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)
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
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(): run.job = "COMPLETED" else: run.job = "RUNNING: %s" % current_workflow.id for job in current_workflow.jobs.itervalues(): if not job.finished: run.job += "\n %s %s %s" % (job.start, job.name, job.description()) print run.job return result
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)
def run_and_get_results(w_list, parameters='', 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 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: try: job_version = v.get_version_number(job.version) except KeyError: # this is a PE or mashup continue 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(): run.job = "COMPLETED" else: run.job = "RUNNING: %s" % current_workflow.id for job in current_workflow.jobs.itervalues(): if not job.finished: run.job += "\n %s %s %s" % (job.start, job.name, job.description()) print run.job return result
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
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)