🎨 Only map synonyms when field is name

lamindb/_can_curate.py

@@ -149,6 +149,11 @@ def _inspect(
     registry = queryset.model
     model_name = registry._meta.model.__name__
 
+    # do not inspect synonyms if the field is not name field
+    inspect_synonyms = True
+    if hasattr(registry, "_name_field") and field != registry._name_field:
+        inspect_synonyms = False
+
     # inspect in the DB
     result_db = inspect(
         df=_filter_query_based_on_organism(
@@ -157,13 +162,14 @@ def _inspect(
         identifiers=values,
         field=field,
         mute=mute,
+        inspect_synonyms=inspect_synonyms,
     )
     nonval = set(result_db.non_validated).difference(result_db.synonyms_mapper.keys())
 
     if len(nonval) > 0 and registry.__get_schema_name__() == "bionty":
         try:
             bionty_result = registry.public(organism=organism, source=source).inspect(
-                values=nonval, field=field, mute=True
+                values=nonval, field=field, mute=True, inspect_synonyms=inspect_synonyms
             )
             bionty_validated = bionty_result.validated
             bionty_mapper = bionty_result.synonyms_mapper
@@ -194,7 +200,7 @@ def _inspect(
                     f" {colors.italic('.from_values()')}"
                 )
 
-            nonval = bionty_result.non_validated
+            nonval = [i for i in bionty_result.non_validated if i not in bionty_mapper]
         # no bionty source is found
         except ValueError:
             logger.warning("no Bionty source found, skipping Bionty validation")

lamindb/_from_values.py

@@ -230,7 +230,16 @@ def create_records_from_source(
     bionty_df = filter_bionty_df_columns(model=model, public_ontology=public_ontology)
 
     # standardize in the bionty reference
-    result = public_ontology.inspect(iterable_idx, field=field.field.name, mute=True)
+    # do not inspect synonyms if the field is not name field
+    inspect_synonyms = True
+    if hasattr(model, "_name_field") and field.field.name != model._name_field:
+        inspect_synonyms = False
+    result = public_ontology.inspect(
+        iterable_idx,
+        field=field.field.name,
+        mute=True,
+        inspect_synonyms=inspect_synonyms,
+    )
     syn_mapper = result.synonyms_mapper
 
     msg_syn: str = ""

tests/core/test_can_validate.py

@@ -117,3 +117,30 @@ def test_set_abbr():
 def test_validate_int():
     result = ln.User.validate([1, 2], field=ln.User.id)
     assert result.sum() == 1
+
+
+def test_synonym_mapping():
+    # only name field can be standardized
+    bt.Gene.from_source(symbol="TNFRSF4", organism="human").save()
+
+    bt_result = bt.Gene.public().inspect(
+        ["ABC1", "TNFRSF4"], field="symbol", organism="human"
+    )
+    assert bt_result.synonyms_mapper == {"ABC1": "HEATR6"}
+
+    bt_result = bt.Gene.public().inspect(
+        ["ABC1", "TNFRSF4"], field="symbol", organism="human", inspect_synonyms=False
+    )
+    assert bt_result.synonyms_mapper == {}
+
+    result = bt.Gene.inspect(
+        ["CD134", "TNFRSF4"], field=bt.Gene.symbol, organism="human"
+    )
+    assert result.synonyms_mapper == {"CD134": "TNFRSF4"}
+
+    result = bt.Gene.inspect(
+        ["CD134", "TNFRSF4"], field=bt.Gene.ensembl_gene_id, organism="human"
+    )
+    assert result.synonyms_mapper == {}
+
+    bt.Gene.filter().delete()

tests/core/test_from_values.py

@@ -118,3 +118,16 @@ def test_from_values_synonyms_aware():
     assert isinstance(records[0].source, bt.Source)
     assert records[0].ontology_id == "CL:0000084"
     bt.CellType.filter().all().delete()
+
+
+def test_standardize():
+    # only name field can be standardized
+    results = bt.Gene.from_values(
+        ["HES4", "TNFRSF4"], field=bt.Gene.ensembl_gene_id, organism="human"
+    )
+    assert len(results) == 0
+
+    results = bt.Gene.from_values(
+        ["HES4", "TNFRSF4"], field=bt.Gene.symbol, organism="human"
+    )
+    assert len(results) == 2