v6.0.0

Overview Backend Changes

This release involves a major repackaging of the backend software to improve the development experience. The backend has been upgraded to use Java Spring Boot v3.1.4. The CORE and MAF modules have been moved to new repositories. All other modules have been compacted into a single source repository. We have also updated the JVM to 21 and many libraries have been updated to address security and performance issues.

More information about this can be found in the Migration Guide.

Module Compaction

As an example all code that was in the service module are now in the src folder. This compaction also means that we now have one pom file. The files in service/src/main/java/org/cbioportal/service are now in /src/main/java/org/cbioportal/service

Properties File Update

We have deprecated the portal.properties file and moved most of the configuration properties to application.properties. Additionally we have added a security.properties file for all security configurations.

Security Updates

Properties used to configure Security have changed, see security.properties reference.
The supported authentication values have been updated and are the following: false, oauth2, optional_oauth2, saml. The optional_oauth2 replaces social_auth. This option allows users to use the site without authentication, but they can optionally log in to save virtual studies and groups.

Developer Experience Improvements

• Update testing and code coverage to github processes (#10561, #10548, #10528)
• Enable hot reloading (#10555)

New Repositories

• CORE - https://github.com/cBioPortal/cbioportal-core
• MAF - https://github.com/cBioPortal/maf

Backend Upgrade Related Commits and Merges

• [RFC72] Spring Boot Upgrade @haynescd @JREastonMarks @inodb @pvannierop (#10425, cbioportal-frontend#4753)
• Update to make /api redirect to springdoc.swagger-ui.path @haynescd (#10533)
• Add Installations Map Redirect @haynescd (#10527)
• Add Sentry jar @haynescd (#10530)
• 6.0.0 fixes for issues identified during testing in prod @haynescd (#10579)
• Add Custom OAuth Authorization @haynescd (#10519)
• Fix CacheMapUtil configurations @haynescd (#10513)
• Fix Cache for StudyViewApplier @haynescd (#10593)
• Add /ln path and update proxy Controller @haynescd (#10531)
• Update to make /api redirect to springdoc.swagger-ui.path @haynescd (#10533)
• Add Installations Map Redirect @haynescd (#10527)
• Hot reloading and Formatting @JREastonMarks (#10555)
• Fix SonarCube Coverage @JREastonMarks (#10548, #10528)
• Fix Auth integration @haynescd @pvannierop (#10560)
• Add 401 response when not authorized exception is thrown instead of redirect @haynescd (#10590)
• Add UUID Dat Support @haynescd (cbioportal-frontend#4837)
• Release 6.0.0 Deployment Documentation @JREastonMarks (#10522)

Other Changes

🧬 Features

• Mutational signature plot with cosmic reference signature @TJMKuijpers (cbioportal-frontend#4771)
• Add structural variant count to datasets page @uklineale (#10582, #10547)

✨ Enhancements

• When bookmark url is too long, prompt user to create a virtual study instead @alisman (cbioportal-frontend#4807)
• Update NDex tooltip @inodb (cbioportal-frontend#4828)
• Change NDEx Tab name @inodb (cbioportal-frontend#4797)
• Add user color configuration for oncoprinter @gblaih (cbioportal-frontend#4817)
• Iframe loader should allow fullscreen functionality @alisman (cbioportal-frontend#4801)
• add arrow buttons to tooltip timeline @uklineale (cbioportal-frontend#4808)

🐛 Bug Fixes

• Show p/q-values in boxplots of comparison clinical tab @gblaih (cbioportal-frontend#4842)
• Update mobxpromise and fix circular dependency caused by onResult @alisman (cbioportal-frontend#4836)
• Prevent clicking within a tooltip from triggering row selection @onursumer (cbioportal-frontend#4821)
• Default visibility of p-value above legend SV plot @TJMKuijpers (cbioportal-frontend#4803)
• Update properties to fix cors issue in backend @haynescd (cbioportal-frontend#4819)
• Fix: data type filter set default value for checkbox @TJMKuijpers (cbioportal-frontend#4804)
• Enable study view action buttons earlier @alisman (cbioportal-frontend#4799)

⚙️ Changes to handle external APIs

• Update civic API @leexgh (cbioportal-frontend#4775)

👷‍♀️ Testing, Configuration & Deployment

• Update screenshots after data changes @alisman (cbioportal-frontend#4835)
• Update test for sample selector mutational signature @TJMKuijpers (cbioportal-frontend#4843)
• Remove demo-rfc72 dockerImage from localdb tests @haynescd (cbioportal-frontend#4805)
• Fix path to config_service for dev and dev builds @alisman (cbioportal-frontend#4824)

📘 Documentation

• Update Authenticating-Users-via-Tokens.md @scvannost (#10501)
• Update News Release - fix formatting @rmadupuri (#10509)
• Update News - Dec 29, 2023 data release @sbabyanusha (#10494)
• Fix link to Architecture overview @pieterlukasse (#10596)

🕵️‍♀️ Full commit logs

• Backend: v5.4.10...v6.0.0
• Frontend: cBioPortal/cbioportal-frontend@v5.4.10...v6.0.0

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning