phc-ingestion 0.10.4__py3-none-any.whl → 0.10.5__py3-none-any.whl

ingestion/nebula/constants.py

@@ -1 +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"

ingestion/nebula/manifest_assembler.py

@@ -1,6 +1,14 @@
 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,
+)
 
 
 class HumanName(TypedDict):
@@ -57,8 +65,8 @@ 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 +88,7 @@ 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:
@@ -121,7 +129,7 @@ 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 +147,15 @@ class ManifestAssembler:
         return {
             "name": "Nebula",
             "indexedDate": datetime.now().strftime("%Y-%m-%d"),
-            "reference": "GRCh38",  # TODO: Get from project?
+            "reference": "GRCh38",
+            "patientId": patient.get("id"),
             "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",
+            "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.dist-info → phc_ingestion-0.10.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.4
+Version: 0.10.5
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.10.4.dist-info → phc_ingestion-0.10.5.dist-info}/RECORD

@@ -27,8 +27,8 @@ ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU
 ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,1777
 ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
 ingestion/nebula/__init__.py,sha256=VauK-rup_N8ZXVohx3HYqHX_PE_WoPyMUhdv2R7al4o,45
-ingestion/nebula/constants.py,sha256=015BkvYnu5JTzFCS3zjqsaFb0emzH4I8ZewpBjMJQfo,29
-ingestion/nebula/manifest_assembler.py,sha256=2nXMfFESs00NeetpizIJlFa8SR0KKqYgK_Xnusdjb58,5616
+ingestion/nebula/constants.py,sha256=thKqSwemdaAwAmKvF4FEVI9l1Ph5ergsnMlx6nWte7E,357
+ingestion/nebula/manifest_assembler.py,sha256=sGZdeMpMT4osOBXlxY9CPZKUJSQXaShT77JJVB30I1s,5704
 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-0.10.4.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.4.dist-info/METADATA,sha256=2bo_7YXbyMWyhO2pJDyGSbMWb_IYdPWgihQDWuB9b6s,677
-phc_ingestion-0.10.4.dist-info/RECORD,,
+phc_ingestion-0.10.5.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.5.dist-info/METADATA,sha256=qf_dLgOkjhiTmAL2LjoyPJWs-38ggs82qXsc8wc66eg,677
+phc_ingestion-0.10.5.dist-info/RECORD,,