toil.server.app

Attributes

version

logger

Classes

ToilBackend

WES backend implemented for Toil to run CWL, WDL, or Toil workflows. This

Functions

get_current_aws_region()

Return the AWS region that the currently configured AWS zone (see

running_on_ec2()

Return True if we are currently running on EC2, and false otherwise.

running_on_ecs()

Return True if we are currently running on Amazon ECS, and false otherwise.

run_app(app[, options])

Run a Gunicorn WSGI server.

parser_with_server_options()

create_app(args)

Create a "connexion.FlaskApp" instance with Toil server configurations.

start_server(args)

Start a Toil server.

Module Contents

toil.server.app.get_current_aws_region()

Return the AWS region that the currently configured AWS zone (see get_current_aws_zone()) is in.

Return type:

Optional[str]

toil.server.app.running_on_ec2()

Return True if we are currently running on EC2, and false otherwise.

Return type:

bool

toil.server.app.running_on_ecs()

Return True if we are currently running on Amazon ECS, and false otherwise.

Return type:

bool

class toil.server.app.ToilBackend(work_dir, state_store, options, dest_bucket_base, bypass_celery=False, wes_dialect='standard')

Bases: toil.server.wes.abstract_backend.WESBackend

WES backend implemented for Toil to run CWL, WDL, or Toil workflows. This class is responsible for validating and executing submitted workflows.

Parameters:

  • work_dir (str)

  • state_store (Optional[str])

  • options (List[str])

  • dest_bucket_base (Optional[str])

  • bypass_celery (bool)

  • wes_dialect (str)

get_runs()

A generator of a list of run ids and their state.

Return type:

Generator[Tuple[str, str], None, None]

get_state(run_id)

Return the state of the workflow run with the given run ID. May raise an error if the workflow does not exist.

Parameters:

run_id (str)

Return type:

str

get_service_info()

Get information about the Workflow Execution Service.

Return type:

Dict[str, Any]

list_runs(page_size=None, page_token=None)

List the workflow runs.

Parameters:

  • page_size (Optional[int])

  • page_token (Optional[str])

Return type:

Dict[str, Any]

run_workflow()

Run a workflow.

Return type:

Dict[str, str]

get_run_log(run_id)

Get detailed info about a workflow run.

Parameters:

run_id (str)

Return type:

Dict[str, Any]

cancel_run(run_id)

Cancel a running workflow.

Parameters:

run_id (str)

Return type:

Dict[str, str]

get_run_status(run_id)

Get quick status info about a workflow run, returning a simple result with the overall state of the workflow run.

Parameters:

run_id (str)

Return type:

Dict[str, str]

get_stdout(run_id)

Get the stdout of a workflow run as a static file.

Parameters:

run_id (str)

Return type:

Any

get_stderr(run_id)

Get the stderr of a workflow run as a static file.

Parameters:

run_id (str)

Return type:

Any

get_health()

Return successfully if the server is healthy.

Return type:

werkzeug.wrappers.response.Response

get_homepage()

Provide a sensible result for / other than 404.

Return type:

werkzeug.wrappers.response.Response

toil.server.app.run_app(app, options=None)

Run a Gunicorn WSGI server.

Parameters:

  • app (object)

  • options (Optional[Dict[str, Any]])

Return type:

None

toil.server.app.version = '7.0.0-d569ea5711eb310ffd5703803f7250ebf7c19576'
toil.server.app.logger
toil.server.app.parser_with_server_options()
Return type:

argparse.ArgumentParser

toil.server.app.create_app(args)

Create a “connexion.FlaskApp” instance with Toil server configurations.

Parameters:

args (argparse.Namespace)

Return type:

connexion.FlaskApp

toil.server.app.start_server(args)

Start a Toil server.

Parameters:

args (argparse.Namespace)

Return type:

None