phc-ingestion 0.10.5__tar.gz → 0.10.7__tar.gz

{phc-ingestion-0.10.5 → phc-ingestion-0.10.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.5
+Version: 0.10.7
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.10.5 → phc-ingestion-0.10.7}/ingestion/nebula/manifest_assembler.py

@@ -9,6 +9,7 @@ from ingestion.nebula.constants import (
     NEBULA_BODY_SITE,
     NEBULA_INDICATION,
 )
+import re
 
 
 class HumanName(TypedDict):
@@ -71,9 +72,16 @@ class ManifestAssembler:
 
         response = self.client.invoke(path, "get", None, params)
         entries = response.get("entry", [])
-        patient = entries[0]["resource"] if len(entries) > 0 else None
 
-        return patient
+        if len(entries) == 0:
+            return None
+
+        if len(entries) > 1:
+            raise RuntimeError(
+                f"Found {len(entries)} patients with kit id {self.kit_id}. Expected 1."
+            )
+
+        return entries[0]["resource"]
 
     def __fetch_resource_by_type_and_reference(
         self,
@@ -91,30 +99,42 @@ class ManifestAssembler:
         except RuntimeError:
             return None
 
-    def __extract_identifier_from_resource(self, resource: Resource | None) -> str:
-        if not resource:
-            return ""
-
+    def __extract_identifier_from_resource(self, resource: Resource) -> str:
         identifiers = resource.get("identifier", [])
         return identifiers[0].get("value", "") if identifiers else ""
 
     def __extract_id_from_reference(self, reference: Reference) -> str:
-        if not reference or not reference.get("reference"):
-            return ""
+        ref_string = reference.get("reference", "")
+        parts = ref_string.split("/")
+        return parts[1] if len(parts) > 1 else parts[0]
 
-        ref_string = reference.get("reference")
-        if not ref_string:
+    def __extract_elation_mrn(self, patient: Patient) -> str:
+        identifier = next(
+            (
+                x
+                for x in patient.get("identifier", [])
+                # if matches LRN format for Elation
+                if re.search(
+                    f"lrn:lo:(dev|us):{self.account_id}:ehr:{self.account_id}:{self.project_id}/Patient",
+                    x.get("system", ""),
+                )
+            ),
+            None,
+        )
+
+        if not identifier:
             return ""
 
-        parts = ref_string.split("/")
-        return parts[1] if len(parts) > 1 else parts[0]
+        return identifier.get("value", "")
 
     def __parse_human_name(self, human_name: list[HumanName] | None):
-        if not human_name or len(human_name) == 0:
-            return None
+        if not human_name:
+            return {}
+
+        human_name = next((x for x in human_name if x.get("use") == "official"), human_name[0])
 
-        last_name = human_name[0].get("family", "")
-        first_name = human_name[0].get("given", [])[0]
+        last_name = human_name.get("family", "")
+        first_name = human_name.get("given", [])[0]
 
         return {
             "lastName": last_name,
@@ -149,7 +169,7 @@ class ManifestAssembler:
             "indexedDate": datetime.now().strftime("%Y-%m-%d"),
             "reference": "GRCh38",
             "patientId": patient.get("id"),
-            "mrn": patient.get("id"),
+            "mrn": self.__extract_elation_mrn(patient),
             "bodySite": NEBULA_BODY_SITE,
             "bodySiteDisplay": NEBULA_BODY_SITE,
             "bodySiteSystem": BODY_SITE_SYSTEM,
@@ -157,10 +177,10 @@ class ManifestAssembler:
             "indication": NEBULA_INDICATION,
             "indicationDisplay": NEBULA_INDICATION,
             "patientInfo": {
-                "lastName": patient_info.get("lastName"),
+                "lastName": patient_info.get("lastName", ""),
                 "dob": datetime.fromisoformat(patient_birth_date).strftime("%Y-%m-%d"),
-                "firstName": patient_info.get("firstName"),
-                "gender": patient["gender"],
+                "firstName": patient_info.get("firstName", ""),
+                "gender": patient.get("gender", ""),
             },
             **(
                 {

{phc-ingestion-0.10.5 → phc-ingestion-0.10.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.10.5"
+version = "0.10.7"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },