planemo.engine package — Planemo 0.75.31.dev0 documentation (original) (raw)
Submodules
planemo.engine.cwltool module
Module contianing the CwlToolEngine implementation of Engine.
class planemo.engine.cwltool.CwlToolEngine(ctx, **kwds)[source]
Bases: BaseEngine
An Engine implementation backed by cwltool.
More information on cwltool can be found at https://github.com/common-workflow-language/cwltool.
handled_runnable_types_: List[RunnableType]_ = [RunnableType.cwl_tool, RunnableType.cwl_workflow]
planemo.engine.factory module
Module contains factory method for building class:Engine objects.
planemo.engine.factory.build_engine(ctx, **kwds)[source]
Build an engine from the supplied planemo configuration.
planemo.engine.factory.engine_context(ctx, **kwds) → Generator[BaseEngine, None, None][source]
A contextlib.contextmanager() engine builder for use with with statements.
https://docs.python.org/2/library/contextlib.html
planemo.engine.factory.is_galaxy_engine(**kwds)[source]
Return True iff the engine configured is GalaxyEngine.
planemo.engine.galaxy module
Module contianing the GalaxyEngine implementation of Engine.
class planemo.engine.galaxy.DockerizedManagedGalaxyEngine(ctx, **kwds)[source]
Bases: LocalManagedGalaxyEngine
An Engine implementation backed by Galaxy running in Docker.
More information on Galaxy can be found at http://galaxyproject.org/.
class planemo.engine.galaxy.ExternalGalaxyEngine(ctx, **kwds)[source]
Bases: GalaxyEngine
An Engine implementation backed by an external Galaxy instance.
ensure_runnables_served(runnables)[source]
Use a context manager and describe Galaxy instance with runnables being served.
rerun(ctx: PlanemoCliContext, rerunnable: Rerunnable, **kwds) → GalaxyBaseRunResponse[source]
class planemo.engine.galaxy.LocalManagedGalaxyEngine(ctx, **kwds)[source]
Bases: GalaxyEngine
An Engine implementation backed by a managed Galaxy.
More information on Galaxy can be found at http://galaxyproject.org/.
ensure_runnables_served(runnables)[source]
Use a context manager and describe Galaxy instance with runnables being served.
class planemo.engine.galaxy.LocalManagedGalaxyEngineWithSingularityDB(ctx, **kwds)[source]
Bases: LocalManagedGalaxyEngine
run(runnables, job_paths, output_collectors: List[Callable] | None = None)[source]
Run a job using a compatible artifact (workflow or tool).
planemo.engine.interface module
Module contianing the Engine abstraction.
class planemo.engine.interface.BaseEngine(ctx, **kwds)[source]
Bases: Engine
Base class providing context and keywords for Engine implementations.
Use subclass’s handled_runnable_types variable to infer can_run.
Default no-op cleanup method.
handled_runnable_types_: List[RunnableType]_ = []
run(runnables, job_paths, output_collectors: List[Callable] | None = None)[source]
Run a job using a compatible artifact (workflow or tool).
test(runnables, test_timeout)[source]
Test runnable artifacts (workflow or tool).
class planemo.engine.interface.Engine[source]
Bases: object
Abstract description of an external process for running tools or workflows.
abstractmethod cleanup()[source]
Release any resources used to run/test with this engine.
abstractmethod run(path, job_path)[source]
Run a job using a compatible artifact (workflow or tool).
abstractmethod test(runnables)[source]
Test runnable artifacts (workflow or tool).
planemo.engine.test module
planemo.engine.test.test_runnables(ctx, runnables, original_paths=None, **kwds)[source]
Return exit code indicating test or failure.
planemo.engine.toil module
Module contianing the ToilEngine implementation of Engine.
class planemo.engine.toil.ToilEngine(ctx, **kwds)[source]
Bases: BaseEngine
An Engine implementation backed by Toil.
More information on toil can be found at https://github.com/BD2KGenomics/toil.
handled_runnable_types_: List[RunnableType]_ = [RunnableType.cwl_tool, RunnableType.cwl_workflow]
Module contents
Module describing planemo.interface.Engine abstraction and implementations.
The main entrypoint is the contextmanager engine_context().
planemo.engine.engine_context(ctx, **kwds) → Generator[BaseEngine, None, None][source]
A contextlib.contextmanager() engine builder for use with with statements.
https://docs.python.org/2/library/contextlib.html
planemo.engine.is_galaxy_engine(**kwds)[source]
Return True iff the engine configured is GalaxyEngine.