phc-ingestion 0.8.41__tar.gz → 0.9.0__tar.gz

{phc-ingestion-0.8.41 → phc-ingestion-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.8.41
+Version: 0.9.0
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.8.41 → phc-ingestion-0.9.0}/ingestion/caris/util/metadata.py

@@ -94,9 +94,13 @@ def extract_metadata(data, prefix, files, source_file_id, log: Logger) -> dict:
     # Get date of collected and received for the specimen
     metadata["receivedDate"] = specimen_details["receivedDate"]
     metadata["collDate"] = specimen_details["collDate"]
+    if specimen_details["specimenId"]:
+        metadata["specimenIds"] = [specimen_details["specimenId"]]
+    if specimen_details["specimenTypes"]:
+        metadata["specimenTypes"] = specimen_details["specimenTypes"]
     metadata["reportDate"] = get_report_date(test_details, log)
 
-    #  Get the date without the time
+    # Get the date without the time
     metadata["indexedDate"] = metadata["reportDate"]
 
     patient = data["patientInformation"]

{phc-ingestion-0.8.41 → phc-ingestion-0.9.0}/ingestion/caris/util/specimen_details.py

@@ -1,5 +1,5 @@
 from logging import Logger
-from typing import TypedDict, cast
+from typing import TypedDict, cast, Optional
 
 
 class SpecimenDetails(TypedDict, total=False):
@@ -8,37 +8,55 @@ class SpecimenDetails(TypedDict, total=False):
     specimenReceivedDate: str
     specimenCollectionDate: str
     specimenSite: str
+    specimenType: str
+    specimenID: str
 
 
 class ParsedSpecimenDetails(TypedDict):
     bodySite: str
     receivedDate: str
     collDate: str
+    specimenId: Optional[str]
+    specimenTypes: Optional[list[str]]
 
 
-def parse_specimen_details(specimen_details: SpecimenDetails) -> ParsedSpecimenDetails:
+def parse_specimen_details(specimen_details: list[SpecimenDetails]) -> ParsedSpecimenDetails:
+    specimen_types: list[str] = []
+    for specimen in specimen_details:
+        specimen_type = specimen.get("specimenType")
+        if specimen_type and specimen_type not in specimen_types:
+            specimen_types.append(specimen_type)
+
     return {
-        "bodySite": specimen_details.get("specimenSite", ""),
-        "receivedDate": specimen_details.get("specimenReceivedDate", ""),
-        "collDate": specimen_details.get("specimenCollectionDate", ""),
+        "bodySite": specimen_details[0].get("specimenSite", ""),
+        "receivedDate": specimen_details[0].get("specimenReceivedDate", ""),
+        "collDate": specimen_details[0].get("specimenCollectionDate", ""),
+        "specimenId": specimen_details[0].get("specimenID"),
+        "specimenTypes": specimen_types if specimen_types else None,
     }
 
 
-def ensure_single_specimen_details(
+def standardize_specimen_details(
     specimen_details: SpecimenDetails | list[SpecimenDetails],
     log: Logger,
-) -> SpecimenDetails:
+) -> list[SpecimenDetails]:
+    """
+    Specimen details can be a single dictionary or a list of dictionaries
+    This function standardizes the input to always be a list of dictionaries
+
+    If it is a list, we expect all the specimens to have the same site and warn otherwise.
+    """
     if isinstance(specimen_details, dict):
-        return specimen_details
+        return [specimen_details]
 
     # Sometimes, we have multiple specimen details
     # In this case, we expect them to all be the same and warn otherwise
-    sites = {specimen["specimenSite"] for specimen in specimen_details}
+    sites = {specimen.get("specimenSite") for specimen in specimen_details}
 
     if len(sites) > 1:
-        log.warn(f"Multiple specimen sites found")
+        log.warning("Multiple specimen sites found")
 
-    return specimen_details[0]
+    return specimen_details
 
 
 def extract_and_parse_specimen_details(data: dict, log: Logger) -> ParsedSpecimenDetails:
@@ -62,6 +80,6 @@ def extract_and_parse_specimen_details(data: dict, log: Logger) -> ParsedSpecime
     if not specimen_details:
         raise ValueError("No specimen details found in data")
 
-    specimen_details = ensure_single_specimen_details(specimen_details, log)
+    specimen_details = standardize_specimen_details(specimen_details, log)
 
     return parse_specimen_details(specimen_details)

{phc-ingestion-0.8.41 → phc-ingestion-0.9.0}/ingestion/foundation/util/ga4gh.py

@@ -190,6 +190,19 @@ def get_test_yml(
     reportDate = str(get_date(signatures.get("Signature").get("ServerTime")))[0:10]
     indexedDate = reportDate
 
+    sample_id = (sample.get("SampleId") or "").strip()
+    block_id = (sample.get("BlockId") or "").strip()
+    if block_id == "N/A":
+        block_id = ""
+
+    specimen_ids = []
+    if sample_id:
+        specimen_ids.append(sample_id)
+    if block_id:
+        specimen_ids.append(block_id)
+
+    specimenType = sample.get("SpecFormat", "").strip()
+
     yaml_file = {
         "name": "Foundation Medicine",
         "reference": "GRCh37",
@@ -216,6 +229,11 @@ def get_test_yml(
         "files": [],
     }
 
+    if specimen_ids:
+        yaml_file["specimenIds"] = specimen_ids
+    if specimenType:
+        yaml_file["specimenTypes"] = [specimenType]
+
     if write_to_manifest["cnv"]:
         yaml_file["files"].append(
             {

{phc-ingestion-0.8.41 → phc-ingestion-0.9.0}/ingestion/generic/process.py

@@ -19,8 +19,12 @@ def process(
         vcf_final = base_vcf_file.replace(".vcf", ".modified.nrm.filtered.vcf")
         if not vcf_final.endswith(".gz"):
             vcf_final = vcf_final + ".gz"
+        # All generic VCF ingestions are germline, so ensure the
+        # sample name is prefixed with "germline_". This matches
+        # the downstream logic in genomic-manifest
+        sample_name = f"germline_{case_id}"
         vcf_line_count = standardize_vcf(
-            vcf_file, vcf_out, out_path, case_id, log, compression=True
+            vcf_file, vcf_out, out_path, sample_name, log, compression=True
         )
 
         # Add to manifest

{phc-ingestion-0.8.41 → phc-ingestion-0.9.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.8.41"
+version = "0.9.0"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },