add injection and test

src/nwbinspector/nwbinspector.py

@@ -604,6 +604,32 @@ def inspect_nwbfile(
             )
 
 
+def _intercept_in_vitro(nwbfile_object: pynwb.NWBFile, checks: Optional[list] = None) -> List[callable]:
+    """If the special 'in_vitro' subject_id is specified, return a truncated list of checks to run."""
+    subject_related_check_names = [
+        "check_subject_exists",
+        "check_subject_id_exists",
+        "check_subject_sex",
+        "check_subject_species_exists",
+        "check_subject_species_form",
+        "check_subject_age",
+        "check_subject_proper_age_range",
+    ]
+    subject_related_dandi_requirements = [
+        check.importance == Importance.CRITICAL for check in checks if check.__name__ in subject_related_check_names
+    ]
+
+    subject = getattr(nwbfile_object, "subject", None)
+    if (
+        any(subject_related_dandi_requirements)
+        and subject is not None
+        and getattr(subject, "subject_id", "") == "in_vitro"
+    ):
+        non_subject_checks = [check for check in checks if check.__name__ not in subject_related_check_names]
+        return non_subject_checks
+    return checks
+
+
 def inspect_nwbfile_object(
     nwbfile_object: pynwb.NWBFile,
     checks: Optional[list] = None,
@@ -651,7 +677,9 @@ def inspect_nwbfile_object(
             checks=checks, config=config, ignore=ignore, select=select, importance_threshold=importance_threshold
         )
 
-    for inspector_message in run_checks(nwbfile=nwbfile_object, checks=checks):
+    subject_dependent_checks = _intercept_in_vitro(nwbfile_object=nwbfile_object, checks=checks)
+
+    for inspector_message in run_checks(nwbfile=nwbfile_object, checks=subject_dependent_checks):
         yield inspector_message
 
 

tests/test_inspector.py

@@ -1,12 +1,12 @@
 import os
-import pytest
 from shutil import rmtree
 from tempfile import mkdtemp
 from pathlib import Path
 from unittest import TestCase
 from datetime import datetime
 
 import numpy as np
+import pynwb
 from pynwb import NWBFile, NWBHDF5IO, TimeSeries
 from pynwb.file import TimeIntervals
 from pynwb.behavior import SpatialSeries, Position
@@ -22,7 +22,7 @@
     check_subject_exists,
     load_config,
 )
-from nwbinspector import inspect_all, inspect_nwbfile, available_checks
+from nwbinspector import inspect_all, inspect_nwbfile, inspect_nwbfile_object, available_checks
 from nwbinspector.register_checks import Severity, InspectorMessage, register_check
 from nwbinspector.tools import make_minimal_nwbfile
 from nwbinspector.utils import FilePathType
@@ -727,3 +727,18 @@ def test_check_unique_identifiers_fail(self):
                 file_path=str(self.tempdir),
             )
         ]
+
+
+def test_dandi_config_in_vitro_injection():
+    """Test that a special subject_id of 'in_vitro' properly excludes meaningless CRITICAL-elevated subject checks."""
+    nwbfile = pynwb.testing.mock.file.mock_NWBFile(
+        subject=pynwb.file.Subject(
+            subject_id="in_vitro", description="A detailed description about the in vitro setup."
+        )
+    )
+    config = load_config(filepath_or_keyword="dandi")
+    importance_threshold = "CRITICAL"
+    messages = list(
+        inspect_nwbfile_object(nwbfile_object=nwbfile, config=config, importance_threshold=importance_threshold)
+    )
+    assert messages == []