xQTL workbench - Manage database and storage

Setup file storage

xQTL can store files in a semi-relational way. In Browse data -> View files you can add an entity which depicts a file, and then upload the content of the file. The content is attached to this entity. Some data matrix storage variants (binary, csv) also use this file storage mechanism. In order to use it, you must set and validate a path on the server where the application is running.

  • Start by clicking to Settings, then select File storage.
  • If not path is set, type one in the box and press Set path.
  • The status of 'does it exist' and 'does it have content' is now updated. Consider if you want to use this location.
  • Press Validate to attempt a mkdir operation if the location does not exist, and attempt to write-read-delete a small test file inside this location next.
  • If this succeeds, you will get a green VALIDATED message. If it fails, you will be informed why at the top, and the message will be UNVALIDATED.
  • Once this path has been set, files will be stored and read from this location.
  • If a path has been set but you are unhappy with it, you can use Delete path. Beware: setting a new path will break existing links to entities and files.

Manage the database

You can find database manipulation tools under Settings, then select Database status. Here you can load the example data, or reset to database to its empty form.

Making the database 'empty' means:

  • The xQTL data tables definitions are reloaded in the database.
  • Users 'admin' and 'anonymous' are loaded.
  • User groups 'biologist' and 'bioinformatician' are loaded.
  • Permissions (as defined in the application GUI XML) are loaded: this means which groups can see which screens and are allowed to write which entities. In this case, the permissions for biologist and bioinformatician are loaded.

Loading the example data results in:

  • The example users 'bio-user' and 'bioinfo-user' are loaded.
  • Additional permissions to give these users functional access to the database are added.
  • The example investigation is loaded, including:
    • Annotations for individuals, chromosomes, etc.
    • Geno- and phenotype dataset, tagged and ready for QTL analysis.
    • The Rqtl analysis with configured parameters, ready to be executed.

Furthermore, you can view the database connection settings and some relevant application generation properties here. In the future we wish to add more database tools for admin, for example, runtime switching of the connection, or running informative queries.

Last modified 12 years ago Last modified on 2011-09-07T10:57:03+02:00