Search result error occurs after docker creation of Rest VV version 2.2.0 #105
Comments
|
Hi @yebean-k . This sounds like the postgres docker container did not build correctly. I think the best thing to do is re-install and see if this fixes the issue. |
|
I also recommend building from master. We do periodic bug fixes between major releases |
|
Hi, I recently cloned GIT and tried to install it, so it seems to be the latest version. - query - log ESC[0mESC[91m2023-07-19 00:27:21 (5.07 MB/s) - ‘input_file.sql.gz’ saved [201476885/201476885] ESC[0mRemoving intermediate container 86a0284cccbb |
|
When I installed Flask 2.3.2 version written in REQUIREMENTS.txt, I got a message that "propagate_exceptions" does not exist. So I installed Flask 2.2.5 version because "propagate_exceptions" disappeared from Flask 2.3.0 version. Could this be a problem? |
|
OK, a couple of things. Firstly you are building from the tagged version Ideally build from master as we regularly test and update. Also, this command will not build the databases needed by VV. Instead, the build instructions are here https://github.com/openvar/rest_variantValidator/blob/master/docs/DOCKER.md Follow these through carefully. Once you have the API running, then you will be able to make url requests and get a JSON response, just as if you were hitting the hosted API at https://rest.variantvalidator.org/. Feel free to give any feedback on the build. Please let me know how you get on |
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
The text was updated successfully, but these errors were encountered: