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Traceback (most recent call last):
File "/home/ubuntu/kg2-code/reactome_mysql_to_kg_jsonl.py", line 933, in <module>
get_nodes(connection, nodes_output, test_mode)
File "/home/ubuntu/kg2-code/reactome_mysql_to_kg_jsonl.py", line 323, in get_nodes
for result in run_sql(nodes_sql, connection):
File "/home/ubuntu/kg2-code/reactome_mysql_to_kg_jsonl.py", line 69, in run_sql
cursor.execute(sql)
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/cursors.py", line 170, in execute
result = self._query(query)
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/cursors.py", line 328, in _query
conn.query(q)
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 517, in query
self._affected_rows = self._read_query_result(unbuffered=unbuffered)
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/cursors.py", line 328, in _query
conn.query(q)
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 517, in query
self._affected_rows = self._read_query_result(unbuffered=unbuffered)
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 732, in _read_query_result
result.read()
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 1075, in read
first_packet = self.connection._read_packet()
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 684, in _read_packet
packet.check_error()
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/protocol.py", line 220, in check_error
err.raise_mysql_exception(self._data)
File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/err.py", line 109, in raise_mysql_exception
raise errorclass(errno, errval)
pymysql.err.ProgrammingError: (1146, "Table 'reactome.Regulation_2_summation' doesn't exist")
Reactome changed their table structure recently and the Regulation_2_summation table no longer exists
The text was updated successfully, but these errors were encountered:
Per Slack DM thread, the plan is to find the most recent Reactome release that does not trigger the above problem, and use that release for building KG2.9.0pre.
Then, after the KG2.9.0pre build is done, we can revisit fixing the Reactome ETL script to address this problem.
Reactome changed their table structure recently and the
Regulation_2_summation
table no longer existsThe text was updated successfully, but these errors were encountered: