phc-ingestion 0.10.7__py3-none-any.whl → 0.10.9__py3-none-any.whl

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
         )

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.dist-info → phc_ingestion-0.10.9.dist-info}/METADATA

@@ -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.dist-info → phc_ingestion-0.10.9.dist-info}/RECORD

@@ -28,8 +28,8 @@ 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=N_19PLdbm9GaptsYfK1whTmVas5qZEtZC6VId_EFVy0,6353
-ingestion/nebula/process.py,sha256=D2ct9tF60ZIP_jZdjvgjfTkhEAkNNEhxaSqa04CtNR8,2237
+ingestion/nebula/manifest_assembler.py,sha256=NaFxmWYiIUXOabP8TTaH3JkvwELVB7Z-TUMN4j_MoaM,6972
+ingestion/nebula/process.py,sha256=NhlaMl6q2nTocWZvTUVMKaq1IghiZKyqSjnWApchnAU,2331
 ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
 ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
 ingestion/nextgen/util/alteration_table.py,sha256=JTWBL1Fqj_pGsH5vwuVEnCUJle2wOBk6VYImHYCF9vg,6129
@@ -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-0.10.7.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.7.dist-info/METADATA,sha256=fPt-rGHMt6ORmjrw1xKM8MDarx9A_b_no3B9UeurMRw,677
-phc_ingestion-0.10.7.dist-info/RECORD,,
+phc_ingestion-0.10.9.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.9.dist-info/METADATA,sha256=5qVLQFXYsuhBOyl6rtGdZ-_YHSCBeX1Zyut3QiMJnI4,677
+phc_ingestion-0.10.9.dist-info/RECORD,,