = tickFont.size * 1.5;
- var y = me.isHorizontal() ? 0 : -lineHeight * (lineCount - 1) / 2;
-
- for (var i = 0; i < lineCount; ++i) {
- // We just make sure the multiline element is a string here..
- context.fillText('' + label[i], 0, y);
- // apply same lineSpacing as calculated @ L#320
- y += lineHeight;
- }
- } else {
- context.fillText(label, 0, 0);
- }
- context.restore();
- }
- });
-
- if (scaleLabel.display) {
- // Draw the scale label
- var scaleLabelX;
- var scaleLabelY;
- var rotation = 0;
- var halfLineHeight = parseLineHeight(scaleLabel) / 2;
-
- if (isHorizontal) {
- scaleLabelX = me.left + ((me.right - me.left) / 2); // midpoint of the width
- scaleLabelY = options.position === 'bottom'
- ? me.bottom - halfLineHeight - scaleLabelPadding.bottom
- : me.top + halfLineHeight + scaleLabelPadding.top;
- } else {
- var isLeft = options.position === 'left';
- scaleLabelX = isLeft
- ? me.left + halfLineHeight + scaleLabelPadding.top
- : me.right - halfLineHeight - scaleLabelPadding.top;
- scaleLabelY = me.top + ((me.bottom - me.top) / 2);
- rotation = isLeft ? -0.5 * Math.PI : 0.5 * Math.PI;
- }
-
- context.save();
- context.translate(scaleLabelX, scaleLabelY);
- context.rotate(rotation);
- context.textAlign = 'center';
- context.textBaseline = 'middle';
- context.fillStyle = scaleLabelFontColor; // render in correct colour
- context.font = scaleLabelFont.font;
- context.fillText(scaleLabel.labelString, 0, 0);
- context.restore();
- }
-
- if (gridLines.drawBorder) {
- // Draw the line at the edge of the axis
- context.lineWidth = helpers.valueAtIndexOrDefault(gridLines.lineWidth, 0);
- context.strokeStyle = helpers.valueAtIndexOrDefault(gridLines.color, 0);
- var x1 = me.left;
- var x2 = me.right + axisWidth;
- var y1 = me.top;
- var y2 = me.bottom + axisWidth;
-
- var aliasPixel = helpers.aliasPixel(context.lineWidth);
- if (isHorizontal) {
- y1 = y2 = options.position === 'top' ? me.bottom : me.top;
- y1 += aliasPixel;
- y2 += aliasPixel;
- } else {
- x1 = x2 = options.position === 'left' ? me.right : me.left;
- x1 += aliasPixel;
- x2 += aliasPixel;
- }
-
- context.beginPath();
- context.moveTo(x1, y1);
- context.lineTo(x2, y2);
- context.stroke();
- }
- }
-});
-
-},{"26":26,"27":27,"35":35,"46":46}],34:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var helpers = require(46);
-var layouts = require(31);
-
-module.exports = {
- // Scale registration object. Extensions can register new scale types (such as log or DB scales) and then
- // use the new chart options to grab the correct scale
- constructors: {},
- // Use a registration function so that we can move to an ES6 map when we no longer need to support
- // old browsers
-
- // Scale config defaults
- defaults: {},
- registerScaleType: function(type, scaleConstructor, scaleDefaults) {
- this.constructors[type] = scaleConstructor;
- this.defaults[type] = helpers.clone(scaleDefaults);
- },
- getScaleConstructor: function(type) {
- return this.constructors.hasOwnProperty(type) ? this.constructors[type] : undefined;
- },
- getScaleDefaults: function(type) {
- // Return the scale defaults merged with the global settings so that we always use the latest ones
- return this.defaults.hasOwnProperty(type) ? helpers.merge({}, [defaults.scale, this.defaults[type]]) : {};
- },
- updateScaleDefaults: function(type, additions) {
- var me = this;
- if (me.defaults.hasOwnProperty(type)) {
- me.defaults[type] = helpers.extend(me.defaults[type], additions);
- }
- },
- addScalesToLayout: function(chart) {
- // Adds each scale to the chart.boxes array to be sized accordingly
- helpers.each(chart.scales, function(scale) {
- // Set ILayoutItem parameters for backwards compatibility
- scale.fullWidth = scale.options.fullWidth;
- scale.position = scale.options.position;
- scale.weight = scale.options.weight;
- layouts.addBox(chart, scale);
- });
- }
-};
-
-},{"26":26,"31":31,"46":46}],35:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-
-/**
- * Namespace to hold static tick generation functions
- * @namespace Chart.Ticks
- */
-module.exports = {
- /**
- * Namespace to hold formatters for different types of ticks
- * @namespace Chart.Ticks.formatters
- */
- formatters: {
- /**
- * Formatter for value labels
- * @method Chart.Ticks.formatters.values
- * @param value the value to display
- * @return {String|Array} the label to display
- */
- values: function(value) {
- return helpers.isArray(value) ? value : '' + value;
- },
-
- /**
- * Formatter for linear numeric ticks
- * @method Chart.Ticks.formatters.linear
- * @param tickValue {Number} the value to be formatted
- * @param index {Number} the position of the tickValue parameter in the ticks array
- * @param ticks {Array<Number>} the list of ticks being converted
- * @return {String} string representation of the tickValue parameter
- */
- linear: function(tickValue, index, ticks) {
- // If we have lots of ticks, don't use the ones
- var delta = ticks.length > 3 ? ticks[2] - ticks[1] : ticks[1] - ticks[0];
-
- // If we have a number like 2.5 as the delta, figure out how many decimal places we need
- if (Math.abs(delta) > 1) {
- if (tickValue !== Math.floor(tickValue)) {
- // not an integer
- delta = tickValue - Math.floor(tickValue);
- }
- }
-
- var logDelta = helpers.log10(Math.abs(delta));
- var tickString = '';
-
- if (tickValue !== 0) {
- var maxTick = Math.max(Math.abs(ticks[0]), Math.abs(ticks[ticks.length - 1]));
- if (maxTick < 1e-4) { // all ticks are small numbers; use scientific notation
- var logTick = helpers.log10(Math.abs(tickValue));
- tickString = tickValue.toExponential(Math.floor(logTick) - Math.floor(logDelta));
- } else {
- var numDecimal = -1 * Math.floor(logDelta);
- numDecimal = Math.max(Math.min(numDecimal, 20), 0); // toFixed has a max of 20 decimal places
- tickString = tickValue.toFixed(numDecimal);
- }
- } else {
- tickString = '0'; // never show decimal places for 0
- }
-
- return tickString;
- },
-
- logarithmic: function(tickValue, index, ticks) {
- var remain = tickValue / (Math.pow(10, Math.floor(helpers.log10(tickValue))));
-
- if (tickValue === 0) {
- return '0';
- } else if (remain === 1 || remain === 2 || remain === 5 || index === 0 || index === ticks.length - 1) {
- return tickValue.toExponential();
- }
- return '';
- }
- }
-};
-
-},{"46":46}],36:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-var helpers = require(46);
-
-defaults._set('global', {
- tooltips: {
- enabled: true,
- custom: null,
- mode: 'nearest',
- position: 'average',
- intersect: true,
- backgroundColor: 'rgba(0,0,0,0.8)',
- titleFontStyle: 'bold',
- titleSpacing: 2,
- titleMarginBottom: 6,
- titleFontColor: '#fff',
- titleAlign: 'left',
- bodySpacing: 2,
- bodyFontColor: '#fff',
- bodyAlign: 'left',
- footerFontStyle: 'bold',
- footerSpacing: 2,
- footerMarginTop: 6,
- footerFontColor: '#fff',
- footerAlign: 'left',
- yPadding: 6,
- xPadding: 6,
- caretPadding: 2,
- caretSize: 5,
- cornerRadius: 6,
- multiKeyBackground: '#fff',
- displayColors: true,
- borderColor: 'rgba(0,0,0,0)',
- borderWidth: 0,
- callbacks: {
- // Args are: (tooltipItems, data)
- beforeTitle: helpers.noop,
- title: function(tooltipItems, data) {
- // Pick first xLabel for now
- var title = '';
- var labels = data.labels;
- var labelCount = labels ? labels.length : 0;
-
- if (tooltipItems.length > 0) {
- var item = tooltipItems[0];
-
- if (item.xLabel) {
- title = item.xLabel;
- } else if (labelCount > 0 && item.index < labelCount) {
- title = labels[item.index];
- }
- }
-
- return title;
- },
- afterTitle: helpers.noop,
-
- // Args are: (tooltipItems, data)
- beforeBody: helpers.noop,
-
- // Args are: (tooltipItem, data)
- beforeLabel: helpers.noop,
- label: function(tooltipItem, data) {
- var label = data.datasets[tooltipItem.datasetIndex].label || '';
-
- if (label) {
- label += ': ';
- }
- label += tooltipItem.yLabel;
- return label;
- },
- labelColor: function(tooltipItem, chart) {
- var meta = chart.getDatasetMeta(tooltipItem.datasetIndex);
- var activeElement = meta.data[tooltipItem.index];
- var view = activeElement._view;
- return {
- borderColor: view.borderColor,
- backgroundColor: view.backgroundColor
- };
- },
- labelTextColor: function() {
- return this._options.bodyFontColor;
- },
- afterLabel: helpers.noop,
-
- // Args are: (tooltipItems, data)
- afterBody: helpers.noop,
-
- // Args are: (tooltipItems, data)
- beforeFooter: helpers.noop,
- footer: helpers.noop,
- afterFooter: helpers.noop
- }
- }
-});
-
-var positioners = {
- /**
- * Average mode places the tooltip at the average position of the elements shown
- * @function Chart.Tooltip.positioners.average
- * @param elements {ChartElement[]} the elements being displayed in the tooltip
- * @returns {Point} tooltip position
- */
- average: function(elements) {
- if (!elements.length) {
- return false;
- }
-
- var i, len;
- var x = 0;
- var y = 0;
- var count = 0;
-
- for (i = 0, len = elements.length; i < len; ++i) {
- var el = elements[i];
- if (el && el.hasValue()) {
- var pos = el.tooltipPosition();
- x += pos.x;
- y += pos.y;
- ++count;
- }
- }
-
- return {
- x: Math.round(x / count),
- y: Math.round(y / count)
- };
- },
-
- /**
- * Gets the tooltip position nearest of the item nearest to the event position
- * @function Chart.Tooltip.positioners.nearest
- * @param elements {Chart.Element[]} the tooltip elements
- * @param eventPosition {Point} the position of the event in canvas coordinates
- * @returns {Point} the tooltip position
- */
- nearest: function(elements, eventPosition) {
- var x = eventPosition.x;
- var y = eventPosition.y;
- var minDistance = Number.POSITIVE_INFINITY;
- var i, len, nearestElement;
-
- for (i = 0, len = elements.length; i < len; ++i) {
- var el = elements[i];
- if (el && el.hasValue()) {
- var center = el.getCenterPoint();
- var d = helpers.distanceBetweenPoints(eventPosition, center);
-
- if (d < minDistance) {
- minDistance = d;
- nearestElement = el;
- }
- }
- }
-
- if (nearestElement) {
- var tp = nearestElement.tooltipPosition();
- x = tp.x;
- y = tp.y;
- }
-
- return {
- x: x,
- y: y
- };
- }
-};
-
-/**
- * Helper method to merge the opacity into a color
- */
-function mergeOpacity(colorString, opacity) {
- var color = helpers.color(colorString);
- return color.alpha(opacity * color.alpha()).rgbaString();
-}
-
-// Helper to push or concat based on if the 2nd parameter is an array or not
-function pushOrConcat(base, toPush) {
- if (toPush) {
- if (helpers.isArray(toPush)) {
- // base = base.concat(toPush);
- Array.prototype.push.apply(base, toPush);
- } else {
- base.push(toPush);
- }
- }
-
- return base;
-}
-
-/**
- * Returns array of strings split by newline
- * @param {String} value - The value to split by newline.
- * @returns {Array} value if newline present - Returned from String split() method
- * @function
- */
-function splitNewlines(str) {
- if ((typeof str === 'string' || str instanceof String) && str.indexOf('\n') > -1) {
- return str.split('\n');
- }
- return str;
-}
-
-
-// Private helper to create a tooltip item model
-// @param element : the chart element (point, arc, bar) to create the tooltip item for
-// @return : new tooltip item
-function createTooltipItem(element) {
- var xScale = element._xScale;
- var yScale = element._yScale || element._scale; // handle radar || polarArea charts
- var index = element._index;
- var datasetIndex = element._datasetIndex;
-
- return {
- xLabel: xScale ? xScale.getLabelForIndex(index, datasetIndex) : '',
- yLabel: yScale ? yScale.getLabelForIndex(index, datasetIndex) : '',
- index: index,
- datasetIndex: datasetIndex,
- x: element._model.x,
- y: element._model.y
- };
-}
-
-/**
- * Helper to get the reset model for the tooltip
- * @param tooltipOpts {Object} the tooltip options
- */
-function getBaseModel(tooltipOpts) {
- var globalDefaults = defaults.global;
- var valueOrDefault = helpers.valueOrDefault;
-
- return {
- // Positioning
- xPadding: tooltipOpts.xPadding,
- yPadding: tooltipOpts.yPadding,
- xAlign: tooltipOpts.xAlign,
- yAlign: tooltipOpts.yAlign,
-
- // Body
- bodyFontColor: tooltipOpts.bodyFontColor,
- _bodyFontFamily: valueOrDefault(tooltipOpts.bodyFontFamily, globalDefaults.defaultFontFamily),
- _bodyFontStyle: valueOrDefault(tooltipOpts.bodyFontStyle, globalDefaults.defaultFontStyle),
- _bodyAlign: tooltipOpts.bodyAlign,
- bodyFontSize: valueOrDefault(tooltipOpts.bodyFontSize, globalDefaults.defaultFontSize),
- bodySpacing: tooltipOpts.bodySpacing,
-
- // Title
- titleFontColor: tooltipOpts.titleFontColor,
- _titleFontFamily: valueOrDefault(tooltipOpts.titleFontFamily, globalDefaults.defaultFontFamily),
- _titleFontStyle: valueOrDefault(tooltipOpts.titleFontStyle, globalDefaults.defaultFontStyle),
- titleFontSize: valueOrDefault(tooltipOpts.titleFontSize, globalDefaults.defaultFontSize),
- _titleAlign: tooltipOpts.titleAlign,
- titleSpacing: tooltipOpts.titleSpacing,
- titleMarginBottom: tooltipOpts.titleMarginBottom,
-
- // Footer
- footerFontColor: tooltipOpts.footerFontColor,
- _footerFontFamily: valueOrDefault(tooltipOpts.footerFontFamily, globalDefaults.defaultFontFamily),
- _footerFontStyle: valueOrDefault(tooltipOpts.footerFontStyle, globalDefaults.defaultFontStyle),
- footerFontSize: valueOrDefault(tooltipOpts.footerFontSize, globalDefaults.defaultFontSize),
- _footerAlign: tooltipOpts.footerAlign,
- footerSpacing: tooltipOpts.footerSpacing,
- footerMarginTop: tooltipOpts.footerMarginTop,
-
- // Appearance
- caretSize: tooltipOpts.caretSize,
- cornerRadius: tooltipOpts.cornerRadius,
- backgroundColor: tooltipOpts.backgroundColor,
- opacity: 0,
- legendColorBackground: tooltipOpts.multiKeyBackground,
- displayColors: tooltipOpts.displayColors,
- borderColor: tooltipOpts.borderColor,
- borderWidth: tooltipOpts.borderWidth
- };
-}
-
-/**
- * Get the size of the tooltip
- */
-function getTooltipSize(tooltip, model) {
- var ctx = tooltip._chart.ctx;
-
- var height = model.yPadding * 2; // Tooltip Padding
- var width = 0;
-
- // Count of all lines in the body
- var body = model.body;
- var combinedBodyLength = body.reduce(function(count, bodyItem) {
- return count + bodyItem.before.length + bodyItem.lines.length + bodyItem.after.length;
- }, 0);
- combinedBodyLength += model.beforeBody.length + model.afterBody.length;
-
- var titleLineCount = model.title.length;
- var footerLineCount = model.footer.length;
- var titleFontSize = model.titleFontSize;
- var bodyFontSize = model.bodyFontSize;
- var footerFontSize = model.footerFontSize;
-
- height += titleLineCount * titleFontSize; // Title Lines
- height += titleLineCount ? (titleLineCount - 1) * model.titleSpacing : 0; // Title Line Spacing
- height += titleLineCount ? model.titleMarginBottom : 0; // Title's bottom Margin
- height += combinedBodyLength * bodyFontSize; // Body Lines
- height += combinedBodyLength ? (combinedBodyLength - 1) * model.bodySpacing : 0; // Body Line Spacing
- height += footerLineCount ? model.footerMarginTop : 0; // Footer Margin
- height += footerLineCount * (footerFontSize); // Footer Lines
- height += footerLineCount ? (footerLineCount - 1) * model.footerSpacing : 0; // Footer Line Spacing
-
- // Title width
- var widthPadding = 0;
- var maxLineWidth = function(line) {
- width = Math.max(width, ctx.measureText(line).width + widthPadding);
- };
-
- ctx.font = helpers.fontString(titleFontSize, model._titleFontStyle, model._titleFontFamily);
- helpers.each(model.title, maxLineWidth);
-
- // Body width
- ctx.font = helpers.fontString(bodyFontSize, model._bodyFontStyle, model._bodyFontFamily);
- helpers.each(model.beforeBody.concat(model.afterBody), maxLineWidth);
-
- // Body lines may include some extra width due to the color box
- widthPadding = model.displayColors ? (bodyFontSize + 2) : 0;
- helpers.each(body, function(bodyItem) {
- helpers.each(bodyItem.before, maxLineWidth);
- helpers.each(bodyItem.lines, maxLineWidth);
- helpers.each(bodyItem.after, maxLineWidth);
- });
-
- // Reset back to 0
- widthPadding = 0;
-
- // Footer width
- ctx.font = helpers.fontString(footerFontSize, model._footerFontStyle, model._footerFontFamily);
- helpers.each(model.footer, maxLineWidth);
-
- // Add padding
- width += 2 * model.xPadding;
-
- return {
- width: width,
- height: height
- };
-}
-
-/**
- * Helper to get the alignment of a tooltip given the size
- */
-function determineAlignment(tooltip, size) {
- var model = tooltip._model;
- var chart = tooltip._chart;
- var chartArea = tooltip._chart.chartArea;
- var xAlign = 'center';
- var yAlign = 'center';
-
- if (model.y < size.height) {
- yAlign = 'top';
- } else if (model.y > (chart.height - size.height)) {
- yAlign = 'bottom';
- }
-
- var lf, rf; // functions to determine left, right alignment
- var olf, orf; // functions to determine if left/right alignment causes tooltip to go outside chart
- var yf; // function to get the y alignment if the tooltip goes outside of the left or right edges
- var midX = (chartArea.left + chartArea.right) / 2;
- var midY = (chartArea.top + chartArea.bottom) / 2;
-
- if (yAlign === 'center') {
- lf = function(x) {
- return x <= midX;
- };
- rf = function(x) {
- return x > midX;
- };
- } else {
- lf = function(x) {
- return x <= (size.width / 2);
- };
- rf = function(x) {
- return x >= (chart.width - (size.width / 2));
- };
- }
-
- olf = function(x) {
- return x + size.width + model.caretSize + model.caretPadding > chart.width;
- };
- orf = function(x) {
- return x - size.width - model.caretSize - model.caretPadding < 0;
- };
- yf = function(y) {
- return y <= midY ? 'top' : 'bottom';
- };
-
- if (lf(model.x)) {
- xAlign = 'left';
-
- // Is tooltip too wide and goes over the right side of the chart.?
- if (olf(model.x)) {
- xAlign = 'center';
- yAlign = yf(model.y);
- }
- } else if (rf(model.x)) {
- xAlign = 'right';
-
- // Is tooltip too wide and goes outside left edge of canvas?
- if (orf(model.x)) {
- xAlign = 'center';
- yAlign = yf(model.y);
- }
- }
-
- var opts = tooltip._options;
- return {
- xAlign: opts.xAlign ? opts.xAlign : xAlign,
- yAlign: opts.yAlign ? opts.yAlign : yAlign
- };
-}
-
-/**
- * Helper to get the location a tooltip needs to be placed at given the initial position (via the vm) and the size and alignment
- */
-function getBackgroundPoint(vm, size, alignment, chart) {
- // Background Position
- var x = vm.x;
- var y = vm.y;
-
- var caretSize = vm.caretSize;
- var caretPadding = vm.caretPadding;
- var cornerRadius = vm.cornerRadius;
- var xAlign = alignment.xAlign;
- var yAlign = alignment.yAlign;
- var paddingAndSize = caretSize + caretPadding;
- var radiusAndPadding = cornerRadius + caretPadding;
-
- if (xAlign === 'right') {
- x -= size.width;
- } else if (xAlign === 'center') {
- x -= (size.width / 2);
- if (x + size.width > chart.width) {
- x = chart.width - size.width;
- }
- if (x < 0) {
- x = 0;
- }
- }
-
- if (yAlign === 'top') {
- y += paddingAndSize;
- } else if (yAlign === 'bottom') {
- y -= size.height + paddingAndSize;
- } else {
- y -= (size.height / 2);
- }
-
- if (yAlign === 'center') {
- if (xAlign === 'left') {
- x += paddingAndSize;
- } else if (xAlign === 'right') {
- x -= paddingAndSize;
- }
- } else if (xAlign === 'left') {
- x -= radiusAndPadding;
- } else if (xAlign === 'right') {
- x += radiusAndPadding;
- }
-
- return {
- x: x,
- y: y
- };
-}
-
-/**
- * Helper to build before and after body lines
- */
-function getBeforeAfterBodyLines(callback) {
- return pushOrConcat([], splitNewlines(callback));
-}
-
-var exports = module.exports = Element.extend({
- initialize: function() {
- this._model = getBaseModel(this._options);
- this._lastActive = [];
- },
-
- // Get the title
- // Args are: (tooltipItem, data)
- getTitle: function() {
- var me = this;
- var opts = me._options;
- var callbacks = opts.callbacks;
-
- var beforeTitle = callbacks.beforeTitle.apply(me, arguments);
- var title = callbacks.title.apply(me, arguments);
- var afterTitle = callbacks.afterTitle.apply(me, arguments);
-
- var lines = [];
- lines = pushOrConcat(lines, splitNewlines(beforeTitle));
- lines = pushOrConcat(lines, splitNewlines(title));
- lines = pushOrConcat(lines, splitNewlines(afterTitle));
-
- return lines;
- },
-
- // Args are: (tooltipItem, data)
- getBeforeBody: function() {
- return getBeforeAfterBodyLines(this._options.callbacks.beforeBody.apply(this, arguments));
- },
-
- // Args are: (tooltipItem, data)
- getBody: function(tooltipItems, data) {
- var me = this;
- var callbacks = me._options.callbacks;
- var bodyItems = [];
-
- helpers.each(tooltipItems, function(tooltipItem) {
- var bodyItem = {
- before: [],
- lines: [],
- after: []
- };
- pushOrConcat(bodyItem.before, splitNewlines(callbacks.beforeLabel.call(me, tooltipItem, data)));
- pushOrConcat(bodyItem.lines, callbacks.label.call(me, tooltipItem, data));
- pushOrConcat(bodyItem.after, splitNewlines(callbacks.afterLabel.call(me, tooltipItem, data)));
-
- bodyItems.push(bodyItem);
- });
-
- return bodyItems;
- },
-
- // Args are: (tooltipItem, data)
- getAfterBody: function() {
- return getBeforeAfterBodyLines(this._options.callbacks.afterBody.apply(this, arguments));
- },
-
- // Get the footer and beforeFooter and afterFooter lines
- // Args are: (tooltipItem, data)
- getFooter: function() {
- var me = this;
- var callbacks = me._options.callbacks;
-
- var beforeFooter = callbacks.beforeFooter.apply(me, arguments);
- var footer = callbacks.footer.apply(me, arguments);
- var afterFooter = callbacks.afterFooter.apply(me, arguments);
-
- var lines = [];
- lines = pushOrConcat(lines, splitNewlines(beforeFooter));
- lines = pushOrConcat(lines, splitNewlines(footer));
- lines = pushOrConcat(lines, splitNewlines(afterFooter));
-
- return lines;
- },
-
- update: function(changed) {
- var me = this;
- var opts = me._options;
-
- // Need to regenerate the model because its faster than using extend and it is necessary due to the optimization in Chart.Element.transition
- // that does _view = _model if ease === 1. This causes the 2nd tooltip update to set properties in both the view and model at the same time
- // which breaks any animations.
- var existingModel = me._model;
- var model = me._model = getBaseModel(opts);
- var active = me._active;
-
- var data = me._data;
-
- // In the case where active.length === 0 we need to keep these at existing values for good animations
- var alignment = {
- xAlign: existingModel.xAlign,
- yAlign: existingModel.yAlign
- };
- var backgroundPoint = {
- x: existingModel.x,
- y: existingModel.y
- };
- var tooltipSize = {
- width: existingModel.width,
- height: existingModel.height
- };
- var tooltipPosition = {
- x: existingModel.caretX,
- y: existingModel.caretY
- };
-
- var i, len;
-
- if (active.length) {
- model.opacity = 1;
-
- var labelColors = [];
- var labelTextColors = [];
- tooltipPosition = positioners[opts.position].call(me, active, me._eventPosition);
-
- var tooltipItems = [];
- for (i = 0, len = active.length; i < len; ++i) {
- tooltipItems.push(createTooltipItem(active[i]));
- }
-
- // If the user provided a filter function, use it to modify the tooltip items
- if (opts.filter) {
- tooltipItems = tooltipItems.filter(function(a) {
- return opts.filter(a, data);
- });
- }
-
- // If the user provided a sorting function, use it to modify the tooltip items
- if (opts.itemSort) {
- tooltipItems = tooltipItems.sort(function(a, b) {
- return opts.itemSort(a, b, data);
- });
- }
-
- // Determine colors for boxes
- helpers.each(tooltipItems, function(tooltipItem) {
- labelColors.push(opts.callbacks.labelColor.call(me, tooltipItem, me._chart));
- labelTextColors.push(opts.callbacks.labelTextColor.call(me, tooltipItem, me._chart));
- });
-
-
- // Build the Text Lines
- model.title = me.getTitle(tooltipItems, data);
- model.beforeBody = me.getBeforeBody(tooltipItems, data);
- model.body = me.getBody(tooltipItems, data);
- model.afterBody = me.getAfterBody(tooltipItems, data);
- model.footer = me.getFooter(tooltipItems, data);
-
- // Initial positioning and colors
- model.x = Math.round(tooltipPosition.x);
- model.y = Math.round(tooltipPosition.y);
- model.caretPadding = opts.caretPadding;
- model.labelColors = labelColors;
- model.labelTextColors = labelTextColors;
-
- // data points
- model.dataPoints = tooltipItems;
-
- // We need to determine alignment of the tooltip
- tooltipSize = getTooltipSize(this, model);
- alignment = determineAlignment(this, tooltipSize);
- // Final Size and Position
- backgroundPoint = getBackgroundPoint(model, tooltipSize, alignment, me._chart);
- } else {
- model.opacity = 0;
- }
-
- model.xAlign = alignment.xAlign;
- model.yAlign = alignment.yAlign;
- model.x = backgroundPoint.x;
- model.y = backgroundPoint.y;
- model.width = tooltipSize.width;
- model.height = tooltipSize.height;
-
- // Point where the caret on the tooltip points to
- model.caretX = tooltipPosition.x;
- model.caretY = tooltipPosition.y;
-
- me._model = model;
-
- if (changed && opts.custom) {
- opts.custom.call(me, model);
- }
-
- return me;
- },
-
- drawCaret: function(tooltipPoint, size) {
- var ctx = this._chart.ctx;
- var vm = this._view;
- var caretPosition = this.getCaretPosition(tooltipPoint, size, vm);
-
- ctx.lineTo(caretPosition.x1, caretPosition.y1);
- ctx.lineTo(caretPosition.x2, caretPosition.y2);
- ctx.lineTo(caretPosition.x3, caretPosition.y3);
- },
- getCaretPosition: function(tooltipPoint, size, vm) {
- var x1, x2, x3, y1, y2, y3;
- var caretSize = vm.caretSize;
- var cornerRadius = vm.cornerRadius;
- var xAlign = vm.xAlign;
- var yAlign = vm.yAlign;
- var ptX = tooltipPoint.x;
- var ptY = tooltipPoint.y;
- var width = size.width;
- var height = size.height;
-
- if (yAlign === 'center') {
- y2 = ptY + (height / 2);
-
- if (xAlign === 'left') {
- x1 = ptX;
- x2 = x1 - caretSize;
- x3 = x1;
-
- y1 = y2 + caretSize;
- y3 = y2 - caretSize;
- } else {
- x1 = ptX + width;
- x2 = x1 + caretSize;
- x3 = x1;
-
- y1 = y2 - caretSize;
- y3 = y2 + caretSize;
- }
- } else {
- if (xAlign === 'left') {
- x2 = ptX + cornerRadius + (caretSize);
- x1 = x2 - caretSize;
- x3 = x2 + caretSize;
- } else if (xAlign === 'right') {
- x2 = ptX + width - cornerRadius - caretSize;
- x1 = x2 - caretSize;
- x3 = x2 + caretSize;
- } else {
- x2 = vm.caretX;
- x1 = x2 - caretSize;
- x3 = x2 + caretSize;
- }
- if (yAlign === 'top') {
- y1 = ptY;
- y2 = y1 - caretSize;
- y3 = y1;
- } else {
- y1 = ptY + height;
- y2 = y1 + caretSize;
- y3 = y1;
- // invert drawing order
- var tmp = x3;
- x3 = x1;
- x1 = tmp;
- }
- }
- return {x1: x1, x2: x2, x3: x3, y1: y1, y2: y2, y3: y3};
- },
-
- drawTitle: function(pt, vm, ctx, opacity) {
- var title = vm.title;
-
- if (title.length) {
- ctx.textAlign = vm._titleAlign;
- ctx.textBaseline = 'top';
-
- var titleFontSize = vm.titleFontSize;
- var titleSpacing = vm.titleSpacing;
-
- ctx.fillStyle = mergeOpacity(vm.titleFontColor, opacity);
- ctx.font = helpers.fontString(titleFontSize, vm._titleFontStyle, vm._titleFontFamily);
-
- var i, len;
- for (i = 0, len = title.length; i < len; ++i) {
- ctx.fillText(title[i], pt.x, pt.y);
- pt.y += titleFontSize + titleSpacing; // Line Height and spacing
-
- if (i + 1 === title.length) {
- pt.y += vm.titleMarginBottom - titleSpacing; // If Last, add margin, remove spacing
- }
- }
- }
- },
-
- drawBody: function(pt, vm, ctx, opacity) {
- var bodyFontSize = vm.bodyFontSize;
- var bodySpacing = vm.bodySpacing;
- var body = vm.body;
-
- ctx.textAlign = vm._bodyAlign;
- ctx.textBaseline = 'top';
- ctx.font = helpers.fontString(bodyFontSize, vm._bodyFontStyle, vm._bodyFontFamily);
-
- // Before Body
- var xLinePadding = 0;
- var fillLineOfText = function(line) {
- ctx.fillText(line, pt.x + xLinePadding, pt.y);
- pt.y += bodyFontSize + bodySpacing;
- };
-
- // Before body lines
- ctx.fillStyle = mergeOpacity(vm.bodyFontColor, opacity);
- helpers.each(vm.beforeBody, fillLineOfText);
-
- var drawColorBoxes = vm.displayColors;
- xLinePadding = drawColorBoxes ? (bodyFontSize + 2) : 0;
-
- // Draw body lines now
- helpers.each(body, function(bodyItem, i) {
- var textColor = mergeOpacity(vm.labelTextColors[i], opacity);
- ctx.fillStyle = textColor;
- helpers.each(bodyItem.before, fillLineOfText);
-
- helpers.each(bodyItem.lines, function(line) {
- // Draw Legend-like boxes if needed
- if (drawColorBoxes) {
- // Fill a white rect so that colours merge nicely if the opacity is < 1
- ctx.fillStyle = mergeOpacity(vm.legendColorBackground, opacity);
- ctx.fillRect(pt.x, pt.y, bodyFontSize, bodyFontSize);
-
- // Border
- ctx.lineWidth = 1;
- ctx.strokeStyle = mergeOpacity(vm.labelColors[i].borderColor, opacity);
- ctx.strokeRect(pt.x, pt.y, bodyFontSize, bodyFontSize);
-
- // Inner square
- ctx.fillStyle = mergeOpacity(vm.labelColors[i].backgroundColor, opacity);
- ctx.fillRect(pt.x + 1, pt.y + 1, bodyFontSize - 2, bodyFontSize - 2);
- ctx.fillStyle = textColor;
- }
-
- fillLineOfText(line);
- });
-
- helpers.each(bodyItem.after, fillLineOfText);
- });
-
- // Reset back to 0 for after body
- xLinePadding = 0;
-
- // After body lines
- helpers.each(vm.afterBody, fillLineOfText);
- pt.y -= bodySpacing; // Remove last body spacing
- },
-
- drawFooter: function(pt, vm, ctx, opacity) {
- var footer = vm.footer;
-
- if (footer.length) {
- pt.y += vm.footerMarginTop;
-
- ctx.textAlign = vm._footerAlign;
- ctx.textBaseline = 'top';
-
- ctx.fillStyle = mergeOpacity(vm.footerFontColor, opacity);
- ctx.font = helpers.fontString(vm.footerFontSize, vm._footerFontStyle, vm._footerFontFamily);
-
- helpers.each(footer, function(line) {
- ctx.fillText(line, pt.x, pt.y);
- pt.y += vm.footerFontSize + vm.footerSpacing;
- });
- }
- },
-
- drawBackground: function(pt, vm, ctx, tooltipSize, opacity) {
- ctx.fillStyle = mergeOpacity(vm.backgroundColor, opacity);
- ctx.strokeStyle = mergeOpacity(vm.borderColor, opacity);
- ctx.lineWidth = vm.borderWidth;
- var xAlign = vm.xAlign;
- var yAlign = vm.yAlign;
- var x = pt.x;
- var y = pt.y;
- var width = tooltipSize.width;
- var height = tooltipSize.height;
- var radius = vm.cornerRadius;
-
- ctx.beginPath();
- ctx.moveTo(x + radius, y);
- if (yAlign === 'top') {
- this.drawCaret(pt, tooltipSize);
- }
- ctx.lineTo(x + width - radius, y);
- ctx.quadraticCurveTo(x + width, y, x + width, y + radius);
- if (yAlign === 'center' && xAlign === 'right') {
- this.drawCaret(pt, tooltipSize);
- }
- ctx.lineTo(x + width, y + height - radius);
- ctx.quadraticCurveTo(x + width, y + height, x + width - radius, y + height);
- if (yAlign === 'bottom') {
- this.drawCaret(pt, tooltipSize);
- }
- ctx.lineTo(x + radius, y + height);
- ctx.quadraticCurveTo(x, y + height, x, y + height - radius);
- if (yAlign === 'center' && xAlign === 'left') {
- this.drawCaret(pt, tooltipSize);
- }
- ctx.lineTo(x, y + radius);
- ctx.quadraticCurveTo(x, y, x + radius, y);
- ctx.closePath();
-
- ctx.fill();
-
- if (vm.borderWidth > 0) {
- ctx.stroke();
- }
- },
-
- draw: function() {
- var ctx = this._chart.ctx;
- var vm = this._view;
-
- if (vm.opacity === 0) {
- return;
- }
-
- var tooltipSize = {
- width: vm.width,
- height: vm.height
- };
- var pt = {
- x: vm.x,
- y: vm.y
- };
-
- // IE11/Edge does not like very small opacities, so snap to 0
- var opacity = Math.abs(vm.opacity < 1e-3) ? 0 : vm.opacity;
-
- // Truthy/falsey value for empty tooltip
- var hasTooltipContent = vm.title.length || vm.beforeBody.length || vm.body.length || vm.afterBody.length || vm.footer.length;
-
- if (this._options.enabled && hasTooltipContent) {
- // Draw Background
- this.drawBackground(pt, vm, ctx, tooltipSize, opacity);
-
- // Draw Title, Body, and Footer
- pt.x += vm.xPadding;
- pt.y += vm.yPadding;
-
- // Titles
- this.drawTitle(pt, vm, ctx, opacity);
-
- // Body
- this.drawBody(pt, vm, ctx, opacity);
-
- // Footer
- this.drawFooter(pt, vm, ctx, opacity);
- }
- },
-
- /**
- * Handle an event
- * @private
- * @param {IEvent} event - The event to handle
- * @returns {Boolean} true if the tooltip changed
- */
- handleEvent: function(e) {
- var me = this;
- var options = me._options;
- var changed = false;
-
- me._lastActive = me._lastActive || [];
-
- // Find Active Elements for tooltips
- if (e.type === 'mouseout') {
- me._active = [];
- } else {
- me._active = me._chart.getElementsAtEventForMode(e, options.mode, options);
- }
-
- // Remember Last Actives
- changed = !helpers.arrayEquals(me._active, me._lastActive);
-
- // Only handle target event on tooltip change
- if (changed) {
- me._lastActive = me._active;
-
- if (options.enabled || options.custom) {
- me._eventPosition = {
- x: e.x,
- y: e.y
- };
-
- me.update(true);
- me.pivot();
- }
- }
-
- return changed;
- }
-});
-
-/**
- * @namespace Chart.Tooltip.positioners
- */
-exports.positioners = positioners;
-
-
-},{"26":26,"27":27,"46":46}],37:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-var helpers = require(46);
-
-defaults._set('global', {
- elements: {
- arc: {
- backgroundColor: defaults.global.defaultColor,
- borderColor: '#fff',
- borderWidth: 2
- }
- }
-});
-
-module.exports = Element.extend({
- inLabelRange: function(mouseX) {
- var vm = this._view;
-
- if (vm) {
- return (Math.pow(mouseX - vm.x, 2) < Math.pow(vm.radius + vm.hoverRadius, 2));
- }
- return false;
- },
-
- inRange: function(chartX, chartY) {
- var vm = this._view;
-
- if (vm) {
- var pointRelativePosition = helpers.getAngleFromPoint(vm, {x: chartX, y: chartY});
- var angle = pointRelativePosition.angle;
- var distance = pointRelativePosition.distance;
-
- // Sanitise angle range
- var startAngle = vm.startAngle;
- var endAngle = vm.endAngle;
- while (endAngle < startAngle) {
- endAngle += 2.0 * Math.PI;
- }
- while (angle > endAngle) {
- angle -= 2.0 * Math.PI;
- }
- while (angle < startAngle) {
- angle += 2.0 * Math.PI;
- }
-
- // Check if within the range of the open/close angle
- var betweenAngles = (angle >= startAngle && angle <= endAngle);
- var withinRadius = (distance >= vm.innerRadius && distance <= vm.outerRadius);
-
- return (betweenAngles && withinRadius);
- }
- return false;
- },
-
- getCenterPoint: function() {
- var vm = this._view;
- var halfAngle = (vm.startAngle + vm.endAngle) / 2;
- var halfRadius = (vm.innerRadius + vm.outerRadius) / 2;
- return {
- x: vm.x + Math.cos(halfAngle) * halfRadius,
- y: vm.y + Math.sin(halfAngle) * halfRadius
- };
- },
-
- getArea: function() {
- var vm = this._view;
- return Math.PI * ((vm.endAngle - vm.startAngle) / (2 * Math.PI)) * (Math.pow(vm.outerRadius, 2) - Math.pow(vm.innerRadius, 2));
- },
-
- tooltipPosition: function() {
- var vm = this._view;
- var centreAngle = vm.startAngle + ((vm.endAngle - vm.startAngle) / 2);
- var rangeFromCentre = (vm.outerRadius - vm.innerRadius) / 2 + vm.innerRadius;
-
- return {
- x: vm.x + (Math.cos(centreAngle) * rangeFromCentre),
- y: vm.y + (Math.sin(centreAngle) * rangeFromCentre)
- };
- },
-
- draw: function() {
- var ctx = this._chart.ctx;
- var vm = this._view;
- var sA = vm.startAngle;
- var eA = vm.endAngle;
-
- ctx.beginPath();
-
- ctx.arc(vm.x, vm.y, vm.outerRadius, sA, eA);
- ctx.arc(vm.x, vm.y, vm.innerRadius, eA, sA, true);
-
- ctx.closePath();
- ctx.strokeStyle = vm.borderColor;
- ctx.lineWidth = vm.borderWidth;
-
- ctx.fillStyle = vm.backgroundColor;
-
- ctx.fill();
- ctx.lineJoin = 'bevel';
-
- if (vm.borderWidth) {
- ctx.stroke();
- }
- }
-});
-
-},{"26":26,"27":27,"46":46}],38:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-var helpers = require(46);
-
-var globalDefaults = defaults.global;
-
-defaults._set('global', {
- elements: {
- line: {
- tension: 0.4,
- backgroundColor: globalDefaults.defaultColor,
- borderWidth: 3,
- borderColor: globalDefaults.defaultColor,
- borderCapStyle: 'butt',
- borderDash: [],
- borderDashOffset: 0.0,
- borderJoinStyle: 'miter',
- capBezierPoints: true,
- fill: true, // do we fill in the area between the line and its base axis
- }
- }
-});
-
-module.exports = Element.extend({
- draw: function() {
- var me = this;
- var vm = me._view;
- var ctx = me._chart.ctx;
- var spanGaps = vm.spanGaps;
- var points = me._children.slice(); // clone array
- var globalOptionLineElements = globalDefaults.elements.line;
- var lastDrawnIndex = -1;
- var index, current, previous, currentVM;
-
- // If we are looping, adding the first point again
- if (me._loop && points.length) {
- points.push(points[0]);
- }
-
- ctx.save();
-
- // Stroke Line Options
- ctx.lineCap = vm.borderCapStyle || globalOptionLineElements.borderCapStyle;
-
- // IE 9 and 10 do not support line dash
- if (ctx.setLineDash) {
- ctx.setLineDash(vm.borderDash || globalOptionLineElements.borderDash);
- }
-
- ctx.lineDashOffset = vm.borderDashOffset || globalOptionLineElements.borderDashOffset;
- ctx.lineJoin = vm.borderJoinStyle || globalOptionLineElements.borderJoinStyle;
- ctx.lineWidth = vm.borderWidth || globalOptionLineElements.borderWidth;
- ctx.strokeStyle = vm.borderColor || globalDefaults.defaultColor;
-
- // Stroke Line
- ctx.beginPath();
- lastDrawnIndex = -1;
-
- for (index = 0; index < points.length; ++index) {
- current = points[index];
- previous = helpers.previousItem(points, index);
- currentVM = current._view;
-
- // First point moves to it's starting position no matter what
- if (index === 0) {
- if (!currentVM.skip) {
- ctx.moveTo(currentVM.x, currentVM.y);
- lastDrawnIndex = index;
- }
- } else {
- previous = lastDrawnIndex === -1 ? previous : points[lastDrawnIndex];
-
- if (!currentVM.skip) {
- if ((lastDrawnIndex !== (index - 1) && !spanGaps) || lastDrawnIndex === -1) {
- // There was a gap and this is the first point after the gap
- ctx.moveTo(currentVM.x, currentVM.y);
- } else {
- // Line to next point
- helpers.canvas.lineTo(ctx, previous._view, current._view);
- }
- lastDrawnIndex = index;
- }
- }
- }
-
- ctx.stroke();
- ctx.restore();
- }
-});
-
-},{"26":26,"27":27,"46":46}],39:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-var helpers = require(46);
-
-var defaultColor = defaults.global.defaultColor;
-
-defaults._set('global', {
- elements: {
- point: {
- radius: 3,
- pointStyle: 'circle',
- backgroundColor: defaultColor,
- borderColor: defaultColor,
- borderWidth: 1,
- // Hover
- hitRadius: 1,
- hoverRadius: 4,
- hoverBorderWidth: 1
- }
- }
-});
-
-function xRange(mouseX) {
- var vm = this._view;
- return vm ? (Math.abs(mouseX - vm.x) < vm.radius + vm.hitRadius) : false;
-}
-
-function yRange(mouseY) {
- var vm = this._view;
- return vm ? (Math.abs(mouseY - vm.y) < vm.radius + vm.hitRadius) : false;
-}
-
-module.exports = Element.extend({
- inRange: function(mouseX, mouseY) {
- var vm = this._view;
- return vm ? ((Math.pow(mouseX - vm.x, 2) + Math.pow(mouseY - vm.y, 2)) < Math.pow(vm.hitRadius + vm.radius, 2)) : false;
- },
-
- inLabelRange: xRange,
- inXRange: xRange,
- inYRange: yRange,
-
- getCenterPoint: function() {
- var vm = this._view;
- return {
- x: vm.x,
- y: vm.y
- };
- },
-
- getArea: function() {
- return Math.PI * Math.pow(this._view.radius, 2);
- },
-
- tooltipPosition: function() {
- var vm = this._view;
- return {
- x: vm.x,
- y: vm.y,
- padding: vm.radius + vm.borderWidth
- };
- },
-
- draw: function(chartArea) {
- var vm = this._view;
- var model = this._model;
- var ctx = this._chart.ctx;
- var pointStyle = vm.pointStyle;
- var rotation = vm.rotation;
- var radius = vm.radius;
- var x = vm.x;
- var y = vm.y;
- var errMargin = 1.01; // 1.01 is margin for Accumulated error. (Especially Edge, IE.)
-
- if (vm.skip) {
- return;
- }
-
- // Clipping for Points.
- if (chartArea === undefined || (model.x >= chartArea.left && chartArea.right * errMargin >= model.x && model.y >= chartArea.top && chartArea.bottom * errMargin >= model.y)) {
- ctx.strokeStyle = vm.borderColor || defaultColor;
- ctx.lineWidth = helpers.valueOrDefault(vm.borderWidth, defaults.global.elements.point.borderWidth);
- ctx.fillStyle = vm.backgroundColor || defaultColor;
- helpers.canvas.drawPoint(ctx, pointStyle, radius, x, y, rotation);
- }
- }
-});
-
-},{"26":26,"27":27,"46":46}],40:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-
-defaults._set('global', {
- elements: {
- rectangle: {
- backgroundColor: defaults.global.defaultColor,
- borderColor: defaults.global.defaultColor,
- borderSkipped: 'bottom',
- borderWidth: 0
- }
- }
-});
-
-function isVertical(bar) {
- return bar._view.width !== undefined;
-}
-
-/**
- * Helper function to get the bounds of the bar regardless of the orientation
- * @param bar {Chart.Element.Rectangle} the bar
- * @return {Bounds} bounds of the bar
- * @private
- */
-function getBarBounds(bar) {
- var vm = bar._view;
- var x1, x2, y1, y2;
-
- if (isVertical(bar)) {
- // vertical
- var halfWidth = vm.width / 2;
- x1 = vm.x - halfWidth;
- x2 = vm.x + halfWidth;
- y1 = Math.min(vm.y, vm.base);
- y2 = Math.max(vm.y, vm.base);
- } else {
- // horizontal bar
- var halfHeight = vm.height / 2;
- x1 = Math.min(vm.x, vm.base);
- x2 = Math.max(vm.x, vm.base);
- y1 = vm.y - halfHeight;
- y2 = vm.y + halfHeight;
- }
-
- return {
- left: x1,
- top: y1,
- right: x2,
- bottom: y2
- };
-}
-
-module.exports = Element.extend({
- draw: function() {
- var ctx = this._chart.ctx;
- var vm = this._view;
- var left, right, top, bottom, signX, signY, borderSkipped;
- var borderWidth = vm.borderWidth;
-
- if (!vm.horizontal) {
- // bar
- left = vm.x - vm.width / 2;
- right = vm.x + vm.width / 2;
- top = vm.y;
- bottom = vm.base;
- signX = 1;
- signY = bottom > top ? 1 : -1;
- borderSkipped = vm.borderSkipped || 'bottom';
- } else {
- // horizontal bar
- left = vm.base;
- right = vm.x;
- top = vm.y - vm.height / 2;
- bottom = vm.y + vm.height / 2;
- signX = right > left ? 1 : -1;
- signY = 1;
- borderSkipped = vm.borderSkipped || 'left';
- }
-
- // Canvas doesn't allow us to stroke inside the width so we can
- // adjust the sizes to fit if we're setting a stroke on the line
- if (borderWidth) {
- // borderWidth shold be less than bar width and bar height.
- var barSize = Math.min(Math.abs(left - right), Math.abs(top - bottom));
- borderWidth = borderWidth > barSize ? barSize : borderWidth;
- var halfStroke = borderWidth / 2;
- // Adjust borderWidth when bar top position is near vm.base(zero).
- var borderLeft = left + (borderSkipped !== 'left' ? halfStroke * signX : 0);
- var borderRight = right + (borderSkipped !== 'right' ? -halfStroke * signX : 0);
- var borderTop = top + (borderSkipped !== 'top' ? halfStroke * signY : 0);
- var borderBottom = bottom + (borderSkipped !== 'bottom' ? -halfStroke * signY : 0);
- // not become a vertical line?
- if (borderLeft !== borderRight) {
- top = borderTop;
- bottom = borderBottom;
- }
- // not become a horizontal line?
- if (borderTop !== borderBottom) {
- left = borderLeft;
- right = borderRight;
- }
- }
-
- ctx.beginPath();
- ctx.fillStyle = vm.backgroundColor;
- ctx.strokeStyle = vm.borderColor;
- ctx.lineWidth = borderWidth;
-
- // Corner points, from bottom-left to bottom-right clockwise
- // | 1 2 |
- // | 0 3 |
- var corners = [
- [left, bottom],
- [left, top],
- [right, top],
- [right, bottom]
- ];
-
- // Find first (starting) corner with fallback to 'bottom'
- var borders = ['bottom', 'left', 'top', 'right'];
- var startCorner = borders.indexOf(borderSkipped, 0);
- if (startCorner === -1) {
- startCorner = 0;
- }
-
- function cornerAt(index) {
- return corners[(startCorner + index) % 4];
- }
-
- // Draw rectangle from 'startCorner'
- var corner = cornerAt(0);
- ctx.moveTo(corner[0], corner[1]);
-
- for (var i = 1; i < 4; i++) {
- corner = cornerAt(i);
- ctx.lineTo(corner[0], corner[1]);
- }
-
- ctx.fill();
- if (borderWidth) {
- ctx.stroke();
- }
- },
-
- height: function() {
- var vm = this._view;
- return vm.base - vm.y;
- },
-
- inRange: function(mouseX, mouseY) {
- var inRange = false;
-
- if (this._view) {
- var bounds = getBarBounds(this);
- inRange = mouseX >= bounds.left && mouseX <= bounds.right && mouseY >= bounds.top && mouseY <= bounds.bottom;
- }
-
- return inRange;
- },
-
- inLabelRange: function(mouseX, mouseY) {
- var me = this;
- if (!me._view) {
- return false;
- }
-
- var inRange = false;
- var bounds = getBarBounds(me);
-
- if (isVertical(me)) {
- inRange = mouseX >= bounds.left && mouseX <= bounds.right;
- } else {
- inRange = mouseY >= bounds.top && mouseY <= bounds.bottom;
- }
-
- return inRange;
- },
-
- inXRange: function(mouseX) {
- var bounds = getBarBounds(this);
- return mouseX >= bounds.left && mouseX <= bounds.right;
- },
-
- inYRange: function(mouseY) {
- var bounds = getBarBounds(this);
- return mouseY >= bounds.top && mouseY <= bounds.bottom;
- },
-
- getCenterPoint: function() {
- var vm = this._view;
- var x, y;
- if (isVertical(this)) {
- x = vm.x;
- y = (vm.y + vm.base) / 2;
- } else {
- x = (vm.x + vm.base) / 2;
- y = vm.y;
- }
-
- return {x: x, y: y};
- },
-
- getArea: function() {
- var vm = this._view;
- return vm.width * Math.abs(vm.y - vm.base);
- },
-
- tooltipPosition: function() {
- var vm = this._view;
- return {
- x: vm.x,
- y: vm.y
- };
- }
-});
-
-},{"26":26,"27":27}],41:[function(require,module,exports){
-'use strict';
-
-module.exports = {};
-module.exports.Arc = require(37);
-module.exports.Line = require(38);
-module.exports.Point = require(39);
-module.exports.Rectangle = require(40);
-
-},{"37":37,"38":38,"39":39,"40":40}],42:[function(require,module,exports){
-'use strict';
-
-var helpers = require(43);
-
-/**
- * @namespace Chart.helpers.canvas
- */
-var exports = module.exports = {
- /**
- * Clears the entire canvas associated to the given `chart`.
- * @param {Chart} chart - The chart for which to clear the canvas.
- */
- clear: function(chart) {
- chart.ctx.clearRect(0, 0, chart.width, chart.height);
- },
-
- /**
- * Creates a "path" for a rectangle with rounded corners at position (x, y) with a
- * given size (width, height) and the same `radius` for all corners.
- * @param {CanvasRenderingContext2D} ctx - The canvas 2D Context.
- * @param {Number} x - The x axis of the coordinate for the rectangle starting point.
- * @param {Number} y - The y axis of the coordinate for the rectangle starting point.
- * @param {Number} width - The rectangle's width.
- * @param {Number} height - The rectangle's height.
- * @param {Number} radius - The rounded amount (in pixels) for the four corners.
- * @todo handle `radius` as top-left, top-right, bottom-right, bottom-left array/object?
- */
- roundedRect: function(ctx, x, y, width, height, radius) {
- if (radius) {
- // NOTE(SB) `epsilon` helps to prevent minor artifacts appearing
- // on Chrome when `r` is exactly half the height or the width.
- var epsilon = 0.0000001;
- var r = Math.min(radius, (height / 2) - epsilon, (width / 2) - epsilon);
-
- ctx.moveTo(x + r, y);
- ctx.lineTo(x + width - r, y);
- ctx.arcTo(x + width, y, x + width, y + r, r);
- ctx.lineTo(x + width, y + height - r);
- ctx.arcTo(x + width, y + height, x + width - r, y + height, r);
- ctx.lineTo(x + r, y + height);
- ctx.arcTo(x, y + height, x, y + height - r, r);
- ctx.lineTo(x, y + r);
- ctx.arcTo(x, y, x + r, y, r);
- ctx.closePath();
- ctx.moveTo(x, y);
- } else {
- ctx.rect(x, y, width, height);
- }
- },
-
- drawPoint: function(ctx, style, radius, x, y, rotation) {
- var type, edgeLength, xOffset, yOffset, height, size;
- rotation = rotation || 0;
-
- if (style && typeof style === 'object') {
- type = style.toString();
- if (type === '[object HTMLImageElement]' || type === '[object HTMLCanvasElement]') {
- ctx.drawImage(style, x - style.width / 2, y - style.height / 2, style.width, style.height);
- return;
- }
- }
-
- if (isNaN(radius) || radius <= 0) {
- return;
- }
-
- ctx.save();
- ctx.translate(x, y);
- ctx.rotate(rotation * Math.PI / 180);
- ctx.beginPath();
-
- switch (style) {
- // Default includes circle
- default:
- ctx.arc(0, 0, radius, 0, Math.PI * 2);
- ctx.closePath();
- break;
- case 'triangle':
- edgeLength = 3 * radius / Math.sqrt(3);
- height = edgeLength * Math.sqrt(3) / 2;
- ctx.moveTo(-edgeLength / 2, height / 3);
- ctx.lineTo(edgeLength / 2, height / 3);
- ctx.lineTo(0, -2 * height / 3);
- ctx.closePath();
- break;
- case 'rect':
- size = 1 / Math.SQRT2 * radius;
- ctx.rect(-size, -size, 2 * size, 2 * size);
- break;
- case 'rectRounded':
- var offset = radius / Math.SQRT2;
- var leftX = -offset;
- var topY = -offset;
- var sideSize = Math.SQRT2 * radius;
-
- // NOTE(SB) the rounded rect implementation changed to use `arcTo`
- // instead of `quadraticCurveTo` since it generates better results
- // when rect is almost a circle. 0.425 (instead of 0.5) produces
- // results visually closer to the previous impl.
- this.roundedRect(ctx, leftX, topY, sideSize, sideSize, radius * 0.425);
- break;
- case 'rectRot':
- size = 1 / Math.SQRT2 * radius;
- ctx.moveTo(-size, 0);
- ctx.lineTo(0, size);
- ctx.lineTo(size, 0);
- ctx.lineTo(0, -size);
- ctx.closePath();
- break;
- case 'cross':
- ctx.moveTo(0, radius);
- ctx.lineTo(0, -radius);
- ctx.moveTo(-radius, 0);
- ctx.lineTo(radius, 0);
- break;
- case 'crossRot':
- xOffset = Math.cos(Math.PI / 4) * radius;
- yOffset = Math.sin(Math.PI / 4) * radius;
- ctx.moveTo(-xOffset, -yOffset);
- ctx.lineTo(xOffset, yOffset);
- ctx.moveTo(-xOffset, yOffset);
- ctx.lineTo(xOffset, -yOffset);
- break;
- case 'star':
- ctx.moveTo(0, radius);
- ctx.lineTo(0, -radius);
- ctx.moveTo(-radius, 0);
- ctx.lineTo(radius, 0);
- xOffset = Math.cos(Math.PI / 4) * radius;
- yOffset = Math.sin(Math.PI / 4) * radius;
- ctx.moveTo(-xOffset, -yOffset);
- ctx.lineTo(xOffset, yOffset);
- ctx.moveTo(-xOffset, yOffset);
- ctx.lineTo(xOffset, -yOffset);
- break;
- case 'line':
- ctx.moveTo(-radius, 0);
- ctx.lineTo(radius, 0);
- break;
- case 'dash':
- ctx.moveTo(0, 0);
- ctx.lineTo(radius, 0);
- break;
- }
-
- ctx.fill();
- ctx.stroke();
- ctx.restore();
- },
-
- clipArea: function(ctx, area) {
- ctx.save();
- ctx.beginPath();
- ctx.rect(area.left, area.top, area.right - area.left, area.bottom - area.top);
- ctx.clip();
- },
-
- unclipArea: function(ctx) {
- ctx.restore();
- },
-
- lineTo: function(ctx, previous, target, flip) {
- if (target.steppedLine) {
- if ((target.steppedLine === 'after' && !flip) || (target.steppedLine !== 'after' && flip)) {
- ctx.lineTo(previous.x, target.y);
- } else {
- ctx.lineTo(target.x, previous.y);
- }
- ctx.lineTo(target.x, target.y);
- return;
- }
-
- if (!target.tension) {
- ctx.lineTo(target.x, target.y);
- return;
- }
-
- ctx.bezierCurveTo(
- flip ? previous.controlPointPreviousX : previous.controlPointNextX,
- flip ? previous.controlPointPreviousY : previous.controlPointNextY,
- flip ? target.controlPointNextX : target.controlPointPreviousX,
- flip ? target.controlPointNextY : target.controlPointPreviousY,
- target.x,
- target.y);
- }
-};
-
-// DEPRECATIONS
-
-/**
- * Provided for backward compatibility, use Chart.helpers.canvas.clear instead.
- * @namespace Chart.helpers.clear
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.clear = exports.clear;
-
-/**
- * Provided for backward compatibility, use Chart.helpers.canvas.roundedRect instead.
- * @namespace Chart.helpers.drawRoundedRectangle
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.drawRoundedRectangle = function(ctx) {
- ctx.beginPath();
- exports.roundedRect.apply(exports, arguments);
-};
-
-},{"43":43}],43:[function(require,module,exports){
-'use strict';
-
-/**
- * @namespace Chart.helpers
- */
-var helpers = {
- /**
- * An empty function that can be used, for example, for optional callback.
- */
- noop: function() {},
-
- /**
- * Returns a unique id, sequentially generated from a global variable.
- * @returns {Number}
- * @function
- */
- uid: (function() {
- var id = 0;
- return function() {
- return id++;
- };
- }()),
-
- /**
- * Returns true if `value` is neither null nor undefined, else returns false.
- * @param {*} value - The value to test.
- * @returns {Boolean}
- * @since 2.7.0
- */
- isNullOrUndef: function(value) {
- return value === null || typeof value === 'undefined';
- },
-
- /**
- * Returns true if `value` is an array, else returns false.
- * @param {*} value - The value to test.
- * @returns {Boolean}
- * @function
- */
- isArray: Array.isArray ? Array.isArray : function(value) {
- return Object.prototype.toString.call(value) === '[object Array]';
- },
-
- /**
- * Returns true if `value` is an object (excluding null), else returns false.
- * @param {*} value - The value to test.
- * @returns {Boolean}
- * @since 2.7.0
- */
- isObject: function(value) {
- return value !== null && Object.prototype.toString.call(value) === '[object Object]';
- },
-
- /**
- * Returns `value` if defined, else returns `defaultValue`.
- * @param {*} value - The value to return if defined.
- * @param {*} defaultValue - The value to return if `value` is undefined.
- * @returns {*}
- */
- valueOrDefault: function(value, defaultValue) {
- return typeof value === 'undefined' ? defaultValue : value;
- },
-
- /**
- * Returns value at the given `index` in array if defined, else returns `defaultValue`.
- * @param {Array} value - The array to lookup for value at `index`.
- * @param {Number} index - The index in `value` to lookup for value.
- * @param {*} defaultValue - The value to return if `value[index]` is undefined.
- * @returns {*}
- */
- valueAtIndexOrDefault: function(value, index, defaultValue) {
- return helpers.valueOrDefault(helpers.isArray(value) ? value[index] : value, defaultValue);
- },
-
- /**
- * Calls `fn` with the given `args` in the scope defined by `thisArg` and returns the
- * value returned by `fn`. If `fn` is not a function, this method returns undefined.
- * @param {Function} fn - The function to call.
- * @param {Array|undefined|null} args - The arguments with which `fn` should be called.
- * @param {Object} [thisArg] - The value of `this` provided for the call to `fn`.
- * @returns {*}
- */
- callback: function(fn, args, thisArg) {
- if (fn && typeof fn.call === 'function') {
- return fn.apply(thisArg, args);
- }
- },
-
- /**
- * Note(SB) for performance sake, this method should only be used when loopable type
- * is unknown or in none intensive code (not called often and small loopable). Else
- * it's preferable to use a regular for() loop and save extra function calls.
- * @param {Object|Array} loopable - The object or array to be iterated.
- * @param {Function} fn - The function to call for each item.
- * @param {Object} [thisArg] - The value of `this` provided for the call to `fn`.
- * @param {Boolean} [reverse] - If true, iterates backward on the loopable.
- */
- each: function(loopable, fn, thisArg, reverse) {
- var i, len, keys;
- if (helpers.isArray(loopable)) {
- len = loopable.length;
- if (reverse) {
- for (i = len - 1; i >= 0; i--) {
- fn.call(thisArg, loopable[i], i);
- }
- } else {
- for (i = 0; i < len; i++) {
- fn.call(thisArg, loopable[i], i);
- }
- }
- } else if (helpers.isObject(loopable)) {
- keys = Object.keys(loopable);
- len = keys.length;
- for (i = 0; i < len; i++) {
- fn.call(thisArg, loopable[keys[i]], keys[i]);
- }
- }
- },
-
- /**
- * Returns true if the `a0` and `a1` arrays have the same content, else returns false.
- * @see http://stackoverflow.com/a/14853974
- * @param {Array} a0 - The array to compare
- * @param {Array} a1 - The array to compare
- * @returns {Boolean}
- */
- arrayEquals: function(a0, a1) {
- var i, ilen, v0, v1;
-
- if (!a0 || !a1 || a0.length !== a1.length) {
- return false;
- }
-
- for (i = 0, ilen = a0.length; i < ilen; ++i) {
- v0 = a0[i];
- v1 = a1[i];
-
- if (v0 instanceof Array && v1 instanceof Array) {
- if (!helpers.arrayEquals(v0, v1)) {
- return false;
- }
- } else if (v0 !== v1) {
- // NOTE: two different object instances will never be equal: {x:20} != {x:20}
- return false;
- }
- }
-
- return true;
- },
-
- /**
- * Returns a deep copy of `source` without keeping references on objects and arrays.
- * @param {*} source - The value to clone.
- * @returns {*}
- */
- clone: function(source) {
- if (helpers.isArray(source)) {
- return source.map(helpers.clone);
- }
-
- if (helpers.isObject(source)) {
- var target = {};
- var keys = Object.keys(source);
- var klen = keys.length;
- var k = 0;
-
- for (; k < klen; ++k) {
- target[keys[k]] = helpers.clone(source[keys[k]]);
- }
-
- return target;
- }
-
- return source;
- },
-
- /**
- * The default merger when Chart.helpers.merge is called without merger option.
- * Note(SB): this method is also used by configMerge and scaleMerge as fallback.
- * @private
- */
- _merger: function(key, target, source, options) {
- var tval = target[key];
- var sval = source[key];
-
- if (helpers.isObject(tval) && helpers.isObject(sval)) {
- helpers.merge(tval, sval, options);
- } else {
- target[key] = helpers.clone(sval);
- }
- },
-
- /**
- * Merges source[key] in target[key] only if target[key] is undefined.
- * @private
- */
- _mergerIf: function(key, target, source) {
- var tval = target[key];
- var sval = source[key];
-
- if (helpers.isObject(tval) && helpers.isObject(sval)) {
- helpers.mergeIf(tval, sval);
- } else if (!target.hasOwnProperty(key)) {
- target[key] = helpers.clone(sval);
- }
- },
-
- /**
- * Recursively deep copies `source` properties into `target` with the given `options`.
- * IMPORTANT: `target` is not cloned and will be updated with `source` properties.
- * @param {Object} target - The target object in which all sources are merged into.
- * @param {Object|Array(Object)} source - Object(s) to merge into `target`.
- * @param {Object} [options] - Merging options:
- * @param {Function} [options.merger] - The merge method (key, target, source, options)
- * @returns {Object} The `target` object.
- */
- merge: function(target, source, options) {
- var sources = helpers.isArray(source) ? source : [source];
- var ilen = sources.length;
- var merge, i, keys, klen, k;
-
- if (!helpers.isObject(target)) {
- return target;
- }
-
- options = options || {};
- merge = options.merger || helpers._merger;
-
- for (i = 0; i < ilen; ++i) {
- source = sources[i];
- if (!helpers.isObject(source)) {
- continue;
- }
-
- keys = Object.keys(source);
- for (k = 0, klen = keys.length; k < klen; ++k) {
- merge(keys[k], target, source, options);
- }
- }
-
- return target;
- },
-
- /**
- * Recursively deep copies `source` properties into `target` *only* if not defined in target.
- * IMPORTANT: `target` is not cloned and will be updated with `source` properties.
- * @param {Object} target - The target object in which all sources are merged into.
- * @param {Object|Array(Object)} source - Object(s) to merge into `target`.
- * @returns {Object} The `target` object.
- */
- mergeIf: function(target, source) {
- return helpers.merge(target, source, {merger: helpers._mergerIf});
- },
-
- /**
- * Applies the contents of two or more objects together into the first object.
- * @param {Object} target - The target object in which all objects are merged into.
- * @param {Object} arg1 - Object containing additional properties to merge in target.
- * @param {Object} argN - Additional objects containing properties to merge in target.
- * @returns {Object} The `target` object.
- */
- extend: function(target) {
- var setFn = function(value, key) {
- target[key] = value;
- };
- for (var i = 1, ilen = arguments.length; i < ilen; ++i) {
- helpers.each(arguments[i], setFn);
- }
- return target;
- },
-
- /**
- * Basic javascript inheritance based on the model created in Backbone.js
- */
- inherits: function(extensions) {
- var me = this;
- var ChartElement = (extensions && extensions.hasOwnProperty('constructor')) ? extensions.constructor : function() {
- return me.apply(this, arguments);
- };
-
- var Surrogate = function() {
- this.constructor = ChartElement;
- };
-
- Surrogate.prototype = me.prototype;
- ChartElement.prototype = new Surrogate();
- ChartElement.extend = helpers.inherits;
-
- if (extensions) {
- helpers.extend(ChartElement.prototype, extensions);
- }
-
- ChartElement.__super__ = me.prototype;
- return ChartElement;
- }
-};
-
-module.exports = helpers;
-
-// DEPRECATIONS
-
-/**
- * Provided for backward compatibility, use Chart.helpers.callback instead.
- * @function Chart.helpers.callCallback
- * @deprecated since version 2.6.0
- * @todo remove at version 3
- * @private
- */
-helpers.callCallback = helpers.callback;
-
-/**
- * Provided for backward compatibility, use Array.prototype.indexOf instead.
- * Array.prototype.indexOf compatibility: Chrome, Opera, Safari, FF1.5+, IE9+
- * @function Chart.helpers.indexOf
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.indexOf = function(array, item, fromIndex) {
- return Array.prototype.indexOf.call(array, item, fromIndex);
-};
-
-/**
- * Provided for backward compatibility, use Chart.helpers.valueOrDefault instead.
- * @function Chart.helpers.getValueOrDefault
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.getValueOrDefault = helpers.valueOrDefault;
-
-/**
- * Provided for backward compatibility, use Chart.helpers.valueAtIndexOrDefault instead.
- * @function Chart.helpers.getValueAtIndexOrDefault
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.getValueAtIndexOrDefault = helpers.valueAtIndexOrDefault;
-
-},{}],44:[function(require,module,exports){
-'use strict';
-
-var helpers = require(43);
-
-/**
- * Easing functions adapted from Robert Penner's easing equations.
- * @namespace Chart.helpers.easingEffects
- * @see http://www.robertpenner.com/easing/
- */
-var effects = {
- linear: function(t) {
- return t;
- },
-
- easeInQuad: function(t) {
- return t * t;
- },
-
- easeOutQuad: function(t) {
- return -t * (t - 2);
- },
-
- easeInOutQuad: function(t) {
- if ((t /= 0.5) < 1) {
- return 0.5 * t * t;
- }
- return -0.5 * ((--t) * (t - 2) - 1);
- },
-
- easeInCubic: function(t) {
- return t * t * t;
- },
-
- easeOutCubic: function(t) {
- return (t = t - 1) * t * t + 1;
- },
-
- easeInOutCubic: function(t) {
- if ((t /= 0.5) < 1) {
- return 0.5 * t * t * t;
- }
- return 0.5 * ((t -= 2) * t * t + 2);
- },
-
- easeInQuart: function(t) {
- return t * t * t * t;
- },
-
- easeOutQuart: function(t) {
- return -((t = t - 1) * t * t * t - 1);
- },
-
- easeInOutQuart: function(t) {
- if ((t /= 0.5) < 1) {
- return 0.5 * t * t * t * t;
- }
- return -0.5 * ((t -= 2) * t * t * t - 2);
- },
-
- easeInQuint: function(t) {
- return t * t * t * t * t;
- },
-
- easeOutQuint: function(t) {
- return (t = t - 1) * t * t * t * t + 1;
- },
-
- easeInOutQuint: function(t) {
- if ((t /= 0.5) < 1) {
- return 0.5 * t * t * t * t * t;
- }
- return 0.5 * ((t -= 2) * t * t * t * t + 2);
- },
-
- easeInSine: function(t) {
- return -Math.cos(t * (Math.PI / 2)) + 1;
- },
-
- easeOutSine: function(t) {
- return Math.sin(t * (Math.PI / 2));
- },
-
- easeInOutSine: function(t) {
- return -0.5 * (Math.cos(Math.PI * t) - 1);
- },
-
- easeInExpo: function(t) {
- return (t === 0) ? 0 : Math.pow(2, 10 * (t - 1));
- },
-
- easeOutExpo: function(t) {
- return (t === 1) ? 1 : -Math.pow(2, -10 * t) + 1;
- },
-
- easeInOutExpo: function(t) {
- if (t === 0) {
- return 0;
- }
- if (t === 1) {
- return 1;
- }
- if ((t /= 0.5) < 1) {
- return 0.5 * Math.pow(2, 10 * (t - 1));
- }
- return 0.5 * (-Math.pow(2, -10 * --t) + 2);
- },
-
- easeInCirc: function(t) {
- if (t >= 1) {
- return t;
- }
- return -(Math.sqrt(1 - t * t) - 1);
- },
-
- easeOutCirc: function(t) {
- return Math.sqrt(1 - (t = t - 1) * t);
- },
-
- easeInOutCirc: function(t) {
- if ((t /= 0.5) < 1) {
- return -0.5 * (Math.sqrt(1 - t * t) - 1);
- }
- return 0.5 * (Math.sqrt(1 - (t -= 2) * t) + 1);
- },
-
- easeInElastic: function(t) {
- var s = 1.70158;
- var p = 0;
- var a = 1;
- if (t === 0) {
- return 0;
- }
- if (t === 1) {
- return 1;
- }
- if (!p) {
- p = 0.3;
- }
- if (a < 1) {
- a = 1;
- s = p / 4;
- } else {
- s = p / (2 * Math.PI) * Math.asin(1 / a);
- }
- return -(a * Math.pow(2, 10 * (t -= 1)) * Math.sin((t - s) * (2 * Math.PI) / p));
- },
-
- easeOutElastic: function(t) {
- var s = 1.70158;
- var p = 0;
- var a = 1;
- if (t === 0) {
- return 0;
- }
- if (t === 1) {
- return 1;
- }
- if (!p) {
- p = 0.3;
- }
- if (a < 1) {
- a = 1;
- s = p / 4;
- } else {
- s = p / (2 * Math.PI) * Math.asin(1 / a);
- }
- return a * Math.pow(2, -10 * t) * Math.sin((t - s) * (2 * Math.PI) / p) + 1;
- },
-
- easeInOutElastic: function(t) {
- var s = 1.70158;
- var p = 0;
- var a = 1;
- if (t === 0) {
- return 0;
- }
- if ((t /= 0.5) === 2) {
- return 1;
- }
- if (!p) {
- p = 0.45;
- }
- if (a < 1) {
- a = 1;
- s = p / 4;
- } else {
- s = p / (2 * Math.PI) * Math.asin(1 / a);
- }
- if (t < 1) {
- return -0.5 * (a * Math.pow(2, 10 * (t -= 1)) * Math.sin((t - s) * (2 * Math.PI) / p));
- }
- return a * Math.pow(2, -10 * (t -= 1)) * Math.sin((t - s) * (2 * Math.PI) / p) * 0.5 + 1;
- },
- easeInBack: function(t) {
- var s = 1.70158;
- return t * t * ((s + 1) * t - s);
- },
-
- easeOutBack: function(t) {
- var s = 1.70158;
- return (t = t - 1) * t * ((s + 1) * t + s) + 1;
- },
-
- easeInOutBack: function(t) {
- var s = 1.70158;
- if ((t /= 0.5) < 1) {
- return 0.5 * (t * t * (((s *= (1.525)) + 1) * t - s));
- }
- return 0.5 * ((t -= 2) * t * (((s *= (1.525)) + 1) * t + s) + 2);
- },
-
- easeInBounce: function(t) {
- return 1 - effects.easeOutBounce(1 - t);
- },
-
- easeOutBounce: function(t) {
- if (t < (1 / 2.75)) {
- return 7.5625 * t * t;
- }
- if (t < (2 / 2.75)) {
- return 7.5625 * (t -= (1.5 / 2.75)) * t + 0.75;
- }
- if (t < (2.5 / 2.75)) {
- return 7.5625 * (t -= (2.25 / 2.75)) * t + 0.9375;
- }
- return 7.5625 * (t -= (2.625 / 2.75)) * t + 0.984375;
- },
-
- easeInOutBounce: function(t) {
- if (t < 0.5) {
- return effects.easeInBounce(t * 2) * 0.5;
- }
- return effects.easeOutBounce(t * 2 - 1) * 0.5 + 0.5;
- }
-};
-
-module.exports = {
- effects: effects
-};
-
-// DEPRECATIONS
-
-/**
- * Provided for backward compatibility, use Chart.helpers.easing.effects instead.
- * @function Chart.helpers.easingEffects
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.easingEffects = effects;
-
-},{"43":43}],45:[function(require,module,exports){
-'use strict';
-
-var helpers = require(43);
-
-/**
- * @alias Chart.helpers.options
- * @namespace
- */
-module.exports = {
- /**
- * Converts the given line height `value` in pixels for a specific font `size`.
- * @param {Number|String} value - The lineHeight to parse (eg. 1.6, '14px', '75%', '1.6em').
- * @param {Number} size - The font size (in pixels) used to resolve relative `value`.
- * @returns {Number} The effective line height in pixels (size * 1.2 if value is invalid).
- * @see https://developer.mozilla.org/en-US/docs/Web/CSS/line-height
- * @since 2.7.0
- */
- toLineHeight: function(value, size) {
- var matches = ('' + value).match(/^(normal|(\d+(?:\.\d+)?)(px|em|%)?)$/);
- if (!matches || matches[1] === 'normal') {
- return size * 1.2;
- }
-
- value = +matches[2];
-
- switch (matches[3]) {
- case 'px':
- return value;
- case '%':
- value /= 100;
- break;
- default:
- break;
- }
-
- return size * value;
- },
-
- /**
- * Converts the given value into a padding object with pre-computed width/height.
- * @param {Number|Object} value - If a number, set the value to all TRBL component,
- * else, if and object, use defined properties and sets undefined ones to 0.
- * @returns {Object} The padding values (top, right, bottom, left, width, height)
- * @since 2.7.0
- */
- toPadding: function(value) {
- var t, r, b, l;
-
- if (helpers.isObject(value)) {
- t = +value.top || 0;
- r = +value.right || 0;
- b = +value.bottom || 0;
- l = +value.left || 0;
- } else {
- t = r = b = l = +value || 0;
- }
-
- return {
- top: t,
- right: r,
- bottom: b,
- left: l,
- height: t + b,
- width: l + r
- };
- },
-
- /**
- * Evaluates the given `inputs` sequentially and returns the first defined value.
- * @param {Array[]} inputs - An array of values, falling back to the last value.
- * @param {Object} [context] - If defined and the current value is a function, the value
- * is called with `context` as first argument and the result becomes the new input.
- * @param {Number} [index] - If defined and the current value is an array, the value
- * at `index` become the new input.
- * @since 2.7.0
- */
- resolve: function(inputs, context, index) {
- var i, ilen, value;
-
- for (i = 0, ilen = inputs.length; i < ilen; ++i) {
- value = inputs[i];
- if (value === undefined) {
- continue;
- }
- if (context !== undefined && typeof value === 'function') {
- value = value(context);
- }
- if (index !== undefined && helpers.isArray(value)) {
- value = value[index];
- }
- if (value !== undefined) {
- return value;
- }
- }
- }
-};
-
-},{"43":43}],46:[function(require,module,exports){
-'use strict';
-
-module.exports = require(43);
-module.exports.easing = require(44);
-module.exports.canvas = require(42);
-module.exports.options = require(45);
-
-},{"42":42,"43":43,"44":44,"45":45}],47:[function(require,module,exports){
-/**
- * Platform fallback implementation (minimal).
- * @see https://github.com/chartjs/Chart.js/pull/4591#issuecomment-319575939
- */
-
-module.exports = {
- acquireContext: function(item) {
- if (item && item.canvas) {
- // Support for any object associated to a canvas (including a context2d)
- item = item.canvas;
- }
-
- return item && item.getContext('2d') || null;
- }
-};
-
-},{}],48:[function(require,module,exports){
-/**
- * Chart.Platform implementation for targeting a web browser
- */
-
-'use strict';
-
-var helpers = require(46);
-
-var EXPANDO_KEY = '$chartjs';
-var CSS_PREFIX = 'chartjs-';
-var CSS_RENDER_MONITOR = CSS_PREFIX + 'render-monitor';
-var CSS_RENDER_ANIMATION = CSS_PREFIX + 'render-animation';
-var ANIMATION_START_EVENTS = ['animationstart', 'webkitAnimationStart'];
-
-/**
- * DOM event types -> Chart.js event types.
- * Note: only events with different types are mapped.
- * @see https://developer.mozilla.org/en-US/docs/Web/Events
- */
-var EVENT_TYPES = {
- touchstart: 'mousedown',
- touchmove: 'mousemove',
- touchend: 'mouseup',
- pointerenter: 'mouseenter',
- pointerdown: 'mousedown',
- pointermove: 'mousemove',
- pointerup: 'mouseup',
- pointerleave: 'mouseout',
- pointerout: 'mouseout'
-};
-
-/**
- * The "used" size is the final value of a dimension property after all calculations have
- * been performed. This method uses the computed style of `element` but returns undefined
- * if the computed style is not expressed in pixels. That can happen in some cases where
- * `element` has a size relative to its parent and this last one is not yet displayed,
- * for example because of `display: none` on a parent node.
- * @see https://developer.mozilla.org/en-US/docs/Web/CSS/used_value
- * @returns {Number} Size in pixels or undefined if unknown.
- */
-function readUsedSize(element, property) {
- var value = helpers.getStyle(element, property);
- var matches = value && value.match(/^(\d+)(\.\d+)?px$/);
- return matches ? Number(matches[1]) : undefined;
-}
-
-/**
- * Initializes the canvas style and render size without modifying the canvas display size,
- * since responsiveness is handled by the controller.resize() method. The config is used
- * to determine the aspect ratio to apply in case no explicit height has been specified.
- */
-function initCanvas(canvas, config) {
- var style = canvas.style;
-
- // NOTE(SB) canvas.getAttribute('width') !== canvas.width: in the first case it
- // returns null or '' if no explicit value has been set to the canvas attribute.
- var renderHeight = canvas.getAttribute('height');
- var renderWidth = canvas.getAttribute('width');
-
- // Chart.js modifies some canvas values that we want to restore on destroy
- canvas[EXPANDO_KEY] = {
- initial: {
- height: renderHeight,
- width: renderWidth,
- style: {
- display: style.display,
- height: style.height,
- width: style.width
- }
- }
- };
-
- // Force canvas to display as block to avoid extra space caused by inline
- // elements, which would interfere with the responsive resize process.
- // https://github.com/chartjs/Chart.js/issues/2538
- style.display = style.display || 'block';
-
- if (renderWidth === null || renderWidth === '') {
- var displayWidth = readUsedSize(canvas, 'width');
- if (displayWidth !== undefined) {
- canvas.width = displayWidth;
- }
- }
-
- if (renderHeight === null || renderHeight === '') {
- if (canvas.style.height === '') {
- // If no explicit render height and style height, let's apply the aspect ratio,
- // which one can be specified by the user but also by charts as default option
- // (i.e. options.aspectRatio). If not specified, use canvas aspect ratio of 2.
- canvas.height = canvas.width / (config.options.aspectRatio || 2);
- } else {
- var displayHeight = readUsedSize(canvas, 'height');
- if (displayWidth !== undefined) {
- canvas.height = displayHeight;
- }
- }
- }
-
- return canvas;
-}
-
-/**
- * Detects support for options object argument in addEventListener.
- * https://developer.mozilla.org/en-US/docs/Web/API/EventTarget/addEventListener#Safely_detecting_option_support
- * @private
- */
-var supportsEventListenerOptions = (function() {
- var supports = false;
- try {
- var options = Object.defineProperty({}, 'passive', {
- get: function() {
- supports = true;
- }
- });
- window.addEventListener('e', null, options);
- } catch (e) {
- // continue regardless of error
- }
- return supports;
-}());
-
-// Default passive to true as expected by Chrome for 'touchstart' and 'touchend' events.
-// https://github.com/chartjs/Chart.js/issues/4287
-var eventListenerOptions = supportsEventListenerOptions ? {passive: true} : false;
-
-function addEventListener(node, type, listener) {
- node.addEventListener(type, listener, eventListenerOptions);
-}
-
-function removeEventListener(node, type, listener) {
- node.removeEventListener(type, listener, eventListenerOptions);
-}
-
-function createEvent(type, chart, x, y, nativeEvent) {
- return {
- type: type,
- chart: chart,
- native: nativeEvent || null,
- x: x !== undefined ? x : null,
- y: y !== undefined ? y : null,
- };
-}
-
-function fromNativeEvent(event, chart) {
- var type = EVENT_TYPES[event.type] || event.type;
- var pos = helpers.getRelativePosition(event, chart);
- return createEvent(type, chart, pos.x, pos.y, event);
-}
-
-function throttled(fn, thisArg) {
- var ticking = false;
- var args = [];
-
- return function() {
- args = Array.prototype.slice.call(arguments);
- thisArg = thisArg || this;
-
- if (!ticking) {
- ticking = true;
- helpers.requestAnimFrame.call(window, function() {
- ticking = false;
- fn.apply(thisArg, args);
- });
- }
- };
-}
-
-// Implementation based on https://github.com/marcj/css-element-queries
-function createResizer(handler) {
- var resizer = document.createElement('div');
- var cls = CSS_PREFIX + 'size-monitor';
- var maxSize = 1000000;
- var style =
- 'position:absolute;' +
- 'left:0;' +
- 'top:0;' +
- 'right:0;' +
- 'bottom:0;' +
- 'overflow:hidden;' +
- 'pointer-events:none;' +
- 'visibility:hidden;' +
- 'z-index:-1;';
-
- resizer.style.cssText = style;
- resizer.className = cls;
- resizer.innerHTML =
- '<div class="' + cls + '-expand" style="' + style + '">' +
- '<div style="' +
- 'position:absolute;' +
- 'width:' + maxSize + 'px;' +
- 'height:' + maxSize + 'px;' +
- 'left:0;' +
- 'top:0">' +
- '</div>' +
- '</div>' +
- '<div class="' + cls + '-shrink" style="' + style + '">' +
- '<div style="' +
- 'position:absolute;' +
- 'width:200%;' +
- 'height:200%;' +
- 'left:0; ' +
- 'top:0">' +
- '</div>' +
- '</div>';
-
- var expand = resizer.childNodes[0];
- var shrink = resizer.childNodes[1];
-
- resizer._reset = function() {
- expand.scrollLeft = maxSize;
- expand.scrollTop = maxSize;
- shrink.scrollLeft = maxSize;
- shrink.scrollTop = maxSize;
- };
- var onScroll = function() {
- resizer._reset();
- handler();
- };
-
- addEventListener(expand, 'scroll', onScroll.bind(expand, 'expand'));
- addEventListener(shrink, 'scroll', onScroll.bind(shrink, 'shrink'));
-
- return resizer;
-}
-
-// https://davidwalsh.name/detect-node-insertion
-function watchForRender(node, handler) {
- var expando = node[EXPANDO_KEY] || (node[EXPANDO_KEY] = {});
- var proxy = expando.renderProxy = function(e) {
- if (e.animationName === CSS_RENDER_ANIMATION) {
- handler();
- }
- };
-
- helpers.each(ANIMATION_START_EVENTS, function(type) {
- addEventListener(node, type, proxy);
- });
-
- // #4737: Chrome might skip the CSS animation when the CSS_RENDER_MONITOR class
- // is removed then added back immediately (same animation frame?). Accessing the
- // `offsetParent` property will force a reflow and re-evaluate the CSS animation.
- // https://gist.github.com/paulirish/5d52fb081b3570c81e3a#box-metrics
- // https://github.com/chartjs/Chart.js/issues/4737
- expando.reflow = !!node.offsetParent;
-
- node.classList.add(CSS_RENDER_MONITOR);
-}
-
-function unwatchForRender(node) {
- var expando = node[EXPANDO_KEY] || {};
- var proxy = expando.renderProxy;
-
- if (proxy) {
- helpers.each(ANIMATION_START_EVENTS, function(type) {
- removeEventListener(node, type, proxy);
- });
-
- delete expando.renderProxy;
- }
-
- node.classList.remove(CSS_RENDER_MONITOR);
-}
-
-function addResizeListener(node, listener, chart) {
- var expando = node[EXPANDO_KEY] || (node[EXPANDO_KEY] = {});
-
- // Let's keep track of this added resizer and thus avoid DOM query when removing it.
- var resizer = expando.resizer = createResizer(throttled(function() {
- if (expando.resizer) {
- return listener(createEvent('resize', chart));
- }
- }));
-
- // The resizer needs to be attached to the node parent, so we first need to be
- // sure that `node` is attached to the DOM before injecting the resizer element.
- watchForRender(node, function() {
- if (expando.resizer) {
- var container = node.parentNode;
- if (container && container !== resizer.parentNode) {
- container.insertBefore(resizer, container.firstChild);
- }
-
- // The container size might have changed, let's reset the resizer state.
- resizer._reset();
- }
- });
-}
-
-function removeResizeListener(node) {
- var expando = node[EXPANDO_KEY] || {};
- var resizer = expando.resizer;
-
- delete expando.resizer;
- unwatchForRender(node);
-
- if (resizer && resizer.parentNode) {
- resizer.parentNode.removeChild(resizer);
- }
-}
-
-function injectCSS(platform, css) {
- // http://stackoverflow.com/q/3922139
- var style = platform._style || document.createElement('style');
- if (!platform._style) {
- platform._style = style;
- css = '/* Chart.js */\n' + css;
- style.setAttribute('type', 'text/css');
- document.getElementsByTagName('head')[0].appendChild(style);
- }
-
- style.appendChild(document.createTextNode(css));
-}
-
-module.exports = {
- /**
- * This property holds whether this platform is enabled for the current environment.
- * Currently used by platform.js to select the proper implementation.
- * @private
- */
- _enabled: typeof window !== 'undefined' && typeof document !== 'undefined',
-
- initialize: function() {
- var keyframes = 'from{opacity:0.99}to{opacity:1}';
-
- injectCSS(this,
- // DOM rendering detection
- // https://davidwalsh.name/detect-node-insertion
- '@-webkit-keyframes ' + CSS_RENDER_ANIMATION + '{' + keyframes + '}' +
- '@keyframes ' + CSS_RENDER_ANIMATION + '{' + keyframes + '}' +
- '.' + CSS_RENDER_MONITOR + '{' +
- '-webkit-animation:' + CSS_RENDER_ANIMATION + ' 0.001s;' +
- 'animation:' + CSS_RENDER_ANIMATION + ' 0.001s;' +
- '}'
- );
- },
-
- acquireContext: function(item, config) {
- if (typeof item === 'string') {
- item = document.getElementById(item);
- } else if (item.length) {
- // Support for array based queries (such as jQuery)
- item = item[0];
- }
-
- if (item && item.canvas) {
- // Support for any object associated to a canvas (including a context2d)
- item = item.canvas;
- }
-
- // To prevent canvas fingerprinting, some add-ons undefine the getContext
- // method, for example: https://github.com/kkapsner/CanvasBlocker
- // https://github.com/chartjs/Chart.js/issues/2807
- var context = item && item.getContext && item.getContext('2d');
-
- // `instanceof HTMLCanvasElement/CanvasRenderingContext2D` fails when the item is
- // inside an iframe or when running in a protected environment. We could guess the
- // types from their toString() value but let's keep things flexible and assume it's
- // a sufficient condition if the item has a context2D which has item as `canvas`.
- // https://github.com/chartjs/Chart.js/issues/3887
- // https://github.com/chartjs/Chart.js/issues/4102
- // https://github.com/chartjs/Chart.js/issues/4152
- if (context && context.canvas === item) {
- initCanvas(item, config);
- return context;
- }
-
- return null;
- },
-
- releaseContext: function(context) {
- var canvas = context.canvas;
- if (!canvas[EXPANDO_KEY]) {
- return;
- }
-
- var initial = canvas[EXPANDO_KEY].initial;
- ['height', 'width'].forEach(function(prop) {
- var value = initial[prop];
- if (helpers.isNullOrUndef(value)) {
- canvas.removeAttribute(prop);
- } else {
- canvas.setAttribute(prop, value);
- }
- });
-
- helpers.each(initial.style || {}, function(value, key) {
- canvas.style[key] = value;
- });
-
- // The canvas render size might have been changed (and thus the state stack discarded),
- // we can't use save() and restore() to restore the initial state. So make sure that at
- // least the canvas context is reset to the default state by setting the canvas width.
- // https://www.w3.org/TR/2011/WD-html5-20110525/the-canvas-element.html
- canvas.width = canvas.width;
-
- delete canvas[EXPANDO_KEY];
- },
-
- addEventListener: function(chart, type, listener) {
- var canvas = chart.canvas;
- if (type === 'resize') {
- // Note: the resize event is not supported on all browsers.
- addResizeListener(canvas, listener, chart);
- return;
- }
-
- var expando = listener[EXPANDO_KEY] || (listener[EXPANDO_KEY] = {});
- var proxies = expando.proxies || (expando.proxies = {});
- var proxy = proxies[chart.id + '_' + type] = function(event) {
- listener(fromNativeEvent(event, chart));
- };
-
- addEventListener(canvas, type, proxy);
- },
-
- removeEventListener: function(chart, type, listener) {
- var canvas = chart.canvas;
- if (type === 'resize') {
- // Note: the resize event is not supported on all browsers.
- removeResizeListener(canvas, listener);
- return;
- }
-
- var expando = listener[EXPANDO_KEY] || {};
- var proxies = expando.proxies || {};
- var proxy = proxies[chart.id + '_' + type];
- if (!proxy) {
- return;
- }
-
- removeEventListener(canvas, type, proxy);
- }
-};
-
-// DEPRECATIONS
-
-/**
- * Provided for backward compatibility, use EventTarget.addEventListener instead.
- * EventTarget.addEventListener compatibility: Chrome, Opera 7, Safari, FF1.5+, IE9+
- * @see https://developer.mozilla.org/en-US/docs/Web/API/EventTarget/addEventListener
- * @function Chart.helpers.addEvent
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.addEvent = addEventListener;
-
-/**
- * Provided for backward compatibility, use EventTarget.removeEventListener instead.
- * EventTarget.removeEventListener compatibility: Chrome, Opera 7, Safari, FF1.5+, IE9+
- * @see https://developer.mozilla.org/en-US/docs/Web/API/EventTarget/removeEventListener
- * @function Chart.helpers.removeEvent
- * @deprecated since version 2.7.0
- * @todo remove at version 3
- * @private
- */
-helpers.removeEvent = removeEventListener;
-
-},{"46":46}],49:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-var basic = require(47);
-var dom = require(48);
-
-// @TODO Make possible to select another platform at build time.
-var implementation = dom._enabled ? dom : basic;
-
-/**
- * @namespace Chart.platform
- * @see https://chartjs.gitbooks.io/proposals/content/Platform.html
- * @since 2.4.0
- */
-module.exports = helpers.extend({
- /**
- * @since 2.7.0
- */
- initialize: function() {},
-
- /**
- * Called at chart construction time, returns a context2d instance implementing
- * the [W3C Canvas 2D Context API standard]{@link https://www.w3.org/TR/2dcontext/}.
- * @param {*} item - The native item from which to acquire context (platform specific)
- * @param {Object} options - The chart options
- * @returns {CanvasRenderingContext2D} context2d instance
- */
- acquireContext: function() {},
-
- /**
- * Called at chart destruction time, releases any resources associated to the context
- * previously returned by the acquireContext() method.
- * @param {CanvasRenderingContext2D} context - The context2d instance
- * @returns {Boolean} true if the method succeeded, else false
- */
- releaseContext: function() {},
-
- /**
- * Registers the specified listener on the given chart.
- * @param {Chart} chart - Chart from which to listen for event
- * @param {String} type - The ({@link IEvent}) type to listen for
- * @param {Function} listener - Receives a notification (an object that implements
- * the {@link IEvent} interface) when an event of the specified type occurs.
- */
- addEventListener: function() {},
-
- /**
- * Removes the specified listener previously registered with addEventListener.
- * @param {Chart} chart -Chart from which to remove the listener
- * @param {String} type - The ({@link IEvent}) type to remove
- * @param {Function} listener - The listener function to remove from the event target.
- */
- removeEventListener: function() {}
-
-}, implementation);
-
-/**
- * @interface IPlatform
- * Allows abstracting platform dependencies away from the chart
- * @borrows Chart.platform.acquireContext as acquireContext
- * @borrows Chart.platform.releaseContext as releaseContext
- * @borrows Chart.platform.addEventListener as addEventListener
- * @borrows Chart.platform.removeEventListener as removeEventListener
- */
-
-/**
- * @interface IEvent
- * @prop {String} type - The event type name, possible values are:
- * 'contextmenu', 'mouseenter', 'mousedown', 'mousemove', 'mouseup', 'mouseout',
- * 'click', 'dblclick', 'keydown', 'keypress', 'keyup' and 'resize'
- * @prop {*} native - The original native event (null for emulated events, e.g. 'resize')
- * @prop {Number} x - The mouse x position, relative to the canvas (null for incompatible events)
- * @prop {Number} y - The mouse y position, relative to the canvas (null for incompatible events)
- */
-
-},{"46":46,"47":47,"48":48}],50:[function(require,module,exports){
-'use strict';
-
-module.exports = {};
-module.exports.filler = require(51);
-module.exports.legend = require(52);
-module.exports.title = require(53);
-
-},{"51":51,"52":52,"53":53}],51:[function(require,module,exports){
-/**
- * Plugin based on discussion from the following Chart.js issues:
- * @see https://github.com/chartjs/Chart.js/issues/2380#issuecomment-279961569
- * @see https://github.com/chartjs/Chart.js/issues/2440#issuecomment-256461897
- */
-
-'use strict';
-
-var defaults = require(26);
-var elements = require(41);
-var helpers = require(46);
-
-defaults._set('global', {
- plugins: {
- filler: {
- propagate: true
- }
- }
-});
-
-var mappers = {
- dataset: function(source) {
- var index = source.fill;
- var chart = source.chart;
- var meta = chart.getDatasetMeta(index);
- var visible = meta && chart.isDatasetVisible(index);
- var points = (visible && meta.dataset._children) || [];
- var length = points.length || 0;
-
- return !length ? null : function(point, i) {
- return (i < length && points[i]._view) || null;
- };
- },
-
- boundary: function(source) {
- var boundary = source.boundary;
- var x = boundary ? boundary.x : null;
- var y = boundary ? boundary.y : null;
-
- return function(point) {
- return {
- x: x === null ? point.x : x,
- y: y === null ? point.y : y,
- };
- };
- }
-};
-
-// @todo if (fill[0] === '#')
-function decodeFill(el, index, count) {
- var model = el._model || {};
- var fill = model.fill;
- var target;
-
- if (fill === undefined) {
- fill = !!model.backgroundColor;
- }
-
- if (fill === false || fill === null) {
- return false;
- }
-
- if (fill === true) {
- return 'origin';
- }
-
- target = parseFloat(fill, 10);
- if (isFinite(target) && Math.floor(target) === target) {
- if (fill[0] === '-' || fill[0] === '+') {
- target = index + target;
- }
-
- if (target === index || target < 0 || target >= count) {
- return false;
- }
-
- return target;
- }
-
- switch (fill) {
- // compatibility
- case 'bottom':
- return 'start';
- case 'top':
- return 'end';
- case 'zero':
- return 'origin';
- // supported boundaries
- case 'origin':
- case 'start':
- case 'end':
- return fill;
- // invalid fill values
- default:
- return false;
- }
-}
-
-function computeBoundary(source) {
- var model = source.el._model || {};
- var scale = source.el._scale || {};
- var fill = source.fill;
- var target = null;
- var horizontal;
-
- if (isFinite(fill)) {
- return null;
- }
-
- // Backward compatibility: until v3, we still need to support boundary values set on
- // the model (scaleTop, scaleBottom and scaleZero) because some external plugins and
- // controllers might still use it (e.g. the Smith chart).
-
- if (fill === 'start') {
- target = model.scaleBottom === undefined ? scale.bottom : model.scaleBottom;
- } else if (fill === 'end') {
- target = model.scaleTop === undefined ? scale.top : model.scaleTop;
- } else if (model.scaleZero !== undefined) {
- target = model.scaleZero;
- } else if (scale.getBasePosition) {
- target = scale.getBasePosition();
- } else if (scale.getBasePixel) {
- target = scale.getBasePixel();
- }
-
- if (target !== undefined && target !== null) {
- if (target.x !== undefined && target.y !== undefined) {
- return target;
- }
-
- if (typeof target === 'number' && isFinite(target)) {
- horizontal = scale.isHorizontal();
- return {
- x: horizontal ? target : null,
- y: horizontal ? null : target
- };
- }
- }
-
- return null;
-}
-
-function resolveTarget(sources, index, propagate) {
- var source = sources[index];
- var fill = source.fill;
- var visited = [index];
- var target;
-
- if (!propagate) {
- return fill;
- }
-
- while (fill !== false && visited.indexOf(fill) === -1) {
- if (!isFinite(fill)) {
- return fill;
- }
-
- target = sources[fill];
- if (!target) {
- return false;
- }
-
- if (target.visible) {
- return fill;
- }
-
- visited.push(fill);
- fill = target.fill;
- }
-
- return false;
-}
-
-function createMapper(source) {
- var fill = source.fill;
- var type = 'dataset';
-
- if (fill === false) {
- return null;
- }
-
- if (!isFinite(fill)) {
- type = 'boundary';
- }
-
- return mappers[type](source);
-}
-
-function isDrawable(point) {
- return point && !point.skip;
-}
-
-function drawArea(ctx, curve0, curve1, len0, len1) {
- var i;
-
- if (!len0 || !len1) {
- return;
- }
-
- // building first area curve (normal)
- ctx.moveTo(curve0[0].x, curve0[0].y);
- for (i = 1; i < len0; ++i) {
- helpers.canvas.lineTo(ctx, curve0[i - 1], curve0[i]);
- }
-
- // joining the two area curves
- ctx.lineTo(curve1[len1 - 1].x, curve1[len1 - 1].y);
-
- // building opposite area curve (reverse)
- for (i = len1 - 1; i > 0; --i) {
- helpers.canvas.lineTo(ctx, curve1[i], curve1[i - 1], true);
- }
-}
-
-function doFill(ctx, points, mapper, view, color, loop) {
- var count = points.length;
- var span = view.spanGaps;
- var curve0 = [];
- var curve1 = [];
- var len0 = 0;
- var len1 = 0;
- var i, ilen, index, p0, p1, d0, d1;
-
- ctx.beginPath();
-
- for (i = 0, ilen = (count + !!loop); i < ilen; ++i) {
- index = i % count;
- p0 = points[index]._view;
- p1 = mapper(p0, index, view);
- d0 = isDrawable(p0);
- d1 = isDrawable(p1);
-
- if (d0 && d1) {
- len0 = curve0.push(p0);
- len1 = curve1.push(p1);
- } else if (len0 && len1) {
- if (!span) {
- drawArea(ctx, curve0, curve1, len0, len1);
- len0 = len1 = 0;
- curve0 = [];
- curve1 = [];
- } else {
- if (d0) {
- curve0.push(p0);
- }
- if (d1) {
- curve1.push(p1);
- }
- }
- }
- }
-
- drawArea(ctx, curve0, curve1, len0, len1);
-
- ctx.closePath();
- ctx.fillStyle = color;
- ctx.fill();
-}
-
-module.exports = {
- id: 'filler',
-
- afterDatasetsUpdate: function(chart, options) {
- var count = (chart.data.datasets || []).length;
- var propagate = options.propagate;
- var sources = [];
- var meta, i, el, source;
-
- for (i = 0; i < count; ++i) {
- meta = chart.getDatasetMeta(i);
- el = meta.dataset;
- source = null;
-
- if (el && el._model && el instanceof elements.Line) {
- source = {
- visible: chart.isDatasetVisible(i),
- fill: decodeFill(el, i, count),
- chart: chart,
- el: el
- };
- }
-
- meta.$filler = source;
- sources.push(source);
- }
-
- for (i = 0; i < count; ++i) {
- source = sources[i];
- if (!source) {
- continue;
- }
-
- source.fill = resolveTarget(sources, i, propagate);
- source.boundary = computeBoundary(source);
- source.mapper = createMapper(source);
- }
- },
-
- beforeDatasetDraw: function(chart, args) {
- var meta = args.meta.$filler;
- if (!meta) {
- return;
- }
-
- var ctx = chart.ctx;
- var el = meta.el;
- var view = el._view;
- var points = el._children || [];
- var mapper = meta.mapper;
- var color = view.backgroundColor || defaults.global.defaultColor;
-
- if (mapper && color && points.length) {
- helpers.canvas.clipArea(ctx, chart.chartArea);
- doFill(ctx, points, mapper, view, color, el._loop);
- helpers.canvas.unclipArea(ctx);
- }
- }
-};
-
-},{"26":26,"41":41,"46":46}],52:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-var helpers = require(46);
-var layouts = require(31);
-
-var noop = helpers.noop;
-
-defaults._set('global', {
- legend: {
- display: true,
- position: 'top',
- fullWidth: true,
- reverse: false,
- weight: 1000,
-
- // a callback that will handle
- onClick: function(e, legendItem) {
- var index = legendItem.datasetIndex;
- var ci = this.chart;
- var meta = ci.getDatasetMeta(index);
-
- // See controller.isDatasetVisible comment
- meta.hidden = meta.hidden === null ? !ci.data.datasets[index].hidden : null;
-
- // We hid a dataset ... rerender the chart
- ci.update();
- },
-
- onHover: null,
-
- labels: {
- boxWidth: 40,
- padding: 10,
- // Generates labels shown in the legend
- // Valid properties to return:
- // text : text to display
- // fillStyle : fill of coloured box
- // strokeStyle: stroke of coloured box
- // hidden : if this legend item refers to a hidden item
- // lineCap : cap style for line
- // lineDash
- // lineDashOffset :
- // lineJoin :
- // lineWidth :
- generateLabels: function(chart) {
- var data = chart.data;
- return helpers.isArray(data.datasets) ? data.datasets.map(function(dataset, i) {
- return {
- text: dataset.label,
- fillStyle: (!helpers.isArray(dataset.backgroundColor) ? dataset.backgroundColor : dataset.backgroundColor[0]),
- hidden: !chart.isDatasetVisible(i),
- lineCap: dataset.borderCapStyle,
- lineDash: dataset.borderDash,
- lineDashOffset: dataset.borderDashOffset,
- lineJoin: dataset.borderJoinStyle,
- lineWidth: dataset.borderWidth,
- strokeStyle: dataset.borderColor,
- pointStyle: dataset.pointStyle,
-
- // Below is extra data used for toggling the datasets
- datasetIndex: i
- };
- }, this) : [];
- }
- }
- },
-
- legendCallback: function(chart) {
- var text = [];
- text.push('<ul class="' + chart.id + '-legend">');
- for (var i = 0; i < chart.data.datasets.length; i++) {
- text.push('<li><span style="background-color:' + chart.data.datasets[i].backgroundColor + '"></span>');
- if (chart.data.datasets[i].label) {
- text.push(chart.data.datasets[i].label);
- }
- text.push('</li>');
- }
- text.push('</ul>');
- return text.join('');
- }
-});
-
-/**
- * Helper function to get the box width based on the usePointStyle option
- * @param labelopts {Object} the label options on the legend
- * @param fontSize {Number} the label font size
- * @return {Number} width of the color box area
- */
-function getBoxWidth(labelOpts, fontSize) {
- return labelOpts.usePointStyle ?
- fontSize * Math.SQRT2 :
- labelOpts.boxWidth;
-}
-
-/**
- * IMPORTANT: this class is exposed publicly as Chart.Legend, backward compatibility required!
- */
-var Legend = Element.extend({
-
- initialize: function(config) {
- helpers.extend(this, config);
-
- // Contains hit boxes for each dataset (in dataset order)
- this.legendHitBoxes = [];
-
- // Are we in doughnut mode which has a different data type
- this.doughnutMode = false;
- },
-
- // These methods are ordered by lifecycle. Utilities then follow.
- // Any function defined here is inherited by all legend types.
- // Any function can be extended by the legend type
-
- beforeUpdate: noop,
- update: function(maxWidth, maxHeight, margins) {
- var me = this;
-
- // Update Lifecycle - Probably don't want to ever extend or overwrite this function ;)
- me.beforeUpdate();
-
- // Absorb the master measurements
- me.maxWidth = maxWidth;
- me.maxHeight = maxHeight;
- me.margins = margins;
-
- // Dimensions
- me.beforeSetDimensions();
- me.setDimensions();
- me.afterSetDimensions();
- // Labels
- me.beforeBuildLabels();
- me.buildLabels();
- me.afterBuildLabels();
-
- // Fit
- me.beforeFit();
- me.fit();
- me.afterFit();
- //
- me.afterUpdate();
-
- return me.minSize;
- },
- afterUpdate: noop,
-
- //
-
- beforeSetDimensions: noop,
- setDimensions: function() {
- var me = this;
- // Set the unconstrained dimension before label rotation
- if (me.isHorizontal()) {
- // Reset position before calculating rotation
- me.width = me.maxWidth;
- me.left = 0;
- me.right = me.width;
- } else {
- me.height = me.maxHeight;
-
- // Reset position before calculating rotation
- me.top = 0;
- me.bottom = me.height;
- }
-
- // Reset padding
- me.paddingLeft = 0;
- me.paddingTop = 0;
- me.paddingRight = 0;
- me.paddingBottom = 0;
-
- // Reset minSize
- me.minSize = {
- width: 0,
- height: 0
- };
- },
- afterSetDimensions: noop,
-
- //
-
- beforeBuildLabels: noop,
- buildLabels: function() {
- var me = this;
- var labelOpts = me.options.labels || {};
- var legendItems = helpers.callback(labelOpts.generateLabels, [me.chart], me) || [];
-
- if (labelOpts.filter) {
- legendItems = legendItems.filter(function(item) {
- return labelOpts.filter(item, me.chart.data);
- });
- }
-
- if (me.options.reverse) {
- legendItems.reverse();
- }
-
- me.legendItems = legendItems;
- },
- afterBuildLabels: noop,
-
- //
-
- beforeFit: noop,
- fit: function() {
- var me = this;
- var opts = me.options;
- var labelOpts = opts.labels;
- var display = opts.display;
-
- var ctx = me.ctx;
-
- var globalDefault = defaults.global;
- var valueOrDefault = helpers.valueOrDefault;
- var fontSize = valueOrDefault(labelOpts.fontSize, globalDefault.defaultFontSize);
- var fontStyle = valueOrDefault(labelOpts.fontStyle, globalDefault.defaultFontStyle);
- var fontFamily = valueOrDefault(labelOpts.fontFamily, globalDefault.defaultFontFamily);
- var labelFont = helpers.fontString(fontSize, fontStyle, fontFamily);
-
- // Reset hit boxes
- var hitboxes = me.legendHitBoxes = [];
-
- var minSize = me.minSize;
- var isHorizontal = me.isHorizontal();
-
- if (isHorizontal) {
- minSize.width = me.maxWidth; // fill all the width
- minSize.height = display ? 10 : 0;
- } else {
- minSize.width = display ? 10 : 0;
- minSize.height = me.maxHeight; // fill all the height
- }
-
- // Increase sizes here
- if (display) {
- ctx.font = labelFont;
-
- if (isHorizontal) {
- // Labels
-
- // Width of each line of legend boxes. Labels wrap onto multiple lines when there are too many to fit on one
- var lineWidths = me.lineWidths = [0];
- var totalHeight = me.legendItems.length ? fontSize + (labelOpts.padding) : 0;
-
- ctx.textAlign = 'left';
- ctx.textBaseline = 'top';
-
- helpers.each(me.legendItems, function(legendItem, i) {
- var boxWidth = getBoxWidth(labelOpts, fontSize);
- var width = boxWidth + (fontSize / 2) + ctx.measureText(legendItem.text).width;
-
- if (lineWidths[lineWidths.length - 1] + width + labelOpts.padding >= me.width) {
- totalHeight += fontSize + (labelOpts.padding);
- lineWidths[lineWidths.length] = me.left;
- }
-
- // Store the hitbox width and height here. Final position will be updated in `draw`
- hitboxes[i] = {
- left: 0,
- top: 0,
- width: width,
- height: fontSize
- };
-
- lineWidths[lineWidths.length - 1] += width + labelOpts.padding;
- });
-
- minSize.height += totalHeight;
-
- } else {
- var vPadding = labelOpts.padding;
- var columnWidths = me.columnWidths = [];
- var totalWidth = labelOpts.padding;
- var currentColWidth = 0;
- var currentColHeight = 0;
- var itemHeight = fontSize + vPadding;
-
- helpers.each(me.legendItems, function(legendItem, i) {
- var boxWidth = getBoxWidth(labelOpts, fontSize);
- var itemWidth = boxWidth + (fontSize / 2) + ctx.measureText(legendItem.text).width;
-
- // If too tall, go to new column
- if (currentColHeight + itemHeight > minSize.height) {
- totalWidth += currentColWidth + labelOpts.padding;
- columnWidths.push(currentColWidth); // previous column width
-
- currentColWidth = 0;
- currentColHeight = 0;
- }
-
- // Get max width
- currentColWidth = Math.max(currentColWidth, itemWidth);
- currentColHeight += itemHeight;
-
- // Store the hitbox width and height here. Final position will be updated in `draw`
- hitboxes[i] = {
- left: 0,
- top: 0,
- width: itemWidth,
- height: fontSize
- };
- });
-
- totalWidth += currentColWidth;
- columnWidths.push(currentColWidth);
- minSize.width += totalWidth;
- }
- }
-
- me.width = minSize.width;
- me.height = minSize.height;
- },
- afterFit: noop,
-
- // Shared Methods
- isHorizontal: function() {
- return this.options.position === 'top' || this.options.position === 'bottom';
- },
-
- // Actually draw the legend on the canvas
- draw: function() {
- var me = this;
- var opts = me.options;
- var labelOpts = opts.labels;
- var globalDefault = defaults.global;
- var lineDefault = globalDefault.elements.line;
- var legendWidth = me.width;
- var lineWidths = me.lineWidths;
-
- if (opts.display) {
- var ctx = me.ctx;
- var valueOrDefault = helpers.valueOrDefault;
- var fontColor = valueOrDefault(labelOpts.fontColor, globalDefault.defaultFontColor);
- var fontSize = valueOrDefault(labelOpts.fontSize, globalDefault.defaultFontSize);
- var fontStyle = valueOrDefault(labelOpts.fontStyle, globalDefault.defaultFontStyle);
- var fontFamily = valueOrDefault(labelOpts.fontFamily, globalDefault.defaultFontFamily);
- var labelFont = helpers.fontString(fontSize, fontStyle, fontFamily);
- var cursor;
-
- // Canvas setup
- ctx.textAlign = 'left';
- ctx.textBaseline = 'middle';
- ctx.lineWidth = 0.5;
- ctx.strokeStyle = fontColor; // for strikethrough effect
- ctx.fillStyle = fontColor; // render in correct colour
- ctx.font = labelFont;
-
- var boxWidth = getBoxWidth(labelOpts, fontSize);
- var hitboxes = me.legendHitBoxes;
-
- // current position
- var drawLegendBox = function(x, y, legendItem) {
- if (isNaN(boxWidth) || boxWidth <= 0) {
- return;
- }
-
- // Set the ctx for the box
- ctx.save();
-
- ctx.fillStyle = valueOrDefault(legendItem.fillStyle, globalDefault.defaultColor);
- ctx.lineCap = valueOrDefault(legendItem.lineCap, lineDefault.borderCapStyle);
- ctx.lineDashOffset = valueOrDefault(legendItem.lineDashOffset, lineDefault.borderDashOffset);
- ctx.lineJoin = valueOrDefault(legendItem.lineJoin, lineDefault.borderJoinStyle);
- ctx.lineWidth = valueOrDefault(legendItem.lineWidth, lineDefault.borderWidth);
- ctx.strokeStyle = valueOrDefault(legendItem.strokeStyle, globalDefault.defaultColor);
- var isLineWidthZero = (valueOrDefault(legendItem.lineWidth, lineDefault.borderWidth) === 0);
-
- if (ctx.setLineDash) {
- // IE 9 and 10 do not support line dash
- ctx.setLineDash(valueOrDefault(legendItem.lineDash, lineDefault.borderDash));
- }
-
- if (opts.labels && opts.labels.usePointStyle) {
- // Recalculate x and y for drawPoint() because its expecting
- // x and y to be center of figure (instead of top left)
- var radius = fontSize * Math.SQRT2 / 2;
- var offSet = radius / Math.SQRT2;
- var centerX = x + offSet;
- var centerY = y + offSet;
-
- // Draw pointStyle as legend symbol
- helpers.canvas.drawPoint(ctx, legendItem.pointStyle, radius, centerX, centerY);
- } else {
- // Draw box as legend symbol
- if (!isLineWidthZero) {
- ctx.strokeRect(x, y, boxWidth, fontSize);
- }
- ctx.fillRect(x, y, boxWidth, fontSize);
- }
-
- ctx.restore();
- };
- var fillText = function(x, y, legendItem, textWidth) {
- var halfFontSize = fontSize / 2;
- var xLeft = boxWidth + halfFontSize + x;
- var yMiddle = y + halfFontSize;
-
- ctx.fillText(legendItem.text, xLeft, yMiddle);
-
- if (legendItem.hidden) {
- // Strikethrough the text if hidden
- ctx.beginPath();
- ctx.lineWidth = 2;
- ctx.moveTo(xLeft, yMiddle);
- ctx.lineTo(xLeft + textWidth, yMiddle);
- ctx.stroke();
- }
- };
-
- // Horizontal
- var isHorizontal = me.isHorizontal();
- if (isHorizontal) {
- cursor = {
- x: me.left + ((legendWidth - lineWidths[0]) / 2),
- y: me.top + labelOpts.padding,
- line: 0
- };
- } else {
- cursor = {
- x: me.left + labelOpts.padding,
- y: me.top + labelOpts.padding,
- line: 0
- };
- }
-
- var itemHeight = fontSize + labelOpts.padding;
- helpers.each(me.legendItems, function(legendItem, i) {
- var textWidth = ctx.measureText(legendItem.text).width;
- var width = boxWidth + (fontSize / 2) + textWidth;
- var x = cursor.x;
- var y = cursor.y;
-
- if (isHorizontal) {
- if (x + width >= legendWidth) {
- y = cursor.y += itemHeight;
- cursor.line++;
- x = cursor.x = me.left + ((legendWidth - lineWidths[cursor.line]) / 2);
- }
- } else if (y + itemHeight > me.bottom) {
- x = cursor.x = x + me.columnWidths[cursor.line] + labelOpts.padding;
- y = cursor.y = me.top + labelOpts.padding;
- cursor.line++;
- }
-
- drawLegendBox(x, y, legendItem);
-
- hitboxes[i].left = x;
- hitboxes[i].top = y;
-
- // Fill the actual label
- fillText(x, y, legendItem, textWidth);
-
- if (isHorizontal) {
- cursor.x += width + (labelOpts.padding);
- } else {
- cursor.y += itemHeight;
- }
-
- });
- }
- },
-
- /**
- * Handle an event
- * @private
- * @param {IEvent} event - The event to handle
- * @return {Boolean} true if a change occured
- */
- handleEvent: function(e) {
- var me = this;
- var opts = me.options;
- var type = e.type === 'mouseup' ? 'click' : e.type;
- var changed = false;
-
- if (type === 'mousemove') {
- if (!opts.onHover) {
- return;
- }
- } else if (type === 'click') {
- if (!opts.onClick) {
- return;
- }
- } else {
- return;
- }
-
- // Chart event already has relative position in it
- var x = e.x;
- var y = e.y;
-
- if (x >= me.left && x <= me.right && y >= me.top && y <= me.bottom) {
- // See if we are touching one of the dataset boxes
- var lh = me.legendHitBoxes;
- for (var i = 0; i < lh.length; ++i) {
- var hitBox = lh[i];
-
- if (x >= hitBox.left && x <= hitBox.left + hitBox.width && y >= hitBox.top && y <= hitBox.top + hitBox.height) {
- // Touching an element
- if (type === 'click') {
- // use e.native for backwards compatibility
- opts.onClick.call(me, e.native, me.legendItems[i]);
- changed = true;
- break;
- } else if (type === 'mousemove') {
- // use e.native for backwards compatibility
- opts.onHover.call(me, e.native, me.legendItems[i]);
- changed = true;
- break;
- }
- }
- }
- }
-
- return changed;
- }
-});
-
-function createNewLegendAndAttach(chart, legendOpts) {
- var legend = new Legend({
- ctx: chart.ctx,
- options: legendOpts,
- chart: chart
- });
-
- layouts.configure(chart, legend, legendOpts);
- layouts.addBox(chart, legend);
- chart.legend = legend;
-}
-
-module.exports = {
- id: 'legend',
-
- /**
- * Backward compatibility: since 2.1.5, the legend is registered as a plugin, making
- * Chart.Legend obsolete. To avoid a breaking change, we export the Legend as part of
- * the plugin, which one will be re-exposed in the chart.js file.
- * https://github.com/chartjs/Chart.js/pull/2640
- * @private
- */
- _element: Legend,
-
- beforeInit: function(chart) {
- var legendOpts = chart.options.legend;
-
- if (legendOpts) {
- createNewLegendAndAttach(chart, legendOpts);
- }
- },
-
- beforeUpdate: function(chart) {
- var legendOpts = chart.options.legend;
- var legend = chart.legend;
-
- if (legendOpts) {
- helpers.mergeIf(legendOpts, defaults.global.legend);
-
- if (legend) {
- layouts.configure(chart, legend, legendOpts);
- legend.options = legendOpts;
- } else {
- createNewLegendAndAttach(chart, legendOpts);
- }
- } else if (legend) {
- layouts.removeBox(chart, legend);
- delete chart.legend;
- }
- },
-
- afterEvent: function(chart, e) {
- var legend = chart.legend;
- if (legend) {
- legend.handleEvent(e);
- }
- }
-};
-
-},{"26":26,"27":27,"31":31,"46":46}],53:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var Element = require(27);
-var helpers = require(46);
-var layouts = require(31);
-
-var noop = helpers.noop;
-
-defaults._set('global', {
- title: {
- display: false,
- fontStyle: 'bold',
- fullWidth: true,
- lineHeight: 1.2,
- padding: 10,
- position: 'top',
- text: '',
- weight: 2000 // by default greater than legend (1000) to be above
- }
-});
-
-/**
- * IMPORTANT: this class is exposed publicly as Chart.Legend, backward compatibility required!
- */
-var Title = Element.extend({
- initialize: function(config) {
- var me = this;
- helpers.extend(me, config);
-
- // Contains hit boxes for each dataset (in dataset order)
- me.legendHitBoxes = [];
- },
-
- // These methods are ordered by lifecycle. Utilities then follow.
-
- beforeUpdate: noop,
- update: function(maxWidth, maxHeight, margins) {
- var me = this;
-
- // Update Lifecycle - Probably don't want to ever extend or overwrite this function ;)
- me.beforeUpdate();
-
- // Absorb the master measurements
- me.maxWidth = maxWidth;
- me.maxHeight = maxHeight;
- me.margins = margins;
-
- // Dimensions
- me.beforeSetDimensions();
- me.setDimensions();
- me.afterSetDimensions();
- // Labels
- me.beforeBuildLabels();
- me.buildLabels();
- me.afterBuildLabels();
-
- // Fit
- me.beforeFit();
- me.fit();
- me.afterFit();
- //
- me.afterUpdate();
-
- return me.minSize;
-
- },
- afterUpdate: noop,
-
- //
-
- beforeSetDimensions: noop,
- setDimensions: function() {
- var me = this;
- // Set the unconstrained dimension before label rotation
- if (me.isHorizontal()) {
- // Reset position before calculating rotation
- me.width = me.maxWidth;
- me.left = 0;
- me.right = me.width;
- } else {
- me.height = me.maxHeight;
-
- // Reset position before calculating rotation
- me.top = 0;
- me.bottom = me.height;
- }
-
- // Reset padding
- me.paddingLeft = 0;
- me.paddingTop = 0;
- me.paddingRight = 0;
- me.paddingBottom = 0;
-
- // Reset minSize
- me.minSize = {
- width: 0,
- height: 0
- };
- },
- afterSetDimensions: noop,
-
- //
-
- beforeBuildLabels: noop,
- buildLabels: noop,
- afterBuildLabels: noop,
-
- //
-
- beforeFit: noop,
- fit: function() {
- var me = this;
- var valueOrDefault = helpers.valueOrDefault;
- var opts = me.options;
- var display = opts.display;
- var fontSize = valueOrDefault(opts.fontSize, defaults.global.defaultFontSize);
- var minSize = me.minSize;
- var lineCount = helpers.isArray(opts.text) ? opts.text.length : 1;
- var lineHeight = helpers.options.toLineHeight(opts.lineHeight, fontSize);
- var textSize = display ? (lineCount * lineHeight) + (opts.padding * 2) : 0;
-
- if (me.isHorizontal()) {
- minSize.width = me.maxWidth; // fill all the width
- minSize.height = textSize;
- } else {
- minSize.width = textSize;
- minSize.height = me.maxHeight; // fill all the height
- }
-
- me.width = minSize.width;
- me.height = minSize.height;
-
- },
- afterFit: noop,
-
- // Shared Methods
- isHorizontal: function() {
- var pos = this.options.position;
- return pos === 'top' || pos === 'bottom';
- },
-
- // Actually draw the title block on the canvas
- draw: function() {
- var me = this;
- var ctx = me.ctx;
- var valueOrDefault = helpers.valueOrDefault;
- var opts = me.options;
- var globalDefaults = defaults.global;
-
- if (opts.display) {
- var fontSize = valueOrDefault(opts.fontSize, globalDefaults.defaultFontSize);
- var fontStyle = valueOrDefault(opts.fontStyle, globalDefaults.defaultFontStyle);
- var fontFamily = valueOrDefault(opts.fontFamily, globalDefaults.defaultFontFamily);
- var titleFont = helpers.fontString(fontSize, fontStyle, fontFamily);
- var lineHeight = helpers.options.toLineHeight(opts.lineHeight, fontSize);
- var offset = lineHeight / 2 + opts.padding;
- var rotation = 0;
- var top = me.top;
- var left = me.left;
- var bottom = me.bottom;
- var right = me.right;
- var maxWidth, titleX, titleY;
-
- ctx.fillStyle = valueOrDefault(opts.fontColor, globalDefaults.defaultFontColor); // render in correct colour
- ctx.font = titleFont;
-
- // Horizontal
- if (me.isHorizontal()) {
- titleX = left + ((right - left) / 2); // midpoint of the width
- titleY = top + offset;
- maxWidth = right - left;
- } else {
- titleX = opts.position === 'left' ? left + offset : right - offset;
- titleY = top + ((bottom - top) / 2);
- maxWidth = bottom - top;
- rotation = Math.PI * (opts.position === 'left' ? -0.5 : 0.5);
- }
-
- ctx.save();
- ctx.translate(titleX, titleY);
- ctx.rotate(rotation);
- ctx.textAlign = 'center';
- ctx.textBaseline = 'middle';
-
- var text = opts.text;
- if (helpers.isArray(text)) {
- var y = 0;
- for (var i = 0; i < text.length; ++i) {
- ctx.fillText(text[i], 0, y, maxWidth);
- y += lineHeight;
- }
- } else {
- ctx.fillText(text, 0, 0, maxWidth);
- }
-
- ctx.restore();
- }
- }
-});
-
-function createNewTitleBlockAndAttach(chart, titleOpts) {
- var title = new Title({
- ctx: chart.ctx,
- options: titleOpts,
- chart: chart
- });
-
- layouts.configure(chart, title, titleOpts);
- layouts.addBox(chart, title);
- chart.titleBlock = title;
-}
-
-module.exports = {
- id: 'title',
-
- /**
- * Backward compatibility: since 2.1.5, the title is registered as a plugin, making
- * Chart.Title obsolete. To avoid a breaking change, we export the Title as part of
- * the plugin, which one will be re-exposed in the chart.js file.
- * https://github.com/chartjs/Chart.js/pull/2640
- * @private
- */
- _element: Title,
-
- beforeInit: function(chart) {
- var titleOpts = chart.options.title;
-
- if (titleOpts) {
- createNewTitleBlockAndAttach(chart, titleOpts);
- }
- },
-
- beforeUpdate: function(chart) {
- var titleOpts = chart.options.title;
- var titleBlock = chart.titleBlock;
-
- if (titleOpts) {
- helpers.mergeIf(titleOpts, defaults.global.title);
-
- if (titleBlock) {
- layouts.configure(chart, titleBlock, titleOpts);
- titleBlock.options = titleOpts;
- } else {
- createNewTitleBlockAndAttach(chart, titleOpts);
- }
- } else if (titleBlock) {
- layouts.removeBox(chart, titleBlock);
- delete chart.titleBlock;
- }
- }
-};
-
-},{"26":26,"27":27,"31":31,"46":46}],54:[function(require,module,exports){
-'use strict';
-
-var Scale = require(33);
-var scaleService = require(34);
-
-module.exports = function() {
-
- // Default config for a category scale
- var defaultConfig = {
- position: 'bottom'
- };
-
- var DatasetScale = Scale.extend({
- /**
- * Internal function to get the correct labels. If data.xLabels or data.yLabels are defined, use those
- * else fall back to data.labels
- * @private
- */
- getLabels: function() {
- var data = this.chart.data;
- return this.options.labels || (this.isHorizontal() ? data.xLabels : data.yLabels) || data.labels;
- },
-
- determineDataLimits: function() {
- var me = this;
- var labels = me.getLabels();
- me.minIndex = 0;
- me.maxIndex = labels.length - 1;
- var findIndex;
-
- if (me.options.ticks.min !== undefined) {
- // user specified min value
- findIndex = labels.indexOf(me.options.ticks.min);
- me.minIndex = findIndex !== -1 ? findIndex : me.minIndex;
- }
-
- if (me.options.ticks.max !== undefined) {
- // user specified max value
- findIndex = labels.indexOf(me.options.ticks.max);
- me.maxIndex = findIndex !== -1 ? findIndex : me.maxIndex;
- }
-
- me.min = labels[me.minIndex];
- me.max = labels[me.maxIndex];
- },
-
- buildTicks: function() {
- var me = this;
- var labels = me.getLabels();
- // If we are viewing some subset of labels, slice the original array
- me.ticks = (me.minIndex === 0 && me.maxIndex === labels.length - 1) ? labels : labels.slice(me.minIndex, me.maxIndex + 1);
- },
-
- getLabelForIndex: function(index, datasetIndex) {
- var me = this;
- var data = me.chart.data;
- var isHorizontal = me.isHorizontal();
-
- if (data.yLabels && !isHorizontal) {
- return me.getRightValue(data.datasets[datasetIndex].data[index]);
- }
- return me.ticks[index - me.minIndex];
- },
-
- // Used to get data value locations. Value can either be an index or a numerical value
- getPixelForValue: function(value, index) {
- var me = this;
- var offset = me.options.offset;
- // 1 is added because we need the length but we have the indexes
- var offsetAmt = Math.max((me.maxIndex + 1 - me.minIndex - (offset ? 0 : 1)), 1);
-
- // If value is a data object, then index is the index in the data array,
- // not the index of the scale. We need to change that.
- var valueCategory;
- if (value !== undefined && value !== null) {
- valueCategory = me.isHorizontal() ? value.x : value.y;
- }
- if (valueCategory !== undefined || (value !== undefined && isNaN(index))) {
- var labels = me.getLabels();
- value = valueCategory || value;
- var idx = labels.indexOf(value);
- index = idx !== -1 ? idx : index;
- }
-
- if (me.isHorizontal()) {
- var valueWidth = me.width / offsetAmt;
- var widthOffset = (valueWidth * (index - me.minIndex));
-
- if (offset) {
- widthOffset += (valueWidth / 2);
- }
-
- return me.left + Math.round(widthOffset);
- }
- var valueHeight = me.height / offsetAmt;
- var heightOffset = (valueHeight * (index - me.minIndex));
-
- if (offset) {
- heightOffset += (valueHeight / 2);
- }
-
- return me.top + Math.round(heightOffset);
- },
- getPixelForTick: function(index) {
- return this.getPixelForValue(this.ticks[index], index + this.minIndex, null);
- },
- getValueForPixel: function(pixel) {
- var me = this;
- var offset = me.options.offset;
- var value;
- var offsetAmt = Math.max((me._ticks.length - (offset ? 0 : 1)), 1);
- var horz = me.isHorizontal();
- var valueDimension = (horz ? me.width : me.height) / offsetAmt;
-
- pixel -= horz ? me.left : me.top;
-
- if (offset) {
- pixel -= (valueDimension / 2);
- }
-
- if (pixel <= 0) {
- value = 0;
- } else {
- value = Math.round(pixel / valueDimension);
- }
-
- return value + me.minIndex;
- },
- getBasePixel: function() {
- return this.bottom;
- }
- });
-
- scaleService.registerScaleType('category', DatasetScale, defaultConfig);
-};
-
-},{"33":33,"34":34}],55:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var helpers = require(46);
-var scaleService = require(34);
-var Ticks = require(35);
-
-module.exports = function(Chart) {
-
- var defaultConfig = {
- position: 'left',
- ticks: {
- callback: Ticks.formatters.linear
- }
- };
-
- var LinearScale = Chart.LinearScaleBase.extend({
-
- determineDataLimits: function() {
- var me = this;
- var opts = me.options;
- var chart = me.chart;
- var data = chart.data;
- var datasets = data.datasets;
- var isHorizontal = me.isHorizontal();
- var DEFAULT_MIN = 0;
- var DEFAULT_MAX = 1;
-
- function IDMatches(meta) {
- return isHorizontal ? meta.xAxisID === me.id : meta.yAxisID === me.id;
- }
-
- // First Calculate the range
- me.min = null;
- me.max = null;
-
- var hasStacks = opts.stacked;
- if (hasStacks === undefined) {
- helpers.each(datasets, function(dataset, datasetIndex) {
- if (hasStacks) {
- return;
- }
-
- var meta = chart.getDatasetMeta(datasetIndex);
- if (chart.isDatasetVisible(datasetIndex) && IDMatches(meta) &&
- meta.stack !== undefined) {
- hasStacks = true;
- }
- });
- }
-
- if (opts.stacked || hasStacks) {
- var valuesPerStack = {};
-
- helpers.each(datasets, function(dataset, datasetIndex) {
- var meta = chart.getDatasetMeta(datasetIndex);
- var key = [
- meta.type,
- // we have a separate stack for stack=undefined datasets when the opts.stacked is undefined
- ((opts.stacked === undefined && meta.stack === undefined) ? datasetIndex : ''),
- meta.stack
- ].join('.');
-
- if (valuesPerStack[key] === undefined) {
- valuesPerStack[key] = {
- positiveValues: [],
- negativeValues: []
- };
- }
-
- // Store these per type
- var positiveValues = valuesPerStack[key].positiveValues;
- var negativeValues = valuesPerStack[key].negativeValues;
-
- if (chart.isDatasetVisible(datasetIndex) && IDMatches(meta)) {
- helpers.each(dataset.data, function(rawValue, index) {
- var value = +me.getRightValue(rawValue);
- if (isNaN(value) || meta.data[index].hidden) {
- return;
- }
-
- positiveValues[index] = positiveValues[index] || 0;
- negativeValues[index] = negativeValues[index] || 0;
-
- if (opts.relativePoints) {
- positiveValues[index] = 100;
- } else if (value < 0) {
- negativeValues[index] += value;
- } else {
- positiveValues[index] += value;
- }
- });
- }
- });
-
- helpers.each(valuesPerStack, function(valuesForType) {
- var values = valuesForType.positiveValues.concat(valuesForType.negativeValues);
- var minVal = helpers.min(values);
- var maxVal = helpers.max(values);
- me.min = me.min === null ? minVal : Math.min(me.min, minVal);
- me.max = me.max === null ? maxVal : Math.max(me.max, maxVal);
- });
-
- } else {
- helpers.each(datasets, function(dataset, datasetIndex) {
- var meta = chart.getDatasetMeta(datasetIndex);
- if (chart.isDatasetVisible(datasetIndex) && IDMatches(meta)) {
- helpers.each(dataset.data, function(rawValue, index) {
- var value = +me.getRightValue(rawValue);
- if (isNaN(value) || meta.data[index].hidden) {
- return;
- }
-
- if (me.min === null) {
- me.min = value;
- } else if (value < me.min) {
- me.min = value;
- }
-
- if (me.max === null) {
- me.max = value;
- } else if (value > me.max) {
- me.max = value;
- }
- });
- }
- });
- }
-
- me.min = isFinite(me.min) && !isNaN(me.min) ? me.min : DEFAULT_MIN;
- me.max = isFinite(me.max) && !isNaN(me.max) ? me.max : DEFAULT_MAX;
-
- // Common base implementation to handle ticks.min, ticks.max, ticks.beginAtZero
- this.handleTickRangeOptions();
- },
- getTickLimit: function() {
- var maxTicks;
- var me = this;
- var tickOpts = me.options.ticks;
-
- if (me.isHorizontal()) {
- maxTicks = Math.min(tickOpts.maxTicksLimit ? tickOpts.maxTicksLimit : 11, Math.ceil(me.width / 50));
- } else {
- // The factor of 2 used to scale the font size has been experimentally determined.
- var tickFontSize = helpers.valueOrDefault(tickOpts.fontSize, defaults.global.defaultFontSize);
- maxTicks = Math.min(tickOpts.maxTicksLimit ? tickOpts.maxTicksLimit : 11, Math.ceil(me.height / (2 * tickFontSize)));
- }
-
- return maxTicks;
- },
- // Called after the ticks are built. We need
- handleDirectionalChanges: function() {
- if (!this.isHorizontal()) {
- // We are in a vertical orientation. The top value is the highest. So reverse the array
- this.ticks.reverse();
- }
- },
- getLabelForIndex: function(index, datasetIndex) {
- return +this.getRightValue(this.chart.data.datasets[datasetIndex].data[index]);
- },
- // Utils
- getPixelForValue: function(value) {
- // This must be called after fit has been run so that
- // this.left, this.top, this.right, and this.bottom have been defined
- var me = this;
- var start = me.start;
-
- var rightValue = +me.getRightValue(value);
- var pixel;
- var range = me.end - start;
-
- if (me.isHorizontal()) {
- pixel = me.left + (me.width / range * (rightValue - start));
- } else {
- pixel = me.bottom - (me.height / range * (rightValue - start));
- }
- return pixel;
- },
- getValueForPixel: function(pixel) {
- var me = this;
- var isHorizontal = me.isHorizontal();
- var innerDimension = isHorizontal ? me.width : me.height;
- var offset = (isHorizontal ? pixel - me.left : me.bottom - pixel) / innerDimension;
- return me.start + ((me.end - me.start) * offset);
- },
- getPixelForTick: function(index) {
- return this.getPixelForValue(this.ticksAsNumbers[index]);
- }
- });
-
- scaleService.registerScaleType('linear', LinearScale, defaultConfig);
-};
-
-},{"26":26,"34":34,"35":35,"46":46}],56:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-var Scale = require(33);
-
-/**
- * Generate a set of linear ticks
- * @param generationOptions the options used to generate the ticks
- * @param dataRange the range of the data
- * @returns {Array<Number>} array of tick values
- */
-function generateTicks(generationOptions, dataRange) {
- var ticks = [];
- // To get a "nice" value for the tick spacing, we will use the appropriately named
- // "nice number" algorithm. See http://stackoverflow.com/questions/8506881/nice-label-algorithm-for-charts-with-minimum-ticks
- // for details.
-
- var factor;
- var precision;
- var spacing;
-
- if (generationOptions.stepSize && generationOptions.stepSize > 0) {
- spacing = generationOptions.stepSize;
- } else {
- var niceRange = helpers.niceNum(dataRange.max - dataRange.min, false);
- spacing = helpers.niceNum(niceRange / (generationOptions.maxTicks - 1), true);
-
- precision = generationOptions.precision;
- if (precision !== undefined) {
- // If the user specified a precision, round to that number of decimal places
- factor = Math.pow(10, precision);
- spacing = Math.ceil(spacing * factor) / factor;
- }
- }
- var niceMin = Math.floor(dataRange.min / spacing) * spacing;
- var niceMax = Math.ceil(dataRange.max / spacing) * spacing;
-
- // If min, max and stepSize is set and they make an evenly spaced scale use it.
- if (!helpers.isNullOrUndef(generationOptions.min) && !helpers.isNullOrUndef(generationOptions.max) && generationOptions.stepSize) {
- // If very close to our whole number, use it.
- if (helpers.almostWhole((generationOptions.max - generationOptions.min) / generationOptions.stepSize, spacing / 1000)) {
- niceMin = generationOptions.min;
- niceMax = generationOptions.max;
- }
- }
-
- var numSpaces = (niceMax - niceMin) / spacing;
- // If very close to our rounded value, use it.
- if (helpers.almostEquals(numSpaces, Math.round(numSpaces), spacing / 1000)) {
- numSpaces = Math.round(numSpaces);
- } else {
- numSpaces = Math.ceil(numSpaces);
- }
-
- precision = 1;
- if (spacing < 1) {
- precision = Math.pow(10, 1 - Math.floor(helpers.log10(spacing)));
- niceMin = Math.round(niceMin * precision) / precision;
- niceMax = Math.round(niceMax * precision) / precision;
- }
- ticks.push(generationOptions.min !== undefined ? generationOptions.min : niceMin);
- for (var j = 1; j < numSpaces; ++j) {
- ticks.push(Math.round((niceMin + j * spacing) * precision) / precision);
- }
- ticks.push(generationOptions.max !== undefined ? generationOptions.max : niceMax);
-
- return ticks;
-}
-
-module.exports = function(Chart) {
-
- var noop = helpers.noop;
-
- Chart.LinearScaleBase = Scale.extend({
- getRightValue: function(value) {
- if (typeof value === 'string') {
- return +value;
- }
- return Scale.prototype.getRightValue.call(this, value);
- },
-
- handleTickRangeOptions: function() {
- var me = this;
- var opts = me.options;
- var tickOpts = opts.ticks;
-
- // If we are forcing it to begin at 0, but 0 will already be rendered on the chart,
- // do nothing since that would make the chart weird. If the user really wants a weird chart
- // axis, they can manually override it
- if (tickOpts.beginAtZero) {
- var minSign = helpers.sign(me.min);
- var maxSign = helpers.sign(me.max);
-
- if (minSign < 0 && maxSign < 0) {
- // move the top up to 0
- me.max = 0;
- } else if (minSign > 0 && maxSign > 0) {
- // move the bottom down to 0
- me.min = 0;
- }
- }
-
- var setMin = tickOpts.min !== undefined || tickOpts.suggestedMin !== undefined;
- var setMax = tickOpts.max !== undefined || tickOpts.suggestedMax !== undefined;
-
- if (tickOpts.min !== undefined) {
- me.min = tickOpts.min;
- } else if (tickOpts.suggestedMin !== undefined) {
- if (me.min === null) {
- me.min = tickOpts.suggestedMin;
- } else {
- me.min = Math.min(me.min, tickOpts.suggestedMin);
- }
- }
-
- if (tickOpts.max !== undefined) {
- me.max = tickOpts.max;
- } else if (tickOpts.suggestedMax !== undefined) {
- if (me.max === null) {
- me.max = tickOpts.suggestedMax;
- } else {
- me.max = Math.max(me.max, tickOpts.suggestedMax);
- }
- }
-
- if (setMin !== setMax) {
- // We set the min or the max but not both.
- // So ensure that our range is good
- // Inverted or 0 length range can happen when
- // ticks.min is set, and no datasets are visible
- if (me.min >= me.max) {
- if (setMin) {
- me.max = me.min + 1;
- } else {
- me.min = me.max - 1;
- }
- }
- }
-
- if (me.min === me.max) {
- me.max++;
-
- if (!tickOpts.beginAtZero) {
- me.min--;
- }
- }
- },
- getTickLimit: noop,
- handleDirectionalChanges: noop,
-
- buildTicks: function() {
- var me = this;
- var opts = me.options;
- var tickOpts = opts.ticks;
-
- // Figure out what the max number of ticks we can support it is based on the size of
- // the axis area. For now, we say that the minimum tick spacing in pixels must be 50
- // We also limit the maximum number of ticks to 11 which gives a nice 10 squares on
- // the graph. Make sure we always have at least 2 ticks
- var maxTicks = me.getTickLimit();
- maxTicks = Math.max(2, maxTicks);
-
- var numericGeneratorOptions = {
- maxTicks: maxTicks,
- min: tickOpts.min,
- max: tickOpts.max,
- precision: tickOpts.precision,
- stepSize: helpers.valueOrDefault(tickOpts.fixedStepSize, tickOpts.stepSize)
- };
- var ticks = me.ticks = generateTicks(numericGeneratorOptions, me);
-
- me.handleDirectionalChanges();
-
- // At this point, we need to update our max and min given the tick values since we have expanded the
- // range of the scale
- me.max = helpers.max(ticks);
- me.min = helpers.min(ticks);
-
- if (tickOpts.reverse) {
- ticks.reverse();
-
- me.start = me.max;
- me.end = me.min;
- } else {
- me.start = me.min;
- me.end = me.max;
- }
- },
- convertTicksToLabels: function() {
- var me = this;
- me.ticksAsNumbers = me.ticks.slice();
- me.zeroLineIndex = me.ticks.indexOf(0);
-
- Scale.prototype.convertTicksToLabels.call(me);
- }
- });
-};
-
-},{"33":33,"46":46}],57:[function(require,module,exports){
-'use strict';
-
-var helpers = require(46);
-var Scale = require(33);
-var scaleService = require(34);
-var Ticks = require(35);
-
-/**
- * Generate a set of logarithmic ticks
- * @param generationOptions the options used to generate the ticks
- * @param dataRange the range of the data
- * @returns {Array<Number>} array of tick values
- */
-function generateTicks(generationOptions, dataRange) {
- var ticks = [];
- var valueOrDefault = helpers.valueOrDefault;
-
- // Figure out what the max number of ticks we can support it is based on the size of
- // the axis area. For now, we say that the minimum tick spacing in pixels must be 50
- // We also limit the maximum number of ticks to 11 which gives a nice 10 squares on
- // the graph
- var tickVal = valueOrDefault(generationOptions.min, Math.pow(10, Math.floor(helpers.log10(dataRange.min))));
-
- var endExp = Math.floor(helpers.log10(dataRange.max));
- var endSignificand = Math.ceil(dataRange.max / Math.pow(10, endExp));
- var exp, significand;
-
- if (tickVal === 0) {
- exp = Math.floor(helpers.log10(dataRange.minNotZero));
- significand = Math.floor(dataRange.minNotZero / Math.pow(10, exp));
-
- ticks.push(tickVal);
- tickVal = significand * Math.pow(10, exp);
- } else {
- exp = Math.floor(helpers.log10(tickVal));
- significand = Math.floor(tickVal / Math.pow(10, exp));
- }
- var precision = exp < 0 ? Math.pow(10, Math.abs(exp)) : 1;
-
- do {
- ticks.push(tickVal);
-
- ++significand;
- if (significand === 10) {
- significand = 1;
- ++exp;
- precision = exp >= 0 ? 1 : precision;
- }
-
- tickVal = Math.round(significand * Math.pow(10, exp) * precision) / precision;
- } while (exp < endExp || (exp === endExp && significand < endSignificand));
-
- var lastTick = valueOrDefault(generationOptions.max, tickVal);
- ticks.push(lastTick);
-
- return ticks;
-}
-
-
-module.exports = function(Chart) {
-
- var defaultConfig = {
- position: 'left',
-
- // label settings
- ticks: {
- callback: Ticks.formatters.logarithmic
- }
- };
-
- var LogarithmicScale = Scale.extend({
- determineDataLimits: function() {
- var me = this;
- var opts = me.options;
- var chart = me.chart;
- var data = chart.data;
- var datasets = data.datasets;
- var isHorizontal = me.isHorizontal();
- function IDMatches(meta) {
- return isHorizontal ? meta.xAxisID === me.id : meta.yAxisID === me.id;
- }
-
- // Calculate Range
- me.min = null;
- me.max = null;
- me.minNotZero = null;
-
- var hasStacks = opts.stacked;
- if (hasStacks === undefined) {
- helpers.each(datasets, function(dataset, datasetIndex) {
- if (hasStacks) {
- return;
- }
-
- var meta = chart.getDatasetMeta(datasetIndex);
- if (chart.isDatasetVisible(datasetIndex) && IDMatches(meta) &&
- meta.stack !== undefined) {
- hasStacks = true;
- }
- });
- }
-
- if (opts.stacked || hasStacks) {
- var valuesPerStack = {};
-
- helpers.each(datasets, function(dataset, datasetIndex) {
- var meta = chart.getDatasetMeta(datasetIndex);
- var key = [
- meta.type,
- // we have a separate stack for stack=undefined datasets when the opts.stacked is undefined
- ((opts.stacked === undefined && meta.stack === undefined) ? datasetIndex : ''),
- meta.stack
- ].join('.');
-
- if (chart.isDatasetVisible(datasetIndex) && IDMatches(meta)) {
- if (valuesPerStack[key] === undefined) {
- valuesPerStack[key] = [];
- }
-
- helpers.each(dataset.data, function(rawValue, index) {
- var values = valuesPerStack[key];
- var value = +me.getRightValue(rawValue);
- // invalid, hidden and negative values are ignored
- if (isNaN(value) || meta.data[index].hidden || value < 0) {
- return;
- }
- values[index] = values[index] || 0;
- values[index] += value;
- });
- }
- });
-
- helpers.each(valuesPerStack, function(valuesForType) {
- if (valuesForType.length > 0) {
- var minVal = helpers.min(valuesForType);
- var maxVal = helpers.max(valuesForType);
- me.min = me.min === null ? minVal : Math.min(me.min, minVal);
- me.max = me.max === null ? maxVal : Math.max(me.max, maxVal);
- }
- });
-
- } else {
- helpers.each(datasets, function(dataset, datasetIndex) {
- var meta = chart.getDatasetMeta(datasetIndex);
- if (chart.isDatasetVisible(datasetIndex) && IDMatches(meta)) {
- helpers.each(dataset.data, function(rawValue, index) {
- var value = +me.getRightValue(rawValue);
- // invalid, hidden and negative values are ignored
- if (isNaN(value) || meta.data[index].hidden || value < 0) {
- return;
- }
-
- if (me.min === null) {
- me.min = value;
- } else if (value < me.min) {
- me.min = value;
- }
-
- if (me.max === null) {
- me.max = value;
- } else if (value > me.max) {
- me.max = value;
- }
-
- if (value !== 0 && (me.minNotZero === null || value < me.minNotZero)) {
- me.minNotZero = value;
- }
- });
- }
- });
- }
-
- // Common base implementation to handle ticks.min, ticks.max
- this.handleTickRangeOptions();
- },
- handleTickRangeOptions: function() {
- var me = this;
- var opts = me.options;
- var tickOpts = opts.ticks;
- var valueOrDefault = helpers.valueOrDefault;
- var DEFAULT_MIN = 1;
- var DEFAULT_MAX = 10;
-
- me.min = valueOrDefault(tickOpts.min, me.min);
- me.max = valueOrDefault(tickOpts.max, me.max);
-
- if (me.min === me.max) {
- if (me.min !== 0 && me.min !== null) {
- me.min = Math.pow(10, Math.floor(helpers.log10(me.min)) - 1);
- me.max = Math.pow(10, Math.floor(helpers.log10(me.max)) + 1);
- } else {
- me.min = DEFAULT_MIN;
- me.max = DEFAULT_MAX;
- }
- }
- if (me.min === null) {
- me.min = Math.pow(10, Math.floor(helpers.log10(me.max)) - 1);
- }
- if (me.max === null) {
- me.max = me.min !== 0
- ? Math.pow(10, Math.floor(helpers.log10(me.min)) + 1)
- : DEFAULT_MAX;
- }
- if (me.minNotZero === null) {
- if (me.min > 0) {
- me.minNotZero = me.min;
- } else if (me.max < 1) {
- me.minNotZero = Math.pow(10, Math.floor(helpers.log10(me.max)));
- } else {
- me.minNotZero = DEFAULT_MIN;
- }
- }
- },
- buildTicks: function() {
- var me = this;
- var opts = me.options;
- var tickOpts = opts.ticks;
- var reverse = !me.isHorizontal();
-
- var generationOptions = {
- min: tickOpts.min,
- max: tickOpts.max
- };
- var ticks = me.ticks = generateTicks(generationOptions, me);
-
- // At this point, we need to update our max and min given the tick values since we have expanded the
- // range of the scale
- me.max = helpers.max(ticks);
- me.min = helpers.min(ticks);
-
- if (tickOpts.reverse) {
- reverse = !reverse;
- me.start = me.max;
- me.end = me.min;
- } else {
- me.start = me.min;
- me.end = me.max;
- }
- if (reverse) {
- ticks.reverse();
- }
- },
- convertTicksToLabels: function() {
- this.tickValues = this.ticks.slice();
-
- Scale.prototype.convertTicksToLabels.call(this);
- },
- // Get the correct tooltip label
- getLabelForIndex: function(index, datasetIndex) {
- return +this.getRightValue(this.chart.data.datasets[datasetIndex].data[index]);
- },
- getPixelForTick: function(index) {
- return this.getPixelForValue(this.tickValues[index]);
- },
- /**
- * Returns the value of the first tick.
- * @param {Number} value - The minimum not zero value.
- * @return {Number} The first tick value.
- * @private
- */
- _getFirstTickValue: function(value) {
- var exp = Math.floor(helpers.log10(value));
- var significand = Math.floor(value / Math.pow(10, exp));
-
- return significand * Math.pow(10, exp);
- },
- getPixelForValue: function(value) {
- var me = this;
- var reverse = me.options.ticks.reverse;
- var log10 = helpers.log10;
- var firstTickValue = me._getFirstTickValue(me.minNotZero);
- var offset = 0;
- var innerDimension, pixel, start, end, sign;
-
- value = +me.getRightValue(value);
- if (reverse) {
- start = me.end;
- end = me.start;
- sign = -1;
- } else {
- start = me.start;
- end = me.end;
- sign = 1;
- }
- if (me.isHorizontal()) {
- innerDimension = me.width;
- pixel = reverse ? me.right : me.left;
- } else {
- innerDimension = me.height;
- sign *= -1; // invert, since the upper-left corner of the canvas is at pixel (0, 0)
- pixel = reverse ? me.top : me.bottom;
- }
- if (value !== start) {
- if (start === 0) { // include zero tick
- offset = helpers.getValueOrDefault(
- me.options.ticks.fontSize,
- Chart.defaults.global.defaultFontSize
- );
- innerDimension -= offset;
- start = firstTickValue;
- }
- if (value !== 0) {
- offset += innerDimension / (log10(end) - log10(start)) * (log10(value) - log10(start));
- }
- pixel += sign * offset;
- }
- return pixel;
- },
- getValueForPixel: function(pixel) {
- var me = this;
- var reverse = me.options.ticks.reverse;
- var log10 = helpers.log10;
- var firstTickValue = me._getFirstTickValue(me.minNotZero);
- var innerDimension, start, end, value;
-
- if (reverse) {
- start = me.end;
- end = me.start;
- } else {
- start = me.start;
- end = me.end;
- }
- if (me.isHorizontal()) {
- innerDimension = me.width;
- value = reverse ? me.right - pixel : pixel - me.left;
- } else {
- innerDimension = me.height;
- value = reverse ? pixel - me.top : me.bottom - pixel;
- }
- if (value !== start) {
- if (start === 0) { // include zero tick
- var offset = helpers.getValueOrDefault(
- me.options.ticks.fontSize,
- Chart.defaults.global.defaultFontSize
- );
- value -= offset;
- innerDimension -= offset;
- start = firstTickValue;
- }
- value *= log10(end) - log10(start);
- value /= innerDimension;
- value = Math.pow(10, log10(start) + value);
- }
- return value;
- }
- });
-
- scaleService.registerScaleType('logarithmic', LogarithmicScale, defaultConfig);
-};
-
-},{"33":33,"34":34,"35":35,"46":46}],58:[function(require,module,exports){
-'use strict';
-
-var defaults = require(26);
-var helpers = require(46);
-var scaleService = require(34);
-var Ticks = require(35);
-
-module.exports = function(Chart) {
-
- var globalDefaults = defaults.global;
-
- var defaultConfig = {
- display: true,
-
- // Boolean - Whether to animate scaling the chart from the centre
- animate: true,
- position: 'chartArea',
-
- angleLines: {
- display: true,
- color: 'rgba(0, 0, 0, 0.1)',
- lineWidth: 1
- },
-
- gridLines: {
- circular: false
- },
-
- // label settings
- ticks: {
- // Boolean - Show a backdrop to the scale label
- showLabelBackdrop: true,
-
- // String - The colour of the label backdrop
- backdropColor: 'rgba(255,255,255,0.75)',
-
- // Number - The backdrop padding above & below the label in pixels
- backdropPaddingY: 2,
-
- // Number - The backdrop padding to the side of the label in pixels
- backdropPaddingX: 2,
-
- callback: Ticks.formatters.linear
- },
-
- pointLabels: {
- // Boolean - if true, show point labels
- display: true,
-
- // Number - Point label font size in pixels
- fontSize: 10,
-
- // Function - Used to convert point labels
- callback: function(label) {
- return label;
- }
- }
- };
-
- function getValueCount(scale) {
- var opts = scale.options;
- return opts.angleLines.display || opts.pointLabels.display ? scale.chart.data.labels.length : 0;
- }
-
- function getPointLabelFontOptions(scale) {
- var pointLabelOptions = scale.options.pointLabels;
- var fontSize = helpers.valueOrDefault(pointLabelOptions.fontSize, globalDefaults.defaultFontSize);
- var fontStyle = helpers.valueOrDefault(pointLabelOptions.fontStyle, globalDefaults.defaultFontStyle);
- var fontFamily = helpers.valueOrDefault(pointLabelOptions.fontFamily, globalDefaults.defaultFontFamily);
- var font = helpers.fontString(fontSize, fontStyle, fontFamily);
-
- return {
- size: fontSize,
- style: fontStyle,
- family: fontFamily,
- font: font
- };
- }
-
- function measureLabelSize(ctx, fontSize, label) {
- if (helpers.isArray(label)) {
- return {
- w: helpers.longestText(ctx, ctx.font, label),
- h: (label.length * fontSize) + ((label.length - 1) * 1.5 * fontSize)
- };
- }
-
- return {
- w: ctx.measureText(label).width,
- h: fontSize
- };
- }
-
- function determineLimits(angle, pos, size, min, max) {
- if (angle === min || angle === max) {
- return {
- start: pos - (size / 2),
- end: pos + (size / 2)
- };
- } else if (angle < min || angle > max) {
- return {
- start: pos - size - 5,
- end: pos
- };
- }
-
- return {
- start: pos,
- end: pos + size + 5
- };
- }
-
- /**
- * Helper function to fit a radial linear scale with point labels
- */
- function fitWithPointLabels(scale) {
- /*
- * Right, this is really confusing and there is a lot of maths going on here
- * The gist of the problem is here: https://gist.github.com/nnnick/696cc9c55f4b0beb8fe9
- *
- * Reaction: https://dl.dropboxusercontent.com/u/34601363/toomuchscience.gif
- *
- * Solution:
- *
- * We assume the radius of the polygon is half the size of the canvas at first
- * at each index we check if the text overlaps.
- *
- * Where it does, we store that angle and that index.
- *
- * After finding the largest index and angle we calculate how much we need to remove
- * from the shape radius to move the point inwards by that x.
- *
- * We average the left and right distances to get the maximum shape radius that can fit in the box
- * along with labels.
- *
- * Once we have that, we can find the centre point for the chart, by taking the x text protrusion
- * on each side, removing that from the size, halving it and adding the left x protrusion width.
- *
- * This will mean we have a shape fitted to the canvas, as large as it can be with the labels
- * and position it in the most space efficient manner
- *
- * https://dl.dropboxusercontent.com/u/34601363/yeahscience.gif
- */
-
- var plFont = getPointLabelFontOptions(scale);
-
- // Get maximum radius of the polygon. Either half the height (minus the text width) or half the width.
- // Use this to calculate the offset + change. - Make sure L/R protrusion is at least 0 to stop issues with centre points
- var largestPossibleRadius = Math.min(scale.height / 2, scale.width / 2);
- var furthestLimits = {
- r: scale.width,
- l: 0,
- t: scale.height,
- b: 0
- };
- var furthestAngles = {};
- var i, textSize, pointPosition;
-
- scale.ctx.font = plFont.font;
- scale._pointLabelSizes = [];
-
- var valueCount = getValueCount(scale);
- for (i = 0; i < valueCount; i++) {
- pointPosition = scale.getPointPosition(i, largestPossibleRadius);
- textSize = measureLabelSize(scale.ctx, plFont.size, scale.pointLabels[i] || '');
- scale._pointLabelSizes[i] = textSize;
-
- // Add quarter circle to make degree 0 mean top of circle
- var angleRadians = scale.getIndexAngle(i);
- var angle = helpers.toDegrees(angleRadians) % 360;
- var hLimits = determineLimits(angle, pointPosition.x, textSize.w, 0, 180);
- var vLimits = determineLimits(angle, pointPosition.y, textSize.h, 90, 270);
-
- if (hLimits.start < furthestLimits.l) {
- furthestLimits.l = hLimits.start;
- furthestAngles.l = angleRadians;
- }
-
- if (hLimits.end > furthestLimits.r) {
- furthestLimits.r = hLimits.end;
- furthestAngles.r = angleRadians;
- }
-
- if (vLimits.start < furthestLimits.t) {
- furthestLimits.t = vLimits.start;
- furthestAngles.t = angleRadians;
- }
-
- if (vLimits.end > furthestLimits.b) {
- furthestLimits.b = vLimits.end;
- furthestAngles.b = angleRadians;
- }
- }
-
- scale.setReductions(largestPossibleRadius, furthestLimits, furthestAngles);
- }
-
- /**
- * Helper function to fit a radial linear scale with no point labels
- */
- function fit(scale) {
- var largestPossibleRadius = Math.min(scale.height / 2, scale.width / 2);
- scale.drawingArea = Math.round(largestPossibleRadius);
- scale.setCenterPoint(0, 0, 0, 0);
- }
-
- function getTextAlignForAngle(angle) {
- if (angle === 0 || angle === 180) {
- return 'center';
- } else if (angle < 180) {
- return 'left';
- }
-
- return 'right';
- }
-
- function fillText(ctx, text, position, fontSize) {
- if (helpers.isArray(text)) {
- var y = position.y;
- var spacing = 1.5 * fontSize;
-
- for (var i = 0; i < text.length; ++i) {
- ctx.fillText(text[i], position.x, y);
- y += spacing;
- }
- } else {
- ctx.fillText(text, position.x, position.y);
- }
- }
-
- function adjustPointPositionForLabelHeight(angle, textSize, position) {
- if (angle === 90 || angle === 270) {
- position.y -= (textSize.h / 2);
- } else if (angle > 270 || angle < 90) {
- position.y -= textSize.h;
- }
- }
-
- function drawPointLabels(scale) {
- var ctx = scale.ctx;
- var opts = scale.options;
- var angleLineOpts = opts.angleLines;
- var pointLabelOpts = opts.pointLabels;
-
- ctx.lineWidth = angleLineOpts.lineWidth;
- ctx.strokeStyle = angleLineOpts.color;
-
- var outerDistance = scale.getDistanceFromCenterForValue(opts.ticks.reverse ? scale.min : scale.max);
-
- // Point Label Font
- var plFont = getPointLabelFontOptions(scale);
-
- ctx.textBaseline = 'top';
-
- for (var i = getValueCount(scale) - 1; i >= 0; i--) {
- if (angleLineOpts.display) {
- var outerPosition = scale.getPointPosition(i, outerDistance);
- ctx.beginPath();
- ctx.moveTo(scale.xCenter, scale.yCenter);
- ctx.lineTo(outerPosition.x, outerPosition.y);
- ctx.stroke();
- ctx.closePath();
- }
-
- if (pointLabelOpts.display) {
- // Extra 3px out for some label spacing
- var pointLabelPosition = scale.getPointPosition(i, outerDistance + 5);
-
- // Keep this in loop since we may support array properties here
- var pointLabelFontColor = helpers.valueAtIndexOrDefault(pointLabelOpts.fontColor, i, globalDefaults.defaultFontColor);
- ctx.font = plFont.font;
- ctx.fillStyle = pointLabelFontColor;
-
- var angleRadians = scale.getIndexAngle(i);
- var angle = helpers.toDegrees(angleRadians);
- ctx.textAlign = getTextAlignForAngle(angle);
- adjustPointPositionForLabelHeight(angle, scale._pointLabelSizes[i], pointLabelPosition);
- fillText(ctx, scale.pointLabels[i] || '', pointLabelPosition, plFont.size);
- }
- }
- }
-
- function drawRadiusLine(scale, gridLineOpts, radius, index) {
- var ctx = scale.ctx;
- ctx.strokeStyle = helpers.valueAtIndexOrDefault(gridLineOpts.color, index - 1);
- ctx.lineWidth = helpers.valueAtIndexOrDefault(gridLineOpts.lineWidth, index - 1);
-
- if (scale.options.gridLines.circular) {
- // Draw circular arcs between the points
- ctx.beginPath();
- ctx.arc(scale.xCenter, scale.yCenter, radius, 0, Math.PI * 2);
- ctx.closePath();
- ctx.stroke();
- } else {
- // Draw straight lines connecting each index
- var valueCount = getValueCount(scale);
-
- if (valueCount === 0) {
- return;
- }
-
- ctx.beginPath();
- var pointPosition = scale.getPointPosition(0, radius);
- ctx.moveTo(pointPosition.x, pointPosition.y);
-
- for (var i = 1; i < valueCount; i++) {
- pointPosition = scale.getPointPosition(i, radius);
- ctx.lineTo(pointPosition.x, pointPosition.y);
- }
-
- ctx.closePath();
- ctx.stroke();
- }
- }
-
- function numberOrZero(param) {
- return helpers.isNumber(param) ? param : 0;
- }
-
- var LinearRadialScale = Chart.LinearScaleBase.extend({
- setDimensions: function() {
- var me = this;
- var opts = me.options;
- var tickOpts = opts.ticks;
- // Set the unconstrained dimension before label rotation
- me.width = me.maxWidth;
- me.height = me.maxHeight;
- me.xCenter = Math.round(me.width / 2);
- me.yCenter = Math.round(me.height / 2);
-
- var minSize = helpers.min([me.height, me.width]);
- var tickFontSize = helpers.valueOrDefault(tickOpts.fontSize, globalDefaults.defaultFontSize);
- me.drawingArea = opts.display ? (minSize / 2) - (tickFontSize / 2 + tickOpts.backdropPaddingY) : (minSize / 2);
- },
- determineDataLimits: function() {
- var me = this;
- var chart = me.chart;
- var min = Number.POSITIVE_INFINITY;
- var max = Number.NEGATIVE_INFINITY;
-
- helpers.each(chart.data.datasets, function(dataset, datasetIndex) {
- if (chart.isDatasetVisible(datasetIndex)) {
- var meta = chart.getDatasetMeta(datasetIndex);
-
- helpers.each(dataset.data, function(rawValue, index) {
- var value = +me.getRightValue(rawValue);
- if (isNaN(value) || meta.data[index].hidden) {
- return;
- }
-
- min = Math.min(value, min);
- max = Math.max(value, max);
- });
- }
- });
-
- me.min = (min === Number.POSITIVE_INFINITY ? 0 : min);
- me.max = (max === Number.NEGATIVE_INFINITY ? 0 : max);
-
- // Common base implementation to handle ticks.min, ticks.max, ticks.beginAtZero
- me.handleTickRangeOptions();
- },
- getTickLimit: function() {
- var tickOpts = this.options.ticks;
- var tickFontSize = helpers.valueOrDefault(tickOpts.fontSize, globalDefaults.defaultFontSize);
- return Math.min(tickOpts.maxTicksLimit ? tickOpts.maxTicksLimit : 11, Math.ceil(this.drawingArea / (1.5 * tickFontSize)));
- },
- convertTicksToLabels: function() {
- var me = this;
-
- Chart.LinearScaleBase.prototype.convertTicksToLabels.call(me);
-
- // Point labels
- me.pointLabels = me.chart.data.labels.map(me.options.pointLabels.callback, me);
- },
- getLabelForIndex: function(index, datasetIndex) {
- return +this.getRightValue(this.chart.data.datasets[datasetIndex].data[index]);
- },
- fit: function() {
- if (this.options.pointLabels.display) {
- fitWithPointLabels(this);
- } else {
- fit(this);
- }
- },
- /**
- * Set radius reductions and determine new radius and center point
- * @private
- */
- setReductions: function(largestPossibleRadius, furthestLimits, furthestAngles) {
- var me = this;
- var radiusReductionLeft = furthestLimits.l / Math.sin(furthestAngles.l);
- var radiusReductionRight = Math.max(furthestLimits.r - me.width, 0) / Math.sin(furthestAngles.r);
- var radiusReductionTop = -furthestLimits.t / Math.cos(furthestAngles.t);
- var radiusReductionBottom = -Math.max(furthestLimits.b - me.height, 0) / Math.cos(furthestAngles.b);
-
- radiusReductionLeft = numberOrZero(radiusReductionLeft);
- radiusReductionRight = numberOrZero(radiusReductionRight);
- radiusReductionTop = numberOrZero(radiusReductionTop);
- radiusReductionBottom = numberOrZero(radiusReductionBottom);
-
- me.drawingArea = Math.min(
- Math.round(largestPossibleRadius - (radiusReductionLeft + radiusReductionRight) / 2),
- Math.round(largestPossibleRadius - (radiusReductionTop + radiusReductionBottom) / 2));
- me.setCenterPoint(radiusReductionLeft, radiusReductionRight, radiusReductionTop, radiusReductionBottom);
- },
- setCenterPoint: function(leftMovement, rightMovement, topMovement, bottomMovement) {
- var me = this;
- var maxRight = me.width - rightMovement - me.drawingArea;
- var maxLeft = leftMovement + me.drawingArea;
- var maxTop = topMovement + me.drawingArea;
- var maxBottom = me.height - bottomMovement - me.drawingArea;
-
- me.xCenter = Math.round(((maxLeft + maxRight) / 2) + me.left);
- me.yCenter = Math.round(((maxTop + maxBottom) / 2) + me.top);
- },
-
- getIndexAngle: function(index) {
- var angleMultiplier = (Math.PI * 2) / getValueCount(this);
- var startAngle = this.chart.options && this.chart.options.startAngle ?
- this.chart.options.startAngle :
- 0;
-
- var startAngleRadians = startAngle * Math.PI * 2 / 360;
-
- // Start from the top instead of right, so remove a quarter of the circle
- return index * angleMultiplier + startAngleRadians;
- },
- getDistanceFromCenterForValue: function(value) {
- var me = this;
-
- if (value === null) {
- return 0; // null always in center
- }
-
- // Take into account half font size + the yPadding of the top value
- var scalingFactor = me.drawingArea / (me.max - me.min);
- if (me.options.ticks.reverse) {
- return (me.max - value) * scalingFactor;
- }
- return (value - me.min) * scalingFactor;
- },
- getPointPosition: function(index, distanceFromCenter) {
- var me = this;
- var thisAngle = me.getIndexAngle(index) - (Math.PI / 2);
- return {
- x: Math.round(Math.cos(thisAngle) * distanceFromCenter) + me.xCenter,
- y: Math.round(Math.sin(thisAngle) * distanceFromCenter) + me.yCenter
- };
- },
- getPointPositionForValue: function(index, value) {
- return this.getPointPosition(index, this.getDistanceFromCenterForValue(value));
- },
-
- getBasePosition: function() {
- var me = this;
- var min = me.min;
- var max = me.max;
-
- return me.getPointPositionForValue(0,
- me.beginAtZero ? 0 :
- min < 0 && max < 0 ? max :
- min > 0 && max > 0 ? min :
- 0);
- },
-
- draw: function() {
- var me = this;
- var opts = me.options;
- var gridLineOpts = opts.gridLines;
- var tickOpts = opts.ticks;
- var valueOrDefault = helpers.valueOrDefault;
-
- if (opts.display) {
- var ctx = me.ctx;
- var startAngle = this.getIndexAngle(0);
-
- // Tick Font
- var tickFontSize = valueOrDefault(tickOpts.fontSize, globalDefaults.defaultFontSize);
- var tickFontStyle = valueOrDefault(tickOpts.fontStyle, globalDefaults.defaultFontStyle);
- var tickFontFamily = valueOrDefault(tickOpts.fontFamily, globalDefaults.defaultFontFamily);
- var tickLabelFont = helpers.fontString(tickFontSize, tickFontStyle, tickFontFamily);
-
- helpers.each(me.ticks, function(label, index) {
- // Don't draw a centre value (if it is minimum)
- if (index > 0 || tickOpts.reverse) {
- var yCenterOffset = me.getDistanceFromCenterForValue(me.ticksAsNumbers[index]);
-
- // Draw circular lines around the scale
- if (gridLineOpts.display && index !== 0) {
- drawRadiusLine(me, gridLineOpts, yCenterOffset, index);
- }
-
- if (tickOpts.display) {
- var tickFontColor = valueOrDefault(tickOpts.fontColor, globalDefaults.defaultFontColor);
- ctx.font = tickLabelFont;
-
- ctx.save();
- ctx.translate(me.xCenter, me.yCenter);
- ctx.rotate(startAngle);
-
- if (tickOpts.showLabelBackdrop) {
- var labelWidth = ctx.measureText(label).width;
- ctx.fillStyle = tickOpts.backdropColor;
- ctx.fillRect(
- -labelWidth / 2 - tickOpts.backdropPaddingX,
- -yCenterOffset - tickFontSize / 2 - tickOpts.backdropPaddingY,
- labelWidth + tickOpts.backdropPaddingX * 2,
- tickFontSize + tickOpts.backdropPaddingY * 2
- );
- }
-
- ctx.textAlign = 'center';
- ctx.textBaseline = 'middle';
- ctx.fillStyle = tickFontColor;
- ctx.fillText(label, 0, -yCenterOffset);
- ctx.restore();
- }
- }
- });
-
- if (opts.angleLines.display || opts.pointLabels.display) {
- drawPointLabels(me);
- }
- }
- }
- });
-
- scaleService.registerScaleType('radialLinear', LinearRadialScale, defaultConfig);
-};
-
-},{"26":26,"34":34,"35":35,"46":46}],59:[function(require,module,exports){
-/* global window: false */
-'use strict';
-
-var moment = require(6);
-moment = typeof moment === 'function' ? moment : window.moment;
-
-var defaults = require(26);
-var helpers = require(46);
-var Scale = require(33);
-var scaleService = require(34);
-
-// Integer constants are from the ES6 spec.
-var MIN_INTEGER = Number.MIN_SAFE_INTEGER || -9007199254740991;
-var MAX_INTEGER = Number.MAX_SAFE_INTEGER || 9007199254740991;
-
-var INTERVALS = {
- millisecond: {
- common: true,
- size: 1,
- steps: [1, 2, 5, 10, 20, 50, 100, 250, 500]
- },
- second: {
- common: true,
- size: 1000,
- steps: [1, 2, 5, 10, 15, 30]
- },
- minute: {
- common: true,
- size: 60000,
- steps: [1, 2, 5, 10, 15, 30]
- },
- hour: {
- common: true,
- size: 3600000,
- steps: [1, 2, 3, 6, 12]
- },
- day: {
- common: true,
- size: 86400000,
- steps: [1, 2, 5]
- },
- week: {
- common: false,
- size: 604800000,
- steps: [1, 2, 3, 4]
- },
- month: {
- common: true,
- size: 2.628e9,
- steps: [1, 2, 3]
- },
- quarter: {
- common: false,
- size: 7.884e9,
- steps: [1, 2, 3, 4]
- },
- year: {
- common: true,
- size: 3.154e10
- }
-};
-
-var UNITS = Object.keys(INTERVALS);
-
-function sorter(a, b) {
- return a - b;
-}
-
-function arrayUnique(items) {
- var hash = {};
- var out = [];
- var i, ilen, item;
-
- for (i = 0, ilen = items.length; i < ilen; ++i) {
- item = items[i];
- if (!hash[item]) {
- hash[item] = true;
- out.push(item);
- }
- }
-
- return out;
-}
-
-/**
- * Returns an array of {time, pos} objects used to interpolate a specific `time` or position
- * (`pos`) on the scale, by searching entries before and after the requested value. `pos` is
- * a decimal between 0 and 1: 0 being the start of the scale (left or top) and 1 the other
- * extremity (left + width or top + height). Note that it would be more optimized to directly
- * store pre-computed pixels, but the scale dimensions are not guaranteed at the time we need
- * to create the lookup table. The table ALWAYS contains at least two items: min and max.
- *
- * @param {Number[]} timestamps - timestamps sorted from lowest to highest.
- * @param {String} distribution - If 'linear', timestamps will be spread linearly along the min
- * and max range, so basically, the table will contains only two items: {min, 0} and {max, 1}.
- * If 'series', timestamps will be positioned at the same distance from each other. In this
- * case, only timestamps that break the time linearity are registered, meaning that in the
- * best case, all timestamps are linear, the table contains only min and max.
- */
-function buildLookupTable(timestamps, min, max, distribution) {
- if (distribution === 'linear' || !timestamps.length) {
- return [
- {time: min, pos: 0},
- {time: max, pos: 1}
- ];
- }
-
- var table = [];
- var items = [min];
- var i, ilen, prev, curr, next;
-
- for (i = 0, ilen = timestamps.length; i < ilen; ++i) {
- curr = timestamps[i];
- if (curr > min && curr < max) {
- items.push(curr);
- }
- }
-
- items.push(max);
-
- for (i = 0, ilen = items.length; i < ilen; ++i) {
- next = items[i + 1];
- prev = items[i - 1];
- curr = items[i];
-
- // only add points that breaks the scale linearity
- if (prev === undefined || next === undefined || Math.round((next + prev) / 2) !== curr) {
- table.push({time: curr, pos: i / (ilen - 1)});
- }
- }
-
- return table;
-}
-
-// @see adapted from http://www.anujgakhar.com/2014/03/01/binary-search-in-javascript/
-function lookup(table, key, value) {
- var lo = 0;
- var hi = table.length - 1;
- var mid, i0, i1;
-
- while (lo >= 0 && lo <= hi) {
- mid = (lo + hi) >> 1;
- i0 = table[mid - 1] || null;
- i1 = table[mid];
-
- if (!i0) {
- // given value is outside table (before first item)
- return {lo: null, hi: i1};
- } else if (i1[key] < value) {
- lo = mid + 1;
- } else if (i0[key] > value) {
- hi = mid - 1;
- } else {
- return {lo: i0, hi: i1};
- }
- }
-
- // given value is outside table (after last item)
- return {lo: i1, hi: null};
-}
-
-/**
- * Linearly interpolates the given source `value` using the table items `skey` values and
- * returns the associated `tkey` value. For example, interpolate(table, 'time', 42, 'pos')
- * returns the position for a timestamp equal to 42. If value is out of bounds, values at
- * index [0, 1] or [n - 1, n] are used for the interpolation.
- */
-function interpolate(table, skey, sval, tkey) {
- var range = lookup(table, skey, sval);
-
- // Note: the lookup table ALWAYS contains at least 2 items (min and max)
- var prev = !range.lo ? table[0] : !range.hi ? table[table.length - 2] : range.lo;
- var next = !range.lo ? table[1] : !range.hi ? table[table.length - 1] : range.hi;
-
- var span = next[skey] - prev[skey];
- var ratio = span ? (sval - prev[skey]) / span : 0;
- var offset = (next[tkey] - prev[tkey]) * ratio;
-
- return prev[tkey] + offset;
-}
-
-/**
- * Convert the given value to a moment object using the given time options.
- * @see http://momentjs.com/docs/#/parsing/
- */
-function momentify(value, options) {
- var parser = options.parser;
- var format = options.parser || options.format;
-
- if (typeof parser === 'function') {
- return parser(value);
- }
-
- if (typeof value === 'string' && typeof format === 'string') {
- return moment(value, format);
- }
-
- if (!(value instanceof moment)) {
- value = moment(value);
- }
-
- if (value.isValid()) {
- return value;
- }
-
- // Labels are in an incompatible moment format and no `parser` has been provided.
- // The user might still use the deprecated `format` option to convert his inputs.
- if (typeof format === 'function') {
- return format(value);
- }
-
- return value;
-}
-
-function parse(input, scale) {
- if (helpers.isNullOrUndef(input)) {
- return null;
- }
-
- var options = scale.options.time;
- var value = momentify(scale.getRightValue(input), options);
- if (!value.isValid()) {
- return null;
- }
-
- if (options.round) {
- value.startOf(options.round);
- }
-
- return value.valueOf();
-}
-
-/**
- * Returns the number of unit to skip to be able to display up to `capacity` number of ticks
- * in `unit` for the given `min` / `max` range and respecting the interval steps constraints.
- */
-function determineStepSize(min, max, unit, capacity) {
- var range = max - min;
- var interval = INTERVALS[unit];
- var milliseconds = interval.size;
- var steps = interval.steps;
- var i, ilen, factor;
-
- if (!steps) {
- return Math.ceil(range / (capacity * milliseconds));
- }
-
- for (i = 0, ilen = steps.length; i < ilen; ++i) {
- factor = steps[i];
- if (Math.ceil(range / (milliseconds * factor)) <= capacity) {
- break;
- }
- }
-
- return factor;
-}
-
-/**
- * Figures out what unit results in an appropriate number of auto-generated ticks
- */
-function determineUnitForAutoTicks(minUnit, min, max, capacity) {
- var ilen = UNITS.length;
- var i, interval, factor;
-
- for (i = UNITS.indexOf(minUnit); i < ilen - 1; ++i) {
- interval = INTERVALS[UNITS[i]];
- factor = interval.steps ? interval.steps[interval.steps.length - 1] : MAX_INTEGER;
-
- if (interval.common && Math.ceil((max - min) / (factor * interval.size)) <= capacity) {
- return UNITS[i];
- }
- }
-
- return UNITS[ilen - 1];
-}
-
-/**
- * Figures out what unit to format a set of ticks with
- */
-function determineUnitForFormatting(ticks, minUnit, min, max) {
- var duration = moment.duration(moment(max).diff(moment(min)));
- var ilen = UNITS.length;
- var i, unit;
-
- for (i = ilen - 1; i >= UNITS.indexOf(minUnit); i--) {
- unit = UNITS[i];
- if (INTERVALS[unit].common && duration.as(unit) >= ticks.length) {
- return unit;
- }
- }
-
- return UNITS[minUnit ? UNITS.indexOf(minUnit) : 0];
-}
-
-function determineMajorUnit(unit) {
- for (var i = UNITS.indexOf(unit) + 1, ilen = UNITS.length; i < ilen; ++i) {
- if (INTERVALS[UNITS[i]].common) {
- return UNITS[i];
- }
- }
-}
-
-/**
- * Generates a maximum of `capacity` timestamps between min and max, rounded to the
- * `minor` unit, aligned on the `major` unit and using the given scale time `options`.
- * Important: this method can return ticks outside the min and max range, it's the
- * responsibility of the calling code to clamp values if needed.
- */
-function generate(min, max, capacity, options) {
- var timeOpts = options.time;
- var minor = timeOpts.unit || determineUnitForAutoTicks(timeOpts.minUnit, min, max, capacity);
- var major = determineMajorUnit(minor);
- var stepSize = helpers.valueOrDefault(timeOpts.stepSize, timeOpts.unitStepSize);
- var weekday = minor === 'week' ? timeOpts.isoWeekday : false;
- var majorTicksEnabled = options.ticks.major.enabled;
- var interval = INTERVALS[minor];
- var first = moment(min);
- var last = moment(max);
- var ticks = [];
- var time;
-
- if (!stepSize) {
- stepSize = determineStepSize(min, max, minor, capacity);
- }
-
- // For 'week' unit, handle the first day of week option
- if (weekday) {
- first = first.isoWeekday(weekday);
- last = last.isoWeekday(weekday);
- }
-
- // Align first/last ticks on unit
- first = first.startOf(weekday ? 'day' : minor);
- last = last.startOf(weekday ? 'day' : minor);
-
- // Make sure that the last tick include max
- if (last < max) {
- last.add(1, minor);
- }
-
- time = moment(first);
-
- if (majorTicksEnabled && major && !weekday && !timeOpts.round) {
- // Align the first tick on the previous `minor` unit aligned on the `major` unit:
- // we first aligned time on the previous `major` unit then add the number of full
- // stepSize there is between first and the previous major time.
- time.startOf(major);
- time.add(~~((first - time) / (interval.size * stepSize)) * stepSize, minor);
- }
-
- for (; time < last; time.add(stepSize, minor)) {
- ticks.push(+time);
- }
-
- ticks.push(+time);
-
- return ticks;
-}
-
-/**
- * Returns the right and left offsets from edges in the form of {left, right}.
- * Offsets are added when the `offset` option is true.
- */
-function computeOffsets(table, ticks, min, max, options) {
- var left = 0;
- var right = 0;
- var upper, lower;
-
- if (options.offset && ticks.length) {
- if (!options.time.min) {
- upper = ticks.length > 1 ? ticks[1] : max;
- lower = ticks[0];
- left = (
- interpolate(table, 'time', upper, 'pos') -
- interpolate(table, 'time', lower, 'pos')
- ) / 2;
- }
- if (!options.time.max) {
- upper = ticks[ticks.length - 1];
- lower = ticks.length > 1 ? ticks[ticks.length - 2] : min;
- right = (
- interpolate(table, 'time', upper, 'pos') -
- interpolate(table, 'time', lower, 'pos')
- ) / 2;
- }
- }
-
- return {left: left, right: right};
-}
-
-function ticksFromTimestamps(values, majorUnit) {
- var ticks = [];
- var i, ilen, value, major;
-
- for (i = 0, ilen = values.length; i < ilen; ++i) {
- value = values[i];
- major = majorUnit ? value === +moment(value).startOf(majorUnit) : false;
-
- ticks.push({
- value: value,
- major: major
- });
- }
-
- return ticks;
-}
-
-function determineLabelFormat(data, timeOpts) {
- var i, momentDate, hasTime;
- var ilen = data.length;
-
- // find the label with the most parts (milliseconds, minutes, etc.)
- // format all labels with the same level of detail as the most specific label
- for (i = 0; i < ilen; i++) {
- momentDate = momentify(data[i], timeOpts);
- if (momentDate.millisecond() !== 0) {
- return 'MMM D, YYYY h:mm:ss.SSS a';
- }
- if (momentDate.second() !== 0 || momentDate.minute() !== 0 || momentDate.hour() !== 0) {
- hasTime = true;
- }
- }
- if (hasTime) {
- return 'MMM D, YYYY h:mm:ss a';
- }
- return 'MMM D, YYYY';
-}
-
-module.exports = function() {
-
- var defaultConfig = {
- position: 'bottom',
-
- /**
- * Data distribution along the scale:
- * - 'linear': data are spread according to their time (distances can vary),
- * - 'series': data are spread at the same distance from each other.
- * @see https://github.com/chartjs/Chart.js/pull/4507
- * @since 2.7.0
- */
- distribution: 'linear',
-
- /**
- * Scale boundary strategy (bypassed by min/max time options)
- * - `data`: make sure data are fully visible, ticks outside are removed
- * - `ticks`: make sure ticks are fully visible, data outside are truncated
- * @see https://github.com/chartjs/Chart.js/pull/4556
- * @since 2.7.0
- */
- bounds: 'data',
-
- time: {
- parser: false, // false == a pattern string from http://momentjs.com/docs/#/parsing/string-format/ or a custom callback that converts its argument to a moment
- format: false, // DEPRECATED false == date objects, moment object, callback or a pattern string from http://momentjs.com/docs/#/parsing/string-format/
- unit: false, // false == automatic or override with week, month, year, etc.
- round: false, // none, or override with week, month, year, etc.
- displayFormat: false, // DEPRECATED
- isoWeekday: false, // override week start day - see http://momentjs.com/docs/#/get-set/iso-weekday/
- minUnit: 'millisecond',
-
- // defaults to unit's corresponding unitFormat below or override using pattern string from http://momentjs.com/docs/#/displaying/format/
- displayFormats: {
- millisecond: 'h:mm:ss.SSS a', // 11:20:01.123 AM,
- second: 'h:mm:ss a', // 11:20:01 AM
- minute: 'h:mm a', // 11:20 AM
- hour: 'hA', // 5PM
- day: 'MMM D', // Sep 4
- week: 'll', // Week 46, or maybe "[W]WW - YYYY" ?
- month: 'MMM YYYY', // Sept 2015
- quarter: '[Q]Q - YYYY', // Q3
- year: 'YYYY' // 2015
- },
- },
- ticks: {
- autoSkip: false,
-
- /**
- * Ticks generation input values:
- * - 'auto': generates "optimal" ticks based on scale size and time options.
- * - 'data': generates ticks from data (including labels from data {t|x|y} objects).
- * - 'labels': generates ticks from user given `data.labels` values ONLY.
- * @see https://github.com/chartjs/Chart.js/pull/4507
- * @since 2.7.0
- */
- source: 'auto',
-
- major: {
- enabled: false
- }
- }
- };
-
- var TimeScale = Scale.extend({
- initialize: function() {
- if (!moment) {
- throw new Error('Chart.js - Moment.js could not be found! You must include it before Chart.js to use the time scale. Download at https://momentjs.com');
- }
-
- this.mergeTicksOptions();
-
- Scale.prototype.initialize.call(this);
- },
-
- update: function() {
- var me = this;
- var options = me.options;
-
- // DEPRECATIONS: output a message only one time per update
- if (options.time && options.time.format) {
- console.warn('options.time.format is deprecated and replaced by options.time.parser.');
- }
-
- return Scale.prototype.update.apply(me, arguments);
- },
-
- /**
- * Allows data to be referenced via 't' attribute
- */
- getRightValue: function(rawValue) {
- if (rawValue && rawValue.t !== undefined) {
- rawValue = rawValue.t;
- }
- return Scale.prototype.getRightValue.call(this, rawValue);
- },
-
- determineDataLimits: function() {
- var me = this;
- var chart = me.chart;
- var timeOpts = me.options.time;
- var unit = timeOpts.unit || 'day';
- var min = MAX_INTEGER;
- var max = MIN_INTEGER;
- var timestamps = [];
- var datasets = [];
- var labels = [];
- var i, j, ilen, jlen, data, timestamp;
-
- // Convert labels to timestamps
- for (i = 0, ilen = chart.data.labels.length; i < ilen; ++i) {
- labels.push(parse(chart.data.labels[i], me));
- }
-
- // Convert data to timestamps
- for (i = 0, ilen = (chart.data.datasets || []).length; i < ilen; ++i) {
- if (chart.isDatasetVisible(i)) {
- data = chart.data.datasets[i].data;
-
- // Let's consider that all data have the same format.
- if (helpers.isObject(data[0])) {
- datasets[i] = [];
-
- for (j = 0, jlen = data.length; j < jlen; ++j) {
- timestamp = parse(data[j], me);
- timestamps.push(timestamp);
- datasets[i][j] = timestamp;
- }
- } else {
- timestamps.push.apply(timestamps, labels);
- datasets[i] = labels.slice(0);
- }
- } else {
- datasets[i] = [];
- }
- }
-
- if (labels.length) {
- // Sort labels **after** data have been converted
- labels = arrayUnique(labels).sort(sorter);
- min = Math.min(min, labels[0]);
- max = Math.max(max, labels[labels.length - 1]);
- }
-
- if (timestamps.length) {
- timestamps = arrayUnique(timestamps).sort(sorter);
- min = Math.min(min, timestamps[0]);
- max = Math.max(max, timestamps[timestamps.length - 1]);
- }
-
- min = parse(timeOpts.min, me) || min;
- max = parse(timeOpts.max, me) || max;
-
- // In case there is no valid min/max, set limits based on unit time option
- min = min === MAX_INTEGER ? +moment().startOf(unit) : min;
- max = max === MIN_INTEGER ? +moment().endOf(unit) + 1 : max;
-
- // Make sure that max is strictly higher than min (required by the lookup table)
- me.min = Math.min(min, max);
- me.max = Math.max(min + 1, max);
-
- // PRIVATE
- me._horizontal = me.isHorizontal();
- me._table = [];
- me._timestamps = {
- data: timestamps,
- datasets: datasets,
- labels: labels
- };
- },
-
- buildTicks: function() {
- var me = this;
- var min = me.min;
- var max = me.max;
- var options = me.options;
- var timeOpts = options.time;
- var timestamps = [];
- var ticks = [];
- var i, ilen, timestamp;
-
- switch (options.ticks.source) {
- case 'data':
- timestamps = me._timestamps.data;
- break;
- case 'labels':
- timestamps = me._timestamps.labels;
- break;
- case 'auto':
- default:
- timestamps = generate(min, max, me.getLabelCapacity(min), options);
- }
-
- if (options.bounds === 'ticks' && timestamps.length) {
- min = timestamps[0];
- max = timestamps[timestamps.length - 1];
- }
-
- // Enforce limits with user min/max options
- min = parse(timeOpts.min, me) || min;
- max = parse(timeOpts.max, me) || max;
-
- // Remove ticks outside the min/max range
- for (i = 0, ilen = timestamps.length; i < ilen; ++i) {
- timestamp = timestamps[i];
- if (timestamp >= min && timestamp <= max) {
- ticks.push(timestamp);
- }
- }
-
- me.min = min;
- me.max = max;
-
- // PRIVATE
- me._unit = timeOpts.unit || determineUnitForFormatting(ticks, timeOpts.minUnit, me.min, me.max);
- me._majorUnit = determineMajorUnit(me._unit);
- me._table = buildLookupTable(me._timestamps.data, min, max, options.distribution);
- me._offsets = computeOffsets(me._table, ticks, min, max, options);
- me._labelFormat = determineLabelFormat(me._timestamps.data, timeOpts);
-
- return ticksFromTimestamps(ticks, me._majorUnit);
- },
-
- getLabelForIndex: function(index, datasetIndex) {
- var me = this;
- var data = me.chart.data;
- var timeOpts = me.options.time;
- var label = data.labels && index < data.labels.length ? data.labels[index] : '';
- var value = data.datasets[datasetIndex].data[index];
-
- if (helpers.isObject(value)) {
- label = me.getRightValue(value);
- }
- if (timeOpts.tooltipFormat) {
- return momentify(label, timeOpts).format(timeOpts.tooltipFormat);
- }
- if (typeof label === 'string') {
- return label;
- }
-
- return momentify(label, timeOpts).format(me._labelFormat);
- },
-
- /**
- * Function to format an individual tick mark
- * @private
- */
- tickFormatFunction: function(tick, index, ticks, formatOverride) {
- var me = this;
- var options = me.options;
- var time = tick.valueOf();
- var formats = options.time.displayFormats;
- var minorFormat = formats[me._unit];
- var majorUnit = me._majorUnit;
- var majorFormat = formats[majorUnit];
- var majorTime = tick.clone().startOf(majorUnit).valueOf();
- var majorTickOpts = options.ticks.major;
- var major = majorTickOpts.enabled && majorUnit && majorFormat && time === majorTime;
- var label = tick.format(formatOverride ? formatOverride : major ? majorFormat : minorFormat);
- var tickOpts = major ? majorTickOpts : options.ticks.minor;
- var formatter = helpers.valueOrDefault(tickOpts.callback, tickOpts.userCallback);
-
- return formatter ? formatter(label, index, ticks) : label;
- },
-
- convertTicksToLabels: function(ticks) {
- var labels = [];
- var i, ilen;
-
- for (i = 0, ilen = ticks.length; i < ilen; ++i) {
- labels.push(this.tickFormatFunction(moment(ticks[i].value), i, ticks));
- }
-
- return labels;
- },
-
- /**
- * @private
- */
- getPixelForOffset: function(time) {
- var me = this;
- var size = me._horizontal ? me.width : me.height;
- var start = me._horizontal ? me.left : me.top;
- var pos = interpolate(me._table, 'time', time, 'pos');
-
- return start + size * (me._offsets.left + pos) / (me._offsets.left + 1 + me._offsets.right);
- },
-
- getPixelForValue: function(value, index, datasetIndex) {
- var me = this;
- var time = null;
-
- if (index !== undefined && datasetIndex !== undefined) {
- time = me._timestamps.datasets[datasetIndex][index];
- }
-
- if (time === null) {
- time = parse(value, me);
- }
-
- if (time !== null) {
- return me.getPixelForOffset(time);
- }
- },
-
- getPixelForTick: function(index) {
- var ticks = this.getTicks();
- return index >= 0 && index < ticks.length ?
- this.getPixelForOffset(ticks[index].value) :
- null;
- },
-
- getValueForPixel: function(pixel) {
- var me = this;
- var size = me._horizontal ? me.width : me.height;
- var start = me._horizontal ? me.left : me.top;
- var pos = (size ? (pixel - start) / size : 0) * (me._offsets.left + 1 + me._offsets.left) - me._offsets.right;
- var time = interpolate(me._table, 'pos', pos, 'time');
-
- return moment(time);
- },
-
- /**
- * Crude approximation of what the label width might be
- * @private
- */
- getLabelWidth: function(label) {
- var me = this;
- var ticksOpts = me.options.ticks;
- var tickLabelWidth = me.ctx.measureText(label).width;
- var angle = helpers.toRadians(ticksOpts.maxRotation);
- var cosRotation = Math.cos(angle);
- var sinRotation = Math.sin(angle);
- var tickFontSize = helpers.valueOrDefault(ticksOpts.fontSize, defaults.global.defaultFontSize);
-
- return (tickLabelWidth * cosRotation) + (tickFontSize * sinRotation);
- },
-
- /**
- * @private
- */
- getLabelCapacity: function(exampleTime) {
- var me = this;
-
- var formatOverride = me.options.time.displayFormats.millisecond; // Pick the longest format for guestimation
-
- var exampleLabel = me.tickFormatFunction(moment(exampleTime), 0, [], formatOverride);
- var tickLabelWidth = me.getLabelWidth(exampleLabel);
- var innerWidth = me.isHorizontal() ? me.width : me.height;
-
- var capacity = Math.floor(innerWidth / tickLabelWidth);
- return capacity > 0 ? capacity : 1;
- }
- });
-
- scaleService.registerScaleType('time', TimeScale, defaultConfig);
-};
-
-},{"26":26,"33":33,"34":34,"46":46,"6":6}]},{},[7])(7)
-});
diff --git a/web/src/main/resources/static/js/pdxFinder.js b/web/src/main/resources/static/js/pdxFinder.js
index 851185c668e0c2007a6d54b6f5fc130f0c9160a8..c414c078ed917e241ba6f8b7236f9a5226e52ef0 100644
--- a/web/src/main/resources/static/js/pdxFinder.js
+++ b/web/src/main/resources/static/js/pdxFinder.js
@@ -466,23 +466,23 @@ function getMolecularDataTable(clickedLink, clickedData) {
/*
<br>
- <span class="small">
- <a target="_blank" href="https://civicdb.org/events/genes/24/summary#gene"
+ Â <span class="small">
+ Â <a target="_blank" href="https://civicdb.org/events/genes/24/summary#gene"
style="text-decoration:none; color:#06369d; text-transform: lowercase;"> civic
- <i class="icon icon-generic" data-icon="x"> </i>
- </a>
+ Â <i class="icon icon-generic" data-icon="x"> </i>
+ Â </a>
</span>
<span class="small">
- <a target="_blank" href="https://civicdb.org/events/genes/24/summary#gene"
+ Â <a target="_blank" href="https://civicdb.org/events/genes/24/summary#gene"
style="text-decoration:none; color:#06369d; text-transform: lowercase;"> cosmic
- <i class="icon icon-generic" data-icon="x"> </i>
- </a>
+ Â <i class="icon icon-generic" data-icon="x"> </i>
+ Â </a>
</span>
<span class="small">
- <a target="_blank" href="https://civicdb.org/events/genes/24/summary#gene"
+ Â <a target="_blank" href="https://civicdb.org/events/genes/24/summary#gene"
style="text-decoration:none; color:#06369d; text-transform: lowercase;"> cravat
- <i class="icon icon-generic" data-icon="x"> </i>
- </a>
+ Â <i class="icon icon-generic" data-icon="x"> </i>
+ Â </a>
</span>
*/
@@ -497,7 +497,7 @@ function displayMolecularDataTable(tableData, clickedData) {
var theadRow = jQuery('<tr>');
var tbody = jQuery('<tbody />');
- if (dataVisibility === true) {
+ if (dataVisibility === true && fullData.length > 1) {
let oneData = fullData[0];
let tableHeaders = Object.keys(oneData);
@@ -528,13 +528,16 @@ function displayMolecularDataTable(tableData, clickedData) {
table.append(tbody);
targetDiv.append(table);
customizeDatatable('molcharDataTable', clickedData[4]);
- } else {
-
+ }
+ else {
let report = `<b style="margin-top: 15px; font-size: 13px; color: #06369d;"> ${tableData.reports[0]} </b> `
targetDiv.append(report);
- $('#download-data').hide();
+ if(dataVisibility === false){
+ $('#download-data').hide();
+ }
}
+
$("#omicDataCount").html(rowCount);
$("#clickedSampleId").html(clickedData[0]);
$("#modelHistology").html(clickedData[1]);
@@ -596,4 +599,8 @@ function customizeDatatable(dTable, presentData) {
oTable.search($(this).val()).draw();
})
+}
+
+function openNewWindow(url){
+ window.open(url,'_blank');
}
\ No newline at end of file
diff --git a/web/src/main/resources/templates/details.html b/web/src/main/resources/templates/details.html
index d0b0879c2c4f56222939e7e802c11a40835c9bff..f25ef162fb04eec5d47ca2b7fe7f5c9b856fbd63 100644
--- a/web/src/main/resources/templates/details.html
+++ b/web/src/main/resources/templates/details.html
@@ -78,624 +78,644 @@
<th:block th:include="fragments/shared :: header"></th:block>
- <div id="content-details">
+ <div id="content">
+
+
<!-- Suggested layout containers -->
- <section id="main-content-area" role="main">
-
- <th:block th:include="fragments/shared :: breadcrumb-search-details"></th:block>
-
- <div id="details-content" class="row-main">
- <!-- Three Grids Section-->
- <section>
- <div id="detail-title" class="row">
- <div id="dt-left">
- <div class="columns medium-4 small-12 margin-top-30">
- <h4 class="pdxBig black"><span class="float-left" th:text="${data.providerName}"> The Jackson Laboratory </span>
- </h4>
- </div>
- <div class="columns medium-4 small-12 margin-top-30">
- <h4 class="pdxBig"><span class="float-left border-color-black"
- th:text="${data.modelId+': '+data.mappedOntologyTermLabel}"></span>
- </h4>
- </div>
- </div>
- <div id="dt-right">
- <div class="columns medium-4 small-12 shiftUp20">
- <!--
- <a th:href="@{'mailto:'+${data.contactProviderUrl+'?subject='+data.modelId}}"
- th:if="${ data.contactProviderUrl != null && #strings.contains(data.contactProviderUrl,'@')}">
- <h4 class="button more uppercase margin-top-large minwidth300 card-3b">Contact Provider</h4>
- </a>
- -->
-
- <a th:href="@{'mailto:'+${data.contactProviderUrl+'?subject='+data.modelId}}"
- th:if="${data.contactProviderUrl != null && #strings.contains(data.contactProviderUrl,'@')}">
- <h4 class="button more uppercase margin-top-large minwidth300 card-3b">Contact Provider</h4>
- </a>
-
- <a th:href="@{${data.contactProviderUrl}}" th:target="_blank"
- th:if="${data.contactProviderUrl != null && #strings.contains(data.contactProviderUrl,'http') }">
- <h4 class="button more uppercase margin-top-large minwidth300 card-3b">Contact Provider</h4>
- </a>
-
-
-
- <a th:href="@{${data.viewDataAtUrl}}" th:target="_blank"
- th:if="${data.viewDataAtUrl != null && #strings.contains(data.viewDataAtUrl,'http')}">
- <h4 class="button outline uppercase margin-top-large minwidth300 shiftUp10 card-3b"
- th:text="${data.viewDataAtLabel}">View at Provider</h4>
- </a>
-
- <a style="visibility: collapse;" th:href="@{'/pdx/'+${data.dataSource}+'/'+${data.modelId}+'/pdf'}"
- th:target="_blank"
- class="button outline uppercase margin-top-large minwidth300 shiftUp10 card-3b">
- <span> Download PDF <i class="icon icon-functional" data-icon="="></i> </span>
- </a>
+ <section id="main-content-area" role="main" style="width: 1200px; margin: auto;">
+
+ <th:block th:include="fragments/shared :: breadcrumb-services"></th:block>
+
+ <div class="row">
+ <nav aria-label="You are here:" role="navigation">
+ <ul class="breadcrumbs columns">
+ <li><a href="/">Home</a></li>
+ <li>
+ Details
+ </li>
+ <li>
+ <span class="show-for-sr">Current: </span> <span th:text="${data.modelId}">Model ID</span>
+ </li>
+ </ul>
+ </nav>
+ </div>
- </div>
- </div>
- <div class="reset-float"></div>
+ <!-- Three Grids Section-->
+ <section>
+ <div class="row">
+
+ <div class="columns medium-4 small-12 margin-top-30">
+ <h4 class="pdxBig"><span class="float-left border-color-black"
+ th:text="${data.modelId+': '+data.mappedOntologyTermLabel}"></span>
+ </h4>
</div>
- </section>
- <hr class="margin-vertical-20 line_v2">
+ <div class="columns medium-4 small-12 margin-top-30" style="margin-top: 0px">
+ <h4 class="pdxBig black"><span class="float-left" th:text="${data.providerName}"> The Jackson Laboratory </span>
+ </h4>
+ </div>
- <!-- Tabs Section -->
- <section class="row large-10 medium-12 expanded" id="detailsData">
- <div class="row large-12 medium-12 expanded">
- <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
+ <div class="columns medium-4 small-12 shiftUp20">
+ <!--
+ <a th:href="@{'mailto:'+${data.contactProviderUrl+'?subject='+data.modelId}}"
+ th:if="${ data.contactProviderUrl != null && #strings.contains(data.contactProviderUrl,'@')}">
+ <h4 class="button more uppercase margin-top-large minwidth300 card-3b">Contact Provider</h4>
+ </a>
+ -->
- <li class="tabs-title is-active">
- <a href="#summary" aria-selected="true" style="font-size: 15px; padding: 15px;"> PDX
- Model </a>
- </li>
+ <a th:href="@{'mailto:'+${data.contactProviderUrl+'?subject='+data.modelId}}"
+ th:if="${data.contactProviderUrl != null && #strings.contains(data.contactProviderUrl,'@')}">
+ <h4 class="button more uppercase margin-top-large minwidth300 card-3b">Contact Provider</h4>
+ </a>
+ <a th:href="@{${data.contactProviderUrl}}" th:target="_blank"
+ th:if="${data.contactProviderUrl != null && #strings.contains(data.contactProviderUrl,'http') }">
+ <h4 class="button more uppercase margin-top-large minwidth300 card-3b">Contact Provider</h4>
+ </a>
- <li class="tabs-title">
- <a href="#patients" style="font-size: 15px; padding: 15px;"> Patient </a>
- </li>
+<!--
+ <a th:href="@{${data.viewDataAtUrl}}" th:target="_blank"
+ th:if="${data.viewDataAtUrl != null && #strings.contains(data.viewDataAtUrl,'http')}">
+ <h4 class="button outline uppercase margin-top-large minwidth300 shiftUp10 card-3b"
+ th:text="${data.viewDataAtLabel}">View at Provider</h4>
+ </a>
+-->
+<!--
+ <a th:href="@{'/pdx/'+${data.dataSource}+'/'+${data.modelId}+'/pdf'}"
+ th:target="_blank"
+ class="button outline uppercase margin-top-large minwidth300 shiftUp10 card-3b">
+ <span> Download PDF <i class="icon icon-functional" data-icon="="></i> </span>
+ </a>
+-->
+ </div>
+ </div>
+ </section>
+ <hr class="margin-vertical-20 line_v2">
- <li th:if="${ #lists.isEmpty(data.molecularDataRows)}"
- class="tabs-title ">
- <a href="#variation" style="font-size: 15px; padding: 15px;" id="variation_data_link"
- onclick="initTabs('0')">
- Molecular Data (0)
- </a>
- </li>
- <li th:if="${ not #lists.isEmpty(data.molecularDataRows) }"
- class="tabs-title ">
- <a href="#variation" style="font-size: 15px; padding: 15px;" id="variation_data_link"
- onclick="initTabs('0')">
- Molecular Data
- (<span th:text="${data.molecularDataEntrySize}"> ... </span>)
- </a>
- </li>
+ <!-- Tabs Section -->
+ <section class="row large-10 medium-12 expanded" id="detailsData" style="width:100%">
+ <div class="row large-12 medium-12 expanded">
+ <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
- <li th:if="${data.dosingStudyNumbers} == 0" class="tabs-title">
- <a href="#dosing_studies" style="font-size: 15px; padding: 15px;">Dosing study (0)</a>
- </li>
+ <li class="tabs-title is-active">
+ <a href="#summary" aria-selected="true" style="font-size: 15px; padding: 15px;"> PDX
+ Model </a>
+ </li>
- <li th:if="${data.dosingStudyNumbers} > 0" class="tabs-title">
- <a href="#dosing_studies" style="font-size: 15px; padding: 15px;">Dosing study (1)</a>
- </li>
- </ul>
- </div>
+ <li class="tabs-title">
+ <a href="#patients" style="font-size: 15px; padding: 15px;"> Patient </a>
+ </li>
- <div class="tabs-content style-2" data-tabs-content="example2-tabs">
- <div class="tabs-panel is-active" id="summary">
- <!-- Summary first row -->
- <div class="row large-12 medium-12 expanded">
+ <li th:if="${ #lists.isEmpty(data.molecularDataRows)}"
+ class="tabs-title ">
+ <a href="#variation" style="font-size: 15px; padding: 15px;" id="variation_data_link"
+ onclick="initTabs('0')">
+ Molecular Data (0)
+ </a>
+ </li>
- <div class="columns medium-12 small-12 margin-top-30 card-3">
- <div class="responsive-table top-space-20">
- <table class="datatable-pdx table-borderedPdx pdx-table head-left">
- <thead>
- <tr>
- <th colspan="2"> Related Models </th>
- </tr>
- </thead>
- <tbody>
- <tr th:if="${not #lists.isEmpty(data.relatedModels)}">
- <th class="text-left"> Models </th>
- <td><span th:each="relMod:${data.relatedModels}"><a th:text="${relMod}"
- th:href="@{'/pdx/'+${data.dataSource}+'/'+${relMod}}"></a> </span>
- </td>
- </tr>
- </tbody>
- </table>
- </div>
- </div>
+ <li th:if="${ not #lists.isEmpty(data.molecularDataRows) }"
+ class="tabs-title ">
+ <a href="#variation" style="font-size: 15px; padding: 15px;" id="variation_data_link"
+ onclick="initTabs('0')">
+ Molecular Data
+ (<span th:text="${data.molecularDataEntrySize}"> ... </span>)
+ </a>
+ </li>
- <div class="columns medium-12 small-12 margin-top-medium card-3">
- <div class="responsive-table top-space-20">
+ <li th:if="${data.dosingStudyNumbers} == 0" class="tabs-title">
+ <a href="#dosing_studies" style="font-size: 15px; padding: 15px;">Dosing study (0)</a>
+ </li>
- <table class="datatable-pdx pdx-table table-borderedPdx head-left">
- <thead>
- <tr>
- <th colspan="6">PDX model Engraftment</th>
- </tr>
- <tr>
- <th> Host Strain Name</th>
- <th> Site</th>
- <th> Type</th>
- <th> Material</th>
- <th> Material Status</th>
- <th>Passage</th>
- </tr>
- </thead>
- <tbody>
- <tr th:each="pdxModel, iter : ${data.pdxModelList}">
- <td th:text="${pdxModel.strainName}"></td>
- <td th:text="${pdxModel.engraftmentSite}" class="capt-text"></td>
- <td th:text="${pdxModel.engraftmentType}" class="capt-text"></td>
- <td th:text="${pdxModel.engraftmentMaterial}" class="capt-text"></td>
- <td th:text="${pdxModel.engraftmentMaterialState}" class="capt-text"></td>
- <td th:text="${pdxModel.passage}" class="capt-text"></td>
- </tr>
- </tbody>
- </table>
- </div>
- </div>
+ <li th:if="${data.dosingStudyNumbers} > 0" class="tabs-title">
+ <a href="#dosing_studies" style="font-size: 15px; padding: 15px;">Dosing study (1)</a>
+ </li>
- <div class="columns medium-12 small-12 margin-top-medium card-3">
- <div class="responsive-table top-space-20">
+ </ul>
- <table class="datatable-pdx pdx-table table-borderedPdx head-left">
- <thead>
- <tr>
- <th colspan="3">Model Quality Control</th>
- </tr>
- <tr>
- <th>Technique</th>
- <th>Description</th>
- <th>Passage</th>
- </tr>
- </thead>
- <tbody>
- <tr th:each="qa, iter : ${data.modelQualityControl}">
- <td th:text="${qa.technique}" class="capt-text"></td>
- <td th:text="${qa.description}" class="capt-text"></td>
- <td th:text="${qa.passage}" class="capt-text"></td>
- </tr>
- </tbody>
- </table>
- </div>
+ </div>
+
+ <div class="tabs-content style-2" data-tabs-content="example2-tabs">
+ <div class="tabs-panel is-active" id="summary">
+
+
+ <!-- Summary first row -->
+ <div class="row large-12 medium-12 expanded">
+
+ <div class="columns medium-12 small-12 margin-top-30 card-3">
+ <div class="responsive-table top-space-20">
+ <table class="datatable-pdx table-borderedPdx pdx-table head-left">
+ <thead>
+ <tr>
+ <th colspan="2"> Related Models </th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:if="${not #lists.isEmpty(data.relatedModels)}">
+ <th class="text-left"> Models </th>
+ <td><span th:each="relMod:${data.relatedModels}"><a th:text="${relMod}"
+ th:href="@{'/pdx/'+${data.dataSource}+'/'+${relMod}}"></a> </span>
+ </td>
+ </tr>
+ </tbody>
+ </table>
</div>
+ </div>
+ <div class="columns medium-12 small-12 margin-top-medium card-3">
+ <div class="responsive-table top-space-20">
+
+ <table class="datatable-pdx pdx-table table-borderedPdx head-left">
+ <thead>
+ <tr>
+ <th colspan="6">PDX model Engraftment</th>
+ </tr>
+ <tr>
+ <th> Host Strain Name</th>
+ <th> Site</th>
+ <th> Type</th>
+ <th> Material</th>
+ <th> Material Status</th>
+ <th>Passage</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="pdxModel, iter : ${data.pdxModelList}">
+ <td th:text="${pdxModel.strainName}"></td>
+ <td th:text="${pdxModel.engraftmentSite}" class="capt-text"></td>
+ <td th:text="${pdxModel.engraftmentType}" class="capt-text"></td>
+ <td th:text="${pdxModel.engraftmentMaterial}" class="capt-text"></td>
+ <td th:text="${pdxModel.engraftmentMaterialState}" class="capt-text"></td>
+ <td th:text="${pdxModel.passage}" class="capt-text"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
+ </div>
- <div th:unless="${#lists.isEmpty(data.publications)}"
- class="columns medium-12 small-12 margin-top-medium card-3">
- <div class="responsive-table top-space-20">
- <table th:each="pub, iter : ${data.publications}" class="datatable-pdx table-borderedPdx pdx-table head-left">
+ <div class="columns medium-12 small-12 margin-top-medium card-3">
+ <div class="responsive-table top-space-20">
+
+ <table class="datatable-pdx pdx-table table-borderedPdx head-left">
+ <thead>
+ <tr>
+ <th colspan="3">Model Quality Control</th>
+ </tr>
+ <tr>
+ <th>Technique</th>
+ <th>Description</th>
+ <th>Passage</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="qa, iter : ${data.modelQualityControl}">
+ <td th:text="${qa.technique}" class="capt-text"></td>
+ <td th:text="${qa.description}" class="capt-text"></td>
+ <td th:text="${qa.passage}" class="capt-text"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
- <thead th:if="${iter.index == 0}">
- <tr><th colspan="2"> Publications</th></tr>
- </thead>
+ </div>
- <tbody>
- <tr>
- <th class="text-left medium-2"> Title </th>
- <td><a th:text="${#strings.capitalizeWords(pub.resultList.result[0].title)}"
- th:href="| https://europepmc.org/article/MED/${pub.resultList.result[0].id} |"
- target="_blank"
- style="white-space: normal;"> Title Text <i class="icon icon-generic" data-icon="x"> </i> </a>
- </td>
- </tr>
- <tr>
- <th class="text-left medium-2">Authors</th>
- <td th:text="${pub.resultList.result[0].authorString}">Bougherara H, NĂ©mati F, Nicolas A, ... Decaudin D.</td>
- </tr>
- <tr>
- <th class="text-left medium-2">Publication year</th>
- <td th:text="${pub.resultList.result[0].pubYear}"> 2017 </td>
- </tr>
- <tr>
- <th class="text-left medium-2"> Journal</th>
- <td th:text="${pub.resultList.result[0].title}"> Journal Title </td>
- </tr>
- <tr>
- <td class="text-left" colspan="2">
-
- <ul class="vertical menu" data-accordion-menu>
- <li>
- <a type="button" th:id="|publication-${iter.index}|" class="primary button card-3b small-2 bold" href="#">
- <span th:id="|btn-text-${iter.index}|"> SHOW ABSTRACT</span> <i class="icon icon-generic" data-icon="P"></i>
- </a>
- <ul class="menu vertical nested topSace10">
- <li>
- <div class="callout card-3" style="white-space: normal; margin-left: -10px;" >
- <p th:text="${pub.resultList.result[0].abstractText}"> </p>
- </div>
- </li>
- </ul>
- </li>
- </ul>
-
- </td>
- </tr>
+ <div th:unless="${#lists.isEmpty(data.publications)}"
+ class="columns medium-12 small-12 margin-top-medium card-3">
+ <div class="responsive-table top-space-20">
+
+ <table th:each="pub, iter : ${data.publications}" class="datatable-pdx table-borderedPdx pdx-table head-left">
+
+ <thead th:if="${iter.index == 0}">
+ <tr><th colspan="2"> Publications</th></tr>
+ </thead>
+
+ <tbody>
+ <tr>
+ <th class="text-left medium-2"> Title </th>
+ <td><a th:text="${#strings.capitalizeWords(pub.resultList.result[0].title)}"
+ th:href="| https://europepmc.org/article/MED/${pub.resultList.result[0].id} |"
+ target="_blank"
+ style="white-space: normal;"> Title Text <i class="icon icon-generic" data-icon="x"> </i> </a>
+ </td>
+ </tr>
+ <tr>
+ <th class="text-left medium-2">Authors</th>
+ <td th:text="${pub.resultList.result[0].authorString}">Bougherara H, NĂ©mati F, Nicolas A, ... Decaudin D.</td>
+ </tr>
+ <tr>
+ <th class="text-left medium-2">Publication year</th>
+ <td th:text="${pub.resultList.result[0].pubYear}"> 2017 </td>
+ </tr>
+ <tr>
+ <th class="text-left medium-2"> Journal</th>
+ <td th:text="${pub.resultList.result[0].title}"> Journal Title </td>
+ </tr>
+
+
+ <tr>
+ <td class="text-left" colspan="2">
+
+ <ul class="vertical menu" data-accordion-menu>
+ <li>
+ <a type="button" th:id="|publication-${iter.index}|" class="primary button card-3b small-2 bold" href="#">
+ <span th:id="|btn-text-${iter.index}|"> SHOW ABSTRACT</span> <i class="icon icon-generic" data-icon="P"></i>
+ </a>
+ <ul class="menu vertical nested topSace10">
+ <li>
+ <div class="callout card-3" style="white-space: normal; margin-left: -10px;" >
+ <p th:text="${pub.resultList.result[0].abstractText}"> </p>
+ </div>
+ </li>
+ </ul>
+ </li>
+ </ul>
- </tbody>
- </table>
+ </td>
+ </tr>
- </div>
- </div>
+ </tbody>
+ </table>
+ </div>
</div>
+
</div>
+ </div>
- <div class="tabs-panel" id="patients">
+ <div class="tabs-panel" id="patients">
+
+ <section class="row large-12 medium-12 expanded" id="detailsData" style="margin-top: 20px;">
+
+
+ <div class="columns medium-12 small-12 margin-top-medium card-3">
+ <div class="responsive-table top-space-20">
+ <table class="datatable-pdx table-borderedPdx pdx-table head-left">
+ <thead>
+ <tr>
+ <th colspan="2"> Patient </th>
+ </tr>
+ </thead>
+ <tbody>
+
+ <tr>
+ <th class="text-left medium-4">Sex</th>
+ <td th:text="${data.patient.gender}"></td>
+ </tr>
+ <tr>
+ <th class="text-left medium-4">Race / Ethnicity</th>
+ <td>
+ <span th:text="${data.race}"></span>
+ <span th:if="${not ( #strings.isEmpty(data.race) || #strings.isEmpty(data.ethnicity) ) }"> / </span>
+ <span th:text="${data.ethnicity}"></span>
+ </td>
+ </tr>
+
+ <tr>
+ <th class="text-left medium-4"> Derived Model </th>
+ <td>
+ <span th:text="${data.modelId}"> present model</span>
+ <span th:each="relMod:${data.relatedModels}">
+ <a th:text="${relMod}" th:href="@{'/pdx/'+${data.dataSource}+'/'+${relMod}}"></a>
+ </span>
+ </td>
+ </tr>
+
+
+ <!--<tr>
+ <th class="text-left medium-4">Primary Tissue</th>
+ <td class="text-left" th:text="${data.primaryTissue}"></td>
+ </tr>
+
+ <tr>
+ <th class="text-left medium-4">Collection Site</th>
+ <td class="text-left" th:text="${data.collectionSite}"></td>
+ </tr>
+
+ <tr>
+ <th class="text-left medium-4">Tumor Type</th>
+ <td class="text-left" th:text="${data.tumorType}"></td>
+ </tr> -->
+
+ </tbody>
+ </table>
+ </div>
+ </div>
- <section class="row large-12 medium-12 expanded" id="detailsData" style="margin-top: 20px;">
- <div class="columns medium-12 small-12 margin-top-medium card-3">
- <div class="responsive-table top-space-20">
- <table class="datatable-pdx table-borderedPdx pdx-table head-left">
- <thead>
- <tr>
- <th colspan="2"> Patient </th>
- </tr>
- </thead>
- <tbody>
+ <div class="columns medium-12 small-12 margin-top-10 card-3">
+ <div class="responsive-table top-space-20">
+ <table class="datatable-pdx pdx-table head-left">
+ <thead>
+ <tr>
+ <th> Patient Tumor Collection For PDX Model </th>
+ </tr>
+ </thead>
+ </table>
+ <table class="pdx-table head-left top-space-n-20">
+ <thead>
+ <th></th>
+ <th:block
+ th:if="${not #lists.isEmpty(data.patient.collectionEvents)}"
+ th:each="event, iter : ${data.patient.collectionEvents}">
+
+ <th th:if="${event.pdxMouse != data.modelId}"
+ th:text="${'Collection '} + ${' (Other Model)'}">
+ Collection
+ </th>
+ <th th:if="${event.pdxMouse == data.modelId}"
+ th:text="${'Collection '} + ${' (Current Model)'}">
+ Collection
+ </th>
+
+ </th:block>
+ </thead>
+ <tbody>
+
+ <th:block
+ th:if="${not #lists.isEmpty(data.patient.collectionEvents)}">
<tr>
- <th class="text-left medium-4">Sex</th>
- <td th:text="${data.patient.gender}"></td>
- </tr>
- <tr>
- <th class="text-left medium-4">Race / Ethnicity</th>
- <td>
- <span th:text="${data.race}"></span>
- <span th:if="${not ( #strings.isEmpty(data.race) || #strings.isEmpty(data.ethnicity) ) }"> / </span>
- <span th:text="${data.ethnicity}"></span>
- </td>
+ <th class="text-left medium-4">Age</th>
+
+ <th:block
+ th:each="event : ${data.patient.collectionEvents}">
+ <td th:text="${event.age}"
+ th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
+ ... AGE ...
+ </td>
+ </th:block>
</tr>
<tr>
- <th class="text-left medium-4"> Derived Model </th>
- <td>
- <span th:text="${data.modelId}"> present model</span>
- <span th:each="relMod:${data.relatedModels}">
- <a th:text="${relMod}" th:href="@{'/pdx/'+${data.dataSource}+'/'+${relMod}}"></a>
- </span>
- </td>
+ <th class="text-left medium-4"> Diagnosis</th>
+
+ <th:block
+ th:each="event : ${data.patient.collectionEvents}">
+ <td th:text="${event.diagnosis}"
+ th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
+ ... DIAGNOSIS ...
+ </td>
+ </th:block>
</tr>
-
- <!--<tr>
- <th class="text-left medium-4">Primary Tissue</th>
- <td class="text-left" th:text="${data.primaryTissue}"></td>
+ <tr>
+ <th class="text-left medium-4"> Type</th>
+
+ <th:block th:each="event : ${data.patient.collectionEvents}">
+ <td th:text="${event.type}"
+ th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
+ ... TYPE ...
+ </td>
+ </th:block>
</tr>
<tr>
- <th class="text-left medium-4">Collection Site</th>
- <td class="text-left" th:text="${data.collectionSite}"></td>
+ <th class="text-left medium0-4"> PDX Mouse</th>
+ <th:block th:each="event : ${data.patient.collectionEvents}">
+ <td th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
+
+ <span th:if="${#strings.equals(event.pdxMouse, data.modelId) }"
+ th:text="${event.pdxMouse}">
+ ... MODELID ...
+ </span>
+
+ <span th:if="${not #strings.equals(event.pdxMouse, data.modelId) }">
+ <a th:text="${event.pdxMouse}"
+ th:href="@{'/pdx/'+${data.dataSource}+'/'+${event.pdxMouse}}"
+ target="_blank"> ... MODELID ... </a>
+ </span>
+ </td>
+
+ </th:block>
</tr>
<tr>
- <th class="text-left medium-4">Tumor Type</th>
- <td class="text-left" th:text="${data.tumorType}"></td>
- </tr> -->
-
- </tbody>
- </table>
- </div>
- </div>
-
-
+ <th class="text-left medium-4">Collection Site</th>
- <div class="columns medium-12 small-12 margin-top-10 card-3">
- <div class="responsive-table top-space-20">
- <table class="datatable-pdx pdx-table head-left">
- <thead>
- <tr>
- <th> Patient Tumor Collection For PDX Model </th>
+ <th:block
+ th:each="event : ${data.patient.collectionEvents}">
+ <td th:text="${event.collectionSite}"
+ th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
+ ... COLLECTION SITE ...
+ </td>
+ </th:block>
</tr>
- </thead>
- </table>
- <table class="pdx-table head-left top-space-n-20">
- <thead>
- <th></th>
- <th:block
- th:if="${not #lists.isEmpty(data.patient.collectionEvents)}"
- th:each="event, iter : ${data.patient.collectionEvents}">
-
- <th th:if="${event.pdxMouse != data.modelId}"
- th:text="${'Collection '} + ${' (Other Model)'}">
- Collection
- </th>
- <th th:if="${event.pdxMouse == data.modelId}"
- th:text="${'Collection '} + ${' (Current Model)'}">
- Collection
- </th>
-
- </th:block>
- </thead>
- <tbody>
-
- <th:block
- th:if="${not #lists.isEmpty(data.patient.collectionEvents)}">
-
- <tr>
- <th class="text-left medium-4">Age</th>
- <th:block
- th:each="event : ${data.patient.collectionEvents}">
- <td th:text="${event.age}"
- th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
- ... AGE ...
- </td>
- </th:block>
- </tr>
-
- <tr>
- <th class="text-left medium-4"> Diagnosis</th>
+ </th:block>
+
+ </tbody>
+ </table>
+
+ <table class="pdx-table head-left">
+ <tbody>
+ <tr>
+ <th class="text-left medium-4"> Grade</th>
+ <td th:if="${#strings.equalsIgnoreCase(data.grade, 'Not Specified') || #strings.equalsIgnoreCase(data.gradeClassification, 'Not Specified')}">
+ <span th:utext="${data.grade}"></span>
+ </td>
+ <td th:if="${not ( #strings.equalsIgnoreCase(data.grade, 'Not Specified') || #strings.equalsIgnoreCase(data.gradeClassification, 'Not Specified') ) }">
+ <span th:utext="${data.grade}"></span>
+ <span th:utext="${'(<b> Classification: </b>'+data.gradeClassification+')'}"></span>
+ </td>
+ </tr>
+
+ <tr>
+ <th class="text-left medium-4"> Stage</th>
+ <td th:if="${#strings.equalsIgnoreCase(data.stage, 'Not Specified') || #strings.equalsIgnoreCase(data.stageClassification, 'Not Specified')}">
+ <span th:utext="${data.stage}"></span>
+ </td>
+ <td th:if="${not ( #strings.equalsIgnoreCase(data.stage, 'Not Specified') || #strings.equalsIgnoreCase(data.stageClassification, 'Not Specified') ) }">
+ <span th:utext="${data.stage}"></span>
+ <span th:utext="${'(<b> Classification: </b>'+data.stageClassification+')'}"></span>
+ </td>
+ </tr>
+ </tbody>
+ </table>
- <th:block
- th:each="event : ${data.patient.collectionEvents}">
- <td th:text="${event.diagnosis}"
- th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
- ... DIAGNOSIS ...
- </td>
- </th:block>
- </tr>
-
- <tr>
- <th class="text-left medium-4"> Type</th>
-
- <th:block th:each="event : ${data.patient.collectionEvents}">
- <td th:text="${event.type}"
- th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
- ... TYPE ...
- </td>
- </th:block>
- </tr>
-
- <tr>
- <th class="text-left medium0-4"> PDX Mouse</th>
- <th:block th:each="event : ${data.patient.collectionEvents}">
- <td th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
-
- <span th:if="${#strings.equals(event.pdxMouse, data.modelId) }"
- th:text="${event.pdxMouse}">
- ... MODELID ...
- </span>
+ </div>
+ </div>
- <span th:if="${not #strings.equals(event.pdxMouse, data.modelId) }">
- <a th:text="${event.pdxMouse}"
- th:href="@{'/pdx/'+${data.dataSource}+'/'+${event.pdxMouse}}"
- target="_blank"> ... MODELID ... </a>
- </span>
- </td>
- </th:block>
- </tr>
- <tr>
- <th class="text-left medium-4">Collection Site</th>
- <th:block
- th:each="event : ${data.patient.collectionEvents}">
- <td th:text="${event.collectionSite}"
- th:class="${#strings.equals(event.pdxMouse, data.modelId) } ? 'highlight-bg' : 'table-focus' ">
- ... COLLECTION SITE ...
- </td>
- </th:block>
- </tr>
- </th:block>
- </tbody>
- </table>
+ <div class="tabs-content style-2" data-tabs-content="example2-tabs">
+ <div class="tabs-panel is-active" id="summary">
- <table class="pdx-table head-left">
- <tbody>
- <tr>
- <th class="text-left medium-4"> Grade</th>
- <td th:if="${#strings.equalsIgnoreCase(data.grade, 'Not Specified') || #strings.equalsIgnoreCase(data.gradeClassification, 'Not Specified')}">
- <span th:utext="${data.grade}"></span>
- </td>
- <td th:if="${not ( #strings.equalsIgnoreCase(data.grade, 'Not Specified') || #strings.equalsIgnoreCase(data.gradeClassification, 'Not Specified') ) }">
- <span th:utext="${data.grade}"></span>
- <span th:utext="${'(<b> Classification: </b>'+data.gradeClassification+')'}"></span>
- </td>
- </tr>
+ <div class="row large-12 medium-12 expanded">
- <tr>
- <th class="text-left medium-4"> Stage</th>
- <td th:if="${#strings.equalsIgnoreCase(data.stage, 'Not Specified') || #strings.equalsIgnoreCase(data.stageClassification, 'Not Specified')}">
- <span th:utext="${data.stage}"></span>
- </td>
- <td th:if="${not ( #strings.equalsIgnoreCase(data.stage, 'Not Specified') || #strings.equalsIgnoreCase(data.stageClassification, 'Not Specified') ) }">
- <span th:utext="${data.stage}"></span>
- <span th:utext="${'(<b> Classification: </b>'+data.stageClassification+')'}"></span>
- </td>
- </tr>
- </tbody>
- </table>
</div>
</div>
+ </div>
+ </section>
+ <!-- Disable Current Treatment Table
+ <section class="row large-12 medium-12 expanded"
+ id="detailsData"
+ style="margin-top: 20px;"
+ th:if="${ #bools.isTrue(data.patient.currentTreatmentExists) } ">
-
-
+ <div class="row large-12 medium-12 expanded">
+ <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
+ <li class="tabs-title is-active"><a href="#initialDiagnosis" aria-selected="true" style="font-size: 15px; padding: 15px;"> Current Therapy </a></li>
+ </ul>
+ </div>
<div class="tabs-content style-2" data-tabs-content="example2-tabs">
<div class="tabs-panel is-active" id="summary">
<div class="row large-12 medium-12 expanded">
+ <div class="columns medium-12 small-12 margin-top-10 card-3">
+ <div class="responsive-table" style="margin-top: 20px;">
+ <table class="pdx-table head-left">
+ <thead>
+ <th> Date Regimen Started </th>
+ <th> Regimen </th>
+ <th> Dose </th>
+ <th> Best Response </th>
+ <th> Duration (Months) </th>
+ </thead>
+ <tbody>
- </div>
- </div>
- </div>
- </section>
-
-
- <!-- Disable Current Treatment Table
- <section class="row large-12 medium-12 expanded"
- id="detailsData"
- style="margin-top: 20px;"
- th:if="${ #bools.isTrue(data.patient.currentTreatmentExists) } ">
-
- <div class="row large-12 medium-12 expanded">
- <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
- <li class="tabs-title is-active"><a href="#initialDiagnosis" aria-selected="true" style="font-size: 15px; padding: 15px;"> Current Therapy </a></li>
- </ul>
- </div>
-
- <div class="tabs-content style-2" data-tabs-content="example2-tabs">
- <div class="tabs-panel is-active" id="summary">
-
- <div class="row large-12 medium-12 expanded">
-
- <div class="columns medium-12 small-12 margin-top-10 card-3">
- <div class="responsive-table" style="margin-top: 20px;">
- <table class="pdx-table head-left">
- <thead>
- <th> Date Regimen Started </th>
- <th> Regimen </th>
- <th> Dose </th>
- <th> Best Response </th>
- <th> Duration (Months) </th>
- </thead>
- <tbody>
-
-
- <th:block th:if="${not #lists.isEmpty(data.patient.treatmentSummaries)}"
- th:each="treatment : ${data.patient.treatmentSummaries}">
- <tr th:if="${ #bools.isTrue(treatment.current) } ">
+ <th:block th:if="${not #lists.isEmpty(data.patient.treatmentSummaries)}"
+ th:each="treatment : ${data.patient.treatmentSummaries}">
- <th class="text-left medium-4"
- th:text="${treatment.treatmentDate+' (Current)'}"> ...DATE... </th>
+ <tr th:if="${ #bools.isTrue(treatment.current) } ">
- <td th:text="${treatment.drugNames}"></td>
- <td th:text="${treatment.dose}"> </td>
+ <th class="text-left medium-4"
+ th:text="${treatment.treatmentDate+' (Current)'}"> ...DATE... </th>
+ <td th:text="${treatment.drugNames}"></td>
+ <td th:text="${treatment.dose}"> </td>
- <td th:text="${treatment.response}"> </td>
- <td th:text="${treatment.duration}"> </td>
- </tr>
+ <td th:text="${treatment.response}"> </td>
+ <td th:text="${treatment.duration}"> </td>
- </th:block>
+ </tr>
- </tbody>
- </table>
- </div>
+ </th:block>
+ </tbody>
+ </table>
</div>
+
</div>
</div>
</div>
- </section> -->
+ </div>
+ </section> -->
- <section class="row large-12 medium-12 expanded"
- id="detailsData"
- style="margin-top: 20px;"
- th:if="${ #bools.isTrue(data.patient.treatmentExists) } ">
+ <section class="row large-12 medium-12 expanded"
+ id="detailsData"
+ style="margin-top: 20px;"
+ th:if="${ #bools.isTrue(data.patient.treatmentExists) } ">
- <div class="row large-12 medium-12 expanded">
- <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
- <li class="tabs-title is-active"><a href="#initialDiagnosis"
- aria-selected="true"
- style="font-size: 15px; padding: 15px;">
- Patient Therapies & Response </a></li>
- </ul>
- </div>
+ <div class="row large-12 medium-12 expanded">
+ <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
+ <li class="tabs-title is-active"><a href="#initialDiagnosis"
+ aria-selected="true"
+ style="font-size: 15px; padding: 15px;">
+ Patient Therapies & Response </a></li>
+ </ul>
+ </div>
- <div class="tabs-content style-2" data-tabs-content="example2-tabs">
- <div class="tabs-panel is-active" id="summary">
+ <div class="tabs-content style-2" data-tabs-content="example2-tabs">
+ <div class="tabs-panel is-active" id="summary">
- <!-- Summary first row -->
- <div class="row large-12 medium-12 expanded">
-
- <div class="columns medium-12 small-12 margin-top-10 card-3">
- <div class="responsive-table" style="margin-top: 20px;">
- <table class="pdx-table head-left">
- <thead>
- <th> Date Regimen Started</th>
- <th> Regimen</th>
- <th> Dose</th>
- <th> Best Response</th>
- <th> Duration (Months)</th>
- </thead>
- <tbody>
+ <!-- Summary first row -->
+ <div class="row large-12 medium-12 expanded">
+ <div class="columns medium-12 small-12 margin-top-10 card-3">
+ <div class="responsive-table" style="margin-top: 20px;">
+ <table class="pdx-table head-left">
+ <thead>
+ <th> Date Regimen Started</th>
+ <th> Regimen</th>
+ <th> Dose</th>
+ <th> Best Response</th>
+ <th> Duration (Months)</th>
+ </thead>
+ <tbody>
- <th:block
- th:if="${not #lists.isEmpty(data.patient.treatmentSummaries)}"
- th:each="treatment : ${data.patient.treatmentSummaries}">
- <tr th:if="${ #bools.isFalse(treatment.current) } ">
+ <th:block
+ th:if="${not #lists.isEmpty(data.patient.treatmentSummaries)}"
+ th:each="treatment : ${data.patient.treatmentSummaries}">
- <th class="text-left medium-4 capt-text"
- th:text="${treatment.treatmentDate}"> ...DATE...
- </th>
+ <tr th:if="${ #bools.isFalse(treatment.current) } ">
- <td th:text="${treatment.drugNames}"></td>
- <td th:text="${treatment.dose}"></td>
- <td th:text="${treatment.response}"></td>
- <td th:text="${treatment.duration}"></td>
+ <th class="text-left medium-4 capt-text"
+ th:text="${treatment.treatmentDate}"> ...DATE...
+ </th>
- </tr>
+ <td th:text="${treatment.drugNames}"></td>
+ <td th:text="${treatment.dose}"></td>
+ <td th:text="${treatment.response}"></td>
+ <td th:text="${treatment.duration}"></td>
- </th:block>
+ </tr>
+ </th:block>
- <th:block
- th:if="${not #lists.isEmpty(data.patient.treatmentSummaries)}"
- th:each="treatment : ${data.patient.treatmentSummaries}">
- <tr th:if="${ #bools.isTrue(treatment.current) } ">
+ <th:block
+ th:if="${not #lists.isEmpty(data.patient.treatmentSummaries)}"
+ th:each="treatment : ${data.patient.treatmentSummaries}">
- <th class="text-left medium-4"
- th:text="${treatment.treatmentDate+' (Current)'}">
- ...DATE...
- </th>
+ <tr th:if="${ #bools.isTrue(treatment.current) } ">
- <td th:text="${treatment.drugNames}"></td>
- <td th:text="${treatment.dose}"></td>
+ <th class="text-left medium-4"
+ th:text="${treatment.treatmentDate+' (Current)'}">
+ ...DATE...
+ </th>
+ <td th:text="${treatment.drugNames}"></td>
+ <td th:text="${treatment.dose}"></td>
- <td th:text="${treatment.response}"></td>
- <td th:text="${treatment.duration}"></td>
- </tr>
+ <td th:text="${treatment.response}"></td>
+ <td th:text="${treatment.duration}"></td>
- </th:block>
+ </tr>
- </tbody>
- </table>
- </div>
+ </th:block>
+ </tbody>
+ </table>
</div>
+
</div>
</div>
</div>
- </section>
+ </div>
+ </section>
- </div>
+ </div>
@@ -706,223 +726,227 @@
- <div class="tabs-panel is-active" id="variation">
+ <div class="tabs-panel is-active" id="variation">
- <div class="row large-12 medium-12 expanded" id="variationTableSummary">
+ <div class="row large-12 medium-12 expanded" id="variationTableSummary">
- <div class="tab hideContent0" role="tabpanel" th:if="${data.molecularDataRows.size() > 0}">
+ <div class="tab hideContent0" role="tabpanel" th:if="${data.molecularDataRows.size() > 0}">
- <div th:if="${not #lists.isEmpty(data.molecularDataRows)}"
- class="row large-12 medium-12 expanded">
+ <div th:if="${not #lists.isEmpty(data.molecularDataRows)}"
+ class="row large-12 medium-12 expanded">
- <div class="columns medium-12 small-12 margin-top-10 card-3">
- <div class="responsive-table" style="margin-top: 20px;">
+ <div class="columns medium-12 small-12 margin-top-10 card-3">
+ <div class="responsive-table" style="margin-top: 20px;">
- <table class="datatable-pdx pdx-table table-borderedPdx head-left" data-tabs
- id="example-tabs">
- <thead>
- <th>Sample ID</th>
- <th>Sample Type</th>
- <th>Engrafted Tumor Passage</th>
- <th>Data Type</th>
- <th>Data Available</th>
- <th>Platform Used</th>
- <th>Raw Data</th>
- </thead>
- <tbody>
+ <table class="datatable-pdx pdx-table table-borderedPdx head-left" data-tabs
+ id="example-tabs">
+ <thead>
+ <th>Sample ID</th>
+ <th>Sample Type</th>
+ <th>Engrafted Tumor Passage</th>
+ <th>Data Type</th>
+ <th>Data Available</th>
+ <th>Platform Used</th>
+ <th>Raw Data</th>
+ </thead>
+ <tbody>
- <tr th:each="dataRow,iter : ${data.molecularDataRows}"
- class="tabs-title" style="float:none; text-transform: capitalize;"
- th:classappend="( ${iter.index} == 0 ) ? 'is-active' : '' ">
-
- <td th:text="${dataRow.sampleId}"> ...</td>
- <td th:text="${dataRow.sampleType}"> ...</td>
- <td th:text="${'Passage '+dataRow.engraftedTumorPassage}"> ...</td>
- <td th:text="${dataRow.molcharType}"> ...</td>
-
- <td>
- <span th:if="${dataRow.isVisible == 'YES' and dataRow.dataAssociated != 'YES'}" th:text="'Data is not available in the Finder'"></span>
- <a th:if="${dataRow.dataAssociated == 'YES' or dataRow.isVisible == 'NO'}" class="molecularDataLink"
- style="color: #06369d; text-decoration: none;"
- data-th-attr="data-tabs-target=${dataRow.dataAvailableLabel}, aria-selected=( ${iter.index} == 0 ) ? 'true' : '' "
- th:title="${dataRow.sampleId+' | '+data.mappedOntologyTermLabel+' | '+dataRow.sampleType+' | '+dataRow.engraftedTumorPassage+' | '+dataRow.platformUsedLabel}"
- th:text="'View data'"
- th:id="${'mc___'+dataRow.molcharId}">
- TAB TITLES
- </a>
- </td>
- <td>
- <a th:if="${dataRow.platformUsedUrl != null or dataRow.platformUsedLabel == ''}" target="_blank"
- style="color: #06369d; text-decoration: none;"
- th:text="${#strings.replace(dataRow.platformUsedLabel,'_',' ')}"
- th:onclick="'window.open(\''+${dataRow.platformUsedUrl}+'\')'">
- ...
- </a>
- <span th:if="${dataRow.platformUsedUrl == null}" th:text="${dataRow.platformUsedLabel}"></span>
- </td>
- <td>
- <a th:text="${dataRow.rawDataLabel}"
- style="color: #06369d; text-decoration: none;"
- th:onclick="'window.open(\' '+${dataRow.rawDataLink}+'\')'">
- ...
- </a>
- <span th:if="${dataRow.rawDataLink == ''} " th:text="'Not Available'" ></span>
- </td>
- </tr>
+ <tr th:each="dataRow,iter : ${data.molecularDataRows}"
+ class="tabs-title" style="float:none; text-transform: capitalize;"
+ th:classappend="( ${iter.index} == 0 ) ? 'is-active' : '' ">
- </tbody>
- </table>
+ <td th:text="${dataRow.sampleId}"> ...</td>
+ <td th:text="${dataRow.sampleType}"> ...</td>
+ <td th:text="${'Passage '+dataRow.engraftedTumorPassage}"> ...</td>
+ <td th:text="${dataRow.molcharType}"> ...</td>
+
+ <td>
+ <span th:if="${dataRow.isVisible == 'YES' and dataRow.dataAssociated != 'YES'}" th:text="'Data is not available in the Finder'"></span>
+ <a th:if="${dataRow.dataAssociated == 'YES' or dataRow.isVisible == 'NO'}" class="molecularDataLink"
+ style="color: #06369d; text-decoration: none;"
+ data-th-attr="data-tabs-target=${dataRow.dataAvailableLabel}, aria-selected=( ${iter.index} == 0 ) ? 'true' : '' "
+ th:title="${dataRow.sampleId+' | '+data.mappedOntologyTermLabel+' | '+dataRow.sampleType+' | '+dataRow.engraftedTumorPassage+' | '+dataRow.platformUsedLabel}"
+ th:text="'View data'"
+ th:id="${'mc___'+dataRow.molcharId}">
+ TAB TITLES
+ </a>
+ </td>
+ <td>
+ <a th:if="${dataRow.platformUsedUrl != null or dataRow.platformUsedLabel == ''}" target="_blank"
+ style="color: #06369d; text-decoration: none;"
+ th:text="${#strings.replace(dataRow.platformUsedLabel,'_',' ')}"
+ th:data-platformurl="${dataRow.platformUsedUrl}"
- </div>
- </div>
+ onclick="openNewWindow(this.getAttribute('data-platformurl'));">
+ ...
+ </a>
+ <span th:if="${dataRow.platformUsedUrl == null}" th:text="${dataRow.platformUsedLabel}"></span>
+ </td>
+ <td>
+ <a th:text="${dataRow.rawDataLabel}"
+ style="color: #06369d; text-decoration: none;"
+ th:attr="onclick=|window.open('${dataRow.rawDataLink}')|">
+ ...
+ </a>
+ <span th:if="${dataRow.rawDataLink == ''} " th:text="'Not Available'" ></span>
+ </td>
+ </tr>
+
+ </tbody>
+ </table>
+
+ </div>
</div>
</div>
</div>
+ </div>
- <div id="omicDataContainer">
- <div class="row large-12 medium-12 expanded top-space-30 ">
- <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
- <li class="tabs-title is-active">
- <a href="#initialDiagnosis"
- aria-selected="true"
- style="font-size: 15px; padding: 15px;">
- Genomic Data (<span id="omicDataCount"></span>) <!-- data.variationDataCount -->
- </a>
- </li>
- </ul>
- </div>
+ <div id="omicDataContainer">
+ <div class="row large-12 medium-12 expanded top-space-30 ">
+ <ul class="tabs style-2" data-deep-link="true" data-tabs id="example2-tabs">
+ <li class="tabs-title is-active">
+ <a href="#initialDiagnosis"
+ aria-selected="true"
+ style="font-size: 15px; padding: 15px;">
+ Genomic Data (<span id="omicDataCount"></span>) <!-- data.variationDataCount -->
+ </a>
+ </li>
+ </ul>
+ </div>
- <div class="columns medium-12 small-12 card-3" style="padding: 15px;">
- <div class="columns medium-6 small-12" id="download-data" style="float: right; margin-top:-65px; margin-right:-30px;">
- <div class="columns medium-5 small-12 text-right" style="padding: 0px;">
- <label class="dropdown">
- <a class="button outline secondary">
- Download Results <i class="icon icon-functional" data-icon="="></i>
- </a>
- <input type="checkbox" class="dd-input" id="test">
-
- <ul class="dd-menu">
- <th:block th:each="dataRow,iter : ${data.molecularDataRows}">
- <li th:if="${dataRow.isVisible == 'YES' and dataRow.dataAssociated == 'YES'}">
- <a th:href="@{'/pdx/'+${data.dataSource}+'/'+${data.modelId}+'/'+${#strings.replace(dataRow.molcharType,' ','-')}+'/'+${dataRow.molcharId}+'/export'}"
- th:text="${#strings.capitalizeWords(dataRow.molcharType)}"> Download ... </a>
- </li>
- </th:block>
- <li class="divider"></li>
- <!--<li>
- <a target="_blank"
- style="color: #06369d; text-decoration: none;"
- th:onclick=" 'window.open(\''+${'https://pdmr.cancer.gov/content/docs/NCI_Cancer_Gene_Panel.pdf'}+'\')' "> Download All </a>
- </li>
- <li>
- <a target="_blank"> Downlload All </a>
- </li>-->
- </ul>
- </label>
- </div>
+ <div class="columns medium-12 small-12 card-3" style="padding: 15px;">
+ <div class="columns medium-6 small-12" id="download-data" style="float: right; margin-top:-65px; margin-right:-30px;">
+ <div class="columns medium-5 small-12 text-right" style="padding: 0px;">
+ <label class="dropdown" style="margin-top: 10px;">
+ <a class="button outline secondary">
+ Download Results <i class="icon icon-functional" data-icon="="></i>
+ </a>
+ <input type="checkbox" class="dd-input" id="test">
+ <ul class="dd-menu">
+ <th:block th:each="dataRow,iter : ${data.molecularDataRows}">
+ <li th:if="${dataRow.isVisible == 'YES' and dataRow.dataAssociated == 'YES'}">
+ <a th:href="@{'/pdx/'+${data.dataSource}+'/'+${data.modelId}+'/'+${#strings.replace(dataRow.molcharType,' ','-')}+'/'+${dataRow.molcharId}+'/export'}"
+ th:text="${#strings.capitalizeWords(dataRow.molcharType)}"> Download ... </a>
+ </li>
+ </th:block>
+
+ <li class="divider"></li>
+ <!--<li>
+ <a target="_blank"
+ style="color: #06369d; text-decoration: none;"
+ th:onclick=" 'window.open(\''+${'https://pdmr.cancer.gov/content/docs/NCI_Cancer_Gene_Panel.pdf'}+'\')' "> Download All </a>
+ </li>
+ <li>
+ <a target="_blank"> Downlload All </a>
+ </li>-->
+ </ul>
+ </label>
+ </div>
- <div id="customSearch" class="columns medium-7 small-12 text-right" style="padding: 0px;">
- <!-- Datatable Search Box -->
- </div>
+ <div id="customSearch" class="columns medium-7 small-12 text-right" style="padding:0px; margin-top:10px">
+ <!-- Datatable Search Box -->
</div>
- <div class="tabs-content" data-tabs-content="example-tabs">
+ </div>
- <div class="tabs-panel is-active"
- style="border-top: 1px solid #5ea88f; margin-top:20px;">
+ <div class="tabs-content" data-tabs-content="example-tabs">
- <hr id="hrTitle" class="hr-text" data-content="THE PLATFORM">
+ <div class="tabs-panel is-active"
+ style="border-top: 1px solid #5ea88f; margin-top:20px;">
- <div class="table-responsive">
+ <hr id="hrTitle" class="hr-text" data-content="THE PLATFORM">
- <h4 class="bLine" th:classappend="( true ) ? '' : 'topSpace50' ">
+ <div class="table-responsive">
- <span class="hdc">Sample ID: </span>
- <b class="black" id="clickedSampleId"></b> <!-- data.techNPassToSampleId['__${technology.key}__'+'__${technology.value[num-1]}__'] -->
+ <h4 class="bLine" th:classappend="( true ) ? '' : 'topSpace50' ">
- <span class="hdc">Histology:</span>
- <b class="black" id="modelHistology"></b> <!-- strings.capitalize(data.diagnosis) -->
+ <span class="hdc">Sample ID: </span>
+ <b class="black" id="clickedSampleId"></b> <!-- data.techNPassToSampleId['__${technology.key}__'+'__${technology.value[num-1]}__'] -->
- <span class="hdc">Tumor Type: </span>
- <b class="black" id="clickedTumorType">Engrafted Tumor</b>
+ <span class="hdc">Histology:</span>
+ <b class="black" id="modelHistology"></b> <!-- strings.capitalize(data.diagnosis) -->
- <span class="hdc">Passage: </span>
- <b class="black" id="clickedPassage"></b>
+ <span class="hdc">Tumor Type: </span>
+ <b class="black" id="clickedTumorType">Engrafted Tumor</b>
- <span class="hdc">Platform: </span>
- <b class="black" id="clickedTech"></b>
+ <span class="hdc">Passage: </span>
+ <b class="black" id="clickedPassage"></b>
- </h4>
+ <span class="hdc">Platform: </span>
+ <b class="black" id="clickedTech"></b>
- <div style="text-align: center;"> <img th:src="@{/images/loading2.gif}" id="preLoader"/> </div>
- <div class="responsive-table" style="margin-top: 20px;" id="variationTableData">
+ </h4>
- </div>
- </div>
+ <div style="text-align: center;"> <img th:src="@{/images/loading2.gif}" id="preLoader"/> </div>
+ <div class="responsive-table" style="margin-top: 20px;" id="variationTableData">
+ </div>
</div>
+
</div>
</div>
</div>
</div>
+ </div>
- <div class="tabs-panel" id="dosing_studies">
- <div th:if="${not #lists.isEmpty(data.dosingStudy)}">
+ <div class="tabs-panel" id="dosing_studies">
+ <div th:if="${not #lists.isEmpty(data.dosingStudy)}">
- <div class="columns medium-12 small-12 margin-top-10 card-3">
- <div class="responsive-table" style="margin-top: 20px;">
+ <div class="columns medium-12 small-12 margin-top-10 card-3">
+ <div class="responsive-table" style="margin-top: 20px;">
- <div th:if="${data.dosingStudyProtocolUrl} != null" class="drug_spacing">
- <a th:href="${data.dosingStudyProtocolUrl}">Dosing study protocol</a>
- </div>
+ <div th:if="${data.dosingStudyProtocolUrl} != null" class="drug_spacing">
+ <a th:href="${data.dosingStudyProtocolUrl}">Dosing study protocol</a>
+ </div>
- <table class="datatable-pdx pdx-table table-borderedPdx head-left">
- <thead>
- <th>Drug</th>
- <th>Dose</th>
- <th>Response</th>
- </thead>
- <tbody>
- <tr th:each="drugData, iter : ${data.dosingStudy}">
- <td th:text="${drugData.drugName}"></td>
- <td th:text="${drugData.dose}"></td>
- <td th:text="${drugData.response}"></td>
- </tr>
- </tbody>
- </table>
+ <table class="datatable-pdx pdx-table table-borderedPdx head-left">
+ <thead>
+ <th>Drug</th>
+ <th>Dose</th>
+ <th>Response</th>
+ </thead>
+ <tbody>
+ <tr th:each="drugData, iter : ${data.dosingStudy}">
+ <td th:text="${drugData.drugName}"></td>
+ <td th:text="${drugData.dose}"></td>
+ <td th:text="${drugData.response}"></td>
+ </tr>
+ </tbody>
+ </table>
- </div>
</div>
-
</div>
- <div th:if="${#lists.isEmpty(data.dosingStudy)}"></div>
</div>
+
+ <div th:if="${#lists.isEmpty(data.dosingStudy)}"></div>
</div>
- </section>
- </div>
+
+ </div>
+ </section>
</section>
- <th:block th:include="fragments/shared :: footer"></th:block>
</div>
-</div>
+ <!-- End suggested layout containers / #content -->
+ <th:block th:include="fragments/shared :: footer"></th:block>
+</div>
<!-- JavaScript -->
-<!--<script type='text/javascript' th:src="@{/js/banner-gdpr.js}"></script>-->
+<script type='text/javascript' th:src="@{/js/banner-gdpr.js}"></script>
<div id="data-protection-message-configuration"
data-message="Your message and links here."
data-service-id="ebi" data-data-protection-version="0.1">
@@ -1023,22 +1047,6 @@
}
</script>
-<div class="box-fixed-notice box-fixed-notice--old-browsers">
- <div class="row-main">
- <form action="/" enctype="multipart/form-data" method="post"> <p class="box-fixed-notice__text">
- You are running an old browser version. We recommend updating your browser to its latest version.
- </p>
- <p class="box-fixed-notice__btn-wrap">
- <a href="/system/your-browser-is-outdated" class="btn btn-white btn-border btn-s">
- <span>More info</span>
- </a>
- <button type="submit" class="btn btn-white btn-border btn-s">
- <span>Close</span>
- </button>
- </p>
- <input name='ufprt' type='hidden' value='lKFncnBaM6PLAWMCyZ6uii0CCveb66W1RDWg3qMNy4WCgWWvBUWX1xJjY62evDRYEvPmouUm6zn6TTNReIzqLBuw7ZXh09ufNDig51U+nuLBvlTuVpmvzfLBQaY+R7XhPg5CzowZxUYkfEmfuMPqRC7GgftaUBX/RKCir0bkaHRpD7bz' /></form> </div>
-</div>
-
<script type="text/javascript">
window.trackDownloads = true;
diff --git a/web/src/main/resources/templates/fragments/filter-components.html b/web/src/main/resources/templates/fragments/filter-components.html
index 41c77efec95790249ac739f7d1f89e99a1236277..ef73836d5318ac18303482688095a64a12f48575 100644
--- a/web/src/main/resources/templates/fragments/filter-components.html
+++ b/web/src/main/resources/templates/fragments/filter-components.html
@@ -18,7 +18,7 @@
<div class="row topSace10">
<div class="columns nospace small-12 large-6">
<input type="text" class="auto-suggest-field-2"
- th:onblur="|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+'0'}','${filterComponent.options2}')|"
+ th:attr="onblur=|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+'0'}','${filterComponent.options2}')|"
th:id="${filterComponent.urlParam}+'_'+${#strings.toLowerCase(filterComponent.param1Name)+'0'}"/>
</div>
@@ -119,13 +119,13 @@
<button th:unless="${filterComponent.active}"
href="#" class="icoButn columns large-2 ORButton"
- th:onclick="|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','1')|">
+ th:attr="onclick=|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','1')|">
OR
</button>
<button th:if="${filterComponent.active}"
href="#" class="icoButn columns large-2 ORButton"
- th:onclick="|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','${#maps.size(filterComponent.selected)}')|">
+ th:attr="onclick=|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','${#maps.size(filterComponent.selected)}')|">
OR
</button>
</div>
@@ -151,7 +151,7 @@
<div class="row topSace10">
<div class="columns nospace small-12 large-6">
<input type="text" class="auto-suggest-field-2"
- th:onblur="|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+'0'}','')|"
+ th:attr="onblur=|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+'0'}','')|"
th:id="${filterComponent.urlParam}+'_'+${#strings.toLowerCase(filterComponent.param1Name)+'0'}"/>
</div>
@@ -168,7 +168,7 @@
style="display:none">
<div class="columns nospace small-12 large-6">
<input type="text" class="auto-suggest-field-2"
- th:onblur="|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+i}','')|"
+ th:attr="onblur=|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+i}','')|"
th:id="${filterComponent.urlParam}+'_'+${#strings.toLowerCase(filterComponent.param1Name)}+${i}"/>
</div>
@@ -189,7 +189,7 @@
<div class="columns nospace small-12 large-6">
<input th:value="${activeComponent.key}"
type="text" class="auto-suggest-field-2"
- th:onblur="|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+iter.index}','')|"
+ th:attr="onblur=|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+iter.index}','')|"
th:id="${filterComponent.urlParam}+'_'+${#strings.toLowerCase(filterComponent.param1Name)}+${iter.index}"/>
</div>
@@ -216,7 +216,7 @@
<div class="columns nospace small-12 large-6">
<input type="text" class="auto-suggest-field-2"
- th:onblur="|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+i}','')|"
+ th:attr="onblur=|selectAllOptionsInMyComponent2(this,'${filterComponent.type}','${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param2Name)+i}','')|"
th:id="${filterComponent.urlParam}+'_'+${#strings.toLowerCase(filterComponent.param1Name)}+${i}"/>
</div>
@@ -239,13 +239,13 @@
<button th:unless="${filterComponent.active}"
href="#" class="icoButn columns large-2 ORButton"
- th:onclick="|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','1')|">
+ th:attr="onclick=|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','1')|">
OR
</button>
<button th:if="${filterComponent.active}"
href="#" class="icoButn columns large-2 ORButton"
- th:onclick="|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','${#maps.size(filterComponent.selected)}')|">
+ th:attr="onclick=|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','${#maps.size(filterComponent.selected)}')|">
OR
</button>
</div>
@@ -326,13 +326,13 @@
<button th:unless="${filterComponent.active}"
href="#" class="icoButn columns large-2 ORButton"
- th:onclick="|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','1')|">
+ th:attr="onclick=|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','1')|">
OR
</button>
<button th:if="${filterComponent.active}"
href="#" class="icoButn columns large-2 ORButton"
- th:onclick="|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','${#lists.size(filterComponent.selected)}')|">
+ th:attr="onclick=|displayMore('${filterComponent.urlParam+ '_'+ #strings.toLowerCase(filterComponent.param1Name)}','${#lists.size(filterComponent.selected)}')|">
OR
</button>
</div>
diff --git a/web/src/main/resources/templates/fragments/shared.html b/web/src/main/resources/templates/fragments/shared.html
index 170b40cd9ac05835cfa08abe67b1f698cb858b80..fceb7a6322e0c0c5fe6f236e9a34a95fd63cc5ec 100644
--- a/web/src/main/resources/templates/fragments/shared.html
+++ b/web/src/main/resources/templates/fragments/shared.html
@@ -523,3 +523,4 @@
</body>
</html>
+
diff --git a/web/src/main/resources/templates/search.html b/web/src/main/resources/templates/search.html
index 1f0737a0cc169e2c1263dbea83fd9c40c6e89c10..7d81907241025dd98b8d8a284b95867de914b5d3 100644
--- a/web/src/main/resources/templates/search.html
+++ b/web/src/main/resources/templates/search.html
@@ -15,14 +15,13 @@
<link rel="icon" th:href="@{/images/favicons/favicon.png}" />
- <script th:src="@{/js/muniweb.aa00301a32be6fbdf120.js}" type="text/javascript"></script>
-
-
+ <script th:src="@{/js/muniweb.aa00301a32be6fbdf120.js}" type="text/javascript"></script>
+
<meta name="apple-mobile-web-app-title" content="EurOPDX Data Portal">
<meta name="application-name" content="EurOPDX Data Portal">
<meta name="msapplication-config"
content="https://ebiwd.github.io/pdx-visual-framework/images/favicons/browserconfig.xml?v=1">
- <meta name="theme-color" content="#0032a0">
+ <meta name="theme-color" content="#0032a0">
<!-- Add information on the life cycle of this page -->
<meta name="ebi:owner" content="PDX"/> <!-- Who should be contacted about changes -->
@@ -31,10 +30,10 @@
<meta name="ebi:expiry" content="2018-01-20"/> <!-- When this content is no longer relevant -->
<link rel="stylesheet" href="https://dev.ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.2/fonts.css"
- type="text/css" media="all"/>
-
+ type="text/css" media="all"/>
+ <!-- Import Choice Library stylesheet-->
<link rel="stylesheet"
- href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/libraries/Choices/assets/styles/css/choices.min.css">
+ href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/libraries/Choices/assets/styles/css/choices.min.css">
<link rel="stylesheet" th:href="@{/css/app.css}" type="text/css" media="all"/>
<link rel="stylesheet" th:href="@{/css/multiple-select.css}">
@@ -64,8 +63,8 @@
<link rel="stylesheet" th:href="@{/css/modifications.css}" />
<link rel="stylesheet" th:href="@{/css/loader.css}"/>
<link rel="stylesheet" th:href="@{/css/style.0373a0d584ab4678ef5f.css}" type="text/css"/>
-
- <script type="text/javascript">
+
+ <script type="text/javascript">
// show loader after click to export button
function btnExport(facetString) {
document.getElementById('search-btn-export-btn').onclick = null;
@@ -73,8 +72,8 @@
document.getElementById('search-btn-export-loader').style.display = "block";
window.location.href = '/data' + facetString;
}
- </script>
-
+ </script>
+
</head>
<body class="level2">
@@ -84,7 +83,7 @@
<div id="skip-to">
<a href="#content">Skip to main content</a>
</div>
-
+
<th:block th:include="fragments/shared :: header"></th:block>
<div id="content">
@@ -93,14 +92,17 @@
<!-- Suggested layout containers -->
<section id="main-content-area" role="main">
-
- <th:block th:include="fragments/shared :: breadcrumb-search"></th:block>
-
-
-
-
-
-
+
+ <th:block th:include="fragments/shared :: breadcrumb-search"></th:block>
+
+
+
+
+
+
+
+
+
<!-- Search FORM Section -->
<section>
@@ -133,8 +135,8 @@
</select>
<span class="form-error margin-top-small">
- You need to enter a search query.
- </span>
+ You need to enter a search query.
+ </span>
</div>
<div class="columns small-1 medium-push-2 small-push-3 margin-bottom-none ">
<input id="search_submit"
@@ -155,18 +157,18 @@
</section>
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
<!-- Search Result and Filter Section -->
@@ -392,19 +394,19 @@
</div>
</td>
+ <td data-title="GENE EXPRESSION" th:if="${#lists.contains(websearch.additionalResultTableHeaders, 'GENE EXPRESSION')}">
+ <th:block th:each="dData : ${model.geneExpression}">
+ <a th:href="@{'/pdx/'+${model.datasource}+'/'+${model.externalId}+'#variation' }"
+ class="size12" th:utext="${dData} + '<br />'">dData</a>
+ </th:block>
+ </td>
-
-
-
-
-
-
-
-
-
-
-
-
+ <td data-title="CYTOGENETICS" th:if="${#lists.contains(websearch.additionalResultTableHeaders, 'CYTOGENETICS')}">
+ <th:block th:each="dData : ${model.cytogenetics}">
+ <a th:href="@{'/pdx/'+${model.datasource}+'/'+${model.externalId}+'#variation' }"
+ class="size12" th:utext="${dData} + '<br />'">dData</a>
+ </th:block>
+ </td>
</tr>
@@ -432,7 +434,7 @@
<li class="pagination-next"
th:classappend="${#strings.equals(websearch.page, #strings.toString(websearch.numPages))} ? 'disabled' ">
- <span th:if="${#strings.equals(websearch.page, #strings.toString(websearch.numPages))}"
+ <span th:if="${#strings.equals(websearch.page, #strings.toString(websearch.numPages))}"
aria-label="Last page">Last </span>
<a th:unless="${#strings.equals(websearch.page, #strings.toString(websearch.numPages))}"
th:href="'?' + ${websearch.facetString} + '&page=' + ${websearch.numPages}"
@@ -459,13 +461,13 @@
</div>
<div class="columns medium-7">
- <button class="button outline secondary"
- id="search-btn-export-btn"
- th:onclick="'btnExport(\'/search/cbio2?' + ${websearch.facetString} + '\')'">
+ <a class="button outline secondary" id="search-btn-export-btn"
+ th:href="@{'/search/cbio2' + '?' + ${websearch.facetString}}">
<span id="search-btn-export-label">Export to cBioPortal</span>
<div class="loader-button-bw" id="search-btn-export-loader"></div>
- </button>
- </div>
+ </a>
+
+ </div>
</div>
@@ -484,7 +486,7 @@
</div>
-
+</div>
<!--<script type='text/javascript' th:src="@{/js/banner-gdpr.js}"></script>-->
@@ -505,8 +507,8 @@
<script type="text/javascript" language="javascript" th:inline="javascript">
- // fix selected value in dropdown menu
- // document.getElementById("search-items-count-dropdown").value = '?'+[[${websearch.facetString}]] + '&size='+[[${websearch.size}]];
+
+
var webFacetSections = [[${websearch.webFacetsContainer.webFacetSections}]];
var searchOptions = [[${websearch.mainSearchFieldOptions}]];
@@ -532,9 +534,7 @@
removeItemButton: true,
// placeholder: false,
// placeholderValue: 'This is a placeholder',
- shouldSort: false,
- shouldSortItems: false,
- maxItemCount: -1, // -1 = infinity
+ maxItemCount: 1,
searchFloor: 0,
searchResultLimit: 10,
noResultsText: 'No results found',
@@ -548,6 +548,8 @@
});
+
+
function conditionallyShowDropdown(str) {
if (str.length < 1) {
mainSearch.hideDropdown();
@@ -688,4 +690,4 @@
<script>App.run({});</script>
</body>
-</html>
\ No newline at end of file
+</html>
diff --git a/web/src/test/java/org/pdxfinder/web/AjaxControllerTest.java b/web/src/test/java/org/pdxfinder/web/AjaxControllerTest.java
index 2231e951362b420b2588b2075f99273908f2eda7..92df285483de58a08179089fcab595da0c54d80e 100644
--- a/web/src/test/java/org/pdxfinder/web/AjaxControllerTest.java
+++ b/web/src/test/java/org/pdxfinder/web/AjaxControllerTest.java
@@ -2,31 +2,24 @@ package org.pdxfinder.web;
import static org.hamcrest.Matchers.*;
-import org.apache.http.entity.ContentType;
-import org.hamcrest.Matchers;
+
import org.junit.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpHeaders;
import org.springframework.http.MediaType;
import org.springframework.test.web.servlet.MockMvc;
-import static org.mockito.Mockito.verify;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
import static org.springframework.test.web.servlet.result.MockMvcResultHandlers.print;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-import org.springframework.test.web.servlet.MvcResult;
-import org.springframework.test.web.servlet.request.MockMvcRequestBuilders;
import org.springframework.test.web.servlet.setup.MockMvcBuilders;
import org.springframework.web.context.WebApplicationContext;
-import static org.mockito.BDDMockito.given;
-
/*
* Created by abayomi on 03/07/2019.
*/
@@ -54,7 +47,7 @@ public class AjaxControllerTest extends BaseTests {
public void getMolecularDataStatAPIOK() throws Exception {
String urlTemplate = "/statistics/molecular-data";
this.mockMvc.perform(get(urlTemplate)).andExpect(status().isOk())
- .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+ .andExpect(content().contentType(MediaType.APPLICATION_JSON))
.andExpect(jsonPath("$.title").exists())
.andExpect(jsonPath("$.title.text", is("")))
.andExpect(jsonPath("$.xAxis").exists())
@@ -78,7 +71,7 @@ public class AjaxControllerTest extends BaseTests {
public void getTreatmentStatAPIOK() throws Exception {
String urlTemplate = "/statistics/patient-treatment/patients";
this.mockMvc.perform(get(urlTemplate)).andExpect(status().isOk())
- .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+ .andExpect(content().contentType(MediaType.APPLICATION_JSON))
.andExpect(jsonPath("$.title").exists())
.andExpect(jsonPath("$.title.text").value("PDX Models Treatment Data"))
.andExpect(jsonPath("$.xAxis").exists())
diff --git a/web/src/test/java/org/pdxfinder/web/IndexControllerTest.java b/web/src/test/java/org/pdxfinder/web/IndexControllerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..f1c247c2aa84ebcff0a3da81244ef61df2d564bf
--- /dev/null
+++ b/web/src/test/java/org/pdxfinder/web/IndexControllerTest.java
@@ -0,0 +1,38 @@
+package org.pdxfinder.web;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.web.servlet.MockMvc;
+import org.springframework.test.web.servlet.setup.MockMvcBuilders;
+import org.springframework.web.context.WebApplicationContext;
+
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+
+public class IndexControllerTest extends BaseTests {
+
+ @Autowired
+ private WebApplicationContext webApplicationContext;
+
+ private MockMvc mockMvc;
+
+
+ @Before
+ public void setup() {
+ mockMvc = MockMvcBuilders.webAppContextSetup(webApplicationContext).build();
+ }
+
+ @Test
+ public void Given_ContextPath_When_ContextPathRootVisited_Then_RedirectToSearch(){
+ try {
+ this.mockMvc.perform(get("/"))
+ .andExpect(redirectedUrl("/search"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+
+}