Accessing ISA data on Github

The ISA GitHub Adapter class

The GitHub API wrapper/adapter may be useful to retrieve ISA datasets (as JSON or Tabs) or configuration files in XML format. The core class, IsaGitHubStorageAdapter can be instantiated with or without authorisation.

Usage without authentication

If authentication is not required to access the required resource, you can directly instantiate an adapter object and use it:

from isatools.io.storage_adapter import IsaGitHubStorageAdapter
from zipfile import ZipFile

adapter = IsaGitHubStorageAdapter()
adapter.retrieve('tests/data/BII-I-1', 'test_out_dir', owner='ISA-tools', repository='isa-api') 
# retrieving a directory (containg either an ISA-tab dataset or a set of configuration files, 
# will return a file-like object containg the zipped content of the directory.
buf = adapter.retrieve('tests/data/BII-I-1', destination='test_out_dir', owner='ISA-tools', 
                       repository='isa-api')
# Default owner is "ISA-tools' and default repo is 'isa-api' so they can actually be omitted. 
# Default destination directory is 'isa-target'
zip_file = ZipFile(buf)
# get the list of the files retrieved from the directory
zip_file.namelist()

# an ISA JSON dataset is returned as a stardard JSON object
json_obj = adapter.retrieve('isatools/sampledata/BII-I-1.json', destination='test_out_dir', 
                            owner='ISA-tools', repository='isa-api', validate_json=True)

# set write_to_file to False to avoid saving the resource to disk
json_obj = adapter.retrieve('isatools/sampledata/BII-I-1.json', write_to_file=False, 
                            owner='ISA-tools', repository='isa-api', validate_json=True)

# retrieving a single configuration file returns an lxml ElementTree object:
xml_obj = adapter.retrieve('isaconfig-2013222/protein_expression_ge.xml', 
                           repository='Configuration-Files')

# get root element for the configuration file
xml_obj.getroot()

Usage with authentication

To access as authenticated user, the recommended way is to instantiate the storage adapter in a with statement:

with IsaGitHubStorageAdapter(username='yourusername', password='yourpw', 
                             note='test_api') as adapter:
    adapter.is_authenticated # true
    # do stuff...

Otherwise you must explicitly call the close() method to delete the current authorisation from the GitHub server

adapter = IsaGitHubStorageAdapter(username='yourusername', password='youpw', note='test_api')
adapter.is_authenticated # True
# do stuff...
adapter.close()