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Releases: SMI/SmiServices

v5.6.0

16 Apr 13:12
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v5.6.0
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v5.6.0

Feature

  • #1735 by rkm. Add support for CohortPackager to process ExtractedFileVerificationMessages in batches
    • Enabled with CohortPackagerOptions.VerificationMessageQueueProcessBatches
    • Process rate configured with CohortPackagerOptions.VerificationMessageQueueFlushTimeSeconds. Defaults to 5 seconds if not set
  • #1746 by rkm. Start to refactor RabbitMqAdapter logic into generic interface
    • Rename IRabbitMqAdapter -> IMessageBroker
    • Move into Smi.Common.Messaging namespace
    • Add MessageBrokerType and MessageBrokerFactory
    • Create ConnectionFactory directly in RabbitMQBroker
    • Tidy unused variables and naming
  • #1749 by rkm. Refactor and simplify extraction reports
    • Generate a single FailureStoreReport which can be further processed depending on the need
    • Removed ReportFormat and ReporterType from CohortPackagerOptions
    • Merge JobReporterBase and FileReporter into JobReporter

Bugfix

  • #1703 by jas88. Update to fix issues in installation script in docs

Change

  • #1729 by rkm. Rename branch references from master to main

Removal

  • #1730 by rkm. Disable services from Windows CI
  • #1747 by rkm. Remove unused JetBrains.Annotations package

What's Changed

  • Disable services from windows CI by @rkm in #1730
  • rename references from master to main by @rkm in #1729
  • Bump IsIdentifiable from 0.2.1 to 0.3.0 by @dependabot in #1731
  • Bump StackExchange.Redis from 2.7.10 to 2.7.17 by @dependabot in #1733
  • Bump org.mockito:mockito-core from 5.9.0 to 5.10.0 in /src/common/com.smi.microservices.parent by @dependabot in #1742
  • Bump codecov/codecov-action from 3.1.4 to 3.1.5 by @dependabot in #1741
  • Bump System.IO.Abstractions.TestingHelpers from 20.0.4 to 20.0.15 by @dependabot in #1740
  • Bump YamlDotNet from 13.7.1 to 15.1.0 by @dependabot in #1738
  • Bump System.IO.Abstractions from 20.0.4 to 20.0.15 by @dependabot in #1737
  • Bump Terminal.Gui from 1.14.1 to 1.15.1 by @dependabot in #1736
  • Feature/cohort packager status batches by @rkm in #1735
  • Bump YamlDotNet from 15.1.0 to 15.1.1 by @dependabot in #1743
  • Bump codecov/codecov-action from 3.1.5 to 4.0.1 by @dependabot in #1744
  • remove JetBrains.Annotations package by @rkm in #1747
  • Start to abstract message brokers by @rkm in #1746
  • Bump Microsoft.NET.Test.Sdk from 17.8.0 to 17.9.0 by @dependabot in #1752
  • Bump HIC.RDMP.Dicom from 7.0.1 to 7.0.2 by @dependabot in #1760
  • Bump ch.qos.logback:logback-classic from 1.4.14 to 1.5.0 in /src/common/com.smi.microservices.parent by @dependabot in #1758
  • Bump NunitXml.TestLogger from 3.1.15 to 3.1.20 by @dependabot in #1764
  • Bump codecov/codecov-action from 4.0.1 to 4.0.2 by @dependabot in #1761
  • Bump StackExchange.Redis from 2.7.17 to 2.7.20 by @dependabot in #1762
  • Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.8.0 to 4.9.2 by @dependabot in #1771
  • Bump StackExchange.Redis from 2.7.20 to 2.7.27 by @dependabot in #1770
  • Bump YamlDotNet from 15.1.1 to 15.1.2 by @dependabot in #1769
  • Bump org.mockito:mockito-core from 5.10.0 to 5.11.0 in /src/common/com.smi.microservices.parent by @dependabot in #1768
  • Bump ch.qos.logback:logback-classic from 1.5.0 to 1.5.2 in /src/common/com.smi.microservices.parent by @dependabot in #1767
  • Bump codecov/codecov-action from 4.0.2 to 4.1.0 by @dependabot in #1766
  • Bump actions/setup-java from 4.0.0 to 4.1.0 by @dependabot in #1765
  • Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.16.1 to 2.16.2 in /src/common/com.smi.microservices.parent by @dependabot in #1777
  • Bump org.apache.maven.plugins:maven-assembly-plugin from 3.6.0 to 3.7.0 in /src/common/com.smi.microservices.parent by @dependabot in #1776
  • Bump com.fasterxml.jackson.core:jackson-databind from 2.16.1 to 2.16.2 in /src/common/com.smi.microservices.parent by @dependabot in #1774
  • Bump ch.qos.logback:logback-classic from 1.5.2 to 1.5.3 in /src/common/com.smi.microservices.parent by @dependabot in #1775
  • Bump softprops/action-gh-release from 1 to 2 by @dependabot in #1773
  • Refactor & simplify extraction reports by @rkm in #1749
  • Bump org.apache.commons:commons-configuration2 from 2.9.0 to 2.10.1 in /src/common/com.smi.microservices.parent by @dependabot in #1784
  • Bump actions/setup-java from 4.1.0 to 4.2.1 by @dependabot in #1783
  • Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.16.2 to 2.17.0 in /src/common/com.smi.microservices.parent by @dependabot in #1781
  • Bump com.fasterxml.jackson.core:jackson-databind from 2.16.2 to 2.17.0 in /src/common/com.smi.microservices.parent by @dependabot in #1780
  • Bump org.apache.maven.plugins:maven-assembly-plugin from 3.7.0 to 3.7.1 in /src/common/com.smi.microservices.parent by @dependabot in #1785
  • Bump Terminal.Gui from 1.15.1 to 1.16.0 by @dependabot in #1790
  • Bump codecov/codecov-action from 4.1.0 to 4.1.1 by @dependabot in #1789
  • Bump StackExchange.Redis from 2.7.27 to 2.7.33 by @dependabot in #1788
  • Bump System.IO.Abstractions.TestingHelpers from 20.0.15 to 21.0.2 by @dependabot in #1787
  • Bump System.IO.Abstractions from 20.0.15 to 21.0.2 by @dependabot in #1786
  • Fix install script issues from JIRA RDMP-78 by @jas88 in #1703
  • Bump codecov/codecov-action from 4.1.1 to 4.2.0 by @dependabot in #1791
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1793
  • Bump codecov/codecov-action from 4.2.0 to 4.3.0 by @dependabot in #1797
  • Bump com.rabbitmq:amqp-client from 5.20.0 to 5.21.0 in /src/common/com.smi.microservices.parent by @dependabot in #1796
  • Bump ch.qos.logback:logback-classic from 1.5.3 to 1.5.5 in /src/common/com.smi.microservices.parent by @dependabot in #1795
  • Bump coverlet.msbuild from 6.0.0 to 6.0.2 by @dependabot in #1794
  • Prepare 5.6.0 release by @rkm in #1798

Full Changelog: v5.5.0...v5.6.0

Contributors

jas88, rkm, and 2 other contributors
Assets 7
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v5.5.0

18 Jan 19:43
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v5.5.0
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v5.5.0

Feature

  • #1583 by rkm. Add DynamicRulesTester application
  • #1599 by rkm. Enable the C# nullable feature and fix all warnings.
  • #1619 by rkm. Add Modality to ExtractFileMessage classes
  • #1622 by rkm. Add LossyImageCompressionMethod to CTP allowlist
  • #1637 by rkm. upgrade to NET7 and C# 11
  • #1663 by karacolada. Add field UserName to ExtractionRequestInfoMessage
  • #1701 by rkm. Adds the ability for consumers to optionally "hold" unprocessable messages so they are not returned to the queue.

Bugfix

  • #1524 by howff. StructuredReport improvements - collect names from anywhere in text body not just in header
  • #1562 by howff. DicomText - Redact all tags which have a data type (VR) of 'DT' (DateTime). It was already doing dates and names.
  • #1611 by howff. CTP_SRAnonTool - implement a full HTML parser (with other sanity checks) for HTML in TextValue in SRs
  • #1639 by rkm. catch any exception raised during file classification. Fixes #1638
  • #1671 by rkm. disable debug logging spam from external CTP libraries
  • #1684 by jas88. Fix SQL in documentation area - missing semicolons causing syntax error
  • #1704 by rkm. Improve quality of log output
  • #1717 by rkm. update CI release script for upload-artifact@v4

Docs

  • #1572 by jas88. Document installation steps for new users

Removal

Update

  • #1664 by jas88. Update RDMP API to reduce casting

What's Changed

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Contributors

jas88, howff, and 4 other contributors
Assets 7
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v5.4.0

25 Apr 13:12
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v5.4.0
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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

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Contributors

jas88, howff, and 5 other contributors
Assets 7
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v5.3.0

08 Nov 20:24
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v5.3.0
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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

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Contributors

jas88, howff, and 5 other contributors
Assets 7
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v5.2.0

10 Aug 14:43
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v5.2.0
224ec42
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v5.2.0

Feature

  • #1254 by tznind. Change
    "Setup" to a library and make it runnable from smi as verb
  • #1255 by tznind. Add support for running RDMP with YamlRepository backend

Bugfix

  • #1241 by rkm. Refactor IsIdentifiableQueueConsumer
    • Improve exception handling to better handle errors caused by IClassifier
    • Remove redundant fileSystemRoot from constructor
    • Add tests
  • #1256 by rkm. Ensure MongoDB service started in Windows CI. Caused by actions/runner-images#5949.

Removal

  • #1251 by rkm. Remove remaining IsIdentifiable code and CI config

What's Changed

Full Changelog: v5.1.3...v5.2.0

Contributors

rkm, dependabot, and tznind
Assets 7
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v5.1.3

21 Jul 16:07
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v5.1.3
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v5.1.3
  • #1229 by dependabot. Bump IsIdentifiable from 0.0.4 to 0.0.5 to fix broken API

What's Changed

Full Changelog: v5.1.2...v5.1.3

Contributors

rkm and dependabot
Assets 8
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v5.1.2

18 Jul 20:36
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v5.1.2
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v5.1.2

Bugfix

  • #1223 by rkm. Fix setup.py in Smi_Common_Python to include all files, regardless of the current directory.

What's Changed

Full Changelog: v5.1.1...v5.1.2

Contributors

rkm
Assets 8
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v5.1.1

18 Jul 12:06
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v5.1.1
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v5.1.1

Bugfix

  • #1216 by jas88. Bugfix: issue #1217, microservices prematurely exiting since RabbitMQ no longer delays completion

What's Changed

  • Bump HIC.RDMP.Plugin.Test from 7.0.13 to 7.0.14 by @dependabot in #1205
  • Bump HIC.RDMP.Plugin from 7.0.13 to 7.0.14 by @dependabot in #1206
  • Bump StackExchange.Redis from 2.6.45 to 2.6.48 by @dependabot in #1208
  • Bump maven-assembly-plugin from 3.3.0 to 3.4.0 in /src/common/com.smi.microservices.parent by @dependabot in #1209
  • Bump System.IO.Abstractions.TestingHelpers from 17.0.18 to 17.0.21 by @dependabot in #1210
  • Bump commons-configuration2 from 2.7 to 2.8.0 in /src/common/com.smi.microservices.parent by @dependabot in #1212
  • Bump System.IO.Abstractions from 17.0.18 to 17.0.21 by @dependabot in #1211
  • Bump maven-assembly-plugin from 3.4.0 to 3.4.1 in /src/common/com.smi.microservices.parent by @dependabot in #1213
  • Bump CsvHelper from 27.2.1 to 28.0.0 by @dependabot in #1214
  • Bump actions/setup-java from 3.4.0 to 3.4.1 by @dependabot in #1215
  • Add wait loop for all Rabbit work to finish before quitting by @jas88 in #1216
  • Bump CsvHelper from 28.0.0 to 28.0.1 by @dependabot in #1218
  • Bump System.IO.Abstractions.TestingHelpers from 17.0.21 to 17.0.23 by @dependabot in #1220
  • Bump System.IO.Abstractions from 17.0.21 to 17.0.23 by @dependabot in #1221
  • Release/v5.1.1 by @rkm in #1222

Full Changelog: v5.1.0...v5.1.1

Contributors

jas88, rkm, and dependabot
Assets 8
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v5.1.0

23 Jun 16:14
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v5.1.0
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v5.1.0

Feature

  • #1074 by rkm. Switch CI to GitHub Actions
  • #1134 by jas88. Remove DeadLetterReprocessor and associated code, more elegant native RabbitMQ approach available if needed.
  • #1190 by howff. Anonymise names and dates in SRs, just in case (useful for demo). Proceed without ID mapping if DB unavailable (useful for testing).
  • #1199 by tznind. Added Setup utility for checking config settings (connection strings, queue setup etc)
  • #1200 by jas88. Add new DicomLoader CLI application for batch-loading DICOM files and archives

Bugfix

  • #1087 by rkm. [CI] Misc. CI fixes
    • Fixes the build scripts to respect any intermediate non-zero return codes
    • Fixes the build scripts to only build linux-x64 and win-x64
    • Fixes the build scripts to select the correct build configuration
    • Removes a bogus test leftover from #1089
    • Temporarily disables a few tests requiring a fix for the leptonica libs
  • #1088 by rkm. Use DirectConnection instead of obsolete ConnectionMode. Fixes #990
  • #1089 by rkm. Remove invalid extraction modality check. Fixes #1059
  • #1128 by jas88. Update RabbitMQ Nuget package and associated API calls
  • #1138 by jas88. Use Chocolatey to install SQL 2019 LocalDB instead of Powershell script
  • #929 by howff. Structured Reports improvements from PR#929
    • Updated documentation
    • Simplify SRAnonTool using external program semehr_anon.py
    • Handle ConceptNameCodeSequence which has VR but no Value
    • Ensure 'replaced' flag is not reset
    • Write replacement DICOM whichever content tag is found
    • Extract metadata from Mongo to go alongside anonymised text
    • Redact numeric DICOM tags with all '9' not all 'X'
    • Allow badly-formatted text content which contains HTML but does not escape non-HTML symbols

Change

  • #1023 by jas88. RabbitMQ tidyup
    • Fix both C# and Java server version check logic
    • Reuse Connection more per RabbitMQ guidance
    • Tidy up some Java exception handling logic

Meta

  • #1082 by rkm. CI: Don't exit early if a single test project has failures

What's Changed

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Contributors

jas88, howff, and 4 other contributors
Assets 8
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v5.0.1

18 Feb 10:50
@SMI-Bot SMI-Bot
v5.0.1
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v5.0.1

Bugfix

  • #1054 by rkm. Swap stderr reading and process.waitFor in SmiCtpProcessor to avoid a deadlock
Assets 9
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