encode_utils

An API and scripts for submitting datasetss to the ENCODE Portal.

encode_utils.AWARD_PROP_NAME = 'award'

The award property name that is common to all ENCODE Portal object profiles.

encode_utils.ALIAS_PROP_NAME = 'aliases'

The aliases property name that is common to almost all ENCODE Portal object profiles. Notably, the following profiles lack this property as of 2018-04-03: [‘access_key_admin’, ‘publication’, ‘award’, ‘organism’, ‘page’, ‘image’, ‘user’, ‘lab’]

encode_utils.LAB_PROP_NAME = 'lab'

The lab property name that is common to all ENCODE Portal object profiles.

encode_utils.LAB = {}

dict. Stores the lab property to the value of the environment variable DCC_LAB to serve as the default lab when submitting an object to the Portal. encode_utils.connection.Connection.post() will use this default if this property doesn’t appear in the payload.

encode_utils.LAB_PREFIX = ''

str. Stores the prefix to add to each record alias when doing a POST operation. Most profiles have an ‘alias’ key, which stores a list of alias names that are useful to the lab. When POSTING objects to the Portal, these aliases must be prefixed with the lab name and end with a colon, and this configuration variable stores that prefix value.

encode_utils.AWARD = {}

dict. Stores the award property to the value of the environment variable DCC_AWARD to act as the default award when submiting an object to the Portal. encode_utils.connection.Connection.post() will use this default if this property doesn’t appear in the payload, and the profile at hand isn’t a member of the list encode_utils.utils.Profile.AWARDLESS_PROFILES.

encode_utils.PROFILES_URL = 'profiles'

The relative ENCODE Portal URL that points to all the profiles (schemas).

encode_utils.DCC_MODES = {'dev': {'url': 'https://test.encodedcc.org'}, 'prod': {'url': 'https://www.encodeproject.org'}}

A hash of known hosts one can connect to, where the key can be passed to the dcc_mode argument when instantiating the connection.Connection class.

encode_utils.TIMEOUT = 60

The timeout in seconds when making HTTP requests via the requests module.

encode_utils.DEBUG_LOGGER_NAME = 'eu_debug'

The name of the debug logging instance.

encode_utils.ERROR_LOGGER_NAME = 'eu_error'

The name of the error logging instance created in encode_utils.connection.Connection(), and referenced elsewhere.

encode_utils.POST_LOGGER_NAME = 'eu_post'

The name of the POST logging instance created in encode_utils.connection.Connection(), and referenced elsewhere.

encode_utils.debug_logger = <Logger eu_debug (DEBUG)>

A logging instance that logs all messages sent to it to STDOUT.

encode_utils.error_logger = <Logger eu_error (ERROR)>

A logging instance that accepts messages at the ERROR level.