def test_copy_folder(self):
client = helpers.get_genomespace_client()
local_test_folder = self._get_test_folder()
remote_folder, _ = self._get_remote_folder()
local_temp_folder = self._get_temp_folder()
client.mkdir(remote_folder)
client.copy(local_test_folder, remote_folder, recurse=True)
client.copy(remote_folder, local_temp_folder, recurse=True)
client.delete(remote_folder, recurse=True)
dcmp = filecmp.dircmp(local_test_folder, local_temp_folder)
self.assertTrue(len(dcmp.same_files) == 3, "Should have copied 3"
" identical files")
self.assertTrue(len(dcmp.left_only) == 0, "Should have no extra files"
" in local fixtures folder")
self.assertTrue(len(dcmp.right_only) == 0, "Should have no extra files"
" in local temp folder")
self.assertTrue(len(dcmp.subdirs) == 1, "Should have exactly one"
" subfolder")
self.assertTrue(len(dcmp.subdirs['folder1'].common) == 2, "Should have"
" exactly 2 files in subfolder")
self.assertTrue(len(dcmp.subdirs['folder1'].left_only) == 0, "Should"
" have no extra files in local subfolder")
self.assertTrue(len(dcmp.subdirs['folder1'].right_only) == 0, "Should"
" have no extra files in copied subfolder")
shutil.rmtree(local_temp_folder)
def test_list(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file_path, remote_name = self._get_remote_file()
client.copy(local_test_file, remote_file_path)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist["contents"]
if f["name"] == remote_name]
self.assertTrue(len(found_file) == 1, "Expected file not found")
client.delete(remote_file_path)
def test_list(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file_path, remote_name = self._get_remote_file()
client.copy(local_test_file, remote_file_path)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist.contents
if f.name == remote_name]
self.assertTrue(len(found_file) == 1, "Expected file not found")
client.delete(remote_file_path)
def test_delete(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file_path, remote_name = self._get_remote_file()
client.copy(local_test_file, remote_file_path)
client.delete(remote_file_path)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist["contents"]
if f["name"] == remote_name]
self.assertTrue(len(found_file) == 0,
"File was found but should have been deleted")
def test_delete(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file_path, remote_name = self._get_remote_file()
client.copy(local_test_file, remote_file_path)
client.delete(remote_file_path)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist.contents
if f.name == remote_name]
self.assertTrue(len(found_file) == 0,
"File was found but should have been deleted")
def test_copy(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file, _ = self._get_remote_file()
local_temp_file = self._get_temp_file()
client.copy(local_test_file, remote_file)
client.copy(remote_file, local_temp_file)
client.delete(remote_file)
self.assertTrue(filecmp.cmp(local_test_file, local_temp_file))
os.remove(local_temp_file)
def test_copy(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file, _ = self._get_remote_file()
local_temp_file = self._get_temp_file()
client.copy(local_test_file, remote_file)
client.copy(remote_file, local_temp_file)
client.delete(remote_file)
self.assertTrue(filecmp.cmp(local_test_file, local_temp_file))
os.remove(local_temp_file)
def test_get_token_expiry(self):
client = helpers.get_genomespace_client()
genomespace_url = helpers.get_genomespace_url()
# no gs-token, as have not yet performed any actions
milliseconds_left = client.get_remaining_token_time(genomespace_url)
self.assertTrue(
milliseconds_left == 0,
"Expected client not yet logged in to have no token expiry time")
# now force a login and hence the client to get a gs-token
client.list(helpers.get_remote_test_folder())
milliseconds_left = client.get_remaining_token_time(genomespace_url)
self.assertTrue(
milliseconds_left > 0,
"Expected a logged in client to have a token expiry time")
def test_delete_wildcard(self):
client = helpers.get_genomespace_client()
local_test_folder = self._get_test_folder()
remote_folder, _ = self._get_remote_folder()
client.mkdir(remote_folder)
client.copy(local_test_folder + "*", remote_folder)
client.delete(remote_folder + "*.txt")
filelist = client.list(remote_folder)
found_file = [f for f in filelist.contents]
self.assertTrue(len(found_file) == 2,
"Two items should be remaining but found: %s"
% (found_file,))
client.delete(remote_folder, recurse=True)
def test_delete_folder(self):
client = helpers.get_genomespace_client()
local_test_folder = self._get_test_folder()
remote_folder, remote_name = self._get_remote_folder()
client.mkdir(remote_folder)
client.copy(local_test_folder, remote_folder, recurse=True)
client.delete(remote_folder, recurse=True)
filelist = client.list(helpers.get_remote_test_folder())
found_folder = [f for f in filelist.contents
if self._adjust_gs_swift_bug(f.name) == remote_name]
self.assertTrue(len(found_folder) == 0,
"Folder was found but should have been deleted")
def test_get_metadata(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file_path, remote_name = self._get_remote_file()
# Set a specific data format
remote_file_path += '?dataformat=http://www.genomespace.org' \
'/datamanager/dataformat/txt'
client.copy(local_test_file, remote_file_path)
metadata = client.get_metadata(remote_file_path)
client.delete(remote_file_path)
self.assertIsInstance(
metadata, GSFileMetadata,
"Expected metadata to be of type GSFileMetadata")
self.assertIsInstance(
metadata.data_format, GSDataFormat,
"Expected metadata's dataFormat to be of type GSDataFormat")
self.assertIsInstance(
metadata.available_data_formats, list,
"Expected metadata's available formats to be of type list")
owner = get_test_username()
self.assertTrue(
metadata.owner['name'] == owner,
"Expected file to owned by uploader")
acl_object = metadata.effective_acl.object
self.assertTrue(
acl_object.object_id.endswith(remote_name),
"Expected acl object path of %s to end with %s" % (
acl_object.object_id, remote_name))
self.assertTrue(
acl_object.object_type == 'DataManagerFileObject',
"Expected acl object type has changed?")
access_control_entries = metadata.effective_acl.access_control_entries
self.assertTrue(
len(access_control_entries) == 2,
"Expected only two entries in ACL")
self.assertTrue(
access_control_entries[0].permission in ('W', 'R'),
"Expected owner to be able to read or write file?")
self.assertTrue(
access_control_entries[0].sid.type in ('User', 'Group'),
"Expected sid type to be either 'User' or 'Group'")
self.assertTrue(
access_control_entries[0].sid.name == owner,
"Expected sid name to be the owner")
def test_mkdir_rmdir(self):
client = helpers.get_genomespace_client()
remote_folder1, remote_name1 = self._get_remote_folder()
client.mkdir(remote_folder1)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist.contents
if self._adjust_gs_swift_bug(f.name) == remote_name1 and
f.is_directory]
self.assertTrue(len(found_file) == 1,
"Expected to find one created folder")
# The recurse is needed to compensate for a bug in GenomeSpace swift
# which creates a .hidden file in each folder
client.delete(remote_folder1, recurse=True)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist.contents
if self._adjust_gs_swift_bug(f.name) == remote_name1]
self.assertTrue(len(found_file) == 0,
"Expected folder to be deleted but it's not")
def test_move(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
local_temp_file = self._get_temp_file()
remote_file1, _ = self._get_remote_file()
remote_file2, _ = self._get_remote_file()
client.copy(local_test_file, remote_file1)
client.move(remote_file1, remote_file2)
client.copy(remote_file2, local_temp_file)
client.delete(remote_file2)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist["contents"]
if f["name"] == remote_file1]
self.assertTrue(len(found_file) == 0,
"File was found but should have been deleted")
self.assertTrue(filecmp.cmp(local_test_file, local_temp_file))
os.remove(local_temp_file)
def test_copy_wildcard(self):
client = helpers.get_genomespace_client()
local_test_folder = self._get_test_folder()
remote_folder, _ = self._get_remote_folder()
local_temp_folder = self._get_temp_folder()
client.mkdir(remote_folder)
client.copy(local_test_folder + "*", remote_folder)
client.copy(remote_folder + "*.txt", local_temp_folder)
client.delete(remote_folder, recurse=True)
dcmp = filecmp.dircmp(local_test_folder, local_temp_folder)
self.assertTrue(len(dcmp.same_files) == 2, "Should have copied 2"
" identical text files")
self.assertTrue(len(dcmp.left_only) == 2, "Should have 1 extra file"
" in local fixtures folder")
self.assertTrue(len(dcmp.right_only) == 0, "Should have no extra files"
" in local temp folder")
shutil.rmtree(local_temp_folder)
def test_move(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
local_temp_file = self._get_temp_file()
remote_file1, remote_name1 = self._get_remote_file()
remote_file2, _ = self._get_remote_file()
client.copy(local_test_file, remote_file1)
client.move(remote_file1, remote_file2)
client.copy(remote_file2, local_temp_file)
client.delete(remote_file2)
filelist = client.list(helpers.get_remote_test_folder())
found_file = [f for f in filelist.contents
if f.name == remote_name1]
self.assertTrue(len(found_file) == 0,
"File was found but should have been moved")
self.assertTrue(filecmp.cmp(local_test_file, local_temp_file))
os.remove(local_temp_file)
def test_get_metadata(self):
client = helpers.get_genomespace_client()
local_test_file = self._get_test_file()
remote_file_path, _ = self._get_remote_file()
# Set a specific data format
remote_file_path += '?dataformat=http://www.genomespace.org' \
'/datamanager/dataformat/txt'
client.copy(local_test_file, remote_file_path)
metadata = client.get_metadata(remote_file_path)
client.delete(remote_file_path)
self.assertIsInstance(
metadata, GSFileMetadata,
"Expected metadata to be of type GSFileMetadata")
self.assertIsInstance(
metadata.dataFormat, GSDataFormat,
"Expected metadata's dataFormat to be of type GSDataFormat")
self.assertIsInstance(
metadata.availableDataFormats, list,
"Expected metadata's available formats to be of type list")