Merge pull request #44 from ImageMarkup/add-anatom-site-special

Author: danlamanna

isic_metadata/fields.py

@@ -191,6 +191,15 @@ class AnatomSiteGeneralEnum(str, Enum):
     oral_genital = "oral/genital"
 
 
+class AnatomSiteSpecialEnum(str, Enum):
+    acral_nos = "acral NOS"
+    nail_nos = "nail NOS"
+    fingernail = "fingernail"
+    toenail = "toenail"
+    acral_palms_soles = "acral palms or soles"
+    oral_genital = "oral or genital"
+
+
 class ColorTintEnum(str, Enum):
     blue = "blue"
     pink = "pink"

isic_metadata/metadata.py

@@ -21,6 +21,7 @@
 from isic_metadata.fields import (
     Age,
     AnatomSiteGeneralEnum,
+    AnatomSiteSpecialEnum,
     BenignMalignantEnum,
     ClinSizeLongDiamMm,
     ColorTintEnum,
@@ -206,6 +207,7 @@ class MetadataRow(BaseModel):
     ) = None
     sex: Literal["male", "female"] | None = None
     anatom_site_general: AnatomSiteGeneralEnum | None = None
+    anatom_site_special: AnatomSiteSpecialEnum | None = None
     benign_malignant: BenignMalignantEnum | None = None
     diagnosis: (
         Annotated[
@@ -442,6 +444,57 @@ 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,
+            ],
+        }
+
+        if self.anatom_site_special.value not in valid_combinations:
+            return self
+
+        if self.anatom_site_general.value not in valid_combinations[self.anatom_site_special.value]:
+            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:

tests/test_fields.py

@@ -7,6 +7,7 @@
 import pytest
 
 from isic_metadata.diagnosis_hierarchical import DiagnosisEnum
+from isic_metadata.fields import AnatomSiteGeneralEnum
 from isic_metadata.metadata import MetadataRow, convert_errors
 
 
@@ -124,3 +125,45 @@ def test_clin_size_long_diam_mm_invalid():
         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"]),
+    ],
+)
+def test_anatom_site_special(anatom_site_special: str, anatom_site_general_values: list[str]):
+    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():
+    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"]