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A context to create cBioPortal docker images

Dockerfile 100.00%

cbioportal docker

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sandertan oplantalech pulyakhina cbioportal jkang-alien pieterlukasse gautric mrc-cu bad-genome chaelir pvannierop luposung brettvanderwerff kcourtet moxgreen amphun

cbioportal-docker's Issues

Cannot upload data into cBioPortal : Checked DB schema version: (expected: 2.7.3) (found: -1)

I have installed cBioPortal using docker and so far I was able to work with it. However, recently I ran into an issue (see this #63) which I got resolved.

But, today I ran into the following issue when I tried to upload a data set.

My command

docker run -it --rm --net cbio-net -v "/media/bioinfo:/study:ro" -v "/media/bioinfo:/outdir" -v "/media/bioinfo/portal.properties:/cbioportal/portal.properties:ro" thehyve/cbioportal:v2.0.1-iss5758 metaImport.py -u http://cbioportal-container:8080/cbioportal -s /study --html=/outdir/.html -v -o

I could see below error

INFO: -: Running validation from cBioPortal version 0-unknown-version-SNAPSHOT
DEBUG: -: Requesting cancertypes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesaliases from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesets from portal at 'http://cbioportal-container:8080/cbioportal'

DEBUG: meta_study.txt: Starting validation of meta file
INFO: meta_study.txt: Validation of meta file complete

DEBUG: meta_fusion.txt: Starting validation of meta file
INFO: meta_fusion.txt: Validation of meta file complete

DEBUG: meta_mutation_file.txt: Starting validation of meta file
INFO: meta_mutation_file.txt: Validation of meta file complete

DEBUG: meta_clinical_sample.txt: Starting validation of meta file
INFO: meta_clinical_sample.txt: Validation of meta file complete

DEBUG: meta_clinical_patient.txt: Starting validation of meta file
INFO: meta_clinical_patient.txt: Validation of meta file complete

DEBUG: data_clinical_sample.txt: Starting validation of file
INFO: data_clinical_sample.txt: Validation of file complete
INFO: data_clinical_sample.txt: Read 110 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_clinical_patient.txt: Starting validation of file
WARNING: data_clinical_patient.txt: Columns OS_MONTHS and/or OS_STATUS not found. Overall survival analysis feature will not be available for this study.
WARNING: data_clinical_patient.txt: Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study.
INFO: data_clinical_patient.txt: Validation of file complete
INFO: data_clinical_patient.txt: Read 110 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_fusion.txt: Starting validation of file
WARNING: data_fusion.txt: lines [3, 5, 7, (1046 more)]: Duplicate entry in fusion data.; values encountered: ['BRAF	673	K80130654	AGTRAP-BRAF (already defined on line 2)', 'BRAF	673	K80130654	CLCN6-BRAF (already defined on line 4)', 'ABL1	25	K80130654	SFPQ-ABL1 (already defined on line 6)', '(322 more)']
WARNING: data_fusion.txt: lines [808, 809]: Entrez gene id is not an integer. This record will not be loaded.; value encountered: 'FOXO4'
INFO: data_fusion.txt: Validation of file complete
INFO: data_fusion.txt: Read 1375 lines. Lines with warning: 1050. Lines with error: 0

DEBUG: merged.maf: Starting validation of file
WARNING: merged.maf: lines [4, 5, 22, (339 more)]: Gene symbol maps to a single Entrez gene id, but is also associated to other genes as an alias. The system will assume the official gene symbol to be the intended one.; values encountered: ['SF3B1', 'KRAS']
WARNING: merged.maf: lines [4, 5, 8, (2875 more)]: No Amino_Acid_Change or HGVSp_Short value. This mutation record will get a generic "MUTATED" flag
INFO: merged.maf: lines [6, 7, 15, (660 more)]: Line will not be loaded due to the variant classification filter. Filtered types: [Silent]; value encountered: 'Silent'
WARNING: merged.maf: lines [358, 359, 906, (36 more)]: Missing value in SWISSPROT column; this column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view.; value encountered: ''
INFO: merged.maf: Validation of file complete
INFO: merged.maf: Read 6502 lines. Lines with warning: 3059. Lines with error: 0

DEBUG: -: Validating case lists

DEBUG: case_lists/cases_sequenced.txt: Starting validation of meta file
INFO: case_lists/cases_sequenced.txt: Validation of meta file complete

INFO: -: Validation of case list folder complete
INFO: -: Validation complete


#######################################################################
Overriding Warnings. Importing study now
#######################################################################

Data loading step using /cbioportal/scripts/target/scripts-2.0.1-SNAPSHOT.jar

Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)
java.sql.SQLException: java.sql.SQLException: Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)
at org.mskcc.cbio.portal.dao.JdbcUtil.getDbConnection(JdbcUtil.java:98)
at org.mskcc.cbio.portal.dao.JdbcUtil.getDbConnection(JdbcUtil.java:80)
at org.mskcc.cbio.portal.dao.DaoInfo.setVersion(DaoInfo.java:56)
at org.mskcc.cbio.portal.dao.DaoInfo.checkVersion(DaoInfo.java:83)
at org.mskcc.cbio.portal.util.VersionUtil.main(VersionUtil.java:41)
Caused by: java.sql.SQLException: Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)
at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2294)
at org.apache.commons.dbcp2.BasicDataSource.createDataSource(BasicDataSource.java:2039)
at org.apache.commons.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1533)
at org.mskcc.cbio.portal.dao.JdbcUtil.getDbConnection(JdbcUtil.java:95)
... 4 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1116)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:344)
at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2333)
at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2370)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2154)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:792)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:381)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:305)
at org.apache.commons.dbcp2.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:39)
at org.apache.commons.dbcp2.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:256)
at org.apache.commons.dbcp2.BasicDataSource.validateConnectionFactory(BasicDataSource.java:2304)
at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2290)
... 7 more
Caused by: java.net.ConnectException: Connection refused (Connection refused)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:244)
at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:257)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:294)
... 23 more
Checked DB schema version: (expected: 2.7.3) (found: -1)
Error, probably due to this version of the portal being out of sync with the database. Run the database migration script located at CBIOPORTAL_SRC/core/src/main/scripts/migrate_db.py before continuing.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error occurred during data loading step. Please fix the problem and run this again to make sure study is completely loaded.
Traceback (most recent call last):
  File "/usr/local/bin/metaImport.py", line 147, in <module>
    cbioportalImporter.main(args)
  File "/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 447, in main
    check_version(jvm_args)
  File "/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 164, in check_version
    run_java(*args)
  File "/cbioportal/core/src/main/scripts/importer/cbioportal_common.py", line 832, in run_java
    raise RuntimeError('Aborting due to error while executing step.')
RuntimeError: Aborting due to error while executing step.

Note that I can still access cBioportal on local host. And the containers are up:

bioinfo@bioinfo-pc$ docker ps -a
CONTAINER ID        IMAGE                               COMMAND                  CREATED             STATUS                  PORTS                    NAMES
e61792bfb7da        mysql:5.7                           "docker-entrypoint.s…"   2 days ago          Up 20 hours             3306/tcp, 33060/tcp      cbioDB
bb744455befd        thehyve/cbioportal:v2.0.1-iss5758   "catalina.sh run"        2 days ago          Up 15 minutes           0.0.0.0:8081->8080/tcp   cbioportal-container

Keycloak documentation incomplete

The documentation at https://github.com/thehyve/cbioportal-docker/blob/master/docs/using-keycloak.md is missing some details regarding how the extra .xml and .jks configuration files should be mounted and configured in the case of using docker.

Session service containers and images remain after following uninstall instructions

The setup downloads images and runs containers for the session service and its database, but the steps to remove all traces of the setup does not clean these up.

cbioDB instructions regarding -p not applicable to basic use-case

for starting the cbioDB container the documentation now contains an example with -p port option.

It would be good to omit this option from the default example and documented as a secondary use case.

Build failing when using `mvn package` instead of `mvn install` on unreleased branch

When I run the build process with this (only including subset of my dockerfile here):

RUN git clone --depth 1 -b chile 'https://github.com/thehyve/cbioportal.git' $PORTAL_HOME
WORKDIR $PORTAL_HOME

RUN mvn -e -DskipTests clean package \
	&& unzip portal/target/cbioportal*.war -d $CATALINA_HOME/webapps/cbioportal \
	&& mv scripts/target/scripts-*.jar /root/ \
	&& mvn clean \
	&& mkdir scripts/target/ \
	&& mv /root/scripts-*.jar scripts/target/

then the build fails with following error:

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Portal Master ...................................... SUCCESS [02:41 min]
[INFO] model .............................................. SUCCESS [  7.814 s]
[INFO] Portal Business Layer .............................. FAILURE [  2.685 s]
[INFO] persistence ........................................ SKIPPED
[INFO] persistence-api .................................... SKIPPED
[INFO] db-scripts ......................................... SKIPPED
[INFO] persistence-mybatis ................................ SKIPPED
[INFO] service ............................................ SKIPPED
[INFO] Portal Web Layer ................................... SKIPPED
[INFO] security ........................................... SKIPPED
[INFO] security-spring .................................... SKIPPED
[INFO] Portal Core ........................................ SKIPPED
[INFO] cBioPortal ......................................... SKIPPED
[INFO] Portal Scripts ..................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:24 min
[INFO] Finished at: 2018-12-18T13:48:07+00:00
[INFO] Final Memory: 40M/714M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project business: Could not resolve dependencies for project org.mskcc.cbio:business:jar:c8076e1ca-SNAPSHOT: Could not find artifact org.mskcc.cbio:model:jar:c8076e1ca-SNAPSHOT -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal on project business: Could not resolve dependencies for project org.mskcc.cbio:business:jar:c8076e1ca-SNAPSHOT: Could not find artifact org.mskcc.cbio:model:jar:c8076e1ca-SNAPSHOT
	at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies(LifecycleDependencyResolver.java:221)
	at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies(LifecycleDependencyResolver.java:128)
	at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved(MojoExecutor.java:245)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:199)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.project.DependencyResolutionException: Could not resolve dependencies for project org.mskcc.cbio:business:jar:c8076e1ca-SNAPSHOT: Could not find artifact org.mskcc.cbio:model:jar:c8076e1ca-SNAPSHOT
	at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve(DefaultProjectDependenciesResolver.java:212)
	at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies(LifecycleDependencyResolver.java:195)
	... 23 more
Caused by: org.eclipse.aether.resolution.DependencyResolutionException: Could not find artifact org.mskcc.cbio:model:jar:c8076e1ca-SNAPSHOT
	at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:384)
	at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve(DefaultProjectDependenciesResolver.java:205)
	... 24 more
Caused by: org.eclipse.aether.resolution.ArtifactResolutionException: Could not find artifact org.mskcc.cbio:model:jar:c8076e1ca-SNAPSHOT
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:444)
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:246)
	at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:367)
	... 25 more
Caused by: org.eclipse.aether.transfer.ArtifactNotFoundException: Could not find artifact org.mskcc.cbio:model:jar:c8076e1ca-SNAPSHOT
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:434)
	... 27 more
[ERROR] 
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :business
ERROR: Service 'cbioportal-container' failed to build: The command '/bin/sh -c mvn -e -DskipTests clean package 	&& unzip portal/target/cbioportal*.war -d $CATALINA_HOME/webapps/cbioportal 	&& mv scripts/target/scripts-*.jar /root/ 	&& mvn clean 	&& mkdir scripts/target/ 	&& mv /root/scripts-*.jar scripts/target/' returned a non-zero code: 1

Interestingly, when I change the word "package" to "install" in the mvn command above, the build process works fine.

Default Catalina JVM mem size low for reasonable use

Documentation or Dockerfile-coded defaults should probably suggest adding -Xms and -Xmx to $CATALINA_OPTS to increase the heap size.

db.use_ssl should be set to true

Would be good to have db.use_ssl=true in our portal.properties. See https://github.com/thehyve/cbioportal-docker/blob/master/portal.properties#L14

How to enable user authentication for local cbioportal instance installed using docker?

Hi again!

So, I have finally setup cbioportal using docker and have successfully uploaded few studies. The next step I want is to set up user authentication into the local cbioportal instance. I know it's feasible .

Where should I begin? Should I look at this link to customize cbioportal

Can you please pin point me to the exact help page?

CI for this repo?

Would be nice to have automated tests for changes in this repo, e.g. when upgrading to a new version of cBioPortal or Keycloak.

Error when using co-expression tab inside the cBioPortal Docker container

The way Docker is configured does not give enough memory for some cBioPortal features (e.g. co-expression tab).

log in for group comparison

Hi,

I updated my docker instance to the release-3.0.1 and tried to use the new group comparison feature. This feature needs a user to log in first but there is no log button available on the interface. So do you have any solutions ?

Best regards
Kevin

Errors when trying last version (1.8.3)

Got this while trying to get the version 1.8.3 working on a client's server:

E: Failed to fetch http://cdn-fastly.deb.debian.org/debian/pool/main/r/requests/python-requests_2.12.4-1_all.deb  Hash Sum mismatch
   Hashes of expected file:
    - SHA256:59dcee64ab8521d72edb7f26030dd00c4c566676875d62d2c0f9d6e760f938ab
    - MD5Sum:df024a773849614ba343c7e35e3ea6b6 [weak]
    - Filesize:111632 [weak]
   Hashes of received file:
    - SHA256:8422e424991aba88cd9887297a0101eea9d864a411bcedcea6806054adfb897d
    - MD5Sum:c7bd2ec018dd1a27bafa0f5116c1969c [weak]
    - Filesize:100986 [weak]
   Last modification reported: Mon, 19 Dec 2016 19:48:26 +0000
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
The command '/bin/sh -c apt-get update && apt-get install -y --no-install-recommends            git             libmysql-java           maven           openjdk-8-jdk           patch       python           python-jinja2           python-mysqldb          python-requests         && rm -rf /var/lib/apt/lists/*  && ln -s /usr/share/java/mysql-connector-java.jar "$CATALINA_HOME"/lib/      && rm -rf $CATALINA_HOME/webapps/*m*' returned a non-zero code: 100

The mysql container worked. This error only happens when building the tomcat image.

Enable backports to stretch

Hi,
I tried to build the image and I got the error:

E: The value 'jessie-backports' is invalid for APT::Default-Release as such a release is not available in the sources

I had to enable first the backports to stretch to be able to build the image.
RUN echo "deb http://ftp.debian.org/debian stretch-backports main" >> /etc/apt/source.list
and changed this
&& apt-get install -y --no-install-recommends -t jessie-backports
to this
&& apt-get install -y --no-install-recommends -t stretch-backports

Thanks

Problem importing test data set.

I am trying to import a test data set by following steps at this link

command

docker run -it --rm --net cbio-net \
>     -v "$PWD/blca_tcga:/study:ro" \
>     -v "$PWD:/outdir" \
>     -v "$PWD/portal.properties:/cbioportal/portal.properties:ro" \
>     thehyve/cbioportal:v2.0.1-iss5758 \
>     metaImport.py \
>         -u http://cbioportal-container:8080/cbioportal \
>         -s /study --html=/outdir/report_blca.html -v -o

Error message

Starting validation...

INFO: -: Running validation from cBioPortal version 0-unknown-version-SNAPSHOT
DEBUG: -: Requesting cancertypes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesaliases from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesets from portal at 'http://cbioportal-container:8080/cbioportal'

DEBUG: meta_mutsig.txt: Starting validation of meta file
WARNING: meta_mutsig.txt: Unrecognized field in meta file; value encountered: 'reference_genome_id'
INFO: meta_mutsig.txt: Validation of meta file complete

DEBUG: meta_rppa.txt: Starting validation of meta file
INFO: meta_rppa.txt: Validation of meta file complete

DEBUG: meta_RNA_Seq_v2_mRNA_median_Zscores.txt: Starting validation of meta file
INFO: meta_RNA_Seq_v2_mRNA_median_Zscores.txt: Validation of meta file complete

DEBUG: meta_gistic_genes_amp.txt: Starting validation of meta file
INFO: meta_gistic_genes_amp.txt: Validation of meta file complete

DEBUG: meta_gistic_genes_del.txt: Starting validation of meta file
INFO: meta_gistic_genes_del.txt: Validation of meta file complete

DEBUG: meta_rppa_Zscores.txt: Starting validation of meta file
INFO: meta_rppa_Zscores.txt: Validation of meta file complete

DEBUG: meta_study.txt: Starting validation of meta file
INFO: meta_study.txt: Validation of meta file complete

DEBUG: meta_mutations_extended.txt: Starting validation of meta file
INFO: meta_mutations_extended.txt: Validation of meta file complete

DEBUG: meta_RNA_Seq_v2_expression_median.txt: Starting validation of meta file
INFO: meta_RNA_Seq_v2_expression_median.txt: Validation of meta file complete

DEBUG: meta_bcr_clinical_sample.txt: Starting validation of meta file
INFO: meta_bcr_clinical_sample.txt: Validation of meta file complete

DEBUG: meta_linear_CNA.txt: Starting validation of meta file
INFO: meta_linear_CNA.txt: Validation of meta file complete

DEBUG: meta_bcr_clinical_patient.txt: Starting validation of meta file
INFO: meta_bcr_clinical_patient.txt: Validation of meta file complete

DEBUG: meta_CNA.txt: Starting validation of meta file
INFO: meta_CNA.txt: Validation of meta file complete

DEBUG: meta_cna_hg19_seg.txt: Starting validation of meta file
INFO: meta_cna_hg19_seg.txt: Validation of meta file complete

DEBUG: -: Retrieving chromosome lengths from 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes'

DEBUG: meta_methylation_hm450.txt: Starting validation of meta file
INFO: meta_methylation_hm450.txt: Validation of meta file complete

DEBUG: data_bcr_clinical_data_sample.txt: Starting validation of file
WARNING: data_bcr_clinical_data_sample.txt: line 1: No data type definition headers found in clinical data file
ERROR: data_bcr_clinical_data_sample.txt: Invalid header comments, file cannot be parsed

ERROR: -: Sample file could not be parsed. Please fix the problems found there first before continuing.


#######################################################################
One or more errors reported above. Please fix your files accordingly
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

The error report could be found here

Could you please help ?

Update to mysql 8

Would be nice to update from Mysql 5.7 to Mysql 8 when updating to the next cBioPortal release (3.0.0).

How to get rid off the cbioportal logo on the local instance of cbioportal ?

Hi,

Is it possible to get rid off the cBioportal image on the left hand side?

If yes :

How to do that ?
And then how to add a new image there ? Is there a flag which I could change in the portal.properties file?

documentation leads to 404

See this link https://github.com/thehyve/cbioportal-docker/blob/f1ae681/docs/adjusting_portal.properties_configuration.md mentioned in https://github.com/thehyve/cbioportal-docker/blob/f1ae681/docs/using-keycloak.md

Add GZIP configuration to catalina

The following needs to be added to catalina configuration server.xml

<Connector executor="tomcatThreadPool"
           ...
  compression="on"
  compressionMinSize="2048"
  noCompressionUserAgents="gozilla, traviata"
  compressableMimeType="text/html,text/xml,application/json,text/plain"
/>

Cannot launch cbioportal: Error response from daemon: OCI runtime create failed

I was successfully able to install cbioportal with docker and also, I was able to upload few data. Today I re-started the machine and to my surprise I cannot no longer launch cBioPortal. When I run below command, I ran into following issue

bioinfo@bioinfo-pc:$docker start cbioportal-container
Error response from daemon: OCI runtime create failed: container_linux.go:345: starting container process caused "process_linux.go:424: container init caused \"rootfs_linux.go:58: mounting \\\"/media/bioinfo/DATA11/08_cbioportal-setup/00_cbioportal_setup/portal.properties\\\" to rootfs \\\"/var/lib/docker/overlay2/9a3af2423e5b8bcb26aeebfd31892d89d05a5fb6882b7d821a18eff55f8eae66/merged\\\" at \\\"/var/lib/docker/overlay2/9a3af2423e5b8bcb26aeebfd31892d89d05a5fb6882b7d821a18eff55f8eae66/merged/cbioportal/portal.properties\\\" caused \\\"not a directory\\\"\"": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
Error: failed to start containers: cbioportal-container

I can see the container though:

bioinfo@bioinfo-pc:$ docker ps -a
CONTAINER ID        IMAGE                               COMMAND                  CREATED             STATUS                        PORTS                    NAMES
5684b649150c        thehyve/cbioportal:v2.0.1-iss5758   "catalina.sh run"        3 days ago          Exited (127) 15 minutes ago   0.0.0.0:8081->8080/tcp   cbioportal-container
19daf67c7aa9        mysql:5.7                           "docker-entrypoint.s…"   3 days ago          Exited (127) 15 minutes ago   3306/tcp, 33060/tcp      cbioDB

Could you please help?

import study failed with SAML authentication

Hi,

I followed the steps at readme to set an authentication to my instance and it works ! However, I can't load data studies anymore since the validateData.py script returns a 401 Client Error for url: http://cbioportal-container:8080/cbioportal/api-legacy/cancertypes (localhost:port/cbioportal/api-legacy/cancertypes is working)

So I would like to know if a solution exists somewhere or if it is a bug to be corrected in the future ?

Best,
Kevin

Security improvement for docker

@fedde-s mentioned this part of https://docs.docker.com/engine/security/security/#linux-kernel-capabilities

As of Docker 1.10 User Namespaces are supported directly by the docker daemon. This feature allows for the root user in a container to be mapped to a non uid-0 user outside the container, which can help to mitigate the risks of container breakout. This facility is available but not enabled by default.

Would be good to add the right documentation steps (or links to it) in this repo to enable this & automate where possible.

add option to support https certificate

For some installations (perhaps most), SSL should be configured for tomcat.

Would be good to have this automated as much as possible.

https://tomcat.apache.org/tomcat-8.0-doc/ssl-howto.html

error database version

Change deployment to catalina ROOT

Change deployment to catalina ROOT so that the final URL reads https://servername.com instead of https://servername.com/cbioportal.

Error while importing data into cbioportal

I am trying to import data into cbioportal and my command is this:

docker run -it --rm --net cbio-net \
     -v "/media/bioinfo/primary1/data_set:/study:ro" \
     -v "$PWD:/outdir" \
     -v "$PWD/portal.properties:/cbioportal/portal.properties:ro" \
     thehyve/cbioportal:v2.0.1-iss5758 \
     metaImport.py \
        -u http://cbioportal-container:8080/cbioportal \
        -s /study --html=/outdir/.html -v -o

I encounter the following error:

INFO: -: Running validation from cBioPortal version 0-unknown-version-SNAPSHOT
DEBUG: -: Requesting cancertypes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesaliases from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesets from portal at 'http://cbioportal-container:8080/cbioportal'

DEBUG: meta_study.txt: Starting validation of meta file
INFO: meta_study.txt: Validation of meta file complete

DEBUG: meta_fusion.txt: Starting validation of meta file
INFO: meta_fusion.txt: Validation of meta file complete

DEBUG: meta_mutation_file.txt: Starting validation of meta file
INFO: meta_mutation_file.txt: Validation of meta file complete

DEBUG: meta_clinical_sample.txt: Starting validation of meta file
INFO: meta_clinical_sample.txt: Validation of meta file complete

DEBUG: meta_clinical_patient.txt: Starting validation of meta file
INFO: meta_clinical_patient.txt: Validation of meta file complete

ERROR: -: **Cancer type of study is neither known to the portal nor defined in a cancer_type file; value encountered: 'mixed**'

my meta_study.txt file looks like this:

type_of_cancer: mixed
cancer_study_identifier: test_2019
name: test_2019
short_name: test_2019
description: test_2019
groups: PUBLIC
add_global_case_list: true

It is weird that I was able to upload the exact same data set with mixed cancer type and now it says that "Cancer type of study is neither known to the portal nor defined in a cancer_type file"

White screen when querying multiple studies

Hi ! I can't submit a query by selecting more than one study, or it returns an empty page. But there is no problem if I select only one study, the Oncoprint view is displayed normally. Is there anybody who can help me to find any explanation to this ?

Regards

Documentation on building other branches says nothing about resolving patch conflicts

The documentation page that explains how to build an alternative branch does not explain what to do when a patch doesn't apply cleanly to the files in that branch; if anything it might be good to make itlink to the page on adjusting the patch by generating a new one.

.jks file does not need to be in classpath

you can refer to them as file:/... . This means that COPY command for these 2 files could be done after the maven step. This would improve/speedup the process when changing any of these files.

Error removing study from cBioportal

I am trying to remove data from cbioportal which I have installed using docker container.

I am running below command (not sure if that is the correct command) and it says that it could not find the file; when the fact remains that the file is indeed present at this location.

bioinfo@bioinfo-pc:~/Desktop$ docker run -it --rm --net cbio-net \
>     -v "$PWD/portal.properties:/cbioportal/portal.properties:ro" \
>     thehyve/cbioportal:v2.0.1-iss5758 \
>     cbioportalImporter.py \
>         -c remove-study \
>         -meta /home/bioinfo/Desktop/meta_study.txt 

Data loading step using /cbioportal/scripts/target/scripts-2.0.1-SNAPSHOT.jar

Checked DB schema version: (expected: 2.7.3) (found: 2.7.3)
meta-file cannot be found: /home/bioinfo/Desktop/meta_study.txt

I checked that the file is present at this location

bioinfo@bioinfo-pc:~/Desktop$ ls /home/bioinfo/Desktop | fold
case_lists
data_clinical_patient.txt
data_clinical_sample.txt
data_log2CNA.txt
meta_clinical_patient.txt
meta_clinical_sample.txt
meta_CNA_log2.txt
meta_study.txt

Any help is highly appreciated!

use jitpack solution for cbioportal artifacts

With Ino's jitpack solution for the project artifacts download (PR #1798) we could even skip git, maven and building altogether!

Problem importing 2 samples under the same cancer study

Hi,

I have 2 samples what I want to import mutation data (from vcf file - 1 / sample ) into local cbioportal under the same cancer study (same cancer study identifier).

So, first I import one sample from a folder structure like this

├── case_lists
│   └── cases_sequenced.txt
├── data_clinical_patient.txt
├── data_clinical_sample.txt
├── meta_clinical_patient.txt
├── meta_clinical_sample.txt
├── meta_study.txt
├── meta_mutation.txt
└── Sample1.maf

1 directory, 8 files

which is successful and then I upload the 2nd sample from a folder structure like this

├── case_lists
│   └── cases_sequenced.txt
├── data_clinical_patient.txt
├── data_clinical_sample.txt
├── meta_clinical_patient.txt
├── meta_clinical_sample.txt
├── meta_study.txt
├── meta_mutation.txt
└── Sample2.maf

1 directory, 8 files

*Notice the maf file names

However, what happens is that the study is removed throwing this message and it replaces my sample1 with sample2

Cancer study with identifier "demo" found in database, removing...

which is not what I want, what I want is to have both of them under the same study.

So, how should I do that ? Any suggestions ? Should I do this first -

merge both the vcf files into a single vcf file
convert the merged vcf file into maf using vcf2maf
and then put the name of merged maf file in the meta_mutation.txt file
and finally import it into cbioportal ?

module is not working properly.

I have followed your instructions to build the cbioportal, but the "network" tab is in a state of loading data and don't appear any word.Could you give me some advice please？

Catalina setting from cBio setup docs missing in context patch

The upstream documentation on how to deploy a cBioPortal server suggests two options that are not applied in the corresponding patch in this setup:

        testOnBorrow="true"
        validationQuery="SELECT 1"

The commit history doesn't tell me why I'd have left these out when I originally made the patch. If it breaks any functionality we should probably fix it, and if not, I wonder if it's still needed in the upstream docs.