Issue ERROR: Zend_Db_Adapter_Exception: SQLSTATE[HY000] [14] unable to open database file (Abstract.php:144)

[Lafrinae]

Server operating system version

CloudLinux 7.9 (Boris Yegorov)

Plesk version and microupdate number

18.0.44

Hello!

A little background, the owner and group were changed recursively to the root of the server. The almost was restored.

[2022-06-27 21:53:56.622] 3633507:62b9d29497ce7 ERR [extension/git] SQLSTATE[HY000] [14] unable to open database file [2022-06-27 21:53:56.783] 3633507:62b9d29497ce7 ERR [panel] SQLSTATE[HY000] [14] unable to open database file [2022-06-27 21:54:00.495] 3633484:62b9d29879032 ERR [panel] SQLSTATE[HY000] [14] unable to open database file:
0: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Adapter/Pdo/Abstract.php:144 Zend_Db_Adapter_Pdo_Abstract->_connect()
1: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Adapter/Pdo/Sqlite.php:137 Zend_Db_Adapter_Pdo_Sqlite->_connect()
2: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Adapter/Abstract.php:460 Zend_Db_Adapter_Abstract->query(string 'PRAGMA table_info("Repositories")', array)
3: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Adapter/Pdo/Abstract.php:238 Zend_Db_Adapter_Pdo_Abstract->query(string 'PRAGMA table_info("Repositories")')
4: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Adapter/Pdo/Sqlite.php:208 Zend_Db_Adapter_Pdo_Sqlite->describeTable(string 'Repositories', NULL null)
5: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Table/Abstract.php:836 Zend_Db_Table_Abstract->_setupMetadata()
6: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Table/Abstract.php:875 Zend_Db_Table_Abstract->_setupPrimaryKey()
7: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Table/Abstract.php:983 Zend_Db_Table_Abstract->info()
8: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Table/Select.php:100 Zend_Db_Table_Select->setTable(object of type PleskExt\Git\Db\Repositories)
9: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Table/Select.php:78 Zend_Db_Table_Select->__construct(object of type PleskExt\Git\Db\Repositories)
10: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Table/Abstract.php:1019 Zend_Db_Table_Abstract->select()
11: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Db/Table/Abstract.php:1376 Zend_Db_Table_Abstract->fetchAll(array)
12: /usr/local/psa/admin/plib/modules/git/controllers/IndexController.php:158 IndexController->getNotificationsForDomain(object of type pm_Domain)
13: /usr/local/psa/admin/plib/modules/git/controllers/IndexController.php:148 IndexController->getNotificationsAction()
14: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Controller/Action.php:516 Zend_Controller_Action->dispatch(string 'getNotificationsAction')
15: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Controller/Dispatcher/Standard.php:308 Zend_Controller_Dispatcher_Standard->dispatch(object of type Zend_Controller_Request_Http, object of type Zend_Controller_Response_Http)
16: /usr/local/psa/admin/plib/vendor/plesk/zf1/library/Zend/Controller/Front.php:954 Zend_Controller_Front->dispatch()
17: /usr/local/psa/admin/plib/pm/Application.php:87 pm_Application->run()
18: /usr/local/psa/admin/htdocs/modules/git/index.php:5 [2022-06-27 21:54:00.496] 3633484:62b9d29879032 ERR [panel] SQLSTATE[HY000] [14] unable to open database file

Plesk repair all not helped.

Redirecting to /bin/systemctl status mysqld.service
● mariadb.service - MariaDB database server
Loaded: loaded (/usr/lib/systemd/system/mariadb.service; enabled; vendor preset: disabled)
Drop-In: /etc/systemd/system/mariadb.service.d
└─limits.conf, migrated-from-my.cnf-settings.conf, tokudb.conf
Active: active (running) since Sun 2022-06-26 17:21:37 +06; 1 day 16h ago
Main PID: 2691294 (mysqld)
Status: "Taking your SQL requests now..."
CGroup: /system.slice/mariadb.service
└─2691294 /usr/sbin/mysqld

Jun 26 17:21:31 pkz68.hoster.kz systemd[1]: Starting MariaDB database server...
Jun 26 17:21:32 pkz68.hoster.kz mysqld[2691294]: 2022-06-26 17:21:32 0 [Note] libgovernor.so found
Jun 26 17:21:32 pkz68.hoster.kz mysqld[2691294]: 2022-06-26 17:21:32 0 [Note] All governors functions found too
Jun 26 17:21:32 pkz68.hoster.kz mysqld[2691294]: 2022-06-26 17:21:32 0 [Note] Governor connected
Jun 26 17:21:32 pkz68.hoster.kz mysqld[2691294]: 2022-06-26 17:21:32 0 [Note] All governors lve function... too
Jun 26 17:21:32 pkz68.hoster.kz mysqld[2691294]: 2022-06-26 17:21:32 0 [Note] /usr/sbin/mysqld (mysqld 1... ...
Jun 26 17:21:32 pkz68.hoster.kz mysqld[2691294]: 2022-06-26 17:21:32 0 [Warning] Could not increase numb...539)
Jun 26 17:21:37 pkz68.hoster.kz systemd[1]: Started MariaDB database server.
Hint: Some lines were ellipsized, use -l to show in full.

So it's ok with mysql.

Please can anyone help with the problem

 

[Bitpalast]

This is not related to a malfunctioning database server, but is related to missing permissions in the individual database directories or files that reside in /var/lib/mysql and the user (database) directories that descend from that path. They ought to be
mysql:mysql and 0700 for the directories
and
mysql:mysql and 0660 for the individual files (*.frm, *.ibd) in the /var/lib/mysql/<user> directories

 

[Lafrinae]

Thank a lot

 

[mow]

This is not related to a malfunctioning database server, but is related to missing permissions in the individual database directories or files that reside in /var/lib/mysql and the user (database) directories that descend from that path. They ought to be
mysql:mysql and 0700 for the directories
and
mysql:mysql and 0660 for the individual files (*.frm, *.ibd) in the /var/lib/mysql/<user> directories

Wouldn't mysql log something if that was the case?
Can't hurt to also check /var/run/mysqld. If the mysql server was not restarted since the permissions were changed, systemd wouldn't have a chance to fix them.