v5.3.0

Feature

• #1259 by rkm. Add support for extraction processing failures
  • Remove IsIdentifiable field from ExtractedFileVerificationMessage and replace with new VerifiedFileStatus enum
  • Update extraction job classes in CohortPackager to store this new field, and handle backwards-incompatibility when reading older extraction logs

Bugfix

• #1285 by howff. Improve the removal of HTML tags from StructuredReport (SR) text
• #1314 by jas88. Replace SharpCompress usage due to buggy LZMA handling to fix issue #1313
• #1350 by tznind. Fix DicomRelationalMapper when running with a YamlRepository backend

Change

• #1270 by tznind. Rename yaml config file IsIdentifiableBaseOptions to IsIdentifiableOptions and removed unused CLI verbs in smi

Meta

• #1261 by jas88. Update caching strategy in CI

What's Changed

• Ensure mongodb service started in Windows CI by @rkm in #1260
• Bump Microsoft.NET.Test.Sdk from 17.2.0 to 17.3.0 by @dependabot in #1262
• Bump SecurityCodeScan.VS2019 from 5.6.3 to 5.6.4 by @dependabot in #1263
• Bump mockito-core from 4.6.1 to 4.7.0 in /src/common/com.smi.microservices.parent by @dependabot in #1265
• Bump NLog from 5.0.1 to 5.0.2 by @dependabot in #1264
• CI update by @jas88 in #1261
• Bump System.IO.Abstractions.TestingHelpers from 17.0.24 to 17.1.1 by @dependabot in #1266
• Bump System.IO.Abstractions from 17.0.24 to 17.1.1 by @dependabot in #1267
• Bump SecurityCodeScan.VS2019 from 5.6.4 to 5.6.5 by @dependabot in #1268
• ii compatibility by @tznind in #1270
• Bump IsIdentifiable from 0.0.5 to 0.0.6 by @dependabot in #1272
• Bump SecurityCodeScan.VS2019 from 5.6.5 to 5.6.6 by @dependabot in #1274
• Bump HIC.FAnsiSql from 2.0.4 to 2.0.5 by @dependabot in #1276
• Bump HIC.RDMP.Dicom from 5.0.10 to 5.0.11 by @dependabot in #1278
• Bump IsIdentifiable from 0.0.6 to 0.0.7 by @dependabot in #1277
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1275
• Bump logback-classic from 1.2.11 to 1.4.0 in /src/common/com.smi.microservices.parent by @dependabot in #1279
• Support extraction validation failure by @rkm in #1259
• Bump HIC.FAnsiSql from 2.0.5 to 3.0.0 by @dependabot in #1281
• Bump Microsoft.NET.Test.Sdk from 17.3.0 to 17.3.1 by @dependabot in #1284
• Bugfix/sr html by @howff in #1285
• Bump HIC.RDMP.Plugin from 7.0.17 to 7.0.18 by @dependabot in #1283
• Bump HIC.RDMP.Plugin.Test from 7.0.17 to 7.0.18 by @dependabot in #1282
• Bump NLog from 5.0.2 to 5.0.3 by @dependabot in #1286
• Bump NLog from 5.0.3 to 5.0.4 by @dependabot in #1288
• Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.2.0 to 4.3.0 by @dependabot in #1287
• Bump jackson-dataformat-yaml from 2.13.3 to 2.13.4 in /src/common/com.smi.microservices.parent by @dependabot in #1294
• Bump jackson-databind from 2.13.3 to 2.13.4 in /src/common/com.smi.microservices.parent by @dependabot in #1293
• Bump HIC.RDMP.Plugin from 7.0.18 to 7.0.19 by @dependabot in #1291
• [Snyk] Security upgrade com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.13.3 to 2.13.4 by @snyk-bot in #1290
• Bump HIC.RDMP.Plugin.Test from 7.0.18 to 7.0.19 by @dependabot in #1292
• Bump SecurityCodeScan.VS2019 from 5.6.6 to 5.6.7 by @dependabot in #1295
• Bump StackExchange.Redis from 2.6.48 to 2.6.66 by @dependabot in #1296
• Bump mockito-core from 4.7.0 to 4.8.0 in /src/common/com.smi.microservices.parent by @dependabot in #1297
• Bump actions/setup-java from 3.4.1 to 3.5.0 by @dependabot in #1300
• Bump HIC.RDMP.Plugin from 7.0.19 to 7.0.20 by @dependabot in #1298
• Bump HIC.RDMP.Plugin.Test from 7.0.19 to 7.0.20 by @dependabot in #1299
• Bump HIC.RDMP.Dicom from 5.0.11 to 5.0.12 by @dependabot in #1301
• Bump amqp-client from 5.15.0 to 5.16.0 in /src/common/com.smi.microservices.parent by @dependabot in #1306
• Bump System.IO.Abstractions.TestingHelpers from 17.1.1 to 17.2.1 by @dependabot in #1304
• Bump Spectre.Console from 0.44.0 to 0.45.0 by @dependabot in #1303
• Bump System.IO.Abstractions from 17.1.1 to 17.2.1 by @dependabot in #1302
• Bump NunitXml.TestLogger from 3.0.117 to 3.0.127 by @dependabot in #1305
• Bump logback-classic from 1.4.0 to 1.4.1 in /src/common/com.smi.microservices.parent by @dependabot in #1307
• Bump System.IO.Abstractions.TestingHelpers from 17.2.1 to 17.2.3 by @dependabot in #1309
• Bump YamlDotNet from 12.0.0 to 12.0.1 by @dependabot in #1308
• Bump System.IO.Abstractions from 17.2.1 to 17.2.3 by @dependabot in #1310
• Bump Terminal.Gui from 1.7.2 to 1.8.0 by @dependabot in #1311
• Bump Terminal.Gui from 1.8.0 to 1.8.2 by @dependabot in #1312
• Feature/libarchive loader by @jas88 in #1314
• Bump Microsoft.NET.Test.Sdk from 17.3.1 to 17.3.2 by @dependabot in #1316
• Bump actions/setup-java from 3.5.0 to 3.5.1 by @dependabot in #1317
• Bump HIC.RDMP.Plugin from 7.0.20 to 8.0.0 by @dependabot in #1320
• Bump HIC.RDMP.Plugin.Test from 7.0.20 to 8.0.0 by @dependabot in #1319
• Bump HIC.RDMP.Dicom from 5.0.12 to 6.0.0 by @dependabot in #1321
• Update dependabot.yml by @jas88 in #1318
• Update dependabot.yml by @jas88 in #1322
• Bump HIC.RDMP.Dicom from 6.0.0 to 6.0.1 by @dependabot in #1323
• Bump actions/setup-dotnet from 2 to 3.0.0 by @dependabot in #1324
• Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.3.0 to 4.3.1 by @dependabot in #1326
• Bump HIC.RDMP.Plugin.Test from 8.0.0 to 8.0.1 by @dependabot in #1325
• Bump logback-classic from 1.4.1 to 1.4.3 in /src/common/com.smi.microservices.parent by @dependabot in #1328
• Bump HIC.RDMP.Plugin from 8.0.0 to 8.0.1 by @dependabot in #1327
• Bump HIC.RDMP.Plugin from 8.0.1 to 8.0.2 by @dependabot in #1329
• Bump HIC.RDMP.Plugin.Test from 8.0.1 to 8.0.2 by @dependabot in #1330
• Bump actions/setup-dotnet from 3.0.0 to 3.0.1 by @dependabot in #1333
• Bump HIC.RDMP.Plugin from 8.0.2 to 8.0.3 by @dependabot in #1332
• Bump HIC.RDMP.Plugin.Test from 8.0.2 to 8.0.3 by @dependabot in #1331
• Bump CsvHelper from 28.0.1 to 29.0.0 by @dependabot in #1335
• Bump YamlDotNet from 12.0.1 to 12.0.2 by @dependabot in #1336
• Bump logback-classic from 1.4.3 to 1.4.4 in /src/common/com.smi.microservices.parent by @dependabot in #1337
• Bump jackson-databind from 2.13.4 to 2.13.4.1 in /src/common/com.smi.microservices.parent by @dependabot in #1338
• [Snyk] Security upgrade protobuf from 3.20.1 to 3.20.2 by @snyk-bot in #1315
• Bump jackson-databind from 2.13.4.1 to 2.13.4.2 in /src/common/com.smi.microservices.parent by @dependabot in #1340
• Bump actions/setup-dotnet from 3.0.1 to 3.0.2 by @dependabot in #1341
• Bump StackExchange.Redis from 2.6.66 to 2.6.70 by @dependabot in #1342
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1343
• Bump actions/setup-java from 3.5.1 to 3.6.0 by @dependabot in #1344
• Bump mockito-core from 4.8.0 to 4.8.1 in /src/common/com.smi.microservices.parent by @dependabot in #1345
• Bump gson from 2.9.1 to 2.10 in /src/common/com.smi.microservices.parent by @dependabot in #1348
• Bump HIC.RDMP.Plugin from 8.0.3 to 8.0.4 by @dependabot in #1346
• Bump HIC.RDMP.Plugin.Test from 8.0.3 to 8.0.4 by @dependabot in #1347
• Remove bad cast that breaks DicomRelationalMapper SMI when running with YamlRepository by @tznind in #1350
• Bump LibArchive.Net from 0.1.1 to 0.1.2 by @dependabot in #1351
• Bump actions/setup-dotnet from 3.0.2 to 3.0.3 by @dependabot in #1352
• Bump NLog from 5.0.4 to 5.0.5 by @dependabot in #1349
• Bump HIC.FAnsiSql from 3.0.0 to 3.0.1 by @dependabot in #1354
• Bump coverlet.msbuild from 3.1.2 to 3.2.0 by @dependabot in #1356
• Bump NUnit3TestAdapter from 4.2.1 to 4.3.0 by @dependabot in #1355
• Bump HIC.RDMP.Plugin from 8.0.4 to 8.0.5 by @dependabot in #1360
• Bump HIC.BadMedicine.Dicom from 0.0.14 to 0.0.15 by @dependabot in #1357
• Bump HIC.RDMP.Dicom from 6.0.1 to 6.0.2 by @dependabot in #1358
• Bump IsIdentifiable from 0.0.7 to 0.0.8 by @dependabot in #1361
• Bump jackson-dataformat-yaml from 2.13.4 to 2.14.0 in /src/common/com.smi.microservices.parent by @dependabot in #1364
• Bump jackson-databind from 2.13.4.2 to 2.14.0 in /src/common/com.smi.microservices.parent by @dependabot in #1363
• Bump JetBrains.Annotations from 2022.1.0 to 2022.3.1 by @dependabot in #1365
• Bump Microsoft.Extensions.Caching.Memory from 6.0.1 to 7.0.0 by @dependabot in #1366
• Bump Microsoft.NET.Test.Sdk from 17.3.2 to 17.4.0 by @dependabot in #1367
• Bump HIC.RDMP.Plugin from 8.0.5 to 8.0.6 by @dependabot in #1369
• Bump HIC.RDMP.Plugin.Test from 8.0.5 to 8.0.6 by @dependabot in #1368
• Release v5.3.0 by @rkm in #1370

Full Changelog: v5.2.0...v5.3.0