AGR Curation v0.26.0

What's Changed

• SCRUM-3027: increase readibility for experimental conditions edition by @abecerra in #1223
• SCRUM-3278 Update to align with LinkML v1.9.0 by @markquintontulloch in #1227
• Added code for health checking by @oblodgett in #1228
• SCRUM-3027: no maximize new dis. anot. form and fix column expansion by @abecerra in #1229
• Added new health page by @oblodgett in #1230
• Remove progress indictor on downloading jars by @oblodgett in #1231
• Fix for down error by @oblodgett in #1232
• Fix typo by @oblodgett in #1233
• Initial Code for top bar to work during indexing by @oblodgett in #1234
• PRmerge/production by @adamgibs in #1236
• PRmerge/beta by @markquintontulloch in #1238
• SCRUM-3290 Fix 500 error on saving row in Experiments table by @markquintontulloch in #1239
• SCRUM-3268 Display latest FMS release as default by @markquintontulloch in #1240
• SCRUM-3268 (update) Display next FMS release instead of latest by @markquintontulloch in #1241
• SCRUM-3290 (update) Fix 'failed to lazily initialize a collection' error by @markquintontulloch in #1242
• pushing out package-lock.json by @adamgibs in #1245
• Added FMS Data Files page by @oblodgett in #1247
• SCRUM-3124 by @adamgibs in #1248
• SCRUM-3220 Add AuditedObject fields to NomenclatureEvents popup by @markquintontulloch in #1249
• SCRUM-3220 (update) Add default value for obsolete by @markquintontulloch in #1250
• SCRUM-3303: bump quarkus version fixes CVE-2023-4853 by @abecerra in #1251
• SCRUM-3128 by @adamgibs in #1252
• SCRUM-199 Load and display constructs by @markquintontulloch in #1254
• SCRUM-199 (update) Load and display constructs by @markquintontulloch in #1255
• SCRUM-199 (update no. 2) Load and display constructs by @markquintontulloch in #1256
• Initial Code for backend child counts by @oblodgett in #1244
• Rename ontology counts migration by @markquintontulloch in #1258
• SCRUM-3132 Add Inheritance Modes to allele detail page by @markquintontulloch in #1257
• SCRUM-3127 Add Secondary IDs to allele detail page by @markquintontulloch in #1260
• SCRUM-3132 (update) Deal with removed or non-selected terms by @markquintontulloch in #1259
• SCRUM-3129 by @adamgibs in #1261
• SCRUM-3316 update rowData directly to fix dropdown bug by @adamgibs in #1262
• SCRUM-3131 & SCRUM-3133 Add Database Status and Related Notes to allele detail page by @markquintontulloch in #1263
• SCRUM-3125: support symbol edition in allele details page by @abecerra in #1264
• SCRUM-3125: fixes for vocabulary search by @abecerra in #1265
• SCRUM-3130 add GermlineTransmissionStatus to AlleleDetailPage by @adamgibs in #1266
• SCRUM-3125: remove the DELETE action for symbol in Allele details by @abecerra in #1267
• SCRUM-3125: remove the -Add Symbol- button completely by @abecerra in #1268
• update AlleleDetailPage validation by @adamgibs in #1269
• SCRUM-3319 (LinkML v1.10.0 update) & SCRUM-3320 (Load & display constructs, 2nd iteration) by @markquintontulloch in #1270
• PRmerge/production by @markquintontulloch in #1277
• SCRUM-3336 Display MOD release version on DataLoads page by @markquintontulloch in #1274
• SCRUM-3200 Display crossReferences in table on allele detail page by @adamgibs in #1279
• SCRUM-3337 Fix failing WB Molecule loads due to FK error by @markquintontulloch in #1278
• SCRUM-3306 Add endpoint to remove unused ConditionRelation and ExperimentalCondition entries by @markquintontulloch in #1280
• SCRUM-3342 Enable removal of is_extinct property from allele detail page by @markquintontulloch in #1281
• Release/v0.26.0-rc1 by @mluypaert in #1285
• Release/v0.26.0 by @mluypaert in #1304

Full Changelog: v0.25.0...v0.26.0

AGR Curation v0.26.0-rc1

What's Changed

• SCRUM-3027: increase readibility for experimental conditions edition by @abecerra in #1223
• SCRUM-3278 Update to align with LinkML v1.9.0 by @markquintontulloch in #1227
• Added code for health checking by @oblodgett in #1228
• SCRUM-3027: no maximize new dis. anot. form and fix column expansion by @abecerra in #1229
• Added new health page by @oblodgett in #1230
• Remove progress indictor on downloading jars by @oblodgett in #1231
• Fix for down error by @oblodgett in #1232
• Fix typo by @oblodgett in #1233
• Initial Code for top bar to work during indexing by @oblodgett in #1234
• PRmerge/production by @adamgibs in #1236
• PRmerge/beta by @markquintontulloch in #1238
• SCRUM-3290 Fix 500 error on saving row in Experiments table by @markquintontulloch in #1239
• SCRUM-3268 Display latest FMS release as default by @markquintontulloch in #1240
• SCRUM-3268 (update) Display next FMS release instead of latest by @markquintontulloch in #1241
• SCRUM-3290 (update) Fix 'failed to lazily initialize a collection' error by @markquintontulloch in #1242
• pushing out package-lock.json by @adamgibs in #1245
• Added FMS Data Files page by @oblodgett in #1247
• SCRUM-3124 by @adamgibs in #1248
• SCRUM-3220 Add AuditedObject fields to NomenclatureEvents popup by @markquintontulloch in #1249
• SCRUM-3220 (update) Add default value for obsolete by @markquintontulloch in #1250
• SCRUM-3303: bump quarkus version fixes CVE-2023-4853 by @abecerra in #1251
• SCRUM-3128 by @adamgibs in #1252
• SCRUM-199 Load and display constructs by @markquintontulloch in #1254
• SCRUM-199 (update) Load and display constructs by @markquintontulloch in #1255
• SCRUM-199 (update no. 2) Load and display constructs by @markquintontulloch in #1256
• Initial Code for backend child counts by @oblodgett in #1244
• Rename ontology counts migration by @markquintontulloch in #1258
• SCRUM-3132 Add Inheritance Modes to allele detail page by @markquintontulloch in #1257
• SCRUM-3127 Add Secondary IDs to allele detail page by @markquintontulloch in #1260
• SCRUM-3132 (update) Deal with removed or non-selected terms by @markquintontulloch in #1259
• SCRUM-3129 by @adamgibs in #1261
• SCRUM-3316 update rowData directly to fix dropdown bug by @adamgibs in #1262
• SCRUM-3131 & SCRUM-3133 Add Database Status and Related Notes to allele detail page by @markquintontulloch in #1263
• SCRUM-3125: support symbol edition in allele details page by @abecerra in #1264
• SCRUM-3125: fixes for vocabulary search by @abecerra in #1265
• SCRUM-3130 add GermlineTransmissionStatus to AlleleDetailPage by @adamgibs in #1266
• SCRUM-3125: remove the DELETE action for symbol in Allele details by @abecerra in #1267
• SCRUM-3125: remove the -Add Symbol- button completely by @abecerra in #1268
• update AlleleDetailPage validation by @adamgibs in #1269
• SCRUM-3319 (LinkML v1.10.0 update) & SCRUM-3320 (Load & display constructs, 2nd iteration) by @markquintontulloch in #1270
• PRmerge/production by @markquintontulloch in #1277
• SCRUM-3336 Display MOD release version on DataLoads page by @markquintontulloch in #1274
• SCRUM-3200 Display crossReferences in table on allele detail page by @adamgibs in #1279
• SCRUM-3337 Fix failing WB Molecule loads due to FK error by @markquintontulloch in #1278
• SCRUM-3306 Add endpoint to remove unused ConditionRelation and ExperimentalCondition entries by @markquintontulloch in #1280
• SCRUM-3342 Enable removal of is_extinct property from allele detail page by @markquintontulloch in #1281
• Release/v0.26.0-rc1 by @mluypaert in #1285

Full Changelog: v0.25.0...v0.26.0-rc1

AGR Curation v0.25.0

What's Changed

• SCRUM-2725 Enable sorting of references by primary xref by @markquintontulloch in #1212
• PRmerge/production by @markquintontulloch in #1215
• PRmerge/beta by @adamgibs in #1217
• SCRUM-3247 Fix short citation display, sorting, and filtering in Literature References table by @markquintontulloch in #1218
• SCRUM-3248 Display uniqueId error message in row edit mode of Disease Annotations table by @markquintontulloch in #1219
• Initial Code for admin token auth by @oblodgett in #1220
• Clean up some error reporting and warning messages. by @oblodgett in #1221
• SCRUM-3255 Display validation errors of hidden fields in row edit mode by @markquintontulloch in #1224
• SCRUM-3156 Update curation system to align with LinkML v1.8.0 by @markquintontulloch in #1222
• SCRUM-3250 Keep the ontology browser term information panel in view while browsing the ontology by @markquintontulloch in #1225
• SCRUM-3126 by @adamgibs in #1226
• Release/v0.25.0-rc1 by @markquintontulloch in #1237
• Hotfix for UI tests by @markquintontulloch in #1275
• Merge back release notes from production by @markquintontulloch in #1273
• Release/v0.25.0 by @markquintontulloch in #1276

Full Changelog: v0.24.0...v0.25.0

AGR Curation v0.25.0-rc1

What's Changed

• SCRUM-2725 Enable sorting of references by primary xref by @markquintontulloch in #1212
• Release/v0.23.0 by @markquintontulloch in #1214
• PRmerge/production by @markquintontulloch in #1215
• PRmerge/beta by @adamgibs in #1217
• SCRUM-3247 Fix short citation display, sorting, and filtering in Literature References table by @markquintontulloch in #1218
• SCRUM-3248 Display uniqueId error message in row edit mode of Disease Annotations table by @markquintontulloch in #1219
• Initial Code for admin token auth by @oblodgett in #1220
• Clean up some error reporting and warning messages. by @oblodgett in #1221
• SCRUM-3255 Display validation errors of hidden fields in row edit mode by @markquintontulloch in #1224
• SCRUM-3156 Update curation system to align with LinkML v1.8.0 by @markquintontulloch in #1222
• SCRUM-3250 Keep the ontology browser term information panel in view while browsing the ontology by @markquintontulloch in #1225
• SCRUM-3126 by @adamgibs in #1226
• Release/v0.25.0-rc1 by @markquintontulloch in #1237

Full Changelog: v0.24.0-rc1...v0.25.0-rc1

AGR Curation v0.24.0

What's Changed

• Allele detail refactor by @adamgibs in #1192
• SCRUM-3172 - Ensure submitted data meets expectations for cleanup code parameters by @markquintontulloch in #1194
• Null check for ref xrefs by @markquintontulloch in #1195
• PRmerge/production by @markquintontulloch in #1196
• SCRUM-2784 add Json Property for citation_short name field in Literat… by @cmpich in #1197
• PRmerge/beta by @markquintontulloch in #1199
• Update EcoTermService to use vocabulary label by @markquintontulloch in #1201
• SCRUM-2340 Add Allele Nomenclature Events by @markquintontulloch in #1200
• SCRUM-2784 adjust jaon field name for citation short to short_citation by @cmpich in #1202
• SCRUM-2784 add short citation text to auto-complete line by @cmpich in #1204
• SCRUM-2340 update - Add missing UI constants by @markquintontulloch in #1203
• SCRUM-3080 Disallow entry of duplicate notes by @markquintontulloch in #1205
• SCRUM-3198 Display allele symbol and curie in header of allele detail page by @markquintontulloch in #1206
• SCRUM-2340 (update) Left-align text in nomenclature list by @markquintontulloch in #1207
• SCRUM-3199 Add species name to allele detail page additional info by @markquintontulloch in #1208
• SCRUM-2784 make short citation show up next to the entry box when sel… by @cmpich in #1210
• SCRUM-3120 by @adamgibs in #1211
• Release/v0.24.0-rc1 by @adamgibs in #1216
• Release/v0.24.0 by @adamgibs in #1235

Full Changelog: v0.23.0...v0.24.0

AGR Curation v0.24.0-rc1

What's Changed

• Allele detail refactor by @adamgibs in #1192
• Release/v0.22.0 by @markquintontulloch in #1193
• SCRUM-3172 - Ensure submitted data meets expectations for cleanup code parameters by @markquintontulloch in #1194
• Null check for ref xrefs by @markquintontulloch in #1195
• PRmerge/production by @markquintontulloch in #1196
• SCRUM-2784 add Json Property for citation_short name field in Literat… by @cmpich in #1197
• PRmerge/beta by @markquintontulloch in #1199
• Update EcoTermService to use vocabulary label by @markquintontulloch in #1201
• SCRUM-2340 Add Allele Nomenclature Events by @markquintontulloch in #1200
• SCRUM-2784 adjust jaon field name for citation short to short_citation by @cmpich in #1202
• SCRUM-2784 add short citation text to auto-complete line by @cmpich in #1204
• SCRUM-2340 update - Add missing UI constants by @markquintontulloch in #1203
• SCRUM-3080 Disallow entry of duplicate notes by @markquintontulloch in #1205
• SCRUM-3198 Display allele symbol and curie in header of allele detail page by @markquintontulloch in #1206
• SCRUM-2340 (update) Left-align text in nomenclature list by @markquintontulloch in #1207
• SCRUM-3199 Add species name to allele detail page additional info by @markquintontulloch in #1208
• SCRUM-2784 make short citation show up next to the entry box when sel… by @cmpich in #1210
• SCRUM-3120 by @adamgibs in #1211
• Release/v0.24.0-rc1 by @adamgibs in #1216

Full Changelog: v0.23.0-rc1...v0.24.0-rc1

AGR Curation v0.23.0

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
• Release/v0.23.0 by @markquintontulloch in #1214

Full Changelog: v0.22.0...v0.23.0

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