phc-ingestion 0.10.14__py3-none-any.whl → 0.10.15__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"):

{phc_ingestion-0.10.14.dist-info → phc_ingestion-0.10.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.14
+Version: 0.10.15
 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-0.10.15.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
@@ -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-0.10.15.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.15.dist-info/METADATA,sha256=WKlso7yXse4-3pnboF_klLG79ocyMFhai3l0HLZ0xHA,678
+phc_ingestion-0.10.15.dist-info/RECORD,,