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Version: v0.1.8

Translate a code through a ConceptMap

cosyte map-codes loads a FHIR R4 ConceptMap you supply and translates one code through it, with @cosyte/terminology. The package ships no terminology content: the map is yours, and an unmapped code is reported as unmapped, never filled in. The examples use gender.conceptmap.json, a synthetic map from FHIR administrative gender to the HL7 v2 table 0001 codes.

Translate a code​

Name the map, the code, and the code's system:

cosyte map-codes gender.conceptmap.json \
  --system http://hl7.org/fhir/administrative-gender --code female --json \
  | jq -c '.result.matches[].target'
{"code":"F","system":"http://terminology.hl7.org/CodeSystem/v2-0001"}

Without --json, the same object is printed indented, and a count of matches goes to stderr. --system names the code's system, which @cosyte/terminology uses to choose the map's groups. --version and --display pass the source code's version and display text through to the translation.

Read the map from stdin​

Pass - in place of the file name:

cat gender.conceptmap.json | cosyte map-codes - --code male --json | jq -r '.result.matches[0].target.code'
M

Branch on whether it mapped​

The exit code is 0 when there is at least one match and 1 when there is none. An unmapped code also prints TERM_TRANSLATE_UNMAPPED on stderr, unless you pass --quiet:

cosyte map-codes gender.conceptmap.json \
  --system http://hl7.org/fhir/administrative-gender --code other > /dev/null; echo "exit $?"
cosyte: map-codes: TERM_TRANSLATE_UNMAPPED (fallback mode: none)
exit 1

The fallback mode is the map's own group.unmapped.mode, which @cosyte/terminology reports and never applies; none means no such fallback applied to this code.

A code and a ConceptMap are reference data, not patient data, so the source code and its target are printed on stdout.

When the map does not load​

A file that is not JSON, or JSON that is not a loadable ConceptMap, exits 65 with CLI_MAP_INVALID and the loader's own code when it gave one:

echo '{"resourceType":"Patient"}' | cosyte map-codes - --code male; echo "exit $?"
cosyte: CLI_MAP_INVALID: the supplied ConceptMap could not be loaded (TERM_CONCEPTMAP_MALFORMED)
exit 65

Reference​