phc-ingestion 0.10.18__py3-none-any.whl → 0.10.20__py3-none-any.whl

ingestion/generic/utils.py

@@ -44,6 +44,7 @@ def check_manifest(manifest_file_path: str, case_id, log: Logger):
             Optional("plasmaTumorFraction"): str,
             Optional("cellPurity"): float,
             Optional("hrdStatus"): str,
+            Optional("specimenIds"): list[str],
         }
     )
 

ingestion/shared_util/fetch_patient.py

@@ -0,0 +1,76 @@
+from typing import Any
+from lifeomic_logging import scoped_logger
+from ingestion.shared_util.lambda_client import LambdaClient
+
+# Constants
+DATASET_SYSTEM = "http://lifeomic.com/fhir/dataset"
+
+
+def fetch_patient(
+    *,
+    elation_id: str,
+    given_name: str,
+    birthdate: str,
+    project_id: str,
+    account_id: str,
+    ingestion_id: str,
+) -> dict[str, Any] | None:
+    """
+    Fetch a patient from the patient-service lambda using Elation ID AND given name AND
+    birthdate.
+
+    Returns:
+        The patient resource if found, None otherwise
+
+    Raises:
+        RuntimeError: When multiple patients are found (ambiguous match)
+    """
+    log_context = {
+        "accountId": account_id,
+        "projectId": project_id,
+        "elationId": elation_id,
+        "ingestionId": ingestion_id,
+    }
+
+    with scoped_logger(__name__, log_context) as log:
+        # Create LambdaClient instance with proper headers
+        client = LambdaClient(
+            "patient-service",
+            {
+                "Content-Type": "application/json",
+                "LifeOmic-Account": account_id,
+                "LifeOmic-Correlation-Id": ingestion_id,
+            },
+        )
+
+        # Search by Elation ID AND given name AND birthdate
+        log.info(
+            f"Searching for patient with Elation ID: {elation_id}, given name: {given_name}, birthdate: {birthdate}"
+        )
+        response = client.invoke(
+            f"/{account_id}/dstu3/Patient",
+            "get",
+            None,
+            {
+                "_tag": f"{DATASET_SYSTEM}|{project_id}",
+                "identifier": elation_id,
+                "name": given_name,
+                "birthdate": birthdate,
+            },
+        )
+        entries = response.get("entry", [])
+
+        if len(entries) == 0:
+            error_msg = f"No patient found with Elation ID: {elation_id}, given name: {given_name}, birthdate: {birthdate}"
+            log.error(error_msg)
+            raise RuntimeError(error_msg)
+
+        if len(entries) > 1:
+            error_msg = f"Found multiple patients when one was expected. Found {len(entries)}. Elation ID {elation_id}, given name {given_name}, birthdate {birthdate}."
+            log.error(error_msg)
+            raise RuntimeError(error_msg)
+
+        log.info(
+            f"Found patient with Elation ID: {elation_id}, given name: {given_name}, birthdate: {birthdate}"
+        )
+        return entries[0]["resource"]

{phc_ingestion-0.10.18.dist-info → phc_ingestion-0.10.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.18
+Version: 0.10.20
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.10.18.dist-info → phc_ingestion-0.10.20.dist-info}/RECORD

@@ -25,7 +25,7 @@ ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd
 ingestion/foundation/util/vcf_etl.py,sha256=GXV5JXswwdyHEEdPsM3Qq8tDPFkvZajrZn5chWgF53k,2266
 ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,1777
-ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
+ingestion/generic/utils.py,sha256=_v3dKqlZK0S99_thSMD4ojkuFbBRWadBcS-RF-lTdJk,2862
 ingestion/nebula/__init__.py,sha256=VauK-rup_N8ZXVohx3HYqHX_PE_WoPyMUhdv2R7al4o,45
 ingestion/nebula/constants.py,sha256=thKqSwemdaAwAmKvF4FEVI9l1Ph5ergsnMlx6nWte7E,357
 ingestion/nebula/manifest_assembler.py,sha256=kcRSy6pixHkuVEK9QSoM-i6ZdLWMSYXw39eKGHvam34,7995
@@ -46,6 +46,7 @@ ingestion/resources/GRCh37_map.csv.gz,sha256=JOEkjtbYrJpIdyoZdCvfJhvvz2dNfkSve7l
 ingestion/resources/GRCh38_map.csv.gz,sha256=qriYO2_buCCb4T6WcuZ-pCwPxMsm0TL2OxAHvJ1cEfA,612373
 ingestion/shared_util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ingestion/shared_util/coords_to_genes.py,sha256=vz9EfgFm3BS6pEPnslbEka8cJKlQZtHJdH2WRCCUMdE,1669
+ingestion/shared_util/fetch_patient.py,sha256=-E-C2m6-fLfKy-r7rSsjZNu_ACGKvdjl1UuB-2gvaJc,2442
 ingestion/shared_util/ga4gh.py,sha256=-jNQj79zspxG67MxHzOfwAhLbb9je55M1h4-i5ri-tU,507
 ingestion/shared_util/gene_to_coords.py,sha256=M-q5ateLSQ4fCF0uMk5TX2uBLRrcZzXqXEf05TPaLsU,876
 ingestion/shared_util/lambda_client.py,sha256=0EdV5nOqe_w-OoDyi72w1P0lk30g1vlTW2sD3ci_Qqw,2695
@@ -59,6 +60,6 @@ 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-0.10.18.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.18.dist-info/METADATA,sha256=ueL73vYHsAoqSag13yqes1-Izpjo-uouBZIIC50VUHM,678
-phc_ingestion-0.10.18.dist-info/RECORD,,
+phc_ingestion-0.10.20.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.20.dist-info/METADATA,sha256=O4v14ntrknbOIU1iPTEoO8kQ8uXVNnNYotDo8YDkQis,678
+phc_ingestion-0.10.20.dist-info/RECORD,,