v5.0.0

What's Changed

• TASK-7693-dev - Upgrade Ubuntu image on GitHub Actions by @juanfeSanahuja in #2587
• TASK-7772 - Upgrade java-driver and MongoDB versions by @pfurio in #2607
• Portpatch 4.1.2 -> 5.0.0-SNAPSHOT by @juanfeSanahuja in #2625
• TASK-8017 - An OpenCGA JUnit test causes a compilation failure by @jtarraga in #2632
• TASK-7809 - Support EMR version 7.5 by @j-coll in #2630
• TASK-7555 - Enable Opencga GRPC Server by @j-coll in #2629
• TASK-7972 - Pyopencga file upload method is not functional by @dapregi in #2628
• TASK-6217 - Solr improvements: Stats and Update by @j-coll in #2601
• TASK-8045 - Update SNAPSHOT policy in pom.xml by @juanfeSanahuja in #2634
• TASK-7922 - Fix: update JWT secret key for new environments by @pfurio in #2621
• TASK-7902 - Missing array of tags in Cohort data model by @pfurio in #2622
• TASK-7834 - OpenCGA start timeout with ~30 organizations -> k8s liveness and readiness probes fail by @pfurio in #2623
• TASK-7944 - Secondary Sample Index Annotation not executed/updated after file delete + index by @j-coll in #2627
• TASK-6346 - Load multiple VCFs with the same name by @j-coll in #2612
• TASK-7983 - Fix the clinical interpretation analysis tool by @jtarraga in #2633
• Implement SHA-256 checksum validation for file uploads by @Copilot in #2636
• TASK-7610 - Extend Workflows data model by @pfurio in #2631
• TASK-7442 - Implement different K8s pool types by @pfurio in #2611
• TASK-8093 - ToolParams not properly detected by @pfurio in #2638
• TASK-6771 - Error running variant-file-delete : IllegalArgumentException: Unknown status ERROR by @j-coll in #2637
• TASK-7645 - Integrated Clinical Preprocessing, Variant Assessment, and Reporting by @pfurio in #2624
• TASK-5564 - Update data sources for CellBase 6.x by @jtarraga in #2640
• TASK-8126 - OpenCGA migrations don't finish by @pfurio in #2639
• TASK-8138 - Xeta40 Integration tests failing by @pfurio in #2641
• TASK-8150 - JUnit tests: Investigate and fix errors by @j-coll in #2642
• TASK-8158 - GRPC doesn't stop streaming on cancelled requests. by @j-coll in #2643
• TASK-8139 - Fix the OpenCGA REST server to use the properly configured ObjectMapper from JacksonUtils by @jtarraga in #2644

New Contributors

• @Copilot made their first contribution in #2636

Full Changelog: v4.1.2...v5.0.0

v4.1.2

What's Changed

• TASK-7958 - Error running Variant-Export (LocalVariantStorageMetadataDBAdaptorFactory) by @j-coll in #2626

Full Changelog: v4.1.1...v4.1.2

v4.1.1

What's Changed

• TASK-7923 - Incomplete variant annotation finishes successfully after skip variant annotation by @j-coll in #2619
• TASK-7905 - Failing OpenCGA Junit tests by @j-coll in #2620

Full Changelog: v4.1.0...v4.1.1

v4.1.0

What's Changed

• TASK-6998 - Fix cohort-sample reference migration by @pfurio in #2510
• TASK-6983 - NPE at DetectIllegalConcurrentFileLoadingsMigration by @j-coll in #2514
• TASK-4682 - Error in VariantExport VCF : Duplicate allele (pre-step to exomiser) by @j-coll in #2527
• TASK-7358 - Memory problem when unlinking some files by @pfurio in #2552
• TASK-7358 - Memory problem when unlinking some files by @pfurio in #2553
• TASK-6880 - CI/CD workflow to delete task docker images on merge fails by @juanfeSanahuja in #2550
• TASK-7330 - Hortonworks maven repositories are down by @j-coll in #2542
• TASK-7511 - Cannot sync more than just one group by @pfurio in #2565
• TASK-7486 - Reset password sent doesn't expire by @pfurio in #2561
• TASK-7605 - CatalogException: User 'opencga' could not be found. by @pfurio in #2575
• TASK-7594 - variant-index: broken "skip-normalization" parameter by @j-coll in #2576
• TASK-7559 - Missing information for the rest response for individuals by @pfurio in #2570
• TASK-7508 - Fail to download files programmatically by @pfurio in #2573
• TASK-7441 - CVDB CLI doesn't work by @juanfeSanahuja in #2568
• TASK-7604 - Variant annotation fails when changing default data release for a CellBase version by @j-coll in #2577
• TASK-7589 - Port Patch 2.12.9 -> 3.2.3 Xetabase 1.10.9 -> 2.2.3 by @juanfeSanahuja in #2574
• TASK-7685 - Login doesn't work with LDAP by @pfurio in #2584
• TASK-7545 - Automatically add users to @members group in studies by @pfurio in #2572
• TASK-7693-rel - Upgrade Ubuntu image on GitHub Actions by @juanfeSanahuja in #2588
• TASK-7531 - Port Patch 2.12.9 -> 3.5.0 XB 1.10.9 - 2.5.0 by @juanfeSanahuja in #2579
• TASK-7130 - Move reset password WebService by @pfurio in #2566
• TASK-5925 - Execute aggregation-family without ArchiveTable for non-gVCF files by @j-coll in #2571
• TASK-7461 - Migrate opencb/docker-hub repositories to zettagenomics-docker-hub by @juanfeSanahuja in #2583
• TASK-7506 - Swagger Issues by @juanfeSanahuja in #2585
• TASK-7524 - Add new Variant output format: JSON_SPARSE by @j-coll in #2580
• TASK-7731 - Portpatch 3.2.3 -> 4.1.0-SNAPSHOT by @juanfeSanahuja in #2598
• Portpatch 3.2.3 -> 3.6.0-SNAPSHOT by @juanfeSanahuja in #2602
• TASK-7770 - pyopencga: clientConfiguration step failing from virtual desktop by @dapregi in #2606
• TASK-7532 - Portpatch 3.5.0 -> 4.1.0-SNAPSHOT by @juanfeSanahuja in #2600
• TASK-7578 - Fix liftover destination folder by @jtarraga in #2578
• TASK-7717 - Unable to delete a folder that was recently created by @pfurio in #2589
• TASK-7671 - OpenCGA Cohort Delete - Array of cohortIds in sample does not get updated after deleting a cohort by @pfurio in #2599
• TASK-7612 - Add missing endpoints to public python and R clients and generate enterprise versions by @juanfeSanahuja in #2582
• TASK-6219 - Automatic Variant Secondary Index by @j-coll in #2495
• TASK-7677 - Support SSO with R client by @pfurio in #2591
• TASK-7817 - Problem with client-builder.sh in Ubuntu 24.04 by @juanfeSanahuja in #2609
• TASK-7718 - Review and fix failed tests by @pfurio in #2610
• TASK-7763 - Swagger Issues II by @juanfeSanahuja in #2608
• TASK-7657 - Automatic Build and Push of ext-tools Docker Image by @juanfeSanahuja in #2590
• TASK-7479 - Variant walker fails when processing contigs with character ":" by @j-coll in #2594
• TASK-7477 - variant_walker.py may skip first variant by @j-coll in #2592
• TASK-5688 - Allow study administrators to synchronise groups from LDAP/Azure by @pfurio in #2521
• TASK-7735 - Duplicated headers on variant-walker output by @j-coll in #2596
• Portpatch 3.6.0 -> 4.1.0-SNAPSHOT by @juanfeSanahuja in #2614
• TASK-7367 - Adapt Biodata models to new COSMIC file version by @jtarraga in #2604
• TASK-7881 - Can't filter by "not equals" with an "AND" operator by @pfurio in #2615
• TASK-7562 - DB prefix for CVDB solr database is not correctly retrieven for cloned environments by @jtarraga in #2581
• TASK-7883 - Modify OpenCGA - CellBase dependency by @juanfeSanahuja in #2616
• TASK-7892 - SIGSEGV error when running CosmicVariantAnnotationExtension by @j-coll in #2617
• TASK-7316 - Memory killed jobs ends with DONE status by @j-coll in #2613

Full Changelog: v4.0.0...v4.1.0

v3.6.0

What's Changed

• TASK-7589 - Port Patch 2.12.9 -> 3.2.3 Xetabase 1.10.9 -> 2.2.3 by @juanfeSanahuja in #2574
• TASK-7685 - Login doesn't work with LDAP by @pfurio in #2584
• Portpatch 3.2.3 -> 3.6.0-SNAPSHOT by @juanfeSanahuja in #2602
• TASK-7770 - pyopencga: clientConfiguration step failing from virtual desktop by @dapregi in #2606
• TASK-7718 - Review and fix failed tests by @pfurio in #2610

Full Changelog: v3.5.0...v3.6.0

v3.5.0

What's Changed

• TASK-6998 - Fix cohort-sample reference migration by @pfurio in #2510
• TASK-6983 - NPE at DetectIllegalConcurrentFileLoadingsMigration by @j-coll in #2514
• TASK-4682 - Error in VariantExport VCF : Duplicate allele (pre-step to exomiser) by @j-coll in #2527
• TASK-7358 - Memory problem when unlinking some files by @pfurio in #2552
• TASK-7358 - Memory problem when unlinking some files by @pfurio in #2553
• TASK-6880 - CI/CD workflow to delete task docker images on merge fails by @juanfeSanahuja in #2550
• TASK-7330 - Hortonworks maven repositories are down by @j-coll in #2542
• TASK-7511 - Cannot sync more than just one group by @pfurio in #2565
• TASK-7486 - Reset password sent doesn't expire by @pfurio in #2561
• TASK-7605 - CatalogException: User 'opencga' could not be found. by @pfurio in #2575
• TASK-7594 - variant-index: broken "skip-normalization" parameter by @j-coll in #2576
• TASK-7508 - Fail to download files programmatically by @pfurio in #2573
• TASK-7604 - Variant annotation fails when changing default data release for a CellBase version by @j-coll in #2577
• TASK-7531 - Port Patch 2.12.9 -> 3.5.0 XB 1.10.9 - 2.5.0 by @juanfeSanahuja in #2579

Full Changelog: v3.4.0...v3.5.0

v3.2.3

What's Changed

• TASK-6998 - Fix cohort-sample reference migration by @pfurio in #2510
• TASK-6983 - NPE at DetectIllegalConcurrentFileLoadingsMigration by @j-coll in #2514
• TASK-4682 - Error in VariantExport VCF : Duplicate allele (pre-step to exomiser) by @j-coll in #2527
• TASK-7330 - Hortonworks maven repositories are down by @j-coll in #2542
• TASK-7589 - Port Patch 2.12.9 -> 3.2.3 Xetabase 1.10.9 -> 2.2.3 by @juanfeSanahuja in #2574
• TASK-7685 - Login doesn't work with LDAP by @pfurio in #2584

Full Changelog: v3.2.2...v3.2.3

v4.0.0

What's Changed

• TASK-6835 - Cellbase dependency error in opencga build by @juanfeSanahuja in #2502
• TASK-6879 - Adapt GitHub Actions, CICD workflows and release scripts to new SDLC by @juanfeSanahuja in #2506
• TASK-6458 - Deployment: Xetabase kubernetes 1.29 compatibility by @juanrizetta in #2501
• TASK-6780 - Port Patch 3.2.1 -> 4.0.0 - Xetabase 2.2.1 -> 3.0.0 by @juanfeSanahuja in #2513
• TASK-7097 - Port Patch 3.3.0 -> 4.0.0 Xetabase 2.3.0 -> 3.0.0 by @juanfeSanahuja in #2519
• TASK-7046 - Add a new field "type" to Notes data model by @pfurio in #2525
• TASK-5662 - Improve .bai and .bw files tracking by @pfurio in #2534
• TASK-7155: Upgrade MongoDB to v7.0 by @pfurio in #2524
• TASK-6446 - Implement quotas management by @pfurio in #2537
• TASK-6765 - Improve VCF Export performance from secondary sample index by @j-coll in #2503
• TASK-6757 - Deployment: Add Jupyter Notebooks feature by @juanfeSanahuja in #2544
• TASK-5914 Update Swagger for OpenCGA by @juanfeSanahuja in #2545
• TASK-7134 - Re-implement Aggregations Stats for all Catalog Browsers by @jtarraga in #2529
• TASK-7214 - Port patch 3.4.0 -> 4.0.0 by @juanfeSanahuja in #2546
• TASK-7192 - Enable Federation Support in XetaBase by @pfurio in #2541
• TASK-6369 - Update R client log-in to include organization parameter by @mbleda in #2543
• TASK-7102 Support SSO with OpenCGA CLI and Python client by @dapregi in #2547
• TASK-7433 - Wrong quotas default value in configuration.yml by @pfurio in #2554
• TASK-6442 - Add Resources Management functionality by @pfurio in #2535
• TASK-7417 - New github workflow to manually delete dockers from DockerHub by @juanfeSanahuja in #2549
• TASK-7429 - Swagger WS body empty and can't be edited by @juanfeSanahuja in #2555
• TASK-5610 - Create the CVDB endpoint analysis/clinical/cvdb/variant/summary and overwrite analysis/clinical/variant by @jtarraga in #2480
• TASK-7439 - Variant Browsers shows a VariantQueryException when running aggregation stats by @jtarraga in #2556
• TASK-6445 - Implement OpenCGA Workflows with NextFlow by @pfurio in #2530
• TASK-7049 - Liftover analysis by @jtarraga in #2548
• TASK-7451 - OpenCGA workflow docker tag is hardcoded by @pfurio in #2558
• TASK-7443 - Some endpoints are not correctly displayed with Swagger by @juanfeSanahuja in #2557
• TASK-7484 - Alignment index error by @jtarraga in #2559
• TASK-7482 - opencga junit tests failed by @pfurio in #2567
• TASK-7486 - Reset password sent doesn't expire by @pfurio in #2562
• TASK-7560 - Problem creating study from federated installation by @pfurio in #2569
• TASK-7481 - Sample Index Configuration completely empty on new studies by @j-coll in #2560

New Contributors

• @mbleda made their first contribution in #2543

Full Changelog: v3.4.0...v4.0.0

v2.12.9

What's Changed

• TASK-4682 - Error in VariantExport VCF : Duplicate allele (pre-step to exomiser) by @j-coll in #2527
• TASK-7330 - Hortonworks maven repositories are down by @j-coll in #2542

Full Changelog: v2.12.8...v2.12.9

v3.4.0

What's Changed

• TASK-6754 - Create cohort with more than 1000 samples lead to MongoDB restarts by @pfurio in #2517
• TASK-7118 - When migrating from XetaBase 1.x to 2.x users can't specify the Organization name by @pfurio in #2523
• TASK-7004 - Variable set creation/update not possible with study admin permission by @pfurio in #2520
• TASK-7207 - Fix Organization migration issue by @pfurio in #2531
• TASK-7187 - admin/users/sync web service doesn't work by @pfurio in #2528
• TASK-7213 - Port Patch 2.0.2 -> 2.4.0 by @juanfeSanahuja in #2533
• TASK-6722 - Variant Walker to enable user defined variant analysis by @j-coll in #2522
• TASK-7225 - Warning events messages still take up a large part of the screen in Variant Browser by @j-coll in #2536
• TASK-7301 - PR approve workflow also runs on PR comment by @juanfeSanahuja in #2538
• TASK-7320 - Compilation failure for hadoop compatibility issues by @j-coll in #2540

Full Changelog: v3.3.0...v3.4.0