v1.7.1 prep#18
Merged
Merged
Conversation
- 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>
Codecov Report✅ All modified and coverable lines are covered by tests. 📢 Thoughts on this report? Let us know! |
![cubic-dev-ai[bot]](https://avatars.githubusercontent.com/in/1082092?s=60&v=4){kind=small}
There was a problem hiding this comment.
2 issues found across 21 files
Tip: cubic can generate docs of your entire codebase and keep them up to date. Try it here.
Re-trigger cubic
- 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.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary by cubic
Prep for v1.7.1: update
uv.lockandCHANGELOG.mdto resolve security advisories, addaiohappyeyeballs, and refresh search examples to match the current dict-shaped response format. No source or runtime API changes vs 1.7.0.uv.lock:idna3.11→3.15,pytest9.0.2→9.0.3,python-dotenv1.2.1→1.2.2,pygments2.19.2→2.20.0.aiohttpand addedaiohappyeyeballs.uv.lock:fhirpy,fhir-resources.httpx,typing_extensions).Written for commit c80ff44. Summary will update on new commits. Review in cubic