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JATOS with MySQL

By default JATOS uses an embedded H2 database and no further setup is necessary but it can be easily configured to work with a MySQL or MariaDB database.

Possible scenarios why one would use an external database are

  • your JATOS will be used by more than a few users (e.g. several research groups or an institute-wide installation)
  • your JATOS will run studies with many participants
  • the expected traffic is rather high (the studies produce a lot of result data)
  • you want to be able to do a regular database backup (with the embedded H2 database this would involve stopping JATOS)
  • higher trust in the reliability of MySQL/MariaDB

Installation​

One could install the external database on the same machine as JATOS is running or on an extra machine depending on ones need.

JATOS requires MySQL >= 5.7 (8.x is fine). JATOS was tested with MariaDB 10.9.7 (other versions likely work too).

There are many manuals out there, e.g. this one. One way to set up MySQL:

  1. Install MySQL

    E.g. on Ubuntu

    sudo apt install mysql-server

  2. Log in to MySQL's command line terminal:

    mysql -u root -p

  3. Create a database for JATOS:

    Character set and collation are important - otherwise you won't have full UTF-8 support

    CREATE DATABASE jatos CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci;

  4. Create a user for JATOS: 

    CREATE USER 'jatosuser'@'localhost' IDENTIFIED BY 'myPassword';

    Remember your username and password. You need them when configuring JATOS later on.

    Leave out the @'localhost' part if the database is not on the same host.

  5. Grant privileges to the new user:

    GRANT ALL PRIVILEGES ON jatos.* TO 'jatosuser'@'localhost';

  6. You can test the new user: log out of MySQL with exit and back in with the newly created user:

    mysql -u jatosuser -p

Appart from giving JATOS access to the database it is not necessary to create any tables - JATOS is doing this automatically.

Now you have to configure JATOS to use your MySQL/MariaDB.

Configure JATOS​

There are three ways to set up JATOS to work with a MySQL/MariaDB database.

The properties starting with db.default are deprecated and shouldn't be used anymore. Use jatos.db.* instead.

Change IP, port, username and password to the ones from your database. The driver is always com.mysql.cj.jdbc.Driver for MySQL or MariaDB.

Always restart JATOS after making any changes to the configuration (e.g. with ./loader.sh restart)

  1. Via config file properties

    The config file, named jatos.conf or production.conf, is located in the JATOS folder, in ./conf folder:

    • in jatos.conf (JATOS version >= 3.8.3) change the properties jatos.db.url, jatos.db.username, and jatos.db.password. The property jatos.db.driver is always com.mysql.cj.jdbc.Driver.

      Example:

      jatos.db.url = "jdbc:mysql://127.0.0.1:3306/jatos?characterEncoding=UTF-8&useJDBCCompliantTimezoneShift=true&useLegacyDatetimeCode=false&serverTimezone=UTC"
      jatos.db.username = "jatosuser"
      jatos.db.password = "mypassword"
      jatos.db.driver = "com.mysql.cj.jdbc.Driver"

    • in production.conf (JATOS version < 3.8.3) change the properties db.default.url, db.default.username, and db.default.password. The property db.default.driver is always com.mysql.cj.jdbc.Driver.

  2. Via command-line arguments

    • JATOS version >= 3.8.3) set the arguments -Djatos.db.url, -Djatos.db.username, and -Djatos.db.password and -Djatos.db.driver (always com.mysql.cj.jdbc.Driver).

      Example:

      -Djatos.db.url = "jdbc:mysql://127.0.0.1:3306/jatos?characterEncoding=UTF-8&useJDBCCompliantTimezoneShift=true&useLegacyDatetimeCode=false&serverTimezone=UTC"
      -Djatos.db.username = "jatosuser"
      -Djatos.db.password = "mypassword"
      -Djatos.db.driver = "com.mysql.cj.jdbc.Driver"

      and use them together with JATOS start command ./loader start:

      ./loader.sh start \
         -Djatos.db.url = "jdbc:mysql://127.0.0.1:3306/jatos?characterEncoding=UTF-8&useJDBCCompliantTimezoneShift=true&useLegacyDatetimeCode=false&serverTimezone=UTC" \
         -Djatos.db.username = "jatosuser" \
         -Djatos.db.password = "mypassword" \
         -Djatos.db.driver = "com.mysql.cj.jdbc.Driver"

    • JATOS version < 3.8.3) set the arguments -Ddb.default.url, -Ddb.default.username, and -Ddb.default.password and -Ddb.default.driver (always com.mysql.cj.jdbc.Driver).

  3. Via environment variables

    Set the variables JATOS_DB_URL, JATOS_DB_USERNAME, JATOS_DB_PASSWORD, and JATOS_DB_DRIVER (always com.mysql.cj.jdbc.Driver).

    Example:

    JATOS_DB_URL="jdbc:mysql://127.0.0.1:3306/jatos?characterEncoding=UTF-8&useJDBCCompliantTimezoneShift=true&useLegacyDatetimeCode=false&serverTimezone=UTC"
    JATOS_DB_USERNAME='jatosuser'
    JATOS_DB_PASSWORD='mypassword'
    JATOS_DB_DRIVER='com.mysql.cj.jdbc.Driver'

You can confirm that JATOS is accessing the correct database by opening JATOS' Administration page in a browser and then click on System Info: The field DB URL should resemble the one from your config. Another way is by looking in the logs: you should see a line after JATOS started similar to this (with your database URI):

14:06:01.760 [info] - p.a.d.DefaultDBApi - Database [default] initialized at jdbc:mysql://localhost/jatos?characterEncoding=UTF-8&useJDBCCompliantTimezoneShift=true&useLegacyDatetimeCode=false&serverTimezone=UTC

Done. Your JATOS uses your MySQL/MariaDB now.

Optional - Deactivate the binary log of your MySQL/MariaDB​

The binary log (also called binlog) serves two purposes: replication and data recovery. More can be found in MariaDB's documentation.

The problem with binary logs is that they can take up quite some disk space depending on the experiments you run on your JATOS. The location of those log files is specified in MySQL/MariaDB's config but on many systems they are under /var/lib/mysql. If you have a single database instance (and therefore do not use replication) and you do not need data recovery (e.g. have a different backup mechanism) than it is safe to deactivate the binary logs.

Add skip-log-bin to the end of your MySQL/MariaDB config (details). On many Linux systems the config is in /etc/mysql/mysql.conf.d/mysqld.cnf.

The part of your mysqld.cnf that configures the binary logs could then look similar to this:

# 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
# binlog_expire_logs_seconds    = 2592000
# max_binlog_size   = 100M
# binlog_do_db          = include_database_name
# binlog_ignore_db      = include_database_name
skip-log-bin

You have to restart MySQL/MariaDB for the changes to take effect.

Optional - Increase max_allowed_packet size in older MySQL/MariaDB databases​

If you have an older MySQL (< 8.x.x) and your experiments will have large result data you might want to increase the max_allowed_packet size. If your result data is larger than the max_allowed_packet JATOS will just return an 'internal server error'. In JATOS' log in will look similar to this:

[ERROR] - g.ErrorHandler - Internal JATOS error
[ERROR] - o.h.e.j.s.SqlExceptionHelper - Packet for query is too large (5,920,824 > 4,194,304). You can change this value on the server by setting the 'max_allowed_packet' variable.
[WARN] - o.h.e.j.s.SqlExceptionHelper - SQL Error: 0, SQLState: S1000

In MySQL, from 8.x.x on, the max_allowed_packet is by default 64MB and this is usually more than enough. But in MySQL versions before 8 it is just 4MB by default and before 5.6.6 it's just 1MB.

To increase the max_allowed_packet size just add it to the end of your MySQL/MariaDB config. On many Linux systems the config is in /etc/mysql/mysql.conf.d/mysqld.cnf. E.g. to set it to 64MB:

max_allowed_packet=64M

You have to restart the database for the changes to take effect.