def _callable_executor_(self, callable, view_args, output_types,
provenance):
output_views = callable(**view_args)
output_views = tuplize(output_views)
# TODO this won't work if the user has annotated their "view API" to
# return a `typing.Tuple` with some number of components. Python will
# return a tuple when there are multiple return values, and this length
# check will fail because the tuple as a whole should be matched up to
# a single output type instead of its components. This is an edgecase
# due to how Python handles multiple returns, and can be worked around
# by using something like `typing.List` instead.
if len(output_views) != len(output_types):
raise TypeError(
"Number of output views must match number of output "
"semantic types: %d != %d"
% (len(output_views), len(output_types)))
output_artifacts = []
for output_view, (semantic_type, view_type) in \
zip(output_views, output_types.values()):
if type(output_view) is not view_type:
raise TypeError(
"Expected output view type %r, received %r" %
(view_type.__name__, type(output_view).__name__))
artifact = qiime.sdk.Artifact._from_view(
semantic_type, output_view, view_type, provenance)
output_artifacts.append(artifact)
if len(output_artifacts) == 1:
return output_artifacts[0]
else:
return tuple(output_artifacts)
def _callable_executor_(self, callable, view_args, output_types,
provenance):
output_views = callable(**view_args)
output_views = tuplize(output_views)
# TODO this won't work if the user has annotated their "view API" to
# return a `typing.Tuple` with some number of components. Python will
# return a tuple when there are multiple return values, and this length
# check will fail because the tuple as a whole should be matched up to
# a single output type instead of its components. This is an edgecase
# due to how Python handles multiple returns, and can be worked around
# by using something like `typing.List` instead.
if len(output_views) != len(output_types):
raise TypeError(
"Number of output views must match number of output "
"semantic types: %d != %d"
% (len(output_views), len(output_types)))
output_artifacts = []
for output_view, (semantic_type, view_type) in \
zip(output_views, output_types.values()):
if type(output_view) is not view_type:
raise TypeError(
"Expected output view type %r, received %r" %
(view_type.__name__, type(output_view).__name__))
artifact = qiime.sdk.Artifact._from_view(
semantic_type, output_view, view_type, provenance.fork())
output_artifacts.append(artifact)
if len(output_artifacts) == 1:
return output_artifacts[0]
else:
return tuple(output_artifacts)
def __getitem__(self, fields):
fields = tuplize(fields)
if len(fields) != len(self.field_names):
raise TypeError("%r takes %d field(s), %d provided."
% (self, len(self.field_names), len(fields)))
for args in zip(self.field_names, fields):
self._validate_field_(*args)
return self._apply_fields_(fields=fields)
def __getitem__(self, fields):
fields = tuplize(fields)
if len(fields) != len(self.field_names):
raise TypeError("%r takes %d field(s), %d provided." %
(self, len(self.field_names), len(fields)))
for args in zip(self.field_names, fields):
self._validate_field_(*args)
return self._apply_fields_(fields=fields)
def callable_wrapper(*args, **kwargs):
provenance = archive.ActionProvenanceCapture(
self.action_type, self.package, self.id)
# This function's signature is rewritten below using
# `decorator.decorator`. When the signature is rewritten, args[0]
# is the function whose signature was used to rewrite this
# function's signature.
args = args[1:]
# TODO this may be able to be simplified once Signature respects
# order.
wrapper_sig = self._callable_sig_converter_(self._callable)
wrapper_sig = inspect.Signature.from_callable(wrapper_sig)
wrapper_params = wrapper_sig.parameters
user_input = {
name: value
for value, name in zip(args, wrapper_params)
}
user_input.update(kwargs)
self.signature.check_types(**user_input)
output_types = self.signature.solve_output(**user_input)
artifacts = {}
for name in self.signature.inputs:
artifact = artifacts[name] = user_input[name]
provenance.add_input(name, artifact)
parameters = {}
for name, (primitive_type, _) in self.signature.parameters.items():
parameter = parameters[name] = user_input[name]
provenance.add_parameter(name, primitive_type, parameter)
view_args = parameters.copy()
for name, (_, view_type) in self.signature.inputs.items():
recorder = provenance.transformation_recorder(name)
view_args[name] = artifacts[name]._view(view_type, recorder)
outputs = self._callable_executor_(self._callable, view_args,
output_types, provenance)
# `outputs` matches a Python function's return: either a single
# value is returned, or it is a tuple of return values. Treat both
# cases uniformly.
outputs_tuple = tuplize(outputs)
for output in outputs_tuple:
output._orphan(self._pid)
if len(outputs_tuple) != len(self.signature.outputs):
raise ValueError(
"Number of callable outputs must match number of outputs "
"defined in signature: %d != %d" %
(len(outputs_tuple), len(self.signature.outputs)))
# Wrap in a Results object mapping output name to value so users
# have access to outputs by name or position.
return Results(self.signature.outputs.keys(), outputs_tuple)
def callable_wrapper(*args, **kwargs):
provenance = archive.ActionProvenanceCapture(
self.action_type, self.package, self.id)
# This function's signature is rewritten below using
# `decorator.decorator`. When the signature is rewritten, args[0]
# is the function whose signature was used to rewrite this
# function's signature.
args = args[1:]
# TODO this may be able to be simplified once Signature respects
# order.
wrapper_sig = self._callable_sig_converter_(self._callable)
wrapper_sig = inspect.Signature.from_callable(wrapper_sig)
wrapper_params = wrapper_sig.parameters
user_input = {name: value for value, name in
zip(args, wrapper_params)}
user_input.update(kwargs)
self.signature.check_types(**user_input)
output_types = self.signature.solve_output(**user_input)
artifacts = {}
for name in self.signature.inputs:
artifact = artifacts[name] = user_input[name]
provenance.add_input(name, artifact)
parameters = {}
for name, (primitive_type, _) in self.signature.parameters.items():
parameter = parameters[name] = user_input[name]
provenance.add_parameter(name, primitive_type, parameter)
view_args = parameters.copy()
for name, (_, view_type) in self.signature.inputs.items():
recorder = provenance.transformation_recorder(name)
view_args[name] = artifacts[name]._view(view_type, recorder)
outputs = self._callable_executor_(self._callable, view_args,
output_types, provenance)
# `outputs` matches a Python function's return: either a single
# value is returned, or it is a tuple of return values. Treat both
# cases uniformly.
outputs_tuple = tuplize(outputs)
for output in outputs_tuple:
output._orphan(self._pid)
if len(outputs_tuple) != len(self.signature.outputs):
raise ValueError(
"Number of callable outputs must match number of outputs "
"defined in signature: %d != %d" %
(len(outputs_tuple), len(self.signature.outputs)))
# Wrap in a Results object mapping output name to value so users
# have access to outputs by name or position.
return Results(self.signature.outputs.keys(), outputs_tuple)
def callable_wrapper(*args, **kwargs):
# This function's signature is rewritten below using
# `decorator.decorator`. When the signature is rewritten, args[0]
# is the function whose signature was used to rewrite this
# function's signature.
args = args[1:]
# TODO this may be able to be simplified once Signature respects
# order.
wrapper_sig = self._callable_sig_converter_(self._callable)
wrapper_sig = inspect.Signature.from_callable(wrapper_sig)
wrapper_params = wrapper_sig.parameters
user_input = {name: value for value, name in
zip(args, wrapper_params)}
user_input.update(kwargs)
self.signature.check_types(**user_input)
output_types = self.signature.solve_output(**user_input)
artifacts = {}
for name in self.signature.inputs:
artifacts[name] = user_input[name]
parameters = {}
for name in self.signature.parameters:
parameters[name] = user_input[name]
view_args = parameters.copy()
for name, (_, view_type) in self.signature.inputs.items():
view_args[name] = artifacts[name].view(view_type)
execution_uuid = uuid.uuid4()
action_reference = (
"%s. Details on plugin, version, website, etc. will also be "
"included, see https://github.com/qiime2/qiime2/issues/26"
% self.id)
artifact_uuids = {name: artifact.uuid for name, artifact in
artifacts.items()}
parameter_references = {name: str(param) for name, param in
parameters.items()}
provenance = qiime.sdk.Provenance(
execution_uuid, action_reference, artifact_uuids,
parameter_references)
outputs = self._callable_executor_(self._callable, view_args,
output_types, provenance)
# `outputs` matches a Python function's return: either a single
# value is returned, or it is a tuple of return values. Treat both
# cases uniformly.
outputs_tuple = tuplize(outputs)
for output in outputs_tuple:
output._orphan(self._pid)
if len(outputs_tuple) != len(self.signature.outputs):
raise ValueError(
"Number of callable outputs must match number of outputs "
"defined in signature: %d != %d" %
(len(outputs_tuple), len(self.signature.outputs)))
# If there is a single output, don't wrap in a Results object to
# match how Python handles single return values. Otherwise, wrap in
# a Results object mapping output name to value so users have
# access to outputs by name or position.
if len(outputs_tuple) == 1:
return outputs_tuple[0]
else:
return Results(self.signature.outputs.keys(),
outputs_tuple)