def import_data(cls, type, view, view_type=None):
type_, type = type, __builtins__['type']
if isinstance(type_, str):
type_ = qiime.sdk.parse_type(type_)
if isinstance(view_type, str):
view_type = qiime.sdk.parse_format(view_type)
if view_type is None:
if type(view) is str or isinstance(view, pathlib.PurePath):
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)
return cls._from_view(type_, view, view_type)
def __eq__(self, other):
return (
type(self) is type(other) and
self.inputs == other.inputs and
self.parameters == other.parameters and
self.outputs == other.outputs
)
def __eq__(self, other):
# Checking the UUID is mostly sufficient but requiring an exact type
# match makes it safer in case `other` is a subclass or a completely
# different type that happens to have a `.uuid` property. We want to
# ensure (as best as we can) that the UUIDs we are comparing are linked
# to the same type of QIIME 2 object.
return (type(self) == type(other) and self.uuid == other.uuid)
def __eq__(self, other):
# Checking the UUID is mostly sufficient but requiring an exact type
# match makes it safer in case `other` is a subclass or a completely
# different type that happens to have a `.uuid` property. We want to
# ensure (as best as we can) that the UUIDs we are comparing are linked
# to the same type of QIIME 2 object.
return (
type(self) == type(other) and
self.uuid == other.uuid
)
def _from_view(cls, view, type_, provenance):
"""
Parameters
----------
view : Python object
View to serialize.
type_ : qiime.plugin.Type
Concrete semantic type of the artifact.
provenance : qiime.sdk.Provenance
Artifact provenance.
"""
if not cls._is_valid_type(type_):
raise TypeError(
"An artifact requires a concrete semantic type, not type %r."
% type_)
if provenance is not None and not isinstance(provenance,
qiime.sdk.Provenance):
raise TypeError(
"`provenance` must be None or an instance of "
"qiime.sdk.Provenance.")
data_layout = cls._get_data_layout(type_)
view_type = type(view)
# TODO better error handling for when `view` cannot be written to
# `type_` data layout.
writer = data_layout.writers[view_type]
writer = functools.partial(writer, view)
artifact = cls.__new__(cls)
artifact._archiver = qiime.core.archiver.Archiver(
uuid.uuid4(), type_, provenance, data_initializer=writer)
return artifact
def _from_view(cls, view, type_, provenance):
"""
Parameters
----------
view : Python object
View to serialize.
type_ : qiime.plugin.Type
Concrete semantic type of the artifact.
provenance : qiime.sdk.Provenance
Artifact provenance.
"""
cls._assert_valid_type(type_)
data_layout = cls._get_data_layout(type_)
view_type = type(view)
# TODO better error handling for when `view` cannot be written to
# `type_` data layout.
writer = data_layout.writers[view_type]
writer = functools.partial(writer, view)
artifact = cls.__new__(cls)
artifact._archiver = qiime.core.archiver.Archiver(
uuid.uuid4(), type_, provenance, data_initializer=writer)
return artifact
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 load(cls, filepath):
"""Factory for loading Artifacts and Visualizations."""
archiver = archive.Archiver.load(filepath)
if Artifact._is_valid_type(archiver.type):
result = Artifact.__new__(Artifact)
elif Visualization._is_valid_type(archiver.type):
result = Visualization.__new__(Visualization)
else:
raise TypeError(
"Cannot load filepath %r into an Artifact or Visualization "
"because type %r is not supported." %
(filepath, archiver.type))
if type(result) is not cls and cls is not Result:
raise TypeError(
"Attempting to load %s with `%s.load`. Use `%s.load` instead."
% (type(result).__name__, cls.__name__, type(result).__name__))
result._archiver = archiver
return result
def load(cls, filepath):
"""Factory for loading Artifacts and Visualizations."""
archiver = qiime.core.archiver.Archiver.load(filepath)
if Artifact._is_valid_type(archiver.type):
result = Artifact.__new__(Artifact)
elif Visualization._is_valid_type(archiver.type):
result = Visualization.__new__(Visualization)
else:
raise TypeError(
"Cannot load filepath %r into an Artifact or Visualization "
"because type %r is not supported."
% (filepath, archiver.type))
if type(result) is not cls and cls is not Result:
raise TypeError(
"Attempting to load %s with `%s.load`. Use `%s.load` instead."
% (type(result).__name__, cls.__name__,
type(result).__name__))
result._archiver = archiver
return result
def import_data(cls, type, view, view_type=None):
type_, type = type, __builtins__['type']
if isinstance(type_, str):
type_ = qiime.sdk.parse_type(type_)
if isinstance(view_type, str):
view_type = qiime.core.util.parse_format(view_type)
if view_type is None:
if type(view) is str or isinstance(view, pathlib.PurePath):
pm = qiime.sdk.PluginManager()
output_dir_fmt = pm.get_directory_format(type_)
if pathlib.Path(view).is_file() and issubclass(
output_dir_fmt, model.SingleFileDirectoryFormatBase):
view_type = output_dir_fmt.file.format
else:
view_type = output_dir_fmt
else:
view_type = type(view)
provenance = ("This artifact was generated by importing data from an "
"external source.")
return cls._from_view(type_, view, view_type, provenance)
