phc-ingestion 0.10.6__py3-none-any.whl → 0.10.8__py3-none-any.whl

ingestion/nebula/manifest_assembler.py

@@ -72,9 +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,
@@ -92,14 +99,11 @@ 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:
+    def __extract_id_from_reference(self, reference: Reference | None) -> str:
         if not reference:
             return ""
 
@@ -110,10 +114,12 @@ 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:
+    def __extract_id_from_reference_list(self, references: list[Reference] | None) -> str:
+        if not references or len(references) == 0:
             return ""
+        return self.__extract_id_from_reference(references[0])
 
+    def __extract_elation_mrn(self, patient: Patient) -> str:
         identifier = next(
             (
                 x
@@ -134,12 +140,9 @@ class ManifestAssembler:
 
     def __parse_human_name(self, human_name: list[HumanName] | None):
         if not human_name:
-            return None
-
-        human_name = next((x for x in human_name if x.get("use") == "official"), None)
+            return {}
 
-        if not human_name:
-            return None
+        human_name = next((x for x in human_name if x.get("use") == "official"), human_name[0])
 
         last_name = human_name.get("family", "")
         first_name = human_name.get("given", [])[0]
@@ -163,11 +166,16 @@ class ManifestAssembler:
             "Organization", patient.get("managingOrganization")
         )
 
-        general_practitioner: Practitioner | None = self.__fetch_resource_by_type_and_reference(
-            "Practitioner", patient.get("generalPractitioner")
-        )
+        # Handle generalPractitioner as a list
+        general_practitioner: Practitioner | None = None
+        general_practitioner_refs: list[Reference] = patient.get("generalPractitioner", [])
+        if general_practitioner_refs:
+            general_practitioner = self.__fetch_resource_by_type_and_reference(
+                "Practitioner",
+                {"reference": self.__extract_id_from_reference_list(general_practitioner_refs)},
+            )
 
-        patient_info = self.__parse_human_name(patient["name"])
+        patient_info = self.__parse_human_name(patient.get("name"))
         practitioner_info = self.__parse_human_name(
             general_practitioner.get("name") if general_practitioner else None
         )
@@ -185,10 +193,10 @@ 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-0.10.6.dist-info → phc_ingestion-0.10.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.6
+Version: 0.10.8
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.10.6.dist-info → phc_ingestion-0.10.8.dist-info}/RECORD

@@ -28,7 +28,7 @@ ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,
 ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
 ingestion/nebula/__init__.py,sha256=VauK-rup_N8ZXVohx3HYqHX_PE_WoPyMUhdv2R7al4o,45
 ingestion/nebula/constants.py,sha256=thKqSwemdaAwAmKvF4FEVI9l1Ph5ergsnMlx6nWte7E,357
-ingestion/nebula/manifest_assembler.py,sha256=OPUnuvzL1Bti_1-4N3fDP22wHtaK__4Bwh5K21Mg-C4,6416
+ingestion/nebula/manifest_assembler.py,sha256=9DME3AlPVvXY2SuR9QBgqfvHh3rJ-DoZRLcJPTonh2E,6974
 ingestion/nebula/process.py,sha256=D2ct9tF60ZIP_jZdjvgjfTkhEAkNNEhxaSqa04CtNR8,2237
 ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
 ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
@@ -59,6 +59,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
 ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
 ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
 ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
-phc_ingestion-0.10.6.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.6.dist-info/METADATA,sha256=IhIQUPLXKsepjBwgwe4ARhaZ2fKrmvsJhsgey1Yui7o,677
-phc_ingestion-0.10.6.dist-info/RECORD,,
+phc_ingestion-0.10.8.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.8.dist-info/METADATA,sha256=y4CsB4FWZJOJR4-qSq1sHl6FCGwu5eXpnI48DLuma40,677
+phc_ingestion-0.10.8.dist-info/RECORD,,