Release RFC72 & cBioPortal v6

[inodb]

Now that we've merged RFC72 changes to the main branch a few more things are remaining to roll out v6 to production

1 Required for release

Configuration

• [x] CORS is missing

Clean Up

• [x] Remove references to portal.properties
• [ ] Add instructions on how to run in IntelliJ or VSCode or Eclipse

Authentication

Security XML has been migrated to an annotation based system. There seems to be a separate OAuth implementation from @pvannierop.

• [x] Try social_auth (is it OAuth?)
• [x] Test saml
  • [x] Add fixes @pvannierop made for SAML
• [x] Fix Microsoft optional_auth @haynescd
• [x] API token. Fix UUID for use with GENIE portal
• [ ] http to https redirect: https://github.com/cBioPortal/cbioportal/issues/10589

Versioning

• [ ] Previously we used maven-external-version plugin to keep track of the version. It pulls the version from git at compile time and sticks it into the pom. There was a change to hardcode a version in the pom. Does the maven-external-version plugin still work?
  • [ ] Update release procedure docs to describe that a manual update of version in pom is necessary: https://github.com/cBioPortal/cbioportal/blob/master/pom.xml#L15

Documentation

• [ ] Security properties EXAMPLE
• [ ] Update instructions on how to run core tests, integration tests
• [x] Release Notes Draft

Caching

• [x] Fix caching map utils @haynescd (https://github.com/cBioPortal/cbioportal/pull/10513)

Deployment

Roll out to all portals:

• [x] Beta portal (https://beta.cbioportal.org)
• [x] MSK beta portal
  • [x] https://github.com/cBioPortal/cbioportal/issues/10580
  • [x] https://github.com/cBioPortal/cbioportal/issues/10583
• [x] Private portal (https://private.cbioportal.mskcc.org)
• [x] Public portal
• [x] MSK portal
  • [ ] https://github.com/cBioPortal/cbioportal/issues/10627 (currently fixed with a hack)
  • [x] https://github.com/cBioPortal/cbioportal/issues/10649
• [x] GENIE Portal (https://genie.cbioportal.org)
  • [x] https://github.com/cBioPortal/cbioportal/issues/10654
• [x] GENIE Private Portal (https://genie-private.cbioportal.org)
• [x] Triage Portal
• [x] Others (sclc, etc)
• [x] More detailed ticket: https://github.com/cBioPortal/cbioportal/issues/10666

Release

• [x] Create tag with proper release notes
• [x] Merge https://github.com/cBioPortal/cbioportal-docker-compose/pull/23 (is manual deletion of servlet API still necessary?)

API Token

• [x] https://github.com/cBioPortal/cbioportal/issues/10581

2. Optional Tasks

Docker Setup

• [x] Improve image, see https://github.com/cBioPortal/cbioportal/issues/10376 (can this be closed?)

Clean Up

• [x] There is a TODO about dispatchservlets, what is this and do we need to do this? File a separate ticket if not essential?

  // TODO Consider creating separate DispatcherServlets as in the original web.xml
  // See: https://stackoverflow.com/a/30686733/11651683

  (Not sure what to do with this, so closed it)

[haynescd]

API token. Data Access Token api was removed @pvannierop This was not removed we updated to only support oAuth2 DAT. UUID can be added back (just didn't test with it)