import os from typing import Any, Dict, Optional, Union from . import load_tool from .context import LoadingContext, RuntimeContext from .errors import WorkflowException from .executors import JobExecutor, SingleJobExecutor from .process import Process from .utils import CWLObjectType class WorkflowStatus(Exception): def __init__(self, out: Optional[CWLObjectType], status: str) -> None: """Signaling exception for the status of a Workflow.""" super().__init__("Completed %s" % status) self.out = out self.status = status class Callable: """Result of ::py:func:`Factory.make`.""" def __init__(self, t: Process, factory: "Factory") -> None: """Initialize.""" self.t = t self.factory = factory def __call__(self, **kwargs): # type: (**Any) -> Union[str, Optional[CWLObjectType]] runtime_context = self.factory.runtime_context.copy() runtime_context.basedir = os.getcwd() out, status = self.factory.executor(self.t, kwargs, runtime_context) if status != "success": raise WorkflowStatus(out, status) else: return out class Factory: """Easy way to load a CWL document for execution.""" loading_context: LoadingContext runtime_context: RuntimeContext def __init__( self, executor: Optional[JobExecutor] = None, loading_context: Optional[LoadingContext] = None, runtime_context: Optional[RuntimeContext] = None, ) -> None: if executor is None: executor = SingleJobExecutor() self.executor = executor if runtime_context is None: self.runtime_context = RuntimeContext() else: self.runtime_context = runtime_context if loading_context is None: self.loading_context = LoadingContext() self.loading_context.singularity = self.runtime_context.singularity self.loading_context.podman = self.runtime_context.podman else: self.loading_context = loading_context def make(self, cwl: Union[str, Dict[str, Any]]) -> Callable: """Instantiate a CWL object from a CWl document.""" load = load_tool.load_tool(cwl, self.loading_context) if isinstance(load, int): raise WorkflowException("Error loading tool") return Callable(load, self)