Release version 1.8.0 with new FHIR resolution features#7
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- Updated the package version to 1.8.0. - Introduced new features in FHIR resolution, including `value_as_concept_id` and `value_as_concept_name` columns in the `resolve_batch()` output for composite concepts. - Added `on_unmapped` argument to `resolve()`, `resolve_batch()`, and `resolve_codeable_concept()` methods, allowing users to specify behavior for unmapped concepts. - Updated documentation and examples to reflect these enhancements, ensuring clarity on new functionalities and usage patterns.
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2 issues found across 8 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="inst/examples/fhir_resolver.R">
<violation number="1" location="inst/examples/fhir_resolver.R:328">
P1: Use `userSelected` (FHIR camelCase) instead of `user_selected` in coding lists. The `resolve_codeable_concept` method serializes the coding list directly to JSON with no name conversion, so `user_selected` will produce the wrong JSON key and the precedence feature will be silently ignored.</violation>
</file>
Reply with feedback, questions, or to request a fix.
Re-trigger cubic
| list( | ||
| system = "http://hl7.org/fhir/sid/icd-10-cm", | ||
| code = "E11.9", | ||
| user_selected = TRUE |
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P1: Use userSelected (FHIR camelCase) instead of user_selected in coding lists. The resolve_codeable_concept method serializes the coding list directly to JSON with no name conversion, so user_selected will produce the wrong JSON key and the precedence feature will be silently ignored.
Prompt for AI agents
Check if this issue is valid — if so, understand the root cause and fix it. At inst/examples/fhir_resolver.R, line 328:
<comment>Use `userSelected` (FHIR camelCase) instead of `user_selected` in coding lists. The `resolve_codeable_concept` method serializes the coding list directly to JSON with no name conversion, so `user_selected` will produce the wrong JSON key and the precedence feature will be silently ignored.</comment>
<file context>
@@ -284,10 +287,78 @@ if (!is.null(best)) {
+ list(
+ system = "http://hl7.org/fhir/sid/icd-10-cm",
+ code = "E11.9",
+ user_selected = TRUE
+ )
+ ),
</file context>
Suggested change
| user_selected = TRUE | |
| userSelected = TRUE |
…esponding tests - Updated the logic in fhir_batch_to_tibble to correctly identify unmapped concepts, ensuring that only explicit concept_id 0 is labeled as "unmapped" while NA ids are treated as resolved. - Added a new test case to verify that a missing standard id does not mislabel the response as "unmapped", maintaining clarity in the output status. - Enhanced overall test coverage for the resolve_batch function to ensure accurate handling of malformed responses.
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Summary by cubic
Release
omophub1.8.0 upgrades the FHIR resolver with Value-as-Concept in batch outputs and a newon_unmappedoption, and refines unmapped labeling to only flag explicitconcept_id0. This reduces 404s in ETL and makes unmapped cases clear and consistent.New Features
resolve(),resolve_batch(), andresolve_codeable_concept()accepton_unmapped("error" default, or "sentinel" to return aconcept_id0 record instead of a 404).value_as_concept_idandvalue_as_concept_namefrom “Maps to value” decomposition (FHIR-to-OMOP IG Value-as-Concept).Behavior Changes
Maps totarget asstatus = "unmapped"withstandard_concept_id = 0(previously "resolved").concept_id0 is labeled"unmapped"; missing/NA standard IDs remain"resolved"to avoid mislabeling.Written for commit a0ab3d3. Summary will update on new commits. Review in cubic