AGR 8.3.0 Release

What's Changed

• KANBAN-741 Create API for Reference page by @Joe-Wdz in #1373
• SCRUM-4072 by @cmpich in #1374
• Added code for converting sitemap from cache to ES by @oblodgett in #1372
• SCRUM-4081 update indexer and API for allele summary documents by @adamgibs in #1375
• Scrum 4072 by @cmpich in #1376
• SCRUM-4072 split transgenic alleles into summary and annotation by @cmpich in #1378
• Added parallel and Sequential modes for each indexer by @oblodgett in #1379
• KANBAN-755 Create API for entity counts on AD page by @Joe-Wdz in #1377
• Limited number of indexers running at a time by @oblodgett in #1380
• handle nonBGI collection is null by @cmpich in #1381
• Fix indexer by @cmpich in #1382
• Allele summary indexer by @cmpich in #1384
• curation library version bump by @VarunReddy1111 in #1385
• update allele summary indexer for indexing optimization by @adamgibs in #1388
• do not run the GeneToGeneOrthologyIndexer in parallel by @cmpich in #1389
• reduce threads for GeneToGene Indexer from 4 to 2 by @cmpich in #1390
• update GeneToGeneOrthologyIndexer by @adamgibs in #1393
• SCRUM-4072 change public site endpoint to use ES: start by @cmpich in #1383
• Change in gene expression annotation end point to use ES instead of C… by @VarunReddy1111 in #1392
• SCRUM-4081 use AlleleSummaryController from curation by @cmpich in #1394
• SCRUM-4072 make download button work by @cmpich in #1395
• remove association api calls from AlleleSummaryCurationIndexer by @cmpich in #1397
• remove parallelization by @cmpich in #1398
• Changes to expression endpoint by @VarunReddy1111 in #1399
• SCRUM-4072 by @cmpich in #1400
• Changes to expression download endpoint by @VarunReddy1111 in #1401
• SCRUM-4072 add targetedGenes, remove duplication by @cmpich in #1403
• SCRUM-4072 fix hasDisease and hasPhenotype in download file by @cmpich in #1404
• update to curation v0.42.9 by @adamgibs in #1405
• SCRUM-4072 by @cmpich in #1406
• Curation library version bump by @VarunReddy1111 in #1407
• Sorting changes for Gene Expression Annotations by @VarunReddy1111 in #1408
• SCRUM-4081 create cursor-based indexer for allele summary indexer by @cmpich in #1409
• Default sorting changes in gene expression annotations by @VarunReddy1111 in #1410
• SCRUM-4072 by @cmpich in #1411
• SCRUM-5380 remove filtering against neo for AGMs by @adamgibs in #1412
• SCRUM-4082 by @cmpich in #1413
• SCRUM-4072 SCRUM-5546 fix filtering on boolean column, on dataProvider column on Disease page by @cmpich in #1414
• SCRUM-4072 fix download file: add targeted genes by @cmpich in #1415
• Scrum 4072 by @cmpich in #1416
• update curation library by @adamgibs in #1417
• do not run any indexer in parallel by @cmpich in #1418
• Revert "do not run any indexer in parallel" by @cmpich in #1419
• SCRUM-4072 do not print construct name in download file if marked as … by @cmpich in #1420
• SCRUM-4072 SCRUM-5553 by @cmpich in #1421
• Scrum 4072 by @cmpich in #1423
• SCRUM-4082 populate primaryExternalId with modInternalId when placeho… by @cmpich in #1424
• SCRUM-4072 handle placeholder == null by @cmpich in #1425
• Consolidation of gene expression annotations by @VarunReddy1111 in #1426
• SCRUM-4072 create mapping info for phylogeneticSortingIndex by @cmpich in #1427
• SCRUM-4072 fix sorting variable by @cmpich in #1428
• Scrum 5363 by @cmpich in #1430
• Gene expression annotations downloads de consolidation changes by @VarunReddy1111 in #1429
• Scrum 4793 by @VarunReddy1111 in #1432
• SCRUM-5602 remove constraint that checks if entities of DAs are found… by @cmpich in #1431
• Changed ExpressionRibbonESService to handle race condition using sync… by @VarunReddy1111 in #1433
• Changes to expression ribbon service by @VarunReddy1111 in #1435
• Changes to consolidation and deconsolidation logic for expression ann… by @VarunReddy1111 in #1436
• curation library version upgrade by @VarunReddy1111 in #1437
• SCRUM-5640 fix agm name for filtering by @adamgibs in #1439
• SCRUM-4993 add additional alleles on view annotations for AGM DAs by @cmpich in #1438
• SCRUM-5640 filter on displayText by @adamgibs in #1440
• SCRUM-5643 create allele download file with correct file name by @cmpich in #1441
• SCRUM-5643 make download file name changes to allele/phenotype sectio… by @cmpich in #1442

New Contributors

• @Joe-Wdz made their first contribution in #1373

Full Changelog: 8.2.0...8.3.0

AGR 8.2.0 Release

What's Changed

• Switched out logging for local application logging by @oblodgett in #1313
• Add go indexer by @adamgibs in #1312
• Update infinispan version by @oblodgett in #1314
• Updated curation library and samtools by @oblodgett in #1315
• Fix cacher by @oblodgett in #1316
• Fix NPE in indexer by @oblodgett in #1317
• Another attempt to fix the indexer by @oblodgett in #1318
• SCRUM-5109 fix download endpoint to be POST instead of GET by @cmpich in #1319
• update to curation library v0.39.1 and fix compile errors by @adamgibs in #1320
• SCRUM-4817 create Affected Genomic Model Indexer for model table on gene page. by @cmpich in #1321
• SCRUM-4073 get API for model table on gene page use ES documents by @cmpich in #1323
• Combine variant indexers by @oblodgett in #1324
• SCRUM4073 fix filtering on model name by @cmpich in #1325
• Removed unused package by @oblodgett in #1327
• Scrum 4073 by @cmpich in #1328
• SCRUM-4073 add sorting by missing phenotype, add fitering on experime… by @cmpich in #1330
• SCRUM-5097 by @adamgibs in #1329
• add mapping for associated phenotype to be sorted by @cmpich in #1331
• SCRUM-4073 fix mapping for variant index by @cmpich in #1332
• Reorged indexer for better throughput and fix indexer errors by @oblodgett in #1333
• Trying to remove errors by @oblodgett in #1335
• Fix variant index by @oblodgett in #1336
• SCRUM-5097 add provider code and remove ribbondetails endpoint by @adamgibs in #1337
• SCRUM-4073 sort by formatText and non-missing phenotypes first by @cmpich in #1338
• Scrum 5078 Refactor by @oblodgett in #1339
• Scrum 5078 by @FB-ping in #1334
• Added creation of directory when doesn't exist by @oblodgett in #1340
• SCRUM-4073 sort on phenotype and disease terms first then on other co… by @cmpich in #1341
• Add DEBUG INFO. Will remove later. by @cmpich in #1342
• SCRUM-5097 update code for DA table download by @adamgibs in #1343
• Add mode DEBUG INFO. Will be removed later. by @cmpich in #1344
• SCRUM-4073 by @cmpich in #1345
• upgrade to v0.39.17 by @cmpich in #1346
• SCRUM-4073 use boolean fields to sort by existence of diseaseAnnotati… by @cmpich in #1347
• SCRUM-4073 fix sorting by case insensitive field by @cmpich in #1348
• SCRUM-4073 sort by disease and phenotype existence by @cmpich in #1349
• Test Claude Code PR Review by @christabone in #1351
• Small Claude Code changes by @christabone in #1352
• Update claude code centralized workflow by @christabone in #1353
• Use centralized Claude review thresholds from .github repo by @christabone in #1354
• Remove obsolete zen tools and API key parameters from Claude workflow by @christabone in #1355
• SCRUM-5263 Prevent partial curie matches when searching for interactions by @markquintontulloch in #1356
• SCRUM-4989 Update Xenopus assembly versions by @markquintontulloch in #1357
• Added logging to accession caching by @VarunReddy1111 in #1359
• Used different method to get Allele Ids. And set key values to plain … by @oblodgett in #1360
• SCRUM-4073 SCRUM-5290 SCRUM-79 by @cmpich in #1361
• SCRUM-4073 upgrade library to 0.40.6 and change authentication from B… by @cmpich in #1362
• SCRUM-4074 upgrade library to 0.40.8 by @cmpich in #1364
• SCRUM-4073 by @cmpich in #1365
• SCRUM-4073 ensure the sorting is in the specified order by @cmpich in #1366
• SCRUM-5306 change GET to POST for expression download on gene page by @cmpich in #1367
• SCRUM-4073 filtering by disease, fix expression download by @cmpich in #1368
• SCRUM-5356 update curation library by @adamgibs in #1370
• SCRUM-5369 add neo models check for AGM indexer by @adamgibs in #1371
• SCRUM-4072 add indexer for transgenic alleles by @cmpich in #1369

Full Changelog: 8.1.0...8.2.0

AGR 8.1.0 Release

What's Changed

• Fail on missing file so that indexer doesn't produce a empty index by @oblodgett in #1228
• Updated ubuntu by @oblodgett in #1229
• SCRUM-4869 populate associated gene to transcript object by @cmpich in #1230
• Updated code for better caching and reruning the indexer in place by @oblodgett in #1226
• Bumped curation version and data modeling changes by @VarunReddy1111 in #1233
• SCRUM-4785 & SCRUM-4786 Index interactions from curation system by @markquintontulloch in #1232
• SCRUM 4067 Adding GeneToGene Paralogy Indexer by @VarunReddy1111 in #1231
• SCRUM-4785 & SCRUM-4786 update - Override customizeObjectMapper by @markquintontulloch in #1236
• Removed unused mapper by @oblodgett in #1234
• SCRUM-4776: index Gene Expression Annotations by @abecerra in #1237
• Bump curation library version by @markquintontulloch in #1238
• SCRUM-4785 & SCRUM-4786 Add null check for interaction subject/object genes by @markquintontulloch in #1239
• Bump curation library version to v0.36.5 by @markquintontulloch in #1241
• Fix for interaction download with reference filter by @VarunReddy1111 in #1244
• Revert "Fix for interaction download with reference filter" by @VarunReddy1111 in #1245
• Make sure that species exists by @oblodgett in #1242
• Scrum 4067 by @VarunReddy1111 in #1240
• SCRUM-4077 SCRUM-4078 SCRUM-4795 SCRUM-4825 Use curation system data for interactions by @markquintontulloch in #1243
• SCRUM-3995 phenotype annotations on gene and allele page by @cmpich in #1235
• SCRUM-3995 add initializer of object by @cmpich in #1248
• Replacing releaseInfo section with ES as datasource by @VarunReddy1111 in #1246
• Scrum 4906 by @oblodgett in #1249
• Updated pom to fix libraries by @oblodgett in #1250
• SCRUM-3998 add genetic entity info for allele and gene phenotype anno… by @cmpich in #1251
• update curation library by @adamgibs in #1252
• Bump library to latest version by @oblodgett in #1253
• SCRUM-3999 filter by source column by @cmpich in #1254
• SCRUM-4077 / SCRUM-4078 / SCRUM-4795 / SCRUM-4825 Various interaction fixes by @markquintontulloch in #1255
• Added dynamic views to the indexer by @oblodgett in #1247
• SCRUM-3999 make gene-page phenotype table filterable by data provider by @cmpich in #1256
• Added log4j depends to the ES util module by @oblodgett in #1257
• Fixed all interfaces by @oblodgett in #1258
• Added missing depends for ES Util by @oblodgett in #1259
• Fix depends by @oblodgett in #1261
• SCRUM-4066 by @adamgibs in #1262
• Fix depends again? by @oblodgett in #1263
• Hopefully the final fix for this by @oblodgett in #1264
• Cleanup log output and remove warnings by @oblodgett in #1265
• Fixed depends for variant indexer by @oblodgett in #1266
• trun off ortho indexer by @adamgibs in #1267
• update how gene DA and EA booleans are indexed by @adamgibs in #1268
• SCRUM-4795 & SCRUM-4825 Add mappings for interaction index fields by @markquintontulloch in #1269
• SCRUM-4795, SCRUM-4825 - Use sort indexes by @markquintontulloch in #1270
• SCRUM-4941 add sorting attribute on phenotypeStatement field by @cmpich in #1271
• Updated field to be keywork so that it can be agged on by @oblodgett in #1272
• SCRUM-4932: add dataProviderCrossReference to FMS expression loads by @abecerra in #1275
• SCRUM-4950 Add alpha smart sorting by @markquintontulloch in #1277
• Revert field change by @oblodgett in #1278
• Added column for allele category field by @oblodgett in #1273
• update to 0.37.3 by @adamgibs in #1280
• SCRUM-4078 Include interactionSource and aggregationDatabase in filter by @markquintontulloch in #1279
• SCRUM-4078 Fix perturbation filters and sort filter options by @markquintontulloch in #1281
• Added and refactored code by @oblodgett in #1276
• jFix depends on log4j by @oblodgett in #1282
• Updated log4j version by @oblodgett in #1283
• Fixed NPE by @oblodgett in #1284
• Reimplement interaction views by @markquintontulloch in #1285
• Turn off debug because of extra logging by @oblodgett in #1286
• Added code to have a searchable boolean on all the documents by @oblodgett in #1287
• SCRUM-4009 Adding Disease Interface and Disease Summary Indexing by @VarunReddy1111 in #1288
• SCRUM-4977 Add padded base to variant sequence by @markquintontulloch in #1290
• SCRUM-4950 & SCRUM-4795 Interaction filter & sorting fixes by @markquintontulloch in #1289
• Fix searchable SCRUM-4816 by @oblodgett in #1291
• Fixed logging with indexer by @oblodgett in #1292
• G2g ortho doc speed up by @oblodgett in #1293
• Fix natural sorting by @markquintontulloch in #1294
• bumped curation version to 0.37.16 by @adamgibs in #1295
• SCRUM-4795 & SCRUM-4925 Fix interaction table source filters by @markquintontulloch in #1296
• SCRUM-4795 & SCRUM-4825 Actually fix natural sorting by @markquintontulloch in #1297
• SCRUM-5005 point source filter to the correct ES field by @cmpich in #1299
• Adjust pattern to deal with all combinations by @markquintontulloch in #1298
• Stop escaping characters in OR search by @markquintontulloch in #1300
• Fix OR search pt 2 - prevent string escaping in helper method too by @markquintontulloch in #1301
• SCRUM-5005 add looping over the last page by @cmpich in #1302
• SCRUM-5005 correct dataProvider name field by @cmpich in #1303
• Upgrade library by @cmpich in #1304
• SCRUM-5038 update gene/expression annotations to take post methods with by @adamgibs in #1305
• Linting and Import cleanup by @oblodgett in #1306
• SCRUM-5034 by @cmpich in #1308
• SCRUM-5040 add neo g...

AGR 8.0.0 Release

What's Changed

• Fix to get stage building again by @oblodgett in #1222
• Add convenience attribute (pubModID) to JSON for diasease annotation by @cmpich in #1223
• use 0.35.3 release, add pubModID to ES document by @cmpich in #1224
• upgrade to v0.35.4 with getPubModId() method by @cmpich in #1225
• SCRUM-4823 Update hard-coded assembly names to current versions by @markquintontulloch in #1227

Full Changelog: 7.5.0...8.0.0

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/...