AGR Curation v0.35.1

What's Changed

• SCRUM-4603 add convenience method for relation plus negation by @cmpich in #1738

Full Changelog: v0.35.0...v0.35.1

AGR Curation v0.35.0

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
• SCRUM-4299 by @adamgibs in #1628
• SCRUM-3952: add ExpressionPattern, TemporalContext and AnatomicalSite by @abecerra in #1627
• Scrum 4305 by @cmpich in #1629
• Release/v0.35.0 rc1 by @VarunReddy1111 in #1633
• Mergeback release v0.35.0-rc1 to alpha by @devopsagr in #1634
• Mergeback release v0.34.2 to alpha by @devopsagr in #1632
• Mergeback release v0.34.3 to alpha by @devopsagr in #1637
• Removed indexing from failing phenotype annotations by @oblodgett in #1635
• SCRUM-3953: ignore the entry -Other- for Uberon terms by @abecerra in #1638
• SCRUM-4176 GFF Loading Part 3 (Parent child associations) by @markquintontulloch in #1639
• Scrum 4303 - P2- HTPDatasetAnnotation loading into persistent store by @VarunReddy1111 in #1641
• SCRUM-4336 Implement Reference caching for data loads by @markquintontulloch in #1642
• SCRUM-4337 Clean up erroneous DO terms by @markquintontulloch in #1643
• SCRUM-3952: Fix stage uberon slim terms by @abecerra in #1647
• SCRUM-4174 (update) Remove Pseudogene: prefix from WB GFF entries by @markquintontulloch in #1644
• SCRUM-4300 by @adamgibs in #1640
• Initial Code for flattening the tables by @oblodgett in #1645
• Updated cluster version by @oblodgett in #1650
• Remove all exceptions after two weeks by @oblodgett in #1648
• upgrade opensearch version by @cmpich in #1651
• Initial code to restructure bulk load file history by @oblodgett in #1653
• Updated UI by @oblodgett in #1654
• Initial Code for removing data provider dups by @oblodgett in #1652
• SCRUM-3952: fix to save exceptions in DB by @abecerra in #1655
• SCRUM-3754 by @adamgibs in #1657
• Remove and add back FK's by @oblodgett in #1656
• Better Count Handling and GFF Load consolidation. by @oblodgett in #1658
• Code for final GFF loads and button fixes. by @oblodgett in #1660
• HTP dataset annotation validation and test cases by @VarunReddy1111 in #1659
• SCRUM 4283 - Removing similarity, length and identity from Paralogy required fields by @VarunReddy1111 in #1661
• Added missing column types and indexes (Merge after Load) by @oblodgett in #1662
• SCRUM-4368 Enable skipping of known issues by @markquintontulloch in #1663
• SCRUM-4424 Integration test base method refactor by @markquintontulloch in #1664
• Fix missing Indexes and Flatten Associations by @oblodgett in #1665
• SCRUM-4429 update data loads page running time by @adamgibs in #1668
• SCRUM-4176 Fix loading of TranscriptGeneAssociations when transcript parent attribute not curie by @markquintontulloch in #1669
• removed dropAndCreateSchemaOnStart by @adamgibs in #1670
• Change in BaseSQLDAO by @VarunReddy1111 in #1671
• Revert "removed dropAndCreateSchemaOnStart" by @adamgibs in #1672
• Changes in BaseSQLDAO by @VarunReddy1111 in #1673
• SCRUM-4436 improve construct association load performance by @cmpich in #1666
• SCRUM-3952: change vocabularyterm to ontologyterm after LinkML change by @abecerra in #1667
• SCRUM-3758 by @adamgibs in #1675
• SCRUM-3757 update ControlledVocabularyTable body templates by @adamgibs in #1676
• Scrum 4452 by @VarunReddy1111 in #1678
• Table body template refactor by @adamgibs in #1679
• UI updates by @adamgibs in #1681
• Updated code for mapped superclass associations by @markquintontulloch in #1680
• Add missing sequence by @markquintontulloch in #1682
• Actually fix missing sequence by @markquintontulloch in #1683
• RGD load and category tag validation change by @VarunReddy1111 in #1685
• Added code to loop through all the loads in counts and check for failed by @va...

AGR Curation v0.35.0-rc2

What's Changed

• SCRUM-4299 by @adamgibs in #1628
• SCRUM-3952: add ExpressionPattern, TemporalContext and AnatomicalSite by @abecerra in #1627
• Scrum 4305 by @cmpich in #1629
• SCRUM-4305 set obsolete / internal variables explicitly when being up… by @cmpich in #1631
• Mergeback release v0.35.0-rc1 to alpha by @devopsagr in #1634
• Mergeback release v0.34.2 to alpha by @devopsagr in #1632
• Updated query to always have an orderBy by @oblodgett in #1636
• Mergeback release v0.34.3 to alpha by @devopsagr in #1637
• Removed indexing from failing phenotype annotations by @oblodgett in #1635
• SCRUM-3953: ignore the entry -Other- for Uberon terms by @abecerra in #1638
• SCRUM-4176 GFF Loading Part 3 (Parent child associations) by @markquintontulloch in #1639
• Scrum 4303 - P2- HTPDatasetAnnotation loading into persistent store by @VarunReddy1111 in #1641
• SCRUM-4336 Implement Reference caching for data loads by @markquintontulloch in #1642
• SCRUM-4337 Clean up erroneous DO terms by @markquintontulloch in #1643
• SCRUM-3952: Fix stage uberon slim terms by @abecerra in #1647
• SCRUM-4174 (update) Remove Pseudogene: prefix from WB GFF entries by @markquintontulloch in #1644
• SCRUM-4300 by @adamgibs in #1640
• Initial Code for flattening the tables by @oblodgett in #1645
• Updated cluster version by @oblodgett in #1650
• Remove all exceptions after two weeks by @oblodgett in #1648
• upgrade opensearch version by @cmpich in #1651
• Initial code to restructure bulk load file history by @oblodgett in #1653
• Updated UI by @oblodgett in #1654
• Initial Code for removing data provider dups by @oblodgett in #1652
• SCRUM-3952: fix to save exceptions in DB by @abecerra in #1655
• SCRUM-3754 by @adamgibs in #1657
• Remove and add back FK's by @oblodgett in #1656
• Better Count Handling and GFF Load consolidation. by @oblodgett in #1658
• Code for final GFF loads and button fixes. by @oblodgett in #1660
• HTP dataset annotation validation and test cases by @VarunReddy1111 in #1659
• SCRUM 4283 - Removing similarity, length and identity from Paralogy required fields by @VarunReddy1111 in #1661
• Added missing column types and indexes (Merge after Load) by @oblodgett in #1662
• SCRUM-4368 Enable skipping of known issues by @markquintontulloch in #1663
• SCRUM-4424 Integration test base method refactor by @markquintontulloch in #1664
• Fix missing Indexes and Flatten Associations by @oblodgett in #1665
• SCRUM-4429 update data loads page running time by @adamgibs in #1668
• SCRUM-4176 Fix loading of TranscriptGeneAssociations when transcript parent attribute not curie by @markquintontulloch in #1669
• removed dropAndCreateSchemaOnStart by @adamgibs in #1670
• Change in BaseSQLDAO by @VarunReddy1111 in #1671
• Revert "removed dropAndCreateSchemaOnStart" by @adamgibs in #1672
• Changes in BaseSQLDAO by @VarunReddy1111 in #1673
• SCRUM-4436 improve construct association load performance by @cmpich in #1666
• SCRUM-3952: change vocabularyterm to ontologyterm after LinkML change by @abecerra in #1667
• SCRUM-3758 by @adamgibs in #1675
• SCRUM-3757 update ControlledVocabularyTable body templates by @adamgibs in #1676
• Scrum 4452 by @VarunReddy1111 in #1678
• Table body template refactor by @adamgibs in #1679
• UI updates by @adamgibs in #1681
• Updated code for mapped superclass associations by @markquintontulloch in #1680
• Add missing sequence by @markquintontulloch in #1682
• Actually fix missing sequence by @markquintontulloch in #1683
• RGD load and category tag validation change by @VarunReddy1111 in #1685
• Added code to loop through all the loads in counts and check for failed by @VarunReddy1111 in #1686
• SCRUM-4426 HTPDATASAMPLE java modeling and tables creation by @VarunReddy1111 in #1684
• Updated schedule for purging by @oblodgett in #1688
• Adding new indexes for htpdatasample by @VarunReddy1111 in #1689
• Added transactional by @oblodgett in #1690
• SCRUM-4118 Implement Expression Atlas load by @cmpich in #1687
• SCRUM-4523 & SCRUM-4254 Split diseaseGeneticModifiers into gene-, allele-, and AGM-specific fields by @markquintontulloch in #1692
• Forgot to observe async all the events after the refactor by @oblodgett in #1694
• SCRUM-4440 add biogrid orc load by @adamgibs in #1693
• ReEnabled indexing for phenotypes by @oblodgett in #1696
• pass down default column width in molecules table by @adamgibs in #1697
• SCRUM-4499 FMS loading of Variant, CuratedVariantGenomicLocationAssociation, and AlleleVariantAssociation objects by @markquintontulloch in #1695
• Release/v0.35.0 rc2 by @VarunReddy1111 in #1705

Full Changelog: v0.35.0-rc1...v0.35.0-rc2

AGR Curation v0.34.3

What's Changed

• Updated query to always have an orderBy by @oblodgett in #1636

Full Changelog: v0.34.2...v0.34.3

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