Common Configuration Errors¶

This guide describes some of the most common configuration problems encountered when installing and configuring VariantValidator, together with their typical causes and recommended solutions.

Invalid SeqRepo database location¶

If the configured SeqRepo database location is incorrect or inaccessible, VariantValidator may fail during initialisation with errors similar to:

Exception ignored in: <bound method UTA_postgresql.__del__ of <vvhgvs.dataproviders.uta.UTA_postgresql object at 0x...>>
...
AttributeError: 'UTA_postgresql' object has no attribute '_pool'

or

NameError: name 'vval' is not defined

These secondary errors occur because the Validator object could not be created successfully.

Cause¶

The seqrepo_location entry in the VariantValidator configuration file does not point to a valid SeqRepo installation.

Solution¶

Verify that the configured SeqRepo directory exists and contains a valid SeqRepo database.

See the Installation Guide for details of configuring SeqRepo.

Running against MariaDB or older MySQL servers¶

When using MariaDB or older MySQL server versions, you may encounter an error similar to:

mysql.connector.errors.NotSupportedError:
MySQL version 5.7.2 and earlier does not support COM_RESET_CONNECTION.

Cause¶

Older MySQL-compatible servers do not support the COM_RESET_CONNECTION command used by newer versions of mysql-connector-python.

Solution¶

Install version 8.0.12 of mysql-connector-python:

pip install "mysql-connector-python==8.0.12" --force-reinstall

After reinstalling the connector, verify the installation by running the VariantValidator test suite:

pytest

For background information, see the relevant Stack Overflow discussion:

https://stackoverflow.com/questions/58044497/is-there-a-way-to-use-pool-reset-connection-from-mysql-connector-python-with-m