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

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 2.8.5 -> 2.12.0 (XB 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

v2.11.0

What's Changed

• TASK-4802 - Port Patch 2.8.2.1 -> 2.8.3 (XB 1.6.3.1 -> XB 1.6.4) by @juanfeSanahuja in #2315
• TASK-4712 - Include not working in project search by @pfurio in #2312
• TASK-4445 - Opencga long test fails by @j-coll in #2293
• TASK-4794 - Missing "FILTER" field in VCF generated (export step) while running Exomiser by @j-coll in #2318
• TASK-4816 - Error fetching original call for INDELs export step from exomiser from complex contigs by @j-coll in #2317
• TASK-4851 - Some Catalog tests are failing - Project include issue by @pfurio in #2322
• TASK-4810 - Port Patch 2.9.2 -> 2.11.0 (XB 1.7.2 -> 1.9.0) by @juanfeSanahuja in #2320
• TASK-4848 - Modifications related to pharmacogenomics causes test failures by @j-coll in #2326
• TASK-4917 - Error generating opencga clients by @pfurio in #2332
• TASK-4913 - Unable to update cellbase-token by @j-coll in #2331
• TASK-4248 - improve usage documentation of REST search endpoint by adding regexp comment by @pfurio in #2327
• TASK-4875 - Port Patch 2.8.4 -> 2.11.0 (XB 1.6.4 -> 1.9.0) by @juanfeSanahuja in #2334
• TASK-4641- Update according to CellBase changes and remove and use VersionUtils from java-common-libs by @jtarraga in #2328
• TASK-4372 - Hadoop ExportSnapshot by @j-coll in #2333
• TASK-4688 - Avoid git.properties collision by @j-coll in #2336

Full Changelog: v2.10.0...v2.11.0

v2.8.3

What's Changed

• TASK-4802 - Port Patch 2.8.2.1 -> 2.8.3 (XB 1.6.3.1 -> XB 1.6.4) by @juanfeSanahuja in #2315
• TASK-4712 - Include not working in project search by @pfurio in #2312
• TASK-4445 - Opencga long test fails by @j-coll in #2293
• TASK-4794 - Missing "FILTER" field in VCF generated (export step) while running Exomiser by @j-coll in #2318
• TASK-4816 - Error fetching original call for INDELs export step from exomiser from complex contigs by @j-coll in #2317
• TASK-4851 - Some Catalog tests are failing - Project include issue by @pfurio in #2322

Full Changelog: v2.8.2.1...v2.8.3

v2.9.2

Full Changelog: v2.9.1...v2.9.2

v2.10.0

What's Changed

• TASK-4289 - Upgrade JVM to 8u372 in opencga Docker by @imedina in #2296
• TASK-4464 - CI/CD - Migrate some test functionality from OpenCB to Xetabase and centralize the regression testing and reporting on it by @juanfeSanahuja in #2304
• TASK-4428 - Ability to handle Ext-Tools for OpenCGA by @imedina in #2303
• TASK-4593 HRDetect analysis not working with the current R library by @jtarraga in #2308
• TASK-4144 Fix structural variation (SV) catalogue counting in signature analysis by @jtarraga in #2310
• TASK-4686 Fix the analysis of pedigree graphs when running with multiple disorders that have ids/names containing multiple words by @jtarraga in #2309
• TASK-4146 - Filtering by gene/region not working for CNVs in sample variant browser by @j-coll in #2307
• TASK-4642 - Incorrect results when running Exomiser on INDELs and Multiallelic by @j-coll in #2306
• TASK-4736 - Error executing junit "VariantHadoopDBWriterTest.loadVariantsBasic" by @j-coll in #2311
• TASK-4667 - Port Patch 1.6.3.1 -> 1.8.0 by @juanfeSanahuja in #2313

Full Changelog: v2.9.1...v2.10.0