cwl_utils.graph_split

Unpacks the result of cwltool –unpack.

Only tested with a single v1.0 workflow.

Attributes

stringify_dict
defaultStreamHandler

Functions

arg_parser()	Build the argument parser.
main()	Console entry point.
run(args)	Split the packed CWL at the path of the first argument.
graph_split(sourceIO, output_dir, output_format, ...)	Loop over the provided packed CWL document and split it up.
rewrite_id(entry, this_id)
rewrite(document, doc_id, output_dir[, pretty])	Rewrite the given element from the CWL $graph.
rewrite_import(document)	Adjust the $import directive.
rewrite_types(field, entry_file, sameself)	Clean up the names of the types.
rewrite_schemadef(document, output_dir[, pretty])	Dump the schemadefs to their own file.
json_dump(entry, output_file)	Output object as JSON.
yaml_dump(entry, output_handle, pretty)	Output object as YAML.

Module Contents

cwl_utils.graph_split.stringify_dict: Callable[[dict[str, Any]], str] | None

cwl_utils.graph_split.defaultStreamHandler

cwl_utils.graph_split.arg_parser()

Build the argument parser.

Return type:

argparse.ArgumentParser

cwl_utils.graph_split.main()

Console entry point.

Return type:

None

cwl_utils.graph_split.run(args)

Split the packed CWL at the path of the first argument.

Parameters:

args (list[str])

Return type:

int

cwl_utils.graph_split.graph_split(sourceIO, output_dir, output_format, mainfile, pretty)

Loop over the provided packed CWL document and split it up.

Parameters:

• sourceIO (IO[str])

• output_dir (pathlib.Path)

• output_format (str)

• mainfile (str)

• pretty (bool)

Return type:

None

cwl_utils.graph_split.rewrite_id(entry, this_id)

Parameters:

• entry (Any)

• this_id (str | None)

Return type:

collections.abc.MutableMapping[Any, Any] | str

cwl_utils.graph_split.rewrite(document, doc_id, output_dir, pretty=False)

Rewrite the given element from the CWL $graph.

Parameters:

• document (Any)

• doc_id (str)

• output_dir (pathlib.Path)

• pretty (bool)

Return type:

set[str]

cwl_utils.graph_split.rewrite_import(document)

Adjust the $import directive.

Parameters:

document (collections.abc.MutableMapping[str, Any])

Return type:

None

cwl_utils.graph_split.rewrite_types(field, entry_file, sameself)

Clean up the names of the types.

Parameters:

• field (Any)

• entry_file (str)

• sameself (bool)

Return type:

None

cwl_utils.graph_split.rewrite_schemadef(document, output_dir, pretty=False)

Dump the schemadefs to their own file.

Parameters:

• document (collections.abc.MutableMapping[str, Any])

• output_dir (pathlib.Path)

• pretty (bool)

Return type:

set[str]

cwl_utils.graph_split.json_dump(entry, output_file)

Output object as JSON.

Parameters:

• entry (Any)

• output_file (pathlib.Path)

Return type:

None

cwl_utils.graph_split.yaml_dump(entry, output_handle, pretty)

Output object as YAML.

Parameters:

• entry (Any)

• output_handle (io.TextIOWrapper)

• pretty (bool)

Return type:

None