phc-ingestion 0.8.37__tar.gz → 0.8.38__tar.gz

{phc-ingestion-0.8.37 → phc-ingestion-0.8.38}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.8.37
+Version: 0.8.38
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.8.37 → phc-ingestion-0.8.38}/ingestion/caris/util/json.py

@@ -84,11 +84,17 @@ def process_caris_json(infile: str, outpath: str, file_name: str, source_file_id
                 ]
 
     # Get patient
-    metadata = extract_metadata(data, file_name, files, source_file_id, log)
+    metadata, is_test_cancelled_permit_vcf_skip = extract_metadata(
+        data, file_name, files, source_file_id, log
+    )
     structural_results = extract_structural(file_name, data, log)
     cnv_results = extract_cnv(file_name, data, log)
     rgel_results = convert_tsv_to_rgel(file_name, files, log)
-    vcf_results = extract_sv(file_name, bool(somatic_filename), bool(germline_filename))
+
+    include_empty = metadata["ihcTests"] and is_test_cancelled_permit_vcf_skip
+    vcf_results = extract_sv(
+        file_name, bool(somatic_filename), bool(germline_filename), include_empty
+    )
 
     # We might not have any of these files but we need an empty json object here.
     file_genome_references = {}
@@ -117,5 +123,7 @@ def process_caris_json(infile: str, outpath: str, file_name: str, source_file_id
         result["somatic_vcf"] = f"{outpath}/{somatic_filename}"
     if germline_filename is not None:
         result["germline_vcf"] = f"{outpath}/{germline_filename}"
+    if not germline_filename and not somatic_filename and include_empty:
+        result["somatic_vcf"] = f"{outpath}/{file_name}.modified.somatic.vcf.gz"
 
     return (result, germline_case_id, file_genome_references, data)

{phc-ingestion-0.8.37 → phc-ingestion-0.8.38}/ingestion/caris/util/metadata.py

@@ -80,6 +80,7 @@ def is_valid_test_entry(test: dict):
 
 # Build up the manifest iteratively because almost everything is optional
 def extract_metadata(data, prefix, files, source_file_id, log: Logger) -> dict:
+    is_test_cancelled_permit_vcf_skip = False
     metadata = {}
 
     test_details = data["testDetails"]
@@ -158,6 +159,13 @@ def extract_metadata(data, prefix, files, source_file_id, log: Logger) -> dict:
     # if not sufficient quantity we won't have test results
     if test_details["reportType"] != "QNS":
         for test in tests:
+            if "test_cancellation_reason" in test:
+                if test["test_cancellation_reason"] == "Quantitation quantity not sufficient":
+                    # capture cancellation reason before bailing
+                    # this is so we can generate an empty vcf so present biomarkers are
+                    # still ingested: https://lifeomic.atlassian.net/browse/PHC-5748
+                    is_test_cancelled_permit_vcf_skip = True
+
             if not is_valid_test_entry(test):
                 continue
             # Sometimes, if there is only a single test result,
@@ -244,4 +252,4 @@ def extract_metadata(data, prefix, files, source_file_id, log: Logger) -> dict:
                 )
 
     active_metadata = {k: v for k, v in metadata.items() if v is not None}
-    return active_metadata
+    return (active_metadata, is_test_cancelled_permit_vcf_skip)

{phc-ingestion-0.8.37 → phc-ingestion-0.8.38}/ingestion/caris/util/vcf.py

@@ -1,11 +1,5 @@
 import datetime
 import gzip
-import io
-import os
-import re
-import subprocess
-import sys
-import zipfile
 
 from logging import Logger
 
@@ -13,8 +7,38 @@ from ingestion.caris.util.tests import safely_extract_tests_from_json_data
 from ingestion.vcf_standardization.standardize import standardize_vcf
 
 
+def create_empty_vcf_zip(prefix):
+    vcf_gzip_path = f"{prefix}.modified.somatic.vcf.gz"
+    content = (
+        """##fileformat=VCFv4.1
+##filedate="""
+        + datetime.datetime.now().isoformat()
+        + """
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=R8,Description="IndelRepeatLength is greater than 8">
+##FILTER=<ID=R8.1,Description="IndelRepeatLength of a monomer is greater than 8">
+##FILTER=<ID=R8.2,Description="IndelRepeatLength of a dimer is greater than 8">
+##FILTER=<ID=sb,Description="Variant strand bias high">
+##FILTER=<ID=sb.s,Description="Variant strand bias significantly high (only for SNV)">
+##FILTER=<ID=rs,Description="Variant with rs (dbSNP) number in a non-core gene">
+##FILTER=<ID=FP,Description="Possibly false positives due to high similarity to off-target regions">
+##FILTER=<ID=NC,Description="Noncoding INDELs on non-core genes">
+##FILTER=<ID=lowDP,Description="low depth variant">
+##FILTER=<ID=Benign,Description="Benign variant">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AF,Number=1,Type=String,Description="Variant Allele Frequency">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	"""
+        + prefix
+        + """
+"""
+    )
+
+    with gzip.open(vcf_gzip_path, "wb") as f:
+        f.write(content.encode("utf-8"))
+
+
 # This is done in next step, we are just adding to yaml
-def extract_sv(prefix, include_somatic: bool, include_germline: bool):
+def extract_sv(prefix, include_somatic: bool, include_germline: bool, include_empty: bool):
     vcfs = []
 
     # Hard-code genome reference for Caris VCFs
@@ -40,6 +64,17 @@ def extract_sv(prefix, include_somatic: bool, include_germline: bool):
             }
         )
 
+    if not vcfs and include_empty:
+        create_empty_vcf_zip(prefix)
+        vcfs.append(
+            {
+                "fileName": f".lifeomic/caris/{prefix}/{prefix}.modified.somatic.nrm.filtered.vcf.gz",
+                "sequenceType": "somatic",
+                "type": "shortVariant",
+                "reference": genome_reference,
+            }
+        )
+
     return vcfs
 
 

{phc-ingestion-0.8.37 → phc-ingestion-0.8.38}/ingestion/foundation/util/vcf_etl.py

@@ -1,6 +1,5 @@
 import gzip
 import xmltodict
-from natsort import natsorted
 from logging import Logger
 import re
 import os

{phc-ingestion-0.8.37 → phc-ingestion-0.8.38}/pyproject.toml

@@ -1,19 +1,20 @@
 [project]
 name = "phc-ingestion"
-version = "0.8.37"
+version = "0.8.38"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },
 ]
 dependencies = [
     "lifeomic-logging>=0.3.2,<0.4.0",
-    "xmltodict==0.13.0",
+    "xmltodict>=0.14.2",
     "natsort==7.1.1",
     "ruamel.yaml==0.17.21",
-    "pandas>=1.5.0,<1.6.0",
+    "pandas>=2.2.3",
     "jsonschema>=4.16.0,<5.0.0",
     "schema>=0.7.5",
     "packaging>=23.1",
+    "numpy>=2.1.2",
 ]
 requires-python = ">=3.11"
 readme = "PYPI.md"