phc-ingestion 0.10.7__tar.gz → 0.10.9__tar.gz

{phc-ingestion-0.10.7 → phc-ingestion-0.10.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.7
+Version: 0.10.9
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.10.7 → phc-ingestion-0.10.9}/ingestion/nebula/manifest_assembler.py

@@ -103,11 +103,22 @@ class ManifestAssembler:
         identifiers = resource.get("identifier", [])
         return identifiers[0].get("value", "") if identifiers else ""
 
-    def __extract_id_from_reference(self, reference: Reference) -> str:
-        ref_string = reference.get("reference", "")
+    def __extract_id_from_reference(self, reference: Reference | None) -> str:
+        if not reference:
+            return ""
+
+        ref_string = reference.get("reference")
+        if not ref_string:
+            return ""
+
         parts = ref_string.split("/")
         return parts[1] if len(parts) > 1 else parts[0]
 
+    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(
             (
@@ -149,17 +160,22 @@ 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("Patient birth date is a required to create a manifest")
+            raise RuntimeError("Patient birth date is required to create a manifest")
 
         organization: Organization | None = self.__fetch_resource_by_type_and_reference(
             "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
         )

{phc-ingestion-0.10.7 → phc-ingestion-0.10.9}/ingestion/nebula/process.py

@@ -1,6 +1,7 @@
 import os
 
 from ingestion.nebula.constants import NEBULA_TEST_TYPE
+from ingestion.shared_util.ga4gh import create_yaml
 from ingestion.vcf_standardization.standardize import standardize_vcf
 from lifeomic_logging import scoped_logger
 from ingestion.nebula.manifest_assembler import ManifestAssembler
@@ -43,6 +44,8 @@ def process(vcf_file, out_path, file_name, source_file_id, ingestion_id, account
             }
         ]
 
+        create_yaml(manifest, file_name)
+
         # Hard-code genome reference for Nebula VCFs
         genome_reference = "GRCh38"
 

{phc-ingestion-0.10.7 → phc-ingestion-0.10.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.10.7"
+version = "0.10.9"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },