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

v2.12.7

What's Changed

• TASK-6535 - Add Haploid call option filter by @imedina in #947

Full Changelog: v2.12.6...v2.12.7

v3.2.0

What's Changed

• TASK-6038 - Migrate build of jsorolla-enterprise to webpack by @jmjuanes in #908
• TASK-6357 - Port Patch 1.10.5 -> 2.2.0 by @juanfeSanahuja in #931
• TASK-5979 - Allow IVA to login with user-pass credentials also when SSO is enabled by @jmjuanes in #924
• TASK-6279 - Hide "Organization" login field by @jmjuanes in #930
• TASK-6386 - Sidebar menu for changing app does not work in some circunstancies by @jmjuanes in #934
• TASK-6385 - Issues with the Study Filter dropdown of Variant Browser by @jmjuanes in #936
• TASK-2523 - Enable the view of the star rating from ClinVar by @imedina in #873
• TASK-6453 - Unable to remove Disease Panels when updating an interpretation by @jmjuanes in #942
• TASK-6452 - Job Retry does not work in job-browser by @jmjuanes in #941
• TASK-6409 - Clinical case can not be created with panel lock ON: value is passed as ON instead of True to OpenCGA by @jmjuanes in #943
• TASK-6430 - IVA redirects to SSO logout page when the logged user is local by @jmjuanes in #939
• TASK-6133 - UI/UX: Review and refine BS5.3.x component styles by @jmjuanes in #945
• TASK-5963 - Clinical Interpretation Improvements by @jmjuanes in #938

Full Changelog: v3.1.0...v3.2.0

v2.12.6

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

Full Changelog: v2.12.5...v2.12.6

v2.12.5

What's Changed

• TASK-6127 - Stock phrases dropdown menu in observations affects previous dropdown menus functionality by @jmjuanes in #910
• TASK-5764 - IVA User projects - Link to VB not working by @gpveronica in #913
• Interpretation create form has the wrong key name for the ID ( "Case id" instead "Interpretation ID") by @Rodielm in #911
• TASK-6081 - Add HGVS column to Variant Browser by @jmjuanes in #912
• TASK-6060 - IVA: Phenotypes added using IVA search tool are not created properly by @gpveronica in #916
• TASK-6128 - Variant Browser: Include new links to export specific variants/queries by @jmjuanes in #920
• TASK-6143 - JSON viewer stops working after trying to preview a JSON FILE by @Rodielm in #918
• TASK-6214 - Variant Browser: passing an URL with characters encoded is not working by @jmjuanes in #922
• TASK-5860 - Extra space added when copying job-id or tool-id from job browser by @gpveronica in #915
• TASK-5931 - File browser showing file sizes in decimal bytes by @Rodielm in #906
• TASK-6093 - Allow IVA to define pre-loaded filters in the Variant Browser, Sample Variant Browser and Catalog Browsers by @jmjuanes in #921
• TASK-6231 - Port Patch 1.10.4.1 -> 1.10.5 by @juanfeSanahuja in #923
• TASK-6023 - Allow to filter by 'genotypes' in the Variant Samples detailed tab by @imedina in #919
• TASK-6167 - Unable to save steiner report by @jmjuanes in #917
• TASK-4451 - Variant and Sample Variant Browser discrepancies and other visualisation details to fix by @imedina in #900
• TASK-6339 - Study filter dropdown is not updated when changing between two projects, each one, with several studies by @jmjuanes in #928

Full Changelog: v2.12.4.1...v2.12.5

v3.1.0

What's Changed

• TASK-5542 - Remove Deleteriousness CADD and SpliceAi from CNV sample browser by @jmjuanes in #855
• TASK-5401 - Split breakpoint annotation for Gene and Gene Feature Overlap in sample variant browser by @jmjuanes in #852
• TASK-5575 - Unable to save variants in Rearrangement Browser by @jmjuanes in #857
• TASK-5559 - Catalog Exception when creating a Clinical Analysis of type FAMILY by @jmjuanes in #854
• TASK-5525 - Export Query in IVA clinical variant export produces API call with not recognized field ("count") by @jmjuanes in #853
• TASK-5494 - File, fileData and sample filters are not kept when applying a saved filter by @jmjuanes in #858
• TASK-5653 - Include OMIM sub-column in Clinical Info colum by @gpveronica in #859
• TASK-5647 - Export Query does not use the filters applied to the VB table by @jmjuanes in #860
• TASK-5503 - IVA variant-grid sub-row is now shown in some circumstances related with clinical primaryHistology field by @jmjuanes in #851
• TASK-5115 - Add genome browser as view in sample variant browsers by @jmjuanes in #862
• TASK-4850 - Single Sign-On (SSO) authentication not working properly by @jmjuanes in #861
• TASK-4487 - DataForm. Make it agnostic and less bound to html generator. by @gpveronica in #863
• PR - IVA Profile/Projects - Missing migration to new config model causes empty view by @gpveronica in #864
• TASK-5765 - Some forms in IVA are displayed narrowed by @jmjuanes in #867
• TASK-5725 - IVA Data-form - Fields with falsy values managed incorrectly by @gpveronica in #869
• PR - IVA Data-form - Clinical Analysis create table not visualised correctly by @gpveronica in #865
• TASK-5791 - Implement SNP search by rsID by @imedina in #879
• TASK-5827 - Port Patch 1.10.3 -> 2.1.0 by @juanfeSanahuja in #882
• TASK-5867 - Port Patch 1.10.3.1 -> 2.1.0 by @juanfeSanahuja in #886
• TASK-5696 - Migrate GitHub Actions to v4 by @juanfeSanahuja in #888
• TASK-1192 - Migrate IVA to new Bootstrap 5.3.x by @Rodielm in #782
• TASK-5566 - Expand and refine CVDB Explorer functionalities by @jmjuanes in #903

Full Changelog: v3.0.0...v3.1.0

v2.12.4.1

What's Changed

• TASK-6144 - Sample column and cohort visualisation issues in the Variant Browser by @jmjuanes in #914

Full Changelog: v2.12.4...v2.12.4.1

v2.12.4

What's Changed

• TASK-5691 - Writing is very slow in comment boxes in observations by @jmjuanes in #877
• TASK-5856 - Port Patch 1.10.3.1 -> 1.10.4 by @juanfeSanahuja in #885
• Sample Variant Download does not display several fields by @imedina in #872
• TASK-5797 - Variant Caller Sample Filter in SVB do not display dropdowns to select comparator and value by @jmjuanes in #876
• TASK-5635 - Inconsistent VCF genotype rendering by @imedina in #875
• TASK-5601 - A locked case in IVA can send exomiser analysis and new interpretations are created by @imedina in #874
• TASK-5854 - Variant Browser and Sample Variant Browser: Cohort Stats Genotype HOM_ALT freq/count data missing from Main Table by @imedina in #883
• TASK-5692 - Add a comment box in the section "Results" in Observations by @jmjuanes in #887
• TASK-5717 - No valid docker image generated when executing docker-build.py script on MacOS by @jmjuanes in #866
• TASK-5946 - Columns section of Variant Browser settings displays escaped HTML content by @jmjuanes in #891
• Add custom genotype 1/2 by @imedina in #868
• TASK-5708 - Actions is listed in the columns dropdown of Clinical Analysis Settings but cannot be hidden by @imedina in #895
• TASK-5834 - Incomplete list of cases in the individual grid by @imedina in #881
• TASK-5674 - IVA Grid toolbar - Checking permissions with wrong parameter by @jmjuanes in #892
• TASK-5852 - In some circumstances selected variants in one interpretation are saved in another interpretation by @jmjuanes in #893
• TASK-5739 - Add stock phrases to report by @jmjuanes in #890
• TASK-5855 - Add Variant ID filter to IVA by @imedina in #884
• TASK-5699 - Fix links to Cellbase in Variant Browser and Sample Variant Browser by @jmjuanes in #870
• TASK-5602 - JOBS browser does not display the events (warnings, errors) in some jobs. Example: individual-qc-run by @imedina in #897
• TASK-5666 - IVA Job Browser - Input parameters type object not displayed by @imedina in #896
• TASK-5597 - Variant browser filter can not add a sample if more than a study is selected by @imedina in #898
• TASK-5744 - Memory leak issue in some views of Case Interpreter by @Rodielm in #889
• TASK-5728 - Fix windowSize in Genome Browser by @jmjuanes in #878
• TASK-6014 - Sample Genotypes columns are hidden in SVB in some circunstancies by @jmjuanes in #902
• TASK-6003 - New selected variants or new changes to primary findings cannot be saved with a specific sample variant browser configuration by @jmjuanes in #901
• TASK-5864 - Variant link route does not work by @imedina in #894
• TASK-6057 - Variant browser config for columns is not refreshing the grid by @jmjuanes in #904
• TASK-6052 - Returned events by variant query endpoint are not displayed in Variant Browser and Sample Variant Browser by @jmjuanes in #905
• TASK-6073 - Variant Browser active filter have important issues to fix by @jmjuanes in #907
• TASK-6119 - The URL for clinical case lacks the clinical case ID by @jmjuanes in #909

Full Changelog: v2.12.3.1...v2.12.4

v2.12.3.1

What's Changed

• TASK-5791 - Implement SNP search by rsID by @imedina in #879

Full Changelog: v2.12.3...v2.12.3.1