phc-ingestion 0.10.5__tar.gz → 0.10.6__tar.gz

{phc-ingestion-0.10.5 → phc-ingestion-0.10.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.5
+Version: 0.10.6
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.10.5 → phc-ingestion-0.10.6}/ingestion/nebula/manifest_assembler.py

@@ -9,6 +9,7 @@ from ingestion.nebula.constants import (
     NEBULA_BODY_SITE,
     NEBULA_INDICATION,
 )
+import re
 
 
 class HumanName(TypedDict):
@@ -99,7 +100,7 @@ class ManifestAssembler:
         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"):
+        if not reference:
             return ""
 
         ref_string = reference.get("reference")
@@ -109,12 +110,39 @@ class ManifestAssembler:
         parts = ref_string.split("/")
         return parts[1] if len(parts) > 1 else parts[0]
 
+    def __extract_elation_mrn(self, patient: Patient) -> str:
+        if not patient:
+            return ""
+
+        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 ""
+
+        return identifier.get("value", "")
+
     def __parse_human_name(self, human_name: list[HumanName] | None):
-        if not human_name or len(human_name) == 0:
+        if not human_name:
+            return None
+
+        human_name = next((x for x in human_name if x.get("use") == "official"), None)
+
+        if not human_name:
             return None
 
-        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 +177,7 @@ 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,

{phc-ingestion-0.10.5 → phc-ingestion-0.10.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.10.5"
+version = "0.10.6"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },