Bug fix: Synonym Sync: Entries without exact mappings (#695)

- The synonym sync template TSVs were being built incorrectly, and were sometimes adding synchronization outputs for cases where the Mondo term and source term had no exact mapping in mondo.sssom.tsv.

src/scripts/sync_synonym.py

@@ -259,6 +259,7 @@ def sync_synonyms(
     #   all_entity_curies(), node() (empty props), node_exists() (no: falsely says 'True', prolly cuz bad xrefs exist)
     source_deleted_ids: Set[CURIE] = set([k for k, v in source_labels.items() if not v])
     mappings_df = mappings_df[~mappings_df['source_id'].isin(source_deleted_ids)]
+    mapping_pairs_set = set(mappings_df[['mondo_id', 'source_id']].apply(tuple, axis=1))
     if len(mappings_df) == 0:
         logging.warning(f'Synonym Sync: No mappings found for source {source_name}. Exiting.')
         return
@@ -337,6 +338,7 @@ def sync_synonyms(
     #  Cases where scope + synonym string are the same
     confirmed_df = mondo_df.merge(source_df, on=['synonym_scope', 'synonym_lower'], how='inner').rename(columns={
         'synonym_x': 'synonym_case_mondo', 'synonym_y': 'synonym_case_source'})  # keep Mondo casing if different
+    confirmed_df = confirmed_df[confirmed_df[['mondo_id', 'source_id']].apply(tuple, axis=1).isin(mapping_pairs_set)]
     confirmed_df = _add_syn_variation_cols(confirmed_df)
     del confirmed_df['mondo_evidence']
     confirmed_df = _common_operations(confirmed_df, outpath_confirmed, mondo_exclusions_df=mondo_exclusions_df)
@@ -347,6 +349,7 @@ def sync_synonyms(
     updated_df = mondo_df.merge(source_df, on=['synonym_lower'], how='inner').rename(columns={
         'synonym_scope_x': 'synonym_scope_mondo', 'synonym_scope_y': 'synonym_scope',
         'synonym_x': 'synonym_case_mondo', 'synonym_y': 'synonym_case_source'})  # keep Mondo casing if different
+    updated_df = updated_df[updated_df[['mondo_id', 'source_id']].apply(tuple, axis=1).isin(mapping_pairs_set)]
     updated_df = _add_syn_variation_cols(updated_df)
     updated_df = updated_df[updated_df['synonym_scope_mondo'] != updated_df['synonym_scope']]
     updated_df = _common_operations(updated_df, outpath_updated, mondo_exclusions_df=mondo_exclusions_df)
@@ -360,6 +363,7 @@ def sync_synonyms(
     source_df_with_mondo_ids['synonym_case_source'] = source_df_with_mondo_ids['synonym']
     # - leave only synonyms that don't exist on given Mondo IDs
     added_df = _filter_a_by_not_in_b(source_df_with_mondo_ids, mondo_df, ['mondo_id', 'synonym_lower'])
+    added_df = added_df[added_df[['mondo_id', 'source_id']].apply(tuple, axis=1).isin(mapping_pairs_set)]
     added_df = _common_operations(added_df, outpath_added, mondo_exclusions_df=mondo_exclusions_df)
     added_df['case'] = 'added'