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   43.6    HL7 v2.x Transmit Flat File
  • Smile CDR CLI (smileutil)
  • 43.0 Introduction
  • 43.1 Bulk Import
  • 43.2 Create FHIR Package
  • 43.3 Execute Script Function
  • 43.4 Export ConceptMap to CSV
  • 43.5 HL7 v2.x Analyze Flat File
  • 43.6 HL7 v2.x Transmit Flat File
  • 43.7 Import CSV to ConceptMap
  • 43.8 Map and Upload CSV Bulk Import File
  • 43.9 Migrate Database
  • 43.10 Clear Database Migration Lock
  • 43.11 Module Config Properties Export
  • 43.12 Reindex Terminology
  • 43.13 Synchronize FHIR Servers
  • 43.14 Upgrade H2 Database File
  • 43.15 Upload Bundle Files
  • 43.16 Upload CSV Bulk Import File
  • 43.17 Upload Sample Dataset
  • 43.18 Upload Terminology
  • 43.19 Generate Realtime Export Schema
  • 43.20 Validate FHIR Resources
    • 43.8    Map and Upload CSV Bulk Import File   
       Table of Contents

    Import CSV to ConceptMap

    43.7.1smileutil: 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: In cases where multiple versions of a given ConceptMap have been loaded, the import-csv-to-conceptmap command will always replace the current version of the specified ConceptMap resource with the imported ConceptMap.

    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.

    43.7.2Usage

      
    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.

    43.7.3Options

     
    • -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 of the ConceptMap to be imported (i.e. ConceptMap.sourceUri).
    • -l (or --logging) – (optional) If specified, verbose logging will be used.
    • -o [target URI] (or --output [target URI]) – (optional) The target value set of the ConceptMap to be imported (i.e. ConceptMap.targetUri).
    • -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.
       43.6    HL7 v2.x Transmit Flat File
  • Smile CDR CLI (smileutil)
  • 43.0 Introduction
  • 43.1 Bulk Import
  • 43.2 Create FHIR Package
  • 43.3 Execute Script Function
  • 43.4 Export ConceptMap to CSV
  • 43.5 HL7 v2.x Analyze Flat File
  • 43.6 HL7 v2.x Transmit Flat File
  • 43.7 Import CSV to ConceptMap
  • 43.8 Map and Upload CSV Bulk Import File
  • 43.9 Migrate Database
  • 43.10 Clear Database Migration Lock
  • 43.11 Module Config Properties Export
  • 43.12 Reindex Terminology
  • 43.13 Synchronize FHIR Servers
  • 43.14 Upgrade H2 Database File
  • 43.15 Upload Bundle Files
  • 43.16 Upload CSV Bulk Import File
  • 43.17 Upload Sample Dataset
  • 43.18 Upload Terminology
  • 43.19 Generate Realtime Export Schema
  • 43.20 Validate FHIR Resources
    • 43.8    Map and Upload CSV Bulk Import File