Release 2.7.0 · StanfordBioinformatics/encode_utils

Updates:

Updated connection.Connection.before_post_file() such that it will calculate file_size now (in addition to md5sum), and that whenever the md5sum needs to be set, the file_size will also be set.

Added connection.Connection.get_biosample_type() to aid in searching for a BiosampleType with a given classification and term_id or term_name.
Added function utils.orient_jpg() which fixes misoriented images, rotating them as necessary. connection.Connection.set_attachment() now calls this if the input file is a JPEG or TIFF.
Added aws_storage.py that includes two classes: S3Upload that simplifies the process of uploading files to a bucket in a specific location with the specified acl, and S3Object which represents an object in a S3 bucket and is internally used for calculating the md5sum and file size when submitting S3 objects to the ENCODE Portal.
Added utils.url_join() which is now used for property joining URL paths, rather than incorrectly with os.path.join since that doesn't construct the right paths on Windows systems.
Added new function in profiles.py called remove_duplicate_associations(). This is called when patching a record so that EU can detect and remove duplicates in array values (when extending arrays).

Added patch to profiles.Profile._set_profile_id() to include exceptional cases, such as antibody_lot records using @id values like '/antibodies/ENCAB719MQZ' instead of the expected '/antibody_lots/ENCAB719MQZ'.