fhir-claml
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aehrc
Transforms ClaML classifications into FHIR code systems.
ClaML to FHIR Transformer
This Spring Boot CLI application transforms a ClaML classification into a FHIR Code System.
Building from source
You will need Maven installed in your computer. You can build the jar file using Maven.
mvn package
Running
You need a JVM to run the application. The only mandatory options are -i and -o.
java -jar fhir-claml-0.0.1-SNAPSHOT.jar -i [input ClaML file] -o [output FHIR JSON file]
The following options are available:
| Parameter | Type | Description |
|---|---|---|
| -applyModifiers | boolean | Apply Modifiers (default: false) |
| -content | string | The extent of the content in this resource. Valid values are not-present, example, fragment, complete and supplement. Defaults to complete. The actual value does not affect the output of the transformation. |
| -d | string | Indicates which ClaML rubric contains the concepts' displays. Default is 'preferred'. |
| -definition | string | Indicates which ClaML rubric contains the concepts' definitions. Default is 'definition'. |
| -designations | string | Comma-separated list of ClaML rubrics that contain the concepts' synonyms. |
| -excludeClassKinds | string | Comma-separated list of class kinds to exclude. |
| -excludeKindlessClasses | boolean | Exclude ClaML classes that do not have kinds (default: false). |
| -help | none | Print the help message. |
| -hierarchyMeaning | string | The hierarchyMeaning of the code system. Allowable values are 'is-a', 'part-of', 'grouped-by', and 'classified-with'. Default is 'is-a'. |
| -i | string | The input ClaML file. |
| -id | string | The technical id of the code system. Required if using PUT to upload the resource to a FHIR server. |
| -o | string | The output FHIR JSON file. |
| -url | string | Canonical identifier of the code system. |
| -valueSet | string | The value set that represents the entire code system. |
| -versionNeeded | none | Flag to indicate if the code system commits to concept permanence across versions. |
| -experimental | boolean | Indicates if the code system is for testing purposes or real usage. Default is 'true'. |
| -status | string | Code system status. Valid values are draft, active, retired and unknown. Default is 'draft'. |
Examples
The ICD-10-GM classification was transformed using the following command:
java -jar fhir-claml-0.0.1-SNAPSHOT.jar -i icd10gm2020syst_claml_20190920.xml -designations preferredLong -o codesystem-icd10gm-2020.json -id icd10gm2020 -url http://hl7.org/fhir/sid/icd-10-gm -valueSet http://hl7.org/fhir/sid/icd-10-gm/vs
Known Issues
-
Inherited modifiers are not currently supported
-
UsageKinds and usage attributes (e.g. for +, * or ! suffixes in ICD) are not yet supported
-
In some Linux environments (including docker deployments), you may need to install some packages to properly support UTF-8 encodings. Andreas Streichardt provided these commands for inclusion in a Dockerfile to fix this (these can be adapted to Linux commands if you need):
# Set the locale
RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
locale-gen
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8```
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