v3.6.1

What's Changed

• TASK-8019 - Remove vulnerable/protestware dependency to improve security by @jmjuanes in #1051

Full Changelog: v3.6.0...v3.6.1

v4.1.0

What's Changed

• TASK-7034 - Unable to display custom indexed fields in Variant Caller Sample Filter by @jmjuanes in #989
• TASK-7205 - Variant Browser infinite loop when using Cellbase v4 by @jmjuanes in #1005
• TASK-7272 - Cohorts column of Variant Browser includes cohorts without calculated stats by @jmjuanes in #1007
• TASK-6933 - IVA Configuration Admin - Unable to select multiple studies by @gpveronica in #1003
• TASK-7325 - IVA Study Admin is setting permissions to NONE when adding a new user to a study by @jmjuanes in #1015
• TASK-7323 - Data is not displayed unless the user switches tabs by @jmjuanes in #1016
• TASK-7476 - Primary findings and reported variants are not visible in Observations by @jmjuanes in #1018
• TASK-7568 - Unable to kill or retry jobs in job browser by @jmjuanes in #1019
• TASK-7600-rel - Deploy IVA Web App Application step fails by @juanfeSanahuja in #1022
• TASK-7600-dev - Deploy IVA Web App Application step fails by @juanfeSanahuja in #1021
• TASK-7581 - Secret invocation from jsorolla workflows fails (branch release-3.x.x) by @juanfeSanahuja in #1023
• TASK-7589 - Port Patch 2.12.8 -> 3.2.2 Xetabase 1.10.9 -> 2.2.3 by @juanfeSanahuja in #1020
• TASK-7373 - Issues in Family Genotype filter by @jmjuanes in #1028
• TASK-7359 - Streamline details view exploration using a modal by @jmjuanes in #1025
• TASK-7415 - Not all nf-core pipelines can be imported through Workflow Import by @jmjuanes in #1024
• TASK-7531 - Port Patch 2.12.8 -> 3.5.0 XB 1.10.9 - 2.5.0 by @juanfeSanahuja in #1027
• TASK-7130 - Move reset password WebService by @jmjuanes in #1026
• TASK-7667 - Minor aesthetic corrections by @jmjuanes in #1032
• TASK-7661 - File Annotations dropdown menu not properly visible by @jmjuanes in #1031
• TASK-7516 - Implement thumbnails view to File Manager by @jmjuanes in #1030
• TASK-7461 - Migrate opencb/docker-hub repositories to zettagenomics-docker-hub by @juanfeSanahuja in #1029
• TASK-7693-rel - Upgrade Ubuntu image on GitHub Actions by @juanfeSanahuja in #1033
• TASK-7710 - Cellbase apiKey not configured by @jmjuanes in #1035
• Portpatch 3.2.2 -> 4.1.0-dev by @juanfeSanahuja in #1036
• TASK-7532 - Port Patch 2.5.0 -> 3.1.0 by @juanfeSanahuja in #1040
• TASK-7789 - Swagger points to the wrong baseUrl by @jmjuanes in #1042
• TASK-7706 - Allow customized reports with templates by @jmjuanes in #1041

Full Changelog: v4.0.0...v4.1.0

v3.6.0

What's Changed

• TASK-7589 - Port Patch 2.12.8 -> 3.2.2 Xetabase 1.10.9 -> 2.2.3 by @juanfeSanahuja in #1020
• Portpatch 3.2.2 -> 3.6.0-dev by @juanfeSanahuja in #1037

Full Changelog: v3.5.0...v3.6.0

v3.5.0

What's Changed

• TASK-7034 - Unable to display custom indexed fields in Variant Caller Sample Filter by @jmjuanes in #989
• TASK-7205 - Variant Browser infinite loop when using Cellbase v4 by @jmjuanes in #1005
• TASK-7272 - Cohorts column of Variant Browser includes cohorts without calculated stats by @jmjuanes in #1007
• TASK-6933 - IVA Configuration Admin - Unable to select multiple studies by @gpveronica in #1003
• TASK-7325 - IVA Study Admin is setting permissions to NONE when adding a new user to a study by @jmjuanes in #1015
• TASK-7323 - Data is not displayed unless the user switches tabs by @jmjuanes in #1016
• TASK-7476 - Primary findings and reported variants are not visible in Observations by @jmjuanes in #1018
• TASK-7568 - Unable to kill or retry jobs in job browser by @jmjuanes in #1019
• TASK-7600-rel - Deploy IVA Web App Application step fails by @juanfeSanahuja in #1022
• TASK-7581 - Secret invocation from jsorolla workflows fails (branch release-3.x.x) by @juanfeSanahuja in #1023
• TASK-7531 - Port Patch 2.12.8 -> 3.5.0 XB 1.10.9 - 2.5.0 by @juanfeSanahuja in #1027

Full Changelog: v3.4.0...v3.5.0

v3.2.2

What's Changed

• TASK-7034 - Unable to display custom indexed fields in Variant Caller Sample Filter by @jmjuanes in #989
• TASK-7205 - Variant Browser infinite loop when using Cellbase v4 by @jmjuanes in #1005
• TASK-7272 - Cohorts column of Variant Browser includes cohorts without calculated stats by @jmjuanes in #1007
• TASK-7589 - Port Patch 2.12.8 -> 3.2.2 Xetabase 1.10.9 -> 2.2.3 by @juanfeSanahuja in #1020

Full Changelog: v3.2.1...v3.2.2

v4.0.0

What's Changed

• TASK-6879 - Adapt GitHub Actions, CICD workflows and release scripts to new SDLC by @juanfeSanahuja in #973
• TASK-6780 - Port Patch 3.2.1 -> 4.0.0 XB 2.2.1 -> 3.0.0 by @jmjuanes in #991
• TASK-7097 - Port Patch 3.3.0 -> 4.0.0 Xetabase 2.3.0 -> 3.0.0 by @jmjuanes in #996
• TASK-7099 - Migrate build of JSorolla to Webpack by @jmjuanes in #1004
• TASK-6559 - Security: IVA Docker - Avoid port 80 and Root privileges by @juanrizetta in #965
• Port patch 3.4.0 -> 4.0.0 by @jmjuanes in #1011
• TASK-5610 - Create the CVDB endpoint analysis/clinical/cvdb/variant/summary and overwrite analysis/clinical/variant by @jmjuanes in #1013
• TASK-6445 - Implement OpenCGA Workflows with NextFlow by @jmjuanes in #1006
• TASK-7049 - Liftover analysis by @jmjuanes in #1012
• TASK-7100 - Redesign IVA User Interface by @jmjuanes in #1014
• TASK-7574 - Secret invocation from jsorolla workflows fails by @juanfeSanahuja in #1017

New Contributors

• @juanrizetta made their first contribution in #965

Full Changelog: v3.4.0...v4.0.0

v2.12.8

What's Changed

• TASK-7034 - Unable to display custom indexed fields in Variant Caller Sample Filter by @jmjuanes in #989
• TASK-7205 - Variant Browser infinite loop when using Cellbase v4 by @jmjuanes in #1005
• TASK-7272 - Cohorts column of Variant Browser includes cohorts without calculated stats by @jmjuanes in #1007

Full Changelog: v2.12.7...v2.12.8

v3.4.0

What's Changed

• TASK-7079 - Summary detail tab is displayed empty for some variants by @jmjuanes in #995
• TASK-7117 - Custom logo in IVA navbar has not a fixed height by @jmjuanes in #998
• TASK-7039 - IVA missing jobs at job monitor by @jmjuanes in #994
• TASK-6930 - Unable to launch variant-stats-index from IVA by @gpveronica in #1001
• TASK-6759 - Catalog forms inline error messages are black by @gpveronica in #999
• TASK-7033 - IVA cannot filter by specific variable types in AnnotationSets by @gpveronica in #997
• TASK-6866 - Issue in genotype filter dropdown in Samples-detail-tab in Variant Browser and Sample Variant Browser by @jmjuanes in #992
• TASK-4846 - Column settings - Grid settings "Clear" or "Discard" buttons unresponsive by @gpveronica in #1002
• TASK-5715 - Move Steiner components to extensions by @jmjuanes in #993
• TASK-6629 - Issues in the Summary and Samples tabs of Variant Browser by @jmjuanes in #1000
• TASK-7256 - Prevent IVA "infinite loading loop" when there is an error getting session info by @jmjuanes in #1008
• TASK-7225 - Warning events messages still take up a large part of the screen in Variant Browser by @jmjuanes in #1009
• TASK-7326 - TypeError when running Jsorolla tests by @jmjuanes in #1010

Full Changelog: v3.3.0...v3.4.0

v3.3.0

What's Changed

• TASK-6879 - Adapt GitHub Actions, CICD workflows and release scripts to new SDLC by @juanfeSanahuja in #972
• TASK-4985 - JSorolla-enterprise version is not correctly displayed by @jmjuanes in #966
• TASK-6839 - Table result/Group by buttons should have horizontal margin between them by @jmjuanes in #971
• TASK-6543 - Steiner Report discussion drop down insertion glitch by @jmjuanes in #967
• TASK-6849 - Saved rearrangements do not show up in report by @jmjuanes in #968
• TASK-6850 - Unable to edit variants in Rearrangement Browser by @jmjuanes in #970
• TASK-6702 - Ability to select the transcript (Mane, Ensembl or RefSeq) in the report. by @jmjuanes in #969
• TASK-6694 - Make the Genome browser Menu Bar always visible by @jmjuanes in #980
• TASK-6854 - Error in variant setting=> transcript filter checkbox selection when clicking in the text values by @gpveronica in #974
• TASK-6312 - IVA Clinical Analysis browser- Priority colour badges not matching by @gpveronica in #981
• TASK-5769 - Lollipops are displaced in variants track in genome browser by @jmjuanes in #978
• TASK-6700 - Update the Steiner tool to include COSMIC count by @jmjuanes in #983
• TASK-5589 - Unable to save grid settings in Variant Interpreter Rearrangement browser by @jmjuanes in #982
• TASK-6869 - Default filters are named differently In Variant Browser and Sample Variant Browser by @gpveronica in #976
• TASK-6838 - Simplify HRDetect Interface for non-advanced users by @jmjuanes in #979
• TASK-6867 - Sample filter in Variant browser is not abled again after deselecting the multiple studies in study filter by @gpveronica in #977
• TASK-6808 - Define Case stages to show in the report by @jmjuanes in #975
• TASK-1232 - Display coverage value in Alignments Track of Genome Browser by @jmjuanes in #984
• TASK-6841 - FILES section (Case info > overview > FILES) has an unnecessary “File” header column by @jmjuanes in #985
• TASK-5245 - Regular users (no admin users) with write clinical analysis permission cannot save variants in the sample variant browser by @imedina in #899
• TASK-6631 - NPE shown in the Sample Browser by @gpveronica in #987
• TASK-6635 - Error in Samples tab of VB when the selected variant has a long ID by @jmjuanes in #986
• TASK-6986 - Study Admin Variant Configuration cannot be edited by @gpveronica in #988

Full Changelog: v3.2.1...v3.3.0

v3.2.1

What's Changed

• TASK-6141 - TypeError when selecting a sample and zygosity genotype visualisation in the Variant Browser by @jmjuanes in #925
• TASK-4951 - Detailed tabs are not cleared when the row in the grid loses focus by @jmjuanes in #927
• TASK-6290 - IVA displays an infinite spinner in the login page when accessing to a tool by URL with SSO mode enabled by @jmjuanes in #926
• TASK-6095 - Variant Browser Sample Filter interaction issues with Study Filter by @jmjuanes in #929
• TASK-6337 - Variant Browser: Warnings displayed take the whole screen by @jmjuanes in #932
• TASK-6058 - Selecting a job in the Jobs drop-down in header bar does not switch to the job browser by @jmjuanes in #933
• TASK-6272: IVA Catalog browser have "Edit" greyed-out in the Actions drop-down for non-admin by @gpveronica in #935
• TASK-6535 - Add Haploid call option filter by @imedina in #947
• TASK-6519 - Unable to unmark a marked element in dropdown list with single selection by @jmjuanes in #951
• TASK-6489 - Unable to view logs for killed jobs in IVA by @jmjuanes in #955
• TASK-6431 - IVA performs queries to OpenCGA adding the token as a query param instead of using the Authorization header by @jmjuanes in #954
• TASK-5889 - Unable to open a clinical analysis using the URL after login by @jmjuanes in #950
• TASK-6340 - IVA instability issues: in certain circumstances the job status notification messages keep being displayed forever and sometimes the filter panel is not shown by @jmjuanes in #953
• TASK-6140 - Create OpenCGA Notes Browser by @jmjuanes in #949
• TASK-6608 - Removing GeneRoleInCancer from Active filter does not unmark them from clinical>GeneRoleInCancer left filter panel (only in variant browser) by @jmjuanes in #958
• TASK-6636 - Job Kill method in JavaScript client of OpenCGA sends the params as POST body data by @jmjuanes in #961
• TASK-6515 - Port Patch 1.10.6(.1) -> 2.2.1 by @imedina in #952
• TASK-6313 - IVA Clinical Analysis Browser - Change Priority or Status not working by @jmjuanes in #957
• TASK-6605 - Clinical filters in Variant Browser have always disabled disease panel filters by xxx even with a disease panel selected by @jmjuanes in #959
• TASK-6494 - Adapt IVA to OpenCGA user data model changes by @jmjuanes in #962
• TASK-4502 - The first default interpretation does not have a Method section by @jmjuanes in #960
• TASK-6637 - Add NA genotype to clinical interpreter genotype filter by @imedina in #956
• TASK-5964 - Clinical Improvements by @jmjuanes in #948
• TASK-4438 - Improve Pharmacogenomics IVA user interfaces by @imedina in #940
• TASK-5809 - Implement new ADMIN UI - Organization section by @gpveronica in #944
• TASK-6783 - IVA TypeError in cohort create when searching for SampleIDs by @gpveronica in #963
• TASK-6708 - Port Patch 2.12.7 -> 3.2.1 (Xetabase 1.10.7 -> 2.2.1) by @jmjuanes in #964

Full Changelog: v3.2.0...v3.2.1