v5.4.0

Feature

• #1489 by howff. CTP_DicomToText has options to control the output formatting (especially redaction of HTML and replacement of newlines)

Bugfix

• #1379 by rkm. Constrain protobuf version to "<3.20.0", since this is the last version which supports python3.6 and we only have 3.6 on the live system.
• #1396 by jas88. Fix some issues encountered loading DICOM to Mongo in HIC deployment
• #1399 by jas88. Revert to [email protected] due to disappearance of 3.7.0
• #1430 by rkm. Add RabbitMQ management port to docker-compose files
• #1431 by rkm. restrict mysql_connector_python version for python 3.6
• #1448 by rkm. Add 0.1% threshold for Codecov to report CI failure
• #1492 by rkm. add codecov token to CI
• #1493 by rkm. ignore BasicRules.yaml in pre-commit codespell config
• #1497 by rkm. Fix MongoDB Windows CI by changing to sc.exe
• #1506 by darshad-github. Fix issue with hidden directories in extraction output paths generated by cohort extractor.
• #1509 by jas88. Change Windows service control operation timeout to 300s since Mongo sometimes takes longer than the default 30s causing timeout errors otherwise

Doc

• #1499 by karacolada. update CTP build docs

Meta

• #1401 by rkm. Condense formatting options into .editorconfig and add more hooks
• #1407 by rkm. Bump SDK to 6.0.403
• #1428 by rkm. Add development support for ARM / M1 Mac
• #1442 by rkm. Switch coverage to Codecov
• #1450 by darshad-github. Update contributing.md with feature branch workflow guidelines
• #1451 by rkm. adopt dotnet central package management (CPM)
• #1468 by rkm. switch rabbitmq docker-compose images to include management plugin
• #1494 by rkm. [actions] replace deprecated set-output with GITHUB_OUTPUT
• #1496 by rkm. add CodeQL scan

What's Changed

• smi-py: constrain protobuf version for python3.6 by @rkm in #1371
• Bump mockito-core from 4.8.1 to 4.9.0 in /src/common/com.smi.microservices.parent by @dependabot in #1377
• Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.3.1 to 4.4.0 by @dependabot in #1376
• smi-py: relax protobuf constraint for python3.6 by @rkm in #1379
• Bump NUnit3TestAdapter from 4.3.0 to 4.3.1 by @dependabot in #1381
• Bump logback-classic from 1.4.4 to 1.4.5 in /src/common/com.smi.microservices.parent by @dependabot in #1383
• Bump jackson-databind from 2.14.0 to 2.14.1 in /src/common/com.smi.microservices.parent by @dependabot in #1386
• Bump jackson-dataformat-yaml from 2.14.0 to 2.14.1 in /src/common/com.smi.microservices.parent by @dependabot in #1385
• Bump StackExchange.Redis from 2.6.70 to 2.6.80 by @dependabot in #1387
• Bump HIC.RDMP.Plugin from 8.0.6 to 8.0.7 by @dependabot in #1389
• Bump Newtonsoft.Json from 13.0.1 to 13.0.2 by @dependabot in #1390
• Bump NLog from 5.0.5 to 5.1.0 by @dependabot in #1391
• Bump System.IO.Abstractions from 17.2.26 to 18.0.1 by @dependabot in #1392
• Bump System.IO.Abstractions.TestingHelpers from 17.2.26 to 18.0.1 by @dependabot in #1393
• Bump actions/setup-java from 3.6.0 to 3.7.0 by @dependabot in #1394
• Feature/dicomloader tidy by @jas88 in #1396
• Bump Moq from 4.18.2 to 4.18.3 by @dependabot in #1397
• Revert to [email protected] by @jas88 in #1399
• Bump YamlDotNet from 12.0.2 to 12.1.0 by @dependabot in #1398
• Bump actions/setup-java from 3.6.0 to 3.8.0 by @dependabot in #1400
• Condense formatting options into .editorconfig and add more hooks by @rkm in #1401
• Bump YamlDotNet from 12.1.0 to 12.2.0 by @dependabot in #1406
• Bump System.IO.Abstractions.TestingHelpers from 18.0.1 to 19.0.1 by @dependabot in #1404
• Bump System.IO.Abstractions from 18.0.1 to 19.0.1 by @dependabot in #1405
• bump SDK to 6.0.403 by @rkm in #1407
• Bump StackExchange.Redis from 2.6.80 to 2.6.86 by @dependabot in #1410
• Bump System.IO.Abstractions.TestingHelpers from 19.0.1 to 19.1.1 by @dependabot in #1408
• Bump System.IO.Abstractions from 19.0.1 to 19.1.1 by @dependabot in #1409
• Bump mockito-core from 4.9.0 to 4.10.0 in /src/common/com.smi.microservices.parent by @dependabot in #1412
• Bump YamlDotNet from 12.2.0 to 12.2.1 by @dependabot in #1411
• Bump actions/setup-java from 3.8.0 to 3.9.0 by @dependabot in #1413
• Bump Microsoft.NET.Test.Sdk from 17.4.0 to 17.4.1 by @dependabot in #1414
• Bump System.IO.Abstractions.TestingHelpers from 19.1.1 to 19.1.5 by @dependabot in #1418
• Bump YamlDotNet from 12.2.1 to 12.3.1 by @dependabot in #1417
• Bump System.IO.Abstractions from 19.1.1 to 19.1.5 by @dependabot in #1416
• Bump LibArchive.Net from 0.1.2 to 0.1.3 by @dependabot in #1420
• Bump mockito-core from 4.10.0 to 4.11.0 in /src/common/com.smi.microservices.parent by @dependabot in #1421
• Bump NLog from 5.1.0 to 5.1.1 by @dependabot in #1422
• Bump Moq from 4.18.3 to 4.18.4 by @dependabot in #1423
• Bump Terminal.Gui from 1.8.2 to 1.9.0 by @dependabot in #1424
• Bump gson from 2.10 to 2.10.1 in /src/common/com.smi.microservices.parent by @dependabot in #1425
• Bump Spectre.Console from 0.45.0 to 0.46.0 by @dependabot in #1426
• Bump StackExchange.Redis from 2.6.86 to 2.6.90 by @dependabot in #1427
• Bump HIC.DicomTypeTranslation from 4.0.1 to 4.0.2 by @dependabot in #1415
• Bump mockito-core from 4.11.0 to 5.0.0 in /src/common/com.smi.microservices.parent by @dependabot in #1429
• restrict mysql_connector_python version for py3.6 by @rkm in #1431
• Bump System.IO.Abstractions from 19.1.5 to 19.1.13 by @dependabot in #1434
• Bump System.IO.Abstractions.TestingHelpers from 19.1.5 to 19.1.13 by @dependabot in #1433
• Bump jackson-databind from 2.14.1 to 2.14.2 in /src/common/com.smi.microservices.parent by @dependabot in #1436
• Bump jackson-dataformat-yaml from 2.14.1 to 2.14.2 in /src/common/com.smi.microservices.parent by @dependabot in #1435
• Bump mockito-core from 5.0.0 to 5.1.0 in /src/common/com.smi.microservices.parent by @dependabot in #1437
• Bump mockito-core from 5.1.0 to 5.1.1 in /src/common/com.smi.microservices.parent by @dependabot in #1439
• Bump NunitXml.TestLogger from 3.0.127 to 3.0.131 by @dependabot in #1438
• Bump System.IO.Abstractions from 19.1.13 to 19.1.14 by @dependabot in #1441
• Bump System.IO.Abstractions.TestingHelpers from 19.1.13 to 19.1.14 by @dependabot in #1440
• add rabbitmq management port to docker-compose by @rkm in #1430
• Add development support for ARM / M1 Mac by @rkm in #1428
• Fix coverage / move to Codecov by @rkm in #1442
• add codecov conf by @rkm in #1448
• Bump actions/setup-java from 3.9.0 to 3.10.0 by @dependabot in #1445
• Bump System.IO.Abstractions from 19.1.14 to 19.1.18 by @dependabot in #1446
• Bump System.IO.Abstractions.TestingHelpers from 19.1.14 to 19.1.18 by @dependabot in #1447
• Update contributing.md with feature branch workflow guidelines by @darshad-github in #1450
• Bump NLog from 5.1.1 to 5.1.2 by @dependabot in #1452
• Bump Microsoft.NET.Test.Sdk from 17.4.1 to 17.5.0 by @dependabot in #1456
• Bump StackExchange.Redis from 2.6.90 to 2.6.96 by @dependabot in #1457
• Bump maven-assembly-plugin from 3.4.2 to 3.5.0 in /src/common/com.smi.microservices.parent by @dependabot in #1459
• Bump YamlDotNet from 12.3.1 to 13.0.1 by @dependabot in #1453
• Bump HIC.DicomTypeTranslation from 4.0.2 to 4.0.3 by @dependabot in #1458
• Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.4.0 to 4.5.0 by @dependabot in #1460
• Bump NUnit3TestAdapter from 4.3.1 to 4.4.2 by @dependabot in #1462
• Bump System.IO.Abstractions from 19.1.18 to 19.2.1 by @dependabot in #1464
• Bump System.IO.Abstractions.TestingHelpers from 19.1.18 to 19.2.1 by @dependabot in #1463
• Bump mockito-core from 5.1.1 to 5.2.0 in /src/common/com.smi.microservices.parent by @dependabot in #1467
• Bump Newtonsoft.Json from 13.0.2 to 13.0.3 by @dependabot in #1466
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1465
• switch rabbitmq docker-compose images to include management plugin by @rkm in #1468
• adopt central package management by @rkm in #1451
• Bump Microsoft.NET.Test.Sdk from 17.4.1 to 17.5.0 by @dependabot in #1469
• Bump NUnit3TestAdapter from 4.3.1 to 4.4.2 by @dependabot in #1478
• Bump System.IO.Abstractions from 19.1.18 to 19.2.1 by @dependabot in #1477
• Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.4.0 to 4.5.0 by @dependabot in #1474
• Bump System.IO.Abstractions.TestingHelpers from 19.1.18 to 19.2.1 by @dependabot in #1471
• Bump NLog from 5.1.1 to 5.1.2 by @dependabot in #1470
• Bump StackExchange.Redis from 2.6.90 to 2.6.96 by @dependabot in #1473
• Bump Newtonsoft.Json from 13.0.2 to 13.0.3 by @dependabot in #1475
• Bump YamlDotNet from 12.3.1 to 13.0.1 by @dependabot in #1476
• Bump YamlDotNet from 13.0.1 to 13.0.2 by @dependabot in #1479
• Bump System.IO.Abstractions.TestingHelpers from 19.2.1 to 19.2.4 by @dependabot in #1482
• Bump System.IO.Abstractions from 19.2.1 to 19.2.4 by @dependabot in #1481
• Bump maven-surefire-plugin from 2.22.2 to 3.0.0 in /src/common/com.smi.microservices.parent by @dependabot in #1487
• Bump maven-surefire-report-plugin from 2.22.2 to 3.0.0 in /src/common/com.smi.microservices.parent by @dependabot in #1486
• Bump logback-classic from 1.4.5 to 1.4.6 in /src/common/com.smi.microservices.parent by @dependabot in #1491
• add codecov token to CI by @rkm in #1492
• [actions] replace deprecated set-output with GITHUB_OUTPUT by @rkm in #1494
• Meta/codespell ignores by @rkm in #1493
• Bump Terminal.Gui from 1.9.0 to 1.10.0 by @dependabot in #1495
• Fix MongoDB Windows CI by @rkm in #1497
• Enable CodeQL Scan by @rkm in #1496
• Bump amqp-client from 5.16.0 to 5.17.0 in /src/common/com.smi.microservices.parent by @dependabot in #1498
• Bump RabbitMQ.Client from 6.4.0 to 6.5.0 by @dependabot in #1500
• Bump maven-resources-plugin from 3.3.0 to 3.3.1 in /src/common/com.smi.microservices.parent by @dependabot in #1501
• Bump actions/setup-java from 3.10.0 to 3.11.0 by @dependabot in #1502
• Update instructions on building SmiServices by @karacolada in #1499
• Bump commons-configuration2 from 2.8.0 to 2.9.0 in /src/common/com.smi.microservices.parent by @dependabot in #1505
• Bump NLog from 5.1.2 to 5.1.3 by @dependabot in #1504
• Bump StackExchange.Redis from 2.6.96 to 2.6.104 by @dependabot in #1507
• DicomText.py - Add options for replacement characters when redacting by @howff in #1489
• Fix/cohort extractor output paths by @darshad-github in #1506
• Bump Terminal.Gui from 1.10.0 to 1.10.1 by @dependabot in #1510
• Change Mongo start timeout on Windows by @jas88 in #1509
• Bump mockito-core from 5.2.0 to 5.3.0 in /src/common/com.smi.microservices.parent by @dependabot in #1512
• Bump System.IO.Abstractions from 19.2.4 to 19.2.9 by @dependabot in #1513
• Bump System.IO.Abstractions.TestingHelpers from 19.2.4 to 19.2.9 by @dependabot in #1511
• Bump codecov/codecov-action from 3.1.1 to 3.1.2 by @dependabot in #1514
• Bump System.IO.Abstractions.TestingHelpers from 19.2.9 to 19.2.11 by @dependabot in #1517
• Bump System.IO.Abstractions from 19.2.9 to 19.2.11 by @dependabot in #1515
• Bump IsIdentifiable from 0.0.9 to 0.1.0 by @dependabot in #1516
• Bump YamlDotNet from 13.0.2 to 13.1.0 by @dependabot in #1521
• Bump System.IO.Abstractions.TestingHelpers from 19.2.11 to 19.2.15 by @dependabot in #1522
• Bump System.IO.Abstractions from 19.2.11 to 19.2.15 by @dependabot in #1523
• Bump System.IO.Abstractions from 19.2.15 to 19.2.16 by @dependabot in #1525
• Bump System.IO.Abstractions.TestingHelpers from 19.2.15 to 19.2.16 by @dependabot in #1526
• Bump logback-classic from 1.4.6 to 1.4.7 in /src/common/com.smi.microservices.parent by @dependabot in #1527
• Bump codecov/codecov-action from 3.1.2 to 3.1.3 by @dependabot in #1528
• Bump System.IO.Abstractions.TestingHelpers from 19.2.16 to 19.2.17 by @dependabot in #1529
• Bump jackson-dataformat-yaml from 2.14.2 to 2.15.0 in /src/common/com.smi.microservices.parent by @dependabot in #1531
• Bump mockito-core from 5.3.0 to 5.3.1 in /src/common/com.smi.microservices.parent by @dependabot in #1532
• Bump jackson-databind from 2.14.2 to 2.15.0 in /src/common/com.smi.microservices.parent by @dependabot in #1533
• Bump System.IO.Abstractions from 19.2.16 to 19.2.17 by @dependabot in #1530
• Replace LGTM badge wiith CodeQL by @jas88 in #1534
• Bump System.IO.Abstractions.TestingHelpers from 19.2.17 to 19.2.18 by @dependabot in #1536
• Bump System.IO.Abstractions from 19.2.17 to 19.2.18 by @dependabot in #1537
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1535
• Release v5.4.0 by @rkm in #1539

New Contributors

• @darshad-github made their first contribution in #1450
• @karacolada made their first contribution in #1499

Full Changelog: v5.3.0...v5.4.0