phenoml 17.2.0 → 17.4.0

package/reference.md

@@ -2673,30 +2673,26 @@ The ID of the FHIR provider to use. Can be either:
 <dl>
 <dd>
 
-Shapes a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows
+Maps a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows
 (person, visit_occurrence, condition_occurrence, drug_exposure,
 procedure_occurrence, measurement, observation).
 
-**Two resolution modes, reported in `mode`.** `mode` reflects which
-resolver is wired, not the path an individual coding took. With a
-concept-resolver configured (the default), `mode` is `"resolved"` and the
-resource's primary clinical coding is resolved to a real OMOP `concept_id`;
-with no resolver configured, `mode` is `"structural"` and every clinical
-and source `concept_id` is `0`. In `"resolved"` mode individual codings can
-still land at `concept_id` `0` without changing the mode: a coding the
-service finds no match for is `UNMAPPED`, and a coding that fell back to the
-structural tier (the resolver was briefly unavailable, or the resource was
-text-only) is surfaced in `scan_summary` (`concept_resolver_note`,
-`construe_resolutions`). A `concept_id` of `0` is "no matching concept" per
-OMOP semantics, deliberately not omitted. Only the primary clinical coding
-is resolved — `gender`/`race`/`ethnicity`/`visit`/`value`/`unit`
-`concept_id`s are always `0`.
-
-In every mode each `*_source_value` carries the verbatim FHIR coding
-(`system#code`), `*_type_concept_id` is set to `32817` (EHR), and the
-response `report` lists one Usagi-shaped entry per source coding describing
-how it resolved (`ALREADY_STANDARD`, `MAPPED`, an `UNCHECKED` suggestion,
-or `UNMAPPED`).
+Each resource's primary clinical coding is resolved to a standard OMOP
+`concept_id`. Alongside the OMOP rows grouped by table (`tables`), the
+response carries `mappings` (how each source coding resolved, linked back
+to the row it produced), `dropped` (resources that could not be shaped
+into a row), `vocab_version` (the OMOP vocabulary release codes were
+resolved against), and a small `summary` of the resolution outcomes.
+
+A `concept_id` of `0` is reported, not omitted (OMOP "no matching
+concept" semantics): it covers both a coding with no standard match
+(`UNMAPPED`) and an unverified suggestion for a text-only resource
+(`UNCHECKED`). Only the primary clinical coding is resolved, so
+`gender`/`race`/`ethnicity`/`visit`/`value`/`unit` `concept_id`s are
+always `0`; the one populated non-resolved concept is measurement
+`operator_concept_id`, set from a value comparator (`<`, `<=`, `>`, `>=`)
+rather than the resolver. Each `*_source_value` carries the verbatim FHIR
+coding (`system#code`), and `*_type_concept_id` is set to `32817` (EHR).
 
 Medication codes are resolved whether they appear inline
 (`medicationCodeableConcept`) or via a `medicationReference` to a contained,
@@ -2704,7 +2700,7 @@ relative (`Type/id`), or bundle-entry (`urn:uuid`) `Medication` resource.
 Resources that cannot be shaped into a row — a medication with no usable
 code, resolvable reference, or display, or any clinical resource whose
 subject/patient reference cannot be tied to a person — are reported under
-`scan_summary.dropped_resources` rather than emitted as blank rows. The
+`dropped` rather than emitted as blank rows. The
 bundle must contain at least one Patient resource.
 </dd>
 </dl>

package/dist/cjs/api/resources/fhir2Omop/types/MappingReportEntry.d.ts

@@ -1,32 +0,0 @@
-/**
- * One source_to_concept_map-style mapping suggestion (Usagi-shaped).
- */
-export interface MappingReportEntry {
-    resource_type?: string | undefined;
-    resource_id?: string | undefined;
-    omop_table?: string | undefined;
-    source_system?: string | undefined;
-    source_code?: string | undefined;
-    source_name?: string | undefined;
-    target_vocabulary?: string | undefined;
-    /**
-     * Standard concept code. Set when a coding is matched by the structural
-     * (construe) tier — an already-standard code taken verbatim, or a
-     * construe-suggested code — which is every match in structural mode and,
-     * in resolved mode, codings for text-only resources or ones that fell back
-     * when the resolver was unavailable. Omitted for codings resolved directly
-     * by the concept-resolver service, which returns the standard concept's
-     * id, name, and vocabulary but not its `concept_code`.
-     */
-    target_code?: string | undefined;
-    target_name?: string | undefined;
-    /**
-     * ALREADY_STANDARD (source already in the target standard vocabulary),
-     * MAPPED (resolved to a standard concept via the OMOP "Maps to" crosswalk
-     * or UMLS-CUI bridge; resolved mode only), UNCHECKED (an unreviewed
-     * construe suggestion; structural / fallback only), or UNMAPPED (no
-     * candidate found).
-     */
-    mapping_status?: string | undefined;
-    note?: string | undefined;
-}

package/dist/cjs/api/resources/fhir2Omop/types/ScanSummary.d.ts

@@ -1,41 +0,0 @@
-import type * as phenoml from "../../../index.js";
-/**
- * White Rabbit-style aggregate profile of the mapping request.
- */
-export interface ScanSummary {
-    total_resources?: number | undefined;
-    resource_counts?: Record<string, number> | undefined;
-    tables_populated?: Record<string, number> | undefined;
-    coding_systems?: Record<string, number> | undefined;
-    codes_already_standard?: number | undefined;
-    codes_normalized?: number | undefined;
-    codes_unmapped?: number | undefined;
-    off_vocab_rate?: number | undefined;
-    dropped_resources?: phenoml.fhir2Omop.DroppedResource[] | undefined;
-    /**
-     * OMOP vocabulary release the resolver mapped against (e.g. "v20240229").
-     * Resolved mode only; empty when no coded concept reached the service.
-     */
-    resolved_vocab_version?: string | undefined;
-    /**
-     * Set when concept resolution was degraded — the resolver was unavailable
-     * for one or more codings, whose `concept_id`s fell back to the structural
-     * (construe) tier. Empty when resolution was clean.
-     */
-    concept_resolver_note?: string | undefined;
-    /**
-     * Count of `concept_id`s chosen via the lower-confidence UMLS-CUI bridge
-     * (no direct OMOP crosswalk existed). Resolved mode only.
-     */
-    concepts_bridged?: number | undefined;
-    /**
-     * Count of codings whose candidate list the resolver capped, so the best
-     * concept may not have been among those returned.
-     */
-    concept_candidates_truncated?: number | undefined;
-    /**
-     * Count of codings resolved via the construe ML extractor — the text-only
-     * or availability fallback path. A non-zero value bills the construe tier.
-     */
-    construe_resolutions?: number | undefined;
-}

package/dist/esm/api/resources/fhir2Omop/types/MappingReportEntry.d.mts

@@ -1,32 +0,0 @@
-/**
- * One source_to_concept_map-style mapping suggestion (Usagi-shaped).
- */
-export interface MappingReportEntry {
-    resource_type?: string | undefined;
-    resource_id?: string | undefined;
-    omop_table?: string | undefined;
-    source_system?: string | undefined;
-    source_code?: string | undefined;
-    source_name?: string | undefined;
-    target_vocabulary?: string | undefined;
-    /**
-     * Standard concept code. Set when a coding is matched by the structural
-     * (construe) tier — an already-standard code taken verbatim, or a
-     * construe-suggested code — which is every match in structural mode and,
-     * in resolved mode, codings for text-only resources or ones that fell back
-     * when the resolver was unavailable. Omitted for codings resolved directly
-     * by the concept-resolver service, which returns the standard concept's
-     * id, name, and vocabulary but not its `concept_code`.
-     */
-    target_code?: string | undefined;
-    target_name?: string | undefined;
-    /**
-     * ALREADY_STANDARD (source already in the target standard vocabulary),
-     * MAPPED (resolved to a standard concept via the OMOP "Maps to" crosswalk
-     * or UMLS-CUI bridge; resolved mode only), UNCHECKED (an unreviewed
-     * construe suggestion; structural / fallback only), or UNMAPPED (no
-     * candidate found).
-     */
-    mapping_status?: string | undefined;
-    note?: string | undefined;
-}

package/dist/esm/api/resources/fhir2Omop/types/ScanSummary.d.mts

@@ -1,41 +0,0 @@
-import type * as phenoml from "../../../index.mjs";
-/**
- * White Rabbit-style aggregate profile of the mapping request.
- */
-export interface ScanSummary {
-    total_resources?: number | undefined;
-    resource_counts?: Record<string, number> | undefined;
-    tables_populated?: Record<string, number> | undefined;
-    coding_systems?: Record<string, number> | undefined;
-    codes_already_standard?: number | undefined;
-    codes_normalized?: number | undefined;
-    codes_unmapped?: number | undefined;
-    off_vocab_rate?: number | undefined;
-    dropped_resources?: phenoml.fhir2Omop.DroppedResource[] | undefined;
-    /**
-     * OMOP vocabulary release the resolver mapped against (e.g. "v20240229").
-     * Resolved mode only; empty when no coded concept reached the service.
-     */
-    resolved_vocab_version?: string | undefined;
-    /**
-     * Set when concept resolution was degraded — the resolver was unavailable
-     * for one or more codings, whose `concept_id`s fell back to the structural
-     * (construe) tier. Empty when resolution was clean.
-     */
-    concept_resolver_note?: string | undefined;
-    /**
-     * Count of `concept_id`s chosen via the lower-confidence UMLS-CUI bridge
-     * (no direct OMOP crosswalk existed). Resolved mode only.
-     */
-    concepts_bridged?: number | undefined;
-    /**
-     * Count of codings whose candidate list the resolver capped, so the best
-     * concept may not have been among those returned.
-     */
-    concept_candidates_truncated?: number | undefined;
-    /**
-     * Count of codings resolved via the construe ML extractor — the text-only
-     * or availability fallback path. A non-zero value bills the construe tier.
-     */
-    construe_resolutions?: number | undefined;
-}