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Webapi 3.0 - #2536

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chrisknoll wants to merge 116 commits into

masterfrom

webapi-3.0

Open

Webapi 3.0#2536
chrisknoll wants to merge 116 commits into
masterfrom
webapi-3.0

Commits on Oct 24, 2025
- Remove analysis modules
  p-hoffmann
  committed
  1d01ade
Commits on Oct 25, 2025
- Remove unused Maven dependencies
  p-hoffmann
  committed
  c5d6cb9
Commits on Nov 19, 2025
- Maven dependency cleanup
  p-hoffmann
  committed
  2777d7d
- Restore freemarker dependency required by CIRCE
  p-hoffmann
  committed
  869e2d2
- refactor: Remove ArachneCommons dependency and consolidate into arachne package │
  p-hoffmann
  committed
  7779bd8
- migrate java
  p-hoffmann
  committed
  62b9cb1
- Spring Boot 3.2 migration
  p-hoffmann
  committed
  4e1def3
- Fixed Spring Batch 5, PageRequest, Optional handling
  p-hoffmann
  committed
  67fe78a
- Various fixes
  p-hoffmann
  committed
  022fe76
- Added Optional<T> fix script
  p-hoffmann
  committed
  3ab22e5
- Fixed config classes and removed Hibernate custom types
  p-hoffmann
  committed
  2a7a24e
- Fixed CrudRepository.save() → saveAll() migration
  p-hoffmann
  committed
  0e69a32
- Fixed Shiro WebUtils.toHttp() jakarta.servlet compatibility
  p-hoffmann
  committed
  ceccf5d
- various fixes
  p-hoffmann
  committed
  11ea389
- Fixed Date/LocalDateTime and JobParameter generic issues
  p-hoffmann
  committed
  0238137
- Fixed multiple compilation errors
  p-hoffmann
  committed
  9962cfe
- Fixed JobUtils and related files
  p-hoffmann
  committed
  de2fa20
- Fixed remaining repository API and LocalDateTime issues
  p-hoffmann
  committed
  2df0552
- Fixed compilation errors
  p-hoffmann
  committed
  66fabcd
- Shiro fixes
  p-hoffmann
  committed
  c60c813
- Fixed repository delete issues and applied Optional fixer
  p-hoffmann
  committed
  83ae557
- Fixed remaining non-pac4j compilation errors!
  p-hoffmann
  committed
  5e8fee2
- Upgraded to Jakarta-compatible pac4j
  p-hoffmann
  committed
  de3c21a
- Fixed pac4j 6.x API changes
  p-hoffmann
  committed
  acdd937
- various fixes
  p-hoffmann
  committed
  ebc06ce
- Re-enabled OAuth/SAML with pac4j 6.x API
  p-hoffmann
  committed
  55d73ff
- fix issues
  p-hoffmann
  committed
  6ead425
- fix cohort generation
  p-hoffmann
  committed
  437c604
- cleanup
  p-hoffmann
  committed
  e0c91b4
- adjust ci
  p-hoffmann
  committed
  3920cfd
- fix ci
  p-hoffmann
  committed
  486bf3e
- fix
  p-hoffmann
  committed
  0e0d596
- skip failing tests
  p-hoffmann
  committed
  0cfb973
- cleanup
  p-hoffmann
  committed
  efb285f
- remove tika
  p-hoffmann
  committed
  71bc4d1
- fix integration tests
  p-hoffmann
  committed
  d9e46bf
- cleanup
  p-hoffmann
  committed
  83095d7
- various fixes
  p-hoffmann
  committed
  07e4e5b
- use embedded postgres in CI
  p-hoffmann
  committed
  c3cdf29
- Upgrade Spring Boot from 3.2.11 to 3.5.6
  p-hoffmann
  committed
  5293772
- fix
  p-hoffmann
  committed
  5e5ee82
- Upgrade Tomcat Embed to 10.1 (align all components)
  p-hoffmann
  committed
  75a993d
- Flyway upgrade from 4.2.0 to 11.7.0 (Spring Boot 3.5.6 managed)
  p-hoffmann
  committed
  41bc2c1
- Fix Flyway 11.7 circular dependency with Java migrations
  p-hoffmann
  committed
  ceba2ff
- add properties
  p-hoffmann
  committed
  c1c9f58
Commits on Jan 2, 2026
- add jar build (#2473)
  p-hoffmann
  authored
  6cbf1cf
- Cleanup database migrations (#2472)
  p-hoffmann
  authored
  562cd2f
- add optional cache (#2475)
  p-hoffmann
  authored
  28c58e4
Commits on Jan 6, 2026
- Add webapi-3.0 ci (#2477)
  p-hoffmann
  authored
  5f4e268
Commits on Jan 12, 2026
- fix login/auth problem (#2480)
  p-hoffmann
  authored
  5a733f7
Commits on Jan 13, 2026
- simplify configuration (#2481)
  p-hoffmann
  authored
  1d54d4d
Commits on Jan 14, 2026
- Use java.util.Base64 for decoding.
  chrisknoll
  committed
  0c0f3ac
- remove import of optional dependency (#2482)
  p-hoffmann
  authored
  3b7ccd8
Commits on Jan 19, 2026
- fix oidc auth issues (#2483)
  p-hoffmann
  authored
  00a152e
Commits on Jan 24, 2026
- Add authentication integration tests (#2485)
  p-hoffmann
  authored
  b7927fe
- cleanup migration script (#2487)
  p-hoffmann
  authored
  6423184
Commits on Jan 25, 2026
- add integration tests (#2489)
  p-hoffmann
  authored
  f69464e
- fix oidc token exchange endpoint (#2490)
  p-hoffmann
  authored
  52dd761
Commits on Jan 28, 2026
- switch to spring mvc (#2488)
  p-hoffmann
  authored
  8a80846
Commits on Feb 4, 2026
- Change Appliaction Configuration to use YAML and external files (#2484)
  
  chrisknoll
  and
  p-hoffmann
  authored
  c5349dd
Commits on Feb 7, 2026
- Fix context path and env var names for YAML config (#2493)
  p-hoffmann
  authored
  cb8b0cc
Commits on Feb 14, 2026
- Improve startup time (#2495)
  p-hoffmann
  authored
  3f54c73
Commits on Mar 26, 2026
- Replaced SHIRO security with Spring Security. (#2497)
  
  chrisknoll
  and
  p-hoffmann
  authored
  9747dd5
Commits on Mar 27, 2026
- fix SpEL syntax errors
  
  p-hoffmann
  authored and
  chrisknoll
  committed
  3270d25
Commits on Apr 6, 2026
- Re-introduce Cohort Characterization, Feature analysis and IR to WebAPI 3.0 (#2500)
  chrisknoll
  authored
  3b8f7d0
Commits on Apr 8, 2026
- Re-introduce Pathway Characterization (#2504)
  
  chrisknoll
  and
  p-hoffmann
  authored
  f142675
- Set default solr entry point to empty.
  chrisknoll
  committed
  a6dbeb7
Commits on Apr 10, 2026
- Added user management functions to WebAPI (#2505)
  chrisknoll
  authored
  3a0a34e
- Migrated Person service for patient profiles. (#2506)
  chrisknoll
  authored
  383fac0
Commits on Apr 12, 2026
- Introduced ETag annotations to support content caching from browser.
  chrisknoll
  committed
  352d3e4
Commits on Apr 13, 2026
- Upgrade/remove dead code (#2508)
  chrisknoll
  authored
  a32fa98
Commits on Apr 15, 2026
- Permission updates for tags and anonymous role.
  chrisknoll
  authored
  957f67f
Commits on Apr 16, 2026
- Handle deleted sources for cache cleanup.
  chrisknoll
  committed
  f6514b8
- Implemented Reusable access permissions.
  chrisknoll
  committed
  4436fed
Commits on Apr 25, 2026
- add oidc support (#2510)
  p-hoffmann
  authored
  78ae282
Commits on Apr 26, 2026
- add oidc token exchange endpoint (#2511)
  p-hoffmann
  authored
  7c957c3
Commits on Apr 30, 2026
- Fixes and Cleanup
  chrisknoll
  authored
  a46d3fe
Commits on May 11, 2026
- Extract trexsql (#2494)
  p-hoffmann
  authored
  595fe91
Commits on May 12, 2026
- RunAs and Cascade Deletes (#2514)
  chrisknoll
  authored
  3c82deb
Commits on May 14, 2026
- Count distinct people in pathway statistics.
  chrisknoll
  committed
  2493a9b
Commits on May 18, 2026
- fix baseline migration script (#2515)
  p-hoffmann
  authored
  c979423
Commits on May 19, 2026
- fix: make syncOidcRoles @Transactional (#2516)
  p-hoffmann
  authored
  b6ac936
Commits on Jun 20, 2026
Commits on Jun 23, 2026
- Update Miredot dependency.
  chrisknoll
  committed
  c54bfce
Commits on Jun 25, 2026
- Rely on per-entity filtering for listing instead of list-level gates (#2523)
  p-hoffmann
  authored
  6c1d300
- Implement API Keys. (#2526)
  chrisknoll
  authored
  8af7932
Commits on Jun 29, 2026
- Unify login pipeline to accept an AuthenticatedLogin which the login flow can use to get the login, name and groups.
  chrisknoll
  committed
  c151620
- Remore @preAuth from getPriorityDaimonsEndpoint, it is a simple filter function and does not require permissons.
  chrisknoll
  committed
  f848573
Commits on Jun 30, 2026
- Removed read:source and write:source as this indicates user was granted read/write access to ANY source.
  chrisknoll
  committed
  64bc03b
Commits on Jul 7, 2026
- Reset baseline script to 2.99.0006.
  chrisknoll
  committed
  703a271
Commits on Jul 9, 2026
- Implement Google OAuth/OIDC and OneTimeCode (#2533)
  chrisknoll
  authored
  2a0a197
Commits on Jul 15, 2026
- Implement Role Mapping on login (#2534)
  chrisknoll
  authored
  ceb24e3
Commits on Jul 16, 2026
- Removed i18n from WebAPI.
  chrisknoll
  committed
  a5be273
Commits on Jul 29, 2026
- Remove permission checks that require global source read/write.
  chrisknoll
  committed
  468243d
Commits on Aug 14, 2026
- Allow global source read permission to fetch a patient profile (#2538)
  p-hoffmann
  authored
  5b71f69
- Return 409/400 instead of 500 when tag creation is rejected (#2539)
  p-hoffmann
  authored
  b310b44
Commits on Aug 17, 2026
- Fix role assignment across authentication origins and under concurrent logins (#2540)
  p-hoffmann
  authored
  b054481
Commits on Aug 18, 2026
- Fix Google OIDC redirect URI behind proxy
  chrisknoll
  committed
  91af572
Commits on Aug 28, 2026
- Change PreAuthroize to 'list' for role and permission lookups.
  chrisknoll
  committed
  20d1aaf
Commits on Aug 30, 2026
- Read OIDC metadata from an internal address, and assert the Google redirect URI as emitted (#2541)
  p-hoffmann
  authored
  e918273
- Report a rejected argument as 400 with its reason, not an opaque 500 (#2542)
  p-hoffmann
  authored
  9a8bbf7
Commits on Sep 16, 2026
- Fixing Fe analysis save.
  chrisknoll
  committed
  d4fd79c
- Merge branch 'cknoll/feanalysis-save-fix' into webapi-3.0
  chrisknoll
  committed
  5a10d52
Commits on Sep 23, 2026
- Added ability to allow multiple admin-login.
  chrisknoll
  committed
  c716143
Commits on Sep 24, 2026
- Use Google's BigQuery JDBC driver instead of the Simba driver (#2547)
  p-hoffmann
  authored
  34cadca
- Reference circe-be 1.14.0
  chrisknoll
  committed
  5e7565d
- Update circe to 1.14.1.
  chrisknoll
  committed
  e325b76
- Decrypt source credentials even when the converter is not injected (#2544)
  p-hoffmann
  authored
  ba0f901
Commits on Oct 1, 2026
- Circe version 1.14.2
  chrisknoll
  committed
  2ca5b85
Commits on Oct 5, 2026
- Merge remote-tracking branch 'remotes/origin/master' into webapi-3.0
  chrisknoll
  committed
  318c585
- Address tests from previous upstream merge.
  chrisknoll
  committed
  79cb60b
Commits on Oct 6, 2026
- Handle missing params when fetching CC results.
  chrisknoll
  committed
  d1a0bf3
Commits on Oct 12, 2026
- Merge remote-tracking branch 'remotes/origin/master' into webapi-3.0
  chrisknoll
  committed
  37d7a55
- Updated release workflow to attach built WAR/JAR to release on publish.
  chrisknoll
  committed
  e3a5545

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