HL7 FHIR code systems on OCL are missing their nested concepts (concept-map-equivalence has 2 of 10 codes)

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python
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调研方向

Start with core/code_systems/serializers.py, especially CodeSystemConceptSerializer and CodeSystemDetailSerializer.create/update, to trace how FHIR CodeSystem concepts are written. Check the existing tests for nested concepts, then verify the HL7 code systems and value sets against the acceptance criteria, including $validate-code for wider. Done means nested concepts and parent relationships are saved, duplicate listings are addressed, and the specified R4 and R5 resources validate.

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描述

component/content component/fhir decision/human-review signal/needs-access signal/well-specified stage/triaged type/bug

Found while following up OpenConceptLab/ocl_issues#2924.

OCL's copy of HL7's R4 ConceptMap equivalence code system (/orgs/HL7/sources/concept-map-equivalence/, loaded 2021-08-19) holds only relatedto and unmatched, its two top-level codes. The eight codes nested under them (equivalent, equal, wider, subsumes, narrower, specializes, inexact, disjoint) are missing. Its value set (/orgs/HL7/collections/concept-map-equivalence/) has no references, so it expands to nothing. Since OpenConceptLab/oclapi2#956, OCL's $translate returns these codes, so OCL can't validate its own answers. R5's concept-map-relationship isn't loaded.

The cause looks general. issue-type also has only its 5 top-level codes out of about 30. The FHIR CodeSystem write still ignores nested concept elements, because CodeSystemConceptSerializer (core/code_systems/serializers.py) reads only code, display, definition, designation and property. Version 4.0.1 of these HL7 code systems also lists each concept twice, in the native API and the FHIR read alike. For example, administrative-gender lists 8 entries for its 4 codes, and resource-types reports a count of 296 and lists each code twice.

Acceptance criteria

  • A FHIR CodeSystem write keeps nested concepts: each child becomes a concept, with its parent recorded in OCL's hierarchy.
  • HL7/concept-map-equivalence holds R4's 10 codes with their displays, each listed once, in a released 4.0.1 version. HL7/collections/concept-map-equivalence references them and expands to the 10.
  • R5's concept-map-relationship code system and value set (5.0.0) are loaded under HL7.
  • The HL7 org's other code systems (270 sources) are checked for missing nested concepts and duplicate listings. The affected ones are reloaded, or listed on this ticket.
  • On openconceptlab.org, $validate-code of wider against http://hl7.org/fhir/ValueSet/concept-map-equivalence answers true.

Components: core/code_systems/serializers.py (CodeSystemConceptSerializer, CodeSystemDetailSerializer.create/update); content in the HL7 org.

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