Beispiel #1
0
    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)
Beispiel #2
0
    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)
Beispiel #3
0
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)
Beispiel #4
0
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)