phc-ingestion 0.10.14__py3-none-any.whl → 0.10.16__py3-none-any.whl

ingestion/caris/util/ihc.py

@@ -121,9 +121,16 @@ def get_ihc_results(data, log) -> list[dict]:
                         )
                         trigger = True
                 if test_results.get("stainPercent"):
-                    if np.isnan(test_results["stainPercent"]) == False:
+                    try:
+                        stain_percent = float(test_results["stainPercent"])
+                        if np.isnan(stain_percent) == False:
+                            log.warning(
+                                f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                            )
+                            trigger = True
+                    except (ValueError, TypeError):
                         log.warning(
-                            f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                            f'IHC test {test_results["biomarkerName"]} has an invalid value for "stainPercent": "{test_results["stainPercent"]}"'
                         )
                         trigger = True
 
@@ -193,9 +200,16 @@ def get_ihc_results(data, log) -> list[dict]:
                     )
                     trigger = True
             if test_results.get("stainPercent"):
-                if np.isnan(test_results["stainPercent"]) == False:
+                try:
+                    stain_percent = float(test_results["stainPercent"])
+                    if not np.isnan(stain_percent):
+                        log.warning(
+                            f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                        )
+                        trigger = True
+                except (ValueError, TypeError):
                     log.warning(
-                        f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                        f'IHC test {test_results["biomarkerName"]} has an invalid value for "stainPercent": "{test_results["stainPercent"]}"'
                     )
                     trigger = True
             if test_results.get("threshold"):

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-0.10.14.dist-info → phc_ingestion-0.10.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.14
+Version: 0.10.16
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.10.14.dist-info → phc_ingestion-0.10.16.dist-info}/RECORD

@@ -5,7 +5,7 @@ ingestion/caris/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hS
 ingestion/caris/util/cnv.py,sha256=Nrc0aoG2k4tmrqHb69hAuXr0adDZIVVJRRjf9_sO91E,4441
 ingestion/caris/util/detect_genome_ref.py,sha256=MpiPa71QmlO3MWvjxPzNdbEHyOhorOcpQWWlwE5BO4c,1640
 ingestion/caris/util/hla.py,sha256=X_t6ngBRvmdG3m4I2_KnPFeWn3BaH-3IWHtOvDbS32A,770
-ingestion/caris/util/ihc.py,sha256=vegxudxHj7tLihrXGbEx_ptwkSsu3YCCB1nZVwoiYXg,12312
+ingestion/caris/util/ihc.py,sha256=1XfFJjvQq9E45cdPX4EPrg2VkXABxbMJP_BOgzA8z7g,13091
 ingestion/caris/util/interpretation.py,sha256=CghNurqeVA5VTBBorU8-ZTN-PVNPnR8wrmTwKCH3568,555
 ingestion/caris/util/json.py,sha256=aifO1hnZwNSS-ZtY20otyGbfIoc23w9HMWJ5D56lhFo,5020
 ingestion/caris/util/metadata.py,sha256=a6NToMtGtIRrlMd3CQwq4IRjGGmIiBA9JFwsATjNEoQ,10287
@@ -22,7 +22,7 @@ ingestion/foundation/util/cnv.py,sha256=YSKCaOBhjZDNXth_GxC-50crDURpTNCMefoHo0uO
 ingestion/foundation/util/fnv.py,sha256=-VstGsBKXM0duC-IpwUkektoTZ9yQUR0IQcDb1HibY0,5937
 ingestion/foundation/util/ga4gh.py,sha256=2oCTR9kvV5EeGZlrR35MfMkNL3nbeJYO88fo0NDDmRo,11304
 ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd8cU3I9YHD5fsXg,405
-ingestion/foundation/util/vcf_etl.py,sha256=ZBrX1XGRz-ymLUEiVcjjqmPZPb-AfD9On8UkZJDa1Dk,2133
+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
@@ -59,6 +59,6 @@ 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-0.10.14.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.14.dist-info/METADATA,sha256=eFtKLSIUt-CxYzOq3I9SsNeg_bb2jw6VByiE6mM0ZD8,678
-phc_ingestion-0.10.14.dist-info/RECORD,,
+phc_ingestion-0.10.16.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.16.dist-info/METADATA,sha256=93pAgQ-3MryemXhW8ucjSC0zGTcbq0tXciquL94S2tY,678
+phc_ingestion-0.10.16.dist-info/RECORD,,