def test_copy_hardlink(self):
"""
Test copy with hardlinks: we create a file in data_dir and try to
link it. This should work unless /tmp don't accept hardlinks.
"""
# Create a file and a directory in data_dir. We don't destroy them
# since they are in /tmp.
_, orig_file_full = tempfile.mkstemp(dir=self.utils.data_dir)
orig_file = os.path.basename(orig_file_full)
to_dir = tempfile.mkdtemp(dir=self.utils.data_dir)
new_file_full = os.path.join(to_dir, orig_file)
# Copy
from_dir = self.utils.data_dir
files_to_copy = [{'root': from_dir, 'name': orig_file}]
Utils.copy_files(files_to_copy, to_dir, use_hardlinks=True)
# Check if file was copied
self.assertTrue(os.path.exists(new_file_full))
# Check if it's really a hardlink. This may fail so we catch
# any exceptions.
orig_file_stat = os.stat(orig_file_full)
new_file_stat = os.stat(new_file_full)
try:
self.assertTrue(orig_file_stat.st_ino == new_file_stat.st_ino)
except Exception:
msg = "In %s: copy worked but hardlinks were not used." % self.id()
print(msg, file=sys.stderr)
def test_copy(self):
from_dir = os.path.dirname(os.path.realpath(__file__))
local_file = 'biomaj_tests.py'
files_to_copy = [{'root': from_dir, 'name': local_file}]
to_dir = self.utils.data_dir
Utils.copy_files(files_to_copy, to_dir)
self.assertTrue(os.path.exists(to_dir + '/biomaj_tests.py'))
def test_uncompress(self):
from_file = {
'root': os.path.dirname(os.path.realpath(__file__)),
'name': 'bank/test.fasta.gz'
}
to_dir = self.utils.data_dir
Utils.copy_files([from_file], to_dir)
Utils.uncompress(os.path.join(to_dir, from_file['name']))
self.assertTrue(os.path.exists(to_dir + '/bank/test.fasta'))
def download(self, local_dir):
'''
Copy local files to local_dir
:param local_dir: Directory where files should be copied
:type local_dir: str
:return: list of downloaded files
'''
self.logger.debug('Local:Download')
Utils.copy_files(self.files_to_download,
local_dir,
use_hardlinks=self.use_hardlinks,
lock=self.mkdir_lock)
for rfile in self.files_to_download:
rfile['download_time'] = 0
return self.files_to_download