Merge pull request #204 from NeurodataWithoutBorders/fix_try_except_pynwb_validation

[Bug] encapsulate nwbfile after io.read() in same try/except

Author: CodyCBakerPhD

nwbinspector/nwbinspector.py

@@ -455,29 +455,29 @@ def inspect_nwb(
     filterwarnings(action="ignore", message="No cached namespaces found in .*")
     filterwarnings(action="ignore", message="Ignoring cached namespace .*")
     with pynwb.NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True, driver=driver) as io:
-        if skip_validate:
+        if not skip_validate:
             validation_errors = pynwb.validate(io=io)
-            if any(validation_errors):
-                for validation_error in validation_errors:
-                    yield InspectorMessage(
-                        message=validation_error.reason,
-                        importance=Importance.PYNWB_VALIDATION,
-                        check_function_name=validation_error.name,
-                        location=validation_error.location,
-                        file_path=nwbfile_path,
-                    )
+            for validation_error in validation_errors:
+                yield InspectorMessage(
+                    message=validation_error.reason,
+                    importance=Importance.PYNWB_VALIDATION,
+                    check_function_name=validation_error.name,
+                    location=validation_error.location,
+                    file_path=nwbfile_path,
+                )
+
         try:
             nwbfile = io.read()
+            for inspector_message in run_checks(nwbfile=nwbfile, checks=checks):
+                inspector_message.file_path = nwbfile_path
+                yield inspector_message
         except Exception as ex:
             yield InspectorMessage(
                 message=traceback.format_exc(),
                 importance=Importance.ERROR,
-                check_function_name=f"{type(ex)}: {str(ex)}",
+                check_function_name=f"During io.read() - {type(ex)}: {str(ex)}",
                 file_path=nwbfile_path,
             )
-        for inspector_message in run_checks(nwbfile, checks=checks):
-            inspector_message.file_path = nwbfile_path
-            yield inspector_message
 
 
 def run_checks(nwbfile: pynwb.NWBFile, checks: list):