def serialize_module(self, module):
"""
Serializes a module to be executed in parallel.
"""
def process_group(group):
group.pipeline.id = None
for module in group.pipeline.module_list:
if module.is_group():
process_group(module)
pipeline = Pipeline(version=vistrails.db.versions.currentVersion)
if module.is_group():
process_group(module)
module = module.do_copy()
pipeline.add_module(module)
return serialize(pipeline)
def serialize_module(self, module):
"""
Serializes a module to be executed in parallel.
"""
def process_group(group):
group.pipeline.id = None
for module in group.pipeline.module_list:
if module.is_group():
process_group(module)
pipeline = Pipeline(version=vistrails.db.versions.currentVersion)
if module.is_group():
process_group(module)
module = module.do_copy()
pipeline.add_module(module)
return serialize(pipeline)
def execute_wf(wf, output_port):
# Save the workflow in a temporary file
temp_wf_fd, temp_wf = tempfile.mkstemp()
try:
f = open(temp_wf, 'w')
f.write(wf)
f.close()
os.close(temp_wf_fd)
# Clean the cache
interpreter = get_default_interpreter()
interpreter.flush()
# Load the Pipeline from the temporary file
vistrail = Vistrail()
locator = XMLFileLocator(temp_wf)
workflow = locator.load(Pipeline)
# Build a Vistrail from this single Pipeline
action_list = []
for module in workflow.module_list:
action_list.append(('add', module))
for connection in workflow.connection_list:
action_list.append(('add', connection))
action = vistrails.core.db.action.create_action(action_list)
vistrail.add_action(action, 0L)
vistrail.update_id_scope()
tag = 'parallel flow'
vistrail.addTag(tag, action.id)
# Build a controller and execute
controller = VistrailController()
controller.set_vistrail(vistrail, None)
controller.change_selected_version(vistrail.get_version_number(tag))
execution = controller.execute_current_workflow(
custom_aliases=None,
custom_params=None,
extra_info=None,
reason='API Pipeline Execution')
# Build a list of errors
errors = []
pipeline = vistrail.getPipeline(tag)
execution_errors = execution[0][0].errors
if execution_errors:
for key in execution_errors:
module = pipeline.modules[key]
msg = '%s: %s' %(module.name, execution_errors[key])
errors.append(msg)
# Get the execution log from the controller
try:
module_log = controller.log.workflow_execs[0].item_execs[0]
except IndexError:
errors.append("Module log not found")
return dict(errors=errors)
else:
machine = controller.log.workflow_execs[0].machines[
module_log.machine_id]
xml_log = serialize(module_log)
machine_log = serialize(machine)
# Get the output value
output = None
serializable = None
if not execution_errors:
executed_module, = execution[0][0].executed
executed_module = execution[0][0].objects[executed_module]
try:
output = executed_module.get_output(output_port)
except ModuleError:
errors.append("Output port not found: %s" % output_port)
return dict(errors=errors)
reg = vistrails.core.modules.module_registry.get_module_registry()
base_classes = inspect.getmro(type(output))
if Module in base_classes:
serializable = reg.get_descriptor(type(output)).sigstring
output = output.serialize()
# Return the dictionary, that will be sent back to the client
return dict(errors=errors,
output=output,
serializable=serializable,
xml_log=xml_log,
machine_log=machine_log)
finally:
os.unlink(temp_wf)
def execute_wf(wf, output_port):
# Save the workflow in a temporary file
temp_wf_fd, temp_wf = tempfile.mkstemp()
try:
f = open(temp_wf, 'w')
f.write(wf)
f.close()
os.close(temp_wf_fd)
# Clean the cache
interpreter = get_default_interpreter()
interpreter.flush()
# Load the Pipeline from the temporary file
vistrail = Vistrail()
locator = XMLFileLocator(temp_wf)
workflow = locator.load(Pipeline)
# Build a Vistrail from this single Pipeline
action_list = []
for module in workflow.module_list:
action_list.append(('add', module))
for connection in workflow.connection_list:
action_list.append(('add', connection))
action = vistrails.core.db.action.create_action(action_list)
vistrail.add_action(action, 0L)
vistrail.update_id_scope()
tag = 'parallel flow'
vistrail.addTag(tag, action.id)
# Build a controller and execute
controller = VistrailController()
controller.set_vistrail(vistrail, None)
controller.change_selected_version(vistrail.get_version_number(tag))
execution = controller.execute_current_workflow(
custom_aliases=None,
custom_params=None,
extra_info=None,
reason='API Pipeline Execution')
# Build a list of errors
errors = []
pipeline = vistrail.getPipeline(tag)
execution_errors = execution[0][0].errors
if execution_errors:
for key in execution_errors:
module = pipeline.modules[key]
msg = '%s: %s' % (module.name, execution_errors[key])
errors.append(msg)
# Get the execution log from the controller
try:
module_log = controller.log.workflow_execs[0].item_execs[0]
except IndexError:
errors.append("Module log not found")
return dict(errors=errors)
else:
machine = controller.log.workflow_execs[0].machines[
module_log.machine_id]
xml_log = serialize(module_log)
machine_log = serialize(machine)
# Get the output value
output = None
serializable = None
if not execution_errors:
executed_module, = execution[0][0].executed
executed_module = execution[0][0].objects[executed_module]
try:
output = executed_module.get_output(output_port)
except ModuleError:
errors.append("Output port not found: %s" % output_port)
return dict(errors=errors)
reg = vistrails.core.modules.module_registry.get_module_registry()
base_classes = inspect.getmro(type(output))
if Module in base_classes:
serializable = reg.get_descriptor(type(output)).sigstring
output = output.serialize()
# Return the dictionary, that will be sent back to the client
return dict(errors=errors,
output=output,
serializable=serializable,
xml_log=xml_log,
machine_log=machine_log)
finally:
os.unlink(temp_wf)