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Merged
danlamanna merged 1 commit into from
May 12, 2026
Merged

Remove anatom_site_general #74

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2 changes: 0 additions & 2 deletions isic_metadata/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
from isic_metadata.diagnosis_hierarchical import DiagnosisEnum
from isic_metadata.fields import (
Age,
AnatomSiteGeneralEnum,
AnatomSiteSpecialEnum,
ClinSizeLongDiamMm,
ColorTintEnum,
Expand All @@ -26,7 +25,6 @@
"FIELD_REGISTRY",
"Age",
"AnatomSiteEnum",
"AnatomSiteGeneralEnum",
"AnatomSiteSpecialEnum",
"ClinSizeLongDiamMm",
"ColorTintEnum",
Expand Down
11 changes: 0 additions & 11 deletions isic_metadata/fields.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,17 +137,6 @@ class MelMitoticIndexEnum(StrEnum):
gt_4 = ">4/mm^2"


class AnatomSiteGeneralEnum(StrEnum):
head_neck = "head/neck"
upper_extremity = "upper extremity"
lower_extremity = "lower extremity"
anterior_torso = "anterior torso"
posterior_torso = "posterior torso"
palms_soles = "palms/soles"
lateral_torso = "lateral torso"
oral_genital = "oral/genital"


class AnatomSiteSpecialEnum(StrEnum):
acral_nos = "acral NOS"
nail_nos = "nail NOS"
Expand Down
57 changes: 0 additions & 57 deletions isic_metadata/metadata.py
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Expand Up @@ -22,7 +22,6 @@
from isic_metadata.diagnosis_hierarchical import DiagnosisEnum
from isic_metadata.fields import (
Age,
AnatomSiteGeneralEnum,
AnatomSiteSpecialEnum,
ClinSizeLongDiamMm,
ColorTintEnum,
Expand Down Expand Up @@ -194,7 +193,6 @@ class MetadataRow(BaseModel):
| None
) = None
sex: Literal["male", "female"] | None = None
anatom_site_general: AnatomSiteGeneralEnum | None = None
anatom_site_special: AnatomSiteSpecialEnum | None = None
anatom_site: (
Annotated[
Expand Down Expand Up @@ -374,7 +372,6 @@ def strip[T](cls, v: T) -> T | None:
return None if v == "" else v

@field_validator(
"anatom_site_general",
"clin_size_long_diam_mm",
"diagnosis_confirm_type",
"mel_mitotic_index",
Expand Down Expand Up @@ -447,60 +444,6 @@ def validate_dermoscopic_fields(self) -> MetadataRow:

return self

@model_validator(mode="after")
def validate_anatom_site_special(self) -> MetadataRow:
if not self.anatom_site_special:
return self

if not self.anatom_site_general:
raise _error_missing_field("anatom_site_special", "anatom_site_general")

valid_combinations = {
AnatomSiteSpecialEnum.acral_nos: [
AnatomSiteGeneralEnum.upper_extremity,
AnatomSiteGeneralEnum.lower_extremity,
AnatomSiteGeneralEnum.palms_soles,
],
AnatomSiteSpecialEnum.nail_nos: [
AnatomSiteGeneralEnum.upper_extremity,
AnatomSiteGeneralEnum.lower_extremity,
AnatomSiteGeneralEnum.palms_soles,
],
AnatomSiteSpecialEnum.fingernail: [
AnatomSiteGeneralEnum.upper_extremity,
AnatomSiteGeneralEnum.palms_soles,
],
AnatomSiteSpecialEnum.toenail: [
AnatomSiteGeneralEnum.lower_extremity,
AnatomSiteGeneralEnum.palms_soles,
],
AnatomSiteSpecialEnum.acral_palms_soles: [
AnatomSiteGeneralEnum.upper_extremity,
AnatomSiteGeneralEnum.lower_extremity,
AnatomSiteGeneralEnum.palms_soles,
],
AnatomSiteSpecialEnum.oral_genital: [
AnatomSiteGeneralEnum.head_neck,
AnatomSiteGeneralEnum.oral_genital,
AnatomSiteGeneralEnum.lower_extremity,
AnatomSiteGeneralEnum.anterior_torso,
AnatomSiteGeneralEnum.posterior_torso,
],
}

if self.anatom_site_special not in valid_combinations:
return self

if self.anatom_site_general not in valid_combinations[self.anatom_site_special]:
raise _error_incompatible_fields(
"anatom_site_special",
"anatom_site_general",
self.anatom_site_special.value,
self.anatom_site_general.value,
)

return self

@model_validator(mode="after")
def validate_tbp_tile_fields(self) -> MetadataRow:
if not self.tbp_tile_type:
Expand Down
6 changes: 0 additions & 6 deletions isic_metadata/registry.py
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Expand Up @@ -46,7 +46,6 @@ class Field:
"dermoscopic_type",
"tbp_tile_type",
"mel_mitotic_index",
"anatom_site_general",
"anatom_site_special",
"color_tint",
"patient_id",
Expand Down Expand Up @@ -201,8 +200,3 @@ class Field:
FIELD_REGISTRY[field].type = "acquisition"
else:
FIELD_REGISTRY[field].type = "clinical"

for field, label in [
("anatom_site_general", "Anatomic Site"),
]:
FIELD_REGISTRY[field].label = label
48 changes: 0 additions & 48 deletions tests/test_fields.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
import pytest

from isic_metadata.diagnosis_hierarchical import DiagnosisEnum
from isic_metadata.fields import AnatomSiteGeneralEnum
from isic_metadata.metadata import MetadataRow, convert_errors


Expand Down Expand Up @@ -118,50 +117,3 @@ def test_clin_size_long_diam_mm_invalid() -> None:
MetadataRow.model_validate({"clin_size_long_diam_mm": "foo"})
assert len(excinfo.value.errors()) == 1
assert "Unable to parse value as a number" in convert_errors(excinfo.value)[0]["msg"]


@pytest.mark.parametrize(
("anatom_site_special", "anatom_site_general_values"),
[
("acral NOS", ["upper extremity", "lower extremity", "palms/soles"]),
("nail NOS", ["upper extremity", "lower extremity", "palms/soles"]),
("fingernail", ["upper extremity", "palms/soles"]),
("toenail", ["lower extremity", "palms/soles"]),
("acral palms or soles", ["upper extremity", "lower extremity", "palms/soles"]),
(
"oral or genital",
["head/neck", "oral/genital", "lower extremity", "anterior torso", "posterior torso"],
),
],
)
def test_anatom_site_special(
anatom_site_special: str, anatom_site_general_values: list[str]
) -> None:
for anatom_site_general_value in anatom_site_general_values:
metadata = MetadataRow.model_validate(
{
"anatom_site_special": anatom_site_special,
"anatom_site_general": anatom_site_general_value,
}
)
assert metadata.anatom_site_special == anatom_site_special
assert metadata.anatom_site_general == anatom_site_general_value

for invalid_anatom_site_general in AnatomSiteGeneralEnum:
if invalid_anatom_site_general.value not in anatom_site_general_values:
with pytest.raises(ValidationError) as excinfo:
MetadataRow.model_validate(
{
"anatom_site_special": anatom_site_special,
"anatom_site_general": invalid_anatom_site_general.value,
}
)
assert len(excinfo.value.errors()) == 1
assert "is incompatible with anatom_site_general" in excinfo.value.errors()[0]["msg"]


def test_anatom_site_special_requires_anatom_site_general() -> None:
with pytest.raises(ValidationError) as excinfo:
MetadataRow.model_validate({"anatom_site_special": "acral NOS"})
assert len(excinfo.value.errors()) == 1
assert "requires setting anatom_site_general" in excinfo.value.errors()[0]["msg"]
23 changes: 0 additions & 23 deletions tests/test_hierarchical_anatom_site.py
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Expand Up @@ -110,29 +110,6 @@ def test_anatom_site_validation_is_idempotent() -> None:
assert metadata == metadata_2


def test_anatom_site_general_and_special_unaffected() -> None:
metadata = MetadataRow.model_validate(
{
"anatom_site_general": "head/neck",
"anatom_site_special": "oral or genital",
}
)
assert metadata.anatom_site_general == "head/neck"
assert metadata.anatom_site_special == "oral or genital"


def test_anatom_site_general_coexists_with_hierarchical() -> None:
metadata = MetadataRow.model_validate(
{
"anatom_site_general": "head/neck",
"anatom_site": "Head and neck:Head:Scalp",
}
)
assert metadata.anatom_site_general == "head/neck"
assert metadata.anatom_site_1 == "Head and neck"
assert metadata.anatom_site_3 == "Scalp"


def test_invalid_anatom_site_raises_error() -> None:
with pytest.raises(ValidationError):
MetadataRow.model_validate({"anatom_site": "Not a real site"})