├── .editorconfig ├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── 1-bug-report.md │ └── config.yml ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml └── workflows │ ├── codeql.yml │ ├── envs.json │ └── main.yml ├── .gitignore ├── .meta ├── codespell-excludes ├── codespell-ignores ├── flake8.conf ├── isort.cfg ├── markdown-link-check.json └── mypy.ini ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── CONTRIBUTORS.md ├── Directory.Build.props ├── Directory.Packages.props ├── Glossary.md ├── LICENSE ├── PACKAGES.md ├── README.md ├── SharedAssemblyInfo.cs ├── SmiServices.sln ├── Tests.md ├── bin ├── README.md ├── checkDocs.py ├── common.py ├── ctp │ ├── ctp_build.py │ ├── ctp_build_test_package.py │ ├── ctp_package.py │ ├── ctp_start_docker_linux.py │ ├── ctp_stop_docker_linux.py │ ├── ctp_test.py │ ├── install_libs.py │ └── java_common.py ├── release │ ├── createReleaseChangelog.py │ ├── missing-news.sh │ └── updateChangelog.py ├── smi │ ├── dotnet_common.py │ ├── downloadCtpAnonJar.py │ ├── downloadRdmpCli.py │ ├── download_tessdata.py │ ├── smi_build.py │ ├── smi_build_test_package.py │ ├── smi_package.py │ ├── smi_start_docker_linux.py │ ├── smi_stop_docker_linux.py │ ├── smi_test.py │ └── writeDatabaseStrings.py └── wait-for.bash ├── codecov.yml ├── coverage.settings ├── data ├── IsIdentifiableRules │ ├── BasicRules.yaml │ ├── InstitutionName.yaml │ ├── Manufacturer.yaml │ ├── SocketRules.yaml │ ├── SurnameFirstnameTitle.yaml │ └── WhiteListRules.yaml ├── ctp │ ├── .gitignore │ └── ctp-allowlist.script ├── logging │ └── Smi.NLog.config ├── microserviceConfigs │ └── default.yaml ├── rabbitmqConfigs │ ├── README.md │ ├── defaultDataLoadConfig.json │ └── defaultExtractConfig.json └── tessdata │ └── .gitignore ├── docs ├── INSTALL.md ├── Images │ ├── ExtractionMicroservices.png │ ├── LoadMicroservices.png │ ├── SmiFlow.svg │ ├── processes.svg │ └── rdmp-tui.png ├── README.md ├── applications │ ├── dicom-directory-processor.md │ ├── dicom-loader.md │ ├── dynamic-rules-tester.md │ ├── extract-images.md │ ├── setup.md │ └── trigger-updates.md ├── config.yaml ├── dev │ └── release-process.md ├── guides │ ├── control-queues.md │ ├── data-loading.md │ ├── extraction.md │ └── img │ │ ├── AfterAccessionDirectory.png │ │ ├── AfterDicomTagReader.png │ │ ├── BindExchange.png │ │ ├── Extraction-Pipeline-2.2.1.png │ │ ├── Extraction-Pipeline-v2.0.png │ │ ├── Extraction-Pipeline-v2.1.png │ │ ├── Extraction-Pipeline-v2.2.png │ │ ├── Extraction-Pipeline-v2.3.png │ │ ├── Extraction-Pipeline.drawio │ │ ├── FinalImageTable.png │ │ ├── FinalStudyTable.png │ │ ├── LostMessages.png │ │ ├── MongoDbCompassAtEnd.png │ │ ├── MongoDbCompassAtStart.png │ │ ├── PeekAccessionDirectory.png │ │ ├── RdmpAllDatabases.png │ │ ├── RdmpGuiCreateDatabase.png │ │ ├── RdmpGuiCreateSuite.png │ │ ├── RdmpGuiLoadCreated.png │ │ ├── RdmpGuiOpenTree.png │ │ ├── RdmpGuiTemplateFile.png │ │ ├── RdmpPlatformDatabases.png │ │ ├── SqlServerIdentifierMapperMappingTable.png │ │ ├── TEST.AccessionDirectoryQueue.png │ │ ├── TEST.ControlExchange.png │ │ └── testfiles.png ├── install.sh ├── metadataTemplate.md ├── metadataTemplate.yaml ├── purge.sh ├── schema.sql └── services │ ├── cohort-extractor.md │ ├── cohort-packager.md │ ├── ctp-anonymiser.md │ ├── dicom-anonymiser.md │ ├── dicom-relational-mapper.md │ ├── dicom-reprocessor.md │ ├── dicom-tag-reader.md │ ├── file-copier.md │ ├── identifier-mapper.md │ ├── is-identifiable.md │ ├── mongodb-populator.md │ └── update-values.md ├── dotnet-tools.json ├── global.json ├── lib ├── ctp │ ├── CTP.jar │ ├── DAT.jar │ ├── RSNA-MIRC-Public-License.pdf │ ├── clibwrapper_jiio.jar │ ├── dcm4che-imageio-rle-2.0.25.jar │ ├── dcm4che.jar │ ├── jai_imageio.jar │ ├── log4j.jar │ ├── pixelmed_codec.jar │ ├── pom.xml │ └── util.jar ├── libleptonica-1.78.0.so ├── libleptonica.so.1.78.0-minimal-centos7 └── libtesseract.so.4.0.1-centos7 ├── news ├── 2146-change.md ├── 2195-fix.md └── README.md ├── nuget.config ├── nunit.runsettings ├── src ├── .gitignore ├── Directory.Build.props ├── SmiServices │ ├── Applications │ │ ├── DicomDirectoryProcessor │ │ │ ├── DicomDirectoryProcessor.cs │ │ │ ├── DicomDirectoryProcessorCliOptions.cs │ │ │ ├── DicomDirectoryProcessorHost.cs │ │ │ └── DirectoryFinders │ │ │ │ ├── AccessionDirectoryLister.cs │ │ │ │ ├── BasicDicomDirectoryFinder.cs │ │ │ │ ├── DicomDirectoryFinder.cs │ │ │ │ ├── IDicomDirectoryFinder.cs │ │ │ │ ├── PacsDirectoryFinder.cs │ │ │ │ └── ZipDicomDirectoryFinder.cs │ │ ├── DicomLoader │ │ │ ├── DicomLoader.cs │ │ │ └── Loader.cs │ │ ├── DynamicRulesTester │ │ │ └── DynamicRulesTester.cs │ │ ├── ExtractImages │ │ │ ├── CohortCsvParser.cs │ │ │ ├── ExtractImages.cs │ │ │ ├── ExtractImagesCliOptions.cs │ │ │ ├── ExtractImagesHost.cs │ │ │ ├── ExtractionMessageSender.cs │ │ │ └── IExtractionMessageSender.cs │ │ ├── Setup │ │ │ ├── EnvironmentProbe.cs │ │ │ ├── MainWindow.Designer.cs │ │ │ ├── MainWindow.cs │ │ │ ├── Setup.cs │ │ │ ├── SetupIsolatedStorage.cs │ │ │ └── SetupSettings.cs │ │ └── TriggerUpdates │ │ │ ├── ITriggerUpdatesSource.cs │ │ │ ├── MapperSource.cs │ │ │ ├── TriggerUpdates.cs │ │ │ ├── TriggerUpdatesFromMapperOptions.cs │ │ │ ├── TriggerUpdatesHost.cs │ │ │ └── TriggerUpdatesOptions.cs │ ├── Common │ │ ├── Events │ │ │ ├── ControlEventHandler.cs │ │ │ ├── FatalErrorEventArgs.cs │ │ │ ├── FatalErrorHandlers.cs │ │ │ ├── MessageResultHandlers.cs │ │ │ └── StopEventHandler.cs │ │ ├── Execution │ │ │ ├── IMicroserviceHost.cs │ │ │ ├── MicroserviceHost.cs │ │ │ └── MicroserviceHostBootstrapper.cs │ │ ├── FansiImplementations.cs │ │ ├── Helpers │ │ │ ├── DateTimeProvider.cs │ │ │ ├── IConsoleInput.cs │ │ │ ├── MicroserviceObjectFactory.cs │ │ │ └── RealConsoleInput.cs │ │ ├── IMessageBroker.cs │ │ ├── MessageSerialization │ │ │ ├── JsonCompatibleDictionary.cs │ │ │ └── JsonConvert.cs │ │ ├── Messages │ │ │ ├── AccessionDirectoryMessage.cs │ │ │ ├── DicomFileMessage.cs │ │ │ ├── Extraction │ │ │ │ ├── ExtractFileCollectionInfoMessage.cs │ │ │ │ ├── ExtractFileMessage.cs │ │ │ │ ├── ExtractMessage.cs │ │ │ │ ├── ExtractedFileStatus.cs │ │ │ │ ├── ExtractedFileStatusMessage.cs │ │ │ │ ├── ExtractedFileVerificationMessage.cs │ │ │ │ ├── ExtractionKey.cs │ │ │ │ ├── ExtractionRequestInfoMessage.cs │ │ │ │ ├── ExtractionRequestMessage.cs │ │ │ │ ├── IExtractMessage.cs │ │ │ │ └── VerifiedFileStatus.cs │ │ │ ├── FatalErrorMessage.cs │ │ │ ├── IFileReferenceMessage.cs │ │ │ ├── IMessage.cs │ │ │ ├── IMessageHeader.cs │ │ │ ├── MessageHeader.cs │ │ │ ├── RabbitMqXDeathHeaders.cs │ │ │ ├── SeriesMessage.cs │ │ │ ├── TagPromotionMessage.cs │ │ │ └── Updating │ │ │ │ └── UpdateValuesMessage.cs │ │ ├── Messaging │ │ │ ├── BackoffProviderFactory.cs │ │ │ ├── BackoffProviderType.cs │ │ │ ├── BatchProducerModel.cs │ │ │ ├── Consumer.cs │ │ │ ├── ControlMessageConsumer.cs │ │ │ ├── ExponentialBackoffProvider.cs │ │ │ ├── IBackoffProvider.cs │ │ │ ├── IConsumer.cs │ │ │ ├── IControlMessageConsumer.cs │ │ │ ├── IControlMessageHandler.cs │ │ │ ├── IProducerModel.cs │ │ │ ├── MessageBrokerFactory.cs │ │ │ ├── MessageBrokerType.cs │ │ │ ├── ProducerModel.cs │ │ │ ├── RabbitMQBroker.cs │ │ │ └── StaticBackoffProvider.cs │ │ ├── MongoDB │ │ │ ├── MongoClientHelpers.cs │ │ │ ├── MongoDocumentHeaders.cs │ │ │ ├── MongoModalityGroups.cs │ │ │ └── MongoQueryParser.cs │ │ ├── Options │ │ │ ├── CliOptions.cs │ │ │ ├── ConsumerOptions.cs │ │ │ ├── EnvironmentVariableDecorator.cs │ │ │ ├── GlobalOptions.cs │ │ │ ├── GlobalOptionsFactory.cs │ │ │ ├── IOptionsDecorator.cs │ │ │ ├── ModalitySpecificRejectorOptions.cs │ │ │ ├── OptionsDecorator.cs │ │ │ ├── ProducerOptions.cs │ │ │ ├── RabbitMqConfigOptions.md │ │ │ └── SmiCliInit.cs │ │ ├── README.md │ │ ├── SmiLogging.cs │ │ ├── TimeTracker.cs │ │ └── ZipHelper.cs │ ├── Microservices │ │ ├── CohortExtractor │ │ │ ├── CohortExtractor.cs │ │ │ ├── CohortExtractorHost.cs │ │ │ ├── ExtractImageCollection.cs │ │ │ ├── ExtractionRequestQueueConsumer.cs │ │ │ ├── ProjectPathResolvers │ │ │ │ ├── IProjectPathResolver.cs │ │ │ │ ├── NoSuffixProjectPathResolver.cs │ │ │ │ ├── ProjectPathResolverConstants.cs │ │ │ │ ├── ProjectPathResolverFactory.cs │ │ │ │ ├── StudySeriesOriginalFilenameProjectPathResolver.cs │ │ │ │ └── StudySeriesSOPProjectPathResolver.cs │ │ │ └── RequestFulfillers │ │ │ │ ├── BlacklistRejector.cs │ │ │ │ ├── ColumnInfoValuesRejector.cs │ │ │ │ ├── ColumnValuesRejector.cs │ │ │ │ ├── Dynamic │ │ │ │ └── DynamicRejector.cs │ │ │ │ ├── ExtractionRequestFulfillerFactory.cs │ │ │ │ ├── ExtractionRequestFulfillerType.cs │ │ │ │ ├── FromCataloguesExtractionRequestFulfiller.cs │ │ │ │ ├── IExtractionRequestFulfiller.cs │ │ │ │ ├── IRejector.cs │ │ │ │ ├── QueryToExecute.cs │ │ │ │ ├── QueryToExecuteColumnSet.cs │ │ │ │ ├── QueryToExecuteResult.cs │ │ │ │ └── RejectAll.cs │ │ ├── CohortPackager │ │ │ ├── AnonFailedMessageConsumer.cs │ │ │ ├── AnonVerificationMessageConsumer.cs │ │ │ ├── CohortPackager.cs │ │ │ ├── CohortPackagerCliOptions.cs │ │ │ ├── CohortPackagerControlMessageHandler.cs │ │ │ ├── CohortPackagerHost.cs │ │ │ ├── ExtractFileCollectionMessageConsumer.cs │ │ │ ├── ExtractJobStorage │ │ │ │ ├── CompletedExtractJobInfo.cs │ │ │ │ ├── ExtractJobInfo.cs │ │ │ │ ├── ExtractJobStatus.cs │ │ │ │ ├── ExtractJobStore.cs │ │ │ │ ├── ExtractionIdentifierRejectionInfo.cs │ │ │ │ ├── FileAnonFailureInfo.cs │ │ │ │ ├── FileVerificationFailureInfo.cs │ │ │ │ ├── IExtractJobStore.cs │ │ │ │ └── MongoDB │ │ │ │ │ ├── MongoExtractJobInfoExtensions.cs │ │ │ │ │ ├── MongoExtractJobStore.cs │ │ │ │ │ └── ObjectModel │ │ │ │ │ ├── MongoCompletedExtractJobDoc.cs │ │ │ │ │ ├── MongoExpectedFilesDoc.cs │ │ │ │ │ ├── MongoExtractJobDoc.cs │ │ │ │ │ ├── MongoExtractionMessageHeaderDoc.cs │ │ │ │ │ └── MongoFileStatusDoc.cs │ │ │ ├── ExtractionRequestInfoMessageConsumer.cs │ │ │ └── JobProcessing │ │ │ │ ├── ExtractJobWatcher.cs │ │ │ │ ├── IExtractJobWatcher.cs │ │ │ │ ├── Notifying │ │ │ │ ├── IJobCompleteNotifier.cs │ │ │ │ ├── JobCompleteNotifierFactory.cs │ │ │ │ └── LoggingNotifier.cs │ │ │ │ └── Reporting │ │ │ │ ├── IJobReporter.cs │ │ │ │ └── JobReporter.cs │ │ ├── DicomAnonymiser │ │ │ ├── Anonymisers │ │ │ │ ├── AnonymiserFactory.cs │ │ │ │ ├── AnonymiserType.cs │ │ │ │ ├── DefaultAnonymiser.cs │ │ │ │ ├── IDicomAnonymiser.cs │ │ │ │ └── SmiCtpAnonymiser.cs │ │ │ ├── DicomAnonymiser.cs │ │ │ ├── DicomAnonymiserConsumer.cs │ │ │ ├── DicomAnonymiserHost.cs │ │ │ └── Helpers │ │ │ │ └── ProcessWrapper.cs │ │ ├── DicomRelationalMapper │ │ │ ├── DicomFileMessageToDatasetListProvider.cs │ │ │ ├── DicomRelationalMapper.cs │ │ │ ├── DicomRelationalMapperHost.cs │ │ │ ├── DicomRelationalMapperQueueConsumer.cs │ │ │ ├── ExplicitListDicomProcessListProvider.cs │ │ │ ├── MigrateRawToStagingWithSelectIntoStatements.cs │ │ │ ├── NLogThrowerDataLoadEventListener.cs │ │ │ ├── Namers │ │ │ │ ├── GuidDatabaseNamer.cs │ │ │ │ ├── GuidTableNamer.cs │ │ │ │ ├── ICanCreateStagingMyself.cs │ │ │ │ └── MyFixedStagingDatabaseNamer.cs │ │ │ ├── ParallelDLEHost.cs │ │ │ └── QueuedImage.cs │ │ ├── DicomReprocessor │ │ │ ├── DicomFileProcessor.cs │ │ │ ├── DicomReprocessor.cs │ │ │ ├── DicomReprocessorCliOptions.cs │ │ │ ├── DicomReprocessorControlMessageHandler.cs │ │ │ ├── DicomReprocessorHost.cs │ │ │ ├── IDocumentProcessor.cs │ │ │ ├── MongoDbReader.cs │ │ │ └── TagPromotionProcessor.cs │ │ ├── DicomTagReader │ │ │ ├── DicomTagReader.cs │ │ │ ├── DicomTagReaderCliOptions.cs │ │ │ ├── Execution │ │ │ │ ├── DicomTagReaderHost.cs │ │ │ │ ├── ParallelTagReader.cs │ │ │ │ ├── SerialTagReader.cs │ │ │ │ └── TagReaderBase.cs │ │ │ └── Messaging │ │ │ │ └── DicomTagReaderConsumer.cs │ │ ├── FileCopier │ │ │ ├── ExtractionFileCopier.cs │ │ │ ├── FileCopier.cs │ │ │ ├── FileCopierHost.cs │ │ │ ├── FileCopyQueueConsumer.cs │ │ │ └── IFileCopier.cs │ │ ├── IdentifierMapper │ │ │ ├── BadPatientIDException.cs │ │ │ ├── IdentifierMapper.cs │ │ │ ├── IdentifierMapperControlMessageHandler.cs │ │ │ ├── IdentifierMapperHost.cs │ │ │ ├── IdentifierMapperQueueConsumer.cs │ │ │ └── Swappers │ │ │ │ ├── ForGuidIdentifierSwapper.cs │ │ │ │ ├── ISwapIdentifiers.cs │ │ │ │ ├── PreloadTableSwapper.cs │ │ │ │ ├── RedisSwapper.cs │ │ │ │ ├── SwapIdentifiers.cs │ │ │ │ ├── TableLookupSwapper.cs │ │ │ │ └── TableLookupWithGuidFallbackSwapper.cs │ │ ├── IsIdentifiable │ │ │ ├── Classifier.cs │ │ │ ├── IClassifier.cs │ │ │ ├── IsIdentifiable.cs │ │ │ ├── IsIdentifiableHost.cs │ │ │ ├── IsIdentifiableQueueConsumer.cs │ │ │ ├── NoChisInAnyColumnsConstraint.cs │ │ │ ├── RejectAllClassifier.cs │ │ │ └── TesseractStanfordDicomFileClassifier.cs │ │ ├── MongoDBPopulator │ │ │ ├── IMongoDbAdapter.cs │ │ │ ├── IMongoDbPopulatorMessageConsumer.cs │ │ │ ├── MongoDBPopulator.cs │ │ │ ├── MongoDbAdapter.cs │ │ │ ├── MongoDbPopulatorHost.cs │ │ │ ├── MongoDbPopulatorMessageConsumer.cs │ │ │ └── Processing │ │ │ │ ├── IMessageProcessor.cs │ │ │ │ ├── ImageMessageProcessor.cs │ │ │ │ ├── MessageProcessor.cs │ │ │ │ └── SeriesMessageProcessor.cs │ │ └── UpdateValues │ │ │ ├── IUpdater.cs │ │ │ ├── UpdateTableAudit.cs │ │ │ ├── UpdateValues.cs │ │ │ ├── UpdateValuesCliOptions.cs │ │ │ ├── UpdateValuesHost.cs │ │ │ ├── UpdateValuesQueueConsumer.cs │ │ │ └── Updater.cs │ ├── Program.cs │ ├── ServiceVerbs.cs │ ├── SmiServices.csproj │ ├── packages.lock.json │ └── runtimes │ │ └── x64 │ │ ├── libleptonica-1.80.0.so │ │ └── libtesseract41.so ├── common │ ├── com.smi.microservices.common │ │ ├── README.md │ │ ├── pom.xml │ │ └── src │ │ │ ├── main │ │ │ └── java │ │ │ │ └── org │ │ │ │ └── smi │ │ │ │ └── common │ │ │ │ ├── execution │ │ │ │ ├── IMicroserviceHost.java │ │ │ │ └── SmiShutdownHook.java │ │ │ │ ├── logging │ │ │ │ ├── SmiLogging.java │ │ │ │ └── SmiLoggingException.java │ │ │ │ ├── messageSerialization │ │ │ │ └── JsonDeserializerWithOptions.java │ │ │ │ ├── messages │ │ │ │ ├── ExtractMessage.java │ │ │ │ ├── FatalLogMessage.java │ │ │ │ ├── IMessage.java │ │ │ │ ├── IMessageHeader.java │ │ │ │ ├── MessageHeader.java │ │ │ │ ├── MessageHeaderFactory.java │ │ │ │ └── SimpleMessage.java │ │ │ │ ├── messaging │ │ │ │ ├── AnyConsumer.java │ │ │ │ ├── IProducerModel.java │ │ │ │ ├── ProducerModel.java │ │ │ │ ├── SimpleConsumer.java │ │ │ │ └── SmiConsumer.java │ │ │ │ ├── options │ │ │ │ ├── ConsumerOptions.java │ │ │ │ ├── GlobalOptions.java │ │ │ │ └── ProducerOptions.java │ │ │ │ ├── rabbitMq │ │ │ │ └── RabbitMqAdapter.java │ │ │ │ └── util │ │ │ │ └── Utils.java │ │ │ └── test │ │ │ └── java │ │ │ └── org │ │ │ └── smi │ │ │ └── common │ │ │ └── test │ │ │ ├── messages │ │ │ └── MessageHeaderTests.java │ │ │ ├── options │ │ │ └── GlobalOptionsTest.java │ │ │ └── rabbitMqAdapter │ │ │ └── RabbitMQAdapterTest.java │ └── com.smi.microservices.parent │ │ ├── README.md │ │ ├── pom.xml │ │ └── res │ │ └── deployDescriptor.xml └── microservices │ └── com.smi.microservices.ctpanonymiser │ ├── .gitignore │ ├── pom.xml │ └── src │ ├── main │ └── java │ │ └── org │ │ └── smi │ │ └── ctpanonymiser │ │ ├── Program.java │ │ ├── execution │ │ ├── CTPAnonymiserHost.java │ │ └── SmiCtpProcessor.java │ │ ├── messages │ │ ├── ExtractFileMessage.java │ │ └── ExtractedFileStatusMessage.java │ │ ├── messaging │ │ └── CTPAnonymiserConsumer.java │ │ └── util │ │ ├── CtpAnonymisationStatus.java │ │ ├── DicomAnonymizerToolBuilder.java │ │ ├── ExtractedFileStatus.java │ │ └── SmiAnonymisationException.java │ └── test │ ├── java │ └── org │ │ └── smi │ │ └── ctpanonymiser │ │ └── test │ │ ├── execution │ │ └── CTPAnonymiserHostTest.java │ │ ├── messages │ │ └── ExtractFileMessageTest.java │ │ └── util │ │ └── DicomAnonymizerToolBuilderTest.java │ └── resources │ ├── .gitignore │ ├── AnonymisedFiles │ └── .gitignore │ ├── dicom-anonymizer.script │ ├── image-000001.dcm │ └── test_SR.dcm ├── tests ├── .gitignore ├── Directory.Build.props ├── SmiServices.IntegrationTests │ ├── Applications │ │ ├── DicomLoader │ │ │ └── DicomLoaderTests.cs │ │ ├── ExtractImages │ │ │ └── ExtractImagesHostTests.cs │ │ └── TriggerUpdates │ │ │ ├── MapperSourceIntegrationTest.cs │ │ │ └── MapperSourceTests.cs │ ├── Common │ │ ├── GlobalOptionsExtensions.cs │ │ ├── HeaderPreservationTest.cs │ │ ├── Messaging │ │ │ ├── ControlMessageConsumerTests.cs │ │ │ └── RabbitMQBrokerTests.cs │ │ ├── MongoDB │ │ │ └── MongoQueryParserTests.cs │ │ └── OptionsTests.cs │ ├── Coverage.cs │ ├── FixtureSetup.cs │ ├── Microservices │ │ ├── CohortExtractor │ │ │ ├── BlacklistRejectorTests.cs │ │ │ ├── ColumnInfoValuesRejectorTests.cs │ │ │ ├── ExtractionSuperTableTests.cs │ │ │ └── FromCataloguesExtractionRequestFulfillerTests.cs │ │ ├── CohortPackager │ │ │ ├── CohortPackagerHostTest.cs │ │ │ └── ProgramTests.cs │ │ ├── DicomAnonymiser │ │ │ ├── Anonymisers │ │ │ │ └── SmiCtpAnonymiserTests.cs │ │ │ ├── DicomAnonymiserHostTests.cs │ │ │ └── FixtureSetup.cs │ │ ├── DicomRelationalMapper │ │ │ ├── DLEBenchmarkingTests │ │ │ │ └── HowFastIsDLETest.cs │ │ │ ├── DicomRelationalMapperHostTests.cs │ │ │ ├── DicomRelationalMapperTests.cs │ │ │ ├── MicroservicesIntegrationTest.cs │ │ │ └── RunMeFirstTests │ │ │ │ ├── RunMeFirstMongoServers.cs │ │ │ │ └── RunMeFirstRdmpTests.cs │ │ ├── DicomTagReader │ │ │ ├── DicomTagReaderHostTests.cs │ │ │ ├── Messaging │ │ │ │ └── DicomTagReaderConsumerTests.cs │ │ │ └── TagReaderTests.cs │ │ ├── FileCopier │ │ │ └── FileCopierHostTest.cs │ │ ├── IdentifierMapper │ │ │ ├── IdentifierMapperTests.cs │ │ │ ├── RedisSwapperTests.cs │ │ │ └── TableLookupWithGuidFallbackSwapperTests.cs │ │ ├── IsIdentifiable │ │ │ └── IsIdentifiableHostTests.cs │ │ ├── MongoDBPopulator │ │ │ ├── MongoDbAdapterTests.cs │ │ │ ├── MongoDbPopulatorHostTests.cs │ │ │ └── Processing │ │ │ │ ├── ImageMessageProcessorTests.cs │ │ │ │ ├── MessageProcessorTests.cs │ │ │ │ └── SeriesMessageProcessorTests.cs │ │ └── UpdateValues │ │ │ └── TestUpdateDatabase.cs │ ├── PostgresFixes.cs │ ├── RequiresExternalService.cs │ ├── RequiresMongoDb.cs │ ├── RequiresRabbit.cs │ ├── RequiresRelationalDb.cs │ ├── SmiServices.IntegrationTests.csproj │ └── packages.lock.json └── SmiServices.UnitTests │ ├── Applications │ ├── DicomDirectoryProcessor │ │ ├── AccessionDirectoryListerTest.cs │ │ ├── DicomDirectoryFinderTest.cs │ │ ├── PacsDirectoryFinderTests.cs │ │ └── ZipDicomDirectoryFinderTests.cs │ ├── DynamicRulesTester │ │ └── ProgramTests.cs │ ├── ExtractImages │ │ ├── CohortCsvParserTests.cs │ │ ├── ExtractImagesCliOptionsTests.cs │ │ ├── ExtractImagesHostTests.cs │ │ └── ExtractionMessageSenderTests.cs │ └── TriggerUpdates │ │ └── MapperSourceUnitTests.cs │ ├── CT.it │ ├── Common │ ├── ArrayHelperTests.cs │ ├── ComplexMessageSerializationTests.cs │ ├── ConsumerTests.cs │ ├── DicomDataGeneratorExtensions.cs │ ├── EquTests.cs │ ├── LoggingTests.cs │ ├── MessageEqualityTests.cs │ ├── Messages │ │ ├── ExtractedFileStatusMessageTests.cs │ │ └── MessageHeaderTest.cs │ ├── Messaging │ │ ├── ExponentialBackoffProviderTests.cs │ │ ├── ProducerModelTests.cs │ │ └── StaticBackoffProviderTests.cs │ ├── MicroserviceTester.cs │ ├── MongoDB │ │ ├── MongoDocumentHeadersTests.cs │ │ ├── MongoModalityGroupsTests.cs │ │ ├── StubMongoCollection.cs │ │ └── StubMongoDatabase.cs │ ├── Options │ │ ├── FileSystemOptionsTests.cs │ │ └── SmiCliInitTests.cs │ ├── TestClassTemplate.cs │ ├── TestData.cs │ ├── TestDateTimeProvider.cs │ ├── TestException.cs │ ├── TestFileSystemHelpers.cs │ ├── TestHelpers.cs │ ├── TestTimeline.cs │ └── ZipHelperTests.cs │ ├── Coverage.cs │ ├── DynamicRules.txt │ ├── FixtureSetup.cs │ ├── LoggerFixture.cs │ ├── Microservices │ ├── CohortExtractor │ │ ├── ColumnValuesRejectorTests.cs │ │ ├── Execution │ │ │ └── RequestFulfillers │ │ │ │ ├── Dynamic │ │ │ │ └── DynamicRejectorTests.cs │ │ │ │ └── QueryToExecuteResultTest.cs │ │ ├── ExtractionRequestMessageTests.cs │ │ ├── FromCataloguesExtractionRequestFulfillerUnitTests.cs │ │ ├── Messaging │ │ │ └── ExtractionRequestQueueConsumerTest.cs │ │ ├── ModalitySpecificRejectorsTests.cs │ │ ├── NoSuffixProjectPathResolverTests.cs │ │ ├── QueryToExecuteTests.cs │ │ ├── StudySeriesOriginalFilenameProjectPathResolverTests.cs │ │ └── StudySeriesSOPProjectPathResolverTests.cs │ ├── CohortPackager │ │ ├── Execution │ │ │ ├── ExtractJobStorage │ │ │ │ ├── CompletedExtractJobInfoTest.cs │ │ │ │ ├── ExtractJobInfoTest.cs │ │ │ │ ├── ExtractJobStoreTest.cs │ │ │ │ ├── ExtractionIdentifierRejectionInfoTest.cs │ │ │ │ ├── FileAnonFailureInfoTest.cs │ │ │ │ ├── MongoDB │ │ │ │ │ ├── MongoExtractJobInfoExtensionsTest.cs │ │ │ │ │ ├── MongoExtractJobStoreTest.cs │ │ │ │ │ └── ObjectModel │ │ │ │ │ │ ├── MongoCompletedExtractJobDocTest.cs │ │ │ │ │ │ ├── MongoExpectedFilesDocTest.cs │ │ │ │ │ │ ├── MongoExtractJobDocTest.cs │ │ │ │ │ │ ├── MongoExtractionMessageHeaderDocTest.cs │ │ │ │ │ │ └── MongoFileStatusDocTest.cs │ │ │ │ └── VerificationFailureInfoTest.cs │ │ │ └── JobProcessing │ │ │ │ ├── ExtractJobWatcherTest.cs │ │ │ │ ├── Notifying │ │ │ │ └── JobCompleteNotifierFactoryTest.cs │ │ │ │ └── Reporting │ │ │ │ └── JobReporterTests.cs │ │ ├── Messaging │ │ │ ├── AnonFailedMessageConsumerTests.cs │ │ │ ├── AnonVerificationMessageConsumerTests.cs │ │ │ ├── CohortPackagerControlMessageHandlerTests.cs │ │ │ ├── ExtractFileCollectionMessageConsumerTests.cs │ │ │ └── ExtractionRequestInfoMessageConsumerTests.cs │ │ └── PathFixtures.cs │ ├── DicomAnonymiser │ │ ├── Anonymisers │ │ │ └── AnonymiserFactoryTests.cs │ │ └── DicomAnonymiserConsumerTests.cs │ ├── DicomRelationalMapper │ │ ├── AutoRoutingAttacherTests.cs │ │ ├── DicomDatasetCollectionSourceTests.cs │ │ ├── DicomRelationalMapperTestHelper.cs │ │ └── Namers │ │ │ └── GuidDatabaseNamerTests.cs │ ├── DicomReprocessor │ │ ├── DicomFileProcessorTest.cs │ │ └── DicomReprocessorCliOptionsTests.cs │ ├── DicomTagReader │ │ └── DicomTagReaderTestHelper.cs │ ├── FileCopier │ │ ├── FileCopierTest.cs │ │ └── FileCopyQueueConsumerTest.cs │ ├── IdentifierMapper │ │ ├── IdentifierMapperUnitTests.cs │ │ └── SwapForFixedValueTester.cs │ ├── IsIdentifiable │ │ ├── IsIdentifiableQueueConsumerTests.cs │ │ ├── NoChisInAnyColumnsConstraintTests.cs │ │ └── TesseractStanfordDicomFileClassifierTests.cs │ ├── MongoDbPopulator │ │ ├── Execution │ │ │ └── Processing │ │ │ │ └── ImageMessageProcessorTests_NoMongo.cs │ │ └── MongoDbPopulatorTestHelper.cs │ └── UpdateValues │ │ ├── TestUpdateValuesMessage.cs │ │ └── UpdateTableAuditTests.cs │ ├── Mongo.yaml │ ├── ProgramTests.cs │ ├── Rabbit.yaml │ ├── RelationalDatabases.yaml │ ├── ServiceVerbsTests.cs │ ├── SmiServices.UnitTests.csproj │ ├── TestCommon │ ├── DisposableTempDir.cs │ ├── TestDirectoryHelpers.cs │ └── TestTimelineAwaiter.cs │ ├── TestData │ ├── FileWithLotsOfTags.dcm │ ├── IM-0001-0013.dcm │ ├── IM-0001-0019.dcm │ ├── IM-0001-0024.dcm │ ├── NotADicomFile.txt │ └── burned-in-text-test.dcm │ ├── TestDatabases.txt │ ├── default.yaml │ └── 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