AttributeError: 'Engine' object has no attribute 'cursor'
drmatthewclark opened this issue · comments
following conda install instructions the system throws an error when computing humanness
AttributeError: 'Engine' object has no attribute 'cursor'
[2024-02-06 13:58:11,833: ERROR/ForkPoolWorker-14] Task biophi.humanization.web.tasks.humanness_task[9fe7dc93-8651-49ab-baec-f3a0386376f5] raised unexpected: HumannessTaskError("'Engine' object has no attribute 'cursor'")
Traceback (most recent call last):
File "/home/mclark/BioPhi/biophi/humanization/web/tasks.py", line 305, in humanness_task
humanness=get_antibody_humanness(
File "/home/mclark/BioPhi/biophi/humanization/methods/humanness.py", line 275, in get_antibody_humanness
vh=get_chain_humanness(vh, params=params) if vh else None,
File "/home/mclark/BioPhi/biophi/humanization/methods/humanness.py", line 321, in get_chain_humanness
peptides = get_chain_oasis_peptides(chain, params=params)
File "/home/mclark/BioPhi/biophi/humanization/methods/humanness.py", line 303, in get_chain_oasis_peptides
oas_hits = get_oas_hits(
File "/home/mclark/BioPhi/biophi/humanization/methods/humanness.py", line 367, in get_oas_hits
return pd.read_sql(statement, params=peptides, con=engine)
File "/home/mclark/.conda/envs/biophi-dev/lib/python3.9/site-packages/pandas/io/sql.py", line 706, in read_sql
return pandas_sql.read_query(
File "/home/mclark/.conda/envs/biophi-dev/lib/python3.9/site-packages/pandas/io/sql.py", line 2739, in read_query
cursor = self.execute(sql, params)
File "/home/mclark/.conda/envs/biophi-dev/lib/python3.9/site-packages/pandas/io/sql.py", line 2673, in execute
cur = self.con.cursor()
AttributeError: 'Engine' object has no attribute 'cursor'
The same error in docker compose setup also
I haven't fully tested it but I think the issue is with Pandas version 2.2. Replacing it with version 2.1.4 made the error go away.
Try to do a connection before you read your query:
engine = create_engine(str_conn)
connection = engine.raw_connection()
df = pd.read_sql(query, con=connection)
If you keep getting the error maybe it's because your pandas version. I got it just for reading purposes but when I tried to send the df into mysql, it failed
Yes, this is definitely pandas >=2.2 that causes this error.
I uninstalled sqlalchemy and pandas then reinstalled and it fixed the problem
Fixed in new biophi build on bioconda, thanks everyone for reporting and sorry for the delay.