Merge branch 'dev' into fix_session_start_time_bug

Author: CodyCBakerPhD

nwbinspector/inspector_tools.py

@@ -3,12 +3,29 @@
 import sys
 from typing import Dict, List
 from pathlib import Path
-from natsort import natsorted
 from enum import Enum
+from datetime import datetime
+from platform import platform
+
+from natsort import natsorted
 
 from .register_checks import InspectorMessage
 from .utils import FilePathType
 
+try:
+    from importlib.metadata import version
+
+    inspector_version = version("nwbinspector")
+except ModuleNotFoundError:  # Remove the except clause when minimal supported version becomes 3.8
+    from pkg_resources import get_distribution
+
+    inspector_version = get_distribution("nwbinspector").version
+
+
+def get_report_header():
+    """Grab basic information from system at time of report generation."""
+    return dict(Timestamp=str(datetime.now().astimezone()), Platform=platform(), NWBInspector_version=inspector_version)
+
 
 def _sort_unique_values(unique_values: list, reverse: bool = False):
     """Technically, the 'set' method applies basic sorting to the unique contents, but natsort is more general."""

nwbinspector/nwbinspector.py

@@ -18,6 +18,7 @@
 
 from . import available_checks
 from .inspector_tools import (
+    get_report_header,
     organize_messages,
     format_organized_results_output,
     print_to_console,
@@ -201,8 +202,12 @@ def inspect_all_cli(
         )
     )
     if json_file_path is not None:
+        if Path(json_file_path).exists() and not overwrite:
+            raise FileExistsError(f"The file {json_file_path} already exists! Specify the '-o' flag to overwrite.")
         with open(file=json_file_path, mode="w") as fp:
-            json.dump(obj=messages, fp=fp, cls=InspectorOutputJSONEncoder)
+            json_report = dict(header=get_report_header(), messages=messages)
+            json.dump(obj=json_report, fp=fp, cls=InspectorOutputJSONEncoder)
+            print(f"{os.linesep*2}Report saved to {str(Path(json_file_path).absolute())}!{os.linesep}")
     if len(messages):
         organized_results = organize_messages(messages=messages, levels=["file_path", "importance"])
         formatted_results = format_organized_results_output(organized_results=organized_results)
@@ -342,6 +347,7 @@ def inspect_nwb(
         )
     nwbfile_path = str(nwbfile_path)
     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:
             validation_errors = pynwb.validate(io=io)