Don't add NCIT term if there is no id

monarch-initiative · Dec 13, 2023 · 52e2816 · 52e2816
1 parent 43ff1c6
commit 52e2816
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/src/oncoexporter/cda/cda_disease_factory.py b/src/oncoexporter/cda/cda_disease_factory.py
@@ -115,7 +115,10 @@ def _get_morphology_ncit_term_from_icdo(self, row) -> Optional[List[PPkt.Ontolog
             ncit_record = self._icdo_to_ncit.get(row['morphology'])
             ontology_term = PPkt.OntologyClass()
             if 'NCIt Code (if present)' not in ncit_record:
-                warnings.warn(f"Couldn't find NCIt Code (if present) in record for ICD-O code {row['morphology']}")
+                warnings.warn(f"Couldn't find 'NCIt Code (if present)' entry in record for ICD-O code {row['morphology']}")
+                return None
+            elif ncit_record['NCIt Code (if present)'] == '':
+                warnings.warn(f"Found empty 'NCIt Code (if present)' entry in record for ICD-O code {row['morphology']}")
                 return None
             else:
                 ontology_term.id = "NCIT:" + ncit_record['NCIt Code (if present)']