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April 10, 2026 21:39
- Introduced a new script `fhir_resolver.py` that demonstrates FHIR-to-OMOP concept resolution using the OMOPHub SDK. - The script includes examples for resolving SNOMED, ICD-10-CM, LOINC, RxNorm codes, and text-only semantic searches. - Added functionality for direct standard lookups, non-standard code mapping, and Phoebe recommendations. - Supports batch resolution and asynchronous usage for improved performance.
- Added support for FHIR type interoperability in the resolver, allowing acceptance of various Coding-like inputs (dicts, TypedDicts, and objects with .system/.code attributes). - Introduced new FHIR type definitions (`Coding`, `CodeableConcept`) and runtime-checkable protocols (`CodingLike`, `CodeableConceptLike`) for structural matching. - Implemented FHIR client interop helpers to configure external libraries (`fhirpy`, `fhir.resources`) with OMOPHub's FHIR Terminology Service. - Enhanced `Fhir.resolve`, `Fhir.resolve_batch`, and `Fhir.resolve_codeable_concept` methods to accept mixed input types. - Updated documentation and examples to reflect new functionalities and usage patterns. - Added comprehensive unit and integration tests to validate new features and ensure compatibility.
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2 issues found across 14 files
Prompt for AI agents (unresolved issues)
Check if these issues are valid — if so, understand the root cause of each and fix them. If appropriate, use sub-agents to investigate and fix each issue separately.
<file name="src/omophub/fhir_interop.py">
<violation number="1" location="src/omophub/fhir_interop.py:77">
P2: Missing `# type: ignore[import-not-found]` on the `fhirpy` import will cause MyPy checks to fail if the optional dependency is not installed in the type-checking environment.</violation>
</file>
<file name="src/omophub/resources/fhir.py">
<violation number="1" location="src/omophub/resources/fhir.py:60">
P2: Filter dict inputs down to the resolver's supported coding keys before building the request body.</violation>
</file>
Reply with feedback, questions, or to request a fix. Tag @cubic-dev-ai to re-run a review.
- Updated example scripts. - Adjusted search and resolution methods in examples to reflect the new API response structures, ensuring consistency across examples. - Improved documentation and comments in example scripts for clarity and better user guidance.
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Summary by cubic
Adds FHIR type interoperability and client helpers so you can pass Coding-like objects directly and connect external FHIR clients to OMOPHub. Examples now read
OMOPHUB_API_KEYfrom the environment and search examples reflect the flat list output.New Features
client.fhir.resolvesupportscoding=(dicts,omophub.types.fhir.Coding, or any object with.system/.code/.display); explicitsystem/codeoverridecoding.resolve_batchaccepts mixed inputs.resolve_codeable_conceptaccepts a CodeableConcept-like object or a list.Coding,CodeableConcept, and runtime protocolsCodingLike,CodeableConceptLikefor duck typing.omophub.fhir_interopaddsget_fhir_server_url(supportsr4,r4b,r5,r6),get_fhirpy_client,get_async_fhirpy_client; re-exported at top-level. NewOMOPHub.fhir_server_url/AsyncOMOPHub.fhir_server_urlreturn the R4 base URL.examples/fhir_interop.py; updated examples and README to use env API key and show flat list results fromsearch.basic.Dependencies
omophub[fhirpy]installsfhirpy>=1.4.0;omophub[fhir-resources]installsfhir.resources>=7.0.0.fhirpyis lazily imported by helpers; no new required dependencies.Written for commit 7f2014f. Summary will update on new commits.