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