phc-ingestion 0.10.17__py3-none-any.whl → 0.10.19__py3-none-any.whl

ingestion/foundation/util/ga4gh.py

@@ -111,17 +111,23 @@ def get_hrd_status(genes) -> Optional[str]:
     hrd_dict = {
         "HRD Positive": "positive",
         "HRD Not Detected": "negative",
+        "HRDsig Positive": "positive",
+        "HRDsig Not Detected": "negative",
+        "HRDsig Negative": "negative",
     }
-    hrd_entry = [
-        entry
-        for entry in genes.get("Gene", {})
-        if entry.get("Name", "") == "Homologous Recombination status"
-    ]
-    if hrd_entry:
-        hrd_val = hrd_entry[0].get("Alterations", "").get("Alteration", "").get("Name", "")
-        return [value for (key, value) in hrd_dict.items() if key == hrd_val][0]
-    else:
+    hrd_entry = next(
+        (
+            entry
+            for entry in genes.get("Gene", {})
+            if entry.get("Name", "") == "Homologous Recombination status"
+            or entry.get("Name", "") == "HRD signature"
+        ),
+        None,
+    )
+    if not hrd_entry:
         return None
+    hrd_val = hrd_entry.get("Alterations", {}).get("Alteration", {}).get("Name", "")
+    return hrd_dict.get(hrd_val, None)
 
 
 def get_test_yml(
@@ -155,6 +161,14 @@ def get_test_yml(
         (prop for prop in properties if prop.get("@key") == "ComprehensiveTumorFractionScore"),
         {},
     ).get("value")
+    hrd_score = next(
+        (
+            prop
+            for prop in properties
+            if prop.get("@key") == "HomologousRecombinationDeficiencyScore"
+        ),
+        {},
+    ).get("value")
     plasma_tumor_fraction_score = None
     if plasma_tumor_fraction_score_value:
         plasma_tumor_fraction_score = get_plasma_tumor_fraction_score_from_value(
@@ -325,5 +339,7 @@ def get_test_yml(
     # add homologous recombination deficiency
     if hrd_status:
         yaml_file["hrdStatus"] = hrd_status
+    if hrd_score != None and is_number(hrd_score):
+        yaml_file["hrdScore"] = float(hrd_score)
 
     return yaml_file

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-0.10.17.dist-info → phc_ingestion-0.10.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.17
+Version: 0.10.19
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.10.17.dist-info → phc_ingestion-0.10.19.dist-info}/RECORD

@@ -20,7 +20,7 @@ ingestion/foundation/process.py,sha256=mzKVVefGZD1HkEi0Hbb9eD_flwGp1S6SZ7FNXZpWn
 ingestion/foundation/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ingestion/foundation/util/cnv.py,sha256=eyTn1lqbo0tmEacnqWuGATt1h9lllTlVlboT8n5C6Ao,4283
 ingestion/foundation/util/fnv.py,sha256=B8tOREYsR45aIGdSj8SPpe7f3L8FlGaIhLe0DSNqCnc,6006
-ingestion/foundation/util/ga4gh.py,sha256=2oCTR9kvV5EeGZlrR35MfMkNL3nbeJYO88fo0NDDmRo,11304
+ingestion/foundation/util/ga4gh.py,sha256=RqyKuntH5Y-dRpr188i2hR8yc1F_An_8Z9DlGsFa0Sw,11779
 ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd8cU3I9YHD5fsXg,405
 ingestion/foundation/util/vcf_etl.py,sha256=GXV5JXswwdyHEEdPsM3Qq8tDPFkvZajrZn5chWgF53k,2266
 ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -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-0.10.17.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.17.dist-info/METADATA,sha256=qYPpPZAUmSeBfcZzMmYCAZrEmN7y01Hve1sKcGEtBSA,678
-phc_ingestion-0.10.17.dist-info/RECORD,,
+phc_ingestion-0.10.19.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.19.dist-info/METADATA,sha256=TJl30skhIPB8AGD-RYwHch6NS2AW3FqaeFXwRO3wAyk,678
+phc_ingestion-0.10.19.dist-info/RECORD,,