encode_utils¶
An API and scripts for submitting datasetss to the ENCODE Portal.
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encode_utils.
AWARD_PROP_NAME
= 'award'¶ The award property name that is common to all ENCODE Portal object profiles.
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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’]
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encode_utils.
LAB_PROP_NAME
= 'lab'¶ The lab property name that is common to all ENCODE Portal object profiles.
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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.
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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.
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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 listencode_utils.utils.Profile.AWARDLESS_PROFILES
.
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encode_utils.
PROFILES_URL
= 'profiles'¶ The relative ENCODE Portal URL that points to all the profiles (schemas).
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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.
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encode_utils.
TIMEOUT
= 60¶ The timeout in seconds when making HTTP requests via the
requests
module.
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encode_utils.
DEBUG_LOGGER_NAME
= 'eu_debug'¶ The name of the debug
logging
instance.
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encode_utils.
ERROR_LOGGER_NAME
= 'eu_error'¶ The name of the error
logging
instance created inencode_utils.connection.Connection()
, and referenced elsewhere.
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encode_utils.
POST_LOGGER_NAME
= 'eu_post'¶ The name of the POST
logging
instance created inencode_utils.connection.Connection()
, and referenced elsewhere.
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encode_utils.
debug_logger
= <Logger eu_debug (DEBUG)>¶ A
logging
instance that logs all messages sent to it to STDOUT.
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encode_utils.
error_logger
= <Logger eu_error (ERROR)>¶ A
logging
instance that accepts messages at the ERROR level.