Settings

Refinery settings are configured in settings_local.py.

Note

You should never edit the settings directly in settings.py to avoid conflicts when upgrading.

Database Settings

DATABASES

Solr Settings

REFINERY_SOLR_BASE_URL = "http://localhost:8983/solr/"

Location of the Solr API.

Email Settings

EMAIL_HOST = 'localhost'

EMAIL_PORT = 25

DEFAULT_FROM_EMAIL = 'webmaster@localhost'

SERVER_EMAIL = 'root@localhost'

The email address that error messages come from, such as those sent to ADMINS and MANAGERS.

Customization Settings

TIME_ZONE = 'America/New_York'

Local time zone for this installation. Choices can be found at http://en.wikipedia.org/wiki/List_of_tz_zones_by_name, although not all choices may be available on all operating systems. On Unix systems, a value of None will cause Django to use the same timezone as the operating system. If running in a Windows environment this must be set to the same as your system time zone.

REFINERY_PUBLIC_GROUP_NAME = "Public"

Set the name of the group that is used to share data with all users (= “the public”)

REFINERY_PUBLIC_GROUP_ID = 100

Do not change this after initialization of your Refinery instance.

ISA_TAB_DIR = ''

FILE_STORE_DIR = 'file_store'

Location of the file store data directory relative to MEDIA_ROOT.

REFINERY_SOLR_SPACE_DYNAMIC_FIELDS = "_"

Used to replaces spaces in the names of dynamic fields in Solr indexing.

REFINERY_CSS = ["styles/css/refinery-style-bootstrap.css", "styles/css/refinery-style-bootstrap-responsive.css", "styles/css/refinery-style.css" ]

List of paths to CSS files used to style Refinery pages (relative to STATIC_URL)

REFINERY_GOOGLE_ANALYTICS_ID = ""

Supply a Google analytics id “UA-...” (if set to “” tracking will be deactivated).

EMAIL_SUBJECT_PREFIX = '[Refinery] '

Prefix for emails sent by Refinery. Should always end with a space.

REFINERY_REPOSITORY_MODE = False

Set to True to activate Refinery repository mode.

ACCOUNT_ACTIVATION_DAYS = 7

Number of days user has to activate their account before it expires.

REFINERY_WELCOME_EMAIL_SUBJECT = 'Welcome to Refinery'

Subject of the welcome email sent to new users.

REFINERY_WELCOME_EMAIL_MESSAGE = 'Please fill out your user profile'

Message body of the welcome email sent to new users.

REFINERY_FILE_SOURCE_MAP = {}

Optional dictionary for translating file URLs into file system paths (and vice versa) format: {‘pattern’: ‘replacement’} where pattern is a string to search for in source and then replace with replacement string. May contain more than one pattern-replacement pair (only the first match will be used).

REFINERY_BANNER = ''

Optional string to display a message near the top of every page (HTML tags allowed).

REFINERY_BANNER_ANONYMOUS_ONLY = False

Optional setting to display REFINERY_BANNER to anonymous users only.

REFINERY_REGISTRATION_CLOSED_MESSAGE = ''

Optional string to display a message when REGISTRATION_OPEN = False (HTML tags allowed).

REFINERY_INNER_NAVBAR_HEIGHT = 20

Set height of navigation bar (e.g. to fit a logo).

REFINERY_MAIN_LOGO = ""

Supply a path to a logo that will become part of the branding (set navbar height correctly!)

REFINERY_EXTERNAL_AUTH = False

Use external authentication system like django-auth-ldap (disables password management URLs)

REFINERY_EXTERNAL_AUTH_MESSAGE = ''

Message to display on password management pages when REFINERY_EXTERNAL_AUTH = True

TAXONOMY_URL = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"

Location of the zip file that contains the entire NCBI taxonomy database

UCSC_URL = "hgdownload.cse.ucsc.edu/admin/hgcentral.sql"

Database of all UCSC genomes, alternate names, and their corresponding organisms.

AE_BASE_QUERY = 'http://www.ebi.ac.uk/arrayexpress/xml/v2/experiments?'

Base query for what kind of ArrayExpress studies to pull in (e.g. only ChIP-Seq studies, or studies updated after a certain date)

AE_BASE_URL = "http://www.ebi.ac.uk/arrayexpress/experiments"

prefix of the URL where all ArrayExpress studies’ MAGE-TAB files can be accessed

Authentication settings

Example for user authentication via LDAP using django-auth-ldap:

from django_auth_ldap.config import LDAPSearch
# Baseline configuration
AUTH_LDAP_SERVER_URI = "ldap://ldap.example.com"
AUTH_LDAP_BIND_DN = ""
AUTH_LDAP_BIND_PASSWORD = ""
AUTH_LDAP_USER_SEARCH = LDAPSearch("OU=Domain Users,DC=rc,DC=Domain",
                                ldap.SCOPE_SUBTREE, "(uid=%(user)s)")
# Populate Django user from the LDAP directory.
AUTH_LDAP_USER_ATTR_MAP = {
   "first_name": "givenName",
   "last_name": "sn",
   "email": "mail"
}
settings.AUTHENTICATION_BACKENDS += (
    'refinery.core.models.RefineryLDAPBackend',
)