AGR 7.5.0 Release

What's Changed

• SCRUM-4518 Switching to Null class example schemas for all end points by @VarunReddy1111 in #1212
• Scrum 4529 by @oblodgett in #1213
• Bump org.infinispan:infinispan-commons from 14.0.17.Final to 14.0.25.Final by @dependabot in #1210
• Added local file caching for better performance on many runs by @oblodgett in #1205
• Removed custom null serializer by @oblodgett in #1214
• SCRUM-4538 upgrade to independent genetic modifier model by @cmpich in #1215
• Fix faulty neo4j query by @cmpich in #1216
• Fix to enable downloading of experimental conditions in associated al… by @VarunReddy1111 in #1217
• Added ameliorated and exacerbated by conditions by @VarunReddy1111 in #1218
• Duplicate condition modifiers and experimental conditions removed for… by @VarunReddy1111 in #1219
• SCRUM-4603 set genetic entity association via getFullRelation by @cmpich in #1220
• Fix for experimental conditions by @VarunReddy1111 in #1221

Full Changelog: 7.4.0...7.5.0

AGR 7.4.0 Release

What's Changed

• Added code to pull shard count into a configuration variable by @oblodgett in #1211

Full Changelog: 7.3.0...7.4.0

AGR 7.3.0 Release

What's Changed

• SCRUM-4150 validate various entities of disease annotation for being … by @cmpich in #1204
• Added code for checkstyle by @oblodgett in #1199
• SCRUM-4150 replace OR to an AND by @cmpich in #1206
• SCRUM-4165 populate the Variant-Species attribute from the Transcript… by @cmpich in #1207
• SCRUM-4165 add gene info to variant object by @cmpich in #1208

Full Changelog: 7.2.0...7.3.0

AGR 7.2.0 Release

What's Changed

• SCRUM-3841 by @cmpich in #1192
• SCRUM-4017 re-order columns in allele download file by @cmpich in #1193
• Bump curation library version by @VarunReddy1111 in #1194
• SCRUM-4017 swap species ID and Name column for model table download file by @cmpich in #1195
• Fix for downloading error disease page genes by @VarunReddy1111 in #1197
• SCRUM-4092 make all disease qualifier names be their original names i… by @cmpich in #1196
• Updated curation library version by @oblodgett in #1200
• SCRUM-4099 fixup species name in filtering option by @cmpich in #1201
• Add variants and Accession endpoint by @oblodgett in #1202
• Updated variants to use versioned files vs hardcoded ones by @oblodgett in #1203

Full Changelog: 7.1.0...7.2.0

AGR 7.1.0 Release

What's Changed

• SCRUM-2016 by @cmpich in #1158
• Sort by @cmpich in #1160
• Add IEA to via orthology DAs by @cmpich in #1161
• Fixed display helper due to commit d920119 by @oblodgett in #1163
• SCRUM-3649 reorder download file columns, adjust filter name for dis… by @cmpich in #1164
• SCRUM-3648 make disease qualifiers all consistent accross via-ortholo… by @cmpich in #1165
• suppress via Orthology records from gene page DA table by @cmpich in #1166
• SCRUM-3649 replace newlines with white spaces, show main entity genet… by @cmpich in #1167
• SCRUM-3649 ensure to set phylogeneticOrderIndex to gene of DA and not… by @cmpich in #1168
• SCRUM-3826 Put the isViaOrthology variable onto the parent so it gets inherited … by @cmpich in #1169
• SCRUM-3649 always use genetic enyity type gene for orthology records by @cmpich in #1170
• SCRUM-3649 set generated Relation name into genetic association type … by @cmpich in #1171
• SCRUM-3649 add parentSlimIDs to AlleleDiseaseAnnotationDocuments by @cmpich in #1172
• SCRUM-3798 Added Null class to disease endpoint by @VarunReddy1111 in #1173
• SCRUM-3847 allow to filter by species through taxon.name.keyword fiel… by @cmpich in #1176
• SCRUM-3872 Bump curation library to v0.31.0 by @markquintontulloch in #1175
• SCRUM-3872 fix API to use getIdentifier() instead of curie by @cmpich in #1177
• SCRUM-3914 fix DAs on gene and allele page: subject.curie -> subject.… by @cmpich in #1178
• SCRUM-3914 SCRUM-3872 fix download logic with entity.getIdentifier, f… by @cmpich in #1179
• Increased client buffer size and default row limit by @VarunReddy1111 in #1180
• SCRUM-3921 fix api call for orthologous records by @cmpich in #1181
• SCRUM-3919 by @cmpich in #1182
• SCRUM-3943 by @cmpich in #1183
• SCRUM-3948: fix operation description in swager by @abecerra in #1184
• Change to fix crashing disease page gene endpoint in swagger by @VarunReddy1111 in #1185
• SCRUM-3948: fix parameter description in swager by @abecerra in #1187
• replace newline with nothing makes all values null for both geneSynop… by @kkarra in #1186
• SCRUM-3957: upgrade curation library to 0.32.0 by @abecerra in #1188
• Changed disease term query parameters for gene table in disease page by @VarunReddy1111 in #1189
• SCRUM-3793: bump library after the hotfix by @abecerra in #1190
• SCRUM-3984 sort diseases case-insensitive for gene table on disease page by @cmpich in #1191

Full Changelog: 7.0.0...7.1.0

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 https://github.com/alliance-genome/...

AGR 6.0.0 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

New Contributors

• @markquintontulloch made their first contribution in #1056

Full Changelog: 5.4.0...6.0.0

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

AGR 5.3.0 Release

What's Changed

• Release 5.1.0 into master by @oblodgett in #947
• SCRUM-1441 fix missing refs by @cmpich in #948
• SCRUM-1219 remove cache index by species by @cmpich in #946
• SCRUM-1883 add two xenbase species by @cmpich in #950
• Update species orderID given new Xenbase species by @chris-grove in #951
• SCRUM-1883 fix orderIDs in the species list by @cmpich in #952
• SCRUM-1968 fix orthologous record order: use phylogenetic ordering by @cmpich in #953
• Changed spaces to tabs by @oblodgett in #955
• Bump aws-java-sdk-s3 from 1.11.475 to 1.12.261 in /agr_java_core by @dependabot in #949
• Bump jackson-databind from 2.11.1 to 2.12.6.1 in /agr_cacher by @dependabot in #960
• Bump jackson-databind from 2.11.1 to 2.12.6.1 in /agr_intermine_data_extractor by @dependabot in #959
• Bump jackson-databind from 2.11.1 to 2.12.6.1 in /agr_java_core by @dependabot in #957
• Bump jackson-databind from 2.11.1 to 2.12.6.1 in /agr_indexer by @dependabot in #956
• Bump jackson-databind from 2.11.0 to 2.12.6.1 in /agr_variant_indexer by @dependabot in #958
• Upgrade Infinispan from 10 to 13 by @oblodgett in #954
• Fix library imports SCRUM-1949 by @oblodgett in #962
• Import and whitespace cleanup by @oblodgett in #961
• Removed chromosome from repo queries by @oblodgett in #964
• Removal of chromosome object from GL by @oblodgett in #965
• SCRUM-2022 add sorting variable to ES search by @cmpich in #967
• pom version mismatch problem? by @kkarra in #971
• Added closable ES client and closes after 3 minutes (SCRUM-2206) by @oblodgett in #979

New Contributors

• @chris-grove made their first contribution in #951

Full Changelog: 5.1.0...5.3.0

AGR 5.1.0 Release

What's Changed

• Bump httpclient from 4.5.10 to 4.5.13 in /agr_java_core by @dependabot in #819
• Bump elasticsearch from 7.9.0 to 7.13.3 in /agr_java_core by @dependabot in #908
• Release 4.1.0 into Master by @oblodgett in #919
• SCRUM-271 merge all pub/ev codes into PAEs by @cmpich in #921
• Scrum-271 release branch by @cmpich in #924
• Bump log4j-api from 2.13.2 to 2.15.0 by @dependabot in #927
• Bump log4j-core from 2.13.2 to 2.15.0 in /agr_schema_validation by @dependabot in #926
• Bump log4j-core from 2.13.2 to 2.15.0 in /agr_java_core by @dependabot in #925
• SCRUM-271 by @cmpich in #922
• Bump elasticsearch from 7.13.3 to 7.14.0 in /agr_java_core by @dependabot in #920
• Bump log4j-api from 2.15.0 to 2.16.0 by @dependabot in #928
• Bump log4j-core from 2.15.0 to 2.16.0 in /agr_java_core by @dependabot in #930
• Bump log4j-core from 2.15.0 to 2.16.0 in /agr_schema_validation by @dependabot in #929
• Bump log4j-api from 2.16.0 to 2.17.0 by @dependabot in #933
• Bump log4j-core from 2.16.0 to 2.17.0 in /agr_schema_validation by @dependabot in #932
• Bump log4j-core from 2.16.0 to 2.17.0 in /agr_java_core by @dependabot in #931
• Bump log4j-core from 2.17.0 to 2.17.1 in /agr_java_core by @dependabot in #934
• Bump log4j-core from 2.17.0 to 2.17.1 in /agr_schema_validation by @dependabot in #935
• Bump log4j-api from 2.17.0 to 2.17.1 by @dependabot in #936
• Release 4.2.0 into master by @oblodgett in #937
• fixed some dependencies versions by @dougli1sqrd in #938
• This needs to get sorted out in the UI not the API by @oblodgett in #939
• fix scrum-251 from release-5.1.0 by @FB-ping in #944
• Fix urls to be the same field name as in neo by @oblodgett in #945

New Contributors

• @dougli1sqrd made their first contribution in #938

Full Changelog: 4.1.0...5.1.0