AGR Curation v0.36.0-rc3

What's Changed

• Mergeback release v0.36.0-rc2 to alpha by @devopsagr in #1796
• Fix migration for deployment in light of resource descriptor changes by @markquintontulloch in #1797
• SCRUM-4721: alpha to beta release/v0.36.0 rc3 by @abecerra in #1799

Full Changelog: v0.36.0-rc2...v0.36.0-rc3

AGR Curation v0.36.0-rc2

What's Changed

• SCRUM-4447 Add gene/phenotypes xrefs by @markquintontulloch in #1748
• Mergeback release v0.36.0-rc1 to alpha by @devopsagr in #1750
• Added indexes for the blue team by @oblodgett in #1752
• Added name to the hash check by @oblodgett in #1751
• Renamed the migration by @oblodgett in #1756
• SCRUM-4617 - add history cleanup job by @adamgibs in #1755
• SCRUM-4163 Add GEO cross-reference load by @markquintontulloch in #1757
• SCRUM-4280 Differentiate labels for different interaction loads by @markquintontulloch in #1759
• Initial code to stop loads by @oblodgett in #1762
• SCRUM-4691 Fix cleanup of interaction loads by @markquintontulloch in #1761
• Added dependencies for loads by @oblodgett in #1764
• SCRUM-4690 Reimplement Expression Atlas xref load by @markquintontulloch in #1760
• Added code to create a new history everytime a current one is run by @oblodgett in #1765
• DA notes and condition relation dialogs fix by @adamgibs in #1767
• SCRUM-4697 Reimplement Biogrid xref load with genus check by @markquintontulloch in #1766
• Add related notes to Genes table by @VarunReddy1111 in #1758
• Fix typo in XBXL Biogrid load by @markquintontulloch in #1769
• SCRUM-4696 Add load order dependency section to README by @markquintontulloch in #1770
• SCRUM-4714 Fix NPE for empty ingest sets by @markquintontulloch in #1771
• SCRUM-4646 add synonym loading for AGMs by @cmpich in #1768
• SCRUM-4647 implementation of secondary IDs for AGMs. by @cmpich in #1772
• SCRUM-4647 add UI part of secondary ID column by @cmpich in #1774
• Add convenience methods by @cmpich in #1775
• Add convenience methods (#1775) by @cmpich in #1776
• Mergeback release v0.35.2 to alpha by @devopsagr in #1778
• SCRUM-4669 AGM STR Associations by @adamgibs in #1773
• Add synonyms to variant by @VarunReddy1111 in #1777
• Added forced stopped job status by @oblodgett in #1780
• SCRUM-4710 disable scheduling of mass indexing by @cmpich in #1779
• add shortCitation to JSON and fix pubModID logic by @cmpich in #1781
• add shortCitation to JSON and fix pubModID logic by @cmpich in #1782
• Mergeback release v0.35.3 to alpha by @devopsagr in #1783
• Use runtime exception by @oblodgett in #1784
• Switched out for runtime exceptions by @oblodgett in #1785
• Add pubModID to Reference object in Json output by @cmpich in #1786
• Mergeback release v0.35.4 to alpha by @devopsagr in #1787
• SCRUM-4657: add references to Variant FMS load by @abecerra in #1788
• SCRUM-4657: rename migration by @abecerra in #1789
• SCRUM-4672 LinkML v2.9.1 migration by @markquintontulloch in #1790
• SCRUM-4748 Fix xref persistence error by @markquintontulloch in #1792
• SCRUM-4672 (update) Drop dataprovider table by @markquintontulloch in #1794
• SCRUM-4721: alpha to beta release v0.36.0-rc2 by @abecerra in #1795

Full Changelog: v0.36.0-rc1...v0.36.0-rc2

AGR Curation v0.35.4

What's Changed

• Add pubModID to Reference object in Json output by @cmpich in #1786

Full Changelog: v0.35.3...v0.35.4

AGR Curation v0.35.3

What's Changed

• add shortCitation to JSON and fix pubModID logic by @cmpich in #1782

Full Changelog: v0.35.2...v0.35.3

AGR Curation v0.35.2

What's Changed

• Add convenience methods (#1775) by @cmpich in #1776

Full Changelog: v0.35.1...v0.35.2

AGR Curation v0.36.0-rc1

What's Changed

• SCRUM-4509 Validation of HTPExpressionDataSampleAnnotation by @VarunReddy1111 in #1698
• MGI load fix by @VarunReddy1111 in #1699
• SCRUM-4442 & SCRUM-4554 VEP result loading by @markquintontulloch in #1700
• SCRUM-4442 (update) Handle amino acids for synonymous variants by @markquintontulloch in #1701
• SCRUM-4442 (update) Skip VEP results for intergenic variants by @markquintontulloch in #1702
• SCRUM-4442 (update) Handle ambiguous codon change by @markquintontulloch in #1703
• SCRUM-4190 GAF load by @cmpich in #1691
• SCRUM-4442 (update) Handle whitespace and lower-case characters in ref/alt sequences for HGVSg identifier generation by @markquintontulloch in #1707
• Mergeback release v0.35.0-rc2 to alpha by @devopsagr in #1706
• Fixed bug with synonyms by @oblodgett in #1710
• SCRUM-4539 Load GeneGenomicLocationAssociation from GFF by @markquintontulloch in #1711
• Fix file history by @oblodgett in #1712
• SCRUM-4561 Fix failing ZFIN TranscriptGeneAssociation and GeneGenomicLocationAssociation loads by @markquintontulloch in #1713
• Added fix for curation cerebro admin link by @oblodgett in #1716
• Adding vocabulary terms to genetic sex vocabulary by @VarunReddy1111 in #1708
• Changed the ES protocol to http by @VarunReddy1111 in #1717
• Add convenience method for genetic modifiers by @cmpich in #1715
• Added other synonym types by @oblodgett in #1718
• Release/v0.35.0 by @VarunReddy1111 in #1719
• Fixing htpdataset table name column by @VarunReddy1111 in #1722
• Mergeback release v0.35.0 to alpha by @devopsagr in #1720
• SCRUM-4571 Orphaned dataprovider cleanup by @markquintontulloch in #1721
• SCRUM-4574 Fix sorting of file histories by date by @markquintontulloch in #1725
• SCRUM-4575 - Fix setCounts() bug for bulk load histories created prior to reporting change by @markquintontulloch in #1724
• SCRUM-4585 Update entity counts page by @markquintontulloch in #1727
• SCRUM-4585 (update) Remove links for entities without tables by @markquintontulloch in #1728
• SCRUM-4585 (update) Remove more dead links by @markquintontulloch in #1729
• SCRUM-4585 (update) Column rename by @markquintontulloch in #1730
• SCRUM-4572 left justify ListDialog columns by @adamgibs in #1731
• SCRUM-3953: load expression experiments afer annotations by @abecerra in #1723
• SCRUM-4606 Add fields to JsonIgnore to fix 400 error on Constructs table by @markquintontulloch in #1732
• SCRUM-4190 by @cmpich in #1714
• SCRUM-3953: add missing XBXL load by @abecerra in #1733
• SCRUM-4606 Added new columns to controlled vocabulary terms by @VarunReddy1111 in #1736
• Adding integration tests for HTP Data Sample by @VarunReddy1111 in #1734
• SCRUM-3953: fix loadType for expression annotations by @abecerra in #1737
• SCRUM-4513 by @adamgibs in #1726
• SCRUM-4603 add convenience method for relation plus negation by @cmpich in #1738
• Mergeback release v0.35.1 to alpha by @devopsagr in #1739
• SCRUM-3953 (update) Fix record counts by @markquintontulloch in #1740
• SCRUM-4608 Fix counts for disease annotation loads by @markquintontulloch in #1741
• SCRUM-4607 add sticky header to data loads page by @adamgibs in #1742
• Scrum 4436 by @cmpich in #1735
• SCRUM-4627 Prevent cleanup of ConstructGenomicEntityAssociation objects if load fails by @markquintontulloch in #1745
• SCRUM-4626 make a unique set of GAF records (geneID,GoTermCurie) by @cmpich in #1744
• SCRUM-4625 fix lazy initialization error by @cmpich in #1746
• SCRUM-4618: add MaTI host info and link by @abecerra in #1747
• SCRUM-4633: release/v0.36.0-rc1 by @abecerra in #1749

Full Changelog: v0.35.0-rc2...v0.36.0-rc1

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