cwl_utils.parser.cwl_v1_1_utils

Attributes

CONTENT_LIMIT

Classes

SrcSink

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, 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 v1.1 input file from a serialized YAML string or a YAML object.
`load_inputfile_by_string`(string, uri[, loadingOptions])	Load a CWL v1.1 input file from a serialized YAML string.
`load_inputfile_by_yaml`(yaml, uri[, loadingOptions])	Load a CWL v1.1 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, linkMerge])	Determine the type for the given sourcenames.

Module Contents

cwl_utils.parser.cwl_v1_1_utils.CONTENT_LIMIT: int = 65536

class cwl_utils.parser.cwl_v1_1_utils.SrcSink

Bases: tuple

src

sink

linkMerge

message

cwl_utils.parser.cwl_v1_1_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_1_utils.check_all_types(src_dict, sinks, 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_1.WorkflowStepInput | cwl_utils.parser.cwl_v1_1.WorkflowOutputParameter])
type_dict (dict[str, Any])

Return type:

dict[str, list[SrcSink]]

cwl_utils.parser.cwl_v1_1_utils.content_limit_respected_read_bytes(f)

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

Truncate content for larger files.

Parameters:: f (IO[bytes])
Return type:: bytes

cwl_utils.parser.cwl_v1_1_utils.content_limit_respected_read(f)

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

Truncate content for larger files.

Parameters:: f (IO[bytes])
Return type:: str

cwl_utils.parser.cwl_v1_1_utils.convert_stdstreams_to_files(clt)

Convert stdin, stdout and stderr type shortcuts to files.

Parameters:: clt (cwl_utils.parser.cwl_v1_1.CommandLineTool)
Return type:: None

cwl_utils.parser.cwl_v1_1_utils.load_inputfile(doc, baseuri=None, loadingOptions=None)

Load a CWL v1.1 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_1_utils.load_inputfile_by_string(string, uri, loadingOptions=None)

Load a CWL v1.1 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_1_utils.load_inputfile_by_yaml(yaml, uri, loadingOptions=None)

Load a CWL v1.1 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_1_utils.type_for_step_input(step, in_)

Determine the type for the given step input.

Parameters:

step (cwl_utils.parser.cwl_v1_1.WorkflowStep)
in_ (cwl_utils.parser.cwl_v1_1.WorkflowStepInput)

Return type:

Any

cwl_utils.parser.cwl_v1_1_utils.type_for_step_output(step, sourcename)

Determine the type for the given step output.

Parameters:

step (cwl_utils.parser.cwl_v1_1.WorkflowStep)
sourcename (str)

Return type:

Any

cwl_utils.parser.cwl_v1_1_utils.type_for_source(process, sourcenames, parent=None, linkMerge=None)

Determine the type for the given sourcenames.

Parameters:

process (cwl_utils.parser.cwl_v1_1.CommandLineTool | cwl_utils.parser.cwl_v1_1.Workflow | cwl_utils.parser.cwl_v1_1.ExpressionTool)
sourcenames (str | list[str])
parent (cwl_utils.parser.cwl_v1_1.Workflow | None)
linkMerge (str | None)

Return type:

Any