check

This page provides the usage information for the rf2 check command.

Command options overview and help

You can also see this information by running rf2 help check from the command line.

Usage:

rf2 check PATH...

Description:

Checks a set of RF2 files and/or archives against the current RF2 Specification

Parameters:
      PATH...   RF2 source files to check.

PATH argument

The rf2 check command accepts arbitrary number of RF2 source file paths. The PATH argument must point to a location of file (NOTE: directories are not supported yet).

For example, consider this command line:

rf2 check SnomedCT_RF2_PRODUCTION_20190131T120000Z.zip

Executing it will print out the RF2 release structure along with certain properties of each file inside the release package. Example output:

SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z.zip
  -type: Release
  SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z
    -type: Directory
    Snapshot
      -type: Directory
      Refset
        -type: Directory
        Metadata
          -type: Directory
          der2_cRefset_MRCMModuleScopeSnapshot_INT_20190131.txt
            -type: cRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, mrcmRuleRefsetId]
            -lines: 3
          der2_ssccRefset_MRCMAttributeRangeSnapshot_INT_20190131.txt
            -type: ssccRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, rangeConstraint, attributeRule, ruleStrengthId, contentTypeId]
            -lines: 119
          der2_cissccRefset_MRCMAttributeDomainSnapshot_INT_20190131.txt
            -type: cissccRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, domainId, grouped, attributeCardinality, attributeInGroupCardinality, ruleStrengthId, contentTypeId]
            -lines: 134
          der2_sssssssRefset_MRCMDomainSnapshot_INT_20190131.txt
            -type: sssssssRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, domainConstraint, parentDomain, proximalPrimitiveConstraint, proximalPrimitiveRefinement, domainTemplateForPrecoordination, domainTemplateForPostcoordination, guideURL]
            -lines: 19
          der2_ciRefset_DescriptionTypeSnapshot_INT_20190131.txt
            -type: ciRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, descriptionFormat, descriptionLength]
            -lines: 3
          der2_ssRefset_ModuleDependencySnapshot_INT_20190131.txt
            -type: ssRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, sourceEffectiveTime, targetEffectiveTime]
            -lines: 3
          der2_cciRefset_RefsetDescriptorSnapshot_INT_20190131.txt
            -type: cciRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, attributeDescription, attributeType, attributeOrder]
            -lines: 167
        Language
          -type: Directory
          der2_cRefset_LanguageSnapshot-en_INT_20190131.txt
            -type: cRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, acceptabilityId]
            -lines: 2831149
        Map
          -type: Directory
          der2_iisssccRefset_ExtendedMapSnapshot_INT_20190131.txt
            -type: iisssccRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, mapGroup, mapPriority, mapRule, mapAdvice, mapTarget, correlationId, mapCategoryId]
            -lines: 174594
          der2_sRefset_SimpleMapSnapshot_INT_20190131.txt
            -type: sRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, mapTarget]
            -lines: 493422
        Content
          -type: Directory
          der2_Refset_SimpleSnapshot_INT_20190131.txt
            -type: Refset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId]
            -lines: 19878
          der2_cRefset_AttributeValueSnapshot_INT_20190131.txt
            -type: cRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, valueId]
            -lines: 535131
          der2_cRefset_AssociationSnapshot_INT_20190131.txt
            -type: cRefset
            -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, targetComponentId]
            -lines: 157369
      Terminology
        -type: Directory
        sct2_sRefset_OWLExpressionSnapshot_INT_20190131.txt
          -type: sRefset
          -header: [id, effectiveTime, active, moduleId, refsetId, referencedComponentId, owlExpression]
          -lines: 224
        sct2_TextDefinition_Snapshot-en_INT_20190131.txt
          -type: TextDefinition
          -header: [id, effectiveTime, active, moduleId, conceptId, languageCode, typeId, term, caseSignificanceId]
          -lines: 5726
        sct2_Identifier_Snapshot_INT_20190131.txt
          -type: Identifier
          -header: [identifierSchemeId, alternateIdentifier, effectiveTime, active, moduleId, referencedComponentId]
          -lines: 0
          -issues:
            -WARN: No validator is registered for column header 'identifierSchemeId'.
            -WARN: No validator is registered for column header 'alternateIdentifier'.
        sct2_Relationship_Snapshot_INT_20190131.txt
          -type: Relationship
          -header: [id, effectiveTime, active, moduleId, sourceId, destinationId, relationshipGroup, typeId, characteristicTypeId, modifierId]
          -lines: 2876521
        sct2_StatedRelationship_Snapshot_INT_20190131.txt
          -type: StatedRelationship
          -header: [id, effectiveTime, active, moduleId, sourceId, destinationId, relationshipGroup, typeId, characteristicTypeId, modifierId]
          -lines: 1024719
        sct2_Description_Snapshot-en_INT_20190131.txt
          -type: Description
          -header: [id, effectiveTime, active, moduleId, conceptId, languageCode, typeId, term, caseSignificanceId]
          -lines: 1451467
        sct2_Concept_Snapshot_INT_20190131.txt
          -type: Concept
          -header: [id, effectiveTime, active, moduleId, definitionStatusId]
          -lines: 466612
...

Validation

The rf2 check command validates each supplied source file and reports problems under the issues property of the corresponding file output.

File Name Validation

RF2 packages are validated against the current Release Package Naming Convention, while RF2 files are validated against the current Release File Naming Convention. If a file cannot be recognized by the currently loaded RF2 Specification (see rf2-spec.yml), the rf2 check command will report the file as Unrecognized type and will not attempt any other validation to run on that file.

Content Validation

On top of the file name validation, rf2 check command provides the ability to validate the actual RF2 content of each RF2 source file. If an RF2 source file is not Unrecognized, then the tool will search for registered validators and run them on the entirety of the file.

Currently supported content validation rules:

• Not empty validation rule (reports if a column is empty)

• Boolean column type validation rule (reports if a column value is not of type Boolean)

• Integer column type validation rule (reports if a column value is not of type Integer)

• SNOMED CT Identifier validation rule (reports invalid SNOMED CT IDs, see SNOMED CT ID specification for more detail)

• Referenced Component ID validation rule (reports if a referenced SNOMED CT ID is invalid or valid but references unexpected SNOMED CT Component, eg. moduleId column should refer to a SNOMED CT Concept)

• EffectiveTime validation rule (reports if an effectiveTime column value is an incorrect ISO-8601 date value)

• ISO-639 validator for languageCode column

Custom validation rules

This feature is currently in design phase and it is planned to be released at the latest with the v1.0.0 release.