def test_7z(self):
self.assertImportFile('some file.1.txt.zip', 'test 7z.txt.zip', 'test 7z.txt')
file_name = import_file(self._file('some folder.tar.gz'), 'some folder.tar.gz')
assert file_name == 'some folder'
assert os.path.isdir('some folder'), "directory not found"
assert os.path.exists('some folder.tar.gz'), "file not found"
shutil.rmtree('some folder')
os.remove('some folder.tar.gz')
file_name = import_file(
self._file('some folder.tar.gz'),
'some folder.tar.gz',
ImportedFormat.COMPRESSED,
)
assert file_name == 'some folder.tar.gz'
assert not os.path.isdir('some folder'), "directory should not exist"
assert os.path.exists('some folder.tar.gz'), "file not found"
file_name = import_file(self._file('some folder 1.zip'), 'some folder 1.zip')
assert file_name == 'some folder 1'
assert os.path.isdir('some folder 1'), "directory not found"
assert os.path.exists('some folder 1.tar.gz'), "file not found"
shutil.rmtree('some folder 1')
os.remove('some folder 1.tar.gz')
file_name = import_file(
self._file('some folder 1.zip'),
'some folder 1.zip',
ImportedFormat.COMPRESSED,
)
assert file_name == 'some folder 1.tar.gz'
assert not os.path.isdir('some folder 1'), "directory should not exist"
assert os.path.exists('some folder 1.tar.gz'), "file not found"
def test_uncompressed_url(self):
responses.add(
responses.GET, 'https://testurl/someslug', status=200, body='some text'
)
import_file('https://testurl/someslug', 'test uncompressed.txt')
assert os.path.exists('test uncompressed.txt'), "file not found"
assert os.path.exists('test uncompressed.txt.gz'), "file not found"
def test_gz_corrupted(self):
with self.assertRaises(
ValueError, msg='invalid gzip file format: corrupted.gz'
):
import_file(self._file('corrupted.gz'), 'corrupted.gz')
with self.assertRaises(
ValueError, msg='invalid gzip file format: corrupted.gz'
):
import_file(
self._file('corrupted.gz'), 'corrupted.gz', ImportedFormat.COMPRESSED
)
def test_gz_url(self):
# Return gzipped file
responses.add(
responses.GET,
'https://testurl/someslug',
status=200,
body=bytes.fromhex(
'1f8b0808a6cea15c0003736f6d652066696c652e312e747874002bcecf4d'
'552849ad28e10200bce62c190a000000'
),
)
import_file('https://testurl/someslug', 'test uncompressed.txt.gz')
assert os.path.exists('test uncompressed.txt'), "file not found"
assert os.path.exists('test uncompressed.txt.gz'), "file not found"
def test_7z_url(self):
# Return zipped file
responses.add(
responses.GET,
'http://testurl/someslug',
status=200,
body=bytes.fromhex(
'504b03041400080008000c5b814e0000000000000000000000000f001000'
'736f6d652066696c652e312e74787455580c009fdaa15cc7d8a15cf50114'
'002bcecf4d552849ad28e10200504b0708bce62c190c0000000a00000050'
'4b010215031400080008000c5b814ebce62c190c0000000a0000000f000c'
'000000000000000040a48100000000736f6d652066696c652e312e747874'
'555808009fdaa15cc7d8a15c504b05060000000001000100490000005900'
'00000000'
),
)
import_file('http://testurl/someslug', 'test uncompressed.txt.zip')
assert os.path.exists('test uncompressed.txt'), "file not found"
assert os.path.exists('test uncompressed.txt.gz'), "file not found"
def assertImportFile(self, src, dst, returned_name):
# Test both
src = self._file(src)
file_name = import_file(src, dst)
assert file_name == returned_name
assert os.path.exists(returned_name), "file not found"
assert os.path.exists(returned_name + '.gz'), "file not found"
os.remove(returned_name)
os.remove(returned_name + '.gz')
# Test extracted
file_name = import_file(src, dst, ImportedFormat.EXTRACTED)
assert file_name == returned_name
assert os.path.exists(returned_name), "file not found"
assert not os.path.exists(returned_name + '.gz'), "file should not exist"
os.remove(returned_name)
# Test compressed
file_name = import_file(src, dst, ImportedFormat.COMPRESSED)
assert file_name == returned_name + '.gz'
assert os.path.exists(returned_name + '.gz'), "file not found"
assert not os.path.exists(returned_name), "file should not exist"
os.remove(returned_name + '.gz')
def import_file(self, imported_format=None, progress_from=0.0, progress_to=None):
"""Import field source file to working directory.
:param imported_format: Import file format (extracted, compressed or both)
:param progress_from: Initial progress value
:param progress_to: Final progress value
:return: Destination file path (if extracted and compressed, extracted path given)
"""
if not hasattr(resolwe_runtime_utils, "import_file"):
raise RuntimeError("Requires resolwe-runtime-utils >= 2.0.0")
if imported_format is None:
imported_format = resolwe_runtime_utils.ImportedFormat.BOTH
return resolwe_runtime_utils.import_file(
src=self.file_temp,
file_name=self.path,
imported_format=imported_format,
progress_from=progress_from,
progress_to=progress_to,
)
def import_file(self, imported_format=None, progress_from=0.0, progress_to=None):
"""Import field source file to working directory.
:param imported_format: Import file format (extracted, compressed or both)
:param progress_from: Initial progress value
:param progress_to: Final progress value
:return: Destination file path (if extracted and compressed, extracted path given)
"""
if not hasattr(resolwe_runtime_utils, 'import_file'):
raise RuntimeError('Requires resolwe-runtime-utils >= 2.0.0')
if imported_format is None:
imported_format = resolwe_runtime_utils.ImportedFormat.BOTH
return resolwe_runtime_utils.import_file(
src=self.file_temp,
file_name=self.path,
imported_format=imported_format,
progress_from=progress_from,
progress_to=progress_to
)
def test_invalid_url(self):
with self.assertRaises(requests.exceptions.ConnectionError):
import_file('http://testurl/someslug', 'test uncompressed.txt.zip')
def test_7z_corrupted(self):
with self.assertRaises(ValueError, msg='failed to extract file: corrupted.zip'):
import_file(self._file('corrupted.zip'), 'corrupted.zip')