Merge pull request #49 from ImageMarkup/deprecate-diagnosis-specific-fields

Deprecate nevus_type/mel_class/mel_type

Author: danlamanna

isic_metadata/metadata.py

@@ -370,26 +370,11 @@ def validate_no_benign_melanoma(self) -> MetadataRow:
 
         return self
 
-    @model_validator(mode="after")
-    def validate_non_nevus_diagnoses(self) -> MetadataRow:
-        if not self.nevus_type:
-            return self
-
-        if not self.diagnosis:
-            raise error_missing_field("nevus_type", "diagnosis")
-
-        if not DiagnosisEnum.is_nevus(self.diagnosis):
-            raise error_incompatible_fields("nevus_type", "diagnosis", field2_value=self.diagnosis)
-
-        return self
-
     @model_validator(mode="after")
     def validate_melanoma_fields(self) -> MetadataRow:
         melanoma_fields: list[str] = [
-            "mel_class",
             "mel_mitotic_index",
             "mel_thick_mm",
-            "mel_type",
             "mel_ulcer",
         ]
 

tests/test_dependent_fields.py

@@ -23,25 +23,12 @@ def test_diagnosis_no_malignant_nevus(benign_malignant: str):
     assert " is incompatible with benign_malignant" in excinfo.value.errors()[0]["msg"]
 
 
-@pytest.mark.parametrize(
-    ("diagnosis", "error_message"),
-    [(None, "requires setting diagnosis"), ("Melanoma Invasive", "is incompatible with diagnosis")],
-)
-def test_nevus_type_needs_nevus_diagnosis(diagnosis: str | None, error_message: str):
-    with pytest.raises(ValidationError) as excinfo:
-        MetadataRow.model_validate({"diagnosis": diagnosis, "nevus_type": "spitz"})
-    assert len(excinfo.value.errors()) == 1
-    assert f"nevus_type {error_message}" in excinfo.value.errors()[0]["msg"]
-
-
 @pytest.mark.parametrize("diagnosis", [None, "Basal cell carcinoma"])
 @pytest.mark.parametrize(
     ("field_name", "field_value"),
     [
-        ("mel_class", "melanoma in situ"),
         ("mel_mitotic_index", "4/mm^2"),
         ("mel_thick_mm", "4mm"),
-        ("mel_type", "nodular melanoma"),
         ("mel_ulcer", True),
     ],
 )

tests/test_fields.py

@@ -37,7 +37,7 @@ def test_non_str_types(
 
 @pytest.mark.parametrize(("emptyish_value"), ["", " ", "\t", None])
 def test_empty_fields_are_omitted(emptyish_value: Any):
-    metadata = MetadataRow.model_validate({"diagnosis": "Benign", "mel_type": emptyish_value})
+    metadata = MetadataRow.model_validate({"diagnosis": "Benign", "mel_ulcer": emptyish_value})
     assert metadata.diagnosis == "Benign"
     assert metadata.mel_thick_mm is None
 
@@ -51,13 +51,13 @@ def test_unstructured_fields():
 @pytest.mark.parametrize(("melanoma_diagnosis"), DiagnosisEnum._melanoma_diagnoses())
 def test_melanoma_fields(melanoma_diagnosis: str):
     with pytest.raises(ValidationError) as excinfo:
-        # mel_class can only be set if diagnosis is melanoma
-        MetadataRow.model_validate({"diagnosis": "Benign", "mel_class": "invasive melanoma"})
+        # mel_ulcer can only be set if diagnosis is melanoma
+        MetadataRow.model_validate({"diagnosis": "Benign", "mel_ulcer": True})
     assert len(excinfo.value.errors()) == 1
-    assert "mel_class is incompatible with diagnosis" in excinfo.value.errors()[0]["msg"]
+    assert "mel_ulcer is incompatible with diagnosis" in excinfo.value.errors()[0]["msg"]
 
-    # mel_class can only be set if diagnosis is melanoma
-    MetadataRow.model_validate({"diagnosis": melanoma_diagnosis, "mel_class": "invasive melanoma"})
+    # mel_ulcer can only be set if diagnosis is melanoma
+    MetadataRow.model_validate({"diagnosis": melanoma_diagnosis, "mel_ulcer": True})
 
 
 @given(age=st.integers(min_value=0).map(str))
@@ -79,11 +79,6 @@ def test_benign_malignant():
     MetadataRow.model_validate({"benign_malignant": "benign"})
 
 
-@pytest.mark.parametrize(("nevus_diagnosis"), DiagnosisEnum._nevus_diagnoses())
-def test_nevus_diagnosis(nevus_diagnosis: str):
-    MetadataRow.model_validate({"diagnosis": nevus_diagnosis, "nevus_type": "blue"})
-
-
 @pytest.mark.parametrize(
     ("raw", "parsed"),
     [

tests/test_hierarchical_diagnosis.py

@@ -52,15 +52,15 @@ def test_single_value_diagnosis_is_favored():
     with pytest.raises(ValidationError) as excinfo:
         MetadataRow.model_validate(
             {
-                "diagnosis": "Melanoma Invasive",
-                "nevus_type": "blue",
+                "diagnosis": "Fibroma, Sclerotic",
+                "mel_ulcer": True,
                 # these should be ignored
                 "diagnosis_1": "Benign",
                 "diagnosis_2": "Benign melanocytic proliferations",
                 "diagnosis_3": "Nevus",
             }
         )
-    assert "Setting nevus_type is incompatible with diagnosis" in excinfo.value.errors()[0]["msg"]
+    assert "Setting mel_ulcer is incompatible with diagnosis" in excinfo.value.errors()[0]["msg"]
 
 
 def test_diagnosis_multiple_levels_is_coerced():