Python VistrailController.execute_current_workflow方法代碼示例

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import execute_current_workflow [as 別名]
 def previewChanges(self, aliases):
     print "previewChanges", aliases
     # we will just execute the pipeline with the given alias dictionary
     controller = VistrailController()
     controller.set_vistrail(self.plot_vistrail, self.locator)
     version = self.plot_vistrail.get_version_number(self.workflow_tag) if self.workflow_tag else controller.get_latest_version_in_graph()
     controller.change_selected_version(version)
     (results, _) = controller.execute_current_workflow(aliases)

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import execute_current_workflow [as 別名]
def run_file(filename, tag_filter=lambda x: True):
    """Loads a .vt file and runs all the tagged versions in it.
    """
    import vistrails.core.db.io
    from vistrails.core.db.locator import FileLocator
    from vistrails.core.system import vistrails_root_directory
    from vistrails.core.vistrail.controller import VistrailController

    filename = os.path.join(vistrails_root_directory(), '..', filename)
    locator = FileLocator(filename)
    loaded_objs = vistrails.core.db.io.load_vistrail(locator)
    controller = VistrailController(loaded_objs[0], locator, *loaded_objs[1:])

    errors = []
    for version, name in controller.vistrail.get_tagMap().iteritems():
        if tag_filter(name):
            controller.change_selected_version(version)
            (result,), _ = controller.execute_current_workflow()
            if result.errors:
                errors.append(("%d: %s" % (version, name), result.errors))

    return errors

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import execute_current_workflow [as 別名]
def run_and_get_results(w_list, parameters='', output_dir=None, 
                        update_vistrail=True, extra_info=None, 
                        reason='Console Mode Execution'):
    """run_and_get_results(w_list: list of (locator, version), parameters: str,
                           output_dir:str, update_vistrail: boolean,
                           extra_info:dict)
    Run all workflows in w_list, and returns an interpreter result object.
    version can be a tag name or a version id.
    
    """
    elements = parameters.split("$&$")
    aliases = {}
    params = []
    result = []
    for locator, workflow in w_list:
        (v, abstractions , thumbnails, mashups)  = load_vistrail(locator)
        controller = VistrailController(v, locator, abstractions, thumbnails,
                                        mashups, auto_save=update_vistrail)
        if isinstance(workflow, basestring):
            version = v.get_version_number(workflow)
        elif isinstance(workflow, (int, long)):
            version = workflow
        elif workflow is None:
            version = controller.get_latest_version_in_graph()
        else:
            msg = "Invalid version tag or number: %s" % workflow
            raise VistrailsInternalError(msg)
        controller.change_selected_version(version)
        
        for e in elements:
            pos = e.find("=")
            if pos != -1:
                key = e[:pos].strip()
                value = e[pos+1:].strip()
            
                if controller.current_pipeline.has_alias(key):
                    aliases[key] = value
                elif 'mashup_id' in extra_info:
                    # new-style mashups can have aliases not existing in pipeline
                    for mashuptrail in mashups:
                        if mashuptrail.vtVersion == version:
                            mashup = mashuptrail.getMashup(extra_info['mashup_id'])
                            c = mashup.getAliasByName(key).component
                            params.append((c.vttype, c.vtid, value))

        if output_dir is not None and controller.current_pipeline is not None:
            # FIXME DAK: why is this always done?!? there is a flag for it...
            if is_running_gui():
                controller.updatePipelineScene()
                base_fname = "%s_%s_pipeline.pdf" % (locator.short_filename, version)
                filename = os.path.join(output_dir, base_fname)
                controller.current_pipeline_scene.saveToPDF(filename)
            else:
                debug.critical("Cannot save pipeline figure when not "
                               "running in gui mode")
            base_fname = "%s_%s_pipeline.xml" % (locator.short_filename, version)
            filename = os.path.join(output_dir, base_fname)
            vistrails.core.db.io.save_workflow(controller.current_pipeline, filename)
        if not update_vistrail:
            conf = get_vistrails_configuration()
            if conf.has('thumbs'):
                conf.thumbs.autoSave = False
        
        jobMonitor = controller.jobMonitor
        current_workflow = jobMonitor.currentWorkflow()
        if not current_workflow:
            for job in jobMonitor.workflows.itervalues():
                try:
                    job_version = int(job.version)
                except ValueError:
                    job_version =  v.get_version_number(job.version)
                if version == job_version:
                    current_workflow = job
                    jobMonitor.startWorkflow(job)
            if not current_workflow:
                current_workflow = JobWorkflow(version)
                jobMonitor.startWorkflow(current_workflow)

        try:
            (results, _) = \
            controller.execute_current_workflow(custom_aliases=aliases,
                                                custom_params=params,
                                                extra_info=extra_info,
                                                reason=reason)
        finally:
            jobMonitor.finishWorkflow()
        new_version = controller.current_version
        if new_version != version:
            debug.log("Version '%s' (%s) was upgraded. The actual "
                      "version executed was %s" % (
                      workflow, version, new_version))
        run = results[0]
        run.workflow_info = (locator.name, new_version)
        run.pipeline = controller.current_pipeline

        if update_vistrail:
            controller.write_vistrail(locator)
        result.append(run)
        if current_workflow.jobs:
            if current_workflow.completed():
#.........這裏部分代碼省略.........

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import execute_current_workflow [as 別名]
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)

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import execute_current_workflow [as 別名]
def run_and_get_results(w_list, parameters='', workflow_info=None, 
                        update_vistrail=True, extra_info=None, 
                        reason='Console Mode Execution'):
    """run_and_get_results(w_list: list of (locator, version), parameters: str,
                           workflow_info:str, update_vistrail: boolean,
                           extra_info:dict)
    Run all workflows in w_list, and returns an interpreter result object.
    version can be a tag name or a version id.
    
    """
    elements = parameters.split("$&$")
    aliases = {}
    result = []
    for locator, workflow in w_list:
        (v, abstractions , thumbnails, mashups)  = load_vistrail(locator)
        controller = VistrailController(v, locator, abstractions, thumbnails, 
                                        mashups, auto_save=update_vistrail)
        if isinstance(workflow, basestring):
            version = v.get_version_number(workflow)
        elif isinstance(workflow, (int, long)):
            version = workflow
        elif workflow is None:
            version = controller.get_latest_version_in_graph()
        else:
            msg = "Invalid version tag or number: %s" % workflow
            raise VistrailsInternalError(msg)
        controller.change_selected_version(version)
        
        for e in elements:
            pos = e.find("=")
            if pos != -1:
                key = e[:pos].strip()
                value = e[pos+1:].strip()
            
                if controller.current_pipeline.has_alias(key):
                    aliases[key] = value
                    
        if workflow_info is not None and controller.current_pipeline is not None:
            # FIXME DAK: why is this always done?!? there is a flag for it...
            if is_running_gui():
                controller.updatePipelineScene()
                base_fname = "%s_%s_pipeline.pdf" % (locator.short_filename, version)
                filename = os.path.join(workflow_info, base_fname)
                controller.current_pipeline_scene.saveToPDF(filename)
            else:
                debug.critical("Cannot save pipeline figure when not "
                               "running in gui mode")
            base_fname = "%s_%s_pipeline.xml" % (locator.short_filename, version)
            filename = os.path.join(workflow_info, base_fname)
            vistrails.core.db.io.save_workflow(controller.current_pipeline, filename)
        if not update_vistrail:
            conf = get_vistrails_configuration()
            if conf.has('thumbs'):
                conf.thumbs.autoSave = False
        
        (results, _) = \
            controller.execute_current_workflow(custom_aliases=aliases,
                                                extra_info=extra_info,
                                                reason=reason)
        new_version = controller.current_version
        if new_version != version:
            debug.warning("Version '%s' (%s) was upgraded. The actual "
                          "version executed was %s" % \
                              (workflow, version, new_version))
        run = results[0]
        run.workflow_info = (locator.name, new_version)
        run.pipeline = controller.current_pipeline

        if update_vistrail:
            controller.write_vistrail(locator)
        result.append(run)
    return result

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import execute_current_workflow [as 別名]
    def execute(workflowJSON):
        ''' Execute a workflow from it's JSON representation
        '''

        debug('convert json to xml')
        workflowXML = json2xml(workflowJSON)

        #temp_wf_fd, temp_wf = tempfile.mkstemp('.xml')

        debug('create temporary file')
        temp_wf_fd, temp_wf = tempfile.mkstemp()
        try:
            f = open(temp_wf, 'w')
            f.write(workflowXML)
            f.close()
            os.close(temp_wf_fd)

            #load workflow temp file into vistrails
            #vt.load_workflow(temp_wf)

            #execute workflow
            #execution = vt.execute()

            debug('Load the Pipeline from the temporary file')
            vistrail = Vistrail()
            locator = XMLFileLocator(temp_wf)
            workflow = locator.load(Pipeline)

            debug('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)

            debug('add actions')
            vistrail.add_action(action, 0L)
            vistrail.update_id_scope()
            tag = 'climatepipes'
            vistrail.addTag(tag, action.id)

            debug('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')

            debug('get result')
            execution_pipeline = execution[0][0]

            if len(execution_pipeline.errors) > 0:
                error("Executing workflow")
                for key in execution_pipeline.errors:
                    error(execution_pipeline.errors[key])
                    print execution_pipeline.errors[key]
                return None

            modules = execution_pipeline.objects

            for id, module in modules.iteritems():
                if isinstance(module, ToGeoJSON):
                    return json.dumps({'result': module.JSON, 'error': None })

        finally:
            os.unlink(temp_wf)