phc-ingestion 0.10.15__tar.gz → 0.10.17__tar.gz

{phc-ingestion-0.10.15 → phc-ingestion-0.10.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.15
+Version: 0.10.17
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.10.15 → phc-ingestion-0.10.17}/ingestion/foundation/util/cnv.py

@@ -42,13 +42,15 @@ def extract_copy_numbers(
     log.info("Extracting copy numbers from xml")
     copy_number_list: dict = {"CopyNumbers": []}
 
-    if "copy-number-alterations" in results_payload_dict["variant-report"].keys():
+    if (
+        "variant-report" in results_payload_dict
+        and "copy-number-alterations" in results_payload_dict["variant-report"].keys()
+    ):
         if (
             results_payload_dict["variant-report"]["copy-number-alterations"] is not None
             and "copy-number-alteration"
             in results_payload_dict["variant-report"]["copy-number-alterations"].keys()
         ):
-
             variants_dict = results_payload_dict["variant-report"]["copy-number-alterations"][
                 "copy-number-alteration"
             ]

{phc-ingestion-0.10.15 → phc-ingestion-0.10.17}/ingestion/foundation/util/fnv.py

@@ -67,7 +67,10 @@ def extract_fusion_variant(
     log.info("Extracting fusion variants from xml")
     fusion_variant_list: dict = {"FusionVariants": []}
 
-    if "rearrangements" in results_payload_dict["variant-report"].keys():
+    if (
+        "variant-report" in results_payload_dict
+        and "rearrangements" in results_payload_dict["variant-report"].keys()
+    ):
         if (
             results_payload_dict["variant-report"]["rearrangements"] is not None
             and "rearrangement" in results_payload_dict["variant-report"]["rearrangements"].keys()

{phc-ingestion-0.10.15 → phc-ingestion-0.10.17}/ingestion/foundation/util/vcf_etl.py

@@ -55,6 +55,9 @@ def get_xml_short_vars(xml_file: str, log):
         xml_short_vars = xml_dict["rr:ResultsReport"]["rr:ResultsPayload"]["variant-report"][
             "short-variants"
         ]["short-variant"]
+    except KeyError as e:
+        log.info(f"Missing key in XML structure for short variants: {str(e)}")
+        return vendsig_dict
     except TypeError:
         log.info("No short variants found in xml")
         return vendsig_dict

{phc-ingestion-0.10.15 → phc-ingestion-0.10.17}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.10.15"
+version = "0.10.17"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },