cwltool.main

Entry point for cwltool.

Module Contents

Classes

ProvLogFormatter

Enforce ISO8601 with both T and Z.

Functions

append_word_to_default_user_agent(word)	Append the specified word to the requests http user agent string if it's not already there.
generate_example_input(inptype, default)	Convert a single input schema into an example.
realize_input_schema(input_types, schema_defs)	Replace references to named typed with the actual types.
generate_input_template(tool)	Generate an example input object for the given CWL process.
load_job_order(args, stdin, fetcher_constructor, ...)
init_job_order(job_order_object, args, process, ...[, ...])
make_relative(base, obj)	Relativize the location URI of a File or Directory object.
printdeps(obj, document_loader, stdout, relative_deps, uri)	Print a JSON representation of the dependencies of the CWL document.
prov_deps(obj, document_loader, uri[, basedir])
find_deps(obj, document_loader, uri[, basedir, nestdirs])	Find the dependencies of the CWL document.
print_pack(loadingContext, uri)	Return a CWL serialization of the CWL document in JSON.
supported_cwl_versions(enable_dev)
setup_schema(args, custom_schema_callback)
setup_provenance(args, runtimeContext[, argsl])
setup_loadingContext(loadingContext, runtimeContext, args)	Prepare a LoadingContext from the given arguments.
make_template(tool, target)	Make a template CWL input object for the give Process.
inherit_reqshints(tool, parent)	Copy down requirements and hints from ancestors of a given process.
choose_target(args, tool, loading_context)	Walk the Workflow, extract the subset matches all the args.targets.
choose_step(args, tool, loading_context)	Walk the given Workflow and extract just args.single_step.
choose_process(args, tool, loadingContext)	Walk the given Workflow and extract just args.single_process.
check_working_directories(runtimeContext)	Make any needed working directories.
print_targets(tool, stdout, loading_context[, prefix])	Recursively find targets for --subgraph and friends.
main([argsl, args, job_order_object, stdin, stdout, ...])
find_default_container(builder[, default_container, ...])	Find a container.
windows_check()	See if we are running on MS Windows and warn about the lack of support.
run(*args, **kwargs)	Run cwltool.

Attributes

docker_exe
ProvOut

cwltool.main.docker_exe: str

cwltool.main.append_word_to_default_user_agent(word)

Append the specified word to the requests http user agent string if it’s not already there.

Parameters:

word (str) –

Return type:

None

cwltool.main.generate_example_input(inptype, default)

Convert a single input schema into an example.

Parameters:

• inptype (Optional[cwltool.utils.CWLOutputType]) –

• default (Optional[cwltool.utils.CWLOutputType]) –

Return type:

Tuple[Any, str]

cwltool.main.realize_input_schema(input_types, schema_defs)

Replace references to named typed with the actual types.

Parameters:

• input_types (MutableSequence[Union[str, cwltool.utils.CWLObjectType]]) –

• schema_defs (MutableMapping[str, cwltool.utils.CWLObjectType]) –

Return type:

MutableSequence[Union[str, cwltool.utils.CWLObjectType]]

cwltool.main.generate_input_template(tool)

Generate an example input object for the given CWL process.

Parameters:

tool (cwltool.process.Process) –

Return type:

cwltool.utils.CWLObjectType

cwltool.main.load_job_order(args, stdin, fetcher_constructor, overrides_list, tool_file_uri)

Parameters:

• args (argparse.Namespace) –

• stdin (IO[Any]) –

• fetcher_constructor (Optional[schema_salad.utils.FetcherCallableType]) –

• overrides_list (List[cwltool.utils.CWLObjectType]) –

• tool_file_uri (str) –

Return type:

Tuple[Optional[cwltool.utils.CWLObjectType], str, schema_salad.ref_resolver.Loader]

cwltool.main.init_job_order(job_order_object, args, process, loader, stdout, print_input_deps=False, relative_deps='primary', make_fs_access=StdFsAccess, input_basedir='', secret_store=None, input_required=True, runtime_context=None)

Parameters:

• job_order_object (Optional[cwltool.utils.CWLObjectType]) –

• args (argparse.Namespace) –

• process (cwltool.process.Process) –

• loader (schema_salad.ref_resolver.Loader) –

• stdout (IO[str]) –

• print_input_deps (bool) –

• relative_deps (str) –

• make_fs_access (Callable[[str], cwltool.stdfsaccess.StdFsAccess]) –

• input_basedir (str) –

• secret_store (Optional[cwltool.secrets.SecretStore]) –

• input_required (bool) –

• runtime_context (Optional[cwltool.context.RuntimeContext]) –

Return type:

cwltool.utils.CWLObjectType

cwltool.main.make_relative(base, obj)

Relativize the location URI of a File or Directory object.

Parameters:

• base (str) –

• obj (cwltool.utils.CWLObjectType) –

Return type:

None

cwltool.main.printdeps(obj, document_loader, stdout, relative_deps, uri, basedir=None, nestdirs=True)

Print a JSON representation of the dependencies of the CWL document.

Parameters:

• obj (cwltool.utils.CWLObjectType) –

• document_loader (schema_salad.ref_resolver.Loader) –

• stdout (IO[str]) –

• relative_deps (str) –

• uri (str) –

• basedir (Optional[str]) –

• nestdirs (bool) –

Return type:

None

cwltool.main.prov_deps(obj, document_loader, uri, basedir=None)

Parameters:

• obj (cwltool.utils.CWLObjectType) –

• document_loader (schema_salad.ref_resolver.Loader) –

• uri (str) –

• basedir (Optional[str]) –

Return type:

cwltool.utils.CWLObjectType

cwltool.main.find_deps(obj, document_loader, uri, basedir=None, nestdirs=True)

Find the dependencies of the CWL document.

Parameters:

• obj (cwltool.utils.CWLObjectType) –

• document_loader (schema_salad.ref_resolver.Loader) –

• uri (str) –

• basedir (Optional[str]) –

• nestdirs (bool) –

Return type:

cwltool.utils.CWLObjectType

cwltool.main.print_pack(loadingContext, uri)

Return a CWL serialization of the CWL document in JSON.

Parameters:

• loadingContext (cwltool.context.LoadingContext) –

• uri (str) –

Return type:

str

cwltool.main.supported_cwl_versions(enable_dev)

Parameters:

enable_dev (bool) –

Return type:

List[str]

cwltool.main.setup_schema(args, custom_schema_callback)

Parameters:

• args (argparse.Namespace) –

• custom_schema_callback (Optional[Callable[[], None]]) –

Return type:

None

class cwltool.main.ProvLogFormatter

Bases: logging.Formatter

Enforce ISO8601 with both T and Z.

formatTime(record, datefmt=None)

Override the default formatTime to include the timezone.

Parameters:

• record (logging.LogRecord) –

• datefmt (Optional[str]) –

Return type:

str

cwltool.main.ProvOut

cwltool.main.setup_provenance(args, runtimeContext, argsl=None)

Parameters:

• args (argparse.Namespace) –

• runtimeContext (cwltool.context.RuntimeContext) –

• argsl (Optional[List[str]]) –

Return type:

Tuple[ProvOut, logging.StreamHandler[ProvOut]]

cwltool.main.setup_loadingContext(loadingContext, runtimeContext, args)

Prepare a LoadingContext from the given arguments.

Parameters:

• loadingContext (Optional[cwltool.context.LoadingContext]) –

• runtimeContext (cwltool.context.RuntimeContext) –

• args (argparse.Namespace) –

Return type:

cwltool.context.LoadingContext

cwltool.main.make_template(tool, target)

Make a template CWL input object for the give Process.

Parameters:

• tool (cwltool.process.Process) –

• target (IO[str]) –

Return type:

None

cwltool.main.inherit_reqshints(tool, parent)

Copy down requirements and hints from ancestors of a given process.

Parameters:

• tool (cwltool.process.Process) –

• parent (cwltool.process.Process) –

Return type:

None

cwltool.main.choose_target(args, tool, loading_context)

Walk the Workflow, extract the subset matches all the args.targets.

Parameters:

• args (argparse.Namespace) –

• tool (cwltool.process.Process) –

• loading_context (cwltool.context.LoadingContext) –

Return type:

Optional[cwltool.process.Process]

cwltool.main.choose_step(args, tool, loading_context)

Walk the given Workflow and extract just args.single_step.

Parameters:

• args (argparse.Namespace) –

• tool (cwltool.process.Process) –

• loading_context (cwltool.context.LoadingContext) –

Return type:

Optional[cwltool.process.Process]

cwltool.main.choose_process(args, tool, loadingContext)

Walk the given Workflow and extract just args.single_process.

Parameters:

• args (argparse.Namespace) –

• tool (cwltool.process.Process) –

• loadingContext (cwltool.context.LoadingContext) –

Return type:

Optional[cwltool.process.Process]

cwltool.main.check_working_directories(runtimeContext)

Make any needed working directories.

Parameters:

runtimeContext (cwltool.context.RuntimeContext) –

Return type:

Optional[int]

cwltool.main.print_targets(tool, stdout, loading_context, prefix='')

Recursively find targets for –subgraph and friends.

Parameters:

• tool (cwltool.process.Process) –

• stdout (IO[str]) –

• loading_context (cwltool.context.LoadingContext) –

• prefix (str) –

Return type:

None

cwltool.main.main(argsl=None, args=None, job_order_object=None, stdin=sys.stdin, stdout=None, stderr=sys.stderr, versionfunc=versionstring, logger_handler=None, custom_schema_callback=None, executor=None, loadingContext=None, runtimeContext=None, input_required=True)

Parameters:

• argsl (Optional[List[str]]) –

• args (Optional[argparse.Namespace]) –

• job_order_object (Optional[cwltool.utils.CWLObjectType]) –

• stdin (IO[Any]) –

• stdout (Optional[IO[str]]) –

• stderr (IO[Any]) –

• versionfunc (Callable[[], str]) –

• logger_handler (Optional[logging.Handler]) –

• custom_schema_callback (Optional[Callable[[], None]]) –

• executor (Optional[cwltool.executors.JobExecutor]) –

• loadingContext (Optional[cwltool.context.LoadingContext]) –

• runtimeContext (Optional[cwltool.context.RuntimeContext]) –

• input_required (bool) –

Return type:

int

cwltool.main.find_default_container(builder, default_container=None, use_biocontainers=None, container_image_cache_path=None)

Find a container.

Parameters:

• builder (cwltool.utils.HasReqsHints) –

• default_container (Optional[str]) –

• use_biocontainers (Optional[bool]) –

• container_image_cache_path (Optional[str]) –

Return type:

Optional[str]

cwltool.main.windows_check()

See if we are running on MS Windows and warn about the lack of support.

Return type:

None

cwltool.main.run(*args, **kwargs)

Run cwltool.

Parameters:

• args (Any) –

• kwargs (Any) –

Return type:

int