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

v3.0.0

What's Changed

• TASK-5300-develop - Class not found org/apache/commons/io/FileUtils by @juanfeSanahuja in #2364
• TASK-5425 - Port Patch 2.12.1 -> 3.0.0 (XB 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 - Add functionality for indexing, querying and aggregating to the CVDB Engine 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 2.12.2 -> 3.0.0 (XB 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 2.8.5 -> 2.12.1 (XB 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