def test_load_module_objects(self):
""" Method to test module objects import from string description.
"""
from capsul.pipeline.pipeline_nodes import Node
node_sub_class = load_objects(
"capsul.pipeline.pipeline_nodes", allowed_instances=[Node])
for sub_class in node_sub_class:
self.assertTrue(issubclass(sub_class, Node))
node_class = load_objects(
"capsul.pipeline.pipeline_nodes", object_name="Node")[0]
self.assertTrue(type(node_class) is type(Node))
def get_process_instance(process_or_id, **kwargs):
""" Return a Process instance given an identifier.
The identifier is either:
* a derived Process class.
* a derived Process class instance.
* a Nipype Interface instance.
* a Nipype Interface class.
* a string description of the class `<module>.<class>`.
* a string description of a function to warp `<module>.<function>`.
* a string description of a pipeline `<module>.<fname>.xml`.
Default values of the process instance are passed as additional parameters.
.. note:
If no process is found an ImportError is raised.
.. note:
If the 'process_or_id' parameter is not valid a ValueError is raised.
.. note:
If the function to warp does not contain a process description in its
docstring ('<process>...</process>') a ValueError is raised.
Parameters
----------
process_or_id: instance or class description (mandatory)
a process/nipype interface instance/class or a string description.
kwargs:
default values of the process instance parameters.
Returns
-------
result: Process
an initialized process instance.
"""
# If the function 'process_or_id' parameter is already a Process
# instance.
if isinstance(process_or_id, Process):
result = process_or_id
# If the function 'process_or_id' parameter is a Process class.
elif isinstance(process_or_id, type) and issubclass(process_or_id, Process):
result = process_or_id()
# If the function 'process_or_id' parameter is already a Nipye
# interface instance, wrap this structure in a Process class
elif isinstance(process_or_id, Interface):
result = nipype_factory(process_or_id)
# If the function 'process_or_id' parameter is an Interface class.
elif isinstance(process_or_id, type) and issubclass(process_or_id, Interface):
result = nipype_factory(process_or_id())
# If the function 'process_or_id' parameter is a class string
# description
elif isinstance(process_or_id, basestring):
# Get the class and module names from the class string description
id_list = process_or_id.split(".")
if id_list[-1] == "xml":
module_name = ".".join(id_list[:-2])
object_name = ".".join(id_list[-2:])
else:
module_name = ".".join(id_list[:-1])
object_name = id_list[-1]
# Try to load the class
module_objects = load_objects(module_name, object_name, allowed_instances=[Process, Interface])
# Expect only one Process
if len(module_objects) != 1:
raise ImportError(
"Found '{0}' process(es) declared in '{1}' when looking for "
"'{2}' class/function/pipeline.".format(len(module_objects), module_name, object_name)
)
# Get the target Process
process_class = module_objects[0]
# Get the process class instance
result = process_class()
# If we have a Nipype interface, wrap this structure in a Process
# class
if isinstance(result, Interface):
result = nipype_factory(result)
else:
raise ValueError(
"Invalid process_or_id argument. "
"Got '{0}' and expect a Process instance/string "
"description or an Interface instance/string "
"description".format(process_or_id)
)
# Set the instance default parameters
for name, value in kwargs.iteritems():
result.set_parameter(name, value)
return result