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# Galactic Database
Updated: Apr 6, 2021
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Useful when presenting. --- # Galactic Database .left[Galaxy uses a database for:] * Galaxy objects and all their relations (users, histories, datasets, workflows) * Job state persistence, job dispatching .left[Galaxy does not use a database for:] * Dataset **contents**: files on disk ??? - Galaxy objects like users, histories, datasets, and workflows are stored in the database. - All job information is likewise stored there. - User and reference data, however, are stored outside of the database. - You will want to backup both user data and your 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` ??? - Galaxy uses SQLAlchemy for interacting with databases. - This allows Galaxy to transparently use sqlite or postgres. --- # 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. ??? - sqlite is fine in development, but should not be used for production. - postgres is the best for any production server. - Do not use mysql if possible. --- # Sizing Galaxy rarely deletes from the database, most objects are *marked* deleted. Allocate at least 20 GB of disk to start, 50+ GB if expanding would be difficult. 8-16 GB memory should be sufficient. Recommended: Run PostgreSQL on a different server for resource isolation. ??? - Data is not removed from the database, so plan accordingly. - Allocated at least 20 GB of disk to start, and 50 if expanding later is difficult. - The RAM usage is usually not significant. - We recommend running the database on a separate server from Galaxy for better isolation. --- # 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:///<db_name>[?host=/var/run/postgresql]` * Network PostgreSQL: `postgresql://[user][:password]@<host>[:5432]/<db_name>` ??? - The parameter database_connection tells galaxy where the database is. - There are several styles, depending on how you connect to your database. --- # New Database On first startup with an empty database, Galaxy creates its schema ??? - On first startup with an empty database, Galaxy creates its schema. --- # Migrations Changes in the Galaxy DB model (when upgrading Galaxy) 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 ``` ??? - Whenever Galaxy is upgraded, there may be changes to the database schema. - These are stored in migration scripts, and you can use the manage db script to up or downgrade. --- # Tuning - Pool If the server logs errors about not having enough database pool connections. | Galaxy config option | default value | usegalaxy.org value | | ------ | ------------- | ------------------- | | `database_engine_option_pool_size` | `5` | `10` | | `database_engine_option_max_overflow` | `10` | `20` | [Values for usegalaxy.org](https://github.com/galaxyproject/usegalaxy-playbook/blob/master/env/main/group_vars/all/galaxy_config_vars.yml) ??? - Databases have a limited number of connection slots. - Galaxy can pool connections, and re-use existing connections from a pool when it needs to query the DB. - There are a couple of options for controlling pooling. - The defaults are generally fine until you see errors. --- # Tuning - Server-side cursors If large database query results are causing memory or response time issues in the Galaxy process, leave it on server (PostgreSQL only, recommended). | Galaxy config option | default value | usegalaxy.org value | | ------ | ------------- | ------------------- | | `database_engine_option_server_side_cursors` | `false` | `true` | ??? - Large queries may slow down Galaxy or the DB. - You can enable server side cursors to help with this. --- # Tuning - Slow query logging Queries slower than this threshold (in s) will be logged at debug level. | Galaxy config option | default value | usegalaxy.org value | | ------ | ------------- | ------------------- | | `slow_query_log_threshold` | `0` | `2` | ??? - If you notice slow responses, you can enable slow query logging. - This will print a message in your Galaxy log if a query takes more than a specified time period. - This can be useful to help you debug issues. --- # Tuning - TS install database Galaxy can track Tool Shed data in a separate DB. | Galaxy config option | default value | usegalaxy.org value | | ------ | ------------- | ------------------- | | `install_database_connection` | value of `database_connection` | SQLite DB in CVMFS | All other database config options but prefixed with `install_` are also available. .left[This allows:] * Bootstrapping fresh Galaxy instances with prebuilt/tested tool sets * Atomic installation/rollback (esp. with SQLite: backup and restore DB file) ??? - Galaxy can track tool shed data in a separate database - This can enable deploying Galaxies with prebuilt tool sets --- # Access through model Python script to access Galaxy's database layer **via the Galaxy model**. ```console (venv)$ python -i scripts/db_shell.py >>> new_user = User('email@example.com', 'secret') >>> new_user.username = 'foo' >>> sa_session.add(new_user) >>> sa_session.flush() >>> sa_session.query(User).all() ``` ??? - You can use the Galaxy python models to interact with the database. - After activating the galaxy virtual environment, you can use the DB shell script to interface. - This can allow scripting tasks like resetting passwords. --- # Useful queries Captured in [gxadmin](/archive/2021-12-01/topics/admin/tutorials/gxadmin/slides.html) ([tutorial](/archive/2021-12-01/topics/admin/tutorials/gxadmin/tutorial.html)) ??? - Many useful DB queries are captured in gxadmin - Look into this if you need to query the database for information like running jobs or recent users. --- ## Thank You! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!
This material is licensed under the Creative Commons Attribution 4.0 International License