AGR Curation v0.36.2

What's Changed

• Release/v0.36.2 by @markquintontulloch in #1845

Full Changelog: v0.36.1...v0.36.2

AGR Curation v0.36.1

What's Changed

• SCRUM-4634: Promote curation R12 S3 beta to prod (as v0.36.1) by @abecerra in #1834

Full Changelog: v0.36.0...v0.36.1

AGR Curation v0.36.0

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
• 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
• 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-4447 Add gene/phenotypes xrefs by @markquintontulloch in #1748
• SCRUM-4633: release/v0.36.0-rc1 by @abecerra in #1749
• 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
• 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
• 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
• 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 m...

AGR Curation v0.36.0-rc6

What's Changed

• Update valid LinkML versions for ingest classes by @markquintontulloch in #1820

Full Changelog: v0.36.0-rc5...v0.36.0-rc6

AGR Curation v0.36.0-rc5

What's Changed

• v0.35.5 Hotfix - Clean up expression_atlas xrefs by @markquintontulloch in #1802
• SCRUM-4762 Removed orphan removal true in ExternalDatabaseEntity by @VarunReddy1111 in #1811
• Prmerge/production by @VarunReddy1111 in #1815

Full Changelog: v0.36.0-rc4...v0.36.0-rc5

AGR Curation v0.35.6

What's Changed

• SCRUM-4762 Removed orphan removal true in ExternalDatabaseEntity by @VarunReddy1111 in #1811

Full Changelog: v0.35.5...v0.35.6

AGR Curation v0.36.0-rc4

What's Changed

• v0.36.0-rc4 Rename and adapt migration in light of hotfix on production by @markquintontulloch in #1804

Full Changelog: v0.36.0-rc3...v0.36.0-rc4

AGR Curation v0.35.5

What's Changed

• v0.35.5 Hotfix - Clean up expression_atlas xrefs by @markquintontulloch in #1802

Full Changelog: v0.35.4...v0.35.5

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