default.yaml

RabbitOptions:
  RabbitMqHostName: "localhost"
  RabbitMqHostPort: 5672
  RabbitMqVirtualHost: "/"
  RabbitMqUserName: "guest"
  RabbitMqPassword: "guest"
  RabbitMqControlExchangeName: "TEST.ControlExchange"
  FatalLoggingExchange: "TEST.FatalLoggingExchange"

LoggingOptions:
  LogConfigFile: ""
  LogsRoot: ""
  TraceLogging: true

FileSystemOptions:
  FileSystemRoot: 'C:\temp'
  ExtractRoot: 'C:\temp'
  # Set this to "*" if your dicom files do not have file extensions
  DicomSearchPattern: "*.dcm"

RDMPOptions:
  CatalogueConnectionString: 'server=localhost\sqlexpress;integrated security=true;database=RDMP_Catalogue'
  DataExportConnectionString: 'server=localhost\sqlexpress;integrated security=true;database=RDMP_DataExport'

  # Alternative to connection strings for if you have RDMP running with a YAML file system backend.  If specified then this will override the connection strings
  YamlDir:
MongoDatabases:
  DicomStoreOptions:
    HostName: "localhost"
    Port: 27017
    UserName: ""
    Password: ""
    DatabaseName: "dicom"
  ExtractionStoreOptions:
    HostName: "localhost"
    Port: 27017
    UserName: ""
    Password: ""
    DatabaseName: "extraction"

DicomRelationalMapperOptions:
  Guid: "6ff062af-5538-473f-801c-ed2b751c7897"
  QueueName: "TEST.AnonymousImageQueue"
  QoSPrefetchCount: 10000
  AutoAck: false
  LoadMetadataId: 1
  DatabaseNamerType: "GuidDatabaseNamer"
  MinimumBatchSize: 10000
  UseInsertIntoForRAWMigration: true
  RetryOnFailureCount: 1
  RetryDelayInSeconds: 60
  RunChecks: true

UpdateValuesOptions:
  QueueName: "TEST.UpdateValuesQueue"
  QoSPrefetchCount: 10000
  AutoAck: false
  #TableInfosToUpdate: 1,2,3 <-set this to limit which tables get updated when no explicit table is listed in the message
  UpdateTimeout: 500 # number of seconds to wait for each UPDATE statement

TriggerUpdatesOptions:
  ExchangeName: "TEST.TriggerUpdatesExchange"
  MaxConfirmAttempts: 1

CohortExtractorOptions:
  QueueName: "TEST.RequestQueue"
  QoSPrefetchCount: 10000
  AutoAck: false
  AllCatalogues: true

  # List of IDs of Catalogues to extract from (in ascending order).
  # Ignored if "AllCatalogues == true"
  OnlyCatalogues: [1, 2, 3]

  # ID(s) of ColumnInfo that contains a list of values which should not have data extracted for them.  e.g. opt out.  The name of the column referenced must match a column in the extraction table
  #RejectColumnInfos: [105,110]

  AuditorType: "SmiServices.Microservices.CohortExtractor.Audit.NullAuditExtractions"
  RequestFulfillerType: "SmiServices.Microservices.CohortExtractor.RequestFulfillers.FromCataloguesExtractionRequestFulfiller"
  ProjectPathResolverType: "SmiServices.Microservices.CohortExtractor.ProjectPathResolvers.DefaultProjectPathResolver"
  ExtractAnonRoutingKey: anon
  ExtractIdentRoutingKey: ident
  # Writes (Producer) to this exchange
  ExtractFilesProducerOptions:
    ExchangeName: "TEST.ExtractFileExchange"
    MaxConfirmAttempts: 1
  # And audits this too
  ExtractFilesInfoProducerOptions:
    ExchangeName: "TEST.FileCollectionInfoExchange"
    MaxConfirmAttempts: 1

CohortPackagerOptions:
  JobWatcherTimeoutInSeconds: 30
  ReporterType: "LoggingReporter"
  NotifierType: "LoggingNotifier"
  ReportFormat: "Combined"
  ReportNewLine: ""
  ExtractRequestInfoOptions:
    QueueName: "TEST.RequestInfoQueue"
    QoSPrefetchCount: 1
    AutoAck: false
  FileCollectionInfoOptions:
    QueueName: "TEST.FileCollectionInfoQueue"
    QoSPrefetchCount: 1
    AutoAck: false
  NoVerifyStatusOptions:
    QueueName: "TEST.ExtractedFileNoVerifyQueue"
    QoSPrefetchCount: 1
    AutoAck: false
  VerificationStatusOptions:
    QueueName: "TEST.ExtractedFileVerifiedQueue"
    QoSPrefetchCount: 1
    AutoAck: false

DicomReprocessorOptions:
  ProcessingMode: "ImageReprocessing"
  ReprocessingProducerOptions:
    ExchangeName: "TEST.IdentifiableImageExchange"
    MaxConfirmAttempts: 1

DicomTagReaderOptions:
  QueueName: "TEST.AccessionDirectoryQueue"
  QoSPrefetchCount: 1
  AutoAck: false
  NackIfAnyFileErrors: true
  ImageProducerOptions:
    ExchangeName: "TEST.IdentifiableImageExchange"
    MaxConfirmAttempts: 1
  SeriesProducerOptions:
    ExchangeName: "TEST.IdentifiableSeriesExchange"
    MaxConfirmAttempts: 1
  FileReadOption: "ReadLargeOnDemand"
  TagProcessorMode: "Serial"
  MaxIoThreads: 1

IdentifierMapperOptions:
  QueueName: "TEST.IdentifiableImageQueue"
  QoSPrefetchCount: 1000
  AutoAck: false
  AnonImagesProducerOptions:
    ExchangeName: "TEST.AnonymousImageExchange"
    MaxConfirmAttempts: 1
  MappingConnectionString: 'Server=localhost\sqlexpress;Integrated Security=true;Initial Catalog=MappingDatabase;'
  MappingDatabaseType: "MicrosoftSQLServer"
  MappingTableName: "MappingTable"
  TimeoutInSeconds: 600
  SwapColumnName: "CHI"
  ReplacementColumnName: "ECHI"
  SwapperType: "SmiServices.Microservices.IdentifierMapper.Swappers.ForGuidIdentifierSwapper"
  AllowRegexMatching: false
  RedisConnectionString: ""

MongoDbPopulatorOptions:
  SeriesQueueConsumerOptions:
    QueueName: "TEST.MongoSeriesQueue"
    QoSPrefetchCount: 1000
    AutoAck: false
  ImageQueueConsumerOptions:
    QueueName: "TEST.MongoImageQueue"
    QoSPrefetchCount: 10000
    AutoAck: false
  MongoDbFlushTime: 30 # Seconds
  FailedWriteLimit: 5

ProcessDirectoryOptions:
  AccessionDirectoryProducerOptions:
    ExchangeName: "TEST.AccessionDirectoryExchange"
    MaxConfirmAttempts: 1

CTPAnonymiserOptions:
  VerifyRoutingKey: verify
  NoVerifyRoutingKey: noverify
  AnonFileConsumerOptions:
    QueueName: "TEST.ExtractFileAnonQueue"
    QoSPrefetchCount: 1
    AutoAck: false
  ExtractFileStatusProducerOptions:
    ExchangeName: "TEST.ExtractedFileStatusExchange"
    MaxConfirmAttempts: 1

DicomAnonymiserOptions:
  AnonymiserType: "DefaultAnonymiser"
  AnonFileConsumerOptions:
    QueueName: "TEST.ExtractFileAnonQueue"
    QoSPrefetchCount: 1
    AutoAck: false
  ExtractFileStatusProducerOptions:
    ExchangeName: "TEST.ExtractedFileStatusExchange"
    MaxConfirmAttempts: 1
  RoutingKeySuccess: verify
  RoutingKeyFailure: noverify
  FailIfSourceWriteable: false
  VirtualEnvPath: "path/to/venv"
  DicomPixelAnonPath: "path/to/dicompixelanon/src/applications/"
  SmiServicesPath: "path/to/SmiServices" # replace with /nfs/smi/home/smi for production
  CtpAnonCliJar: "path/to/ctp-anon-cli/ctp-anon-cli-0.5.0.jar" # replace with /nfs/smi/home/smi/bin/ctp-anon-cli-0.5.0.jar for production
  CtpAllowlistScript: "path/to/SmiServices/data/ctp/ctp-whitelist.script" # replace with /nfs/smi/home/smi/configs/ctp-whitelist.script for production
  SRAnonymiserToolPath: "path/to/StructuredReports/src/applications/SRAnonTool/CTP_SRAnonTool.sh"

FileCopierOptions:
  NoVerifyRoutingKey: noverify
  QueueName: "TEST.ExtractFileIdentQueue"
  QoSPrefetchCount: 1
  AutoAck: false
  CopyStatusProducerOptions:
    ExchangeName: "TEST.ExtractedFileStatusExchange"
    MaxConfirmAttempts: 1

ExtractImagesOptions:
  MaxIdentifiersPerMessage: 1000
  ExtractionRequestProducerOptions:
    ExchangeName: "TEST.RequestExchange"
    MaxConfirmAttempts: 1
  ExtractionRequestInfoProducerOptions:
    ExchangeName: "TEST.RequestInfoExchange"
    MaxConfirmAttempts: 1

IsIdentifiableServiceOptions:
  QueueName: "TEST.ExtractedFileToVerifyQueue"
  QoSPrefetchCount: 1
  AutoAck: false
  IsIdentifiableProducerOptions:
    ExchangeName: "TEST.ExtractedFileVerifiedExchange"
    MaxConfirmAttempts: 1
  ClassifierType: "SmiServices.Microservices.IsIdentifiable.TesseractStanfordDicomFileClassifier"
  DataDirectory: ""

IsIdentifiableOptions:
  #Optional. Full connection string to the database storing the Allowlist of valid entries
  AllowlistConnectionString:
  #Optional. The DBMS provider of the Allowlist table e.g. MySql
  AllowlistDatabaseType:
  #Optional. The unqualified name of the Allowlist table
  AllowlistTableName:
  #Optional. The column in AllowlistTableName which contains the Allowlist elements
  AllowlistColumn:

  #Optional. Path to a CSV file containing a single untitled column of Allowlist values
  AllowlistCsv:

  #Optional. Generate a report on the proportion of values failing validation (for each column)
  #ColumnReport: true

  #Optional. Generate a report listing every unique value failing validation (and the column the value failed in)
  #ValuesReport: true

  #Optional. Generate a full failure storage report that persists Failure objects in a manner that they can be retrieved.
  #StoreReport: true

  #Optional - If specified reports will be generated in the given folder.  If not specified, current directory is used (unless an alternate destination option is picked)
  DestinationCsvFolder:
  #Optional - If specified, the given separator will be used instead of ,.  Includes support for \t for tab and \r\n
  DestinationCsvSeparator:
  #Optional - If specified all tabs, newlines (\r and \n) and 2+ spaces will be stripped from the values written as output (applies to all output formats)
  DestinationNoWhitespace:

  #Optional. Full connection string to the database in which to store the report results
  DestinationConnectionString:
  #Optional. The DBMS provider of DestinationConnectionString e.g. MySql
  DestinationDatabaseType:

  #Optional. If specified postcodes will not be reported as failures
  IgnorePostcodes: false
  #Optional. Comma separated list of columns/tags which should be ignored and not processed
  SkipColumns:
  #Optional. If set and using a 7 class NER model then DATE and TIME objects will not be considered failures.
  IgnoreDatesInText:
  #Optional. Set to control the max size of the in-memory store of processed before the get written out to any destinations. Only makes sense for reports that don't perform any aggregation across the data
  MaxCacheSize:

  #Optional. Filename of additional rules in yaml format.
  RulesFile:
  #Optional. Directory of additional rules in yaml format.
  RulesDirectory:
  #Optional.  Maximum number of answers to cache per column.
  MaxValidationCacheSize:

IsIdentifiableReviewerOptions:
  #Location of database connection strings file (for issuing UPDATE statements)
  TargetsFile:
  #File containing rules for ignoring validation errors
  IgnoreList:
  #File containing rules for when to issue UPDATE statements
  RedList:
  #Sets the user interface to use a specific color palette yaml file
  Theme: