cwl_utils.parser.utils

CWL parser utility functions.

Functions

`convert_stdstreams_to_files`(process)	Convert stdin, stdout and stderr type shortcuts to files.
`load_inputfile_by_uri`(version, path[, loadingOptions])	Load a CWL input file from a URI or a path.
`load_inputfile`(version, doc[, baseuri, loadingOptions])	Load a CWL input file from a serialized YAML string or a YAML object.
`load_inputfile_by_string`(version, string, uri[, ...])	Load a CWL input file from a serialized YAML string.
`load_inputfile_by_yaml`(version, yaml, uri[, ...])	Load a CWL input file from a YAML object.
`load_step`(step)
`static_checker`(workflow)	Check if all source and sink types of a workflow are compatible before run time.
`type_for_source`(process, sourcenames[, parent, ...])	Determine the type for the given sourcenames.
`type_for_step_input`(step, in_, cwlVersion)	Determine the type for the given step output.
`type_for_step_output`(step, sourcename, cwlVersion)	Determine the type for the given step output.
`param_for_source_id`(process, sourcenames[, parent, ...])

Module Contents

cwl_utils.parser.utils.convert_stdstreams_to_files(process)

Convert stdin, stdout and stderr type shortcuts to files.

Parameters:: process (cwl_utils.parser.Process)
Return type:: None

cwl_utils.parser.utils.load_inputfile_by_uri(version, path, loadingOptions=None)

Load a CWL input file from a URI or a path.

Parameters:

version (str)
path (str | pathlib.Path)
loadingOptions (cwl_utils.parser.LoadingOptions | None)

Return type:

Any

cwl_utils.parser.utils.load_inputfile(version, doc, baseuri=None, loadingOptions=None)

Load a CWL input file from a serialized YAML string or a YAML object.

Parameters:

version (str)
doc (Any)
baseuri (str | None)
loadingOptions (cwl_utils.parser.LoadingOptions | None)

Return type:

Any

cwl_utils.parser.utils.load_inputfile_by_string(version, string, uri, loadingOptions=None)

Load a CWL input file from a serialized YAML string.

Parameters:

version (str)
string (str)
uri (str)
loadingOptions (cwl_utils.parser.LoadingOptions | None)

Return type:

Any

cwl_utils.parser.utils.load_inputfile_by_yaml(version, yaml, uri, loadingOptions=None)

Load a CWL input file from a YAML object.

Parameters:

version (str)
yaml (Any)
uri (str)
loadingOptions (cwl_utils.parser.LoadingOptions | None)

Return type:

Any

cwl_utils.parser.utils.load_step(step)

Parameters:: step (cwl_utils.parser.WorkflowStep)
Return type:: cwl_utils.parser.Process

cwl_utils.parser.utils.static_checker(workflow)

Check if all source and sink types of a workflow are compatible before run time.

Parameters:: workflow (cwl_utils.parser.Workflow)
Return type:: None

cwl_utils.parser.utils.type_for_source(process, sourcenames, parent=None, linkMerge=None, pickValue=None)

Determine the type for the given sourcenames.

Parameters:

process (cwl_utils.parser.Process)
sourcenames (str | list[str])
parent (cwl_utils.parser.Workflow | None)
linkMerge (str | None)
pickValue (str | None)

Return type:

Any

cwl_utils.parser.utils.type_for_step_input(step, in_, cwlVersion)

Determine the type for the given step output.

Parameters:

step (cwl_utils.parser.WorkflowStep)
in_ (cwl_utils.parser.WorkflowStepInput)
cwlVersion (str)

Return type:

Any

cwl_utils.parser.utils.type_for_step_output(step, sourcename, cwlVersion)

Determine the type for the given step output.

Parameters:

step (cwl_utils.parser.WorkflowStep)
sourcename (str)
cwlVersion (str)

Return type:

Any

cwl_utils.parser.utils.param_for_source_id(process, sourcenames, parent=None, scatter_context=None)

Parameters:

process (cwl_utils.parser.CommandLineTool | cwl_utils.parser.Workflow | cwl_utils.parser.ExpressionTool)
sourcenames (str | list[str])
parent (cwl_utils.parser.Workflow | None)
scatter_context (list[tuple[int, str] | None] | None)

Return type: