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 gene check for orthology index by @adamgibs in #1309
• SCRUM-5080 upgrade curation library to 0.37.24 by @cmpich in #1310

Full Changelog: 8.0.0...8.1.0