phenoml 17.0.1 → 17.2.0

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "phenoml",
-    "version": "17.0.1",
+    "version": "17.2.0",
     "private": false,
     "repository": {
         "type": "git",
@@ -121,6 +121,17 @@
             },
             "default": "./dist/cjs/api/resources/fhir/exports.js"
         },
+        "./fhir2Omop": {
+            "import": {
+                "types": "./dist/esm/api/resources/fhir2Omop/exports.d.mts",
+                "default": "./dist/esm/api/resources/fhir2Omop/exports.mjs"
+            },
+            "require": {
+                "types": "./dist/cjs/api/resources/fhir2Omop/exports.d.ts",
+                "default": "./dist/cjs/api/resources/fhir2Omop/exports.js"
+            },
+            "default": "./dist/cjs/api/resources/fhir2Omop/exports.js"
+        },
         "./fhirProvider": {
             "import": {
                 "types": "./dist/esm/api/resources/fhirProvider/exports.d.mts",
@@ -220,12 +231,12 @@
             },
             "default": "./dist/cjs/api/resources/workflows/exports.js"
         },
-        "./openapi.json": "./openapi/openapi.json",
-        "./package.json": "./package.json"
+        "./package.json": "./package.json",
+        "./openapi.json": "./openapi/openapi.json"
     },
     "files": [
-        "dist",
         "openapi",
+        "dist",
         "reference.md",
         "README.md",
         "LICENSE"

package/reference.md

@@ -2656,6 +2656,165 @@ The ID of the FHIR provider to use. Can be either:
 </dl>
 
 
+</dd>
+</dl>
+</details>
+
+## Fhir2Omop
+<details><summary><code>client.fhir2Omop.<a href="/src/api/resources/fhir2Omop/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateOmopResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Shapes 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`).
+
+Medication codes are resolved whether they appear inline
+(`medicationCodeableConcept`) or via a `medicationReference` to a contained,
+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
+bundle must contain at least one Patient resource.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhir2Omop.create({
+    fhir_resources: {
+        "resourceType": "Bundle",
+        "type": "collection",
+        "entry": [
+            {
+                "resource": {
+                    "resourceType": "Patient",
+                    "id": "patient-1",
+                    "gender": "female",
+                    "birthDate": "1985-07-22"
+                }
+            },
+            {
+                "resource": {
+                    "resourceType": "Condition",
+                    "id": "condition-1",
+                    "subject": {
+                        "reference": "Patient/patient-1"
+                    },
+                    "code": {
+                        "coding": [
+                            {
+                                "system": "http://snomed.info/sct",
+                                "code": "44054006",
+                                "display": "Type 2 diabetes mellitus"
+                            }
+                        ]
+                    },
+                    "onsetDateTime": "2024-01-15"
+                }
+            },
+            {
+                "resource": {
+                    "resourceType": "MedicationRequest",
+                    "id": "medreq-1",
+                    "status": "active",
+                    "subject": {
+                        "reference": "Patient/patient-1"
+                    },
+                    "medicationReference": {
+                        "reference": "#med0"
+                    },
+                    "authoredOn": "2024-01-16",
+                    "contained": [
+                        {
+                            "resourceType": "Medication",
+                            "id": "med0",
+                            "code": {
+                                "coding": [
+                                    {
+                                        "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
+                                        "code": "860975",
+                                        "display": "metformin hydrochloride 500 MG"
+                                    }
+                                ]
+                            }
+                        }
+                    ]
+                }
+            }
+        ]
+    }
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhir2Omop.CreateOmopRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir2OmopClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
 </dd>
 </dl>
 </details>