Confluence not starting after mysql upgrade

[Johan Johansson]

I have Confluence 7.3.1 with mysql version 5.7.27 on Linux 64 bit.

After the upgrade of mysql (from v 5.5) Confluence is no longer starting.

The error message I get is 

ERROR [Catalina-utility-1] [confluence.setup.dbcheck.MySQLChecker] checkIsolationLevel MySQL isolation level could not be read. Isolation level must be 'READ-COMMITTED'. See http://confluence.atlassian.com/x/GAtmDg

When logging in to the mysql both the global and the session isolation level is READ-COMMITTED. So I dont get this error message.

I have tried to add the parameter to the connection string to, but to no avail.

The upgrade was made on error but unfortunately we didnt use it for a long time so we no longer have a backup of the one before the upgrade.. 

EDIT:

Anyway, after fiddling for ages with mysql, I have been able to get forward, but still I get startup errors. Does anyone have an idea what this means:

2020-03-10 13:47:01,387 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.GroupMembersCache] error Loading group members from database failed: could not extract ResultSet
2020-03-10 13:47:01,403 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.CacheUpdateReceiver] error Failed to initialize evaluator cache
Failed to initialize evaluator cache^C
informa_jojo@jiratest2:~$
informa_jojo@jiratest2:~$ ERROR [perm-delta-cache-receiver] [engine.jdbc.spi.SqlExceptionHelper]2020-03-10 13:47:01,386 ERROR [perm-delta-cache-receiver] [engine.jdbc.spi.SqlExceptionHelper] logExceptions Unknown column 'hibernatem0_.child_user_id' in 'where clause'
-bash: ERROR: command not found
informa_jojo@jiratest2:~$ 2020-03-10 13:47:01,387 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.GroupMembersCache] error Loading group members from database failed: could not extract ResultSet
-bash: 2020-03-10: command not found
informa_jojo@jiratest2:~$ 2020-03-10 13:47:01,403 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.CacheUpdateReceiver] error Failed to initialize evaluator cache
-bash: 2020-03-10: command not found

thanks

any ideas please?

Many thanks

[Johan Johansson · Accepted solution]

Anyway, I was finally able to get it up and running.

It turned out I had imported the database dump with foregin key checks active, so some data had not been imported. So recreating the database with that turned off did the trick.

[Nicolas Werle [Decadis AG]]

Hi @Johan Johansson ,

can you please provide your my.cnf file (usually to find under /etc/my.cnf) so that we can investigate further? 
Many thanks in advance. 
Best, 
Nicolas

[Johan Johansson]

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
#
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port = 3306
socket = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket = /var/run/mysqld/mysqld.sock
nice = 0

[mysqld]
#
# * Basic Settings
#
user = mysql
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
port = 3306
basedir = /usr
datadir = /var/lib/mysql
tmpdir = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
character-set-server=utf8
collation-server=utf8_bin
transaction-isolation=READ-COMMITTED
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address = 127.0.0.1
#
# * Fine Tuning
#
key_buffer = 16M
max_allowed_packet = 256M
thread_stack = 192K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover = BACKUP
#max_connections = 100
#table_cache = 64
#thread_concurrency = 10
#
# * Query Cache Configuration
#
query_cache_limit = 1M
query_cache_size = 16M
#
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file = /var/log/mysql/mysql.log
#general_log = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#slow_query_log_file = /var/log/mysql/mysql-slow.log
#slow_query_log = 1
#long_query_time = 2
#log_queries_not_using_indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
#binlog_do_db = include_database_name
#binlog_ignore_db = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem
innodb_log_file_size=256M

[mysqldump]
quick
quote-names
max_allowed_packet = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/