Merge branch 'dev' into order_of_images

Author: CodyCBakerPhD

nwbinspector/nwbinspector.py

@@ -8,7 +8,7 @@
 from pathlib import Path
 from collections.abc import Iterable
 from enum import Enum
-from typing import Optional, List
+from typing import Union, Optional, List
 from concurrent.futures import ProcessPoolExecutor, as_completed
 from types import FunctionType
 from warnings import filterwarnings, warn
@@ -278,7 +278,7 @@ def inspect_all(
     config: Optional[dict] = None,
     ignore: OptionalListOfStrings = None,
     select: OptionalListOfStrings = None,
-    importance_threshold: Importance = Importance.BEST_PRACTICE_SUGGESTION,
+    importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
     n_jobs: int = 1,
     skip_validate: bool = False,
     progress_bar: bool = True,
@@ -305,7 +305,7 @@ def inspect_all(
         Names of functions to skip.
     select: list of strings, optional
         Names of functions to pick out of available checks.
-    importance_threshold : string, optional
+    importance_threshold : string or Importance, optional
         Ignores tests with an assigned importance below this threshold.
         Importance has three levels:
             CRITICAL
@@ -336,6 +336,9 @@ def inspect_all(
         Common options are 'draft' or 'published'.
         Defaults to the most recent published version, or if not published then the most recent draft version.
     """
+    importance_threshold = (
+        Importance[importance_threshold] if isinstance(importance_threshold, str) else importance_threshold
+    )
     modules = modules or []
     if progress_bar_options is None:
         progress_bar_options = dict(position=0, leave=False)
@@ -410,7 +413,7 @@ def inspect_nwb(
     config: dict = None,
     ignore: OptionalListOfStrings = None,
     select: OptionalListOfStrings = None,
-    importance_threshold: Importance = Importance.BEST_PRACTICE_SUGGESTION,
+    importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
     driver: str = None,
     skip_validate: bool = False,
 ) -> List[InspectorMessage]:
@@ -431,7 +434,7 @@ def inspect_nwb(
         Names of functions to skip.
     select: list, optional
         Names of functions to pick out of available checks.
-    importance_threshold : string, optional
+    importance_threshold : string or Importance, optional
         Ignores tests with an assigned importance below this threshold.
         Importance has three levels:
             CRITICAL
@@ -447,6 +450,9 @@ def inspect_nwb(
         Skip the PyNWB validation step. This may be desired for older NWBFiles (< schema version v2.10).
         The default is False, which is also recommended.
     """
+    importance_threshold = (
+        Importance[importance_threshold] if isinstance(importance_threshold, str) else importance_threshold
+    )
     if any(x is not None for x in [config, ignore, select, importance_threshold]):
         checks = configure_checks(
             checks=checks, config=config, ignore=ignore, select=select, importance_threshold=importance_threshold

tests/test_inspector.py

@@ -330,7 +330,7 @@ def test_inspect_nwb(self):
         ]
         self.assertCountEqual(first=test_results, second=true_results)
 
-    def test_inspect_nwb_importance_threshold(self):
+    def test_inspect_nwb_importance_threshold_as_importance(self):
         test_results = list(
             inspect_nwb(
                 nwbfile_path=self.nwbfile_paths[0], checks=self.checks, importance_threshold=Importance.CRITICAL
@@ -361,6 +361,35 @@ def test_inspect_nwb_importance_threshold(self):
         ]
         self.assertCountEqual(first=test_results, second=true_results)
 
+    def test_inspect_nwb_importance_threshold_as_string(self):
+        test_results = list(
+            inspect_nwb(nwbfile_path=self.nwbfile_paths[0], checks=self.checks, importance_threshold="CRITICAL")
+        )
+        true_results = [
+            InspectorMessage(
+                message=(
+                    "Data may be in the wrong orientation. Time should be in the first dimension, and is "
+                    "usually the longest dimension. Here, another dimension is longer."
+                ),
+                importance=Importance.CRITICAL,
+                check_function_name="check_data_orientation",
+                object_type="SpatialSeries",
+                object_name="my_spatial_series",
+                location="/processing/behavior/Position/my_spatial_series",
+                file_path=self.nwbfile_paths[0],
+            ),
+            InspectorMessage(
+                message="The length of the first dimension of data does not match the length of timestamps.",
+                importance=Importance.CRITICAL,
+                check_function_name="check_timestamps_match_first_dimension",
+                object_type="TimeSeries",
+                object_name="test_time_series_3",
+                location="/acquisition/test_time_series_3",
+                file_path=self.nwbfile_paths[0],
+            ),
+        ]
+        self.assertCountEqual(first=test_results, second=true_results)
+
     def test_command_line_runs_cli_only(self):
         console_output_file = self.tempdir / "test_console_output.txt"
         os.system(

tests/unit_tests/test_tables.py

@@ -1,6 +1,7 @@
 import platform
 import json
 from unittest import TestCase
+from packaging import version
 
 import numpy as np
 from hdmf.common import DynamicTable, DynamicTableRegion
@@ -17,6 +18,7 @@
     check_single_row,
     check_table_values_for_dict,
 )
+from nwbinspector.utils import get_package_version
 
 
 class TestCheckDynamicTableRegion(TestCase):
@@ -237,16 +239,27 @@ def test_check_single_row_ignore_electrodes():
     table = ElectrodeTable(
         name="electrodes",  # default name when building through nwbfile
     )
-    table.add_row(
-        x=np.nan,
-        y=np.nan,
-        z=np.nan,
-        imp=np.nan,
-        location="unknown",
-        filtering="unknown",
-        group=ElectrodeGroup(name="test_group", description="", device=Device(name="test_device"), location="unknown"),
-        group_name="test_group",
-    )
+    if get_package_version(name="pynwb") >= version.Version("2.1.0"):
+        table.add_row(
+            location="unknown",
+            group=ElectrodeGroup(
+                name="test_group", description="", device=Device(name="test_device"), location="unknown"
+            ),
+            group_name="test_group",
+        )
+    else:
+        table.add_row(
+            x=np.nan,
+            y=np.nan,
+            z=np.nan,
+            imp=np.nan,
+            location="unknown",
+            filtering="unknown",
+            group=ElectrodeGroup(
+                name="test_group", description="", device=Device(name="test_device"), location="unknown"
+            ),
+            group_name="test_group",
+        )
     assert check_single_row(table=table) is None