Merge pull request #144 from NeurodataWithoutBorders/fix_session_start_time_bug

[Bug]: session_start_time not readable

Author: CodyCBakerPhD

nwbinspector/__init__.py

@@ -6,3 +6,4 @@
 from .checks.time_series import *
 from .checks.tables import *
 from .checks.ecephys import *
+from .checks.ogen import *

nwbinspector/nwbinspector.py

@@ -276,7 +276,6 @@ def inspect_all(
         importlib.import_module(module)
     # Filtering of checks should apply after external modules are imported, in case those modules have their own checks
     checks = configure_checks(config=config, ignore=ignore, select=select, importance_threshold=importance_threshold)
-
     if n_jobs != 1:
 
         # max_workers for threading is a different concept to number of processes; from the documentation

nwbinspector/register_checks.py

@@ -6,6 +6,17 @@
 from typing import Optional
 
 import h5py
+from pynwb import NWBFile
+from pynwb.file import Subject
+from pynwb.ecephys import Device, ElectrodeGroup
+
+KNOWN_LOCATIONS = {
+    NWBFile: "/",
+    Subject: "/subject",
+    Device: "/general/devices",
+    ElectrodeGroup: "/general/extracellular_ephys/",
+    # TODO: add ophys equivalents
+}
 
 
 class Importance(Enum):
@@ -71,7 +82,7 @@ class InspectorMessage:
     check_function_name: str = ""
     object_type: str = ""
     object_name: str = ""
-    location: str = ""
+    location: Optional[str] = None
     file_path: str = ""
 
 
@@ -154,7 +165,7 @@ def auto_parse(check_function, obj, result: Optional[InspectorMessage] = None):
         return auto_parsed_result
 
 
-def parse_location(neurodata_object) -> str:
+def parse_location(neurodata_object) -> Optional[str]:
     """Infer the human-readable path of the object within an NWBFile by tracing its parents."""
     if neurodata_object.parent is None:
         return "/"
@@ -165,22 +176,4 @@ def parse_location(neurodata_object) -> str:
         for field in neurodata_object.fields.values():
             if isinstance(field, h5py.Dataset):
                 return "/".join(field.parent.name.split("/")[:-1]) + "/"
-    try:
-        # General case for nested modules not containing Datasets
-        level = neurodata_object
-        level_names = []
-        while level.parent.name != "root":
-            level_names.append(level.parent.name)
-            level = level.parent
-        # Determine which field of the NWBFile contains the previous recent level
-        invalid_field_names = ["timestamps_reference_time", "session_start_time"]
-        possible_fields = level.parent.fields
-        for field_name in invalid_field_names:
-            if field_name in possible_fields:
-                possible_fields.pop(field_name)
-        for field_name, field in possible_fields.items():
-            if level.name in field:
-                level_names.append(field_name)
-        return "/" + "/".join(level_names[::-1]) + "/"
-    except Exception:
-        return ""
+    return KNOWN_LOCATIONS.get(type(neurodata_object))

tests/test_inspector.py

@@ -16,8 +16,11 @@
     check_regular_timestamps,
     check_data_orientation,
     check_timestamps_match_first_dimension,
+    check_session_start_time_old_date,
+    check_description,
+    available_checks,
 )
-from nwbinspector.nwbinspector import inspect_all, inspect_nwb, configure_checks
+from nwbinspector.nwbinspector import inspect_all, inspect_nwb
 from nwbinspector.register_checks import Severity, InspectorMessage, register_check
 from nwbinspector.utils import FilePathType
 from nwbinspector.tools import make_minimal_nwbfile
@@ -402,7 +405,6 @@ def iterable_check_function(table: DynamicTable):
                 check_function_name="iterable_check_function",
                 object_type="TimeIntervals",
                 object_name="test_table",
-                location="/acquisition/",
                 file_path=self.nwbfile_paths[0],
             ),
             InspectorMessage(
@@ -411,7 +413,6 @@ def iterable_check_function(table: DynamicTable):
                 check_function_name="iterable_check_function",
                 object_type="TimeIntervals",
                 object_name="test_table",
-                location="/acquisition/",
                 file_path=self.nwbfile_paths[0],
             ),
         ]

tests/unit_tests/test_ecephys.py

@@ -89,7 +89,6 @@ def test_check_electrical_series_wrong_dims(self):
             check_function_name="check_electrical_series_dims",
             object_type="ElectricalSeries",
             object_name="elec_series",
-            location="/acquisition/",
         )
 
     def test_check_electrical_series_flipped(self):
@@ -112,7 +111,6 @@ def test_check_electrical_series_flipped(self):
             check_function_name="check_electrical_series_dims",
             object_type="ElectricalSeries",
             object_name="elec_series",
-            location="/acquisition/",
         )
 
     def test_pass(self):
@@ -138,7 +136,6 @@ def test_trigger_check_electrical_series_reference_electrodes_table(self):
         dyn_tab.add_column("name", "desc")
         for i in range(5):
             dyn_tab.add_row(name=1)
-
         dynamic_table_region = DynamicTableRegion(
             name="electrodes", description="I am wrong", data=[0, 1, 2, 3, 4], table=dyn_tab
         )

tests/unit_tests/test_nwbfile_metadata.py

@@ -204,7 +204,7 @@ def test_check_subject_sex():
         check_function_name="check_subject_sex",
         object_type="Subject",
         object_name="subject",
-        location="",
+        location="/subject",
     )
 
 

tests/unit_tests/test_ophys.py

@@ -11,7 +11,7 @@
     check_roi_response_series_dims,
     check_roi_response_series_link_to_plane_segmentation,
 )
-from nwbinspector.register_checks import InspectorMessage, Importance, Severity
+from nwbinspector.register_checks import InspectorMessage, Importance
 
 
 class TestCheckRoiResponseSeries(TestCase):
@@ -84,7 +84,6 @@ def test_check_flipped_dims(self):
             check_function_name="check_roi_response_series_dims",
             object_type="RoiResponseSeries",
             object_name="RoiResponseSeries",
-            location="/processing/ophys/",
         )
 
     def test_check_wrong_dims(self):
@@ -110,7 +109,6 @@ def test_check_wrong_dims(self):
             check_function_name="check_roi_response_series_dims",
             object_type="RoiResponseSeries",
             object_name="RoiResponseSeries",
-            location="/processing/ophys/",
         )
 
     def test_pass_check_roi_response_series_dims(self):
@@ -134,7 +132,6 @@ def test_check_roi_response_series_link_to_plane_segmentation(self):
         dt.add_column("a", "desc")
         for _ in range(5):
             dt.add_row(a=1)
-
         dtr = DynamicTableRegion(name="n", description="desc", data=[0, 1, 2, 3, 4], table=dt)
         roi_resp_series = RoiResponseSeries(
             name="RoiResponseSeries",
@@ -152,7 +149,6 @@ def test_check_roi_response_series_link_to_plane_segmentation(self):
             check_function_name="check_roi_response_series_link_to_plane_segmentation",
             object_type="RoiResponseSeries",
             object_name="RoiResponseSeries",
-            location="/processing/ophys/",
         )
 
     def test_pass_check_roi_response_series_link_to_plane_segmentation(self):