feat!: moa disease conflict resolution should follow therapy conflict…

… resolution

src/metakb/transformers/moa.py

@@ -497,6 +497,65 @@ def _get_therapeutic_substitute_group(
         :return: None, since not supported by MOA
         """
 
+    def _resolve_concept_discrepancy(
+        self,
+        cached_id: str,
+        cached_obj: MappableConcept,
+        cached_label: str,
+        moa_concept_label: str,
+        is_disease: bool = False,
+    ) -> None:
+        """Resolve conflict where MOA disease or therapy resolve to same normalized
+        concept
+
+        The min label will be used as the primary label for the mappable concept, and
+        the other label will be added as an alias in extensions.
+        The cache will be updated with updated object.
+        The cached object will be removed from ``self.processed_data``
+
+        :param cached_id: ID found in cache
+        :param cached_obj: Mappable concept found in cache for ``cached_id``. This will
+            be mutated
+        :param cached_label: Label for ``cached_obj``
+        :param moa_concept_label: MOA concept label
+        :param is_disease: ``True`` if ``cached_obj`` is a disease. ``False`` if
+            ``cached_obj`` is a therapy
+        """
+        logger.debug(
+            "MOA %s and %s resolve to same concept %s",
+            moa_concept_label,
+            cached_label,
+            cached_id,
+        )
+        alias = max(moa_concept_label, cached_label)
+        cached_obj.label = min(moa_concept_label, cached_label)
+        extensions = cached_obj.extensions or []
+
+        aliases_ext = next(
+            (ext for ext in extensions if ext.name == "aliases"),
+            None,
+        )
+        if aliases_ext:
+            if cached_obj.label in aliases_ext.value:
+                aliases_ext.value.remove(cached_obj.label)
+            aliases_ext.value.append(alias)
+        else:
+            extensions.append(Extension(name="aliases", value=[alias]))
+            cached_obj.extensions = extensions
+
+        if is_disease:
+            self.processed_data.conditions = [
+                c for c in self.processed_data.conditions if c.id != cached_obj.id
+            ]
+            cache = self._cache.conditions
+        else:
+            self.processed_data.therapies = [
+                t for t in self.processed_data.therapies if t.id != cached_id
+            ]
+            cache = self._cache.normalized_therapies
+
+        cache[cached_id] = cached_obj
+
     def _get_therapy(self, therapy_id: str, therapy: dict) -> MappableConcept:
         """Get Therapy mappable concept for a MOA therapy name.
 
@@ -525,37 +584,13 @@ def _resolve_therapy_discrepancy(
             therapy_norm_obj = self._cache.normalized_therapies[cached_id]
             og_therapy_norm_label = therapy_norm_obj.label
             if moa_concept_label != og_therapy_norm_label:
-                logger.debug(
-                    "MOA therapy %s and %s resolve to same concept %s",
-                    moa_concept_label,
-                    og_therapy_norm_label,
+                self._resolve_concept_discrepancy(
                     cached_id,
+                    therapy_norm_obj,
+                    og_therapy_norm_label,
+                    moa_concept_label,
+                    is_disease=False,
                 )
-                alias = max(moa_concept_label, og_therapy_norm_label)
-                therapy_norm_obj.label = min(moa_concept_label, og_therapy_norm_label)
-                extensions = therapy_norm_obj.extensions or []
-
-                aliases_ext = next(
-                    (
-                        ext
-                        for ext in therapy_norm_obj.extensions
-                        if ext.name == "aliases"
-                    ),
-                    None,
-                )
-                if aliases_ext:
-                    if therapy_norm_obj.label in aliases_ext.value:
-                        aliases_ext.value.remove(therapy_norm_obj.label)
-                    aliases_ext.value.append(alias)
-                else:
-                    extensions.append(Extension(name="aliases", value=[alias]))
-                    therapy_norm_obj.extensions = extensions
-
-                # Remove from processed (it will be added back in _add_therapy)
-                self.processed_data.therapies = [
-                    t for t in self.processed_data.therapies if t.id != cached_id
-                ]
-                self._cache.normalized_therapies[cached_id] = therapy_norm_obj
             return therapy_norm_obj
 
         mappings = []
@@ -630,23 +665,18 @@ def _add_disease(self, disease: dict) -> MappableConcept | None:
         oncotree_kv = [f"{oncotree_key}:{oncotree_value}"]
         blob = json.dumps(oncotree_kv, separators=(",", ":")).encode("ascii")
         disease_id = sha512t24u(blob)
-
         moa_disease = self._cache.conditions.get(disease_id)
         if moa_disease:
             source_disease_name = disease["name"]
             if source_disease_name != moa_disease.label:
-                if not moa_disease.extensions:
-                    moa_disease.extensions = [
-                        Extension(name="aliases", value=[source_disease_name])
-                    ]
-                else:
-                    for ext in moa_disease.extensions:
-                        if (
-                            ext.name == "aliases"
-                            and source_disease_name not in ext.value
-                        ):
-                            ext.value.append(source_disease_name)
-                            break
+                self._resolve_concept_discrepancy(
+                    disease_id,
+                    moa_disease,
+                    moa_disease.label,
+                    source_disease_name,
+                    is_disease=True,
+                )
+                self.processed_data.conditions.append(moa_disease)
             return moa_disease
 
         moa_disease = None

tests/data/transformers/therapeutic/moa_harvester_conflict.json → tests/data/transformers/therapeutic/moa_harvester_conflicts.json

@@ -6,9 +6,9 @@
             "deprecated": false,
             "description": "The U.S. Food and Drug Administration (FDA) granted approval to selpercatinib for the treatment of adult patients with locally advanced or metastatic non-small cell lung cancer (NSCLC) with a RET gene fusion, as detected by an FDA-approved test.",
             "disease": {
-                "name": "Non-Small Cell Lung Cancer",
-                "oncotree_code": "NSCLC",
-                "oncotree_term": "Non-Small Cell Lung Cancer"
+                "name": "Myelodysplastic Syndromes",
+                "oncotree_code": "MDS",
+                "oncotree_term": "Myelodysplastic Syndromes"
             },
             "therapy": {
                 "name": "Selpercatinib",
@@ -40,9 +40,9 @@
             "deprecated": false,
             "description": "Certain missesnse mutations may predict resistance to RET inhibitors",
             "disease": {
-                "name": "Medullary Thyroid Cancer",
-                "oncotree_code": "THME",
-                "oncotree_term": "Medullary Thyroid Cancer"
+                "name": "Myelodysplasia",
+                "oncotree_code": "MDS",
+                "oncotree_term": "Myelodysplasia"
             },
             "therapy": {
                 "name": "LOXO-292",

tests/unit/transformers/test_moa_transformer_therapeutic.py

@@ -404,11 +404,11 @@ def test_moa_cdm_not_normalizable(
 
 
 @pytest.mark.asyncio()
-async def test_moa_therapy_conflict(normalizers):
-    """Test that MOA therapy conflict merges concept correctly"""
+async def test_moa_concept_conflicts(normalizers):
+    """Test that MOA therapy and disease conflict resolution works correctly"""
     t = MoaTransformer(
         data_dir=DATA_DIR,
-        harvester_path=DATA_DIR / "moa_harvester_conflict.json",
+        harvester_path=DATA_DIR / "moa_harvester_conflicts.json",
         normalizers=normalizers,
     )
     harvested_data = t.extract_harvested_data()
@@ -428,3 +428,18 @@ async def test_moa_therapy_conflict(normalizers):
         "name": "aliases",
         "value": ["Selpercatinib"],
     }
+
+    conditions = t.processed_data.conditions
+    assert len(conditions) == 1
+
+    condition = conditions[0]
+    assert condition.id == "moa.normalize.disease.ncit:C3247"
+    assert condition.label == "Myelodysplasia"
+    condition_alias_ext = next(
+        (ext for ext in condition.extensions if ext.name == "aliases"),
+        None,
+    )
+    assert condition_alias_ext.model_dump(exclude_none=True) == {
+        "name": "aliases",
+        "value": ["Myelodysplastic Syndromes"],
+    }