From 68587e03af953179d71f1311a72d654ced7e101c Mon Sep 17 00:00:00 2001
From: 456130 <456130@mail.muni.cz>
Date: Wed, 31 Jul 2019 16:45:25 +0200
Subject: [PATCH] moved cbioapp to data-lodint repo

---
 .gitlab-ci.yml                   |  16 +--
 builds/cbioapp/Dockerfile        |  45 -------
 builds/cbioapp/context.xml       |  37 ------
 builds/cbioapp/log4j.properties  |  19 ---
 builds/cbioapp/logo_EurOPDX.png  | Bin 10869 -> 0 bytes
 builds/cbioapp/portal.properties | 218 -------------------------------
 builds/cbioapp/settings.xml      |  10 --
 builds/cbioapp/start.sh          |   8 --
 8 files changed, 8 insertions(+), 345 deletions(-)
 delete mode 100644 builds/cbioapp/Dockerfile
 delete mode 100644 builds/cbioapp/context.xml
 delete mode 100644 builds/cbioapp/log4j.properties
 delete mode 100644 builds/cbioapp/logo_EurOPDX.png
 delete mode 100644 builds/cbioapp/portal.properties
 delete mode 100644 builds/cbioapp/settings.xml
 delete mode 100644 builds/cbioapp/start.sh

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c4c6068..79cc7ef 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,14 +13,14 @@ stages:
     - echo -n $CI_REGISTRY_PASSWORD | docker login -u "$CI_REGISTRY_USER" --password-stdin  $CI_REGISTRY
 #   - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
 
-cBioApp build:
-    stage: build
-    <<: *docker-login
-    image: docker:latest
-    script:
-        - docker build --pull -t "${CI_REGISTRY_IMAGE}:app${CI_COMMIT_SHA}" ./builds/cbioapp
-        - docker push "$CI_REGISTRY_IMAGE:app${CI_COMMIT_SHA}"
-    when: manual
+# cBioApp build:
+#     stage: build
+#     <<: *docker-login
+#     image: docker:latest
+#     script:
+#         - docker build --pull -t "${CI_REGISTRY_IMAGE}:app${CI_COMMIT_SHA}" ./builds/cbioapp
+#         - docker push "$CI_REGISTRY_IMAGE:app${CI_COMMIT_SHA}"
+#     when: manual
 
 cBioDb build:
     stage: build
diff --git a/builds/cbioapp/Dockerfile b/builds/cbioapp/Dockerfile
deleted file mode 100644
index 74132b3..0000000
--- a/builds/cbioapp/Dockerfile
+++ /dev/null
@@ -1,45 +0,0 @@
-ARG TAG=2.0.0
-FROM cbioportal/cbioportal:$TAG AS build
-MAINTAINER Luboslav Pivarc <456130@muni.cz>
-COPY ./log4j.properties /cbioportal/src/main/resources/log4j.properties
-COPY ./portal.properties /cbioportal/src/main/resources/portal.properties
-COPY ./settings.xml /root/.m2/settings.xml
-COPY ./context.xml /usr/local/tomcat/conf/context.xml
-COPY ./logo_EurOPDX.png /cbioportal/portal/src/main/webapp/images/logo_EurOPDX.png
-
-RUN mvn -DskipTests clean install
-
-RUN ls $PORTAL_HOME/portal/target/
-
-FROM tomcat:8-jre8
-MAINTAINER Luboslav Pivarc <456130@muni.cz>
-ENV APP_NAME="cbioportal" \
-    PORTAL_HOME="/cbioportal"
-#======== Install Prerequisites ===============#
-RUN apt-get update && apt-get install -y --no-install-recommends \
-        libmysql-java \
-        patch \
-        python3 \
-        python3-jinja2 \
-        python3-mysqldb \
-        python3-requests \
-    && ln -s /usr/share/java/mysql-connector-java.jar "$CATALINA_HOME"/lib/ \
-    && rm -rf $CATALINA_HOME/webapps/examples \
-    && rm -rf /var/lib/apt/lists/*
-
-#======== Copy from first stage ===========================#
-
-COPY --from=build $PORTAL_HOME/portal/target/cbioportal.war $CATALINA_HOME/webapps/cbioportal.war
-COPY --from=build $PORTAL_HOME/core/src/main/scripts/ $PORTAL_HOME/core/src/main/scripts/
-COPY --from=build $PORTAL_HOME/scripts/target/scripts*.jar $PORTAL_HOME/scripts/target/
-
-COPY --from=build /usr/local/tomcat/conf/context.xml /usr/local/tomcat/conf/context.xml
-COPY --from=build /cbioportal/src/main/resources/portal.properties /cbioportal/portal.properties
-COPY ./data-loading /etc/data-loading
-COPY ./start.sh /start.sh
-
-RUN chmod +x /start.sh
-WORKDIR $PORTAL_HOME
-EXPOSE 8080
-#======== symbol links & subtitute db host & run app ===============#
-CMD  /start.sh
diff --git a/builds/cbioapp/context.xml b/builds/cbioapp/context.xml
deleted file mode 100644
index 1da4e84..0000000
--- a/builds/cbioapp/context.xml
+++ /dev/null
@@ -1,37 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  Licensed to the Apache Software Foundation (ASF) under one or more
-  contributor license agreements.  See the NOTICE file distributed with
-  this work for additional information regarding copyright ownership.
-  The ASF licenses this file to You under the Apache License, Version 2.0
-  (the "License"); you may not use this file except in compliance with
-  the License.  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
--->
-<!-- The contents of this file will be loaded for each web application -->
-<Context>
-
-    <!-- Default set of monitored resources. If one of these changes, the    -->
-    <!-- web application will be reloaded.                                   -->
-    <WatchedResource>WEB-INF/web.xml</WatchedResource>
-    <WatchedResource>${catalina.base}/conf/web.xml</WatchedResource>
-
-    <!-- Uncomment this to disable session persistence across Tomcat restarts -->
-    <!--
-    <Manager pathname="" />
-    -->
-
-    <Resource name="jdbc/cbioportal" auth="Container" type="javax.sql.DataSource"
-       maxActive="100" maxIdle="30" maxWait="10000"
-       username="cbio" password="P@ssword1"
-       driverClassName="com.mysql.jdbc.Driver"
-       connectionProperties="zeroDateTimeBehavior=convertToNull;"
-       url="jdbc:mysql://cbiodb:3306/cbioportal"/>
-</Context>
diff --git a/builds/cbioapp/log4j.properties b/builds/cbioapp/log4j.properties
deleted file mode 100644
index 964f33b..0000000
--- a/builds/cbioapp/log4j.properties
+++ /dev/null
@@ -1,19 +0,0 @@
-# Change INFO to DEBUG, if you want to see debugging info on underlying libraries we use.
-log4j.rootLogger=INFO, a
-
-# Change INFO to DEBUG, if you want see debugging info on our packages and spring security packages.
-log4j.category.org.mskcc=INFO
-log4j.logger.org.springframework.security=INFO
-
-# Use the JVM option, e.g.: "java -DPORTAL_HOME=/pathto/portal_homedir",
-# or - "java -DPORTAL_HOME=$PORTAL_HOME", where PORTAL_HOME is shell (environment) variable.
-
-## IMPORTANT - THRESHOLD SHOULD NOT BE DEBUG FOR PRODUCTION, CREDENTIALS CAN BE DISPLAYED!
-
-log4j.appender.a = org.apache.log4j.rolling.RollingFileAppender
-log4j.appender.a.rollingPolicy = org.apache.log4j.rolling.TimeBasedRollingPolicy
-log4j.appender.a.rollingPolicy.FileNamePattern = ${java.io.tmpdir}/cbioportal.log.%d.gz
-log4j.appender.a.File = ${java.io.tmpdir}/cbioportal.log
-log4j.appender.a.layout = org.apache.log4j.PatternLayout
-log4j.appender.a.layout.ConversionPattern = %d{yyyy-MM-dd HH:mm:ss} [%t] %-5p %c - %m%n
-log4j.appender.a.append = true
\ No newline at end of file
diff --git a/builds/cbioapp/logo_EurOPDX.png b/builds/cbioapp/logo_EurOPDX.png
deleted file mode 100644
index 1aa9f993c49b96914889a84078e44a0feeb813ed..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/builds/cbioapp/portal.properties b/builds/cbioapp/portal.properties
deleted file mode 100644
index c39b3cc..0000000
--- a/builds/cbioapp/portal.properties
+++ /dev/null
@@ -1,218 +0,0 @@
-# app name
-app.name=cbioportal1
-
-# database
-db.user=cbio
-db.password=P@ssword1
-db.host=cbiodb
-db.portal_db_name=cbioportal
-db.driver=com.mysql.jdbc.Driver
-db.connection_string=jdbc:mysql://cbiodb/
-db.tomcat_resource_name=jdbc/cbioportal
-# this should normally be set to false. In some cases you could set this to true (e.g. for testing a feature of a newer release that is not related to the schema change in expected db version above):
-db.suppress_schema_version_mismatch_errors=false
-app.version=${timestamp}
-db.version=${db.version}
-
-# web page cosmetics
-skin.title=EurOPDX cBioPortal
-skin.email_contact=it at europdx eu
-skin.authorization_message=Access to this portal is only available to authorized users of EurOPDX consortium.
-skin.example_study_queries=tcga\ntcga -provisional\ntcga -moratorium\ntcga OR icgc\n-"cell line"\nprostate mskcc\nesophageal OR stomach\nserous\nbreast
-skin.data_sets_header=The portal currently contains data from the following cancer genomics studies.  The table below lists the number of available samples per data type and tumor.
-skin.data_sets_footer=
-#skin.examples_right_column_html=<ul><li><a href="case.do#/patient?studyId=ucec_tcga_pub&caseId=TCGA-BK-A0CC">Patient view of an endometrial cancer case</a></li></ul>
-
-# documentation pages
-#skin.documentation.baseurl=https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/
-skin.documentation.baseurl=https://gitlab.ics.muni.cz/europdx/cbioportal/cbio-public-info/raw/master/
-skin.documentation.markdown=true
-skin.documentation.faq=FAQ.md
-skin.documentation.about=About-Us.md
-skin.documentation.skin.news=News.md
-skin.documentation.oql=Onco-Query-Language.md
-
-# setting controlling the logos
-skin.right_logo=logo_EurOPDX.png
-skin.tag_line_image=tag_line.png
-
-# setting controlling which tabs to hide.
-skin.show_news_tab=true
-skin.show_data_tab=true
-skin.show_web_api_tab=true
-skin.show_r_matlab_tab=true
-skin.show_tutorials_tab=false
-skin.show_faqs_tab=true
-skin.show_tools_tab=true
-skin.show_about_tab=true
-
-# settings controlling the whats new blurb
-skin.right_nav.whats_new_blurb=<a class="twitter-timeline" href="https://twitter.com/europdx" data-tweet-limit="1"> Tweets by @EurOPDX </a>
-
-# setting controlling the blurb
-skin.blurb=<p>Welcome to the european instance of cBioPortal which provides <b>visualization</b>, <b>analysis</b> and <b>download</b> of large-scale cancer genomics datasets of EurOPDX consortium. This portal is run by <a href="https://www.cerit-sc.cz/about/news/cerit-sc-member-participates-in-eu-h2020-project-as-the-it-task-leader">Masaryk University</a> for <a href="https://cordis.europa.eu/project/rcn/212589_en.html">EDIReX: European Distributed Infrastructure for Research on patient-derived cancer Xenografts</a> project with kind support of cBioPortal developers from Weill Cornell Medicine (WCM, New York, NY, USA).</p><p>Please adhere to <u><a href="http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines"> the TCGA publication guidelines</a></u> when using TCGA data in your publications.</p> <p><b>Please cite</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/23550210">Gao et al. <i>Sci. Signal.</i> 2013</a> &amp;  <a href="http://cancerdiscovery.aacrjournals.org/content/2/5/401.abstract">Cerami et al. <i>Cancer Discov.</i> 2012</a> when publishing results based on cBioPortal.</p>
-
-# setting controlling the footer
-skin.footer= | <a href="http://www.mskcc.org/mskcc/html/44.cfm">MSKCC</a> | <a href="http://europdx.eu/">EurOPDX</a> | <a href="http://www.ics.muni.cz/">ICS MU</a>
-
-# setting controlling html for the contact
-skin.login.contact_html=If you think you have received this message in error, please contact us at <a style="color:#FF0000" href="mailto:europdx-cbioportal@googlegroups.com">europdx-cbioportal@googlegroups.com</a>
-
-# setting controlling the saml registration
-skin.login.saml.registration_html=Sign in
-
-# settings controlling what to show in the right navigation bar
-skin.right_nav.show_data_sets=true
-skin.right_nav.show_examples=true
-skin.right_nav.show_testimonials=false
-
-# settings controlling what to show in the right navigation bar
-skin.study_view.link_text=To build your own case set, try out our enhanced Study View.
-
-# authentication
-## is authorization enabled at all? (true, false)
-authorization=false
-## enable and set this property to specify a study group to be used to identify public studies for which no specific authorization entries are needed in the `authorities` table
-# always_show_study_group=
-## which method of authentication to use (false, googleplus, saml, openid, ad, ldap, noauthsessionservice)
-authenticate=false
-## Should the permissions for groups and users be filtered by this instance's app.name?
-## (true means the system only handles "CBIOPORTAL:someGroupPermission" groups, false means "someGroupPermission" works)
-filter_groups_by_appname=true
-## settings to connect to googleplus auth infrastructure
-googleplus.consumer.key=
-googleplus.consumer.secret=
-
-## SAML settings
-saml.sp.metadata.entityid=
-saml.idp.metadata.location=
-saml.idp.metadata.entityid=
-# saml keystore settings:
-saml.keystore.location=
-saml.keystore.password=
-saml.keystore.private-key.key=
-saml.keystore.private-key.password=
-saml.keystore.default-key=
-# How to send SAML request messages to the IDP.
-# Set to "specificBinding" to configure specific binding:
-saml.idp.comm.binding.settings=defaultBinding
-# Configure the specific binding if above is specificBinding. Leave empty if defaultBinding.
-# Options: bindings:HTTP-POST, bindings:HTTP-Redirect, bindings:PAOS, profiles:holder-of-key:SSO:browser
-saml.idp.comm.binding.type=
-# Change this to configure your custom UserDetails parser (default: org.cbioportal.security.spring.authentication.saml.SAMLUserDetailsServiceImpl)
-saml.custom.userservice.class=org.cbioportal.security.spring.authentication.saml.SAMLUserDetailsServiceImpl
-# Change this to configure to configure a custom logout URL: (default: /login.jsp?logout_success=true)
-saml.logout.url=/login.jsp?logout_success=true
-
-## settings to connect to an Active Directory domain controller
-ad.domain=
-ad.url=
-## configuration for the LDAP access
-ldap.user_search_base=DC=example,DC=com
-ldap.url=ldap://ldap.example.com
-ldap.manager.dn=CN=manager-user,DC=example,DC=com
-ldap.manager.password=PASSWORD
-## The following attributes for are good for ActiveDirectory, for OpenLDAP use "uid" for username
-ldap.attributes.username=sAMAccountName
-#ldap.attributes.username=uid
-ldap.attributes.last_name=sn
-ldap.attributes.given_name=givenName
-ldap.attributes.email=mail
-
-# study view settings
-# always show studies with this group
-always_show_study_group=
-mdacc.heatmap.study.meta.url=//bioinformatics.mdanderson.org/study2url?studyid=
-mdacc.heatmap.study.url=//bioinformatics.mdanderson.org/TCGA/NGCHMPortal/?
-
-# patient view settings
-patient_view_placeholder=false
-patient_view_genomic_overview_cna_cutoff=0.2,1.5
-digitalslidearchive.iframe.url=http://cancer.digitalslidearchive.net/index_mskcc.php?slide_name=
-digitalslidearchive.meta.url=http://cancer.digitalslidearchive.net/local_php/get_slide_list_from_db_groupid_not_needed.php?slide_name_filter=
-tumor_image.url=http://cbio.mskcc.org/cancergenomics/tcga-tumor-images/
-tcga_path_report.url=https://github.com/cbioportal/datahub/raw/master/tcga/pathology_reports/pathology_reports.txt
-mdacc.heatmap.patient.url=//bioinformatics.mdanderson.org/TCGA/NGCHMPortal/?participant=
-mdacc.heatmap.meta.url=//bioinformatics.mdanderson.org/participant2maps?participant=
-
-# various url's
-segfile.url=http://cbio.mskcc.org/cancergenomics/gdac-portal/seg/
-
-# Enable OncoKB annotation (true, false)
-show.oncokb=true
-
-# Enable Chang's hotspot list (true, false)
-show.hotspot=true
-hotspots.url=http://cancerhotspots.org/api/
-
-# Enable Civic variant annotation (true, false)
-show.civic=false
-
-# Link to My Cancer Genome. Please disable (set to false) when using cBioPortal with patient identifiable data due My Cancer Genome license restrictions.
-mycancergenome.show=true
-
-# igv bam linking
-igv.bam.linking=
-# colon delimited
-igv.bam.linking.studies=
-openssl.binary=
-signature.key=
-encryption.key=
-broad.bam.url=
-broad.bam.checking.url=
-
-# pathway settings
-include_networks=true
-pathway_commons.url=http://www.pathwaycommons.org/pc2
-
-# bitly, please use your bitly user and apiKey
-bitly.url=
-# the new API uses the v3 of bitly API, and a java library to make the API call, so you only need to provide the access token
-bitly.access.token=
-
-# google analytics
-google_analytics_profile_id=UA-120520301-1
-
-# genomespace linking
-genomespace=true
-
-# set this to true if you update cancer studies in your production database without shutting the web server
-recache_study_after_update=false
-
-# session-service url: http://[host]:[port]/[session_service_app]/api/sessions/[portal_instance]/
-# example session-service url: http://localhost:8080/session_service/api/sessions/public_portal/
-# see: https://github.com/cBioPortal/session-service
-# excluding this value or setting it to an empty string will revert to the previous bookmarking method
-# WARNING: do not use session service with authenticate=false
-#  either use authentication or change to authenticate=noauthsessionservice
-session.service.url=
-# Only allow requests from here:
-#  e.g. session.service.origin=http://dashi-dev.cbio.mskcc.org:8080
-session.service.origin=*
-
-# disabled tabs, | delimited
-# possible values: cancer_types_summary, mutual_exclusivity, plots, mutations, co_expression, enrichments, survival, network, download, bookmark, IGV
-disabled_tabs=
-
-# study ids and categories to force to top of study selector
-# format is category1#study1a,study1b,study1c;category2#study2
-priority_studies=
-
-# species and genomic information
-species=human
-ncbi.build=37
-ucsc.build=hg19
-
-# default view in oncoprint (sample, patient (default))
-oncoprint.defaultview=patient
-
-# OncoPrint driver mutation annotations
-# oncoprint.custom_driver_annotation.binary.menu_label=Custom driver annotation
-# oncoprint.custom_driver_annotation.tiers.menu_label=Custom driver tiers
-# oncoprint.custom_driver_annotation.default=true
-# oncoprint.custom_driver_tiers_annotation.default=true
-# oncoprint.oncokb_hotspots.default=custom
-# oncoprint.hide_vus.default=false
-
-# Custom gene sets
-# querypage.setsofgenes.location=file:/<path>
diff --git a/builds/cbioapp/settings.xml b/builds/cbioapp/settings.xml
deleted file mode 100644
index 55f7437..0000000
--- a/builds/cbioapp/settings.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-  <servers>
-    <server>
-      <id>settingsKey</id>
-      <username>cbio</username>
-      <password>P@ssword1</password>
-   </server>
- </servers>
-</settings>
\ No newline at end of file
diff --git a/builds/cbioapp/start.sh b/builds/cbioapp/start.sh
deleted file mode 100644
index f3d2532..0000000
--- a/builds/cbioapp/start.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh
-find $PWD/core/src/main/scripts/ -type f -executable \! -name '*.pl'  -print0 | xargs -0 -- ln -st /usr/local/bin
-
-sed -i "s/cbiodb/${DBHOST}/g" /cbioportal/portal.properties &&
-sed -i "s/cbiodb/$DBHOST/g" /usr/local/tomcat/conf/context.xml
-
-mv $CATALINA_HOME/webapps/cbioportal.war $CATALINA_HOME/webapps/${MOVE}.war
-sh $CATALINA_HOME/bin/catalina.sh run
-- 
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