v6.3.7

🧬 Features

• Add posibility to create and drop published virtual studies with custom IDs @forus (#11611)

✨ Enhancements

• Refactor enrichments endpoint @alisman (#11617)

🐛 Bug Fixes

• Handle empty list for clinical data fetch and update wrong sample count in test @dippindots (#11693)

🐛 Bug Fixes

• Fix broken patient clinical data SQL @onursumer (#11710)
• Fix display of study icon for virtual studies @alisman (cbioportal-frontend#5269)
• Fix bugs in OncoPrint's tabular download due to OQL @oplantalech (cbioportal-frontend#5188)
• fix eager loading of clinical data @alisman (cbioportal-frontend#5261)

📘 Documentation

• Update Architecture-Overview.md with corrected links @chiang-sh (#11675)

🧹 Cleanup & Refactoring 🔧

• Update cache key generation logic in CustomKeyGenerator @alisman (#11686)

👷‍♀️ Testing, Configuration & Deployment

• Handle empty list for clinical data fetch and update wrong sample count in test @dippindots (#11693)
• Delete long cache key test for CustomKeyGeneratorTest @dippindots (#11697)
• Add more null checks for api validation tests @onursumer (cbioportal-frontend#5263)
• Update patient cohort navigation screenshot @gblaih (cbioportal-frontend#5262)

🧰 Maintenance

• Fix high security vulnerabilities @gblaih (#11717)

🕵️‍♀️ Full commit logs

• Backend: v6.3.6...v6.3.7
• Frontend: cBioPortal/cbioportal-frontend@v6.3.6...v6.3.7

🏷Notes on versioning and release procedure

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

v6.3.6

✨ Enhancements

• Adjust caching behavior (move some resources to from general to static and vice versa) @alisman (#11663)
• Study view: eagerly load data for charts menu so you don't have to wait @alisman (cbioportal-frontend#5260)

🐛 Bug Fixes

• Request for copy number segments on study view should fail silently @alisman (cbioportal-frontend#5258)

👷‍♀️ Testing, Configuration & Deployment

• update remote e2e screenshots @alisman (cbioportal-frontend#5252)

🧰 Maintenance

• Update lodash @alisman (cbioportal-frontend#5256)

📘 Documentation

• Update FAQ for CDA studies @jamesqo (#11671)

🧹 Cleanup & Refactoring 🔧

• Migrate clinical-data endpoint to clean architecture with ClickHouse support @fuzhaoyuan (#11425)

🕵️‍♀️ Full commit logs

• Backend: v6.3.5...v6.3.6
• Frontend: cBioPortal/cbioportal-frontend@v6.3.5...v6.3.6

🏷Notes on versioning and release procedure

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

v6.3.5

✨ Enhancements

• Render the comparison page tabs without waiting for data @onursumer (cbioportal-frontend#5191)

🏎 Performance Tweaks

• Update StudyRepository cache to static cache and institute keyword condition @alisman (#11659)

🧰 Maintenance

• Resurrect Darwin->cBio link. It was accidentally dropped when cBio->DDP link was decomissioned. @n1zea144 (#11660)

🕵️‍♀️ Full commit logs

• Backend: v6.3.4...v6.3.5
• Frontend: cBioPortal/cbioportal-frontend@v6.3.4...v6.3.5

🏷Notes on versioning and release procedure

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

v6.3.4

🧬 Features

• RFC93: Custom variant annotation filter in study view page @FlorisVleugels (cbioportal-frontend#5118)

✨ Enhancements

• App should fallback gracefully when Redis cache is unavailable @dippindots (#11647)
• Lazy load detailed sample treatment counts for comparison @onursumer (cbioportal-frontend#5240)

🐛 Bug Fixes

• Add special case for null start end values for numerical study view filters @gblaih (#11637)
• add property to set default view oncoprint @TJMKuijpers (#11503)
• Fix study view pie chart numbers being cut off @gblaih (cbioportal-frontend#5247)
• Fix await of sample-list service when loading filters from url @alisman (cbioportal-frontend#5246)
• Add samples to the treatments endpoint @onursumer (#11628)

👷‍♀️ Testing, Configuration & Deployment

• Update screenshots to reflect oncokb update and data ordering changes @gblaih (cbioportal-frontend#5248)
• Update screenshots for download tab alteration table ordering @gblaih (cbioportal-frontend#5245)

📘 Documentation

• Extend documentation for timeline specimen event types @alisman (#11657)
• Correct profiles and commands for tests in README @gblaih (#11649)
• Correct e2e command in README.md @alisman (#11648)

🧰 Maintenance

• Restore jitpack config @dippindots (#11643)

🕵️‍♀️ Full commit logs

• Backend: v6.3.3...v6.3.4
• Frontend: cBioPortal/cbioportal-frontend@v6.3.3...v6.3.4

🏷Notes on versioning and release procedure

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

v6.3.3

🧬 Features

• RFC95: Generating Study data files @forus (#11482)
• Rfc95 study download @forus (cbioportal-frontend#5185)

✨ Enhancements

• Update legacy path in namespace controllers @Floris-Hyve (#11622)
• add markdown link check on pull request @gritsynad (#11606)
• update to utilize pull_request_target @haynescd (#11619)
• Use new count of alterationsInProfiled genes as numerator in study vi… @alisman (cbioportal-frontend#5213)
• Clinical timeline: Apply line chart to all numerical tracks in MEASUREMENTS parent track @alisman (cbioportal-frontend#5218)

🐛 Bug Fixes

• Fix get all samples of patient in a study endpoint returning 500 error for invalid patient id @gblaih (#11626)
• Restore sample check endpoint for CIS @alisman (#11623)
• Fix Clinical Data NA Count Bug with Cross-Study Attribute Level Conflict Resolution @fuzhaoyuan (#11603)
• Prevent user from entering empty value in user selection filters on study view @gblaih (cbioportal-frontend#5242)
• In local development mode (frontend dev server) clickhouse api endpoints broken @alisman (cbioportal-frontend#5235)
• Turn off the CH studies endpoint @alisman (cbioportal-frontend#5236)

📘 Documentation

• Update News-Genie.md @sbabyanusha (#11631)

👷‍♀️ Testing, Configuration & Deployment

• Fix Sonar Github Action to pass secret @haynescd (#11620)
• Add e2e testing @haynescd (#11613)
• Update screenshot for results mutations tab cosmic removal @gblaih (cbioportal-frontend#5244)
• Increase selected info wait timeout to stabilize study view tests @gblaih (cbioportal-frontend#5243)
• Update mutation frequencies screenshot @gblaih (cbioportal-frontend#5238)
• Stabilize mrna enrichments screenshot test @gblaih (cbioportal-frontend#5239)
• Fix comparison alterations tab and breadcrumbs localdb tests @gblaih (cbioportal-frontend#5234)
• Fix removing filters e2e remote test @gblaih (cbioportal-frontend#5232)

🎨 Style Tweaks

• Update citation link in "Visualize Your Data" page @leexgh (cbioportal-frontend#5241)

🧰 Maintenance

• Upgrade to spring boot 3.5 @gblaih (#11608)
• Fx07014 @alisman (cbioportal-frontend#5230)

🕵️‍♀️ Full commit logs

• Backend: v6.3.2...v6.3.3
• Frontend: cBioPortal/cbioportal-frontend@v6.3.2...v6.3.3

🏷Notes on versioning and release procedure

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

v6.3.2

✨ Enhancements

• Add configuration for google tag manager embed @alisman (#11602)
• Rename table header to 'Data Types' and remove 'Molecular Profile' @viveak910 (cbioportal-frontend#5210)

🐛 Bug Fixes

• Return 404 error for virtual study endpoint when given invalid study id @gblaih (#11604)
• Add On-Panel Alteration Count @fuzhaoyuan (#11587)
• Fix CNA frequency in legacy @fuzhaoyuan (#11565)
• Fix filter checked state when navigating back to home page @gblaih (cbioportal-frontend#5193)

⚙️ REST API Changes

• Add JSON field customMetaData as string in Resource Definition endpoints @dippindots (#11580)

📘 Documentation

• fix link to the Backend-Code-Organization.md in Architecture-Overview.md @gritsynad (#11596)
• fix broken links in CONTRIBUTING.md @Vignesh-JavaDev (#11590)

🧹 Cleanup & Refactoring 🔧

• Refactor SessionServiceController HTTP calls @gulshan2052 (#11581)

👷‍♀️ Testing, Configuration & Deployment

• Automate ArgoCD deployment for new blue/green master portals @zainasir (#11586)
• Adjust localdb assertion after adjustment to backend alteration frequ… @alisman (cbioportal-frontend#5212)

🧰 Maintenance

• Remove references to Darwin/DDP @ao508 (#11572)
• Remove newsletter banner @alisman (cbioportal-frontend#5217)

🕵️‍♀️ Full commit logs

• Backend: v6.3.1...v6.3.2
• Frontend: cBioPortal/cbioportal-frontend@v6.3.1...v6.3.2

🏷Notes on versioning and release procedure

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

v6.3.1

🐛 Bug Fixes

• Fix Study DTO to adhere to what frontend expects @haynescd (#11573)

🧰 Maintenance

• Remove Cosmic and MyCancerGenome visualization and related resources @onursumer (cbioportal-frontend#5199)

✨ Enhancements

• Add aria-label attribute and column header to fix the aria-input-field-name and aria-command-name 508 issues @johnyesit (cbioportal-frontend#5206)
• Add pie chart download options to table download options on study view @gblaih (cbioportal-frontend#5192)
• Add aria-label attribute to fix the svg-img-alt-related 508 issues @johnyesit (cbioportal-frontend#5203)

🗄 Database Migration

• clickhouse.sql fixes @sheridancbio (#11577)

👷‍♀️ Testing, Configuration & Deployment

• Update screenshots after frequency calculation fix @alisman (cbioportal-frontend#5205)

🕵️‍♀️ Full commit logs

• Backend: v6.3.0...v6.3.1
• Frontend: cBioPortal/cbioportal-frontend@v6.3.0...v6.3.1

🏷Notes on versioning and release procedure

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

v6.3.0

📝 Migration Guide

This major release involves a database migration. See migration guide before upgrading. Note: the migration code was introduced in pre-release v6.2.2.

✨ Enhancements

• Update legend with filtered categories in Plots tab @rishisulakhe (cbioportal-frontend#5130)

🐛 Bug Fixes

• Fix freqency error in ClickHouse @fuzhaoyuan (#11447)
• Fix mutation frequency in legacy @fuzhaoyuan (#11533)
• Fixes 11541. Enrichments service should only return items where a gene is altered in at least one group @alisman (cbioportal-frontend#5190)

📘 Documentation

• Add database migration guide for v6.3.0 @zainasir (#11546)
• Add about page to news @inodb (#11529)
• Fix link of pdf tutorial slides 6 @thomasmarwitz (#11535)

👷‍♀️ Testing, Configuration & Deployment

• Fix integration test after database migration @dippindots (#11547)
• Filter out genes subject to off-panel issue in validator @alisman (cbioportal-frontend#5197)
• Fix failing screenshot tests for results view mutations table oncokb annotation @gblaih (cbioportal-frontend#5195)
• Increase timeout for group comparison clinical tab categorical table screenshot test @onursumer (cbioportal-frontend#5189)

🕵️‍♀️ Full commit logs

• Backend: v6.2.2...v6.3.0
• Frontend: cBioPortal/cbioportal-frontend@v6.2.2...v6.3.0

🏷Notes on versioning and release procedure

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

v6.2.2

✨ Enhancements

• Add aria-label attribute to fix the button name-related 508 issues @johnyesit (cbioportal-frontend#5187)
• Add alt attribute to fix the image-alt-related 508 issues @johnyesit (cbioportal-frontend#5183)
• Add aria-label attribute to fix the link-name-related and the select-name-related 508 issues @johnyesit (cbioportal-frontend#5182)
• Add tabIndex attribute to fix the scrollable-region-focus-related 508 issues and add aria-label attribute to some of the input fields to fix the label-related 508 issues @johnyesit (cbioportal-frontend#5171)

🐛 Bug Fixes

• Serialize Web Param used in Authorization @haynescd (#11530)
• Make the "fetchGenericAssayData()" method more robust against possible NPEs @KingAlex1985 (#11504)
• Fix comparison page category table numbers @onursumer (cbioportal-frontend#5184)

🗄 Database Migration

• Add CUSTOM_METADATA column into resource_definition table @dippindots (#11536)
• correct the DROP table statement order @sheridancbio (#11444)
• Use BIGINT primary key for clinical_event table @jamesqo (#11399)
• Add schema versioning for derived tables @sheridancbio (#11446)

📘 Documentation

• Add schema versioning for derived tables @sheridancbio (#11446)
• Add docs references to clickhouse update tools @sheridancbio (#11453)
• Update News.md @sbabyanusha (#11528)

🧹 Cleanup & Refactoring 🔧

• remove mvn-external-version deps @inodb (#11499)

👷‍♀️ Testing, Configuration & Deployment

• Use of path URL for comparison and pathways subtab @rishisulakhe (cbioportal-frontend#5162)
• Java style formatter @teesamuel (#11406)
• Update patient table screenshot @gblaih (cbioportal-frontend#5181)
• Revert study view screenshots affected by frequency change @gblaih (cbioportal-frontend#5180)
• Enable validation for the new alteration enrichments and samples endpoints @onursumer (cbioportal-frontend#5176)

🧰 Maintenance

• Update cbioportal-core v1.0.10 @dippindots (#11538)
• Temporarily disable 3D Structure viewer @onursumer (cbioportal-frontend#5186)

🎨 Style Tweaks

• Change NA to Not Profiled in gene-specific CNA chart @lllinging (cbioportal-frontend#5135)

🕵️‍♀️ Full commit logs

• Backend: v6.2.1...v6.2.2
• Frontend: cBioPortal/cbioportal-frontend@v6.2.1...v6.2.2

🏷Notes on versioning and release procedure

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

v6.2.1

🐛 Bug Fixes

• Revert "Fix for frequency in multi-study view (#11331)" @alisman (#11508)
• Enable table search for genomic start and end positions @onursumer (cbioportal-frontend#5168)
• Fix issue parsing custom data input @alisman (cbioportal-frontend#5165)
• Hide pie button if user unauthorized @FlorisVleugels (cbioportal-frontend#5164)

⚙️ REST API Changes

• Clickhousify alteration enrichments @haynescd (#11454)
• Clickhousify samples endpoint @onursumer (#11393)

📘 Documentation

• Add chromoscope video to how-tos @tmazor (#11513)
• Update About-Us.md - add Guizela @pieterlukasse (#11497)
• Update example link in File-Formats @dippindots (#11495)
• Add link to new about page @inodb (cbioportal-frontend#5160)
• Update Visualize.tsx to include SE4BIO @pieterlukasse (cbioportal-frontend#5163)

🔐 Security

• Extract groups from OAuth JWT token @pnartowski (#11430)

👷‍♀️ Testing, Configuration & Deployment

• Fix prettier version for circleci config @onursumer (cbioportal-frontend#5170)
• remove duplicate plugins from maven central profile @zainasir (#11498)
• Add lang attribute to html tag for 508 compliance @alisman (#11510)
• Add backend SPA forwarding support for result view comparison and pathways subtabs new routes @rishisulakhe (#11500)
• Allow clickhousifying of the public API client @onursumer (cbioportal-frontend#5120)
• Restrict docker image builds to master and tags @zainasir (#11520)
• Automate master portal image deployment @zainasir (#11517)
• Fix screenshot tracking and restore completeResults and imageCompare in circleci @gblaih (#11521)
• Fix localdb tests on junit @gblaih (#11509)
• Update url navigation to fix failing e2e localdb tests on backend and restore localdb errors screenshots @gblaih (cbioportal-frontend#5175)
• Fix prettier version for circleci config @onursumer (cbioportal-frontend#5170)
• Revert test changes affected by frequency fix @gblaih (cbioportal-frontend#5169)
• Stabilize flaky unprofiled samples oncoprint and breadcrumbs tests @gblaih (cbioportal-frontend#5161)
• Improve prettier check in circleci tests @zainasir (cbioportal-frontend#5166)
• Fix e2e localdb oncoprint don't cluster test @gblaih (cbioportal-frontend#5159)
• Stabilize gsva plots tab geneset selection test @gblaih (cbioportal-frontend#5158)
• Stabilize clicking query by gene tests @gblaih (cbioportal-frontend#5157)

🕵️‍♀️ Full commit logs

• Backend: v6.2.0...v6.2.1
• Frontend: cBioPortal/cbioportal-frontend@v6.2.0...v6.2.1

🏷Notes on versioning and release procedure

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