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CQ: add expert consultant tables and fix source/sckan mapping cleanup #69

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Merged
dbrnz merged 3 commits into from
Mar 10, 2026
+12 −0
Merged

CQ: add expert consultant tables and fix source/sckan mapping cleanup #69

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6caa92a
CQ: manage inserts and updates for feature_expert_consultants (#68).
napakalas Mar 6, 2026
9eaacf7
CQ: delete stale path_node_mappings entries where source_id appears i…
napakalas Mar 6, 2026
b4496c9
CQ: relocate the deletion of feature_expert_consultants before featur…
napakalas Mar 9, 2026
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12 changes: 12 additions & 0 deletions mapknowledge/competency/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,8 +134,10 @@ def __delete_source_from_tables(self, cursor, source: KnowledgeSource):
cursor.execute('DELETE FROM path_phenotypes WHERE source_id=%s', (source_id, ))
cursor.execute('DELETE FROM path_properties WHERE source_id=%s', (source_id, ))
cursor.execute('DELETE FROM path_node_mappings WHERE source_id=%s', (source_id, ))
cursor.execute('DELETE FROM path_node_mappings WHERE sckan_id=%s', (source_id, ))
cursor.execute('DELETE FROM path_nodes WHERE source_id=%s', (source_id, ))
cursor.execute('DELETE FROM feature_types WHERE source_id=%s', (source_id, ))
cursor.execute('DELETE FROM feature_expert_consultants WHERE source_id=%s', (source_id, ))
cursor.execute('DELETE FROM feature_terms WHERE source_id=%s', (source_id, ))

def __update_anatomical_types(self, cursor):
Expand Down Expand Up @@ -238,6 +240,16 @@ def __update_connectivity(self, cursor, knowledge: KnowledgeList, show_progress=
cursor.executemany('INSERT INTO path_node_mappings (source_id, path_id, node_id, sckan_id, sckan_node_id) VALUES (%s, %s, %s, %s, %s) ON CONFLICT DO NOTHING',
node_mappings)

# Expert consultants
expert_consultants = record.get('expert-consultants', [])
cursor.executemany('INSERT INTO expert_consultants (expert_id) VALUES (%s) ON CONFLICT DO NOTHING',
((expert,) for expert in expert_consultants))

# Path expert consultants
with cursor.copy("COPY feature_expert_consultants (source_id, term_id, expert_id) FROM STDIN") as copy:
for expert in expert_consultants:
copy.write_row((source_id, path_id, expert))

if progress_bar is not None:
progress_bar.update(1)
if progress_bar is not None:
Expand Down