cwl_utils.inputs_schema_gen

Generate JSON Schema from CWL inputs object.

Attributes

`defaultStreamHandler`
`PRIMITIVE_TYPES_MAPPING`
`JSON_TEMPLATE_PATH`
`InputType`

Classes

JSONSchemaProperty

Generate a JSON schema property from a CWL input parameter.

Functions

`get_is_required_from_input_parameter`(input_parameter)	Given an input parameter, return if it is required.
`generate_json_schema_property_from_input_parameter`(...)	Given an input parameter, generate a JSON schema property.
`generate_definition_from_schema`(schema)	Given a schema, generate a JSON schema definition.
`cwl_to_jsonschema`(cwl_obj)	cwl_obj: A CWL Object.
`get_property_dependencies`(property_dict, input_json_schema)	Recursively collect all dependencies for a property.
`slim_definitions`(input_json_schema)	Slim down the schema to only the definitions that are used by the properties.
`arg_parser`()	Build the argument parser.
`parse_args`(args)	Parse the command line arguments.
`main`()	Console entry point.
`get_cwl_url`(url)	Conform to uri format.
`run`(args)	Run the main program.

Module Contents

cwl_utils.inputs_schema_gen.defaultStreamHandler

cwl_utils.inputs_schema_gen.PRIMITIVE_TYPES_MAPPING

cwl_utils.inputs_schema_gen.JSON_TEMPLATE_PATH

cwl_utils.inputs_schema_gen.InputType

class cwl_utils.inputs_schema_gen.JSONSchemaProperty(name, type_, description='', required=False)

Generate a JSON schema property from a CWL input parameter.

Parameters:

name (str)
type_ (Union[InputType, list[InputType], str, Any])
description (Optional[str])
required (Optional[bool])

name: str

type_: InputType | list[InputType] | str | Any

description = ''

required = False

type_dict

generate_type_dict()

Generate the type dict for a property from a CWL input parameter type.

Return type:: dict[str, Any]

generate_type_dict_from_type(type_item)

Generate the type dict for a property from a CWL input parameter type.

We call this function for each type in the type_ list In the case there are multiple types, each dict is added to the oneOf list

Parameters:: type_item (Any)
Return type:: dict[str, Any]

generate_type_dict_from_type_list(type_)

Given a list of types, generate a JSON schema property dict wrapped in oneOf list.

Parameters:: type_ (list[InputType])
Return type:: dict[str, Any]

to_dict()

Return as a dictionary.

Return type:: dict[str, Any]

cwl_utils.inputs_schema_gen.get_is_required_from_input_parameter(input_parameter)

Given an input parameter, return if it is required.

Parameters:: input_parameter (cwl_utils.parser.WorkflowInputParameter)
Return type:: bool

cwl_utils.inputs_schema_gen.generate_json_schema_property_from_input_parameter(input_parameter)

Given an input parameter, generate a JSON schema property.

Parameters:: input_parameter (cwl_utils.parser.WorkflowInputParameter)
Returns:
Return type:: JSONSchemaProperty

cwl_utils.inputs_schema_gen.generate_definition_from_schema(schema)

Given a schema, generate a JSON schema definition.

Parameters:: schema (cwl_utils.parser.InputRecordSchema)
Returns:
Return type:: dict[str, Any]

cwl_utils.inputs_schema_gen.cwl_to_jsonschema(cwl_obj)

cwl_obj: A CWL Object.

Returns:: A JSONSchema object.
Example:: cwl_obj = load_document_by_uri(<CWL_URL>) jsonschema = cwl_to_jsonschema(cwl_inputs)

Parameters:: cwl_obj (Union[cwl_utils.parser.Workflow, cwl_utils.parser.CommandLineTool])
Return type:: Any

cwl_utils.inputs_schema_gen.get_property_dependencies(property_dict, input_json_schema, existing_property_dependencies=None)

Recursively collect all dependencies for a property.

Parameters:

property_dict (dict[str, Any])
input_json_schema (dict[str, Any])
existing_property_dependencies (Optional[list[Any]])

Return type:

list[str]

cwl_utils.inputs_schema_gen.slim_definitions(input_json_schema)

Slim down the schema to only the definitions that are used by the properties.

Traverse the properties and return all definitions that are used. Remove all other definitions.

Parameters:: input_json_schema (dict[str, Any])
Return type:: dict[str, Any]

cwl_utils.inputs_schema_gen.arg_parser()

Build the argument parser.

Return type:: argparse.ArgumentParser

cwl_utils.inputs_schema_gen.parse_args(args)

Parse the command line arguments.

Parameters:: args (list[str])
Return type:: argparse.Namespace

cwl_utils.inputs_schema_gen.main()

Console entry point.

Return type:: None

cwl_utils.inputs_schema_gen.get_cwl_url(url)

Conform to uri format.

If no scheme, then assert is a local file path and exists if scheme is file, then assert is a local file path and exists If scheme is not file, then assert is a valid Web URL Return either the url or the local path as a uri.

Parameters:: url (str)
Return type:: str

cwl_utils.inputs_schema_gen.run(args)

Run the main program.

Parameters:: args (argparse.Namespace)
Return type:: int