cwl_utils.expression_refactor

CWL Expression refactoring tool for CWL.

Attributes

defaultStreamHandler
save_type

Classes

saveCWL

Shortcut type for CWL v1.x parse.save().

Functions

arg_parser()	Build the argument parser.
parse_args(args)	Parse the command line options.
add_input_to_process(process, cwlVersion, name, ...)
cltool_inputs_to_etool_inputs(tool, cwlVersion)
empty_inputs(process_or_step, cwlVersion[, parent])
etool_to_cltool(etool, cwlVersion[, expressionLib])
find_expressionLib(processes)	Return the expressionLib from the highest priority InlineJavascriptRequirement.
generate_etool_from_expr2(expr, cwlVersion, target, inputs)	Generate an ExpressionTool to achieve the same result as the given expression.
get_command_input_parameter(…)
get_command_line_binding(…)
get_inline_javascript_requirement(…)
get_input_for_id(name, tool)	Determine the CommandInputParameter for the given input name.
load_step(step, replace_etool, skip_command_line1, ...)	If the step's Process is not inline, load and process it.
process_CommandLineTool_output(ctool, cwlVersion, outp_id)
remove_JSReq(process, skip_command_line1)	Since the InlineJavascriptRequirement is longer needed, remove it.
main()	Console entry point.
run(args)	Collect the arguments and run.
refactor(args)	Primary processing loop.

Module Contents

cwl_utils.expression_refactor.defaultStreamHandler

cwl_utils.expression_refactor.save_type

class cwl_utils.expression_refactor.saveCWL

Bases: Protocol

Shortcut type for CWL v1.x parse.save().

__call__(val, top=True, base_url='', relative_uris=True)

Must use this instead of a Callable due to the keyword args.

Parameters:

• val (Any)

• top (bool)

• base_url (str)

• relative_uris (bool)

Return type:

save_type

cwl_utils.expression_refactor.arg_parser()

Build the argument parser.

Return type:

argparse.ArgumentParser

cwl_utils.expression_refactor.parse_args(args)

Parse the command line options.

Parameters:

args (list[str])

Return type:

argparse.Namespace

cwl_utils.expression_refactor.add_input_to_process(process, cwlVersion, name, inptype, loadingOptions)

Parameters:

• process (cwl_utils.parser.Process)

• cwlVersion (Literal['v1.0', 'v1.1', 'v1.2'])

• name (str)

• inptype (Any)

• loadingOptions (schema_salad.runtime.LoadingOptions)

Return type:

None

cwl_utils.expression_refactor.cltool_inputs_to_etool_inputs(tool, cwlVersion)

Parameters:

• tool (cwl_utils.parser.CommandLineTool)

• cwlVersion (Literal['v1.0', 'v1.1', 'v1.2'])

Return type:

collections.abc.Sequence[cwl_utils.parser.WorkflowInputParameter]

cwl_utils.expression_refactor.empty_inputs(process_or_step, cwlVersion, parent=None)

Parameters:

• process_or_step (cwl_utils.parser.Process | cwl_utils.parser.WorkflowStep)

• cwlVersion (Literal['v1.0', 'v1.1', 'v1.2'])

• parent (cwl_utils.parser.Workflow | None)

Return type:

dict[str, Any]

cwl_utils.expression_refactor.etool_to_cltool(etool, cwlVersion, expressionLib=None)

Parameters:

• etool (cwl_utils.parser.ExpressionTool)

• cwlVersion (Literal['v1.0', 'v1.1', 'v1.2'])

• expressionLib (list[str] | None)

Return type:

cwl_utils.parser.CommandLineTool

cwl_utils.expression_refactor.find_expressionLib(processes)

Return the expressionLib from the highest priority InlineJavascriptRequirement.

processes: should be in order of least important to most important (Workflow, WorkflowStep, … CommandLineTool/ExpressionTool)

Parameters:

processes (collections.abc.Sequence[cwl_utils.parser.Process | cwl_utils.parser.WorkflowStep])

Return type:

list[str] | None

cwl_utils.expression_refactor.generate_etool_from_expr2(expr, cwlVersion, target, inputs, self_name=None, process=None, extra_processes=None)

Generate an ExpressionTool to achieve the same result as the given expression.

Parameters:

• expr (str)

• cwlVersion (Literal['v1.0', 'v1.1', 'v1.2'])

• target (cwl_utils.parser.CommandInputParameter | cwl_utils.parser.WorkflowInputParameter | cwl_utils.parser.OperationInputParameter)

• inputs (collections.abc.Sequence[cwl_utils.parser.CommandInputParameter | cwl_utils.parser.CommandOutputParameter | cwl_utils.parser.WorkflowInputParameter])

• self_name (str | None)

• process (cwl_utils.parser.Process | None)

• extra_processes (collections.abc.Sequence[cwl_utils.parser.Process | cwl_utils.parser.WorkflowStep] | None)

Return type:

cwl_utils.parser.ExpressionTool

cwl_utils.expression_refactor.get_command_input_parameter(cwlVersion: Literal['v1.0'], id_: str, type_: Any) → cwl_utils.parser.cwl_v1_0.CommandInputParameter

cwl_utils.expression_refactor.get_command_input_parameter(cwlVersion: Literal['v1.1'], id_: str, type_: Any) → cwl_utils.parser.cwl_v1_1.CommandInputParameter

cwl_utils.expression_refactor.get_command_input_parameter(cwlVersion: Literal['v1.2'], id_: str, type_: Any) → cwl_utils.parser.cwl_v1_2.CommandInputParameter

cwl_utils.expression_refactor.get_command_line_binding(cwlVersion: Literal['v1.0'], valueFrom: str | None = ..., loadContents: bool | None = ...) → cwl_utils.parser.cwl_v1_0.CommandLineBinding

cwl_utils.expression_refactor.get_command_line_binding(cwlVersion: Literal['v1.1'], valueFrom: str | None = ..., loadContents: bool | None = ...) → cwl_utils.parser.cwl_v1_1.CommandLineBinding

cwl_utils.expression_refactor.get_command_line_binding(cwlVersion: Literal['v1.2'], valueFrom: str | None = ..., loadContents: bool | None = ...) → cwl_utils.parser.cwl_v1_2.CommandLineBinding

cwl_utils.expression_refactor.get_inline_javascript_requirement(etool: cwl_utils.parser.ExpressionTool, cwlVersion: Literal['v1.0'], expression_lib: list[str] | None) → cwl_utils.parser.cwl_v1_0.InlineJavascriptRequirement

cwl_utils.expression_refactor.get_inline_javascript_requirement(etool: cwl_utils.parser.ExpressionTool, cwlVersion: Literal['v1.1'], expression_lib: list[str] | None) → cwl_utils.parser.cwl_v1_1.InlineJavascriptRequirement

cwl_utils.expression_refactor.get_inline_javascript_requirement(etool: cwl_utils.parser.ExpressionTool, cwlVersion: Literal['v1.2'], expression_lib: list[str] | None) → cwl_utils.parser.cwl_v1_2.InlineJavascriptRequirement

cwl_utils.expression_refactor.get_input_for_id(name, tool)

Determine the CommandInputParameter for the given input name.

Parameters:

• name (str)

• tool (cwl_utils.parser.Process)

Return type:

cwl_utils.parser.CommandInputParameter | cwl_utils.parser.WorkflowInputParameter | cwl_utils.parser.OperationInputParameter | None

cwl_utils.expression_refactor.load_step(step, replace_etool, skip_command_line1, skip_command_line2)

If the step’s Process is not inline, load and process it.

Parameters:

• step (cwl_utils.parser.WorkflowStep)

• replace_etool (bool)

• skip_command_line1 (bool)

• skip_command_line2 (bool)

Return type:

bool

cwl_utils.expression_refactor.process_CommandLineTool_output(ctool, cwlVersion, outp_id)

Parameters:

• ctool (cwl_utils.parser.CommandLineTool)

• cwlVersion (Literal['v1.0', 'v1.1', 'v1.2'])

• outp_id (str)

Return type:

None

cwl_utils.expression_refactor.remove_JSReq(process, skip_command_line1)

Since the InlineJavascriptRequirement is longer needed, remove it.

Parameters:

• process (cwl_utils.parser.CommandLineTool | cwl_utils.parser.WorkflowStep | cwl_utils.parser.Workflow)

• skip_command_line1 (bool)

Return type:

None

cwl_utils.expression_refactor.main()

Console entry point.

Return type:

None

cwl_utils.expression_refactor.run(args)

Collect the arguments and run.

Parameters:

args (list[str])

Return type:

int

cwl_utils.expression_refactor.refactor(args)

Primary processing loop.

Parameters:

args (argparse.Namespace)

Return type:

int