def workflow_from_graph(graph, temp_map={}, shared_map={},
transfers=[{}, {}], shared_paths={},
disabled_nodes=set(), forbidden_temp=set(),
jobs_priority=0, steps={}, current_step='',
study_config={}):
""" Convert a CAPSUL graph to a soma-workflow workflow
Parameters
----------
graph: Graph (mandatory)
a CAPSUL graph
temp_map: dict (optional)
temporary files to replace by soma_workflow TemporaryPath objects
shared_map: dict (optional)
shared translated paths maps (global to pipeline).
This dict is updated when needed during the process.
transfers: list of 2 dicts (optional)
File transfers dicts (input / ouput), indexed by process, then by
file path.
shared_paths: dict (optional)
holds information about shared resource paths from soma-worflow
section in study config.
If not specified, no translation will be used.
jobs_priority: int (optional, default: 0)
set this priority on soma-workflow jobs.
steps: dict (optional)
node name -> step name dict
current_step: str (optional)
the parent node step name
study_config: StydyConfig instance (optional)
used only for iterative nodes, to be passed to create sub-workflows
Returns
-------
workflow: tuple (jobs, dependencies, groups, root_jobs)
the corresponding soma-workflow workflow definition (to be passed
to Workflow constructor)
"""
jobs = {}
groups = {}
root_jobs = {}
dependencies = set()
group_nodes = {}
ordered_nodes = graph.topological_sort()
proc_keys = dict([(node[1] if isinstance(node[1], Graph)
else node[1][0].process, i)
for i, node in enumerate(ordered_nodes)])
# Go through all graph nodes
for node_name, node in six.iteritems(graph._nodes):
# If the the node meta is a Graph store it
if isinstance(node.meta, Graph):
group_nodes[node_name] = node
# Otherwise convert all the processes in meta as jobs
else:
sub_jobs = {}
for pipeline_node in node.meta:
process = pipeline_node.process
if pipeline_node in disabled_nodes:
continue
step_name = current_step or steps.get(pipeline_node.name)
if isinstance(process, ProcessIteration):
# iterative node
group_nodes.setdefault(
node_name, []).append(pipeline_node)
elif (not isinstance(process, Pipeline) and
isinstance(process, Process)):
job = build_job(process, temp_map, shared_map,
transfers, shared_paths,
forbidden_temp=forbidden_temp,
name=pipeline_node.name,
priority=jobs_priority,
step_name=step_name)
sub_jobs[process] = job
root_jobs[process] = [job]
#node.job = job
jobs.update(sub_jobs)
# Recurrence on graph node
for node_name, node in six.iteritems(group_nodes):
if isinstance(node, list):
# iterative nodes
for i, it_node in enumerate(node):
process = it_node.process
sub_workflows = build_iteration(
process, step_name, temp_map,
shared_map, transfers, shared_paths, disabled_nodes,
{}, steps, study_config={})
(sub_jobs, sub_deps, sub_groups, sub_root_jobs) = \
sub_workflows
group = build_group(node_name, six_values(sub_root_jobs))
groups.setdefault(process, []).append(group)
root_jobs.setdefault(process, []).append(group)
groups.update(sub_groups)
jobs.update(sub_jobs)
dependencies.update(sub_deps)
else:
# sub-pipeline
wf_graph = node.meta
step_name = current_step or steps.get(node_name, '')
(sub_jobs, sub_deps, sub_groups, sub_root_jobs) \
= workflow_from_graph(
wf_graph, temp_map, shared_map, transfers,
shared_paths, disabled_nodes,
jobs_priority=jobs_priority,
steps=steps, current_step=step_name)
group = build_group(node_name, six_values(sub_root_jobs))
groups[node.meta] = group
root_jobs[node.meta] = [group]
jobs.update(sub_jobs)
groups.update(sub_groups)
dependencies.update(sub_deps)
# Add dependencies between a source job and destination jobs
for node_name, node in six.iteritems(graph._nodes):
# Source job
if isinstance(node.meta, list):
if isinstance(node.meta[0].process, ProcessIteration):
sjobs = groups.get(node.meta[0].process)
if not sjobs:
continue # disabled
elif node.meta[0].process in jobs:
sjobs = [jobs[node.meta[0].process]]
else:
continue # disabled node
else:
sjobs = [groups[node.meta]]
# Destination jobs
for dnode in node.links_to:
if isinstance(dnode.meta, list):
if isinstance(dnode.meta[0].process, ProcessIteration):
djobs = groups.get(dnode.meta[0].process)
if not djobs:
continue # disabled
elif dnode.meta[0].process in jobs:
djobs = [jobs[dnode.meta[0].process]]
else:
continue # disabled node
else:
djobs = groups[dnode.meta]
if not isinstance(djobs, list):
djobs = [djobs]
for djob in djobs:
dependencies.update([(sjob, djob) for sjob in sjobs])
# sort root jobs/groups
root_jobs_list = []
for p, js in six.iteritems(root_jobs):
root_jobs_list.extend([(proc_keys[p], p, j) for j in js])
root_jobs_list.sort()
root_jobs = OrderedDict([x[1:] for x in root_jobs_list])
return jobs, dependencies, groups, root_jobs
def create_xml_pipeline(module, name, xml_file):
"""
Create a pipeline class given its Capsul XML 2.0 representation.
Parameters
----------
module: str (mandatory)
name of the module for the created Pipeline class (the Python module is
not modified).
name: str (mandatory)
name of the new pipeline class
xml_file: str (mandatory)
name of file containing the XML description or XML string.
"""
if os.path.exists(xml_file):
xml_pipeline = ET.parse(xml_file).getroot()
else:
xml_pipeline = ET.fromstring(xml_file)
version = xml_pipeline.get('capsul_xml')
if version and version != '2.0':
raise ValueError('Only Capsul XML 2.0 is supported, not %s' % version)
class_name = xml_pipeline.get('name')
if class_name:
if name is None:
name = class_name
elif name != class_name:
raise KeyError('pipeline name (%s) and requested object name '
'(%s) differ.' % (class_name, name))
elif name is None:
name = os.path.basename(xml_file).rsplit('.', 1)[0]
builder = PipelineConstructor(module, name)
exported_parameters = set()
for child in xml_pipeline:
if child.tag == 'doc':
builder.set_documentation(child.text.strip())
elif child.tag == 'process':
process_name = child.get('name')
module = child.get('module')
args = (process_name, module)
kwargs = {}
nipype_usedefault = []
iterate = []
iteration = child.get('iteration')
if iteration:
iterate = [x.strip() for x in iteration.split(',')]
for process_child in child:
if process_child.tag == 'set':
name = process_child.get('name')
value = process_child.get('value')
value = string_to_value(value)
if value is not None:
kwargs[name] = value
kwargs.setdefault('make_optional', []).append(name)
elif process_child.tag == 'nipype':
name = process_child.get('name')
usedefault = process_child.get('usedefault')
if usedefault == 'true':
nipype_usedefault.append(name)
copyfile = process_child.get('copyfile')
if copyfile == 'true':
kwargs.setdefault('inputs_to_copy', []).append(name)
elif copyfile == 'discard':
kwargs.setdefault('inputs_to_copy', []).append(name)
kwargs.setdefault('inputs_to_clean', []).append(name)
else:
raise ValueError('Invalid tag in <process>: %s' %
process_child.tag)
if iterate:
kwargs['iterative_plugs'] = iterate
builder.add_iterative_process(*args, **kwargs)
else:
builder.add_process(*args, **kwargs)
for name in nipype_usedefault:
builder.call_process_method(process_name, 'set_usedefault',
name, True)
enabled = child.get('enabled')
if enabled == 'false':
builder.set_node_enabled(process_name, False)
elif child.tag == 'switch':
switch_name = child.get('name')
value = child.get('switch_value')
kwargs = {'export_switch': False}
if value:
kwargs['switch_value'] = value
inputs = []
outputs = []
for process_child in child:
if process_child.tag == 'input':
name = process_child.get('name')
inputs.append(name)
elif process_child.tag == 'output':
name = process_child.get('name')
outputs.append(name)
optional = process_child.get('optional')
if optional == 'true':
kwargs.setdefault('make_optional', []).append(name)
builder.add_switch(switch_name, inputs, outputs, **kwargs)
enabled = child.get('enabled')
if enabled == 'false':
builder.set_node_enabled(switch_name, False)
elif child.tag == 'link':
source = child.get('source')
dest = child.get('dest')
weak_link = child.get('weak_link')
if weak_link == 'true':
weak_link = True
else:
weak_link = False
if '.' in source:
if '.' in dest:
builder.add_link('%s->%s' % (source, dest),
weak_link=weak_link)
elif dest in exported_parameters:
builder.add_link('%s->%s' % (source, dest),
weak_link=weak_link)
else:
node, plug = source.rsplit('.', 1)
builder.export_parameter(node,
plug,
dest,
weak_link=weak_link)
exported_parameters.add(dest)
elif source in exported_parameters:
builder.add_link('%s->%s' % (source, dest))
else:
node, plug = dest.rsplit('.', 1)
builder.export_parameter(node,
plug,
source,
weak_link=weak_link)
exported_parameters.add(source)
elif child.tag == 'processes_selection':
selection_parameter = child.get('name')
selection_groups = OrderedDict()
for select_child in child:
if select_child.tag == 'processes_group':
group_name = select_child.get('name')
group = selection_groups[group_name] = []
for group_child in select_child:
if group_child.tag == 'process':
group.append(group_child.get('name'))
else:
raise ValueError('Invalid tag in <processes_group>'
'<process>: %s' % group_child.tag)
else:
raise ValueError(
'Invalid tag in <processes_selection>: %s' %
select_child.tag)
builder.add_processes_selection(selection_parameter,
selection_groups)
elif child.tag == 'pipeline_steps':
for step_child in child:
step_name = step_child.get('name')
enabled = step_child.get('enabled')
if enabled == 'false':
enabled = False
else:
enabled = True
nodes = []
for step_node in step_child:
nodes.append(step_node.get('name'))
builder.add_pipeline_step(step_name, nodes, enabled)
elif child.tag == 'gui':
for gui_child in child:
if gui_child.tag == 'position':
name = gui_child.get('name')
x = float(gui_child.get('x'))
y = float(gui_child.get('y'))
builder.set_node_position(name, x, y)
elif gui_child.tag == 'zoom':
builder.set_scene_scale_factor(
float(gui_child.get('level')))
else:
raise ValueError('Invalid tag in <gui>: %s' %
gui_child.tag)
else:
raise ValueError('Invalid tag in <pipeline>: %s' % child.tag)
return builder.pipeline
class ProcessAttributes(Controller):
'''
This is the base class for managing attributes for a process.
'''
def __init__(self, process, schema_dict):
super(ProcessAttributes, self).__init__()
self._process = process
self._schema_dict = schema_dict
self.editable_attributes = OrderedDict()
self.parameter_attributes = {}
def __getinitargs__(self):
# needed for self.copy()
return (self._process, self._schema_dict)
def set_parameter_attributes(self, parameter, schema, editable_attributes,
fixed_attibute_values):
if parameter in self.parameter_attributes:
raise KeyError('Attributes already set for parameter %s' %
parameter)
if isinstance(editable_attributes, six.string_types) or isinstance(
editable_attributes, EditableAttributes):
editable_attributes = [editable_attributes]
parameter_editable_attributes = []
for ea in editable_attributes:
add_editable_attributes = False
if isinstance(ea, six.string_types):
key = ea
ea = self.editable_attributes.get(key)
if ea is None:
ea = getattr(self._schema_dict[schema], key)()
self.editable_attributes[key] = ea
add_editable_attributes = True
elif isinstance(ea, EditableAttributes):
key = ea
if key not in self.editable_attributes:
self.editable_attributes[key] = ea
add_editable_attributes = True
else:
raise TypeError(
'Invalid value for editable attributes: {0}'.format(ea))
parameter_editable_attributes.append(ea)
if add_editable_attributes:
for name, trait in six.iteritems(ea.user_traits()):
self.add_trait(name, trait)
f = SomaPartial(set_attribute, ea)
self.on_trait_change(f, name)
self.parameter_attributes[parameter] = (parameter_editable_attributes,
fixed_attibute_values)
def get_parameters_attributes(self):
pa = {}
for parameter, trait in six.iteritems(self._process.user_traits()):
if trait.output:
if hasattr(self._process, 'id'):
process_name = self._process.id
else:
process_name = self._process.name
attributes = {
'generated_by_process': process_name,
'generated_by_parameter': parameter
}
else:
attributes = {}
editable_fixed = self.parameter_attributes.get(parameter, ([], {}))
editable_attributes, fixed_attibute_values = editable_fixed
for ea in editable_attributes:
for attribute in ea.user_traits():
value = getattr(ea, attribute)
attributes[attribute] = value
attributes.update(fixed_attibute_values)
if attributes:
pa[parameter] = attributes
return pa
def __init__(self, process, schema_dict):
super(ProcessAttributes, self).__init__()
self._process = process
self._schema_dict = schema_dict
self.editable_attributes = OrderedDict()
self.parameter_attributes = {}
def __init__(self,
controller,
parent=None,
name=None,
live=False,
hide_labels=False,
select_controls=None,
editable_labels=False):
""" Method to initilaize the ControllerWidget class.
Parameters
----------
controller: derived Controller instance (mandatory)
a class derived from the Controller class we want to parametrize
with a widget.
parent: QtGui.QWidget (optional, default None)
the controller widget parent widget.
name: (optional, default None)
the name of this controller widget
live: bool (optional, default False)
if True, synchronize the edited values in the widget with the
controller values on the fly,
otherwise, wait the synchronization instruction to update the
controller values.
hide_labels: bool (optional, default False)
if True, don't show the labels associated with the controls
select_controls: str (optional, default None)
parameter to select specific conrtoller traits. Authorized options
are 'inputs' or 'outputs'.
editable_labels: bool (optional, default False)
if True, labels (trait keys) may be edited by the user, their
modification will trigger a signal.
"""
# Inheritance
super(ControllerWidget, self).__init__(parent)
QtCore.QResource.registerResource(
os.path.join(os.path.dirname(os.path.dirname(__file__)),
'resources', 'widgets_icons.rcc'))
# Class parameters
self.controller = controller
self.live = live
self.hide_labels = hide_labels
self.select_controls = select_controls
# Parameter to store the connection status between the
# controller widget and the controller
self.connected = False
# Parameter to store all the controller widget controls:
# the keys correspond to the control name (a control name is
# associated to a controller trait with the same name), the
# dictionary elements are 4-uplets of the form (trait, control_class,
# control_instance, control_label).
self._controls = {}
self._keys_connections = {}
self.editable_labels = editable_labels
# If possilbe, set the widget name
if name:
self.setObjectName(name)
# Create the layout of the controller widget
# We will add all the controls to this layout
self._grid_layout = QtGui.QGridLayout()
self._grid_layout.setAlignment(QtCore.Qt.AlignTop)
self._grid_layout.setSpacing(3)
self._grid_layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self._grid_layout)
self._groups = OrderedDict()
# Create all the layout controls associated with the controller values
# we want to tune (ie the user traits)
self._create_controls()
self.connect_keys()
# Start the event loop that check for wrong edited fields (usefull
# when we work off line, otherwise the traits make the job but it is
# still user friendly).
self._check()
# Set the synchrinization between this object and the input controller:
# 1) synchronize the edited values in the widget with the controller
# values on the fly
if self.live:
self.connect()
# 2) initialize the controller widget with the controller values and
# wait synchronization instructions to update the controller values.
else:
self.update_controller_widget()
class ControllerWidget(QtGui.QWidget):
""" Class that create a widget to set the controller parameters.
"""
# Parameter to store the mapping between the string trait descriptions and
# the associated control classes
_defined_controls = {}
def __init__(self,
controller,
parent=None,
name=None,
live=False,
hide_labels=False,
select_controls=None,
editable_labels=False):
""" Method to initilaize the ControllerWidget class.
Parameters
----------
controller: derived Controller instance (mandatory)
a class derived from the Controller class we want to parametrize
with a widget.
parent: QtGui.QWidget (optional, default None)
the controller widget parent widget.
name: (optional, default None)
the name of this controller widget
live: bool (optional, default False)
if True, synchronize the edited values in the widget with the
controller values on the fly,
otherwise, wait the synchronization instruction to update the
controller values.
hide_labels: bool (optional, default False)
if True, don't show the labels associated with the controls
select_controls: str (optional, default None)
parameter to select specific conrtoller traits. Authorized options
are 'inputs' or 'outputs'.
editable_labels: bool (optional, default False)
if True, labels (trait keys) may be edited by the user, their
modification will trigger a signal.
"""
# Inheritance
super(ControllerWidget, self).__init__(parent)
QtCore.QResource.registerResource(
os.path.join(os.path.dirname(os.path.dirname(__file__)),
'resources', 'widgets_icons.rcc'))
# Class parameters
self.controller = controller
self.live = live
self.hide_labels = hide_labels
self.select_controls = select_controls
# Parameter to store the connection status between the
# controller widget and the controller
self.connected = False
# Parameter to store all the controller widget controls:
# the keys correspond to the control name (a control name is
# associated to a controller trait with the same name), the
# dictionary elements are 4-uplets of the form (trait, control_class,
# control_instance, control_label).
self._controls = {}
self._keys_connections = {}
self.editable_labels = editable_labels
# If possilbe, set the widget name
if name:
self.setObjectName(name)
# Create the layout of the controller widget
# We will add all the controls to this layout
self._grid_layout = QtGui.QGridLayout()
self._grid_layout.setAlignment(QtCore.Qt.AlignTop)
self._grid_layout.setSpacing(3)
self._grid_layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self._grid_layout)
self._groups = OrderedDict()
# Create all the layout controls associated with the controller values
# we want to tune (ie the user traits)
self._create_controls()
self.connect_keys()
# Start the event loop that check for wrong edited fields (usefull
# when we work off line, otherwise the traits make the job but it is
# still user friendly).
self._check()
# Set the synchrinization between this object and the input controller:
# 1) synchronize the edited values in the widget with the controller
# values on the fly
if self.live:
self.connect()
# 2) initialize the controller widget with the controller values and
# wait synchronization instructions to update the controller values.
else:
self.update_controller_widget()
#
# Public members
#
def is_valid(self):
""" Check that all edited fields are correct.
Returns
-------
valid: bool
True if all the controller widget controls are correctly filled,
False otherwise
"""
# Initilaized the output
valid = True
# Go through all the controller widget controls
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
# Unpack the control item
trait, control_class, control_instance, control_label = control
# Call the current control specific check method
valid = control_class.is_valid(control_instance)
# Stop checking if a wrong control has been found
if not valid:
break
return valid
def update_controller(self):
""" Update the controller.
At the end the controller traits values will match the controller
widget user defined parameters.
"""
# Go through all the controller widget controls
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
# Unpack the control item
trait, control_class, control_instance, control_label = control
# Call the current control specific update controller method
control_class.update_controller(self, control_name,
control_instance)
def update_controller_widget(self):
""" Update the controller widget.
At the end the controller widget user editable parameters will match
the controller traits values.
"""
# Go through all the controller widget controls
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
# Unpack the control item
trait, control_class, control_instance, control_label = control
# Call the current control specific update controller widget
# method
control_class.update_controller_widget(self, control_name,
control_instance)
def connect(self):
""" Connect the controller trait and the controller widget controls
At the end al control will be connected with the associated trait, and
when a 'user_traits_changed' signal is emited, the controls are updated
(ie, deleted if necessary).
"""
# If the controller and controller widget are not yet connected
if not self.connected:
# Go through all the controller widget controls
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
# Unpack the control item
trait, control_class, control_instance, control_label \
= control
# Call the current control specific connection method
logger.debug("Connecting control '{0}: {1}'...".format(
control_name, control_instance))
control_class.connect(self, control_name, control_instance)
# Add an event connected with the 'user_traits_changed' controller
# signal: update the controls
self.controller.on_trait_change(self.update_controls,
"user_traits_changed",
dispatch='ui')
# if 'visible_groups' is a trait, connect it to groups
if self.controller.trait('visible_groups'):
self.controller.on_trait_change(self.groups_vibility_changed,
'visible_groups',
dispatch='ui')
# Update the controller widget values
self.update_controller_widget()
# Update the connection status
self.connected = True
def connect_keys(self):
if not self.editable_labels or self._keys_connections:
return
keys_connect = {}
# Go through all the controller widget controls
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
hook1 = partial(self.__class__._key_modified,
weakref.proxy(self), control_name)
hook2 = partial(self.__class__._delete_key,
weakref.proxy(self), control_name)
#control = self._controls[control_name]
label_control = control[3]
if isinstance(label_control, tuple):
label_control = label_control[0]
label_control.userModification.connect(hook1)
label_control.buttonPressed.connect(hook2)
keys_connect[control_name] = (label_control, hook1, hook2)
self._keys_connections = keys_connect
def disconnect(self):
""" Disconnect the controller trait and the controller widget controls
"""
# If the controller and controller widget are connected
if self.connected:
# Remove the 'update_controls' event connected with the
# 'user_traits_changed' controller signal
self.controller.on_trait_change(self.update_controls,
"user_traits_changed",
remove=True)
# if 'visible_groups' is a trait, connect it to groups
if self.controller.trait('visible_groups'):
self.controller.on_trait_change(self.groups_vibility_changed,
'visible_groups',
remove=True)
# Go through all the controller widget controls
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
# Unpack the control item
trait, control_class, control_instance, control_label \
= control
# Call the current control specific disconnection method
control_class.disconnect(self, control_name,
control_instance)
# Update the connection status
self.connected = False
def disconnect_keys(self):
for control_name, connections in six.iteritems(self._keys_connections):
label_widget, hook1, hook2 = connections
label_widget.userModification.disconnect(hook1)
label_widget.buttonPressed.disconnect(hook2)
self._keys_connections = {}
def update_controls(self):
""" Event to refresh controller widget controls and intern parameters.
The refresh is done off line, ie. we need first to disconnect the
controller and the controller widget.
"""
# Get the controller traits
user_traits = self.controller.user_traits()
# Assess the refreshing is done off line
was_connected = self.connected
if was_connected:
self.disconnect()
self.disconnect_keys()
# Go through all the controller widget controls
to_remove_controls = []
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
# Message
logger.debug(
"Check if we need to update '{0}': trait in '{1}' "
"different from '{2}'?".format(
control_name, control, user_traits.get(control_name)))
# Unpack the control item
trait, control_class, control_instance, control_label = control
# If the the controller trait is different from the trait
# associated with the control
if user_traits.get(control_name) != trait:
# Close and schedule for deletation the control widget
control_instance.close()
control_instance.deleteLater()
# Close and schedule for deletation the control labels
if isinstance(control_label, tuple):
for label in control_label:
label.close()
label.deleteLater()
elif control_label:
control_label.close()
control_label.deleteLater()
# Store the controls to be removed
to_remove_controls.append(control_name)
# Delete all dead controls from the class '_controls' intern parameter
for control_name in to_remove_controls:
logger.debug("Delete control '{0}'.".format(control_name))
del self._controls[control_name]
# Recreate all the layout controls associated with the controller
# values we want to tune (ie the user_traits): this procedure check
# if the control has not already been created.
self._create_controls()
# Restore the connection status
if was_connected:
self.connect()
self.connect_keys()
# Update the widget geometry
self.updateGeometry()
#
# Private members
#
def _check(self):
""" Check that all edited fields are correct.
At the end the controls with wrong values will be colored in red.
"""
# Go through all the controller widget controls
for control_name, control_groups in six.iteritems(self._controls):
for group_name, control in six.iteritems(control_groups):
# Unpack the control item
trait, control_class, control_instance, control_label = control
# Call the current control specific check method
control_class.check(control_instance)
def _create_controls(self):
""" Method that will create a control for each user trait of the
controller.
Controller trait parameters that cannot be maped to controls
will not appear in the user interface.
"""
# Select only the controller traits of interest
all_traits = self.controller.user_traits()
if self.select_controls is None:
selected_traits = all_traits
elif self.select_controls == "inputs":
selected_traits = dict(
(trait_name, trait)
for trait_name, trait in six.iteritems(all_traits)
if trait.output == False)
elif self.select_controls == "outputs":
selected_traits = dict(
(trait_name, trait)
for trait_name, trait in six.iteritems(all_traits)
if trait.output == True)
else:
raise Exception(
"Unrecognized 'select_controls' option '{0}'. Valid "
"options are 'inputs' or 'outputs'.".format(
self.select_controls))
# Go through all the controller user traits
skipped = set(['visible_groups'])
for trait_name, trait in six.iteritems(selected_traits):
if trait_name in skipped:
continue
# Create the widget
self.create_control(trait_name, trait)
def create_control(self, trait_name, trait):
""" Create a control associated to a trait.
Parameters
----------
trait_name: str (mandatory)
the name of the trait from which we want to create a control. The
control widget will share the same name
trait: Trait (mandatory)
a trait item
"""
# Search if the current trait has already been processed
control_groups = self._controls.get(trait_name)
control_instances = []
control_labels = []
# If no control has been found in the class intern parameters
if control_groups is None:
# Call the search function that will map the trait type to the
# corresponding control type
control_class = self.get_control_class(trait)
# If no control has been found, skip this trait and print
# an error message. Note that the parameter will not be
# accessible in the user interface.
if control_class is None:
logger.error("No control defined for trait '{0}': {1}. This "
"parameter will not be accessible in the "
"user interface.".format(trait_name,
trait_ids(trait)))
return
# handle groups
layouts = []
groups = trait.groups
if groups:
for group in groups:
group_widget = self._groups.get(group)
if group_widget is None:
group_widget = self._create_group_widget(group)
self._groups[group] = group_widget
layouts.append(group_widget.hideable_widget.layout())
else:
layouts.append(self._grid_layout)
group = None
for i, layout in enumerate(layouts):
if groups:
group = groups[i]
control_instance, control_label \
= self._create_control_in_layout(trait_name, trait,
layout, group)
control_instances.append(control_instance)
if control_label:
if not isinstance(control_label, tuple):
control_label = [control_label]
control_labels += list(control_label)
if isinstance(control_label[0], QtGui.QLabel):
control_label[0].setTextInteractionFlags(
QtCore.Qt.TextSelectableByKeyboard
| QtCore.Qt.TextSelectableByMouse)
# Otherwise, the control associated with the current trait name is
# already inserted in the grid layout, just unpack the values
# contained in the private '_controls' class parameter
else:
for group, control in six.iteritems(control_groups):
trait, control_class, control_instance, control_label = control
control_instances.append(control_instance)
if control_label:
if isinstance(control_label, tuple):
control_labels += list(control_label)
else:
control_labels.append(control_label)
# Each trait has a hidden property. Take care of this information
hide = (getattr(trait, 'hidden', False)
or getattr(trait, 'unused', False))
# Show/Hide the control and associated labels
for control_instance in control_instances:
control_instance.setVisible(not hide)
for label in control_labels:
label.setVisible(not hide)
## Show the control and associated labels
#else:
#for control_instance in control_instances:
#control_instance.show()
#for label in control_labels:
#label.show()
def _create_group_widget(self, group):
group_widget = QtGui.QGroupBox()
last_row = self._grid_layout.rowCount()
self._grid_layout.addWidget(group_widget, last_row, 0, 1, 2)
lay1 = QtGui.QVBoxLayout()
lay1.setContentsMargins(0, 0, 0, 0)
lay2 = QtGui.QHBoxLayout()
lay1.addLayout(lay2)
lay2.setContentsMargins(10, 0, 0, 0)
lay2.addWidget(QtGui.QLabel('<html><em>%s</em></html>' % group))
lay2.addStretch(1)
icon = QtGui.QIcon()
icon.addPixmap(
QtGui.QPixmap(_fromUtf8(":/soma_widgets_icons/nav_down")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
group_widget.fold_button = QtGui.QPushButton(icon, '')
group_widget.fold_button.setFixedSize(30, 20)
lay2.addWidget(group_widget.fold_button)
widget = QtGui.QWidget()
group_widget.setLayout(lay1)
lay1.addWidget(widget)
group_widget.hideable_widget = widget
layout = QtGui.QGridLayout()
widget.setLayout(layout)
layout.setAlignment(QtCore.Qt.AlignTop)
layout.setSpacing(3)
layout.setContentsMargins(5, 5, 5, 5)
group_widget.setAlignment(QtCore.Qt.AlignLeft)
visible_groups = getattr(self.controller, 'visible_groups', set())
if group in visible_groups:
show = True
else:
show = False
group_widget.hideable_widget.setVisible(show)
if not show:
icon = QtGui.QIcon()
icon.addPixmap(
QtGui.QPixmap(_fromUtf8(":/soma_widgets_icons/nav_right")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
group_widget.fold_button.setIcon(icon)
#group_widget.fold_button.clicked.connect(SomaPartial(
#self._toggle_group_visibility, group))
# FIXME: if we use this, self gets deleted somewhere. This is not
# normal.
group_widget.fold_button.clicked.connect(
partial(self.__class__._toggle_group_visibility, weak_proxy(self),
group))
return group_widget
def _set_group_visibility(self, group, checked):
group_widget = self._groups[group]
group_widget.hideable_widget.setVisible(checked)
icon = QtGui.QIcon()
if checked:
icon.addPixmap(
QtGui.QPixmap(_fromUtf8(":/soma_widgets_icons/nav_down")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
else:
icon.addPixmap(
QtGui.QPixmap(_fromUtf8(":/soma_widgets_icons/nav_right")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
group_widget.fold_button.setIcon(icon)
def _toggle_group_visibility(self, group, checked=False):
visible_groups = getattr(self.controller, 'visible_groups', set())
if group in visible_groups:
show = False
visible_groups.remove(group)
else:
show = True
visible_groups.add(group)
self._set_group_visibility(group, show)
self.controller.visible_groups = visible_groups
def _create_control_in_layout(self, trait_name, trait, layout, group=None):
# Call the search function that will map the trait type to the
# corresponding control type
control_class = self.get_control_class(trait)
# FIXME: for now we use a hack for compound/either traits, until
# we write a "real" GUI for them
if isinstance(trait.trait_type, (traits.TraitCompound, traits.Either)):
# compound trait: use the 1st
trait = trait.handler.handlers[0].as_ctrait()
# Create the control instance and associated label
if self.editable_labels:
label_class = DeletableLineEdit
else:
label_class = QtGui.QLabel
control_instance, control_label = control_class.create_widget(
self, trait_name, getattr(self.controller, trait_name), trait,
label_class)
control_class.is_valid(control_instance)
# If the trait contains a description, insert a tool tip to the
# control instance
tooltip = ""
if trait.desc:
tooltip = "<b>" + trait_name + ":</b> " + trait.desc
control_instance.setToolTip(tooltip)
# Get the last empty row in the grid layout
# Trick: If the grid layout is empty check the element 0
# (not realistic but te grid layout return None)
last_row = layout.rowCount()
widget_item = layout.itemAtPosition(last_row, 1)
while widget_item is None and last_row > 0:
last_row -= 1
widget_item = layout.itemAtPosition(last_row, 1)
last_row += 1
# If the control has no label, append the control in a two
# columns span area of the grid layout
if control_label is None:
# Grid layout 'addWidget' parameters: QWidget, int row,
# int column, int rowSpan, int columnSpan
layout.addWidget(control_instance, last_row, 0, 1, 2)
# If the control has two labels, add a first row with the
# labels (one per column), and add the control in
# the next row of the grid layout in the second column
elif isinstance(control_label, tuple):
# Get the number of label
nb_of_labels = len(control_label)
# If more than two labels are detected, print an error message.
# We actually consider only the two first labels and skip the
# others
if nb_of_labels > 2:
logger.error("To many labels associated with control "
"'{0}': {1}. Only consider the two first "
"labels and skip the others".format(
trait_name, control_label))
# Append each label in different columns
if not self.hide_labels:
layout.addWidget(control_label[0], last_row, 0)
if nb_of_labels >= 2:
layout.addWidget(control_label[1], last_row, 1)
# Append the control in the next row in the second column
layout.addWidget(control_instance, last_row + 1, 1)
# Otherwise, append the label and control in two separate
# columns of the grid layout
else:
# Append the label in the first column
if not self.hide_labels:
layout.addWidget(control_label, last_row, 0)
# Append the control in the second column
layout.addWidget(control_instance, last_row, 1, 1, 1)
# Store some informations about the inserted control in the
# private '_controls' class parameter
# Keys: the trait names
# Parameters: the trait - the control name - the control - and
# the labels associated with the control
self._controls.setdefault(trait_name,
{})[group] = (trait, control_class,
control_instance,
control_label)
return control_instance, control_label
def _key_modified(self, old_key):
""" Dict / open controller key modification callback
"""
control_groups = self._controls[old_key]
control_labels = []
for group_name, control in six.iteritems(control_groups):
control_labels += control[3]
for control_label in control_labels:
key = str(control_label.text())
was_connected = self.connected
if was_connected:
self.disconnect()
self.disconnect_keys()
controller = self.controller
trait = controller.trait(old_key)
controller.add_trait(key, trait)
setattr(controller, key, getattr(controller, old_key))
controller.remove_trait(old_key)
self._controls[key] = self._controls[old_key]
del self._controls[old_key]
if was_connected:
self.connect()
# reconnect label widget
self.connect_keys()
# self.update_controls() # not even needed
if hasattr(self, 'main_controller_def'):
main_control_class, controller_widget, control_name, frame = \
self.main_controller_def
main_control_class.update_controller(controller_widget,
control_name, frame)
# self.update_controller()
def _delete_key(self, key):
""" Dict / open controller key deletion callback
"""
controller = self.controller
trait = controller.trait(key)
controller.remove_trait(key)
self.update_controls()
if hasattr(self, 'main_controller_def'):
main_control_class, controller_widget, control_name, frame = \
self.main_controller_def
main_control_class.update_controller(controller_widget,
control_name, frame)
# self.update_controller()
def groups_vibility_changed(self):
visible_groups = self.controller.visible_groups or set()
for group, group_widget in six.iteritems(self._groups):
if group in visible_groups:
show = True
else:
show = False
self._set_group_visibility(group, show)
#
# Class Methods
#
@classmethod
def get_control_class(cls, trait):
""" Find the control associated with the input trait.
The mapping is defined in the global class parameter
'_defined_controls'.
Parameters
----------
cls: ControllerWidget (mandatory)
a ControllerWidget class
trait: Trait (mandatory)
a trait item
Returns
-------
control_class: class
the control class associated with the input trait.
If no match has been found, return None
"""
# Initilaize the output variable
control_class = None
# Go through the trait string description: can have multiple element
# when either trait is used
# Todo:: we actualy need to create all the controls and let the user
# choose which one he wants to fill.
for trait_id in trait_ids(trait):
# Recursive construction: consider only the top level
trait_id = trait_id.split("_")[0]
# Try to get the control class
control_class = cls._defined_controls.get(trait_id)
# Stop when we have a match
if control_class is not None:
break
return control_class
class ProcessAttributes(Controller):
'''
This is the base class for managing attributes for a process.
It stores attributes associated with a Process, for each of its parameters.
Attribute values can be accessed "globally" (for the whole process) as
ProcessAttributes instance traits.
Or each parameter attributes set may be accessed individually, using
:meth:`get_parameters_attributes()`.
To define attributes for a process, the programmer may subclass
ProcessAttributes and define some EditableAttributes in it. Each
EditableAttributes is a group of attributes (traits in the EditableAttributes instance or subclass).
A ProcessAttributes subclass should be registered to a factory to be linked
to a process name, using the `factory_id` class variable.
See Capsul :ref:`advanced usage doc <completion>` for details.
'''
def __init__(self, process, schema_dict):
super(ProcessAttributes, self).__init__()
self._process = process
self._schema_dict = schema_dict
self.editable_attributes = OrderedDict()
self.parameter_attributes = {}
def __getinitargs__(self):
# needed for self.copy()
return (self._process, self._schema_dict)
def set_parameter_attributes(self,
parameter,
schema,
editable_attributes,
fixed_attibute_values,
allow_list=True):
'''
Set attributes associated with a single process parameter.
Parameters
----------
parameter: str
process parameter name
schema: str
schema used for it (input, output, shared)
editable_attributes: str, EditableAttributes instance, or list of them
EditableAttributes or id containing attributes traits
fixed_attibute_values: dict (str/str)
values of non-editable attributes
allow_list: bool
if True (the default), it the process parameter is a list, then
attributes are transformed into lists.
'''
if parameter in self.parameter_attributes:
if schema == 'link':
return # this is just a lower priority
raise KeyError('Attributes already set for parameter %s' %
parameter)
process = self._process
if isinstance(process, ProcessNode):
process = process.process
if parameter not in process._instance_traits():
print('WARNING: parameter', parameter, 'not in process',
process.name)
return
if isinstance(editable_attributes, six.string_types) \
or isinstance(editable_attributes, EditableAttributes):
editable_attributes = [editable_attributes]
parameter_editable_attributes = []
for ea in editable_attributes:
add_editable_attributes = False
if isinstance(ea, six.string_types):
key = ea
ea = self.editable_attributes.get(key)
if ea is None:
ea = getattr(self._schema_dict[schema], key)()
self.editable_attributes[key] = ea
add_editable_attributes = True
elif isinstance(ea, EditableAttributes):
key = ea
if key not in self.editable_attributes:
self.editable_attributes[key] = ea
add_editable_attributes = True
else:
raise TypeError(
'Invalid value for editable attributes: {0}'.format(ea))
parameter_editable_attributes.append(ea)
if add_editable_attributes:
is_list = allow_list \
and isinstance(process.trait(parameter).trait_type,
traits.List)
for name in list(ea.user_traits().keys()):
# don't use items() since traits may change during iter.
trait = ea.trait(name)
if is_list:
trait = traits.List(trait)
ea.remove_trait(name)
ea.add_trait(name, trait)
if name in self.user_traits():
if not is_list \
and isinstance(self.trait(name).trait_type,
traits.List):
# a process attribute trait may have been changed
# into a list. Here we assume attributes are only
# strings (at this point - it can be changed at
# higher lever afterwards), so change it back into
# a single value trait.
self.remove_trait(name)
self.add_trait(name, trait)
# else don't add it again: this way non-list versions
# of attributes get priority. If both exist, lists
# should get one single value (otherwise there is an
# ambiguity or inconsistency), so the attribute should
# not be a list.
else:
self.add_trait(name, trait)
f = SomaPartial(set_attribute, ea)
self.on_trait_change(f, name)
self.parameter_attributes[parameter] = (parameter_editable_attributes,
fixed_attibute_values)
def get_parameters_attributes(self):
''' Get attributes for each process parameter
'''
pa = {}
process = self._process
if isinstance(process, ProcessNode):
process = process.process
for parameter, trait in six.iteritems(process.user_traits()):
if trait.output:
if hasattr(process, 'id'):
process_name = process.id
else:
process_name = process.name
attributes = {
'generated_by_process': process_name,
'generated_by_parameter': parameter
}
else:
attributes = {}
editable_fixed = self.parameter_attributes.get(parameter, ([], {}))
editable_attributes, fixed_attibute_values = editable_fixed
for ea in editable_attributes:
for attribute in ea.user_traits():
value = getattr(ea, attribute)
attributes[attribute] = value
attributes.update(fixed_attibute_values)
if attributes:
pa[parameter] = attributes
return pa
def copy(self, with_values=True):
''' overloads :meth:`soma.Controller.copy`
'''
other = self.__class__(self._process, self._schema_dict)
ea_map = {}
for parameter, pa in six.iteritems(self.parameter_attributes):
if parameter not in other.parameter_attributes:
# otherwise assume this has been done in a subclass constructor
eas, fa = pa
oeas = []
for ea in eas:
oea = ea_map.get(ea)
if oea is None:
oea = ea.copy()
oeas.append(oea)
other.set_parameter_attributes(parameter,
'',
oeas,
fa,
allow_list=False)
# copy the values
if with_values:
for name in self.user_traits():
#print('copy attribs:', self, name, getattr(self, name))
#print(' to:', other.trait(name).trait_type)
#if isinstance(other.trait(name).trait_type, traits.List):
#print(' ', other.trait(name).inner_traits[0].trait_type)
#if isinstance(self.trait(name).trait_type, traits.List):
#print(' self list:', self.trait(name).inner_traits[0].trait_type)
setattr(other, name, getattr(self, name))
return other
def copy_to_single(self, with_values=True):
''' Similar to :meth:`copy`, excepts that it converts list attributes
into single values. This is useful within the completion system
infrastructure, to get from an attributes set containing lists
(process parameters which are lists), a single value allowing to
determine a single path.
This method is merely useful to the end user.
'''
other = ProcessAttributes(self._process, self._schema_dict)
ea_map = {}
for parameter, pa in six.iteritems(self.parameter_attributes):
if parameter not in other.parameter_attributes:
# otherwise assume this has been done in a subclass constructor
eas, fa = pa
oeas = []
for ea in eas:
oea = ea_map.get(ea)
if oea is None:
oea = EditableAttributes()
for name, trait in six.iteritems(ea.user_traits()):
if isinstance(trait.trait_type, traits.List):
trait = trait.inner_traits[0]
oea.add_trait(name, trait)
ea_map[ea] = oea
oeas.append(oea)
other.set_parameter_attributes(parameter,
'',
oeas,
fa,
allow_list=False)
# copy the values
if with_values:
for name in self.user_traits():
value = getattr(self, name)
if isinstance(value, list):
if len(value) != 0:
value = value[0]
else:
value = self.trait(name).inner_traits[0].default
if value is not None:
setattr(other, name, value)
return other
def __init__(self, process, schema_dict):
super(ProcessAttributes, self).__init__()
self._process = process
self._schema_dict = schema_dict
self.editable_attributes = OrderedDict()
self.parameter_attributes = {}
class ProcessAttributes(Controller):
'''
This is the base class for managing attributes for a process.
'''
def __init__(self, process, schema_dict):
super(ProcessAttributes, self).__init__()
self._process = process
self._schema_dict = schema_dict
self.editable_attributes = OrderedDict()
self.parameter_attributes = {}
def set_parameter_attributes(self, parameter, schema, editable_attributes, fixed_attibute_values):
if parameter in self.parameter_attributes:
raise KeyError('Attributes already set for parameter %s' % parameter)
if isinstance(editable_attributes, six.string_types) or isinstance(editable_attributes, EditableAttributes):
editable_attributes = [editable_attributes]
parameter_editable_attributes = []
for ea in editable_attributes:
add_editable_attributes = False
if isinstance(ea, six.string_types):
key = ea
ea = self.editable_attributes.get(key)
if ea is None:
ea = getattr(self._schema_dict[schema], key)()
self.editable_attributes[key] = ea
add_editable_attributes = True
elif isinstance(ea, EditableAttributes):
key = ea
if key not in self.editable_attributes:
self.editable_attributes[key] = ea
add_editable_attributes = True
else:
raise TypeError('Invalid value for editable attributes: {0}'.format(ea))
parameter_editable_attributes.append(ea)
if add_editable_attributes:
for name, trait in six.iteritems(ea.user_traits()):
self.add_trait(name, trait)
f = SomaPartial(set_attribute, ea)
self.on_trait_change(f, name)
self.parameter_attributes[parameter] = (parameter_editable_attributes, fixed_attibute_values)
def get_parameters_attributes(self):
pa = {}
for parameter, trait in six.iteritems(self._process.user_traits()):
if trait.output:
if hasattr(self._process, 'id'):
process_name = self._process.id
else:
process_name = self._process.name
attributes = {
'generated_by_process': process_name,
'generated_by_parameter': parameter}
else:
attributes = {}
editable_fixed = self.parameter_attributes.get(parameter, ([], {}))
editable_attributes, fixed_attibute_values = editable_fixed
for ea in editable_attributes:
for attribute in ea.user_traits():
value = getattr(ea, attribute)
attributes[attribute] = value
attributes.update(fixed_attibute_values)
if attributes:
pa[parameter] = attributes
return pa
