cwltool.checker
Static checking of CWL workflow connectivity.
Module Contents
Functions
|
Check if the source and sink types are correct. |
|
Return the merge flattened type of the source type. |
|
Check for identical type specifications, ignoring extra keys like inputBinding. |
|
|
|
Check if all source and sink types of a workflow are compatible before run time. |
|
Given a list of sinks, check if their types match with the types of their sources. |
|
Check if a workflow has circular dependency. |
|
Get the dependency tree in the form of adjacency list. |
|
Perform depth first search. |
|
Extract step id from either input or output fields. |
|
|
|
Check if a step contains a http://commonwl.org/cwltool#Loop requirement with all outputMethod. |
|
Check http://commonwl.org/cwltool#Loop requirement compatibility with other directives. |
Attributes
- cwltool.checker.check_types(srctype, sinktype, linkMerge, valueFrom)
Check if the source and sink types are correct.
- Raises:
WorkflowException – If there is an unrecognized linkMerge type
- Parameters:
- Return type:
Union[Literal[pass], Literal[warning], Literal[exception]]
- cwltool.checker.merge_flatten_type(src)
Return the merge flattened type of the source type.
- Parameters:
src (cwltool.utils.SinkType) –
- Return type:
cwltool.utils.CWLOutputType
- cwltool.checker.can_assign_src_to_sink(src, sink, strict=False)
Check for identical type specifications, ignoring extra keys like inputBinding.
In non-strict comparison, at least one source type must match one sink type, except for ‘null’. In strict comparison, all source types must match at least one sink type.
- cwltool.checker.missing_subset(fullset, subset)
- Parameters:
fullset (List[Any]) –
subset (List[Any]) –
- Return type:
List[Any]
- cwltool.checker.static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs, param_to_step)
Check if all source and sink types of a workflow are compatible before run time.
- Raises:
ValidationException – If any incompatibilities are detected.
- Parameters:
workflow_inputs (List[cwltool.utils.CWLObjectType]) –
workflow_outputs (MutableSequence[cwltool.utils.CWLObjectType]) –
step_inputs (MutableSequence[cwltool.utils.CWLObjectType]) –
step_outputs (List[cwltool.utils.CWLObjectType]) –
param_to_step (Dict[str, cwltool.utils.CWLObjectType]) –
- Return type:
None
- cwltool.checker.SrcSink
- cwltool.checker.check_all_types(src_dict, sinks, sourceField, param_to_step)
Given a list of sinks, check if their types match with the types of their sources.
- Raises:
WorkflowException – if there is an unrecognized linkMerge value (from
check_types()
)ValidationException – if a sourceField is missing
- Parameters:
- Return type:
Dict[str, List[SrcSink]]
- cwltool.checker.circular_dependency_checker(step_inputs)
Check if a workflow has circular dependency.
- Raises:
ValidationException – If a circular dependency is detected.
- Parameters:
step_inputs (List[cwltool.utils.CWLObjectType]) –
- Return type:
None
- cwltool.checker.get_dependency_tree(step_inputs)
Get the dependency tree in the form of adjacency list.
- cwltool.checker.processDFS(adjacency, traversal_path, processed, cycles)
Perform depth first search.
- cwltool.checker.get_step_id(field_id)
Extract step id from either input or output fields.
- cwltool.checker.is_conditional_step(param_to_step, parm_id)
- cwltool.checker.is_all_output_method_loop_step(param_to_step, parm_id)
Check if a step contains a http://commonwl.org/cwltool#Loop requirement with all outputMethod.
- cwltool.checker.loop_checker(steps)
Check http://commonwl.org/cwltool#Loop requirement compatibility with other directives.
- Raises:
ValidationException – If there is an incompatible combination between cwltool:loop and ‘scatter’ or ‘when’.
- Parameters:
steps (Iterator[MutableMapping[str, Any]]) –
- Return type:
None