def get_windows_safe_factory(runtime_context=None, # type: RuntimeContext loading_context=None, # type: LoadingContext executor=None # type: Any ): # type: (...) -> Factory if onWindows(): if not runtime_context: runtime_context = RuntimeContext() runtime_context.find_default_container = functools.partial( force_default_container, windows_default_container_id) runtime_context.use_container = True runtime_context.default_container = windows_default_container_id return Factory(executor, loading_context, runtime_context)
def get_windows_safe_factory(runtime_context=None, # type: RuntimeContext loading_context=None, # type: LoadingContext executor=None # type: Any ): # type: (...) -> Factory if onWindows(): if not runtime_context: runtime_context = RuntimeContext() runtime_context.find_default_container = functools.partial( force_default_container, windows_default_container_id) runtime_context.use_container = True runtime_context.default_container = windows_default_container_id return Factory(executor, loading_context, runtime_context)
def cwlmain( self, argsl=None, # type: List[str] args=None, # type: argparse.Namespace job_order_object=None, # type: MutableMapping[Text, Any] stdin=sys.stdin, # type: IO[Any] stdout=None, # type: Union[TextIO, codecs.StreamWriter] stderr=sys.stderr, # type: IO[Any] versionfunc=versionstring, # type: Callable[[], Text] logger_handler=None, # custom_schema_callback=None, # type: Callable[[], None] executor=None, # type: Callable[..., Tuple[Dict[Text, Any], Text]] loadingContext=None, # type: LoadingContext runtimeContext=None # type: RuntimeContext ): # type: (...) -> int if not stdout: stdout = codecs.getwriter('utf-8')(sys.stdout) _logger.removeHandler(defaultStreamHandler) if logger_handler: stderr_handler = logger_handler else: stderr_handler = logging.StreamHandler(stderr) _logger.addHandler(stderr_handler) try: if args is None: args = arg_parser().parse_args(argsl) if args.workflow and "--outdir" not in argsl: outputPath = args.workflow.split('/')[-1].split('.')[0] setattr( args, "outdir", os.getcwd() + "/" + outputPath + "/" + datetime.datetime.now().strftime('%Y-%m-%d-%H%M')) if runtimeContext is None: runtimeContext = RuntimeContext(vars(args)) else: runtimeContext = runtimeContext.copy() rdflib_logger = logging.getLogger("rdflib.term") rdflib_logger.addHandler(stderr_handler) rdflib_logger.setLevel(logging.ERROR) if args.quiet: _logger.setLevel(logging.WARN) if runtimeContext.debug: _logger.setLevel(logging.DEBUG) rdflib_logger.setLevel(logging.DEBUG) if args.timestamps: formatter = logging.Formatter("[%(asctime)s] %(message)s", "%Y-%m-%d %H:%M:%S") stderr_handler.setFormatter(formatter) # version if args.version: return versionfunc(), 0 else: _logger.info(versionfunc()) if args.print_supported_versions: return "\n".join(supportedCWLversions(args.enable_dev)), 0 if not args.workflow: if os.path.isfile("CWLFile"): setattr(args, "workflow", "CWLFile") else: _logger.error("") _logger.error( "CWL document required, no input file was provided") arg_parser().print_help() return "CWL document required, no input file was provided", 1 if args.relax_path_checks: command_line_tool.ACCEPTLIST_RE = command_line_tool.ACCEPTLIST_EN_RELAXED_RE if args.ga4gh_tool_registries: ga4gh_tool_registries[:] = args.ga4gh_tool_registries if not args.enable_ga4gh_tool_registry: del ga4gh_tool_registries[:] if custom_schema_callback: custom_schema_callback() elif args.enable_ext: res = pkg_resources.resource_stream(__name__, 'extensions.yml') use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read()) res.close() else: use_standard_schema("v1.0") if loadingContext is None: loadingContext = LoadingContext(vars(args)) else: loadingContext = loadingContext.copy() loadingContext.disable_js_validation = \ args.disable_js_validation or (not args.do_validate) loadingContext.construct_tool_object = getdefault( loadingContext.construct_tool_object, workflow.default_make_tool) loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver) try: uri, tool_file_uri = resolve_tool_uri( args.workflow, resolver=loadingContext.resolver, fetcher_constructor=loadingContext.fetcher_constructor) except: return "Can't find file " + args.workflow, 0 try_again_msg = "" if args.debug else ", try again with --debug for more information" try: job_order_object, input_basedir, jobloader = load_job_order( args, stdin, loadingContext.fetcher_constructor, loadingContext.overrides_list, tool_file_uri) if args.overrides: loadingContext.overrides_list.extend( load_overrides( file_uri(os.path.abspath(args.overrides)), tool_file_uri)) document_loader, workflowobj, uri = fetch_document( uri, resolver=loadingContext.resolver, fetcher_constructor=loadingContext.fetcher_constructor) if args.print_deps: # printdeps(workflowobj, document_loader, stdout, args.relative_deps, uri) result = returndeps(workflowobj, document_loader, stdout, args.relative_deps, uri) return result, 0 document_loader, avsc_names, processobj, metadata, uri \ = validate_document(document_loader, workflowobj, uri, enable_dev=loadingContext.enable_dev, strict=loadingContext.strict, preprocess_only=(args.print_pre or args.pack), fetcher_constructor=loadingContext.fetcher_constructor, skip_schemas=args.skip_schemas, overrides=loadingContext.overrides_list, do_validate=loadingContext.do_validate) if args.print_pre: # stdout.write(json_dumps(processobj, indent=4)) return json_dumps(processobj, indent=4), 0 loadingContext.overrides_list.extend( metadata.get("cwltool:overrides", [])) tool = make_tool(document_loader, avsc_names, metadata, uri, loadingContext) if args.make_template: yaml.safe_dump(generate_input_template(tool), sys.stdout, default_flow_style=False, indent=4, block_seq_indent=2) return yaml.safe_dump(generate_input_template(tool), indent=4), 0 if args.validate: _logger.info("Tool definition is valid") return "Tool definition is valid", 0 if args.pack: stdout.write( print_pack(document_loader, processobj, uri, metadata)) return print_pack(document_loader, processobj, uri, metadata), 0 if args.print_rdf: stdout.write( printrdf(tool, document_loader.ctx, args.rdf_serializer)) return printrdf(tool, document_loader.ctx, args.rdf_serializer), 0 if args.print_dot: printdot(tool, document_loader.ctx, stdout) return "args.print_dot still not solved", 0 except (validate.ValidationException) as exc: _logger.error(u"Tool definition failed validation:\n%s", exc, exc_info=args.debug) infor = "Tool definition failed validation:\n%s" + exc + args.debug return infor, 1 except (RuntimeError, WorkflowException) as exc: _logger.error(u"Tool definition failed initialization:\n%s", exc, exc_info=args.debug) infor = "Tool definition failed initialization:\n%s" + exc + args.debug return infor, 1 except Exception as exc: _logger.error( u"I'm sorry, I couldn't load this CWL file%s.\nThe error was: %s", try_again_msg, exc if not args.debug else "", exc_info=args.debug) return "I'm sorry, I couldn't load this CWL file", 1 if isinstance(tool, int): return tool, 0 # If on MacOS platform, TMPDIR must be set to be under one of the # shared volumes in Docker for Mac # More info: https://dockstore.org/docs/faq if sys.platform == "darwin": default_mac_path = "/private/tmp/docker_tmp" if runtimeContext.tmp_outdir_prefix == DEFAULT_TMP_PREFIX: runtimeContext.tmp_outdir_prefix = default_mac_path for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"): if getattr(runtimeContext, dirprefix) and getattr( runtimeContext, dirprefix) != DEFAULT_TMP_PREFIX: sl = "/" if getattr(runtimeContext, dirprefix).endswith("/") or dirprefix == "cachedir" \ else "" setattr( runtimeContext, dirprefix, os.path.abspath(getattr(runtimeContext, dirprefix)) + sl) if not os.path.exists( os.path.dirname(getattr(runtimeContext, dirprefix))): try: os.makedirs( os.path.dirname( getattr(runtimeContext, dirprefix))) except Exception as e: _logger.error("Failed to create directory: %s", e) infor = "Failed to create directory: %s" + e + "" return infor, 1 if args.cachedir: if args.move_outputs == "move": runtimeContext.move_outputs = "copy" runtimeContext.tmp_outdir_prefix = args.cachedir runtimeContext.secret_store = getdefault( runtimeContext.secret_store, SecretStore()) try: initialized_job_order_object = init_job_order( job_order_object, args, tool, jobloader, stdout, print_input_deps=args.print_input_deps, relative_deps=args.relative_deps, input_basedir=input_basedir, secret_store=runtimeContext.secret_store) except SystemExit as err: return err.code if not executor: if args.parallel: executor = MultithreadedJobExecutor() else: executor = SingleJobExecutor() assert executor is not None if isinstance(initialized_job_order_object, int): return initialized_job_order_object try: runtimeContext.basedir = input_basedir del args.workflow del args.job_order conf_file = getattr(args, "beta_dependency_resolvers_configuration", None) # Text use_conda_dependencies = getattr(args, "beta_conda_dependencies", None) # Text job_script_provider = None # type: Optional[DependenciesConfiguration] if conf_file or use_conda_dependencies: runtimeContext.job_script_provider = DependenciesConfiguration( args) runtimeContext.find_default_container = \ functools.partial(find_default_container, args) runtimeContext.make_fs_access = getdefault( runtimeContext.make_fs_access, StdFsAccess) (out, status) = executor(tool, initialized_job_order_object, runtimeContext, logger=_logger) # This is the workflow output, it needs to be written if out is not None: def loc_to_path(obj): for field in ("path", "nameext", "nameroot", "dirname"): if field in obj: del obj[field] if obj["location"].startswith("file://"): obj["path"] = uri_file_path(obj["location"]) visit_class(out, ("File", "Directory"), loc_to_path) # Unsetting the Generation fron final output object visit_class(out, ("File", ), MutationManager().unset_generation) if isinstance(out, string_types): stdout.write(out) else: stdout.write( json_dumps( out, indent=4, # type: ignore ensure_ascii=False)) stdout.write("\n") if hasattr(stdout, "flush"): stdout.flush() # type: ignore if status != "success": _logger.warning(u"Final process status is %s", status) infor = "Final process status is %s" + status + "" return infor, 1 _logger.info(u"Final process status is %s", status) return out, status except (validate.ValidationException) as exc: _logger.error(u"Input object failed validation:\n%s", exc, exc_info=args.debug) infor = "Input object failed validation:\n%s" + exc + args.debug return infor, 1 except UnsupportedRequirement as exc: _logger.error( u"Workflow or tool uses unsupported feature:\n%s", exc, exc_info=args.debug) infor = "Workflow or tool uses unsupported feature:\n%s" + exc + args.debug return infor, 3 except WorkflowException as exc: _logger.error(u"Workflow error%s:\n%s", try_again_msg, strip_dup_lineno(six.text_type(exc)), exc_info=args.debug) infor = "Workflow error%s:\n%s" + try_again_msg + strip_dup_lineno( six.text_type(exc)) + args.debug return infor, 1 except Exception as exc: _logger.error(u"Unhandled error%s:\n %s", try_again_msg, exc, exc_info=args.debug) infor = "Unhandled error%s:\n %s" + try_again_msg + exc + args.debug return infor, 1 finally: _logger.removeHandler(stderr_handler) _logger.addHandler(defaultStreamHandler)