v5.0.0

Feature

• #1040 by tznind. Updated to latest dotnet sdk (net6)
• #973 by rkm. Adds the basis for a new "DicomAnonymiser" microservice, which can be used in place of the existing Java CTP service. It supports pluggable anonymisers through the
  IDicomAnonymiser interface. No implementations are provided in this PR.

Bugfix

• #1010 by rkm. Update CI script to pull tessdata file from the new branch name (main not master)
• #1050 by rkm. Disable coverage upload which is currently broken for .NET 6
• #1052 by rkm. Ensure any errors encountered when running SRAnonTool are handled properly and produce an appropriate status message.
• #885 by howff. Always convert PHI to XML regardless of annotation_mode setting.
• #914 by rkm. Fix #913; error if file extraction command is re-run after being cancelled
• #915 by rkm. Fix #891; jobId not created until extraction is completed.
• #917 by rkm. Ensure control exchange exists for ExtractImagesHostTests
• #926 by rkm. Fixes the current CI issues by restricting the creation of the ControlExchange to the RequiresRabbit test decorator.
• #931 by rkm. Ensure the python version used in CI runs is exactly what we specify
• #968 by rkm. Remove reference to System.Drawing.Common
• #976 by jas88. Fix issue
  #921 - erroneous stripping of root path to empty string in GlobalOptions
• #981 by rkm. Fix deprecated python collections import for py310+
• #987 by rkm. Treat all build warnings as errors, and fix or disable existing ones. Also remove unused System.Security.AccessControl package.

Meta

• #923 by rkm. Allow newer minor SDK versions to build the sln. global.json specifies the minimum version which will be used in the CI.
• #986 by rkm. Add missing reference to NLog.

v4.0.0

Feature

• #849 by jas88. CTPAnonymiser refactoring
  • Reduce memory footprint (issue #837)
  • Simplify RabbitMQ message handling
  • Stop creating temporary copy of input file - no longer needed in EPCC environment without Lustre FS (per issue #836)
  • Add checks input file is readable not just extant, hopefully fixing issue #533
• #861 by rkm. Add Equ to automatically implement equality members for classes.
• #878 by rkm. Update RDMP packages with replacement of System.Data.SqlClient with Microsoft.Data.SqlClient. Replace usages of same in codebase

Bugfix

• #764 by howff. Clean up the Python code lint after running pylint3
• #841 by tznind. Fixed bug when disposing CsvDestination instances that have not begun writing any output
• #880 by tznind. Fixed edge case in IdentifierMapper when a dicom tag has illegal multiplicity in PatientID field

Meta

• #843 by rkm. Add pre-commit and codespell. Fix all current spelling mistakes
• #844 by rkm. Fixup regex in codespell config
• #855 by rkm. Specify dotnet SDK version in global.json
• #859 by rkm. Bump LangVersion to 9.0
• #876 by rkm. Add check and error message for missing coveralls token
• #877 by rkm. Fix setting replication for MongoDB in Windows CI pipelines

Removal

• #848 by rkm. Removed NationalPACSAccessionNumber from all metadata

v3.2.1

Bugfix

• #834 by tznind. Improved logging and fixed yaml options not being respected in IsIdentifiableReviewer

v3.2.0

Feature

• #795 by tznind. Added support for specifying IsIdentifiable CLI options in the yaml config files instead of command line (command line will always take precedence if both are specified)
• #797 by tznind. Added custom themes to IsIdentifiableReviewer. Use flag --theme mytheme.yaml
• #801 by tznind. Added help and cancel buttons to custom pattern dialog in reviewer
• #802 by tznind. Added IsIdentifiableReviewer settings into main yaml config
• #818 by tznind. Added Rules Manager to IsIdentifiable Reviewer

Bugfix

• #787 by rkm. Fix the call to the release changelog script
• #788 by rkm. Require all CI tests to pass before packaging runs
• #789 by rkm. Don't upload coverage for tagged builds
• #796 by tznind. Fixed bug opening corrupted reports in IsIdentifiableReviewer crashing the application
• #806 by tznind. Replace use of GlobalColorScheme with the proper static members in Terminal.Gui that will propagate correctly for all windows without having to set them manually.
• #811 by rkm. Fix coverage task always running even if a previous task failed

Doc

• #823 by tznind. Refresh documentation for IsIdentifiableReviewer

v3.1.0

Feature

• #759 by tznind. Added parallelisation to load process in IsIdentifiableReviewer rules view

Bugfix

• #756 by howff. Open CSV file read-only
• #771 by tznind. IsIdentifiableReviewer:
  • Added --usc (UseSystemConsole) for alternative display driver based on System.Console
  • Removed modal dialog that could cause errors opening a previously completed report
  • Added label with currently opened file and fixed ignore/update labels
  • Added spinner indicator for when loading the Next report in sequential mode takes a while
  • Fixed bug where Ctrl+Q in Ignore/Update with custom patterns in RulesView results in hard crash
• #785 by tznind. Fixed bug with multiple enumeration during loading very large failure reports in IsIdentifiableReviewer

Meta

• #773 by rkm. Add code coverage
• #775 by rkm. Move useful scripts from .azure-pipelines/scripts to utils. Update utils/README.md.
• #781 by rkm. Fixup coverage variables between pushes/PRs

v3.0.2

Bugfix

• #745 by tznind. Fixed
  reviewer tree view refresh/async code

v3.0.1

Feature

• #738 by rkm. Improvements to CLI user experience
  • Immediately verify that the config file (GlobalOptions) we've loaded is somewhat valid
  • Improve visibility of exception messages on CLI exit

Bugfix

• #737 by rkm. Switch ordering of annotations in ExtractImagesCliOption to fix a runtime exception.

Meta

• #736 by rkm. Remove .NET Core 2.2 runtime from the Azure Pipelines builds

v3.0.0

Feature

• #702 by rkm. Replace Java ExtractorCLI with C# ExtractImages service
  • Breaking Existing scripts and documentation
  • Breaking Change ExtractorClOptions -> ExtractImagesOptions in YAML
    configs
• #713 by rkm. Upgrade all projects and related CI scripts to net5.
• #734 by tznind. Updated to RDMP 5.0.0 (and Dicom Plugin 3.0.0)

Bugfix

• #708 by rkm. Add nuget.config file to fix flaky issues with Azure CI Runners. Ref:
  • NuGet/Home#10586
  • actions/runner-images#3038
• #714 by rkm. Fixup current LGTM alerts.
• #715 by rkm. Revert to the hack-y method of fixing the Nuget cache for Azure Windows agents.
• #722 by rkm. Remove workaround for Windows agents in Azure CI since fixed upstream. Ref:
  • actions/runner-images#3038

v2.1.1

Bugfix

• #697 by rkm. Fixes #695. Removes the checks preventing modality being specified with other extraction
  keys
• #698 by rkm. CohortExtractor database queries that crash during execution are now logged
• #701 by howff. Several improvements to Python code for handling unusually-formatted SR documents.
• #704 by rkm. Fix ReportNewLine being incorrectly set to a pre-escaped string. Fixes #703

Doc

• #672 by howff. IsIdentifiableReviewer document updated

v2.1.0

Feature

• #676 by tznind. Improvements to IsIdentifiable Reviewer
  • Tab based navigation
  • Better pattern generation for overlapping failure parts
  • Fixed sequential mode always showing failures covered by existing UPDATE rules
  • Fixed tree view not adapting as new rules are added e.g. when used to interactively process many failures
• #690 by tznind. Added ModalitySpecificRejectorOptions

Bugfix

• #678 by rkm. Fix log directory naming for single-entrypoint app. Fixes #677
• #681 by howff. Fix Python packaging when run from repo root dir
• #684 by howff.
  • Minor fixes to python for compatibility (eg. semehr using python2)
  • Use a unique temporary directory for input and output files
  • Enable extraction from MongoDB by StudyDate (the only field other than FilePath which has an index)
• #688 by howff. Reword the CohortExtractor log/info messages as it's not just patients which can be rejected

Meta

• #668 by rkm. Add note to the releasing documentation to alert the Mattermost channel