.. _pheno_db:

Phenotype Database Configuration
================================

The configuration file for a single phenotype database follows the general
INI format. Its filename can be freely chosen, however, it **must** contain a
``phenoDB`` section - this will indicate that it is a phenotype database
configuration file.  This configuration file must properly describe a single
phenotype database. Its properties, which must belong to the ``phenoDB``
section, are explained below.

Example Configuration
---------------------

.. code-block:: ini

  [phenoDB]
  name = phenotypeDatabaseName
  dbfile = %(wd)s/pheno.db
  browser_dbfile = %(wd)s/browser/pheno_browser.db
  browser_images_dir = %(wd)s/browser/images/
  browser_images_url = /static/phenotypeDatabaseName/browser/images/


[phenoDB]
---------

name
____

.. code-block:: ini

  name = <pheno db name>

This is the unique name of the phenotype database. It can be used in the
configuration files of studies and datasets to attach the phenotype
database to them.

dbfile
______

.. code-block:: ini

  dbfile = <sqlite3 pheno db path>

The path to the SQLite3 phenotype database file, relative to the
configuration file.

browser_dbfile
______________

.. code-block:: ini

  browser_dbfile = <sqlite3 pheno browser db path>

The path to the SQLite3 phenotype **browser** database file, relative to the
configuration file.

browser_images_dir
__________________

.. code-block:: ini

  browser_images_dir = <images directory path>

The path to the directory containing the measure images for the browser,
relative to the configuration file.

browser_images_url
__________________

.. code-block:: ini

  browser_images_url = /static/<images directory path>/

The path to the directory containing the measure images for the browser,
relative to the *static root directory*. The trailing slash is required.