Labcodeset to FHIR transformation

A stand-alone command-line tool that transforms Nederlandse Labcodeset XML to a collection of FHIR resources, specifically

Type	URI	Description
CodeSystem supplement	http://labterminologie.nl/cs/labconcepts	CodeSystem supplement containing Dutch translations and properties as defined in the Labcodeset XML file
ValueSet	http://labterminologie.nl/vs/labconcepts	ValueSet containing the unique set of LOINC codes referenced by the Labcodeset XML file - note this contains LOINC codes in any state, not just active codes
CodeSystem fragment	http://unitsofmeasure.org	Fragment of the UCUM CodeSystem containing the union of UCUM expressions referenced by Labcodeset and the "common" FHIR UCUM ValueSet. Language for this CodeSystem is nl_NL, and Dutch display terms are used where available with the English terms set as designations
ValueSet	http://labterminologie.nl/vs/labconcepts-ucum	ValueSet containing the unique set of UCUM expressions referenced by Labcodeset
ConceptMap	http://labterminologie.nl/cm/labconcepts-ucum	ConceptMap containing mappings for each LOINC code in Labcodeset where a unit is expressed
ValueSet	http://labterminologie.nl/vs/labconcepts-materials	ValueSet containing the unique set of SNOMED CT "material" codes referenced by Labcodeset
ConceptMap	http://labterminologie.nl/cm/labconcepts-materials	ConceptMap containing mappings from LOINC codes in Labcodeset that reference one or more SNOMED CT "material" codes
ValueSet	http://labterminologie.nl/vs/labconcepts-ordinal-xxx	A set of ValueSets, one for each "ordinal" list included in the Labcodeset XML file where xxx in the URI is replaced with the OID of the ordinal set
ConceptMap	http://labterminologie.nl/cm/labconcepts-outcomes	ConceptMap containing mappings from LOINC codes in Labcodeset to either a SNOMED CT Reference Set identifier or a ValueSet OID depending upon which is listed in Labcodeset for that LOINC code.

Build

mvn clean package

This will build a file called ./target/labcodeset-transforms-jar-with-dependencies.jar

If you just want to run it, you can simply download the labcodeset-transforms-jar-with-dependencies.jar from the prebuilt release packages and skip to the next step.

Run

The program requires a few command line parameters to execute, they are desribed by the usage message if you don't supply the correct parameters.

    usage: java -jar labcodeset-transforms-jar-with-dependencies.jar [-clientId <client_id>] [-clientSecret <client_secret>]
           -fhirEndpoint <fhir endpoint> -labcodesetFile <file_path> -loincVersion <loinc_version> [-outputDir <directory>]
           [-tokenEndpoint <token _endpoint>]
     -clientId <client_id>              Client id part of client credentials to use with the token endpoint to get a bearer
                                        token for use with the specified FHIR endpoin - optional if authorisation is
                                        required for the FHIR endpoint
     -clientSecret <client_secret>      Client secret part of client credentials to use with the token endpoint to get a
                                        bearer token for use with the specified FHIR endpoin  - optional if authorisation is
                                        required for the FHIR endpoint
     -fhirEndpoint <fhir endpoint>      FHIR terminology endpoint containing the appropriate LOINC and SNOMED CT-NL versions
                                        to reference during the transformation
     -labcodesetFile <file_path>        File path to the Labcodeset XML file to transform
     -loincVersion <loinc_version>      Version of LOINC this Labcodeset XML file has been built with
     -outputDir <directory>             Location to output the resulting FHIR resources and Bundle - defaults to the
                                        directory the program was executed from if not specified
     -tokenEndpoint <token _endpoint>   Token endpoint URL to get a bearer token with for the specified endpoint - optional
                                        if authorisation is required for the FHIR endpoint

Following is an example execution

    java -jar labcodeset-transforms-jar-with-dependencies.jar \
        -fhirEndpoint https://r4.ontoserver.csiro.au/fhir \
        -labcodesetFile /some/path/labcodeset.xml \
        -loincVersion 2.69

Output

The transform will produce one JSON file for each of the generated resource as well as a Bundle resource JSON file containing all of the resources as a convenience.

The file names of the generated JSON files will contain the version number inside each of the resources, and the Bundle resource file name will carry the Labcodeset version it was generated from.