Data Database

Debug Information

Image: docker.io/bitnami/mariadb-galera:11.1.3-debian-11-r8

Ports: 3306/tcp
JDBC: jdbc://mariadb:<hostname>:3306

Debug Information

Image: dbrepo/data-db-sidecar:1.4.5

Ports: 8080/tcp

Overview¶

The Data Database contains the research data. In the default configuration, only one database of this type is deployed. Any number of MariaDB ata databases can be integrated into DBRepo, even non-empty databases. The database needs to be registered in the Metadata Database to be visible in the User Interface and usable from e.g. the Python Library.

Architecture¶

Sidecar¶

We deploy a sidecar that handles the CSV-file upload/download operations between the Storage Service and the Data Database using a Python Flask application and the boto3 client until MariaDB supports S3 natively.

Data¶

The procedures require the user-generated databases to have the same collation (because of comparison operations). Ensure that the Data Database has the character set utf8mb4 and collation utf8mb4_general_ci in your my.cfg:

[mysqld]
character_set_server=utf8mb4
collation_server=utf8mb4_general_ci

We observed this unexpected behavior for the MariaDB Galera chart powered by Bitnami and had to set extra flags. We could not observe this behavior with the MariaDB Galera container image itself.

mariadb-galera:
  extraFlags: "--character-set-server=utf8mb4 --collation-server=utf8mb4_general_ci"

Backup¶

Export all databases with --skip-lock-tables option for MariaDB Galera clusters as it is not supported currently by MariaDB Galera.

Terminal

mariadb \
    -u <privilegedUsername> \
    -p<privilegedPassword> \
    --complete-insert \
    --skip-lock-tables \
    --skip-add-locks \
    --all-databases > dump.sql

Restore¶

Terminal

mariadb \
    -u <privilegedUsername> \
    -p<privilegedPassword> < dump.sql

Limitations¶

(none)

Do you miss functionality? Do these limitations affect you?

We strongly encourage you to help us implement it as we are welcoming contributors to open-source software and get in contact with us, we happily answer requests for collaboration with attached CV and your programming experience!

Security¶

(none)