AGR Curation v0.23.0-rc1

What's Changed

• SCRUM-3086 Incorporate default value for 'negated' into disease annotation uniqueId in bulk loads by @markquintontulloch in #1173
• SCRUM-3009 by @adamgibs in #1176
• Release v0.22.0-rc1 mergeback by @mluypaert in #1177
• Reorganised other links. by @mluypaert in #1179
• Alternative fix for file checking by @oblodgett in #1181
• SCRUM-2248 Fail loads with invalid URL with correct status by @markquintontulloch in #1180
• SCRUM-2784 by @cmpich in #1178
• SCRUM-2248 update fix for null by @oblodgett in #1183
• SCRUM-3117 Display status of latest file for load by @markquintontulloch in #1185
• SCRUM-3121 by @adamgibs in #1188
• PRmerge/beta (v0.22.0-rc2, SCRUM-3143) mergeback to alpha by @mluypaert in #1189
• SCRUM-3167 Add label to Vocabulary and VocabularyTermSet by @markquintontulloch in #1187
• SCRUM-3167 update - Fix variable names by @markquintontulloch in #1190
• SCRUM-3167 update - UI fix by @markquintontulloch in #1191
• Release/v0.23.0-rc1 by @markquintontulloch in #1198

Full Changelog: v0.22.0-rc2...v0.23.0-rc1

AGR Curation v0.22.0

What's Changed

• SCRUM-1778 Autosuggest tooltip updates by @markquintontulloch in #1129
• SCRUM-2621_mem-monitoring by @mluypaert in #1130
• PRmerge/beta by @markquintontulloch in #1134
• SCRUM-2710 Implement loading of orthology data by @markquintontulloch in #1131
• SCRUM-2710 (update) Handle mismatch between HUMAN datatype and OMIM dataProvider by @markquintontulloch in #1135
• deployment instructions correction by @mluypaert in #1136
• SCRUM-3040 Fix enabling of Keep Edits button for Allele synonyms by @markquintontulloch in #1137
• SCRUM-3038 Fix sorting on updatedBy and createdBy fields by @markquintontulloch in #1138
• SCRUM-3019 Enable clearing of non-required dropdown fields by @markquintontulloch in #1132
• SCRUM-2710 (update) Logging improvements by @markquintontulloch in #1140
• PRmerge/production by @markquintontulloch in #1143
• Scrum 3030 by @adamgibs in #1144
• SCRUM-3030 reset buttons are disabled during row edit by @adamgibs in #1145
• SCRUM-2451, SCRUM-2452, SCRUM-2454, SCRUM-3036 Add MPO, MPATH, MI, and UBERON ontologies by @markquintontulloch in #1146
• SCRUM-3050 Add Rat Strain (RS) ontology by @markquintontulloch in #1148
• SCRUM-3056 Enable loading of XB genes and orthology by @markquintontulloch in #1152
• SCRUM-3051 Fix disappearing loads in Data Loads page by @markquintontulloch in #1153
• SCRUM-2454 (update) Make UBERONTerm an AnatomicalTerm by @markquintontulloch in #1151
• SCRUM-2901 by @adamgibs in #1149
• SCRUM-3030 by @adamgibs in #1150
• SCRUM-3057 Load Pathway Ontology by @markquintontulloch in #1154
• Allele load speedup by @oblodgett in #1147
• SCRUM-3059 & SCRUM-3060 Load Cell Ontology (CL) and Clinical Measurement Ontology (CMO) by @markquintontulloch in #1155
• updated transaction timeout by @oblodgett in #1156
• Added update refresh interval on all indexes endpoint by @oblodgett in #1157
• Fix integer equality check in getCuriePrefixFromTaxonId method by @markquintontulloch in #1158
• Code for quarkus upgrade 3.2 by @oblodgett in #998
• Revert merge pull request #998 (SCRUM-2814) by @mluypaert in #1162
• GH actions updates (including PR-validation ignore edits removal) by @mluypaert in #1161
• SCRUM-3062 Load Biological Spatial Ontology (BSPO) by @markquintontulloch in #1159
• Gh actions fixes by @mluypaert in #1163
• Remove vocabterm xrefs by @markquintontulloch in #1164
• Attempt 1 to fix gh-actions EB deployment using AWS roles by @mluypaert in #1165
• Attempt 2 to fix gh-actions EB deployment using AWS roles by @mluypaert in #1166
• Fix failed to lazily initialize... error by @markquintontulloch in #1167
• SCRUM-3037 (cleanup) Remove temp endpoint by @markquintontulloch in #1168
• PRmerge/production by @markquintontulloch in #1170
• SCRUM-3073 Clean up disease annotations based on subject DataProvider by @markquintontulloch in #1171
• Remove pagination option from findAllIds by @markquintontulloch in #1172
• Release v0.22.0-rc1 by @mluypaert in #1174
• SCRUM-3143 RGD obsoletion fix by @mluypaert in #1186
• Release/v0.22.0 by @markquintontulloch in #1193

Full Changelog: v0.21.0...v0.22.0

AGR Curation v0.22.0-rc2

What's Changed

• SCRUM-3143 RGD obsoletion fix by @mluypaert in #1186

Full Changelog: v0.22.0-rc1...v0.22.0-rc2

AGR Curation release v0.22.0-rc1

What's Changed

• SCRUM-1778 Autosuggest tooltip updates by @markquintontulloch in #1129
• SCRUM-2621_mem-monitoring by @mluypaert in #1130
• PRmerge/beta by @markquintontulloch in #1134
• SCRUM-2710 Implement loading of orthology data by @markquintontulloch in #1131
• SCRUM-2710 (update) Handle mismatch between HUMAN datatype and OMIM dataProvider by @markquintontulloch in #1135
• deployment instructions correction by @mluypaert in #1136
• SCRUM-3040 Fix enabling of Keep Edits button for Allele synonyms by @markquintontulloch in #1137
• SCRUM-3038 Fix sorting on updatedBy and createdBy fields by @markquintontulloch in #1138
• SCRUM-3019 Enable clearing of non-required dropdown fields by @markquintontulloch in #1132
• SCRUM-2710 (update) Logging improvements by @markquintontulloch in #1140
• PRmerge/production by @markquintontulloch in #1143
• Scrum 3030 by @adamgibs in #1144
• SCRUM-3030 reset buttons are disabled during row edit by @adamgibs in #1145
• SCRUM-2451, SCRUM-2452, SCRUM-2454, SCRUM-3036 Add MPO, MPATH, MI, and UBERON ontologies by @markquintontulloch in #1146
• SCRUM-3050 Add Rat Strain (RS) ontology by @markquintontulloch in #1148
• SCRUM-3056 Enable loading of XB genes and orthology by @markquintontulloch in #1152
• SCRUM-3051 Fix disappearing loads in Data Loads page by @markquintontulloch in #1153
• SCRUM-2454 (update) Make UBERONTerm an AnatomicalTerm by @markquintontulloch in #1151
• SCRUM-2901 by @adamgibs in #1149
• SCRUM-3030 by @adamgibs in #1150
• SCRUM-3057 Load Pathway Ontology by @markquintontulloch in #1154
• Allele load speedup by @oblodgett in #1147
• SCRUM-3059 & SCRUM-3060 Load Cell Ontology (CL) and Clinical Measurement Ontology (CMO) by @markquintontulloch in #1155
• updated transaction timeout by @oblodgett in #1156
• Added update refresh interval on all indexes endpoint by @oblodgett in #1157
• Fix integer equality check in getCuriePrefixFromTaxonId method by @markquintontulloch in #1158
• Code for quarkus upgrade 3.2 by @oblodgett in #998
• Revert merge pull request #998 (SCRUM-2814) by @mluypaert in #1162
• GH actions updates (including PR-validation ignore edits removal) by @mluypaert in #1161
• SCRUM-3062 Load Biological Spatial Ontology (BSPO) by @markquintontulloch in #1159
• Gh actions fixes by @mluypaert in #1163
• Remove vocabterm xrefs by @markquintontulloch in #1164
• Attempt 1 to fix gh-actions EB deployment using AWS roles by @mluypaert in #1165
• Attempt 2 to fix gh-actions EB deployment using AWS roles by @mluypaert in #1166
• Fix failed to lazily initialize... error by @markquintontulloch in #1167
• SCRUM-3037 (cleanup) Remove temp endpoint by @markquintontulloch in #1168
• PRmerge/production by @markquintontulloch in #1170
• SCRUM-3073 Clean up disease annotations based on subject DataProvider by @markquintontulloch in #1171
• Remove pagination option from findAllIds by @markquintontulloch in #1172
• Release v0.22.0-rc1 by @mluypaert in #1174

Full Changelog: v0.21.0...v0.22.0-rc1

AGR Curation v0.21.0

What's Changed

• Updated shards for cluster experiment by @oblodgett in #1050
• Added notes back but turned off keyword indexing by @oblodgett in #1051
• SCRUM-2947: release v0.19.0 by @abecerra in #1054
• Updated README search index UI instructions by @mluypaert in #1055
• Prmerge/beta by @adamgibs in #1057
• PRmerge/beta by @markquintontulloch in #1062
• Added missing indexes and added fetch types to speed up queries by @oblodgett in #1059
• Fix issue with header column by @oblodgett in #1065
• SCRUM-2916 Display MOD xrefs first for references by @markquintontulloch in #1066
• SCRUM-2976 Add AuditedObject fields to AGM table by @markquintontulloch in #1067
• SCRUM-2883: Added database user and privileges instructions to README by @mluypaert in #1063
• SCRUM-2932 - Revert subselects by @oblodgett in #1071
• SCRUM-2834 Loading of entities using secondary IDs for ontologies by @markquintontulloch in #1068
• PRmerge/beta by @adamgibs in #1072
• PRmerge/beta by @markquintontulloch in #1074
• Changed agg query to be more than 10 by @oblodgett in #1075
• Attempt to get better performance by @oblodgett in #1077
• SCRUM-2894 Prevent loading of files without LinkML schema version by @markquintontulloch in #1076
• SCRUM-2834 (update) Add new ontology fields to sort constants by @markquintontulloch in #1078
• SCRUM-2946 - Improve error reporting for failed data loads by @markquintontulloch in #1080
• SCRUM-2917: left aligning the column contents by @abecerra in #1064
• SCRUM-2983 added indexedEmbedded include depth to gene and allele DAs by @adamgibs in #1079
• SCRUM-2991 Include all fields (depth 2) in asserted/inferred gene/allele indexes by @markquintontulloch in #1081
• SCRUM-2991 (update) includeDepth instead of includePath for missed field by @markquintontulloch in #1082
• SCRUM-2796 Highlight obsolete rows by @markquintontulloch in #1084
• SCRUM-2991 update - Update with field index and remove filtering on undisplayed fields by @markquintontulloch in #1083
• SCRUM-2915 Hierarchical and alphabetised display of Ontology data tables by @markquintontulloch in #1085
• SCRUM-2915 (update) Update ontology order by @markquintontulloch in #1086
• SCRUM-2786 (update) Update highlight colour for obsolete rows by @markquintontulloch in #1088
• SCRUM-2883: Updated deployment instructions by @mluypaert in #1087
• removed default visible columns from AGM table by @adamgibs in #1089
• README deployment step instruction improvements, SCRUM-2884 by @mluypaert in #1090
• SCRUM-2600: Upgrade to Node 18 by @abecerra in #1091
• SCRUM-2287 Load RO Ontology by @markquintontulloch in #1092
• SCRUM-2911 added row duplication functionality by @adamgibs in #1095
• SCRUM-2338 Load and display allele_database_status attribute by @markquintontulloch in #1094
• SCRUM-2338 (update) Return sorted results for vocab term dropdowns by @markquintontulloch in #1097
• Remove duplicate SlotAnnotation table indexes by @markquintontulloch in #1096
• SCRUM-2448 - Load DPO Ontology by @markquintontulloch in #1098
• Correct migration version by @markquintontulloch in #1099
• SCRUM-2338 (update) Add internal column to database and germline status popups by @markquintontulloch in #1101
• PRmerge/production by @adamgibs in #1102
• Added code to remove many elastic search fields by @oblodgett in #1103
• Slimmed down a few more fields by @oblodgett in #1104
• SCRUM-3006 Add dataProvider to Allele table by @markquintontulloch in #1105
• SCRUM-1206 Load MMO Ontology by @markquintontulloch in #1106
• SCRUM-3006 (update) Sort entries in multiselect dropdowns by @markquintontulloch in #1107
• SCRUM-2828 Prevent loading of duplicate notes by @markquintontulloch in #1108
• SCRUM-3007 Add DataProvider to Gene and AGM tables by @markquintontulloch in #1109
• SCRUM-2447 Load Ascomycete Phenotype Ontology by @markquintontulloch in #1110
• SCRUM-2911 notes and conditions open on duplication by @adamgibs in #1111
• SCRUM-2447 (update) Add namespace column to APO table by @markquintontulloch in #1112
• SCRUM-2447 (update) Fix filter for ontology namespace column by @markquintontulloch in #1114
• SCRUM-3005 Related Note dialog display updates by @markquintontulloch in #1113
• SCRUM-2453 Load Vertebrate Trait Ontology by @markquintontulloch in #1115
• SCRUM-2911 disabled duplication during row edit by @adamgibs in #1116
• Scrum 2982 - Indexing improvements. by @oblodgett in #1117
• SCRUM-3008 Use consensus set of defining properties for DAs by @markquintontulloch in #1118
• Fixed bug with refresh interval on index everything vs a single type by @oblodgett in #1119
• Add keyword indexes for Allele references by @markquintontulloch in #1120
• SCRUM-3021 Switch order of name and curie in tree display by @markquintontulloch in #1122
• SCRUM-2911 conditions appear in condition relation form table by @adamgibs in #1123
• Add more keyword indexes by @markquintontulloch in #1124
• SCRUM-3021 (update) Alphabetize nodes in tree display by @markquintontulloch in #1125
• SCRUM-3021 (update) Sort obsolete terms in tree by @markquintontulloch in #1126
• SCRUM-2707 Entity and DTO classes for Orthology by @markquintontulloch in #1121
• Revert "Use custom SCSS classes" by @adamgibs in #1127
• SCRUM-3005 (update) Custom SCSS class reimplementation by @markquintontulloch in #1128
• Release/v0.21.0 rc1 by @markquintontulloch in #1133
• PRmerge/production by @markquintontulloch in #1142
• Release/v0.21.0 by @markquintontulloch in #1169

Full Changelog: v0.20.1...v0.21.0

AGR Curation v0.20.1

What's Changed

• Release/v0.20.1 by @markquintontulloch in #1141

Full Changelog: v0.20.0...v0.20.1

AGR Curation Prerelease v0.21.0-rc1

What's Changed

• Updated shards for cluster experiment by @oblodgett in #1050
• Added notes back but turned off keyword indexing by @oblodgett in #1051
• SCRUM-2947: release v0.19.0 by @abecerra in #1054
• Updated README search index UI instructions by @mluypaert in #1055
• Prmerge/beta by @adamgibs in #1057
• PRmerge/beta by @markquintontulloch in #1062
• Added missing indexes and added fetch types to speed up queries by @oblodgett in #1059
• Fix issue with header column by @oblodgett in #1065
• SCRUM-2916 Display MOD xrefs first for references by @markquintontulloch in #1066
• SCRUM-2976 Add AuditedObject fields to AGM table by @markquintontulloch in #1067
• SCRUM-2883: Added database user and privileges instructions to README by @mluypaert in #1063
• SCRUM-2932 - Revert subselects by @oblodgett in #1071
• SCRUM-2834 Loading of entities using secondary IDs for ontologies by @markquintontulloch in #1068
• PRmerge/beta by @adamgibs in #1072
• PRmerge/beta by @markquintontulloch in #1074
• Changed agg query to be more than 10 by @oblodgett in #1075
• Attempt to get better performance by @oblodgett in #1077
• SCRUM-2894 Prevent loading of files without LinkML schema version by @markquintontulloch in #1076
• SCRUM-2834 (update) Add new ontology fields to sort constants by @markquintontulloch in #1078
• SCRUM-2946 - Improve error reporting for failed data loads by @markquintontulloch in #1080
• SCRUM-2917: left aligning the column contents by @abecerra in #1064
• SCRUM-2983 added indexedEmbedded include depth to gene and allele DAs by @adamgibs in #1079
• SCRUM-2991 Include all fields (depth 2) in asserted/inferred gene/allele indexes by @markquintontulloch in #1081
• SCRUM-2991 (update) includeDepth instead of includePath for missed field by @markquintontulloch in #1082
• SCRUM-2796 Highlight obsolete rows by @markquintontulloch in #1084
• SCRUM-2991 update - Update with field index and remove filtering on undisplayed fields by @markquintontulloch in #1083
• SCRUM-2915 Hierarchical and alphabetised display of Ontology data tables by @markquintontulloch in #1085
• SCRUM-2915 (update) Update ontology order by @markquintontulloch in #1086
• SCRUM-2786 (update) Update highlight colour for obsolete rows by @markquintontulloch in #1088
• SCRUM-2883: Updated deployment instructions by @mluypaert in #1087
• removed default visible columns from AGM table by @adamgibs in #1089
• README deployment step instruction improvements, SCRUM-2884 by @mluypaert in #1090
• SCRUM-2600: Upgrade to Node 18 by @abecerra in #1091
• SCRUM-2287 Load RO Ontology by @markquintontulloch in #1092
• SCRUM-2911 added row duplication functionality by @adamgibs in #1095
• SCRUM-2338 Load and display allele_database_status attribute by @markquintontulloch in #1094
• SCRUM-2338 (update) Return sorted results for vocab term dropdowns by @markquintontulloch in #1097
• Remove duplicate SlotAnnotation table indexes by @markquintontulloch in #1096
• SCRUM-2448 - Load DPO Ontology by @markquintontulloch in #1098
• Correct migration version by @markquintontulloch in #1099
• Release/v0.20.0 by @adamgibs in #1100
• SCRUM-2338 (update) Add internal column to database and germline status popups by @markquintontulloch in #1101
• PRmerge/production by @adamgibs in #1102
• Added code to remove many elastic search fields by @oblodgett in #1103
• Slimmed down a few more fields by @oblodgett in #1104
• SCRUM-3006 Add dataProvider to Allele table by @markquintontulloch in #1105
• SCRUM-1206 Load MMO Ontology by @markquintontulloch in #1106
• SCRUM-3006 (update) Sort entries in multiselect dropdowns by @markquintontulloch in #1107
• SCRUM-2828 Prevent loading of duplicate notes by @markquintontulloch in #1108
• SCRUM-3007 Add DataProvider to Gene and AGM tables by @markquintontulloch in #1109
• SCRUM-2447 Load Ascomycete Phenotype Ontology by @markquintontulloch in #1110
• SCRUM-2911 notes and conditions open on duplication by @adamgibs in #1111
• SCRUM-2447 (update) Add namespace column to APO table by @markquintontulloch in #1112
• SCRUM-2447 (update) Fix filter for ontology namespace column by @markquintontulloch in #1114
• SCRUM-3005 Related Note dialog display updates by @markquintontulloch in #1113
• SCRUM-2453 Load Vertebrate Trait Ontology by @markquintontulloch in #1115
• SCRUM-2911 disabled duplication during row edit by @adamgibs in #1116
• Scrum 2982 - Indexing improvements. by @oblodgett in #1117
• SCRUM-3008 Use consensus set of defining properties for DAs by @markquintontulloch in #1118
• Fixed bug with refresh interval on index everything vs a single type by @oblodgett in #1119
• Add keyword indexes for Allele references by @markquintontulloch in #1120
• SCRUM-3021 Switch order of name and curie in tree display by @markquintontulloch in #1122
• SCRUM-2911 conditions appear in condition relation form table by @adamgibs in #1123
• Add more keyword indexes by @markquintontulloch in #1124
• SCRUM-3021 (update) Alphabetize nodes in tree display by @markquintontulloch in #1125
• SCRUM-3021 (update) Sort obsolete terms in tree by @markquintontulloch in #1126
• SCRUM-2707 Entity and DTO classes for Orthology by @markquintontulloch in #1121
• Revert "Use custom SCSS classes" by @adamgibs in #1127
• SCRUM-3005 (update) Custom SCSS class reimplementation by @markquintontulloch in #1128
• Release/v0.21.0 rc1 by @markquintontulloch in #1133

Full Changelog: v0.20.0-rc4...v0.21.0-rc1

AGR Curation v0.20.0

What's Changed

• SCRUM-2333, SCRUM-2334, SCRUM- 2341 - Add allele functional impacts, germline transmission status, and notes by @markquintontulloch in #1033
• SCRUM-2898: beta to prod release by @abecerra in #1037
• SCRUM-2897: alpha to beta release by @abecerra in #1039
• SCRUM-2341 (update) Increase number of terms returned by search for CV dropdown by @markquintontulloch in #1036
• SCRUM-2334 update - Fix display for functional impacts by @markquintontulloch in #1040
• SCRUM-2341 update - Allele note UI updates by @markquintontulloch in #1041
• SCRUM-2341 update - Add missing term to allele note vocabulary by @markquintontulloch in #1042
• Updated ngram count SCRUM-2930 by @oblodgett in #1043
• Fix for indexes and constraints by @oblodgett in #1044
• added private only view by @adamgibs in #1046
• SCRUM-2900 added more mock table data and tests by @adamgibs in #1047
• Scrum 2932 added no cleanup feature by @oblodgett in #1045
• Bump for Release by @oblodgett in #1049
• Release/v0.20.0 rc1 by @adamgibs in #1056
• PRmerge/production by @markquintontulloch in #1060
• Release/v0.20.0-rc2 by @markquintontulloch in #1061
• SCRUM-2970 Fix issue with header column by @adamgibs in #1070
• SCRUM-2977 Truncate values in Note freeText field indexes by @markquintontulloch in #1073
• Release/v0.20.0 by @adamgibs in #1100

Full Changelog: v0.19.1...v0.20.0

AGR Curation v0.20.0-rc4

What's Changed

• SCRUM-2977 Truncate values in Note freeText field indexes by @markquintontulloch in #1073

Full Changelog: v0.20.0-rc3...v0.20.0-rc4

AGR Curation v0.20.0-rc3

What's Changed

• SCRUM-2970 Fix issue with header column by @adamgibs in #1070

Full Changelog: v0.20.0-rc2...v0.20.0-rc3