Add support for hierarchical anatomic site

isic/core/tests/test_metadata_download.py

@@ -15,6 +15,7 @@ def image_with_metadata(image):
         {
             "age": 32,
             "diagnosis": "Nevus",
+            "anatom_site": "Scalp",
             "patient_id": "supersecretpatientid",
             "lesion_id": "supersecretlesionid",
             "rcm_case_id": "supersecretrcmcaseid",
@@ -34,6 +35,9 @@ def test_image_metadata_csv_rows_correct(image_with_metadata):
     row = next(rows)
     assert row == {
         "age_approx": image_with_metadata.accession.age_approx,
+        "anatom_site_1": "Head and neck",
+        "anatom_site_2": "Head",
+        "anatom_site_3": "Scalp",
         "attribution": image_with_metadata.accession.attribution,
         "copyright_license": image_with_metadata.accession.copyright_license,
         "diagnosis_1": "Benign",
@@ -55,6 +59,9 @@ def test_staff_image_metadata_csv_rows_correct(image_with_metadata):
     assert row == {
         "age_approx": image_with_metadata.accession.age_approx,
         "age": image_with_metadata.accession.age,
+        "anatom_site_1": "Head and neck",
+        "anatom_site_2": "Head",
+        "anatom_site_3": "Scalp",
         "attribution": image_with_metadata.accession.attribution,
         "cohort_id": image_with_metadata.accession.cohort_id,
         "cohort": image_with_metadata.accession.cohort.name,

isic/core/tests/test_search.py

@@ -30,10 +30,12 @@ def searchable_images(image_factory, _search_index):
         image_factory(
             public=True,
             accession__short_diagnosis="melanoma",
+            accession__short_anatom_site="scalp",
         ),
         image_factory(
             public=False,
             accession__short_diagnosis="nevus",
+            accession__short_anatom_site="forearm",
         ),
     ]
     for image in images:
@@ -193,6 +195,14 @@ def test_core_api_image_search(searchable_images, staff_client):
     assert r.status_code == 200, r.json()
     assert r.json()["count"] == 1, r.json()
 
+    r = staff_client.get("/api/v2/images/search/", {"query": "anatom_site_3:Scalp"})
+    assert r.status_code == 200, r.json()
+    assert r.json()["count"] == 1, r.json()
+
+    r = staff_client.get("/api/v2/images/search/", {"query": 'anatom_site_1:"Upper extremity"'})
+    assert r.status_code == 200, r.json()
+    assert r.json()["count"] == 1, r.json()
+
 
 @pytest.mark.django_db
 def test_core_api_image_search_private_image(private_searchable_image, authenticated_client):
@@ -346,6 +356,16 @@ def test_core_api_image_faceting_structure(searchable_images, client):
         "present_count": 1,
     }, r.json()
 
+    assert len(r.json()["anatom_site_3"]["buckets"]) == 1, r.json()
+    assert r.json()["anatom_site_3"]["meta"] == {
+        "missing_count": 0,
+        "present_count": 1,
+    }, r.json()
+    assert r.json()["anatom_site_1"]["meta"] == {
+        "missing_count": 0,
+        "present_count": 1,
+    }, r.json()
+
 
 @pytest.mark.parametrize(
     "client_",

isic/core/tests/test_view_image_list.py

@@ -16,6 +16,7 @@ def test_image_list_metadata_download_view(mocker, staff_client, mailoutbox, use
             "patient_id": "bar",
             "rcm_case_id": "baz",
             "diagnosis": "Melanoma Invasive",
+            "anatom_site": "Scalp",
             "image_type": "RCM: macroscopic",
         },
         ignore_image_check=True,
@@ -41,6 +42,9 @@ def test_image_list_metadata_download_view(mocker, staff_client, mailoutbox, use
         "public",
         "age",
         "age_approx",
+        "anatom_site_1",
+        "anatom_site_2",
+        "anatom_site_3",
         "diagnosis_1",
         "diagnosis_2",
         "diagnosis_3",
@@ -67,6 +71,9 @@ def test_image_list_metadata_download_view(mocker, staff_client, mailoutbox, use
         image.public,
         "57",
         "55",
+        "Head and neck",
+        "Head",
+        "Scalp",
         "Malignant",
         "Malignant melanocytic proliferations (Melanoma)",
         "Melanoma Invasive",

isic/ingest/migrations/0036_add_anatom_site_hierarchical_fields.py

@@ -0,0 +1,39 @@
+# Generated by Django 5.2.3 on 2026-02-19 16:44
+
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("ingest", "0035_alter_distinctnessmeasure_checksum"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="accession",
+            name="anatom_site_1",
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name="accession",
+            name="anatom_site_2",
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name="accession",
+            name="anatom_site_3",
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name="accession",
+            name="anatom_site_4",
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name="accession",
+            name="anatom_site_5",
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+    ]

isic/ingest/models/accession.py

@@ -76,6 +76,11 @@ class AccessionMetadata(models.Model):
     sex = models.CharField(max_length=6, null=True, blank=True)
     anatom_site_general = models.CharField(max_length=255, null=True, blank=True)
     anatom_site_special = models.CharField(max_length=255, null=True, blank=True)
+    anatom_site_1 = models.CharField(max_length=255, null=True, blank=True)
+    anatom_site_2 = models.CharField(max_length=255, null=True, blank=True)
+    anatom_site_3 = models.CharField(max_length=255, null=True, blank=True)
+    anatom_site_4 = models.CharField(max_length=255, null=True, blank=True)
+    anatom_site_5 = models.CharField(max_length=255, null=True, blank=True)
     diagnosis_1 = models.CharField(max_length=255, null=True, blank=True)
     diagnosis_2 = models.CharField(max_length=255, null=True, blank=True)
     diagnosis_3 = models.CharField(max_length=255, null=True, blank=True)

isic/ingest/tests/factories.py

@@ -4,7 +4,7 @@
 
 import factory
 import factory.django
-from isic_metadata.fields import DiagnosisEnum
+from isic_metadata.fields import AnatomSiteEnum, DiagnosisEnum
 
 from isic.core.models import CopyrightLicense
 from isic.factories import UserFactory
@@ -182,6 +182,24 @@ def short_diagnosis(self, create: bool, extracted: Any, **kwargs: Any) -> None:
         if create:
             self.save()
 
+    @factory.post_generation
+    def short_anatom_site(self, create: bool, extracted: Any, **kwargs: Any) -> None:  # noqa: FBT001
+        if extracted is None:
+            return
+
+        if extracted == "scalp":
+            anatom_site = AnatomSiteEnum.head_and_neck_head_scalp
+        elif extracted == "forearm":
+            anatom_site = AnatomSiteEnum.upper_extremity_forearm
+        else:
+            raise ValueError(f"Unknown short_anatom_site: {extracted}")
+
+        for key, value in AnatomSiteEnum.as_dict(anatom_site).items():
+            setattr(self, key, value)
+
+        if create:
+            self.save()
+
 
 class AccessionReviewFactory(factory.django.DjangoModelFactory):
     class Meta:

isic/ingest/tests/test_metadata.py

@@ -397,6 +397,28 @@ def test_accession_update_metadata_iddx(user, imageless_accession) -> None:
     assert imageless_accession.metadata_versions.count() == 1
 
 
+@pytest.mark.django_db
+def test_accession_update_metadata_anatom_site(user, imageless_accession) -> None:
+    imageless_accession.update_metadata(user, {"anatom_site": "Scalp"})
+    assert imageless_accession.metadata == {
+        "anatom_site_1": "Head and neck",
+        "anatom_site_2": "Head",
+        "anatom_site_3": "Scalp",
+    }
+    assert imageless_accession.metadata_versions.count() == 1
+
+
+@pytest.mark.django_db
+def test_accession_remove_metadata_anatom_site(user, imageless_accession) -> None:
+    imageless_accession.update_metadata(user, {"anatom_site": "Scalp"})
+    imageless_accession.remove_metadata(user, ["anatom_site_3"])
+    assert imageless_accession.metadata == {
+        "anatom_site_1": "Head and neck",
+        "anatom_site_2": "Head",
+    }
+    assert imageless_accession.metadata_versions.count() == 2
+
+
 @pytest.mark.django_db
 def test_accession_update_metadata_idempotent(user, imageless_accession) -> None:
     imageless_accession.update_metadata(user, {"sex": "male", "foo": "bar", "baz": "qux"})

isic/ingest/utils/metadata.py

@@ -127,7 +127,15 @@ def validate_internal_consistency(
     return _validate_df_consistency(rows)
 
 
-def validate_archive_consistency(  # noqa: C901
+def _reassemble_hierarchical_fields(values: dict[str, Any]) -> None:
+    """Reassemble level fields (e.g. diagnosis_1..5) into colon-separated parent fields."""
+    for field_name in ["diagnosis", "anatom_site"]:
+        level_fields = [f"{field_name}_{i}" for i in range(1, 6) if f"{field_name}_{i}" in values]
+        if any(values[f] for f in level_fields):
+            values[field_name] = ":".join(values[f] for f in level_fields if values[f])
+
+
+def validate_archive_consistency(
     rows: csv.DictReader, cohort: Cohort
 ) -> tuple[ColumnRowErrors, list[Problem]]:
     """
@@ -173,13 +181,7 @@ def accession_values_to_metadata_dict(accession_values: dict[str, Any]) -> dict[
                     ]
                     del accession_values[f"{field.relation_name}__{field.internal_id_name}"]
 
-            diagnosis_fields = [
-                f"diagnosis_{i}" for i in range(1, 6) if f"diagnosis_{i}" in accession_values
-            ]
-            if any(accession_values[field] for field in diagnosis_fields):
-                accession_values["diagnosis"] = ":".join(
-                    accession_values[field] for field in diagnosis_fields if accession_values[field]
-                )
+            _reassemble_hierarchical_fields(accession_values)
 
             return {k: v for (k, v) in accession_values.items() if v is not None}
 

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
   "gdal",
   "google-analytics-data",
   "elasticsearch",
-  "isic-metadata",
+  "isic-metadata>=4.12.0",
   "jaro-winkler",
   "numpy",
   "pandas",