cwl_utils.parser.cwl_v1_2_utils

Attributes

CONTENT_LIMIT

SrcSink

Exceptions

WorkflowException

Common base class for all non-exit exceptions.

Functions

can_assign_src_to_sink(src, sink[, strict])

Check for identical type specifications, ignoring extra keys like inputBinding.

check_all_types(src_dict, sinks, param_to_step, type_dict)

Given a list of sinks, check if their types match with the types of their sources.

check_types(srctype, sinktype, linkMerge[, valueFrom])

Check if the source and sink types are correct.

content_limit_respected_read_bytes(f)

Read file content up to 64 kB as a byte array.

content_limit_respected_read(f)

Read file content up to 64 kB as an utf-8 encoded string.

convert_stdstreams_to_files(clt)

Convert stdin, stdout and stderr type shortcuts to files.

load_inputfile(doc[, baseuri, loadingOptions])

Load a CWL v1.2 input file from a serialized YAML string or a YAML object.

load_inputfile_by_string(string, uri[, loadingOptions])

Load a CWL v1.2 input file from a serialized YAML string.

load_inputfile_by_yaml(yaml, uri[, loadingOptions])

Load a CWL v1.2 input file from a YAML object.

merge_flatten_type(src)

Return the merge flattened type of the source type.

type_for_step_input(step, in_)

Determine the type for the given step input.

type_for_step_output(step, sourcename)

Determine the type for the given step output.

type_for_source(process, sourcenames[, parent, ...])

Determine the type for the given sourcenames.

param_for_source_id(process, sourcenames[, parent, ...])

Find the process input parameter that matches one of the given sourcenames.

Module Contents

exception cwl_utils.parser.cwl_v1_2_utils.WorkflowException

Bases: Exception

Inheritance diagram of cwl_utils.parser.cwl_v1_2_utils.WorkflowException

Common base class for all non-exit exceptions.

cwl_utils.parser.cwl_v1_2_utils.CONTENT_LIMIT: int
cwl_utils.parser.cwl_v1_2_utils.SrcSink
cwl_utils.parser.cwl_v1_2_utils.can_assign_src_to_sink(src, sink, strict=False)

Check for identical type specifications, ignoring extra keys like inputBinding.

src: admissible source types sink: admissible sink types

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.

Parameters:
  • src (Any) –

  • sink (Any) –

  • strict (bool) –

Return type:

bool

cwl_utils.parser.cwl_v1_2_utils.check_all_types(src_dict, sinks, param_to_step, type_dict)

Given a list of sinks, check if their types match with the types of their sources.

Parameters:
Return type:

Dict[str, List[SrcSink]]

cwl_utils.parser.cwl_v1_2_utils.check_types(srctype, sinktype, linkMerge, valueFrom=None)

Check if the source and sink types are correct.

Acceptable types are “pass”, “warning”, or “exception”.

Parameters:
  • srctype (Any) –

  • sinktype (Any) –

  • linkMerge (Optional[str]) –

  • valueFrom (Optional[str]) –

Return type:

str

cwl_utils.parser.cwl_v1_2_utils.content_limit_respected_read_bytes(f)

Read file content up to 64 kB as a byte array.

Throw exception for larger files (see https://www.commonwl.org/v1.2/Workflow.html#Changelog).

Parameters:

f (IO[bytes]) –

Return type:

bytes

cwl_utils.parser.cwl_v1_2_utils.content_limit_respected_read(f)

Read file content up to 64 kB as an utf-8 encoded string.

Throw exception for larger files (see https://www.commonwl.org/v1.2/Workflow.html#Changelog).

Parameters:

f (IO[bytes]) –

Return type:

str

cwl_utils.parser.cwl_v1_2_utils.convert_stdstreams_to_files(clt)

Convert stdin, stdout and stderr type shortcuts to files.

Parameters:

clt (cwl_utils.parser.cwl_v1_2.CommandLineTool) –

Return type:

None

cwl_utils.parser.cwl_v1_2_utils.load_inputfile(doc, baseuri=None, loadingOptions=None)

Load a CWL v1.2 input file from a serialized YAML string or a YAML object.

Parameters:
Return type:

Any

cwl_utils.parser.cwl_v1_2_utils.load_inputfile_by_string(string, uri, loadingOptions=None)

Load a CWL v1.2 input file from a serialized YAML string.

Parameters:
Return type:

Any

cwl_utils.parser.cwl_v1_2_utils.load_inputfile_by_yaml(yaml, uri, loadingOptions=None)

Load a CWL v1.2 input file from a YAML object.

Parameters:
Return type:

Any

cwl_utils.parser.cwl_v1_2_utils.merge_flatten_type(src)

Return the merge flattened type of the source type.

Parameters:

src (Any) –

Return type:

Any

cwl_utils.parser.cwl_v1_2_utils.type_for_step_input(step, in_)

Determine the type for the given step input.

Parameters:
Return type:

Any

cwl_utils.parser.cwl_v1_2_utils.type_for_step_output(step, sourcename)

Determine the type for the given step output.

Parameters:
Return type:

Any

cwl_utils.parser.cwl_v1_2_utils.type_for_source(process, sourcenames, parent=None, linkMerge=None, pickValue=None)

Determine the type for the given sourcenames.

Parameters:
Return type:

Any

cwl_utils.parser.cwl_v1_2_utils.param_for_source_id(process, sourcenames, parent=None, scatter_context=None)

Find the process input parameter that matches one of the given sourcenames.

Parameters:
Return type:

Union[List[cwl_utils.parser.cwl_v1_2.WorkflowInputParameter], cwl_utils.parser.cwl_v1_2.WorkflowInputParameter]