Search result error occurs after docker creation of Rest VV version 2.2.0 #105
Description
Hi,
I'm trying to install rest VV (version 2.2.0).
Since the Docker build finished without errors, I tested the Variant Validator inside Docker.
Then I got this error message.
I think the postgresql connection is the problem.
Can you help me??
Thank you.
query
variant_validator.py -v 'NC_000017.11:g.50198002C>A' -g GRCh38 -t mane -s individual -f json -m -o stdout
error message
Lost connection to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11; attempting reconnect
Reconnected to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11
Lost connection to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11; attempting reconnect
Reconnected to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11
Lost connection to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11; attempting reconnect
Reconnected to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11
Lost connection to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11; attempting reconnect
Reconnected to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11
Lost connection to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11; attempting reconnect
Reconnected to postgresql://uta_admin:[email protected]:54320/vvta/vvta_2022_11
CRITICAL: <class 'RuntimeError'> generator didn't stop after throw()
Traceback (most recent call last):
File "/usr/local/lib/python3.10/site-packages/vvhgvs/dataproviders/uta.py", line 585, in _get_cursor
yield cur
File "/usr/local/lib/python3.10/site-packages/vvhgvs/dataproviders/uta.py", line 220, in _fetchall
cur.execute(sql, *args)
File "/usr/local/lib/python3.10/site-packages/psycopg2/extras.py", line 146, in execute
return super().execute(query, vars)
psycopg2.errors.ObjectNotInPrerequisiteState: materialized view "tx_exon_aln_mv" has not been populated
HINT: Use the REFRESH MATERIALIZED VIEW command.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.10/site-packages/VariantValidator/modules/vvMixinCore.py", line 1343, in validate
lifted_response = liftover(genomic_position_info[g_p_key]['hgvs_genomic_description'],
File "/usr/local/lib/python3.10/site-packages/VariantValidator/modules/liftover.py", line 167, in liftover
options = validator.hdp.get_tx_mapping_options(tx)
File "/usr/local/lib/python3.10/site-packages/vvhgvs/decorators/lru_cache.py", line 186, in wrapper
result = user_function(*args, **kwds)
File "/usr/local/lib/python3.10/site-packages/vvhgvs/dataproviders/uta.py", line 453, in get_tx_mapping_options
rows = self._fetchall(self._queries['tx_mapping_options'], [tx_ac])
File "/usr/local/lib/python3.10/site-packages/vvhgvs/dataproviders/uta.py", line 219, in _fetchall
with self._get_cursor() as cur:
File "/usr/local/lib/python3.10/contextlib.py", line 185, in exit
raise RuntimeError("generator didn't stop after throw()")
RuntimeError: generator didn't stop after throw()
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/bin/variant_validator.py", line 48, in
output = validator.validate(variant, args.genome, args.transcripts)
File "/usr/local/lib/python3.10/site-packages/VariantValidator/modules/vvMixinCore.py", line 1442, in validate
raise fn.VariantValidatorError('Validation error')
VariantValidator.modules.utils.VariantValidatorError: Validation error