Fix issues in examples#19
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- 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.
- 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.
- Added new package `aiohappyeyeballs` version 2.6.2 with source and wheel details. - Updated `aiohttp` to version 3.13.5, including its dependencies and corresponding source and wheel information. - Enhanced package management for improved compatibility and functionality. Co-authored-by: alex-omophub <sdk@omophub.com>
- Adjusted the `basic_search`, `filtered_search`, and `bulk_lexical_search` functions to handle the updated response format from the `client.search` methods, ensuring that results are accessed correctly from the returned dictionaries. - Enhanced comments in the code to clarify the structure of the responses and improve overall documentation for better user understanding.
- Updated `basic_search`, `filtered_search`, and `bulk_lexical_search` functions to directly access results from the `client.search` methods, simplifying the code structure. - Enhanced comments to clarify the response formats and improve documentation for better user understanding.
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Summary by cubic
Fixes and polishes example scripts to match the latest API responses, removes hardcoded API keys, and adds a new
fhir_resolver.pyexample. Also updatesuv.lockand CHANGELOG for a 1.7.1 maintenance release with security patches and no runtime API changes.New Features
fhir_resolver.pyexample for FHIR-to-OMOP concept resolution.Bug Fixes
Dependencies
uv.lock; addedaiohappyeyeballsand bumpedaiohttp.fhirpy,fhir-resources.idna3.15,pytest9.0.3,python-dotenv1.2.2,pygments2.20.0.httpx,typing_extensions).Written for commit ee08fca. Summary will update on new commits. Review in cubic