AGR 7.0.0 Release

What's Changed

• Bump jackson-databind from 2.13.4.1 to 2.13.4.2 in /agr_cacher by @dependabot in #1042
• Bump jackson-databind from 2.13.4 to 2.13.4.2 in /agr_intermine_data_extractor by @dependabot in #1038
• Bump jackson-databind from 2.13.4.1 to 2.13.4.2 in /agr_indexer by @dependabot in #1039
• Bump jackson-databind from 2.13.4.1 to 2.13.4.2 in /agr_variant_indexer by @dependabot in #1040
• Bump jackson-databind from 2.13.4.1 to 2.13.4.2 in /agr_java_core by @dependabot in #1041
• Release 5.4.0 by @oblodgett in #1049
• SCRUM-2851 upgrade OGM driver from 3.x to 4.0.4 by @cmpich in #1052
• SCRUM 2851 fix cacher after neo4j upgrade by @cmpich in #1053
• SCRUM-2727 create new field on DiseseAnnotationDocument: PubmedPubModID by @cmpich in #1051
• Fixed queries by @oblodgett in #1055
• Merge Code from master to release by @oblodgett in #1057
• SCRUM-2913 Fix Neo queries by @markquintontulloch in #1056
• SCRUM-2727 turn pubmedPubModId into a collection by @cmpich in #1059
• SCRUM-2727 filter disease association table.reference column against PubMedID/PubModID by @cmpich in #1060
• SCRUM-2727 escape colon in string throught QueryParser.escape() by @cmpich in #1062
• Remove obsoletes for now by @oblodgett in #1064
• Updated curation software version by @oblodgett in #1063
• SCRUM-2723 deleted subtype hack code by @adamgibs in #1065
• SCRUM-2704 add paralogy chacher infrastructure plus new endpoint for paralogy by @cmpich in #1066
• SCRUM-2704 by @cmpich in #1068
• SCRUM-2823 include all DA attributes in download file by @cmpich in #1067
• SCRUM-2704 add note / summary to note column in download file by @cmpich in #1070
• SCRUM-2704 add a few more attributes to download logic by @cmpich in #1071
• SCRUM-2704 handle null dataProvider and null crossReferences by @cmpich in #1073
• SCRUM-2824 add diseaseQualifier into ES, mapping of vocabulary term by @cmpich in #1076
• SCRUM-2823 fix evidence code Column of disease annotation table on gene page by @cmpich in #1075
• SCRUM-2823 add GeneticModifierNames to download file by @cmpich in #1077
• SCRUM-2823 upgrade curation library by @cmpich in #1078
• Scrum 2824 by @cmpich in #1080
• SCRUM-2824 adjust mapping of qualifier names by @cmpich in #1081
• SCRUM-2824 by @cmpich in #1082
• SCRUM-2824 use mapped strings for disease qualifiers in download file by @cmpich in #1083
• Added fix for consolidation via SGD by @oblodgett in #1084
• Fixed logic for consolidation of gene disease annotations by @oblodgett in #1085
• SCRUM-3091 add new genetic entityt association column to download file by @cmpich in #1087
• Added code for species ordering by @oblodgett in #1086
• SCRUM-3091 fix column header name by @cmpich in #1088
• Turn on query debugging by @oblodgett in #1089
• Added fix for keyword field by @oblodgett in #1090
• Fix for speciesorder sort field by @oblodgett in #1091
• Added code for fixing sorting on species order by @oblodgett in #1092
• Fix Compile Error and change Github checks by @oblodgett in #1093
• SCRUM-3217 fix multiple selections to search against keyword (full string) by @cmpich in #1094
• Fix Cacher to remove unused fields for disease annotations from Neo SCRUM-3228 by @oblodgett in #1095
• SCRUM-3221 replace old fields on Paralogus object with length, identity, similarity and rank by @cmpich in #1096
• SCRUM-3221 make identity a string not a float by @cmpich in #1098
• Removed logging by @oblodgett in #1097
• Added code to fix reference errors by @oblodgett in #1099
• SCRUM-3221 turn all float types into String types in Paralogous class by @cmpich in #1100
• SCRUM-3221 turn all integer types into String types in Paralogous class by @cmpich in #1101
• SCRUM-3221 make ParalogBean the class type for the Paralogy cacher object by @cmpich in #1102
• SCRUM-3257 by @cmpich in #1103
• strip multiple newlines in synopsis by @kkarra in #1105
• SCRUM-3257 make escaping come after splitting off | selection list by @cmpich in #1104
• Scrum-3280 Fix NPE with DA download file by @oblodgett in #1106
• SCRUM-3280 enable Json on publicationJoins object by @cmpich in #1107
• SCRUM-3251 SCRUM-3280 by @cmpich in #1108
• Fixed code for indexer by @oblodgett in #1111
• SCRUM-3280 undo logic for download file as publicationJoins got revived. by @cmpich in #1110
• Fix indexer by @oblodgett in #1112
• Fix NPE by @oblodgett in #1113
• Fixed sitemap for alleles by @oblodgett in #1114
• SCRUM-3251 check that GeneticModifiers are valid gene/allele or AGM entities by @cmpich in #1116
• Removed host based sitemap by @oblodgett in #1117
• SCRUM-3251 by @cmpich in #1118
• SCRUM-3303: bump quarkus version by @abecerra in #1119
• SCRUM-3305 fix variant category filtering bug by @cmpich in #1120
• SCRUM-3286 Update curation library to v0.25.0 by @markquintontulloch in #1121
• Initial Code for quarkus 3.4 upgrade by @oblodgett in #1122
• Fix indexer and cacher logging. by @oblodgett in #1123
• SCRUM-2392 adjust allele/disease endpoint to retrieve allele disease annotations by @cmpich in #1124
• Added fix for logging and neo driver upgrade by @oblodgett in #1125
• SCRUM-2392 refactor allele diesease endpoint to re-use ES service cod… by @cmpich in #1126
• Updated pom and docker scripts by @oblodgett in #1127
• Attempt 2 to fix logs by @oblodgett in #1128
• SCRUM-2392 refactor ES query logic, shared among gene and allele, fix… by @cmpich in #1129
• Bump curation version to v0.26.0 (SCRUM-3367) by @mluypaert in #1130
• SCRUM-3431 update to curation v0.27.0 by @mluypaert in #1132
• SCRUM-2393 make inferred or asserted AlleleDAs have is_implicated_in … by @cmpich in #1134
• SCRUM-2388 fix allele disease annotation download file by @cmpich in #1135
• SCRUM-2393 fix indexer to populate upper level disease qualifiers for Allele disease annotations by @cmpich in #1136
• Updated neo4j driver and updated timeout by @oblodgett in #1137
• SCRUM-2393: Removal of columns in download file by @abecerra in #1139
• Added qualifiers to consolidation key by @oblodgett in #1140
• The NPE will get you every time by @oblodgett in #1141
• Removed unused extractors by @oblodgett in #1144
• Updated data extractor by @oblodgett in #1143
• Changed endpoint to pull annotations SCRUM-3588 by @oblodgett in #1145
• Added debug code by @oblodgett in #1146
• SCRUM-3315: create a new list of evidence codes by @abecerra in #1147
• SCRUM-3315: add checks for getEvidenceCodes returning null by @abecerra in #1148
• SCRUM-3509: bump curation library version to v0.28.0 by @abecerra in #1149
• SCRUM-3509: upgrade curation library to 0.28.2 by @abecerra in #1150
• SCRUM-3361: fix dataProvider filter by @abecerra in #1151
• SCRUM-3361 search data provider in two places: dataProvider and secondaryDataProvider by @cmpich in #1153
• SCRUM-3674 bump curation library version by @adamgibs in #1154
• SCRUM-3669 do not suppress negated DAs on allele page by @cmpich in #1155
• SCRUM-3716 Bump curation library version by @VarunReddy1111 in #1157
• SCRUM-3697 by @cmpich in #1156

New Contributors

• @markquintontulloch made their first contribution in #1056
• @VarunReddy1111 made their first contribution in #1157

Full Changelog: 5.4.0...7.0.0