1

Did an update of the MySQL Workbench to version 8.0.18 on Mac OS X Catalina and since then my databases don't show up anymore neither does my website start on localhost because of a connection error.

In the folder: OS X ~/Library/Application\ Support/MySQL/Workbench/ I deleted the wb_options.xml and wb_state.xml files and restarted Workbench but no databases are shown.

Tried to get to a command line where I can enter these commands:

echo 'export PATH=/usr/local/mysql/bin:$PATH' >> ~/.bash_profile
. ~/.bash_profile
mysql -u root -p
mysql> SET GLOBAL innodb_fast_shutdown = 1;
mysql_upgrade -u root -p

Output:

➜  mysql mysql -u root -p            
Enter password: 
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 48
Server version: 8.0.18 MySQL Community Server - GPL

Copyright (c) 2000, 2019, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> SET GLOBAL innodb_fast_shhutdown = 1;
ERROR 1193 (HY000): Unknown system variable 'innodb_fast_shhutdown'

mysql> SET GLOBAL innodb_fast_shutdown = 1;
Query OK, 0 rows affected (0,00 sec)

mysql> mysql_upgrade -u root -p

No further output.

Had a look at wb.log:

07:45:48 [INF][      Workbench]: Starting up Workbench
07:45:48 [INF][   WBContext UI]: Initializing workbench context UI with these values:
      base dir: /Applications/MySQLWorkbench 2.app/Contents/Resources
    plugin path: /Applications/MySQLWorkbench 2.app/Contents/PlugIns
    struct path: /Applications/MySQLWorkbench 2.app/Contents/Resources/grt
    module path: /Applications/MySQLWorkbench 2.app/Contents/PlugIns:/Applications/MySQLWorkbench 2.app/Contents/Resources/plugins
    library path: /Applications/MySQLWorkbench 2.app/Contents/Resources/libraries
    user data dir: /Users/<USERNAME>/Library/Application Support/MySQL/Workbench
      open at start: -psn_0_5371167
    open type:
    run at startup:
    run type:
    Force SW rendering: No
    Force OpenGL: No
    quit when done: No
07:45:48 [INF][      WBContext]: WbContext::init
07:45:48 [INF][      WBA]: Looking for extension modules for WBA...
07:45:48 [INF][      WBA]: 0 extension modules found
07:45:48 [WRN][      grt]: /Users/<USERNAME>/Library/Application Support/MySQL/Workbench/connections.xml:27: link 'D61B9071-5CA5-47E8-AF17-EC4DB12CA9B2' <object GrtObject> key=owner could not be resolved**
07:45:48 [INF][      WBContext]: System info:
  MySQL Workbench Community (GPL) for Mac OS X version 8.0.18 CE build 15329599 (64 bit)
  Configuration Directory: /Users/<USERNAME>/Library/Application Support/MySQL/Workbench
  Data Directory: /Applications/MySQLWorkbench 2.app/Contents/Resources
    Cairo Version: 1.10.2   OS: macOS 10.15.x Catalina x86_64   CPU: 8x Intel(R) Core(TM) i7-4870HQ CPU @ 2.50GHz - 16.00GiB RAM No video adapter info available

07:45:48 [ERR][      WBContext]: Unknown file type -psn_0_5371167
07:45:59 [ERR][  GRTDispatcher]: exception in grt execute_task, continuing: Exception: Access denied for user 'root'@'localhost' (using password: NO) 07:45:59 [ERR][  GRTDispatcher]: worker: task 'execute sql queries' has failed with error:.Access denied for user
'root'@'localhost' (using password: NO) 07:46:06 [ERR][SQL Editor Form]: Can't restore default schema (develop): Unknown database
'develop' 07:46:06 [ERR][SQL Editor Form]: Can't restore default schema (develop): Unknown database 'develop' 07:46:06 [INF][SQL Editor
Form]: Opened connection 'Local instance 3306' to MySQL Community Server - GPL version 8.0.18 07:46:35
[INF][wb_admin_control.py:query_server_installation_info:860]: Currently connected to MySQL server version '8.0.18', conn status = True, active plugins = ['INNODB_INDEXES', 'sha256_password', 'INNODB_CMPMEM_RESET', 'INNODB_BUFFER_POOL_STATS', 'CSV', 'mysql_native_password', 'INNODB_FT_BEING_DELETED', 'INNODB_BUFFER_PAGE', 'INNODB_CMP_PER_INDEX_RESET', 'INNODB_TABLESTATS', 'ARCHIVE', 'INNODB_FT_INDEX_CACHE', 'INNODB_CMP', 'INNODB_FT_CONFIG', 'InnoDB', 'INNODB_FT_DEFAULT_STOPWORD', 'INNODB_TRX', 'binlog', 'INNODB_TABLES', 'INNODB_COLUMNS', 'INNODB_CMPMEM', 'INNODB_FT_INDEX_TABLE', 'sha2_cache_cleaner', 'MEMORY', 'PERFORMANCE_SCHEMA', 'BLACKHOLE', 'caching_sha2_password', 'INNODB_SESSION_TEMP_TABLESPACES', 'INNODB_CACHED_INDEXES',
'TempTable', 'INNODB_VIRTUAL', 'MRG_MYISAM', 'INNODB_CMP_PER_INDEX', 'INNODB_FT_DELETED', 'mysqlx_cache_cleaner', 'INNODB_TABLESPACES',
'INNODB_METRICS', 'mysqlx', 'MyISAM', 'INNODB_TEMP_TABLE_INFO', 'INNODB_CMP_RESET', 'keyring_file', 'ngram', 'INNODB_BUFFER_PAGE_LRU']
07:46:49 [WRN][wb_admin_control.py:exec_query:623]: Error executing query SELECT name, timer_name FROM performance_schema.setup_timers: 
07:47:32 [WRN][         mforms]: Resource file not found: mysql-logo-80.png
07:47:33 [WRN][         mforms]: Resource file not found: mysql-logo-80.png
07:53:38 [WRN][         mforms]: Resource file not found: db.StoredProcedure.16x16.png
07:53:38 [WRN][         mforms]: Resource file not found: db.Function.16x16.png
07:53:38 [WRN][         mforms]: Resource file not found: db.Grants.16x16.png
07:54:04 [INF][      Workbench]: Shutting down Workbench
07:54:04 [INF][      Workbench]: Workbench shutdown done ➜  log

Highlighted a line noticing connections.xml could not be resolved. Don't know what the impact is of this notice.

Any help is highly appreciated!

Thank you for your time.

UPDATE 1:

➜  bin mysql_upgrade -u root -p
Enter password: 
The mysql_upgrade client is now deprecated. The actions executed by
the upgrade client are now done by the server. To upgrade, please
start the new MySQL binary with the older data directory. Repairing
user tables is done automatically. Restart is not required after
upgrade. The upgrade process automatically starts on running a new
MySQL binary with an older data directory. To avoid accidental
upgrades, please use the --upgrade=NONE option with the MySQL binary.
The option --upgrade=FORCE is also provided to run the server upgrade
sequence on demand. It may be possible that the server upgrade fails
due to a number of reasons. In that case, the upgrade sequence will
run again during the next MySQL server start. If the server upgrade
fails repeatedly, the server can be started with the --upgrade=MINIMAL
option to start the server without executing the upgrade sequence,
thus allowing users to manually rectify the problem. ➜  bin

UPDATE 2

Tried to connect to the database via the commandline, and my best guess is that my databases are gone :(

➜ bin echo 'export PATH=/usr/local/mysql/bin:$PATH' >> ~/.bash_profile ➜ bin . ~/.bash_profile ➜ bin mysql -u root -p -h 127.0.0.1 develop Enter password: ERROR 1049 (42000): Unknown database 'develop'

Is there by any change a possibility to check if the database 'develop' really is gone? If so, is it possible to recover it with TimeMachine?

I don't know what happend, but upgrading the Workbench has become a nightmare to me.

user2037412
  • 164
  • 1
  • 11
  • your last command `> mysql_upgrade -u root -p` should NOT be run inside mysql... so after `mysql> SET GLOBAL` do `mysql> quit` and then `> mysql_upgrade -u root -p` – Holger Will Dec 20 '19 at 07:00
  • Thanks. But no luck. Edit the OP with this command and the message I got. – user2037412 Dec 20 '19 at 07:22
  • :-( you have: `Access denied for user 'root'@'localhost' (using password: NO) ` in your logs as well... so maybe that answers will help: https://stackoverflow.com/questions/2995054/access-denied-for-user-rootlocalhost-using-passwordno – Holger Will Dec 20 '19 at 07:51
  • Thanks. Tried to follow the steps, but f.i. the command ‘service’ is not found by zsh. Stuck in how to proceed and get my databases back. – user2037412 Dec 20 '19 at 16:54

1 Answers1

0

The warning you highlighted is about a deserialization problem for a file and is nothing serious.

You real problem is that you cannot connect. You passed a parameter to Workbench 07:45:48 [ERR][ WBContext]: Unknown file type -psn_0_5371167 which it tries to interpret as connection name. See also the context initialization values at the top of the log file. There's an entry open at start: -psn_0_5371167 which confirms what I mention above. Try launching Workbench without any parameter.

According to this question the PSN parameter is a process serial number, which is passed to a GUI app only on first start. Did you ever try another start of Workbench since you downloaded it?

Side note: Workbench really should be aware of such a parameter and ignore it.

Mike Lischke
  • 48,925
  • 16
  • 119
  • 181
  • Thanks. I launch MySQL workbench as an app not from the command line. How can I prevent any parameter when I start Workbench? – user2037412 Dec 20 '19 at 11:04
  • Have started Workbench several times after I got the famous 'open from the internet' message. Agree with your side note Mike. – user2037412 Dec 20 '19 at 16:02