fix possible column error in omop_teva

aphp · Jun 10, 2024 · 20545e2 · 20545e2
1 parent 36c63a9
commit 20545e2
Showing 1 changed file with 9 additions and 3 deletions.
diff --git a/eds_scikit/plot/omop_teva.py b/eds_scikit/plot/omop_teva.py
@@ -101,9 +101,15 @@ def generate_omop_teva(
         else:
             try:
                 table = data._read_table(table_name)
-                table = table.merge(
-                    visit_occurrence, on="visit_occurrence_id", how="left"
-                )
+                drop_columns = (set(visit_occurrence.columns).intersection(table.columns)).difference(["visit_occurrence_id"])
+                if drop_columns:
+                    table = table.merge(
+                        visit_occurrence.drop(columns=drop_columns), on="visit_occurrence_id", how="left"
+                    )
+                else:
+                    table = table.merge(
+                        visit_occurrence, on="visit_occurrence_id", how="left"
+                    )
             except AttributeError:
                 raise Exception(
                     f"No {table_name} table in input data object. Skipping procedure_occurrence."