phc-ingestion 0.10.4__tar.gz → 0.10.6__tar.gz

{phc-ingestion-0.10.4 → phc-ingestion-0.10.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.4
+Version: 0.10.6
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

phc-ingestion-0.10.6/ingestion/nebula/constants.py

@@ -0,0 +1,7 @@
+NEBULA_TEST_TYPE = "WGS-30x"
+DATASET_SYSTEM = "http://lifeomic.com/fhir/dataset"
+NEBULA_KIT_ID_SYSTEM = "http://lifeomic.com/fhir/nebula-kit-id"
+BODY_SITE_SYSTEM = "http://lifeomic.com/fhir/sequence-body-site"
+NEBULA_BODY_SITE = "Buccal Swab"
+INDICATION_SYSTEM = "http://lifeomic.com/fhir/sequence-indication"
+NEBULA_INDICATION = "Genetic Health Screening"

{phc-ingestion-0.10.4 → phc-ingestion-0.10.6}/ingestion/nebula/manifest_assembler.py

@@ -1,6 +1,15 @@
 from typing import Optional, TypedDict, Any
 from datetime import datetime
 from ingestion.shared_util.lambda_client import LambdaClient
+from ingestion.nebula.constants import (
+    DATASET_SYSTEM,
+    NEBULA_KIT_ID_SYSTEM,
+    BODY_SITE_SYSTEM,
+    INDICATION_SYSTEM,
+    NEBULA_BODY_SITE,
+    NEBULA_INDICATION,
+)
+import re
 
 
 class HumanName(TypedDict):
@@ -57,8 +66,8 @@ class ManifestAssembler:
     def __fetch_patient_by_kit_id(self) -> Optional[Patient]:
         path = f"/{self.account_id}/dstu3/Patient"
         params = {
-            "_tag": f"http://lifeomic.com/fhir/dataset|{self.project_id}",
-            "identifier": f"http://lifeomic.com/fhir/nebula-kit-id|{self.kit_id}",
+            "_tag": f"{DATASET_SYSTEM}|{self.project_id}",
+            "identifier": f"{NEBULA_KIT_ID_SYSTEM}|{self.kit_id}",
         }
 
         response = self.client.invoke(path, "get", None, params)
@@ -80,7 +89,7 @@ class ManifestAssembler:
 
         try:
             return self.client.invoke(path, "get")
-        except RuntimeError as e:
+        except RuntimeError:
             return None
 
     def __extract_identifier_from_resource(self, resource: Resource | None) -> str:
@@ -91,7 +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")
@@ -101,12 +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,
@@ -121,7 +157,7 @@ class ManifestAssembler:
             raise RuntimeError(f"Patient with kit id {self.kit_id} not found")
         patient_birth_date = patient.get("birthDate")
         if not patient_birth_date:
-            raise RuntimeError(f"Patient birth date is a required to create a manifest")
+            raise RuntimeError("Patient birth date is a required to create a manifest")
 
         organization: Organization | None = self.__fetch_resource_by_type_and_reference(
             "Organization", patient.get("managingOrganization")
@@ -139,14 +175,15 @@ class ManifestAssembler:
         return {
             "name": "Nebula",
             "indexedDate": datetime.now().strftime("%Y-%m-%d"),
-            "reference": "GRCh38",  # TODO: Get from project?
-            "mrn": patient.get("id"),
-            "bodySite": "Buccal Swab",
-            "bodySiteDisplay": "Buccal Swab",
-            "bodySiteSystem": "http://lifeomic.com/fhir/sequence-body-site",
-            "indicationSystem": "http://lifeomic.com/fhir/sequence-indication",
-            "indication": "Genetic Health Screening",
-            "indicationDisplay": "Genetic Health Screening",
+            "reference": "GRCh38",
+            "patientId": patient.get("id"),
+            "mrn": self.__extract_elation_mrn(patient),
+            "bodySite": NEBULA_BODY_SITE,
+            "bodySiteDisplay": NEBULA_BODY_SITE,
+            "bodySiteSystem": BODY_SITE_SYSTEM,
+            "indicationSystem": INDICATION_SYSTEM,
+            "indication": NEBULA_INDICATION,
+            "indicationDisplay": NEBULA_INDICATION,
             "patientInfo": {
                 "lastName": patient_info.get("lastName"),
                 "dob": datetime.fromisoformat(patient_birth_date).strftime("%Y-%m-%d"),

{phc-ingestion-0.10.4 → phc-ingestion-0.10.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.10.4"
+version = "0.10.6"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },

phc-ingestion-0.10.4/ingestion/nebula/constants.py

@@ -1 +0,0 @@
-NEBULA_TEST_TYPE = "WGS-30x"