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 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• TASK-6201 - Outdated variant stats of running operations are not returned by @j-coll in #2445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
• 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

v3.0.0

What's Changed

• TASK-5300-develop - Class not found org/apache/commons/io/FileUtils by @juanfeSanahuja in #2364
• TASK-5425 - PortPatch 1.10.1 -> 2.0.0 by @juanfeSanahuja in #2368
• TASK-4437 - Update general dependencies from dependabot (security alerts) by @juanfeSanahuja in #2373
• TASK-5444 - Fix OpenCB repository versions to conform to XetaBase 2.0.0 version by @juanfeSanahuja in #2383
• TASK-5475 - The version of Java (11.0.21) used to run our analysis is deprecated, and SonarCloud no longer supports it. by @juanfeSanahuja in #2384
• TASK-1294 - Remove deprecated VariableSet fields by @pfurio in #2376
• TASK-4158 by @jtarraga in #2379
• TASK-5609 - Can't merge into develop (v3.0.0) by @pfurio in #2391
• TASK-5622 Fix Junit test (assert fails) by @jtarraga in #2392
• TASK-4436 - Deployment Update Hadoop HDI and EMR versions. Clean older versions. by @j-coll in #2387
• TASK-4389 - OpenCGA Catalog - Organizations by @pfurio in #2375
• TASK-5663 - Failing tests on v3.0.0 by @j-coll in #2401
• TASK-5232 - Deployment: Update Solr version by @juanfeSanahuja in #2370
• TASK-5618 - Port Patch 1.10.2 -> 2.0.0 by @juanfeSanahuja in #2408

Full Changelog: v2.12.2...v3.0.0

v2.12.3

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

Full Changelog: v2.12.2...v2.12.3

v2.12.2

What's Changed

• TASK-5349 - Add new clinical report web service to update the report information by @pfurio in #2369
• TASK-5450 Update signature.tools.lib package to fix HRDetect analysis by @jtarraga in #2371
• TASK-5404 - There are two implementations of SLF4J and log lines appear at the beginning of the result of each CLI command by @juanfeSanahuja in #2372
• TASK-5475 - The version of Java (11.0.21) used to run our analysis is deprecated, and SonarCloud no longer supports it. by @juanfeSanahuja in #2385
• TASK-5482 - Opencga-enterprise CLI could not be generated by @juanfeSanahuja in #2377
• TASK-5501 Modify resources README file by @jtarraga in #2378
• TASK-5452 - "Wrong number of arguments" launching MR operation by @j-coll in #2374
• TASK-5511 - opencga.sh CLI option --json-data-model produces malformed JSON by @juanfeSanahuja in #2386
• TASK-5580 - The model webservice client must have an input parameter by @juanfeSanahuja in #2388

Full Changelog: v2.12.1...v2.12.2

v2.12.1

What's Changed

• TASK-2254 - Error processing job output - malformed VCF and disk quota exceeded by @pfurio in #2352
• TASK-5166 - The CLI upload service does not display error messages. by @juanfeSanahuja in #2355
• TASK-5279 - Port Patch 1.6.6 -> 1.10.1 by @juanfeSanahuja in #2360
• TASK-5160 - CLI fails if involves a call to meta/model by @juanfeSanahuja in #2357
• TASK-5300-release-2.12.x - Class not found org/apache/commons/io/FileUtils by @juanfeSanahuja in #2363
• TASK-5198 - Catalog changes to improve Clinical reports by @pfurio in #2365
• TASK-5190 Fix Exomiser parameter "analysisMode" by @jtarraga in #2361
• TASK-5113 SVs not being displayed in genome plot (circos) by @jtarraga in #2362
• TASK-5006 - Exomiser fails in the opencga by @juanrizetta in #2359
• TASK-5373 - Error compiling opencga-enterprise - ClinicalAnalyst changes by @pfurio in #2366
• TASK-5394 - NoClassDefFoundError: org/apache/logging/log4j/spi/AbstractLoggerAdapter by @j-coll in #2367

Full Changelog: v2.12.0...v2.12.1

v2.12.0

What's Changed

• TASK-4913 - Unable to update cellbase-token by @j-coll in #2329
• TASK-4688 - Avoid git.properties collision by @j-coll in #2335
• TASK-5027 - NullPointerException executing JUnit tests SampleIndexOnlyVariantQueryExecutor by @j-coll in #2340
• TASK-4938 - OpenCGA VariantExport tests sometimes throw a ConcurrentModificationException by @j-coll in #2338
• TASK-4945 - OpenCGA Status not being updated by @j-coll in #2339
• TASK-4853 - OutOfMemoryError running CatalogStorageMetadataSynchronizer by @j-coll in #2324
• TASK-4843 - CLI Fails uploading file by @juanfeSanahuja in #2323
• TASK-4210 - Catalog delete operations may not check if data is used in Clinical Analyses by @pfurio in #2343
• TASK-5038 Update signature.tools.lib package to fix fitting and HRDetect analysis by @jtarraga in #2346
• TASK-4684 - AggregateFamily overwrites multiallelic information by @j-coll in #2321
• TASK-5083 - Sample - Case junit test not working by @pfurio in #2347
• TASK-4872 - NullPointerException at variant-secondary-sample-index by @j-coll in #2342
• TASK-4873 - Unable to update CellBase version by @j-coll in #2344
• TASK-4770 Error running migration calculate_pedigree_graph by @jtarraga in #2314
• TASK-4889 - Broken custom commands in CLI by @j-coll in #2348
• TASK-5092 - The CICD to delete docker on merge fails by @juanfeSanahuja in #2349
• TASK-4899 - Abnormally slow variant-index postLoad for files with thousands of samples by @j-coll in #2345
• TASK-5092 - The CICD to delete docker on merge fails by @juanfeSanahuja in #2351
• TASK-5120 - Port Patch 1.6.5 - > 1.10.0 by @juanfeSanahuja in #2353
• TASK-5055 - ERROR CLI Opencga-enterprise by @juanfeSanahuja in #2354
• TASK-2095 - Duplicated libraries at opencga/build/libs by @juanfeSanahuja in #2341

Full Changelog: v2.11.0...v2.12.0

v2.8.5

What's Changed

• TASK-2254 - Error processing job output - malformed VCF and disk quota exceeded by @pfurio in #2352
• TASK-5166 - The CLI upload service does not display error messages. by @juanfeSanahuja in #2355

Full Changelog: v2.8.4...v2.8.5

v2.8.4

What's Changed

• TASK-4913 - Unable to update cellbase-token by @j-coll in #2329
• TASK-4688 - Avoid git.properties collision by @j-coll in #2335
• TASK-5027 - NullPointerException executing JUnit tests SampleIndexOnlyVariantQueryExecutor by @j-coll in #2340
• TASK-4938 - OpenCGA VariantExport tests sometimes throw a ConcurrentModificationException by @j-coll in #2338
• TASK-4945 - OpenCGA Status not being updated by @j-coll in #2339
• TASK-4853 - OutOfMemoryError running CatalogStorageMetadataSynchronizer by @j-coll in #2324
• TASK-4843 - CLI Fails uploading file by @juanfeSanahuja in #2323
• TASK-4210 - Catalog delete operations may not check if data is used in Clinical Analyses by @pfurio in #2343
• TASK-5038 Update signature.tools.lib package to fix fitting and HRDetect analysis by @jtarraga in #2346
• TASK-4684 - AggregateFamily overwrites multiallelic information by @j-coll in #2321
• TASK-5083 - Sample - Case junit test not working by @pfurio in #2347
• TASK-4872 - NullPointerException at variant-secondary-sample-index by @j-coll in #2342
• TASK-4873 - Unable to update CellBase version by @j-coll in #2344
• TASK-4770 Error running migration calculate_pedigree_graph by @jtarraga in #2314
• TASK-4889 - Broken custom commands in CLI by @j-coll in #2348
• TASK-5092 - The CICD to delete docker on merge fails by @juanfeSanahuja in #2349
• TASK-4899 - Abnormally slow variant-index postLoad for files with thousands of samples by @j-coll in #2345
• TASK-5092 - The CICD to delete docker on merge fails by @juanfeSanahuja in #2351

Full Changelog: v2.8.3...v2.8.4