Unable to deploy version 5 of cbioportal

[Carlos Espinosa]

Hi, I'm trying to redeploy version 5 of cbioportal because version 6 broke SAML login and it no longer works at our institution. And without SAML authentication/authorization (https://github.com/cBioPortal/cbioportal/issues/11818#issuecomment-3610432109) it's a no go. However when trying to build version 5 I keep getting the following error. I believe it's the same error as described here: https://github.com/cBioPortal/cbioportal/issues/9844 

cbioportal  | [INFO] ------------------------------------------------------------------------

cbioportal  | [INFO] Reactor Summary for Portal Master 5.4.5-dirty-SNAPSHOT:

cbioportal  | [INFO] 

cbioportal  | [INFO] Portal Master ...................................... SUCCESS [ 44.937 s]

cbioportal  | [INFO] persistence ........................................ SUCCESS [  4.390 s]

cbioportal  | [INFO] persistence-connections ............................ SUCCESS [ 21.025 s]

cbioportal  | [INFO] model .............................................. SUCCESS [ 16.646 s]

cbioportal  | [INFO] Portal utils ....................................... SUCCESS [  3.563 s]

cbioportal  | [INFO] persistence-api .................................... SUCCESS [ 16.357 s]

cbioportal  | [INFO] db-scripts ......................................... SUCCESS [  0.796 s]

cbioportal  | [INFO] persistence-mybatis ................................ SUCCESS [  6.168 s]

cbioportal  | [INFO] security ........................................... SUCCESS [  5.247 s]

cbioportal  | [INFO] permission-evaluator ............................... SUCCESS [  1.478 s]

cbioportal  | [INFO] service ............................................ FAILURE [  3.281 s]

cbioportal  | [INFO] security-spring .................................... SKIPPED

cbioportal  | [INFO] Portal Web Layer ................................... SKIPPED

cbioportal  | [INFO] Portal utils ....................................... SKIPPED

cbioportal  | [INFO] Portal Core ........................................ SKIPPED

cbioportal  | [INFO] cBioPortal ......................................... SKIPPED

cbioportal  | [INFO] Portal Scripts ..................................... SKIPPED

cbioportal  | [INFO] ------------------------------------------------------------------------

cbioportal  | [INFO] BUILD FAILURE

cbioportal  | [INFO] ------------------------------------------------------------------------

cbioportal  | [INFO] Total time:  02:51 min

cbioportal  | [INFO] Finished at: 2025-12-09T22:32:32Z

cbioportal  | [INFO] ------------------------------------------------------------------------

cbioportal  | [ERROR] Failed to execute goal on project service: Could not resolve dependencies for project org.mskcc.cbio:service:jar:5.4.5-dirty-SNAPSHOT: Could not find artifact com.github.cbioportal:session-service:jar:model:v0.5.0 in alfresco (https://artifacts.alfresco.com/nexus/content/repositories/public/) -> [Help 1]

cbioportal  | [ERROR] 

cbioportal  | [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.

cbioportal  | [ERROR] Re-run Maven using the -X switch to enable full debug logging.

cbioportal  | [ERROR] 

cbioportal  | [ERROR] For more information about the errors and possible solutions, please read the following articles:

cbioportal  | [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

cbioportal  | [ERROR] 

cbioportal  | [ERROR] After correcting the problems, you can resume the build with the command

cbioportal  | [ERROR]   mvn <args> -rf :service

cbioportal  | NOTE: Picked up JDK_JAVA_OPTIONS:  --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.invoke=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED

Reaching out here because this is a huge blocker and some guidance would be appreciated. I feel like I've exhausted all my options for making a deployment work.

[Gaofei Zhao]

Hi Carlos,

Regarding your issue with deploying version 5 of cBioPortal, the build failure is due to a dependency resolution problem. You should be able to resolve this by replacing the version string for the session-service dependency from v0.5.0 to 0.5.0 in your build configuration:

<dependency>

<groupId>com.github.cbioportal</groupId>

<artifactId>session-service</artifactId>

<classifier>model</classifier>

<version>0.5.0</version>

</dependency>

If you decide to give version 6 another try and want to configure SAML/Keycloak, here are some resources that may be helpful:

- Keycloak/SAML Documentation

- v5 to v6 Migration Guide

- Example Production SAML Configuration: You can see how SAML-related parameters are configured in our production deployment file here

I hope this helps you get your deployment working.

Best,

Gaofei

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[Sachin Kumar]

I can help if you need

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/CAKYhKrCkW1fwUvZyQi5NK4_MXA8wEJij4C2-tbCSg3TJ6nb5kQ%40mail.gmail.com.

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Thanks & Regards

Sachin Kumar
PRS-I @ NISER

HP: lazyminnd