Map C. elegans sex XX/XO to hermaphrodite/male

dandi/consts.py

@@ -39,6 +39,8 @@
     "species",
     "strain",
     "subject_id",
+    # CElegansSubject of ndx-subjects fixes `sex` to "O" and keeps XX/XO here
+    "c_elegans_sex",
 )
 
 metadata_nwb_dandi_fields = ("cell_id", "slice_id", "tissue_sample_id", "probe_ids")

dandi/metadata/util.py

@@ -297,8 +297,31 @@ def timedelta2duration(delta: timedelta) -> str:
 }
 
 
+def _is_c_elegans(species: Any) -> bool:
+    """Whether NWB ``subject.species`` designates *Caenorhabditis elegans*"""
+    if not isinstance(species, str):
+        return False
+    species = species.strip().lower()
+    return (
+        species in ("c. elegans", "caenorhabditis elegans")
+        or species.startswith("caenorhabditis elegans ")
+        or species.endswith("/ncbitaxon_6239")
+    )
+
+
 def extract_sex(metadata: dict) -> models.SexType | None:
     value = metadata.get("sex", None)
+    c_elegans_sex = metadata.get("c_elegans_sex")
+    is_c_elegans = _is_c_elegans(metadata.get("species"))
+    if (
+        isinstance(c_elegans_sex, str)
+        and c_elegans_sex.strip().lower() in ("xx", "xo")
+        and (value is None or value.strip().lower() in ("", "o", "other"))
+    ):
+        # CElegansSubject of ndx-subjects records the sex there and fixes
+        # `sex` to "O"
+        value = c_elegans_sex
+        is_c_elegans = True
     if value is not None and value != "":
         value_orig = value.strip()
         value = value_orig.lower()
@@ -311,6 +334,14 @@ def extract_sex(metadata: dict) -> models.SexType | None:
         elif value == "hermaphrodite":
             value_id = "http://purl.obolibrary.org/obo/PATO_0001340"
             value = "Hermaphrodite"
+        elif value in ["xx", "xo"] and is_c_elegans:
+            # nwbinspector requires XX (hermaphrodite) or XO (male) for C. elegans
+            if value == "xx":
+                value_id = "http://purl.obolibrary.org/obo/PATO_0001340"
+                value = "Hermaphrodite"
+            else:
+                value_id = "http://purl.obolibrary.org/obo/PATO_0000384"
+                value = "Male"
         elif value in ["unknown", "u"]:
             value_id = None
             value = "Unknown"

dandi/tests/test_metadata.py

@@ -1199,6 +1199,79 @@ def test_extract_sex(sex: str, identifier: str | None, name: str) -> None:
     assert rec.name == name
 
 
+@pytest.mark.ai_generated
+@pytest.mark.parametrize(
+    "species",
+    [
+        "Caenorhabditis elegans",
+        "C. elegans",
+        "Caenorhabditis elegans - Roundworm",
+        "http://purl.obolibrary.org/obo/NCBITaxon_6239",
+    ],
+)
+@pytest.mark.parametrize(
+    "sex,identifier,name",
+    [
+        ("XX", "http://purl.obolibrary.org/obo/PATO_0001340", "Hermaphrodite"),
+        ("XO", "http://purl.obolibrary.org/obo/PATO_0000384", "Male"),
+        ("xo", "http://purl.obolibrary.org/obo/PATO_0000384", "Male"),
+    ],
+)
+def test_extract_sex_c_elegans(
+    species: str, sex: str, identifier: str, name: str
+) -> None:
+    # nwbinspector requires these chromosomal codes for C. elegans
+    rec = extract_sex({"sex": sex, "species": species})
+    assert rec is not None
+    assert str(rec.identifier) == identifier
+    assert rec.name == name
+
+
+@pytest.mark.ai_generated
+@pytest.mark.parametrize("sex", ["O", "other", None])
+@pytest.mark.parametrize(
+    "c_elegans_sex,identifier,name",
+    [
+        ("XX", "http://purl.obolibrary.org/obo/PATO_0001340", "Hermaphrodite"),
+        ("xo", "http://purl.obolibrary.org/obo/PATO_0000384", "Male"),
+    ],
+)
+def test_extract_sex_ndx_subjects_c_elegans(
+    sex: str | None, c_elegans_sex: str, identifier: str, name: str
+) -> None:
+    # CElegansSubject of ndx-subjects fixes `sex` to "O" and records the
+    # actual sex in `c_elegans_sex`
+    rec = extract_sex(
+        {
+            "sex": sex,
+            "c_elegans_sex": c_elegans_sex,
+            "species": "Caenorhabditis elegans",
+        }
+    )
+    assert rec is not None
+    assert str(rec.identifier) == identifier
+    assert rec.name == name
+
+
+@pytest.mark.ai_generated
+def test_extract_sex_c_elegans_sex_does_not_override_explicit_sex() -> None:
+    rec = extract_sex({"sex": "M", "c_elegans_sex": "XX"})
+    assert rec is not None
+    assert rec.name == "Male"
+
+
+@pytest.mark.ai_generated
+@pytest.mark.parametrize("species", [None, "Mus musculus", "Drosophila melanogaster"])
+@pytest.mark.parametrize("sex", ["XX", "XO"])
+def test_extract_sex_chromosomal_other_species(species: str | None, sex: str) -> None:
+    # outside of C. elegans, XX/XO do not unambiguously designate a sex
+    metadata = {"sex": sex}
+    if species is not None:
+        metadata["species"] = species
+    with pytest.raises(ValueError, match="Cannot interpret sex field"):
+        extract_sex(metadata)
+
+
 @pytest.mark.parametrize(
     "species",
     [