cwl_utils.parser

Submodules

• cwl_utils.parser.cwl_v1_0
• cwl_utils.parser.cwl_v1_0_utils
• cwl_utils.parser.cwl_v1_1
• cwl_utils.parser.cwl_v1_1_utils
• cwl_utils.parser.cwl_v1_2
• cwl_utils.parser.cwl_v1_2_utils
• cwl_utils.parser.latest
• cwl_utils.parser.utils

Package Contents

Functions

cwl_version(yaml)	Return the cwlVersion of a YAML object.
load_document_by_uri(path[, loadingOptions, load_all])	Load a CWL object from a URI or a path.
load_document(doc[, baseuri, loadingOptions, id_, ...])	Load a CWL object from a serialized YAML string or a YAML object.
load_document_by_string(string, uri[, loadingOptions, ...])	Load a CWL object from a serialized YAML string.
load_document_by_yaml(yaml, uri[, loadingOptions, ...])	Load a CWL object from a YAML object.
save(val[, top, base_url, relative_uris])	Convert a CWL Python object into a JSON/YAML serializable object.
is_process(v)	Test to see if the object is a CWL v1.x Python Process object.
version_split(version)	Split a cwlVersion value into its numerical components.

Attributes

LoadingOptions	Type union for a CWL v1.x LoadingOptions object.
Saveable	Type union for a CWL v1.x Saveable object.
InputParameter	Type union for a CWL v1.x InputParameter object.
OutputParameter	Type union for a CWL v1.x OutputParameter object.
Workflow
WorkflowTypes	Type union for a CWL v1.x Workflow object.
WorkflowInputParameter	Type union for a CWL v1.x WorkflowInputParameter object.
WorkflowOutputParameter	Type union for a CWL v1.x WorkflowOutputParameter object.
WorkflowStep	Type union for a CWL v1.x WorkflowStep object.
WorkflowStepInput	Type union for a CWL v1.x WorkflowStepInput object.
WorkflowStepOutput	Type union for a CWL v1.x WorkflowStepOutput object.
CommandLineTool	Type union for a CWL v1.x CommandLineTool object.
CommandLineBinding	Type union for a CWL v1.x CommandLineBinding object.
CommandOutputParameter	Type union for a CWL v1.x CommandOutputParameter object.
ExpressionTool	Type union for a CWL v1.x ExpressionTool object.
DockerRequirement
DockerRequirementTypes	Type union for a CWL v1.x DockerRequirement object.
Process	Type Union for a CWL v1.x Process object.
ProcessRequirement	Type Union for a CWL v1.x ProcessRequirement object.
ProcessRequirementTypes
SoftwareRequirement
SoftwareRequirementTypes	Type union for a CWL v1.x SoftwareRequirement object.
ArraySchema	Type Union for a CWL v1.x ArraySchema object.
EnumSchema	Type Union for a CWL v1.x EnumSchema object.
RecordSchema	Type Union for a CWL v1.x RecordSchema object.
File	Type Union for a CWL v1.x File object.
SecondaryFileSchema	Type Union for a CWL v1.x SecondaryFileSchema object.
Directory	Type Union for a CWL v1.x Directory object.
Dirent	Type Union for a CWL v1.x Dirent object.

exception cwl_utils.parser.GraphTargetMissingException

Bases: WorkflowException

When a $graph is encountered and there is no target and no main/#main.

cwl_utils.parser.LoadingOptions

Type union for a CWL v1.x LoadingOptions object.

cwl_utils.parser.Saveable

Type union for a CWL v1.x Saveable object.

cwl_utils.parser.InputParameter

Type union for a CWL v1.x InputParameter object.

cwl_utils.parser.OutputParameter

Type union for a CWL v1.x OutputParameter object.

cwl_utils.parser.Workflow

cwl_utils.parser.WorkflowTypes = ()

Type union for a CWL v1.x Workflow object.

cwl_utils.parser.WorkflowInputParameter

Type union for a CWL v1.x WorkflowInputParameter object.

cwl_utils.parser.WorkflowOutputParameter

Type union for a CWL v1.x WorkflowOutputParameter object.

cwl_utils.parser.WorkflowStep

Type union for a CWL v1.x WorkflowStep object.

cwl_utils.parser.WorkflowStepInput

Type union for a CWL v1.x WorkflowStepInput object.

cwl_utils.parser.WorkflowStepOutput

Type union for a CWL v1.x WorkflowStepOutput object.

cwl_utils.parser.CommandLineTool

Type union for a CWL v1.x CommandLineTool object.

cwl_utils.parser.CommandLineBinding

Type union for a CWL v1.x CommandLineBinding object.

cwl_utils.parser.CommandOutputParameter

Type union for a CWL v1.x CommandOutputParameter object.

cwl_utils.parser.ExpressionTool

Type union for a CWL v1.x ExpressionTool object.

cwl_utils.parser.DockerRequirement

cwl_utils.parser.DockerRequirementTypes = ()

Type union for a CWL v1.x DockerRequirement object.

cwl_utils.parser.Process

Type Union for a CWL v1.x Process object.

cwl_utils.parser.ProcessRequirement

Type Union for a CWL v1.x ProcessRequirement object.

cwl_utils.parser.ProcessRequirementTypes = ()

cwl_utils.parser.SoftwareRequirement

cwl_utils.parser.SoftwareRequirementTypes = ()

Type union for a CWL v1.x SoftwareRequirement object.

cwl_utils.parser.ArraySchema

Type Union for a CWL v1.x ArraySchema object.

cwl_utils.parser.EnumSchema

Type Union for a CWL v1.x EnumSchema object.

cwl_utils.parser.RecordSchema

Type Union for a CWL v1.x RecordSchema object.

cwl_utils.parser.File

Type Union for a CWL v1.x File object.

cwl_utils.parser.SecondaryFileSchema

Type Union for a CWL v1.x SecondaryFileSchema object.

cwl_utils.parser.Directory

Type Union for a CWL v1.x Directory object.

cwl_utils.parser.Dirent

Type Union for a CWL v1.x Dirent object.

cwl_utils.parser.cwl_version(yaml)

Return the cwlVersion of a YAML object.

Parameters:

yaml (Any) – ruamel.yaml object for a CWL document

Raises:

ValidationException – If yaml is not a MutableMapping.

Return type:

Optional[str]

cwl_utils.parser.load_document_by_uri(path, loadingOptions=None, load_all=False)

Load a CWL object from a URI or a path.

Parameters:

• path (Union[str, pathlib.Path]) –

• loadingOptions (Optional[LoadingOptions]) –

• load_all (bool) –

Return type:

Any

cwl_utils.parser.load_document(doc, baseuri=None, loadingOptions=None, id_=None, load_all=False)

Load a CWL object from a serialized YAML string or a YAML object.

Parameters:

• doc (Any) –

• baseuri (Optional[str]) –

• loadingOptions (Optional[LoadingOptions]) –

• id_ (Optional[str]) –

• load_all (bool) –

Return type:

Any

cwl_utils.parser.load_document_by_string(string, uri, loadingOptions=None, id_=None, load_all=False)

Load a CWL object from a serialized YAML string.

Parameters:

• string (str) –

• uri (str) –

• loadingOptions (Optional[LoadingOptions]) –

• id_ (Optional[str]) –

• load_all (bool) –

Return type:

Any

cwl_utils.parser.load_document_by_yaml(yaml, uri, loadingOptions=None, id_=None, load_all=False)

Load a CWL object from a YAML object.

Parameters:

• yaml (Any) –

• uri (str) –

• loadingOptions (Optional[LoadingOptions]) –

• id_ (Optional[str]) –

• load_all (bool) –

Return type:

Any

cwl_utils.parser.save(val, top=True, base_url='', relative_uris=True)

Convert a CWL Python object into a JSON/YAML serializable object.

Parameters:

• val (Optional[Union[Saveable, MutableSequence[Saveable]]]) –

• top (bool) –

• base_url (str) –

• relative_uris (bool) –

Return type:

Any

cwl_utils.parser.is_process(v)

Test to see if the object is a CWL v1.x Python Process object.

Parameters:

v (Any) –

Return type:

bool

cwl_utils.parser.version_split(version)

Split a cwlVersion value into its numerical components.

Parameters:

version (str) –

Return type:

MutableSequence[int]