v3.2.1

What's Changed

• TASK-6136 - OpenCGA-Storage tests failed on OpenCGA 2.12.x by @j-coll in #2457
• TASK-5895 - HBaseLockManager Inconsistent lock status by @j-coll in #2459
• TASK-6311 - Error querying by CompoundHet - Require exactly one study by @j-coll in #2471
• TASK-6436 - OpenCGA-Storage test failed on release-2.12.x branch by @j-coll in #2478
• TASK-6345 - Cohort and sample double association is missing by @pfurio in #2473
• TASK-6596 - Error loading long variants: DocValuesField "variantId" is too large, must be <=32766 by @j-coll in #2490
• TASK-5516 Speed-up CVDB queries by @jtarraga in #2465
• TASK-6568 - Missing tagsAction in notes/update by @pfurio in #2485
• TASK-6492 - Clinical Case query failed with cvCt value loss_of_function by @jtarraga in #2492
• TASK-6558 - Issue indexing variants with length 0 (i.e. start > end) and CIEND by @j-coll in #2484
• TASK-6626 - CLI file update sets empty attributes object by @pfurio in #2489
• TASK-6703 - Fix junit tests by @j-coll in #2493
• TASK-6636 - Job Kill method in JavaScript client of OpenCGA sends the params as POST body data by @juanfeSanahuja in #2494
• TASK-6399 - CI/CD: Include save reports option for tasks workflows by @juanfeSanahuja in #2477
• TASK-6515 - Port Patch 2.12.6.1 -> 3.2.1 (XB 1.10.6.1 -> 2.2.1) by @juanfeSanahuja in #2491
• Task 6255 Update Exomiser Docker image to v14.0.0 by @jtarraga in #2462
• TASK-6494 - Improve our current Password Policy for built-in authentication in OpenCGA by @pfurio in #2488
• TASK-5964 - Clinical Improvements by @pfurio in #2474
• TASK-6789 - Variant query fails with large skip values by @j-coll in #2498
• TASK-6737 - Force parameter is not recognised in the variant delete operation by @j-coll in #2497
• TAKS-6756 - Error deleting files from archive table by @j-coll in #2496
• TASK-5448 - Add mandatory variant setup step by @j-coll in #2454
• TASK-6708 - Port Patch 2.12.7 -> 3.2.1 (Xetabase 1.10.7 -> 2.2.1) by @juanfeSanahuja in #2499
• TASK-6807 - Pull request approve workflow Fail by @juanfeSanahuja in #2500

Full Changelog: v3.2.0...v3.2.1

v2.12.7

What's Changed

• TASK-6345 - Cohort and sample double association is missing by @pfurio in #2473
• TASK-6558 - Issue indexing variants with length 0 (i.e. start > end) and CIEND by @j-coll in #2484
• TASK-6703 - Fix junit tests by @j-coll in #2493
• TASK-6789 - Variant query fails with large skip values by @j-coll in #2498

Full Changelog: v2.12.6...v2.12.7

v2.12.6.1

What's Changed

• TASK-6596 - Error loading long variants: DocValuesField "variantId" is too large, must be <=32766 by @j-coll in #2490

Full Changelog: v2.12.6...v2.12.6.1

v3.2.0

What's Changed

• TASK-2306 - Family index error is raised when variant-secondary-sample-index is run for non-family samples by @j-coll in #2406
• TASK-5668 - Linked file not shown under sample when retrieving an Individual by @pfurio in #2409
• TASK-5716 - Renaming a file is not reflected on the list of files contained by samples by @pfurio in #2410
• TASK-5796 - Replace status.name indexes for status.id by @pfurio in #2423
• TASK-6007 - OpenCGA tests fails by @j-coll in #2426
• TASK-5563 - Secondary sample index and CellBase issue - NotPresentExceptionConsequenceTypeMixinConsequenceTypeConverter error by @j-coll in #2417
• Task 5603 Exomiser: Single sample Case run as trio family by @jtarraga in #2425
• TASK-5858 - Fix alignment and coverage index analyses in blob storage by @jtarraga in #2416
• TASK-5878 - Unable to filter by dbSNP (rsIds) and HGVS id in variant browser by @j-coll in #2427
• TASK-6082 - Fix pom.xml to include the src/test/resources folder by @jtarraga in #2433
• TASK-5877 - Accept non-normalized variant ID filtering by variant by @j-coll in #2418
• TASK-5876 - Outdated variant stats are not returned by @j-coll in #2431
• TASK-6117 - Fix JUnit VariantOperationsTest:testCellbaseConfigure test by @jtarraga in #2435
• TASK-6183 - Email can't be used as a userId by @pfurio in #2441
• TASK-6172 - Improve HGVS queries by @imedina in #2440
• TASK-6201 - Outdated variant stats of running operations are not returned by @j-coll in #2445
• TASK-5932 - Format filter autocomplete is broken "The results could not be loaded" by @pfurio in #2436
• TASK-5535 - "Unlink file" action does not remove files from ClinicalAnalysis or relatedFiles by @pfurio in #2437
• TASK-6231 - Port Patch 1.10.4.1 -> 1.10.5 by @juanfeSanahuja in #2448
• TASK-464 - Login - Forgot Password option by @juanfeSanahuja in #2439
• TASK-6240 - Symbolic inversions not indexed during data load by @j-coll in #2450
• TASK-6005 - Error loading variants : "Row length 45522 is > 32767" by @j-coll in #2449
• TASK-5888 - REST Error : 414 URI too large and 431 Header too large by @j-coll in #2443
• TASK-6256 - Main OpenCGA v3.0.0 migration loses track of previous migration executions by @pfurio in #2452
• TASK-6078 - Concurrent variant-index from same sample without --load-multi-file-data by @j-coll in #2442
• TASK-5980 - REST Admin - Endpoint GET /admin/users/search only allowed for opencga user, not for organization admin/owner by @pfurio in #2438
• TASK-6305 - Error executing migrations. "requires additional parameters and need to be run manually." by @j-coll in #2456
• TASK-6302 - Improve clients auto-generation process by @j-coll in #2455
• TASK-6281 - Port Patch 2.0.0.1 -> 2.2.0 by @juanfeSanahuja in #2464
• TASK-6357 - Port Patch 1.10.5 -> 2.2.0 by @juanfeSanahuja in #2463
• TASK-4970 - New CI/CD should be triggered when a PR is approved for OpenCGA repository by @juanfeSanahuja in #2467
• TASK-6322 - Study admins should be able to update Project by @pfurio in #2458
• TASK-5979 - Automatize validation of SSO with CAS for OpenCGA Enterprise 2.x.x by @pfurio in #2461
• TASK-6413 - Allow migrations from 3.0.0.1 to 3.2.x by @pfurio in #2470
• TASK-6013 - Extend User Management capabilities by @pfurio in #2432
• TASK-6089 - Automation: Optimise Job management by @pfurio in #2476
• TASK-6345 - Cohort and sample double association is missing by @pfurio in #2472
• TASK-5960 - Update python client log-in to include organization parameter by @dapregi in #2468
• TASK-6266 - OpenCGA-Storage test failed on develop branch by @j-coll in #2481
• TASK-6522 - NoSuchMethodError okhttp3 in opencga-enterprise by @j-coll in #2483

Full Changelog: v3.1.0...v3.2.0

v2.12.6

What's Changed

• TASK-6136 - OpenCGA-Storage tests failed on OpenCGA 2.12.x by @j-coll in #2457
• TASK-5895 - HBaseLockManager Inconsistent lock status by @j-coll in #2459
• TASK-6311 - Error querying by CompoundHet - Require exactly one study by @j-coll in #2471
• TASK-6436 - OpenCGA-Storage test failed on release-2.12.x branch by @j-coll in #2478

Full Changelog: v2.12.5...v2.12.6

v2.12.5

What's Changed

• TASK-5932 - Format filter autocomplete is broken "The results could not be loaded" by @pfurio in #2436
• TASK-5535 - "Unlink file" action does not remove files from ClinicalAnalysis or relatedFiles by @pfurio in #2437
• TASK-6231 - Port Patch 2.12.4.1 -> 2.12.5 (XB 1.10.4.1 -> 1.10.5) by @juanfeSanahuja in #2448
• TASK-464 - Login - Forgot Password option by @juanfeSanahuja in #2439
• TASK-6240 - Symbolic inversions not indexed during data load by @j-coll in #2450
• TASK-6005 - Error loading variants : "Row length 45522 is > 32767" by @j-coll in #2449
• TASK-5888 - REST Error : 414 URI too large and 431 Header too large by @j-coll in #2443
• TASK-6078 - Concurrent variant-index from same sample without --load-multi-file-data by @j-coll in #2442
• TASK-6305 - Error executing migrations. "requires additional parameters and need to be run manually." by @j-coll in #2456

Full Changelog: v2.12.4.1...v2.12.5

v3.0.0.1

What's Changed

• TASK-6256 - Main OpenCGA v3.0.0 migration loses track of previous migration executions by @pfurio in #2452

Full Changelog: v3.0.0...v3.0.0.1

v3.1.0

What's Changed

• TASK-5670 - Exception deploying opencga on Apache Tomcat by @j-coll in #2399
• TASK-5493 - Error in variant-index-annotation : "Private sources has changed" by @j-coll in #2395
• TASK-5556 - OpenCGA CLI --json-data-model does not produce parseable JSONS by @juanfeSanahuja in #2394
• TASK-5624 - jq parse error - extra slf4j library by @j-coll in #2402
• TASK-5645 - Fix alignment and coverage index operations by @jtarraga in #2398
• TASK-5439 - Update Junit test Cellbase and save infra resources by @jtarraga in #2400
• TASK-5741 - Jobs tag not being propagated at variant-index-launcher by @j-coll in #2407
• TASK-5827 - Port Patch 2.12.3 -> 3.1.0 (XB 1.10.3 -> 2.1.0) by @juanfeSanahuja in #2414
• TASK-5807 - Automatic docker tag doesn't include hadoop flavour by @j-coll in #2415
• TASK-5754 - Deployment: Update solr to 8.11.3 by @juanfeSanahuja in #2411
• TASK-5696 - Migrate GitHub Actions to v4 by @juanfeSanahuja in #2419
• TASK-5869 - OpenCGA throws a NullPointerException when trying to refresh session by @pfurio in #2420
• TASK-5659 - Fix Organizations small issues found during testing by @pfurio in #2403
• TASK-5804 - Organization updates can be performed by any user by @pfurio in #2424
• TASK-5716 - Renaming a file is not reflected on the list of files contained by samples by @pfurio in #2413
• TASK-5836 - Properly implement new Notes functionality by @pfurio in #2421
• TASK-6019 - Note migration may raise errors by @pfurio in #2429
• TASK-5922 - Organization info doesn't return array of projects by @pfurio in #2422
• TASK-5923 - Organization returns authentication origins secretKey by @pfurio in #2428
• TASK-6032 - User info does not return projects by @pfurio in #2430
• TASK-6185 - Modify release workflows for OpenCB and Enterprise to include all 4 Hadoop flavors by @juanfeSanahuja in #2447
• TASK-6209 - Error executing MapReduce operations in emr6.13 by @j-coll in #2446
• TASK-6245 - Main OpenCGA v3 migration is broken by @pfurio in #2451

Full Changelog: v3.0.0...v3.1.0

v2.12.4.1

What's Changed

• TASK-6183 - Email can't be used as a userId by @pfurio in #2441
• TASK-6172 - Improve HGVS queries by @imedina in #2440
• TASK-6201 - Outdated variant stats of running operations are not returned by @j-coll in #2445

Full Changelog: v2.12.4...v2.12.4.1

v2.12.4

What's Changed

• TASK-2306 - Family index error is raised when variant-secondary-sample-index is run for non-family samples by @j-coll in #2406
• TASK-5668 - Linked file not shown under sample when retrieving an Individual by @pfurio in #2409
• TASK-5716 - Renaming a file is not reflected on the list of files contained by samples by @pfurio in #2410
• TASK-5796 - Replace status.name indexes for status.id by @pfurio in #2423
• TASK-6007 - OpenCGA tests fails by @j-coll in #2426
• TASK-5563 - Secondary sample index and CellBase issue - NotPresentExceptionConsequenceTypeMixinConsequenceTypeConverter error by @j-coll in #2417
• TASK-5603 - Exomiser: Single sample Case run as trio family by @jtarraga in #2425
• TASK-5858 - Fix alignment and coverage index analyses in blob storage by @jtarraga in #2416
• TASK-5878 - Unable to filter by dbSNP (rsIds) and HGVS id in variant browser by @j-coll in #2427
• TASK-6082 - Fix pom.xml to include the src/test/resources folder by @jtarraga in #2433
• TASK-5877 - Accept non-normalized variant ID filtering by variant by @j-coll in #2418
• TASK-5876 - Outdated variant stats are not returned by @j-coll in #2431
• TASK-6117 - Fix JUnit VariantOperationsTest:testCellbaseConfigure test by @jtarraga in #2435

Full Changelog: v2.12.3...v2.12.4