def test_single_file(self):
self.make_file(b"Normal text\nand things\n", "foobarbaz.txt")
self.assertEqual(
util.md5sum_directory(self.test_path),
collections.OrderedDict([("foobarbaz.txt", "93b048d0202e4b06b658f3aef1e764d3")]),
)
def test_sorted_decent(self):
nested_dir = self.test_path / "beta"
nested_dir.mkdir()
filepath = (nested_dir / "10").relative_to(self.test_path)
self.make_file(b"10", filepath)
filepath = (nested_dir / "1").relative_to(self.test_path)
self.make_file(b"1", filepath)
filepath = (nested_dir / "2").relative_to(self.test_path)
self.make_file(b"2", filepath)
nested_dir = self.test_path / "alpha"
nested_dir.mkdir()
filepath = (nested_dir / "foo").relative_to(self.test_path)
self.make_file(b"foo", filepath)
filepath = (nested_dir / "bar").relative_to(self.test_path)
self.make_file(b"bar", filepath)
self.make_file(b"z", "z")
self.assertEqual(
list(util.md5sum_directory(self.test_path).items()),
[
("z", "fbade9e36a3f36d3d676c1b808451dd7"),
("alpha/bar", "37b51d194a7513e45b56f6524f2d51f2"),
("alpha/foo", "acbd18db4cc2f85cedef654fccc4a4d8"),
("beta/1", "c4ca4238a0b923820dcc509a6f75849b"),
("beta/10", "d3d9446802a44259755d38e6d163e820"),
("beta/2", "c81e728d9d4c2f636f067f89cc14862c"),
],
)
def test_sorted_decent(self):
nested_dir = self.test_path / 'beta'
nested_dir.mkdir()
filepath = (nested_dir / '10').relative_to(self.test_path)
self.make_file(b'10', filepath)
filepath = (nested_dir / '1').relative_to(self.test_path)
self.make_file(b'1', filepath)
filepath = (nested_dir / '2').relative_to(self.test_path)
self.make_file(b'2', filepath)
nested_dir = self.test_path / 'alpha'
nested_dir.mkdir()
filepath = (nested_dir / 'foo').relative_to(self.test_path)
self.make_file(b'foo', filepath)
filepath = (nested_dir / 'bar').relative_to(self.test_path)
self.make_file(b'bar', filepath)
self.make_file(b'z', 'z')
self.assertEqual(list(util.md5sum_directory(self.test_path).items()), [
('z', 'fbade9e36a3f36d3d676c1b808451dd7'),
('alpha/bar', '37b51d194a7513e45b56f6524f2d51f2'),
('alpha/foo', 'acbd18db4cc2f85cedef654fccc4a4d8'),
('beta/1', 'c4ca4238a0b923820dcc509a6f75849b'),
('beta/10', 'd3d9446802a44259755d38e6d163e820'),
('beta/2', 'c81e728d9d4c2f636f067f89cc14862c'),
])
def test_single_file(self):
self.make_file(b'Normal text\nand things\n', 'foobarbaz.txt')
self.assertEqual(
util.md5sum_directory(self.test_path),
collections.OrderedDict([('foobarbaz.txt',
'93b048d0202e4b06b658f3aef1e764d3')]))
def test_nested_empty_directories(self):
(self.test_path / 'foo').mkdir()
(self.test_path / 'foo' / 'bar').mkdir()
(self.test_path / 'baz').mkdir()
self.assertEqual(util.md5sum_directory(self.test_path),
collections.OrderedDict())
def test_can_use_string(self):
nested_dir = self.test_path / "bar"
nested_dir.mkdir()
filepath = (nested_dir / "foo.baz").relative_to(self.test_path)
self.make_file(b"anything at all", filepath)
self.assertEqual(
util.md5sum_directory(str(self.test_path)),
collections.OrderedDict([("bar/foo.baz", "dcc0975b66728be0315abae5968379cb")]),
)
def test_can_use_string(self):
nested_dir = self.test_path / 'bar'
nested_dir.mkdir()
filepath = (nested_dir / 'foo.baz').relative_to(self.test_path)
self.make_file(b'anything at all', filepath)
self.assertEqual(
util.md5sum_directory(str(self.test_path)),
collections.OrderedDict([('bar/foo.baz',
'dcc0975b66728be0315abae5968379cb')]))
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_nested_empty_directories(self):
(self.test_path / "foo").mkdir()
(self.test_path / "foo" / "bar").mkdir()
(self.test_path / "baz").mkdir()
self.assertEqual(util.md5sum_directory(self.test_path), collections.OrderedDict())
def test_empty_directory(self):
self.assertEqual(util.md5sum_directory(self.test_path), collections.OrderedDict())
def test_empty_directory(self):
self.assertEqual(util.md5sum_directory(self.test_path),
collections.OrderedDict())
