def bound_callable(*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:]
ctx = context_factory()
# Set up a scope under which we can track destructable references
# if something goes wrong, the __exit__ handler of this context
# manager will clean up. (It also cleans up when things go right)
with ctx as scope:
provenance = self._ProvCaptureCls(self.type, self.package,
self.id)
scope.add_reference(provenance)
# Collate user arguments
user_input = {
name: value
for value, name in zip(args,
self.signature.signature_order)
}
user_input.update(kwargs)
# Type management
self.signature.check_types(**user_input)
output_types = self.signature.solve_output(**user_input)
callable_args = {}
# Record parameters
for name, spec in self.signature.parameters.items():
parameter = callable_args[name] = user_input[name]
provenance.add_parameter(name, spec.qiime_type, parameter)
# Record and transform inputs
for name, spec in self.signature.inputs.items():
artifact = user_input[name]
provenance.add_input(name, artifact)
if artifact is None:
callable_args[name] = None
elif spec.has_view_type():
recorder = provenance.transformation_recorder(name)
if qtype.is_collection_type(spec.qiime_type):
# Always put in a list. Sometimes the view isn't
# hashable, which isn't relevant, but would break
# a Set[SomeType].
callable_args[name] = [
a._view(spec.view_type, recorder)
for a in user_input[name]
]
else:
callable_args[name] = artifact._view(
spec.view_type, recorder)
else:
callable_args[name] = artifact
# Execute
outputs = self._callable_executor_(scope, callable_args,
output_types, provenance)
if len(outputs) != len(self.signature.outputs):
raise ValueError(
"Number of callable outputs must match number of "
"outputs defined in signature: %d != %d" %
(len(outputs), 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 qiime2.sdk.Results(self.signature.outputs.keys(),
outputs)
def test_set_primitive_type(self):
self.assertTrue(is_collection_type(Set[Int % Range(5)]))
self.assertTrue(is_primitive_type(Set[Int % Range(5)]))
self.assertFalse(is_semantic_type(Set[Int % Range(5)]))
def test_set_semantic_type(self):
Foo = SemanticType('Foo')
self.assertTrue(is_collection_type(Set[Foo]))
self.assertTrue(is_semantic_type(Set[Foo]))
self.assertFalse(is_primitive_type(Set[Foo]))
def bound_callable(*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:]
ctx = context_factory()
# Set up a scope under which we can track destructable references
# if something goes wrong, the __exit__ handler of this context
# manager will clean up. (It also cleans up when things go right)
with ctx as scope:
provenance = self._ProvCaptureCls(
self.type, self.package, self.id)
scope.add_reference(provenance)
# Collate user arguments
user_input = {name: value for value, name in
zip(args, self.signature.signature_order)}
user_input.update(kwargs)
# Type management
self.signature.check_types(**user_input)
output_types = self.signature.solve_output(**user_input)
callable_args = {}
# Record parameters
for name, spec in self.signature.parameters.items():
parameter = callable_args[name] = user_input[name]
provenance.add_parameter(name, spec.qiime_type, parameter)
# Record and transform inputs
for name, spec in self.signature.inputs.items():
artifact = user_input[name]
provenance.add_input(name, artifact)
if artifact is None:
callable_args[name] = None
elif spec.has_view_type():
recorder = provenance.transformation_recorder(name)
if qtype.is_collection_type(spec.qiime_type):
# Always put in a list. Sometimes the view isn't
# hashable, which isn't relevant, but would break
# a Set[SomeType].
callable_args[name] = [
a._view(spec.view_type, recorder)
for a in user_input[name]]
else:
callable_args[name] = artifact._view(
spec.view_type, recorder)
else:
callable_args[name] = artifact
# Execute
outputs = self._callable_executor_(scope, callable_args,
output_types, provenance)
if len(outputs) != len(self.signature.outputs):
raise ValueError(
"Number of callable outputs must match number of "
"outputs defined in signature: %d != %d" %
(len(outputs), 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 qiime2.sdk.Results(self.signature.outputs.keys(),
outputs)
def test_set_primitive_type(self):
self.assertTrue(is_collection_type(Set[Int % Range(5)]))
self.assertTrue(is_primitive_type(Set[Int % Range(5)]))
self.assertFalse(is_semantic_type(Set[Int % Range(5)]))
def test_set_semantic_type(self):
Foo = SemanticType('Foo')
self.assertTrue(is_collection_type(Set[Foo]))
self.assertTrue(is_semantic_type(Set[Foo]))
self.assertFalse(is_primitive_type(Set[Foo]))
