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

v2.2.2

What's Changed

• fixed url for pyopencga by @pamag in #1821
• client: improve catalog notebook #1716 by @lauralopezreal in #1808
• Fix token auto-refreshing by @dapregi in #1830
• Python Notebook Improvements by @lauralopezreal in #1836
• Fix wait_for_job status functionality by @dapregi in #1911
• TASK-512 by @j-coll in #1914
• TASK-512 by @j-coll in #1915
• TASK-516 by @j-coll in #1916
• TASK-515 by @j-coll in #1917
• TASK-529 by @j-coll in #1918
• TASK-532 by @j-coll in #1919
• #TASK-531 by @pfurio in #1921
• TASK-530 by @pfurio in #1920
• TASK-530 by @pfurio in #1922
• TASK-537 by @pfurio in #1923
• TASK-453 by @j-coll in #1924
• TASK-536 by @j-coll in #1925
• TASK-557 by @j-coll in #1926
• TASK-561 by @j-coll in #1927
• TASK-529 by @j-coll in #1928
• TASK-565 by @pfurio in #1929
• TASK-569 by @jtarraga in #1931
• TASK-602 by @pfurio in #1934
• TASK-564 by @pfurio in #1933
• TASK-613 by @j-coll in #1936
• TASK-618 by @j-coll in #1937
• TASK-620 by @j-coll in #1938
• TASK-625 by @pfurio in #1939
• TASK-632 by @j-coll in #1940
• TASK-566 by @j-coll in #1945
• TASK-632 by @j-coll in #1946
• TASK-621 by @j-coll in #1947
• TASK-649 by @j-coll in #1949
• TASK-671 by @j-coll in #1956
• TASK-686 by @j-coll in #1957
• TASK-691 by @pfurio in #1958
• TASK-702 by @pfurio in #1960
• TASK-618 by @j-coll in #1963
• TASK-708 by @j-coll in #1964
• TASK-709 by @pfurio in #1965
• TASK-710 by @pfurio in #1966
• TASK-804 by @pfurio in #1978
• TASK-947 by @j-coll in #1994
• TASK-960 by @j-coll in #1996

Full Changelog: v2.1.2...v2.2.2

v2.3.0

What's Changed

• Fix wait_for_job functionality by @dapregi in #1905
• TASK-508 - Update OpenCGA dependencies by @imedina in #1912
• TASK-552 - Add new field 'locked' to the interpretation data model by @pfurio in #1932
• TASK-425 - Allow cases to lock panels if interpretation contain at least one case panel by @pfurio in #1935
• TASK-668 - Upgrade Jersey lib to fix Java 11 compatibility issue by @imedina in #1952
• TASK-669 - Make OpenCGA Docker Compose version configurable by @imedina in #1953
• TASK-359 - Rename deleted collections by @pfurio in #1962
• TASK-550 - Create a default SampleIndexConfiguration when study is created by @pfurio in #1961
• TASK-354 - Configure CellBase host when creating a new project by @juanfeSanahuja in #1955
• TASK-630 - Fully private HDInsight deployments by @j-coll in #1968
• TASK-734 - Missing internal field in DiseasePanel data model by @pfurio in #1969
• TASK-665 - OpenCGA cli shell: list studdies need to have "\n" or ", " between studies by @juanfeSanahuja in #1954
• TASK-504 - Code maintaince by @j-coll in #1971
• TASK-323 - Autoincrement version by @pfurio in #1970
• TASK-428 - Rename OpenCGA Variant Storage Secondary Index names by @juanfeSanahuja in #1967
• TASK-807 - JWT secret key issue by @pfurio in #1972
• TASK-815 - Logger Appender TXT file not being used on log4j2.xml by @j-coll in #1975
• TASK-697 - Panel import timeout by @pfurio in #1973
• TASK-707 - Fix JUnit tests by @pfurio in #1974
• TASK-781 - Allow clinical users to define a default filter in the study configuration by @pfurio in #1977
• TASK-451 - Random "hconnection-0xHHHHHH closed" using Apache Phoenix by @j-coll in #1976
• TASK-521 - OpenCGA Command Line improvements by @j-coll in #1948

Full Changelog: v2.2.1...v2.3.0

v2.2.1

What's Changed

• Fix wait_for_job status functionality by @dapregi in #1911
• TASK-512 by @j-coll in #1914
• TASK-512 by @j-coll in #1915
• TASK-516 by @j-coll in #1916
• TASK-515 by @j-coll in #1917
• TASK-529 by @j-coll in #1918
• TASK-532 by @j-coll in #1919
• #TASK-531 by @pfurio in #1921
• TASK-530 by @pfurio in #1920
• TASK-530 by @pfurio in #1922
• TASK-537 by @pfurio in #1923
• TASK-453 by @j-coll in #1924
• TASK-536 by @j-coll in #1925
• TASK-557 by @j-coll in #1926
• TASK-561 by @j-coll in #1927
• TASK-529 by @j-coll in #1928
• TASK-565 by @pfurio in #1929
• TASK-569 by @jtarraga in #1931
• TASK-602 by @pfurio in #1934
• TASK-564 by @pfurio in #1933
• TASK-613 by @j-coll in #1936
• TASK-618 by @j-coll in #1937
• TASK-620 by @j-coll in #1938
• TASK-625 by @pfurio in #1939
• TASK-632 by @j-coll in #1940
• TASK-566 by @j-coll in #1945
• TASK-632 by @j-coll in #1946
• TASK-621 by @j-coll in #1947
• TASK-649 by @j-coll in #1949
• TASK-671 by @j-coll in #1956
• TASK-686 by @j-coll in #1957
• TASK-691 by @pfurio in #1958
• TASK-702 by @pfurio in #1960
• TASK-618 by @j-coll in #1963
• TASK-708 by @j-coll in #1964
• TASK-709 by @pfurio in #1965
• TASK-710 by @pfurio in #1966

New Contributors

• @jtarraga made their first contribution in #1931

Full Changelog: v2.2.0...v2.2.1