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Upload term descendants to competency database #80

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Upload term descendants to competency database #80

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9 changes: 8 additions & 1 deletion mapknowledge/competency/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,7 @@ def __delete_source_from_tables(self, cursor, source: KnowledgeSource):
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_relationship 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 @@ -258,7 +259,6 @@ def __update_connectivity(self, cursor, knowledge: KnowledgeList, show_progress=
def __update_features(self, cursor, knowledge: KnowledgeList):
#=============================================================
source_id = knowledge.source.source_id
cursor.execute('DELETE FROM feature_terms WHERE source_id=%s', (source_id, ))

for record in knowledge.knowledge:
if source_id == clean_knowledge_source(record.get('source', '')):
Expand All @@ -272,6 +272,13 @@ def __update_features(self, cursor, knowledge: KnowledgeList):
if (term_type:=record.get('type')) is not None:
copy.write_row([source_id, record['id'], term_type])

# Feature relationships
with cursor.copy("COPY feature_relationship (source_id, feature_0, feature_1, relationship) FROM STDIN") as copy:
for record in knowledge.knowledge:
if source_id == clean_knowledge_source(record.get('source', '')):
for descendant in record.get('descendants', []):
copy.write_row([source_id, descendant, record['id'], 'descendant-ancestor'])

def __update_knowledge_source(self, cursor, source: KnowledgeSource):
#====================================================================
cursor.execute('''INSERT INTO knowledge_sources (source_id, sckan_id, description)
Expand Down