name: inverse layout: true class: center, middle, inverse
--- # Galactic Database --- # Defaults * Galaxy uses the [SQLAlchemy](http://www.sqlalchemy.org/) database abstraction layer. This allows for different database servers to be plugged in. * By default Galaxy automatically creates and uses an [SQLite](https://sqlite.org/) database during the first startup. * The database is in the file `database/universe.sqlite` --- # Choices * SQLite * Useful for single-user Galaxy or development. * **PostgreSQL** * The recommended standard for anything serious. * ~~MySQL~~ * Supported by SQLAlchemy but Galaxy is not tested against it. --- # Configuration `database_connection` is specified as a [database URL](http://docs.sqlalchemy.org/en/latest/core/engines.html#database-urls) in `galaxy.yml` * Default SQLite: `sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE` * Local PostgreSQL (socket) `postgresql://<user>:<password>@/<db_name>?host=/var/run/postgresql` * Network PostgreSQL: `postgresql://<user>:<password>@<host>:5432/<db_name>` --- # Tuning - Pool If the server logs errors about not having enough database pool connections. * `database_engine_option_pool_size: 5` (10 on Main) * `database_engine_option_max_overflow: 10` (20 on Main) ??? Values for Main are available at https://github.com/galaxyproject/usegalaxy-playbook/blob/master/env/main/group_vars/galaxyservers/vars.yml --- # Tuning - Server-side cursors If large database query results are causing memory or response time issues in the Galaxy process, leave it on server. * `database_engine_option_server_side_cursors: False` (True on Main, PostgreSQL only, recommended) --- # Tuning - Slow query logging Queries slower than this threshold (in s) will be logged at debug level `slow_query_log_threshold: 0` (5000 on Main) --- # Tuning - TS install database Galaxy can track Tool Shed data in a separate DB. ```ini install_database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE ``` This allows: * Bootstrapping fresh Galaxy instances with prebuilt/tested tool sets * Atomic installation/rollback (esp. with SQLite) ??? All other database config options but prefixed with `install_` are also available. --- # Migrations Changes in the Galaxy DB model are captured incrementally in the form of [atomic scripts](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/model/migrate/versions). Each script can both upgrade and downgrade a DB. ```console $ ./manage_db.sh upgrade $ ./manage_db.sh downgrade --version=132 ``` --- # Access through model Python script to access Galaxy's database layer **via the Galaxy models**. ```console $ python -i scripts/db_shell.py >>> new_user = User('firstname.lastname@example.org', 'secret') >>> new_user.username = 'foo' >>> sa_session.add(new_user) >>> sa_session.flush() >>> sa_session.query(User).all() ``` ??? Need to be inside the Galaxy virtualenv for this to work --- # Other Databases * The Reports app is hooked to the Galaxy DB to present data in useful format. * The Tool Shed app has its own database. --- ## Thank you! This material is the result of a collaborative work. Thanks the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors (Martin Čech, Nicola Soranzo) !
.footnote[Found a typo? Something is wrong in this tutorial?
Edit it on [GitHub](https://github.com/galaxyproject/training-material/tree/master/topics/admin/tutorials/database/slides.html)]