Accept C. elegans sex from ndx-subjects' c_elegans_sex

changelog_entries/774.fix.md

@@ -0,0 +1 @@
+Fixed `check_subject_sex` flagging C. elegans subjects stored as `CElegansSubject` of ndx-subjects, which fixes `sex` to `"O"` and records `XX` (hermaphrodite) or `XO` (male) in `c_elegans_sex`. `sex` `"O"` or unset is now accepted when `c_elegans_sex` is `XX` or `XO`.

docs/best_practices/nwbfile_metadata.rst

@@ -231,6 +231,8 @@ The ``sex`` of the :ref:`nwb-schema:sec-Subject` should be specified as a single
 following four possibilities: "M" (male), "F" (female), "U" (unknown), or "O" (other, for asexual species).
 
 C. elegans are an exception to this rule. For C. elegans, the sex should either be "XO" (male) or "XX" (hermaphrodite).
+The ``CElegansSubject`` type of the `ndx-subjects <https://github.com/catalystneuro/ndx-subjects>`_ extension
+fixes ``sex`` to "O" and records "XO" or "XX" in its ``c_elegans_sex`` field instead, which is also accepted.
 
 Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_sex`
 

src/nwbinspector/checks/_nwbfile_metadata.py

@@ -334,7 +334,12 @@ def _check_subject_sex_defaults(sex: str) -> Optional[InspectorMessage]:
 def _check_subject_sex_c_elegans(sex: str) -> Optional[InspectorMessage]:
     """Check if the subject sex has been specified properly for the C. elegans species."""
     if sex not in ("XO", "XX"):
-        return InspectorMessage(message="For C. elegans, Subject.sex should be 'XO' (male) or 'XX' (hermaphrodite).")
+        return InspectorMessage(
+            message=(
+                "For C. elegans, Subject.sex should be 'XO' (male) or 'XX' (hermaphrodite), "
+                "or 'O' with 'XO' or 'XX' in `c_elegans_sex` (CElegansSubject of ndx-subjects)."
+            )
+        )
 
     return None
 
@@ -346,6 +351,10 @@ def check_subject_sex(subject: Subject) -> Optional[InspectorMessage]:
 
     Best Practice: :ref:`best_practice_subject_sex`
     """
+    # CElegansSubject of the ndx-subjects extension fixes `sex` to "O" and records
+    # XX (hermaphrodite) or XO (male) in a separate `c_elegans_sex` field
+    if getattr(subject, "c_elegans_sex", None) in ("XO", "XX") and subject.sex in (None, "", "O"):
+        return None
     if subject and not subject.sex:
         return InspectorMessage(message="Subject.sex is missing.")
     if subject.species in ("Caenorhabditis elegans", "C. elegans"):

tests/unit_tests/test_nwbfile_metadata.py

@@ -413,7 +413,10 @@ def test_check_subject_sex_caenorhabditis_elegans_default_sex():
     subject = Subject(subject_id="001", species="Caenorhabditis elegans", sex="F")
 
     assert check_subject_sex(subject=subject) == InspectorMessage(
-        message="For C. elegans, Subject.sex should be 'XO' (male) or 'XX' (hermaphrodite).",
+        message=(
+            "For C. elegans, Subject.sex should be 'XO' (male) or 'XX' (hermaphrodite), "
+            "or 'O' with 'XO' or 'XX' in `c_elegans_sex` (CElegansSubject of ndx-subjects)."
+        ),
         importance=Importance.CRITICAL,
         check_function_name="check_subject_sex",
         object_type="Subject",
@@ -426,7 +429,10 @@ def test_check_subject_sex_c_elegans_default_sex():
     subject = Subject(subject_id="001", species="C. elegans", sex="F")
 
     assert check_subject_sex(subject=subject) == InspectorMessage(
-        message="For C. elegans, Subject.sex should be 'XO' (male) or 'XX' (hermaphrodite).",
+        message=(
+            "For C. elegans, Subject.sex should be 'XO' (male) or 'XX' (hermaphrodite), "
+            "or 'O' with 'XO' or 'XX' in `c_elegans_sex` (CElegansSubject of ndx-subjects)."
+        ),
         importance=Importance.CRITICAL,
         check_function_name="check_subject_sex",
         object_type="Subject",
@@ -447,6 +453,38 @@ def test_check_subject_sex_c_elegans_xx_sex():
     assert check_subject_sex(subject) is None
 
 
+class _CElegansSubject(Subject):
+    """Stand-in for CElegansSubject of ndx-subjects, which adds a ``c_elegans_sex`` field."""
+
+    def __init__(self, c_elegans_sex=None, **kwargs):
+        super().__init__(**kwargs)
+        self.c_elegans_sex = c_elegans_sex
+
+
+@pytest.mark.parametrize("sex", ["O", None])
+@pytest.mark.parametrize("c_elegans_sex", ["XX", "XO"])
+def test_check_subject_sex_c_elegans_ndx_subjects(sex, c_elegans_sex):
+    subject = _CElegansSubject(subject_id="001", species="Caenorhabditis elegans", sex=sex, c_elegans_sex=c_elegans_sex)
+
+    assert check_subject_sex(subject) is None
+
+
+def test_check_subject_sex_c_elegans_ndx_subjects_invalid():
+    subject = _CElegansSubject(subject_id="001", species="Caenorhabditis elegans", sex="O", c_elegans_sex="F")
+
+    assert check_subject_sex(subject=subject) == InspectorMessage(
+        message=(
+            "For C. elegans, Subject.sex should be 'XO' (male) or 'XX' (hermaphrodite), "
+            "or 'O' with 'XO' or 'XX' in `c_elegans_sex` (CElegansSubject of ndx-subjects)."
+        ),
+        importance=Importance.CRITICAL,
+        check_function_name="check_subject_sex",
+        object_type="_CElegansSubject",
+        object_name="subject",
+        location="/general/subject",
+    )
+
+
 def test_pass_check_subject_age_with_dob():
     subject = Subject(subject_id="001", sex="F", date_of_birth=datetime.now().astimezone())
     assert check_subject_age(subject) is None