v1.8.1 prep#22
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>
- 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.
- Upgraded `actions/setup-python` from v5 to v6 for improved Python setup. - Updated `actions/upload-artifact` from v5 to v7 to enhance artifact handling. - Changed `actions/download-artifact` from v5 to v8 for better download capabilities.
- Updated CHANGELOG for version 1.8.1, documenting the change in API endpoint for semantic search. - Refactored `Search` and `AsyncSearch` classes to call the new canonical path `/search/semantic` instead of the deprecated `/concepts/semantic-search`. - Adjusted unit tests to reflect the updated endpoint in mock responses.
- Streamlined the code in the `AsyncSearch` class by consolidating the API request to a single line for improved readability and maintainability.
![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 10 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="CHANGELOG.md">
<violation number="1" location="CHANGELOG.md:8">
P2: The `[Unreleased]` link still points to `v1.7.1...HEAD`. Update it to `v1.8.1...HEAD` now that v1.8.1 is the latest release, consistent with the pattern used by all prior version links.</violation>
<violation number="2" location="CHANGELOG.md:8">
P2: Missing link definitions for `[1.8.1]` and `[1.8.0]`. Add reference-style link definitions at the bottom of the file so the version headings render as clickable links.</violation>
</file>
Reply with feedback, questions, or to request a fix.
Re-trigger cubic
| @@ -5,6 +5,37 @@ All notable changes to this project will be documented in this file. | |||
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), | |||
There was a problem hiding this comment.
P2: The [Unreleased] link still points to v1.7.1...HEAD. Update it to v1.8.1...HEAD now that v1.8.1 is the latest release, consistent with the pattern used by all prior version links.
Prompt for AI agents
Check if this issue is valid — if so, understand the root cause and fix it. At CHANGELOG.md, line 8:
<comment>The `[Unreleased]` link still points to `v1.7.1...HEAD`. Update it to `v1.8.1...HEAD` now that v1.8.1 is the latest release, consistent with the pattern used by all prior version links.</comment>
<file context>
@@ -5,6 +5,37 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [1.8.1] - 2026-06-01
+
+### Changed
</file context>
| @@ -5,6 +5,37 @@ All notable changes to this project will be documented in this file. | |||
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), | |||
There was a problem hiding this comment.
P2: Missing link definitions for [1.8.1] and [1.8.0]. Add reference-style link definitions at the bottom of the file so the version headings render as clickable links.
Prompt for AI agents
Check if this issue is valid — if so, understand the root cause and fix it. At CHANGELOG.md, line 8:
<comment>Missing link definitions for `[1.8.1]` and `[1.8.0]`. Add reference-style link definitions at the bottom of the file so the version headings render as clickable links.</comment>
<file context>
@@ -5,6 +5,37 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [1.8.1] - 2026-06-01
+
+### Changed
</file context>
Codecov Report✅ All modified and coverable lines are covered by tests. 📢 Thoughts on this report? Let us know! |
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
Preps v1.8.1 by moving semantic search to the canonical
/search/semanticendpoint and enhancing the FHIR resolver withon_unmapped, FHIRuserSelectedsupport, and richer typed outputs. Includes docs/examples and CI updates.New Features
on_unmappedtoresolve(),resolve_batch(), andresolve_codeable_concept(); accepts FHIRuserSelected(mapped touser_selected) and prefers it inresolve_codeable_concept().FhirResolutionwithvalue_as_concept,value_target_field,concept_map_id, andmapping_note; examples and README updated.Refactors
/search/semantic(server keeps the old path aliased); tests updated.actions/setup-pythontov6,actions/upload-artifacttov7, andactions/download-artifacttov8.Written for commit 3512066. Summary will update on new commits.