encode_utils.profiles¶

Contains a Profile class for working with profiles on the ENCODE Portal. Note that the terms ‘profile’ and ‘schema’ are used interchangeably in this package.

encode_utils.profiles.DEBUG_LOGGER = <Logger eu_debug.encode_utils.profiles (DEBUG)>¶: A debug logging instance.

encode_utils.profiles.ERROR_LOGGER = <Logger eu_error.encode_utils.profiles (ERROR)>¶: An error logging instance.

exception encode_utils.profiles.UnknownProfile[source]¶

Bases: Exception

Raised when the profile ID in question doesn’t match any known profile ID.

class encode_utils.profiles.Profiles(dcc_url)[source]¶

Bases: object

Encapsulates knowledge about the existing profiles on the Portal and contains useful methods for working with a given profile.

A defining purpose of this class is to validate the profile ID specified in a POST payload passed to encode_utils.connection.Connection.post(). This class is used to ensure that the profile specified there is a known profile on the Portal.

Parameters:	dcc_url – str. The portal URL being submitted to. dcc_url – str. The dcc_url as specified by Connection.dcc_mode.url.

FILE_PROFILE_ID = 'file'¶: Constant storing the file.json profile’s ID. This is asserted for inclusion in Profile.PROFILES.

SUBMITTED_FILE_PROP_NAME = 'submitted_file_name'¶: Constant storing a property name of the file.json profile. The stored name is asserted for inclusion in the set of File properties.

MD5SUM_NAME_PROP_NAME = 'md5sum'¶: Constant storing a property name of the file.json profile. The stored name is asserted for inclusion in the set of File properties.

FILE_SIZE_PROP_NAME = 'file_size'¶: Constant sotring a property name of the file.json profile.

profiles¶: Constant (dict) set to the return value of the function self.get_profiles(). See documentation there for details.

profiles_with_property(property_name)[source]¶

Returns a list of profile names that have a given property.

Parameters:	property_name – str. The name of the property.
Returns:	list of profile names.

get_profile_from_id(at_id)[source]¶

Normalizes the profile_id so that it matches the format of the profile IDs stored in self.profiles, and ensures that the normalized profile ID is a member of this list.

Parameters:	at_id – str. An @id from the portal, e.g. /biosamples/ENCBS123ABC/
Returns:	The normalized profile ID.
Return type:	str
Raises:	`UnknownProfile` – The normalized profile ID is not a member of the list self.profiles.

remove_duplicate_associations(associations)[source]¶

Checks for duplicates in array properties containing string elements. Need to be careful as some cases can be tricky, i.e.

[‘/documents/id1’, ‘id1’]

Such a duplicate should be identified and removed, leaving us with [“id1”].

Parameters:	associations – list.
Returns:	Deduplicated list.