v2.4.3

What's Changed

• TASK-1593 - Variant-export-run : opencga-internal unknown parameter '--compress' by @j-coll in #2071
• TASK-1587 - The parameters of the body give an error by @juanfeSanahuja in #2068
• TASK-1519 - Variant Export in different output formats fails by @j-coll in #2072
• TASK-1120 - Errors in model MetaWS when class not found by @imedina in #2077
• TASK-1189 - Logout on expired session by @juanfeSanahuja in #2074
• TASK-1431 - CLi: error when using --host param by @juanfeSanahuja in #2075
• TASK-1487 - CLI: "Server Not Found" hidden by "Incorrect user or password" by @juanfeSanahuja in #2076
• TASK-563 - CLI: WS under the admin section are not in opencga.sh nor opencga-admin.sh by @juanfeSanahuja in #2067
• TASK-1280 - Port Patch Version 1.1.3 by @j-coll in #2082
• TASK-1254 - Cannot run program "hadoop-ssh.sh" Permission denied by @j-coll in #2065
• TASK-1194 - Add new fields to Catalog data model by @pfurio in #2079
• TASK-1386 - Shorten catalog indexed field variables by @pfurio in #2080
• TASK-1285 - Fix acl behaviour by @pfurio in #2083
• TASK-1664 - Error during migration of TASK-1470 by @pfurio in #2078
• TASK-1706 - NPE in variant export while avro serialization by @j-coll in #2085
• TASK-1708 - Variant export TPED fails if no output file name is provided by @j-coll in #2086
• TASK-1711 - Variant Export PARQUET wrong generated file by @j-coll in #2087
• TASK-1274 - VariantQueryException: Cannot Export VCF - Missing gene regions by @j-coll in #2088
• TASK-1713 - Variant Export using MR when should be using iterator on small queries by @j-coll in #2089
• TASK-1715 - Missing PopulationFrequency filters at VariantFilterBuilder by @j-coll in #2090
• TASK-1732 - Variant Export skips MapReduce for long queries using sample index by @j-coll in #2095
• TASK-1726 - Job aborted without enough error details by @j-coll in #2093
• TASK-1734 - Variant export MapReduce is filling the worker node disk by @j-coll in #2092
• TASK-1735 - Variant export : Sample 'mySample:1/1' not found by @j-coll in #2094
• TASK-1746 - Variant query/export from sample index with covered queries does not need variants table intersection by @j-coll in #2096
• TASK-1722 - Fix internal interpreter CLI name by @imedina in #2091
• TASK-1752 - Filter by chromosome-Linked segregation doesn't filter by chromosome by @j-coll in #2100
• TASK-1751 - Error during migration of TASK-1664 by @pfurio in #2098
• TASK-1756 - Variant export ClassCastException: java.lang.Double cannot be cast to java.lang.Float by @j-coll in #2102
• TASK-1537 - Fix the Exomiser wrapper analysis: it fails when multiple studies exist by @jtarraga in #2101
• TASK-1750 - Fix RGA performance issues by @pfurio in #2097
• TASK-1751 - Error during migration of TASK-1664 by @pfurio in #2103
• TASK-1481 - Fix the alignment command: coverage-index-run by @jtarraga in #2104
• TASK-1576 - Fix the inferred sex analysis: the karyotypic sex inferred is missing by @jtarraga in #2105
• TASK-1760 - Fix exomiser interpretation analysis by @jtarraga in #2106
• TASK-1497 - Fix the variant command: relatedness-run by @jtarraga in #2107
• TASK-1763 - Filter by chromosome-linked segregation at "sample" param. Defect of TASK-1752 by @j-coll in #2108

Full Changelog: v2.4.2...v2.4.3

v2.4.2

What's Changed

• TASK-1082 - CLI: Remove Collection parameters except primitive and string type lists by @juanfeSanahuja in #2066
• TASK-1472 - Review variant discussions don't show who and when were written by @pfurio in #2070
• TASK-1470 - Error in IVA Case explorer when searching by sample id by @pfurio in #2069
• TASK-1387 - Undesired behaviour in link-run operation by @pfurio in #2073

Full Changelog: v2.4.1...v2.4.2

v2.3.3

What's Changed

• TASK-1593 - Variant-export-run : opencga-internal unknown parameter '--compress' by @j-coll in #2071
• TASK-1587 - The parameters of the body give an error by @juanfeSanahuja in #2068
• TASK-1519 - Variant Export in different output formats fails by @j-coll in #2072

Full Changelog: v2.3.2...v2.3.3

v2.2.5

What's Changed

• TASK-1593 by @j-coll in #2071
• TASK-1587 by @juanfeSanahuja in #2068
• TASK-1519 by @j-coll in #2072

Full Changelog: v2.2.4...v2.2.5

v2.4.1

What's Changed

• TASK-1253 - ClassNotFound executing MapReduce by @j-coll in #2024
• TASK-1260 - hadoop-scp.sh: 43: Syntax error: "(" unexpected by @j-coll in #2025
• TASK-1279 - Port Patch Version 1.1.2 by @j-coll in #2032
• TASK-1280 - Port Patch Version 1.1.3 by @j-coll in #2033
• TASK-1341 - Cannot create clinical case with large number of files by @pfurio in #2040
• TASK-1385 - Fix the internal command line parser to run the Exomiser analysis by @juanfeSanahuja in #2047
• TASK-1303 - NPE: Missing authentication section by @pfurio in #2034
• TASK-694 - Mongo server address not showing in logs by @pfurio in #2022
• TASK-1270 - Autogenerated CLI updates send wrong data to server by @juanfeSanahuja in #2041
• TASK-1250 - NullPointerException querying for gene with unreachable cellbase by @j-coll in #2038
• TASK-1158 - Errors in model WS meta/api by @juanfeSanahuja in #2023
• TASK-1456 - RGA Knockout - Solr Timeout indexing result by @j-coll in #2054
• TASK-845 - job browser in opencga-test for demouser study platinum produce NullPointExeption errors (works well with other users) by @pfurio in #2021
• TASK-1297 - Missing mandatory parameter url by @pfurio in #2036
• TASK-1292 - Missing mandatory parameter url??? by @pfurio in #2037
• TASK-1282 - OpenCGA Catalog search complaining about permissions by @pfurio in #2052
• TASK-1344 - Empty smtp server configuration by @juanfeSanahuja in #2049
• TASK-1291 - Could not create file by @pfurio in #2051
• TASK-1284 - --permissions parameter is mandatory by @pfurio in #2035
• TASK-1197 - ERROR updating multiple samples through the CLI by @pfurio in #2026
• TASK-894 - RGA Knockout - Exception obtaining CompoundHeterozygous knockout variants by @j-coll in #2059
• TASK-1495 - RGA Knockout - Unable to regenerate the aux collection by @j-coll in #2061
• TASK-1459 - Fix the procedure to download the Exomiser data once by @jtarraga in #2055
• TASK-1370 - Fix clinical/variant/query by filling in the interpretation fields by @jtarraga in #2053
• TASK-923 - RGA solr hosts not configured in k8s by @juanrizetta in #2058
• TASK-1092 - Support sample name mapping when indexing variants by @j-coll in #2048

Full Changelog: v2.4.0...v2.4.1

v2.3.2

What's Changed

• TASK-1208 - "IllegalArgumentException: Unsupported object type: java.lang.String" at VariantBrowser by @j-coll in #2018
• TASK-1341 - Cannot create clinical case with large number of files by @pfurio in #2040
• TASK-1270 - Autogenerated CLI updates send wrong data to server by @juanfeSanahuja in #2041
• TASK-1250 - NullPointerException querying for gene with unreachable cellbase by @j-coll in #2038
• TASK-1456 - RGA Knockout - Solr Timeout indexing result by @j-coll in #2054
• TASK-894 - RGA Knockout - Exception obtaining CompoundHeterozygous knockout variants by @j-coll in #2059
• TASK-1495 - RGA Knockout - Unable to regenerate the aux collection by @j-coll in #2061

Full Changelog: v2.3.1...v2.3.2

v2.2.4

What's Changed

• TASK-1341 by @pfurio in #2040
• TASK-1270 by @juanfeSanahuja in #2041
• TASK-1250 by @j-coll in #2038
• TASK-1456 by @j-coll in #2054
• TASK-894 by @j-coll in #2059
• TASK-1495 by @j-coll in #2061

Full Changelog: v2.2.3...v2.2.4

v2.2.3

What's Changed

• TASK-1070 by @j-coll in #2016

Full Changelog: v2.2.2...v2.2.3

v2.4.0

What's Changed

• TASK-814 - Upgrade JWT library dependency by @pfurio in #1989
• TASK-814 - Upgrade JWT library dependency by @pfurio in #1990
• TASK-803 - Add due-date filter to Clinical Analysis Browser and Case Portal by @pfurio in #1992
• TASK-473 - Missing filter for source in disease panel browser by @pfurio in #1993
• TASK-804 - LDAP connection hangs - for develop by @j-coll in #1986
• TASK-803 - Add due-date filter to Clinical Analysis Browser and Case Portal by @pfurio in #1995
• TASK-1036 - OpenCGA Storage Hadoop EMR6.1 doesn't compile with mvn 3.8.5 by @j-coll in #2001
• TASK-926 - Add pyopencga and R package generation to CI/CD pipeline by @juanfeSanahuja in #1999
• TASK-607 - Automatically close cases by @pfurio in #2000
• TASK-944 - Create a new Meta web service by @juanfeSanahuja in #1997
• TASK-868 - Test Data Generator improvements by @juanfeSanahuja in #2003
• TASK-452 - opencga CLI: service meta only has the endpoint API by @juanfeSanahuja in #2007
• TASK-551 - Migrate Hadoop tests to version HDP 3.1 by @j-coll in #2006
• TASK-831 - Update "Pathogenic/Reported Variant Database" (aka CVA) index by @jtarraga in #2002
• TASK-1208 - "IllegalArgumentException: Unsupported object type: java.lang.String" at VariantBrowser by @j-coll in #2018
• TASK-1221 - Corpasome template version is not synchronized with OpenCGA version by @j-coll in #2019
• TASK-830 - Add Exomiser as an automatic interpreter by @imedina in #2020

Full Changelog: v2.3.1...v2.4.0

v2.3.1

What's Changed

• TASK-804 - LDAP connection hangs by @pfurio in #1978
• TASK-869 - OpenCGA in K8S fails to startup by @j-coll in #1982
• TASK-889 - OpenCGA returns a NullPointerException when trying to update a variant by @pfurio in #1984
• TASK-885 - Fix AutoIncrementVersion migration by @pfurio in #1981
• TASK-804 for release-2.3.x by @j-coll in #1985
• TASK-935 - pyopencga limit and name fix by @dapregi in #1991
• TASK-889 - OpenCGA returns a NullPointerException when trying to update a variant by @pfurio in #1987
• TASK-885 - Fix AutoIncrementVersion migration by @pfurio in #1988
• TASK-947 - Transcript flags are missed in Variants from projects using CB4.x by @j-coll in #1994
• TASK-960 - Annotation with CB4 using CB5 client ignores the transcript flags by @j-coll in #1996
• TASK-1052 - opencga install/setup fails on new database environment by @pfurio in #2004
• TASK-966 - SVB: Query by large panel+lof+missense timeouts after 3 minutes by @j-coll in #1998
• TASK-789 - 1KGenomes Allele Frequenciess are discordant between Variant Browser ("1000G") and Case Portal's Sample Variant Browser ("1kG_phase3") by @j-coll in #2005
• TASK-1084 - Port Patch Version 1.0.2 by @imedina in #2011
• TASK-1100 - Project configured cellbase being ignored in VariantStorageManager by @pfurio in #2012
• TASK-1147 - Family roles not set properly by @pfurio in #2015
• TASK-1070 - Implement variant prune operation by @j-coll in #2016
• TASK-1185 - IndexOutOfBoundsException when indexing second variant file from a sample by @j-coll in #2017

Full Changelog: v2.3.0...v2.3.1