def import_data(cls, type, view, view_type=None):
type_, type = type, __builtins__['type']
is_format = False
if isinstance(type_, str):
type_ = qiime.sdk.parse_type(type_)
if isinstance(view_type, str):
view_type = qiime.sdk.parse_format(view_type)
is_format = True
if view_type is None:
if type(view) is str or isinstance(view, pathlib.PurePath):
is_format = True
pm = qiime.sdk.PluginManager()
output_dir_fmt = pm.get_directory_format(type_)
if pathlib.Path(view).is_file():
if not issubclass(output_dir_fmt,
model.SingleFileDirectoryFormatBase):
raise ValueError("Importing %r requires a"
" directory, not %s"
% (output_dir_fmt.__name__, view))
view_type = output_dir_fmt.file.format
else:
view_type = output_dir_fmt
else:
view_type = type(view)
format_ = None
md5sums = None
if is_format:
path = pathlib.Path(view)
if path.is_file():
md5sums = {path.name: util.md5sum(path)}
elif path.is_dir():
md5sums = util.md5sum_directory(path)
else:
raise ValueError("Path '%s' does not exist." % path)
format_ = view_type
provenance_capture = archive.ImportProvenanceCapture(format_, md5sums)
return cls._from_view(type_, view, view_type, provenance_capture)
def import_data(cls, type, view, view_type=None):
type_, type = type, __builtins__['type']
is_format = False
if isinstance(type_, str):
type_ = qiime.sdk.parse_type(type_)
if isinstance(view_type, str):
view_type = qiime.sdk.parse_format(view_type)
is_format = True
if view_type is None:
if type(view) is str or isinstance(view, pathlib.PurePath):
is_format = True
pm = qiime.sdk.PluginManager()
output_dir_fmt = pm.get_directory_format(type_)
if pathlib.Path(view).is_file():
if not issubclass(output_dir_fmt,
model.SingleFileDirectoryFormatBase):
raise ValueError("Importing %r requires a"
" directory, not %s" %
(output_dir_fmt.__name__, view))
view_type = output_dir_fmt.file.format
else:
view_type = output_dir_fmt
else:
view_type = type(view)
format_ = None
md5sums = None
if is_format:
path = pathlib.Path(view)
if path.is_file():
md5sums = {path.name: util.md5sum(path)}
elif path.is_dir():
md5sums = util.md5sum_directory(path)
else:
raise ValueError("Path '%s' does not exist." % path)
format_ = view_type
provenance_capture = archive.ImportProvenanceCapture(format_, md5sums)
return cls._from_view(type_, view, view_type, provenance_capture)
def test_can_use_string(self):
string_path = str(self.make_file(b"Normal text\nand things\n"))
self.assertEqual(util.md5sum(string_path), "93b048d0202e4b06b658f3aef1e764d3")
def test_large_file(self):
path = self.make_file(b"verybigfile" * (1024 * 50))
self.assertEqual(util.md5sum(path), "27d64211ee283283ad866c18afa26611")
def test_single_byte_file(self):
self.assertEqual(util.md5sum(self.make_file(b"a")), "0cc175b9c0f1b6a831c399e269772661")
def test_empty_file(self):
self.assertEqual(util.md5sum(self.make_file(b"")), "d41d8cd98f00b204e9800998ecf8427e")
def test_large_file(self):
path = self.make_file(b'verybigfile' * (1024 * 50))
self.assertEqual(util.md5sum(path), '27d64211ee283283ad866c18afa26611')
def test_single_byte_file(self):
self.assertEqual(util.md5sum(self.make_file(b'a')),
'0cc175b9c0f1b6a831c399e269772661')
def test_empty_file(self):
self.assertEqual(util.md5sum(self.make_file(b'')),
'd41d8cd98f00b204e9800998ecf8427e')
def test_can_use_string(self):
string_path = str(self.make_file(b'Normal text\nand things\n'))
self.assertEqual(util.md5sum(string_path),
'93b048d0202e4b06b658f3aef1e764d3')