cwl_utils.parser

Submodules

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.

Exceptions

GraphTargetMissingException

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

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.

Package Contents

exception cwl_utils.parser.GraphTargetMissingException

Bases: WorkflowException

Inheritance diagram of cwl_utils.parser.GraphTargetMissingException

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:
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:
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:
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]