AGR Curation v0.35.0-rc1

What's Changed

• SCRUM-4174 Load entities without location information from GFF by @markquintontulloch in #1594
• Change to use stringlist template for synonyms column in controlled vocabulary by @VarunReddy1111 in #1595
• SCRUM-4174 (update) Fix previous migration errors by @markquintontulloch in #1596
• SCRUM-4174 (update) Fix total record count by @markquintontulloch in #1597
• SCRUM-4174 (update) Don't store curie as modEntityId as not unique by @markquintontulloch in #1598
• SCRUM-3820 Implement loading and display of geneType by @markquintontulloch in #1599
• Mergeback release v0.34.0-rc1 to alpha by @devopsagr in #1601
• SCRUM-2190 Replace DPO ontology with full FlyBase controlled vocabulary by @markquintontulloch in #1602
• SCRUM-2190 update - Switch DPO for FBCV on dashboard by @markquintontulloch in #1603
• SCRUM-4185 updated executor, service, and validator by @adamgibs in #1591
• SCRUM-4236 add CSS for rowEdit column min width by @adamgibs in #1604
• SCRUM-4185 fix dataProvider loading error by @adamgibs in #1605
• SCRUM-4259 fix construct table error by @adamgibs in #1606
• SCRUM-4259 update by @markquintontulloch in #1607
• SCRUM-4174 (update) Add data provider prefix to modInternalId by @markquintontulloch in #1608
• SCRUM-4187 by @adamgibs in #1610
• Remove FBCV terms attached to phenotypeannotations by @markquintontulloch in #1612
• Mergeback release v0.34.0 to alpha by @devopsagr in #1614
• Mergeback release v0.34.1 to alpha by @devopsagr in #1616
• Betafix/vocabuifix by @VarunReddy1111 in #1617
• Update README.md by @VarunReddy1111 in #1618
• SCRUM-4175 GFF Loading Part 2 (Load location associations) by @markquintontulloch in #1611
• SCRUM-4188 by @adamgibs in #1619
• SCRUM-4175 (update) Return assembly name so available for association loads by @markquintontulloch in #1620
• SCRUM-4175 (update) Remove reverse associations by @markquintontulloch in #1621
• skip SQTR Gene Association test for now by @adamgibs in #1624
• Replaced structural reasoner with ELK reasoner by @VarunReddy1111 in #1622
• SCRUM-4277 added obsolete filtering to all mod settings by @adamgibs in #1625
• SCRUM-4277 add filter to default mod by @adamgibs in #1626
• Adding HTPexpressiondatasetannotation entities by @VarunReddy1111 in #1609
• Release/v0.35.0 rc1 by @VarunReddy1111 in #1633

New Contributors

• @devopsagr made their first contribution in #1601

Full Changelog: v0.34.1...v0.35.0-rc1

AGR Curation v0.34.2

What's Changed

• SCRUM-4305 set obsolete / internal variables explicitly when being up… by @cmpich in #1631

Full Changelog: v0.34.1...v0.34.2

AGR Curation v0.34.1

What's Changed

• Release/v0.34.1 by @VarunReddy1111 in #1615

Full Changelog: v0.34.0...v0.34.1

AGR Curation v0.34.0

What's Changed

• Mergeback release v0.33.0-rc1 to alpha by @mluypaert in #1533
• Initial Code for short circuiting loads once a high error rate is met. SCRUM-3871 by @oblodgett in #1534
• Mergeback release v0.33.0 to alpha by @mluypaert in #1536
• Fixed sorting bug in literature references table by @VarunReddy1111 in #1538
• SCRUM-4057 Fix foreign key errors in gene/allele cleanup by @markquintontulloch in #1539
• Change update message for DTO loads by @markquintontulloch in #1540
• SCRUM-4062 Set obsolete/internal to false for FMS loads by @markquintontulloch in #1541
• Added migration file and created GeneToGeneParalogy class (SCRUM-4063) by @VarunReddy1111 in #1537
• Added paralogy executor, DTO's, service and validator by @VarunReddy1111 in #1542
• SCRUM 4088 - Added Controller and Interface for Paralogy by @VarunReddy1111 in #1543
• Fixed history reporting on all exec's by @oblodgett in #1545
• Added Check Style by @oblodgett in #1546
• Remove old config file by @oblodgett in #1547
• Mergeback release v0.33.1 to alpha by @mluypaert in #1549
• Added debug param for all API calls by @oblodgett in #1551
• Fixed random negative boost error by @oblodgett in #1552
• Removed token operator by @oblodgett in #1553
• Speed up interactions by @oblodgett in #1555
• Added code to speed up loads and fixed alt id search by @oblodgett in #1554
• SCRUM-4114 Handle duplicate interaction refs by @markquintontulloch in #1556
• SCRUM-4062 (update) Avoid duplication caused by condition relations not being submitted in secondary annotations by @markquintontulloch in #1557
• SCRUM-4146 Fix orthology cleanup by @markquintontulloch in #1559
• SCRUM-4159 Fix lookup of human genes by xrefs by @markquintontulloch in #1560
• SCRUM-4062 Handle invalid phenotype terms when searching for primary annotation by @markquintontulloch in #1561
• SCRUM-4160 Handle duplicate xrefs in bulk GenomicEntity loads by @markquintontulloch in #1562
• Remove count query as no pagination is passed in by @oblodgett in #1563
• SCRUM-4107 Turn off auxiliary cleanup for associated annotations by @markquintontulloch in #1564
• SCRUM-4137 include SGD background strain into unique ID generation by @cmpich in #1565
• SCRUM-4018 by @adamgibs in #1567
• SCRUM-4018 fix for migration error by @adamgibs in #1568
• SCRUM-4089 Implement Paralogy Validator and test cases by @VarunReddy1111 in #1566
• SCRUM-3708 fixes by @markquintontulloch in #1569
• SCRUM-3951 Fix reference synchronisation by @markquintontulloch in #1571
• SCRUM-4137 add SGD background String info to uniqueID from DieseaseAn… by @cmpich in #1570
• SCRUM-4090 Paralogy Load clean up by @VarunReddy1111 in #1572
• Added rule to disallow trailing whitespace by @oblodgett in #1573
• Add prettier by @adamgibs in #1574
• SCRUM-4162 change to have multiple error messages in download file by @VarunReddy1111 in #1575
• More checkstyle checks by @oblodgett in #1576
• SCRUM-4186 Migration for OMIM to MIM switch by @markquintontulloch in #1578
• SCRUM-3708: add initial load of gene expressions by @abecerra in #1558
• SCRUM-4113 remove name, curie, and modInternalId from DA subject filter by @adamgibs in #1577
• SCRUM-3708: bump migration prefix by @abecerra in #1579
• SCRUM-4137 Fix cleanup error by @markquintontulloch in #1580
• SCRUM-4148 added OR token operator back to multiselect filter by @adamgibs in #1581
• SCRUM-4191 Turn off failure limit for paralogy and interaction loads by @markquintontulloch in #1582
• SCRUM-3708: replace modId per AGRId in in GeneExpression uniqueId by @abecerra in #1583
• SCRUM-4183 by @adamgibs in #1584
• SCRUM-3708: fix validation for evidence by @abecerra in #1585
• SCRUM-3951 (update) Fix NPE by @markquintontulloch in #1586
• SCRUM-4204 Sort file history by date load started by @markquintontulloch in #1587
• SCRUM-4209 Report loads as 'FAILED' when stopped due to exceeding failure rate cutoff by @markquintontulloch in #1588
• SCRUM-4210 Reset error message on file reload by @markquintontulloch in #1589
• Added migration to add all the category tags into vocabulary by @VarunReddy1111 in #1590
• SCRUM-4228 Remove error rate column from data loads page by @markquintontulloch in #1592
• SCRUM-4227 Fix null error on file history dropdown for files with no history by @markquintontulloch in #1593
• Release/v0.34.0 rc1 by @markquintontulloch in #1600
• Release v0.34.0 by @markquintontulloch in #1613

Full Changelog: v0.33.1...v0.34.0

AGR Curation v0.34.0-rc1

What's Changed

• Mergeback release v0.33.0-rc1 to alpha by @mluypaert in #1533
• Initial Code for short circuiting loads once a high error rate is met. SCRUM-3871 by @oblodgett in #1534
• Release/v0.33.0 by @VarunReddy1111 in #1535
• Mergeback release v0.33.0 to alpha by @mluypaert in #1536
• Fixed sorting bug in literature references table by @VarunReddy1111 in #1538
• SCRUM-4057 Fix foreign key errors in gene/allele cleanup by @markquintontulloch in #1539
• Change update message for DTO loads by @markquintontulloch in #1540
• SCRUM-4062 Set obsolete/internal to false for FMS loads by @markquintontulloch in #1541
• Added migration file and created GeneToGeneParalogy class (SCRUM-4063) by @VarunReddy1111 in #1537
• Added paralogy executor, DTO's, service and validator by @VarunReddy1111 in #1542
• SCRUM 4088 - Added Controller and Interface for Paralogy by @VarunReddy1111 in #1543
• Fixed history reporting on all exec's by @oblodgett in #1545
• Added Check Style by @oblodgett in #1546
• Remove old config file by @oblodgett in #1547
• Removed public view for asserted genes and inffered gene crossreferences by @oblodgett in #1548
• Mergeback release v0.33.1 to alpha by @mluypaert in #1549
• Added debug param for all API calls by @oblodgett in #1551
• Fixed random negative boost error by @oblodgett in #1552
• Removed token operator by @oblodgett in #1553
• Speed up interactions by @oblodgett in #1555
• Added code to speed up loads and fixed alt id search by @oblodgett in #1554
• SCRUM-4114 Handle duplicate interaction refs by @markquintontulloch in #1556
• SCRUM-4062 (update) Avoid duplication caused by condition relations not being submitted in secondary annotations by @markquintontulloch in #1557
• SCRUM-4146 Fix orthology cleanup by @markquintontulloch in #1559
• SCRUM-4159 Fix lookup of human genes by xrefs by @markquintontulloch in #1560
• SCRUM-4062 Handle invalid phenotype terms when searching for primary annotation by @markquintontulloch in #1561
• SCRUM-4160 Handle duplicate xrefs in bulk GenomicEntity loads by @markquintontulloch in #1562
• Remove count query as no pagination is passed in by @oblodgett in #1563
• SCRUM-4107 Turn off auxiliary cleanup for associated annotations by @markquintontulloch in #1564
• SCRUM-4137 include SGD background strain into unique ID generation by @cmpich in #1565
• SCRUM-4018 by @adamgibs in #1567
• SCRUM-4018 fix for migration error by @adamgibs in #1568
• SCRUM-4089 Implement Paralogy Validator and test cases by @VarunReddy1111 in #1566
• SCRUM-3708 fixes by @markquintontulloch in #1569
• SCRUM-3951 Fix reference synchronisation by @markquintontulloch in #1571
• SCRUM-4137 add SGD background String info to uniqueID from DieseaseAn… by @cmpich in #1570
• SCRUM-4090 Paralogy Load clean up by @VarunReddy1111 in #1572
• Added rule to disallow trailing whitespace by @oblodgett in #1573
• Add prettier by @adamgibs in #1574
• SCRUM-4162 change to have multiple error messages in download file by @VarunReddy1111 in #1575
• More checkstyle checks by @oblodgett in #1576
• SCRUM-4186 Migration for OMIM to MIM switch by @markquintontulloch in #1578
• SCRUM-3708: add initial load of gene expressions by @abecerra in #1558
• SCRUM-4113 remove name, curie, and modInternalId from DA subject filter by @adamgibs in #1577
• SCRUM-3708: bump migration prefix by @abecerra in #1579
• SCRUM-4137 Fix cleanup error by @markquintontulloch in #1580
• SCRUM-4148 added OR token operator back to multiselect filter by @adamgibs in #1581
• SCRUM-4191 Turn off failure limit for paralogy and interaction loads by @markquintontulloch in #1582
• SCRUM-3708: replace modId per AGRId in in GeneExpression uniqueId by @abecerra in #1583
• SCRUM-4183 by @adamgibs in #1584
• SCRUM-3708: fix validation for evidence by @abecerra in #1585
• SCRUM-3951 (update) Fix NPE by @markquintontulloch in #1586
• SCRUM-4204 Sort file history by date load started by @markquintontulloch in #1587
• SCRUM-4209 Report loads as 'FAILED' when stopped due to exceeding failure rate cutoff by @markquintontulloch in #1588
• SCRUM-4210 Reset error message on file reload by @markquintontulloch in #1589
• Added migration to add all the category tags into vocabulary by @VarunReddy1111 in #1590
• SCRUM-4228 Remove error rate column from data loads page by @markquintontulloch in #1592
• SCRUM-4227 Fix null error on file history dropdown for files with no history by @markquintontulloch in #1593
• Release/v0.34.0 rc1 by @markquintontulloch in #1600

Full Changelog: v0.33.0-rc1...v0.34.0-rc1

AGR Curation v0.33.1

What's Changed

• Removed public view for asserted genes and inffered gene crossreferences by @oblodgett in #1548

Full Changelog: v0.33.0...v0.33.1

AGR Curation v0.33.0

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
• Release/v0.33.0 by @VarunReddy1111 in #1535

Full Changelog: v0.32.1...v0.33.0

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