phc-ingestion 0.10.14__tar.gz → 0.10.15__tar.gz

{phc-ingestion-0.10.14 → phc-ingestion-0.10.15}/PKG-INFO

@@ -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 → phc-ingestion-0.10.15}/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 → phc-ingestion-0.10.15}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.10.14"
+version = "0.10.15"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },