v2.7.0

What's Changed

• TASK-2551 - Remove /user/create webservice by @pfurio in #2232
• TASK-612 - OpenCGA files/link raises a NullPointExeption if it has no read access to the file by @pfurio in #2241
• TASK-2549 - Role and modeOfInheritance changes in Panel data model by @pfurio in #2238
• TASK-2270 - Review and update JUnit Tests by @j-coll in #2251

Full Changelog: v2.6.1.1...v2.7.0

v2.6.1.1

What's Changed

• TASK-3908 - Unable to search for shared projects by @j-coll in #2248

Full Changelog: v2.6.1...v2.6.1.1

v2.4.13.1

What's Changed

• TASK-3908 - Unable to search for shared projects by @j-coll in #2248

Full Changelog: v2.4.13...v2.4.13.1

v2.6.1

What's Changed

• TASK-2259 - Disk quota exceeded by @jtarraga in #2220
• TASK-2539 - Sample and Individual not properly associated by @pfurio in #2223
• TASK-3813 - Fix gene coverage stats analysis when using CellBase data release by @jtarraga in #2234
• TASK-1973 - Project limit not working by @pfurio in #2194
• TASK-1574 - Unexpected "Killed" job at Kubernetes by @j-coll in #2243
• TASK-2530 - Error working with files with URL codes (e.g. %A3) in their name by @j-coll in #2244
• TASK-1304 - Sample.internal sampleGenotypeIndex and annotationIndex fields not updated in catalog after annotation and sample genotype index run by @j-coll in #2233
• TASK-3836 - Fix CellBase data release usage by @jtarraga in #2242
• TASK-3874 - Releases are not naming the opencga-ext-tools properly by @juanfeSanahuja in #2245
• TASK-3864 - Exomiser not finding samples when Individual and sample IDs are not the same by @jtarraga in #2246
• TASK-2531 - Virtual File by @j-coll in #2229
• TASK-1682 - Role in cancer filter not filtering properly by @j-coll in #2173
• TASK-2012 - python rest client: inconsistent parameter strings by @dapregi in #2153
• TASK-3893 - Clinical variant query failed in test environment with current 2.4.13 snapshot by @pfurio in #2247
• TASK-3837 - Remove opencga-storage-mongodb dependencies by @j-coll in #2240

Full Changelog: v2.6.0.1...v2.6.1

v2.4.13

What's Changed

• TASK-2259 - Disk quota exceeded by @jtarraga in #2220
• TASK-2539 - Sample and Individual not properly associated by @pfurio in #2223
• TASK-1973 - Project limit not working by @pfurio in #2194
• TASK-1574 - Unexpected "Killed" job at Kubernetes by @j-coll in #2243
• TASK-2530 - Error working with files with URL codes (e.g. %A3) in their name by @j-coll in #2244
• TASK-1304 - Sample.internal sampleGenotypeIndex and annotationIndex fields not updated in catalog after annotation and sample genotype index run by @j-coll in #2233
• TASK-3874 - Releases are not naming the opencga-ext-tools properly by @juanfeSanahuja in #2245
• TASK-3864 - Exomiser not finding samples when Individual and sample IDs are not the same by @jtarraga in #2246
• TASK-2531 - Virtual File by @j-coll in #2229
• TASK-1682 - Role in cancer filter not filtering properly by @j-coll in #2173
• TASK-2012 - python rest client: inconsistent parameter strings by @dapregi in #2153
• TASK-3893 - Clinical variant query failed in test environment with current 2.4.13 snapshot by @pfurio in #2247

Full Changelog: v2.4.12...v2.4.13

v2.6.0.1

What's Changed

• TASK-3822 - Case report cannot be accessed after opencga update by @pfurio in #2235
• TASK-3796 - Migration 'add_cellbase_data_release' failed with message: Error executing operation configureCellbase by @j-coll in #2237

Full Changelog: v2.6.0...v2.6.0.1

v2.6.0

What's Changed

• TASK-2297 - Upgrade MongoDB version to 5.0.14 by @pfurio in #2222
• TASK-2242 - Improve mutational signature analysis by @jtarraga in #2216
• TASK-1201 - Use dataRelease from Cellbase in OpenCGA by @j-coll in #2226
• TASK-2390 - Improvements in multi-repository development by @juanfeSanahuja in #2225
• TASK-2274 - HRDetect analysis for mutational signatures by @jtarraga in #2217
• TASK-2303 - Remove hybrid selection (HS) metrics from alignment QC analysis by @jtarraga in #2227
• TASK-1290 - Improve file upload parameters by @juanfeSanahuja in #2221
• TASK-2438 - Add variant query param "geneRoleInCancer" by @j-coll in #2228
• TASK-2294 - Include homalt count from aggregated vcf files by @j-coll in #2215

Full Changelog: v2.4.12...v2.6.0

v2.4.12

What's Changed

• TASK-2437 - Operation jobs jam on duplicated operations by @j-coll in #2206
• TASK-2484 - Error fetching jobs to reuse with multiple studies with the same id by @j-coll in #2213
• TASK-2421 - Operation 'variant-stats-index' ignores the AggregationMappingFile by @j-coll in #2202
• TASK-2387 - Fix interpretation save by @jtarraga in #2198
• TASK-2364 - RegionTooBusyException - StoreTooBusy - Above parallelPutToStoreThreadLimit(10) by @j-coll in #2203
• TASK-2014 - Panel intersection between panel and single position regions (chr:pos) not working by @j-coll in #2218
• TASK-2342 - Error at variant-index "SQLException: ERROR 201 (22000): Illegal data" by @j-coll in #2195
• TASK-1323 - NPE at operations variant-configure by @juanfeSanahuja in #2212
• TASK-2204 - Variant query issue when using includeInterpretation by @jtarraga in #2188
• TASK-2418 - Interpretation create forces to contain all panels by @pfurio in #2205
• TASK-2496 - Error running variant-index : ClassCastException: java.net.URI cannot be cast to java.lang.String by @j-coll in #2214
• TASK-2316 - Fix sample file when executing Exomiser with families by @jtarraga in #2191
• TASK-2357 - Cohort Browser error when trying to filter by more than one cohort type by @pfurio in #2199
• TASK-2347 - Distinct should not return null values by @pfurio in #2192
• TASK-2300 - Unable to filter by gene using HGNC ID by @j-coll in #2204
• TASK-2511 - Error in upload file by @juanfeSanahuja in #2219

Full Changelog: v2.4.11...v2.4.12

v2.4.10.1

What's Changed

• TASK-2437 - Operation jobs jam on duplicated operations by @j-coll in #2206

Full Changelog: v2.4.10...v2.4.10.1

v2.4.11

What's Changed

• TASK-2167 - Fix multi-sample (family) Exomiser analysis by @jtarraga in #2176
• TASK-2263 - Unable to variant-prune after variant-study-delete by @j-coll in #2185
• TASK-2285 - Error running variant-prune - "cohort ALL not found in variant" by @j-coll in #2186
• TASK-2337 - Interpretation locking inconsistency issue: a locked secondary interpretation can not be promoted to primary, but a locked primary can be demoted to secondary by @pfurio in #2193
• TASK-2276 - TPED exports more samples than expected when using PhoenixVariantTableInputFormat by @j-coll in #2196
• TASK-2381 - Multiple HBase connections opened at MapReduce by @j-coll in #2197
• TASK-1087 - Job variant-family indexing - OutOfMemoryError, although job status listed as DONE by @j-coll in #2181
• TASK-2290 - Fix disorder filter split by @pfurio in #2189
• TASK-2227 - VariantExportParams includeGenotype and includeSampleId should be boolean instead of String by @j-coll in #2180
• TASK-2420 - Sample-variant-stats error 'Unable to index with indexId='ALL' if query is not empty' by @j-coll in #2201

Full Changelog: v2.4.10...v2.4.11