AGR Curation v0.33.0-rc1

What's Changed

• SCRUM-3803 by @adamgibs in #1508
• Mergeback release v0.32.0-rc1 to alpha by @mluypaert in #1511
• Fix for go and chebi ontologies to load obsoletes by @oblodgett in #1512
• SCRUM-3809 (update) Ensure search by xref loads genes belonging to source MOD by @markquintontulloch in #1513
• SCRUM-3803 update modTableState to have defaultColumnNames and by @adamgibs in #1514
• SCRUM-3944 Fix deletion FK errors for FMS bulk load cleanup by @markquintontulloch in #1515
• Remove obsoletes by @oblodgett in #1516
• SCRUM-3809 (update) Remove duplicate code and handle IDs with prefix not in enum by @markquintontulloch in #1517
• SCRUM-3929 Implement SARS-CoV-2 gene load by @markquintontulloch in #1518
• Add empty list check for ResourceDescriptorPages by @markquintontulloch in #1519
• SCRUM-3723: merge back v0.32.0 to alpha by @abecerra in #1521
• SCRUM-3967 Use curie to get/delete references by @markquintontulloch in #1523
• SCRUM-3894 upgrade React by @adamgibs in #1524
• Change to exclude redundant entities from dashboard by @VarunReddy1111 in #1522
• Added DB fields back to ES so blue team could sort on them by @oblodgett in #1525
• Mergeback release v0.32.1 to alpha by @mluypaert in #1528
• SCRUM-3960 Change to make obsolete column default filtering to false … by @VarunReddy1111 in #1526
• New entity fix by @adamgibs in #1529
• SCRUM-3968 Compact styling of data tables along with refactoring of respective data tables by @VarunReddy1111 in #1530
• Fixing the row width in Literature References Table on reset by @VarunReddy1111 in #1531
• Release/v0.33.0 rc1 by @VarunReddy1111 in #1532

Full Changelog: v0.32.1...v0.33.0-rc1

AGR Curation v0.32.1

What's Changed

• Release v0.32.1 by @markquintontulloch in #1527

Full Changelog: v0.32.0...v0.32.1

AGR Curation v0.32.0

What's Changed

• Mergeback release v0.31.0-rc1 to alpha by @mluypaert in #1463
• Added initial sample code for graphql by @oblodgett in #1464
• Added graphql UI by @oblodgett in #1466
• Added inital documentation for search payload by @oblodgett in #1465
• SCRUM 2755 Mod specific fields are made required in new annotation pop up form by @VarunReddy1111 in #1467
• SCRUM-3712 Missed AGM Phenotype Annotation code by @markquintontulloch in #1468
• SCRUM-2755 Changed the mod related setting specifically to ZFIN by @VarunReddy1111 in #1469
• SCRUM-3857 Fix vocabulary term lookup when creating experiments by @markquintontulloch in #1470
• SCRUM-2755 code changes to fix errors persisting even after clicking on save and add … by @VarunReddy1111 in #1473
• Update README.md by @oblodgett in #1474
• SCRUM-3686 by @adamgibs in #1477
• SCRUM-3806 Load Molecular Genetic Interaction data from FMS by @markquintontulloch in #1472
• Mergeback release v0.31.0 to alpha by @mluypaert in #1476
• SCRUM-3857 update default rows per page by @adamgibs in #1478
• SCRUM-3806 (update) Add identifierId to uniqueId by @markquintontulloch in #1479
• Added code to better handle concurrent threads and chnaged logging by @oblodgett in #1480
• SCRUM-3807 Implement loading of genetic interactions from FMS (phase 1) by @markquintontulloch in #1481
• Fix filter fieldName by @markquintontulloch in #1483
• SCRUM-3868 (update) Fix incorrect error reporting by @markquintontulloch in #1484
• SCRUM-3806 (update) Add filter fields by @markquintontulloch in #1485
• SCRUM-3686 (update) Another reporting fix by @markquintontulloch in #1488
• SCRUM-3765 Species Table refactoring by @VarunReddy1111 in #1487
• SCRUM-3711 Importing Allele Phenotype Annotation into Persistent store by @VarunReddy1111 in #1482
• Fix indentation by @oblodgett in #1489
• SCRUM-3753 by @adamgibs in #1491
• Refactor to remove some classes SCRUM-3711.2 by @oblodgett in #1490
• Ignore invalid entries in phenotypeTermIdentifier field by @markquintontulloch in #1492
• Increase column size by @markquintontulloch in #1493
• Increase reporting interval for bulk loads by @markquintontulloch in #1494
• More column width changes by @markquintontulloch in #1495
• Fix migration name by @markquintontulloch in #1496
• SCRUM-3711 refactor by @markquintontulloch in #1486
• Increase uniqueId width further by @markquintontulloch in #1497
• Added functionality to OR filters together rather than and by @oblodgett in #1499
• Added better messaging to error by @oblodgett in #1498
• Fixed NPE by @oblodgett in #1500
• SCRUM-3883 Add phenotype xrefs & load RGD reference for OMIM/ORPHA xrefs by @markquintontulloch in #1501
• SCRUM-3808 Implement loading of GenomicEntity xrefs from DQM submissions by @markquintontulloch in #1502
• SCRUM-3809 Enable loading of interactions by interactor xrefs by @markquintontulloch in #1503
• SCRUM-3808 (update) Add RefSeq and Ensembl to interaction prefix enum by @markquintontulloch in #1504
• Add MIM prefix to phenotype load reference logic by @markquintontulloch in #1505
• Fix FK error on DataProvider xref update by @markquintontulloch in #1506
• SCRUM-3884 Fixed the ontology tree view bug by @VarunReddy1111 in #1507
• Release/v0.32.0 rc1 by @abecerra in #1510
• SCRUM-3723: deploy beta to production - release/v0.32.0 by @abecerra in #1520

Full Changelog: v0.31.0...v0.32.0

AGR Curation v0.32.0-rc1

What's Changed

• Mergeback release v0.31.0-rc1 to alpha by @mluypaert in #1463
• Added initial sample code for graphql by @oblodgett in #1464
• Added graphql UI by @oblodgett in #1466
• Added inital documentation for search payload by @oblodgett in #1465
• SCRUM 2755 Mod specific fields are made required in new annotation pop up form by @VarunReddy1111 in #1467
• SCRUM-3712 Missed AGM Phenotype Annotation code by @markquintontulloch in #1468
• SCRUM-2755 Changed the mod related setting specifically to ZFIN by @VarunReddy1111 in #1469
• SCRUM-3857 Fix vocabulary term lookup when creating experiments by @markquintontulloch in #1470
• SCRUM-2755 code changes to fix errors persisting even after clicking on save and add … by @VarunReddy1111 in #1473
• Update README.md by @oblodgett in #1474
• SCRUM-3686 by @adamgibs in #1477
• SCRUM-3806 Load Molecular Genetic Interaction data from FMS by @markquintontulloch in #1472
• Mergeback release v0.31.0 to alpha by @mluypaert in #1476
• SCRUM-3857 update default rows per page by @adamgibs in #1478
• SCRUM-3806 (update) Add identifierId to uniqueId by @markquintontulloch in #1479
• Added code to better handle concurrent threads and chnaged logging by @oblodgett in #1480
• SCRUM-3807 Implement loading of genetic interactions from FMS (phase 1) by @markquintontulloch in #1481
• Fix filter fieldName by @markquintontulloch in #1483
• SCRUM-3868 (update) Fix incorrect error reporting by @markquintontulloch in #1484
• SCRUM-3806 (update) Add filter fields by @markquintontulloch in #1485
• SCRUM-3686 (update) Another reporting fix by @markquintontulloch in #1488
• SCRUM-3765 Species Table refactoring by @VarunReddy1111 in #1487
• SCRUM-3711 Importing Allele Phenotype Annotation into Persistent store by @VarunReddy1111 in #1482
• Fix indentation by @oblodgett in #1489
• SCRUM-3753 by @adamgibs in #1491
• Refactor to remove some classes SCRUM-3711.2 by @oblodgett in #1490
• Ignore invalid entries in phenotypeTermIdentifier field by @markquintontulloch in #1492
• Increase column size by @markquintontulloch in #1493
• Increase reporting interval for bulk loads by @markquintontulloch in #1494
• More column width changes by @markquintontulloch in #1495
• Fix migration name by @markquintontulloch in #1496
• SCRUM-3711 refactor by @markquintontulloch in #1486
• Increase uniqueId width further by @markquintontulloch in #1497
• Added functionality to OR filters together rather than and by @oblodgett in #1499
• Added better messaging to error by @oblodgett in #1498
• Fixed NPE by @oblodgett in #1500
• SCRUM-3883 Add phenotype xrefs & load RGD reference for OMIM/ORPHA xrefs by @markquintontulloch in #1501
• SCRUM-3808 Implement loading of GenomicEntity xrefs from DQM submissions by @markquintontulloch in #1502
• SCRUM-3809 Enable loading of interactions by interactor xrefs by @markquintontulloch in #1503
• SCRUM-3808 (update) Add RefSeq and Ensembl to interaction prefix enum by @markquintontulloch in #1504
• Add MIM prefix to phenotype load reference logic by @markquintontulloch in #1505
• Fix FK error on DataProvider xref update by @markquintontulloch in #1506
• SCRUM-3884 Fixed the ontology tree view bug by @VarunReddy1111 in #1507
• Release/v0.32.0 rc1 by @abecerra in #1510

Full Changelog: v0.31.0...v0.32.0-rc1

AGR Curation v0.31.0

What's Changed

• Mergeback release v0.30.0-rc1 to alpha by @mluypaert in #1429
• Fix for failing ontologies by @oblodgett in #1430
• Mergeback release v0.30.0 to alpha by @mluypaert in #1432
• SCRUM-3718: upgrade github actions to nodejs 20 by @abecerra in #1434
• SCRUM-3515 LinkML v2.2.0 migration by @markquintontulloch in #1435
• SCRUM-3515 update - Remove set_session_replica_role statements by @markquintontulloch in #1436
• SCRUM-3661 Persistent Settings of Disease Annotation's - new annotation pop up form by @VarunReddy1111 in #1433
• Updated refresh interval to only be set while indexing by @oblodgett in #1437
• SCRUM-3515 UI fixes by @markquintontulloch in #1438
• Remove refresh interval altogether by @oblodgett in #1439
• SCRUM-3515 validation fix by @markquintontulloch in #1440
• SCRUM-2714 by @adamgibs in #1442
• SCRUM-3593 override search endpoint to use different JSON View to rem… by @cmpich in #1441
• SCRUM-3770 Speed up ID retrieval for filtered ID lists by @markquintontulloch in #1443
• SCRUM 3694 Adding the GENO Term ontology into persistent store by @VarunReddy1111 in #1444
• SCRUM-3740 Adding Null class response body for swagger get end points by @VarunReddy1111 in #1446
• add getIdentifier to EditorTooltip by @adamgibs in #1445
• Fix indentations by @oblodgett in #1447
• Added code to speed up closure queries by @oblodgett in #1448
• SCRUM-3740 Adding Null body request and response to Base interfaces end points by @VarunReddy1111 in #1449
• SCRUM-3740 Removed the response codes and changed Request body schema to String class by @VarunReddy1111 in #1451
• SCRUM-3738: force fetching the evidence list by @abecerra in #1450
• SCRUM-3249 Fixed unnecessary expansion glyphs in ontology tree view by @VarunReddy1111 in #1452
• Added code to remove exceptions every Saturday from history that is t… by @oblodgett in #1453
• SCRUM-3625 & SCRUM-3626 Prevent multiple 'is_allele_of' allele-gene associations and duplicate associations by @markquintontulloch in #1455
• SCRUM-3712 Load AGM Phenotype Annotation data from FMS by @markquintontulloch in #1454
• SCRUM-3779 Added warning and provided openAPI definition download link on swagger page by @VarunReddy1111 in #1456
• SCRUM-3752 refactored the AGM table templates by @VarunReddy1111 in #1457
• SCRUM-3712 (update) Infer primary annotation if not in load file by @markquintontulloch in #1458
• SCRUM-3794 by @adamgibs in #1459
• SCRUM-3823 Fix lazy loading error for Molecule load by @markquintontulloch in #1460
• Release/v0.31.0-rc1 by @markquintontulloch in #1462
• Release/v0.31.0 by @markquintontulloch in #1475

Full Changelog: v0.30.0...v0.31.0

AGR Curation v0.31.0-rc1

What's Changed

• Mergeback release v0.30.0-rc1 to alpha by @mluypaert in #1429
• Fix for failing ontologies by @oblodgett in #1430
• Release/v0.30.0 by @adamgibs in #1431
• Mergeback release v0.30.0 to alpha by @mluypaert in #1432
• SCRUM-3718: upgrade github actions to nodejs 20 by @abecerra in #1434
• SCRUM-3515 LinkML v2.2.0 migration by @markquintontulloch in #1435
• SCRUM-3515 update - Remove set_session_replica_role statements by @markquintontulloch in #1436
• SCRUM-3661 Persistent Settings of Disease Annotation's - new annotation pop up form by @VarunReddy1111 in #1433
• Updated refresh interval to only be set while indexing by @oblodgett in #1437
• SCRUM-3515 UI fixes by @markquintontulloch in #1438
• Remove refresh interval altogether by @oblodgett in #1439
• SCRUM-3515 validation fix by @markquintontulloch in #1440
• SCRUM-2714 by @adamgibs in #1442
• SCRUM-3593 override search endpoint to use different JSON View to rem… by @cmpich in #1441
• SCRUM-3770 Speed up ID retrieval for filtered ID lists by @markquintontulloch in #1443
• SCRUM 3694 Adding the GENO Term ontology into persistent store by @VarunReddy1111 in #1444
• SCRUM-3740 Adding Null class response body for swagger get end points by @VarunReddy1111 in #1446
• add getIdentifier to EditorTooltip by @adamgibs in #1445
• Fix indentations by @oblodgett in #1447
• Added code to speed up closure queries by @oblodgett in #1448
• SCRUM-3740 Adding Null body request and response to Base interfaces end points by @VarunReddy1111 in #1449
• SCRUM-3740 Removed the response codes and changed Request body schema to String class by @VarunReddy1111 in #1451
• SCRUM-3738: force fetching the evidence list by @abecerra in #1450
• SCRUM-3249 Fixed unnecessary expansion glyphs in ontology tree view by @VarunReddy1111 in #1452
• Added code to remove exceptions every Saturday from history that is t… by @oblodgett in #1453
• SCRUM-3625 & SCRUM-3626 Prevent multiple 'is_allele_of' allele-gene associations and duplicate associations by @markquintontulloch in #1455
• SCRUM-3712 Load AGM Phenotype Annotation data from FMS by @markquintontulloch in #1454
• SCRUM-3779 Added warning and provided openAPI definition download link on swagger page by @VarunReddy1111 in #1456
• SCRUM-3752 refactored the AGM table templates by @VarunReddy1111 in #1457
• SCRUM-3712 (update) Infer primary annotation if not in load file by @markquintontulloch in #1458
• SCRUM-3794 by @adamgibs in #1459
• SCRUM-3823 Fix lazy loading error for Molecule load by @markquintontulloch in #1460
• Release/v0.31.0-rc1 by @markquintontulloch in #1462

Full Changelog: v0.30.0-rc1...v0.31.0-rc1

AGR Curation v0.30.0

What's Changed

• Added Filter fields and Show all button in add annotation pop-up by @VarunReddy1111 in #1416
• SCRUM-2756 Changing the position of the pop up page to always stay on top by @VarunReddy1111 in #1417
• added internal field to the dropdown by @VarunReddy1111 in #1419
• SCRUM-3665/SCRUM-2744 - Added set to MOD default button by @VarunReddy1111 in #1421
• Mergeback release v0.29.0-rc1 to alpha by @mluypaert in #1420
• Mergeback release v0.29.0 to alpha by @mluypaert in #1423
• Fix typos ( SCRUM-2744) by @VarunReddy1111 in #1425
• SCRUM-2744 Changed mod default button name and Added XBStaff by @VarunReddy1111 in #1426
• Updated defaults by @oblodgett in #1427
• Release/v0.30.0 rc1 by @VarunReddy1111 in #1428
• Release/v0.30.0 by @adamgibs in #1431

Full Changelog: v0.29.0...v0.30.0

AGR Curation v0.30.0-rc1

What's Changed

• Added Filter fields and Show all button in add annotation pop-up by @VarunReddy1111 in #1416
• SCRUM-2756 Changing the position of the pop up page to always stay on top by @VarunReddy1111 in #1417
• added internal field to the dropdown by @VarunReddy1111 in #1419
• SCRUM-3665/SCRUM-2744 - Added set to MOD default button by @VarunReddy1111 in #1421
• Mergeback release v0.29.0-rc1 to alpha by @mluypaert in #1420
• Release/v0.29.0 by @adamgibs in #1422
• Mergeback release v0.29.0 to alpha by @mluypaert in #1423
• Fix typos ( SCRUM-2744) by @VarunReddy1111 in #1425
• SCRUM-2744 Changed mod default button name and Added XBStaff by @VarunReddy1111 in #1426
• Updated defaults by @oblodgett in #1427
• Release/v0.30.0 rc1 by @VarunReddy1111 in #1428

Full Changelog: v0.29.0-rc1...v0.30.0-rc1

AGR Curation v0.29.0

What's Changed

• Mergeback release v0.28.0-rc1 to alpha by @mluypaert in #1357
• SCRUM-3536 add LoadingOverlay to AlleleDetailPage by @adamgibs in #1358
• SCRUM-3536 add text to LoadingOverlay by @adamgibs in #1359
• SCRUM-3343: increase field names sizes - make buttons subtler by @abecerra in #1360
• Added SlackNotifier class to trigger slack notification for a failed … by @VarunReddy1111 in #1361
• Renamed endpoint for search endpoints by @oblodgett in #1363
• added more null checks by @VarunReddy1111 in #1362
• added the failed loads to dataloads page by @VarunReddy1111 in #1364
• SCRUM-3551: Move buttons at the right of the field name by @abecerra in #1365
• SCRUM-3354 by @adamgibs in #1366
• SCRUM-3354 by @adamgibs in #1367
• SCRUM-3354 more bug fixes by @adamgibs in #1368
• SCRUM-3354 backend update - validate associations with subject entities by @markquintontulloch in #1369
• SCRUM-3354 by @adamgibs in #1371
• Removing empty spaces and styling data tables for compact presentation by @VarunReddy1111 in #1370
• Added margins to all the columns in disease annotations table by @VarunReddy1111 in #1372
• Added a new endpoint to download the exception messages for a data load by @VarunReddy1111 in #1376
• Mergeback release v0.27.4 to alpha by @mluypaert in #1374
• Added the button for downloading exceptions file by @VarunReddy1111 in #1378
• Mergeback release v0.28.0-rc2 to alpha by @mluypaert in #1386
• Mergeback release v0.28.0 to alpha by @mluypaert in #1389
• SCRUM-2016 add View.ForPublic on GeneToGeneOrthology entity by @cmpich in #1390
• Made modifications to the dataloads components and dataload service by @VarunReddy1111 in #1391
• SCRUM-3613 Fix failures on FB Construct load by @markquintontulloch in #1392
• Mergeback release v0.28.1 to alpha by @mluypaert in #1399
• Mergeback release v0.28.2 to alpha by @mluypaert in #1404
• SCRUM-3620 - Fix failing Construct Association loads by @markquintontulloch in #1405
• SCRUM-3354 by @adamgibs in #1394
• SCRUM-3630 Fix cryptic error reporting from null response in ontology curie/secondaryId search by @markquintontulloch in #1406
• SCRUM-3633 Fix copy-paste error in Allele DTO validation code by @markquintontulloch in #1407
• SCRUM-3631 Fix 500 error on Construct page when displaying entries with secondary IDs by @markquintontulloch in #1408
• SCRUM-3634 Fix gene load cleanup error when gene involved in obsolete orthology pair by @markquintontulloch in #1409
• Fix JsonMappingException for allele/updateDetail endpoint by @markquintontulloch in #1395
• SCRUM-3640 Fix DTO validation repeated error bug by @markquintontulloch in #1411
• Set obsolete/internal when loading by @markquintontulloch in #1412
• Mergeback release v0.28.3 to alpha by @mluypaert in #1414
• Aga deletion backend by @adamgibs in #1415
• Release/v0.29.0 rc1 by @adamgibs in #1418
• Release/v0.29.0 by @adamgibs in #1422

Full Changelog: v0.28.3...v0.29.0

AGR Curation v0.29.0-rc1

What's Changed

• Mergeback release v0.28.0-rc1 to alpha by @mluypaert in #1357
• SCRUM-3536 add LoadingOverlay to AlleleDetailPage by @adamgibs in #1358
• SCRUM-3536 add text to LoadingOverlay by @adamgibs in #1359
• SCRUM-3343: increase field names sizes - make buttons subtler by @abecerra in #1360
• Added SlackNotifier class to trigger slack notification for a failed … by @VarunReddy1111 in #1361
• Renamed endpoint for search endpoints by @oblodgett in #1363
• added more null checks by @VarunReddy1111 in #1362
• added the failed loads to dataloads page by @VarunReddy1111 in #1364
• SCRUM-3551: Move buttons at the right of the field name by @abecerra in #1365
• SCRUM-3354 by @adamgibs in #1366
• SCRUM-3354 by @adamgibs in #1367
• SCRUM-3354 more bug fixes by @adamgibs in #1368
• SCRUM-3354 backend update - validate associations with subject entities by @markquintontulloch in #1369
• SCRUM-3354 by @adamgibs in #1371
• Removing empty spaces and styling data tables for compact presentation by @VarunReddy1111 in #1370
• Added margins to all the columns in disease annotations table by @VarunReddy1111 in #1372
• Added a new endpoint to download the exception messages for a data load by @VarunReddy1111 in #1376
• Mergeback release v0.27.4 to alpha by @mluypaert in #1374
• Added the button for downloading exceptions file by @VarunReddy1111 in #1378
• Mergeback release v0.28.0-rc2 to alpha by @mluypaert in #1386
• SCRUM-3511: deployment to production by @abecerra in #1388
• Mergeback release v0.28.0 to alpha by @mluypaert in #1389
• SCRUM-2016 add View.ForPublic on GeneToGeneOrthology entity by @cmpich in #1390
• Made modifications to the dataloads components and dataload service by @VarunReddy1111 in #1391
• SCRUM-3613 Fix failures on FB Construct load by @markquintontulloch in #1392
• SCRUM-3605 serialize sgdStrainBackground, add to ForPublic view by @cmpich in #1398
• Mergeback release v0.28.1 to alpha by @mluypaert in #1399
• SCRUM-3605 serialize dateCreated, add to ForPublic view by @cmpich in #1403
• Mergeback release v0.28.2 to alpha by @mluypaert in #1404
• SCRUM-3620 - Fix failing Construct Association loads by @markquintontulloch in #1405
• SCRUM-3354 by @adamgibs in #1394
• SCRUM-3630 Fix cryptic error reporting from null response in ontology curie/secondaryId search by @markquintontulloch in #1406
• SCRUM-3633 Fix copy-paste error in Allele DTO validation code by @markquintontulloch in #1407
• SCRUM-3631 Fix 500 error on Construct page when displaying entries with secondary IDs by @markquintontulloch in #1408
• SCRUM-3634 Fix gene load cleanup error when gene involved in obsolete orthology pair by @markquintontulloch in #1409
• Fix JsonMappingException for allele/updateDetail endpoint by @markquintontulloch in #1395
• SCRUM-3640 Fix DTO validation repeated error bug by @markquintontulloch in #1411
• Set obsolete/internal when loading by @markquintontulloch in #1412
• SCRUM-3641 Fix DA retrieval and cleanup logic by @markquintontulloch in #1413
• Mergeback release v0.28.3 to alpha by @mluypaert in #1414
• Aga deletion backend by @adamgibs in #1415
• Release/v0.29.0 rc1 by @adamgibs in #1418

Full Changelog: v0.28.0-rc2...v0.29.0-rc1