Source code for WDL.runtime

The recommended way to run a WDL workflow programmatically is to invoke ``miniwdl run`` as a
subprocess, capturing its JSON standard output. This leverages its logging, configuration, and
flexible input loading features; and avoids conflicting with the runtime's thread pools and signal
handlers. Alternatively, it's possible to call ```` directly if needed.
# pyre-strict
from typing import Union, Dict, Tuple, Any
from .. import Tree, Value, Env
from . import config
from . import task
from . import workflow
from . import _statusbar
from .error import RunFailed, CommandFailed, Terminated, OutputError, DownloadFailed, error_json
from .task import run_local_task
from .workflow import run_local_workflow

[docs]def run( cfg: config.Loader, exe: Union[Tree.Task, Tree.Workflow], inputs: Env.Bindings[Value.Base], **run_kwargs: Dict[str, Any], ) -> Tuple[str, Env.Bindings[Value.Base]]: """ Run the task or workflow given the inputs environment and configuration, returning the outputs environment. ``inputs`` may be parsed from a JSON dict using :func:`~WDL.values_from_json`, which can also validate them; see example below. :param run_id: a run identifier used in logs and filenames; defaults to executable name :param run_dir: directory under which to create a timestamp-named subdirectory for this run (defaults to current working directory). If the final path component is ``.`` then operate in run_dir directly. Typical usage: .. code-block:: python import WDL import WDL.runtime # Convert JSON-like inputs dict to WDL environment, validating them against exe's available # and required inputs. The dict keys should NOT be namespaced by the executable name; # if namespaces are present, then add to effectively remove them. inputs_env = WDL.values_from_json(inputs_dict, exe.available_inputs, exe.required_inputs) # Load configuration (see below) cfg = WDL.runtime.config.Loader(logging.getLogger(__name__)) # Run executable run_subdir, outputs_env =, exe, inputs_env, run_dir="/tmp") # Generate JSON-like outputs dict, with keys namespaced by the executable name outputs_dict = WDL.values_to_json(outputs_env, """ if "max_tasks" in run_kwargs and isinstance(exe, Tree.Task): del run_kwargs["max_tasks"] # N/A to run_local_task entrypoint = run_local_task if isinstance(exe, Tree.Task) else run_local_workflow return entrypoint(cfg, exe, inputs, **run_kwargs) # pyre-ignore