Error setting up MySQL: Table 'mysql.plugin' doesn't exist

Question

I have a MySQL 5.7 instance running without problems on Ubuntu 16, but when i try to install any other package or try to update existing ones through apt-get, i get the following error:

# apt-get upgrade

Setting up mysql-server-5.7 (5.7.20-0ubuntu0.16.04.1) ...
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
mysql_upgrade: [ERROR] 1146: Table 'mysql.plugin' doesn't exist
mysql_upgrade failed with exit status 5
 dpkg: error processing package mysql-server-5.7 (--configure):
  subprocess installed post-installation script returned error exit status 1
No apport report written because the error message indicates its a followup error from a previous failure.
dpkg: dependency problems prevent configuration of mysql-server:
mysql-server depends on mysql-server-5.7; however:
Package mysql-server-5.7 is not configured yet.

dpkg: error processing package mysql-server (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 mysql-server-5.7
 mysql-server

And if i run a mysqlcheck, it looks like some of the system tables exists but others are missing:

mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.engine_cost
Error    : Table 'mysql.engine_cost' doesn't exist
status   : Operation failed
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.gtid_executed
Error    : Table 'mysql.gtid_executed' doesn't exist
status   : Operation failed
mysql.help_category
Error    : Table 'mysql.help_category' doesn't exist
status   : Operation failed
mysql.help_keyword
Error    : Table 'mysql.help_keyword' doesn't exist
status   : Operation failed
mysql.help_relation
Error    : Table 'mysql.help_relation' doesn't exist
status   : Operation failed
mysql.help_topic
Error    : Table 'mysql.help_topic' doesn't exist
status   : Operation failed
mysql.innodb_index_stats
Error    : Table 'mysql.innodb_index_stats' doesn't exist
status   : Operation failed
mysql.innodb_table_stats
Error    : Table 'mysql.innodb_table_stats' doesn't exist
status   : Operation failed
mysql.ndb_binlog_index                             OK
mysql.plugin
Error    : Table 'mysql.plugin' doesn't exist
status   : Operation failed
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.server_cost
Error    : Table 'mysql.server_cost' doesn't exist
status   : Operation failed
mysql.servers
Error    : Table 'mysql.servers' doesn't exist
status   : Operation failed
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone
Error    : Table 'mysql.time_zone' doesn't exist
status   : Operation failed
mysql.time_zone_leap_second
Error    : Table 'mysql.time_zone_leap_second' doesn't exist
status   : Operation failed
mysql.time_zone_name
Error    : Table 'mysql.time_zone_name' doesn't exist
status   : Operation failed
mysql.time_zone_transition
Error    : Table 'mysql.time_zone_transition' doesn't exist
status   : Operation failed
mysql.time_zone_transition_type
Error    : Table 'mysql.time_zone_transition_type' doesn't exist
status   : Operation failed
mysql.user                                         OK
sys.sys_config
Error    : Table 'sys.sys_config' doesn't exist
status   : Operation failed

However, the database is correctly running and if I manually check through an SQL, it looks like the tables exist.

mysql> SHOW TABLES;
+---------------------------+
| Tables_in_mysql           |
+---------------------------+
| columns_priv              |
| db                        |
| engine_cost               |
| event                     |
| func                      |
| general_log               |
| gtid_executed             |
| help_category             |
| help_keyword              |
| help_relation             |
| help_topic                |
| innodb_index_stats        |
| innodb_table_stats        |
| ndb_binlog_index          |
| plugin                    |
| proc                      |
| procs_priv                |
| proxies_priv              |
| server_cost               |
| servers                   |
| slave_master_info         |
| slave_relay_log_info      |
| slave_worker_info         |
| slow_log                  |
| tables_priv               |
| time_zone                 |
| time_zone_leap_second     |
| time_zone_name            |
| time_zone_transition      |
| time_zone_transition_type |
| user                      |
+---------------------------+

I use the innodb_file_per_table=1 setting, and the owner of /var/lib/mysql directory is correctly set to mysql user.

I would like to fix this issue without dumping existing data, but i'm running out of ideas.

Answer 1

Try running:

bash-4.2# mysql_install_db --user=mysql --ldata=/var/lib/mysql/
Installing MariaDB/MySQL system tables in '/var/lib/mysql/' ...
OK

This should install the system tables in data directory. Then restart mysql/mariadb service.

Answer 2

Finally the only thing that solved the problem was to purge and reinstall the mysql library making a backup of the database and restoring it after all the process:

# Backup database
time mysqldump -u root -p database > /var/backups/restore_backup.sql

# Backup config and data
mv /var/lib/mysql /tmp/backups/mysql-lib.bak
cp /etc/mysql/my.cnf /tmp/backups/my.cnf.bak

# Purge library
sudo apt-get remove --purge mysql-server mysql-client mysql-common
sudo apt-get autoremove
sudo apt-get autoclean

# Reinstall
sudo apt-get update
sudo apt-get install mysql-server

# Restore config
cp /tmp/backups/my.cnf.bak /etc/mysql/my.cnf
sudo service mysql restart

# Create database
mysql -u root -p
mysql> CREATE DATABASE database;

# Restore backup
time mysql -u root -p database < /var/backups/restore_backup.sql