AGR 5.4.0 Release

What's Changed

• fix scrum-251 for missing allele count for disease by @FB-ping in #943
• SCRUM-2013 create indexer stub to retrieve DiseaseAnnotation records by @cmpich in #969
• SCRUM-2011 add indexer to Main class to be automatically included in indexing by @cmpich in #970
• SCRUM-2014 retrieve disease annotations and filter them by privacy and existence in Neo4j by @cmpich in #973
• Bump jackson-databind from 2.13.4 to 2.13.4.1 in /agr_indexer by @dependabot in #978
• Bump jackson-databind from 2.12.6.1 to 2.13.4.1 in /agr_intermine_data_extractor by @dependabot in #975
• Bump jackson-databind from 2.13.4 to 2.13.4.1 in /agr_cacher by @dependabot in #976
• Bump jackson-databind from 2.13.4 to 2.13.4.1 in /agr_java_core by @dependabot in #977
• Bump jackson-databind from 2.12.6.1 to 2.13.4.1 in /agr_variant_indexer by @dependabot in #974
• Scrum-2015 expansion by @cmpich in #980
• Release 5.3.0 by @oblodgett in #981
• Scrum 2015 by @oblodgett in #983
• Added primary gene annotation by @oblodgett in #984
• Added default token by @oblodgett in #985
• SCRUM-2354 - Initial Code to switch out Thorntail for Quarkus by @oblodgett in #987
• Refactored for 7.14.0 client by @oblodgett in #994
• SCRUM-2442 add all pubs when merging DAs for gene associations on dis… by @cmpich in #996
• SCRUM-2019 convert disease ribbon to use persistent store data by @cmpich in #997
• SCRUM-2374 fix filter options on disease annotation table by @cmpich in #999
• SCRUM-2019 add parent IDs for each disease term by @cmpich in #1001
• Fix for this PR by @oblodgett in #1002
• Added fix for closing repository when finished by @oblodgett in #1003
• retrieve referenceID from cross references by @cmpich in #1005
• Added PR validation by @oblodgett in #1006
• SCRUM-2029 fix filter name for gene column by @cmpich in #1007
• Added code to fix this for SGD by @oblodgett in #1008
• Updated version of curation software due to deployment SCRUM-2534 by @oblodgett in #1010
• SCRUM-2019 make ribbon clicks be honored by the table. by @cmpich in #1012
• SCRUM-2374 make wild card query case-insensitive by @cmpich in #1013
• SCRUM-2019 SCRUM-2029 SCRUM-2418 show full data provider info, date created and evidence code, consolidate multiple basedOn Genes into single column in download file, fix DOID:OTHER ribbon category by @cmpich in #1015
• Scrum 2551 by @oblodgett in #1016
• SCRUM-2374 make keyword filter searches not use wild card queries by @cmpich in #1018
• Updated default tag for linux env. by @christabone in #1019
• SCRUM-2409 filter on negated flag by @cmpich in #1020
• Added sorting by @oblodgett in #1022
• SCRUM-2409 SCRUM-2374 SCRUM-2570 by @oblodgett in #1023
• Updated sort field by @oblodgett in #1024
• SCRUM-2409 print out diseaseRelatonNegation attribute instead of dise… by @cmpich in #1026
• Code to remove annotation facets by @oblodgett in #1025
• Added nested field for crossReferences by @oblodgett in #1027
• Import cleanup by @oblodgett in #1029
• fix download issues: disease and provider column by @cmpich in #1030
• SCRUM-2684 honor the include-negated-annotation flag by @cmpich in #1031
• SCRUM-2697 escape filter values by @cmpich in #1033
• SCRUM-2720 fix case when AGM.subtype is null by @cmpich in #1034
• SCRUM-2721: backend trick for Saccharomyces cerevisia by @abecerra in #1036
• Added fix for data extractor by @oblodgett in #1037
• Fix for changing the type to string vs enum by @oblodgett in #1035
• SCRUM-2721: fixing SC by @abecerra in #1043
• SCRUM-2721: add filter for both SC and SC288C by @abecerra in #1044
• SCRUM-2721: add filter for SC288C only by @abecerra in #1045
• SCRUM-2721: moving SC288C trick to getDiseaseAnnotationsRibbonDetails by @abecerra in #1046
• SCRUM-2721: fix in taxon by @abecerra in #1047

New Contributors

• @christabone made their first contribution in #1019
• @abecerra made their first contribution in #1036

Full Changelog: 5.3.0...5.4.0