48.7.1smileutil: Import CSV to ConceptMap

The import-csv-to-conceptmap command can be used to import a CSV file of terminology mappings and store it as a ConceptMap resource.

Note: The import-csv-to-conceptmap command will always replace any existing ConceptMap that has the same URL with the newly imported ConceptMap. If multiple versions of a ConceptMap exist, it will replace the current version. This is done using a conditional update operation based on the ConceptMap URL.

The first row of the CSV file is expected to include the following headers:

• SOURCE_CODE_SYSTEM – ConceptMap.group.source
• SOURCE_CODE_SYSTEM_VERSION – ConceptMap.group.sourceVersion
• TARGET_CODE_SYSTEM – ConceptMap.group.target
• TARGET_CODE_SYSTEM_VERSION – ConceptMap.group.targetVersion
• SOURCE_CODE – ConceptMap.group.element.code
• SOURCE_DISPLAY – ConceptMap.group.element.display
• TARGET_CODE – ConceptMap.group.element.target.code
• TARGET_DISPLAY – ConceptMap.group.element.target.display
• EQUIVALENCE – ConceptMap.group.element.target.equivalence (ConceptMapEquivalence)
• COMMENT – ConceptMap.group.element.target.comment

An example CSV file that describes the mapping of FHIR to HL7v2 for Administrative Gender would appear as follows:

SOURCE_CODE_SYSTEM,SOURCE_CODE_SYSTEM_VERSION,TARGET_CODE_SYSTEM,TARGET_CODE_SYSTEM_VERSION,SOURCE_CODE,SOURCE_DISPLAY,TARGET_CODE,TARGET_DISPLAY,EQUIVALENCE,COMMENT
http://hl7.org/fhir/administrative-gender,,http://hl7.org/fhir/v2/0001,,male,Male,M,Male,equal,
http://hl7.org/fhir/administrative-gender,,http://hl7.org/fhir/v2/0001,,female,Female,F,Female,equal,
http://hl7.org/fhir/administrative-gender,,http://hl7.org/fhir/v2/0001,,other,Other,A,Ambiguous,wider,
http://hl7.org/fhir/administrative-gender,,http://hl7.org/fhir/v2/0001,,unknown,Unknown,U,Unknown,equal,

These terminology mappings could then be imported with the following command:

bin/smileutil import-csv-to-conceptmap -v "r4" -t "http://localhost:8000/" -u "http://hl7.org/fhir/ConceptMap/cm-administrative-gender-v2" -s "active" -i "http://hl7.org/fhir/ValueSet/administrative-gender" -o "http://hl7.org/fhir/ValueSet/v2-0001" -f "input.csv" -l

Note the source and target value sets are provided when invoking the command.

48.7.2Usage

bin/smileutil import-csv-to-conceptmap -v "r4" -t "http://localhost:8000/" -u "http://example.com/conceptmap" -s "active" -i "http://example.com/valueset/1" -o "http://example.com/valueset/2" -f "input.csv" -l

In the example above, http://localhost:8000/ is the FHIR endpoint to which the mappings will be uploaded.

48.7.3Options

• -b [username:password] (or --basic-auth [username:password]) – (optional) If specified, provides a username and password that will be supplied to the server in an HTTP Basic Authorization header in the form of "username:password". If the value supplied is "PROMPT", smileutil will prompt the user to enter credentials interactively.
• --bearer-token [token] – (optional) If specified, provides a bearer token that will be supplied to the server in an HTTP Authorization header. If the value supplied is "PROMPT", smileutil will prompt the user to enter a bearer token interactively.
• --debug – Enable debug mode.
• -f [filename] (or --filename [filename]) – The path and filename of the CSV file to be imported (e.g. ./input.csv).
• -hp [header] (or --header-passthrough [header]) – If specified, this argument specifies headers to include in the generated request.
• -i [source URI] (or --input [source URI]) – (optional) The source value set URI of the ConceptMap to be imported. This sets the ConceptMap.sourceUri field, which identifies the source ValueSet containing the source concepts.
• -l (or --logging) – (optional) If specified, verbose logging will be used.
• -o [target URI] (or --output [target URI]) – (optional) The target value set URI of the ConceptMap to be imported. This sets the ConceptMap.targetUri field, which identifies the target ValueSet which provides context for the mappings.
• -s [ConceptMap Status] (or --status [ConceptMap Status]) – The status of the ConceptMap resource to be imported (i.e. ConceptMap.status).
• -t [base URL] (or --target [base URL]) – This argument should point to the base URL of the target FHIR server endpoint.
• -u [ConceptMap URL] (or --url [ConceptMap URL]) – The URL of the ConceptMap resource to be imported/exported (i.e. ConceptMap.url).
• -v [version] (or --fhir-version [version]) – (optional) The version of FHIR supported by the server.
• --tls-auth [filename] – (optional) If specified, this parameter supplies a path and filename for a Smile Util TLS JSON Authentication File that will be used to authenticate target FHIR server endpoints secured through HTTPS.