Unable to access WP Toolkit: A table must have a primary key, but none was found for table ‘Instances’

Symptoms

• The following warning appears in the Plesk GUI when accessing the WP Toolkit page in Plesk:

  Warning: WP Toolkit has detected a possible inconsistency of its database. It is strongly suggested to contact Plesk support and open a support ticket.

• The following error occurs on the attempt to access WP Toolkit:

  Zend_Db_Table_Exception
  A table must have a primary key, but none was found for table 'Instances'

• The following errors do occur on the attempt to access WP Toolkit:

  Server Error500
  Zend_Db_Statement_Exception
  SQLSTATE[HY000]: General error: 1 no such column: serverId

  PLESK_ERROR:  Zend_Db_Statement_Exception
  A table must have a primary key, but none was found for table 'RemoteServers' 

• An attempt to check the WordPress plugins updates fails with the following error:

  WP Toolkit has found WordPress files at the following path: Path /var/www/vhosts/example.com/httpdocs
  However, it does not seem that this WordPress website is working. Try restoring the website from a backup or cleaning up the redundant files.

• The output of the following commands shows that WP Toolkit SQLITE3 database, used to store information about instances, does not contain any WordPress-related tables:

  # sqlite3 /usr/local/psa/var/modules/wp-toolkit/wp-toolkit.sqlite3
  sqlite> .tables
  StatisticsMeasurements version

• Backups are created with the warning: 

  backup_restore_helper utility returned incorrect result. Extension with ID 5 cannot be backuped. Please, contact your service provider 

Cause

WP Toolkit SQLITE3 database was not created correctly or has been corrupted.

Resolution

It is required to reinstall WP Toolkit. It is possible to do that via Plesk Interface or via SSH.