Commit 68587e03 authored by Ľuboslav Pivarč's avatar Ľuboslav Pivarč
Browse files

moved cbioapp to data-lodint repo

parent 669acab2
Pipeline #21400 skipped with stages
......@@ -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${CI_COMMIT_SHA}"
# when: manual
cBioDb build:
stage: build
......
ARG TAG=2.0.0
FROM cbioportal/cbioportal:$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 $PORTAL_HOME
EXPOSE 8080
#======== symbol links & subtitute db host & run app ===============#
CMD /start.sh
<?xml version="1.0" encoding="UTF-8"?>
<!--
Licensed to the Apache Software Foundation (ASF) under one or more
contributor license agreements. See the NOTICE file distributed with
this work for additional information regarding copyright ownership.
The ASF licenses this file to You under the Apache License, Version 2.0
(the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-->
<!-- The contents of this file will be loaded for each web application -->
<Context>
<!-- Default set of monitored resources. If one of these changes, the -->
<!-- web application will be reloaded. -->
<WatchedResource>WEB-INF/web.xml</WatchedResource>
<WatchedResource>${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>
# 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 = ${java.io.tmpdir}/cbioportal.log
log4j.appender.a.layout = org.apache.log4j.PatternLayout
log4j.appender.a.layout.ConversionPattern = %d{yyyy-MM-dd HH:mm:ss} [%t] %-5p %c - %m%n
log4j.appender.a.append = true
\ No newline at end of file
# app name
app.name=cbioportal1
# database
db.user=cbio
db.password=P@ssword1
db.host=cbiodb
db.portal_db_name=cbioportal
db.driver=com.mysql.jdbc.Driver
db.connection_string=jdbc:mysql://cbiodb/
db.tomcat_resource_name=jdbc/cbioportal
# this should normally be set to false. In some cases you could set this to true (e.g. for testing a feature of a newer release that is not related to the schema change in expected db version above):
db.suppress_schema_version_mismatch_errors=false
app.version=${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>
<?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
#!/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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