cwl_utils.parser.cwl_v1_2_utils

Attributes

CONTENT_LIMIT

Classes

Functions

`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.
`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.
`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.

Module Contents

cwl_utils.parser.cwl_v1_2_utils.CONTENT_LIMIT: int = 65536

class cwl_utils.parser.cwl_v1_2_utils.SrcSink

Bases: tuple

src

sink

linkMerge

message

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:

src_dict (dict[str, Any])
sinks (collections.abc.MutableSequence[cwl_utils.parser.cwl_v1_2.WorkflowStepInput | cwl_utils.parser.cwl_v1_2.WorkflowOutputParameter])
param_to_step (dict[str, cwl_utils.parser.cwl_v1_2.WorkflowStep])
type_dict (dict[str, Any])

Return type:

dict[str, list[SrcSink]]

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:

doc (Any)
baseuri (str | None)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

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:

string (Any)
uri (str)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

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:

yaml (Any)
uri (str)
loadingOptions (schema_salad.runtime.LoadingOptions | None)

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:

step (cwl_utils.parser.cwl_v1_2.WorkflowStep)
in_ (cwl_utils.parser.cwl_v1_2.WorkflowStepInput)

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:

step (cwl_utils.parser.cwl_v1_2.WorkflowStep)
sourcename (str)

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:

process (cwl_utils.parser.cwl_v1_2.CommandLineTool | cwl_utils.parser.cwl_v1_2.Workflow | cwl_utils.parser.cwl_v1_2.ExpressionTool)
sourcenames (str | list[str])
parent (cwl_utils.parser.cwl_v1_2.Workflow | None)
linkMerge (str | None)
pickValue (str | None)

Return type:

Any