v1.8.0 prep#21
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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.
* Enhance FHIR resolution capabilities and response structure
- Updated CHANGELOG to reflect the release of version 1.8.0. - Added new functions in `fhir_resolver.py` for resolving administrative gender, user-selected codes, and unmapped sentinel handling, enhancing FHIR resolution capabilities.
- Added examples demonstrating the resolution of administrative gender, user-selected coding, and unmapped sentinel handling. - Included information on handling composite concepts and the acceptance of various Coding-like inputs in the resolver. - Updated documentation to clarify the functionality and usage of the FHIR resolver methods.
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Summary by cubic
Prepare v1.8.0 by enhancing the FHIR resolver with
userSelectedsupport,on_unmappedsentinel handling across sync and async clients, and typed fields for composite and IG ConceptMap resolutions. Docs, examples, tests, and the lockfile are updated.New Features
resolve,resolve_batch, andresolve_codeable_concept(sync and async) accepton_unmapped=("error"|"sentinel");"sentinel"returns aconcept_id0 record.userSelectedtouser_selected; a user-selected coding beats vocabulary preference inresolve_codeable_concept. Input typing addsCoding.user_selected.value_as_concept/value_target_fieldand IG ConceptMap metadata (concept_map_id,mapping_note).user_selectedprecedence, andon_unmapped="sentinel".Dependencies
uv.lock: addedaiohappyeyeballs, bumpedaiohttp, and locked optional FHIR extras (fhirpy,fhir-resources).httpx,typing_extensionsunchanged).Written for commit a887c47. Summary will update on new commits. Review in cubic