def get_library_contents(gi, path):
"""
Return the contents of a data library
Returns a list of LibraryFolder and LibraryDataset
instances representing the contents of the specified
Galaxy data library.
FIXME: should filter on full path (currently
lists everything)
Arguments:
gi (GalaxyInstance): bioblend GalaxyInstance
path (str): path of the data library to fetch
the contents of
Returns:
list: list of folders and datasets.
"""
logging.debug("Path '%s'" % path)
lib_client = galaxy.libraries.LibraryClient(gi)
library_name, folder_path = split_library_path(path)
logging.debug("library_name '%s'" % library_name)
library_id = library_id_from_name(gi, library_name)
if library_id is None:
print "No library '%s'" % library_name
return
# Get library contents
contents = []
for item in lib_client.show_library(library_id, contents=True):
if item['type'] == 'folder':
contents.append(LibraryFolder(item))
else:
contents.append(LibraryDataset(item))
return contents
def get_library_contents(gi,path):
"""
Return the contents of a data library
Returns a list of LibraryFolder and LibraryDataset
instances representing the contents of the specified
Galaxy data library.
FIXME: should filter on full path (currently
lists everything)
Arguments:
gi (GalaxyInstance): bioblend GalaxyInstance
path (str): path of the data library to fetch
the contents of
Returns:
list: list of folders and datasets.
"""
logging.debug("Path '%s'" % path)
lib_client = galaxy.libraries.LibraryClient(gi)
library_name,folder_path = split_library_path(path)
logging.debug("library_name '%s'" % library_name)
library_id = library_id_from_name(gi,library_name)
if library_id is None:
print "No library '%s'" % library_name
return
# Get library contents
contents = []
for item in lib_client.show_library(library_id,contents=True):
if item['type'] == 'folder':
contents.append(LibraryFolder(item))
else:
contents.append(LibraryDataset(item))
return contents
def test_library_and_multiple_folders_trailing_slash(self):
self.assertEqual(
split_library_path('Test Library 2/Run 11/Fastqs/'),
('Test Library 2','/Run 11/Fastqs'))
def test_library_and_folder_trailing_slash(self):
self.assertEqual(split_library_path('Test Library 2/Run 11/'),
('Test Library 2','/Run 11'))
def test_library_and_folder(self):
self.assertEqual(split_library_path('Test Library 2/Run 11'),
('Test Library 2','/Run 11'))
def test_library_name_with_spaces(self):
self.assertEqual(split_library_path('Test Library 2'),
('Test Library 2','/'))
def test_library_name_trailing_slash(self):
self.assertEqual(split_library_path('TestLibrary/'),
('TestLibrary','/'))
def test_library_name_only(self):
self.assertEqual(split_library_path('TestLibrary'),
('TestLibrary','/'))
def test_library_and_multiple_folders_trailing_slash(self):
self.assertEqual(split_library_path('Test Library 2/Run 11/Fastqs/'),
('Test Library 2', '/Run 11/Fastqs'))
def test_library_and_folder_trailing_slash(self):
self.assertEqual(split_library_path('Test Library 2/Run 11/'),
('Test Library 2', '/Run 11'))
def test_library_and_folder(self):
self.assertEqual(split_library_path('Test Library 2/Run 11'),
('Test Library 2', '/Run 11'))
def test_library_name_with_spaces(self):
self.assertEqual(split_library_path('Test Library 2'),
('Test Library 2', '/'))
def test_library_name_trailing_slash(self):
self.assertEqual(split_library_path('TestLibrary/'),
('TestLibrary', '/'))
def test_library_name_only(self):
self.assertEqual(split_library_path('TestLibrary'),
('TestLibrary', '/'))