def test_atomic_write_transparent_on_success(self):
_, tempfile_path = mkstemp()
os.remove(tempfile_path) # We reuse the path, not the file itself
with atomic_write(tempfile_path) as f:
f.write('success')
with open(tempfile_path, 'rb') as f:
self.assertEqual('success', f.read())
os.remove(tempfile_path)
def test_atomic_write_transparent_on_success(self):
_, tempfile_path = mkstemp()
os.remove(tempfile_path) # We reuse the path, not the file itself
with atomic_write(tempfile_path) as f:
f.write('success')
with open(tempfile_path, 'rb') as f:
self.assertEqual('success', f.read())
os.remove(tempfile_path)
def test_atomic_write_deletes_on_fail(self):
_, tempfile_path = mkstemp()
os.remove(tempfile_path) # We reuse the path, not the file itself
try:
with atomic_write(tempfile_path) as f:
f.write('fail')
raise Exception
except Exception:
pass
self.assertFalse(exists(tempfile_path))
def test_atomic_write_deletes_on_fail(self):
_, tempfile_path = mkstemp()
os.remove(tempfile_path) # We reuse the path, not the file itself
try:
with atomic_write(tempfile_path) as f:
f.write('fail')
raise Exception
except Exception:
pass
self.assertFalse(exists(tempfile_path))
def download_picrust_files(output_path, with_confidence, gg_version,
type_of_prediction, force):
if not os.path.exists(output_path):
print('Creating output directory {path}...'.format(path=output_path))
os.mkdir(output_path)
elif not os.path.isdir(output_path):
print('Error: {path} already exists but is not a directory!'.format(
path=output_path))
exit(1)
try:
files_to_download = [
FILES[('16s', gg_version)], FILES[(type_of_prediction, gg_version)]
]
except KeyError:
msg = ('Error: {type_of_prediction} predictions not available for'
' GreenGenes {gg_version}')
print(
msg.format(gg_version=gg_version,
type_of_prediction=type_of_prediction))
exit(1)
if with_confidence:
try:
ci_files = [
FILES[('16s_ci', gg_version)],
FILES[(type_of_prediction + '_ci', gg_version)],
]
except KeyError:
msg = 'Error: CI files not available for {gg_version}'
print(msg.format(gg_version=gg_version))
exit(1)
files_to_download.extend(ci_files)
print('Downloading files to {path}...'.format(path=output_path))
for filename in files_to_download:
if 'variances' not in filename:
url = urljoin(BASE_URL, gg_version + '/' + filename)
else:
url = urljoin(BASE_URL, gg_version + '/variances/' + filename)
file_path = os.path.join(DATA_DIR, filename)
if os.path.exists(file_path) and not force:
msg = 'Skipping download of {filename}: file already exists.'
print(msg.format(filename=filename))
continue
else:
print('Downloading {filename}...'.format(filename=filename))
try:
response = urlopen(url)
with atomic_write(file_path) as f:
f.write(response.read())
except HTTPError as e:
msg = 'There was a problem downloading {filename}: {exception}.'
print(msg.format(filename=filename, exception=e))
exit(1)
print('Done.')