Add missing type hints to utils,

* removed duplicate type entries in parser,
* fixed test function docs

Author: alexiswl

cwl_utils/inputs_schema_gen.py

@@ -238,7 +238,8 @@ def get_is_required_from_input_parameter(
 def generate_json_schema_property_from_input_parameter(
     input_parameter: WorkflowInputParameter,
 ) -> JSONSchemaProperty:
-    """Given an input parameter, generate a JSON schema property.
+    """
+    Given an input parameter, generate a JSON schema property.
 
     :param input_parameter:
     :return:
@@ -319,14 +320,16 @@ def generate_definition_from_schema(schema: InputRecordSchema) -> Dict[str, Any]
 
 
 def cwl_to_jsonschema(cwl_obj: Union[Workflow, CommandLineTool]) -> Any:
-    """cwl_obj: A CWL Object.
+    """
+    cwl_obj: A CWL Object.
 
     Returns:
         A JSONSchema object.
 
     Example:
         cwl_obj = load_document_by_uri(<CWL_URL>)
         jsonschema = cwl_to_jsonschema(cwl_inputs)
+
     """
     # Initialise the schema from the workflow input json schema template
     with open(JSON_TEMPLATE_PATH, "r") as template_h:
@@ -559,7 +562,8 @@ def main() -> None:
 
 
 def get_cwl_url(url: str) -> str:
-    """Conform to uri format.
+    """
+    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

cwl_utils/parser/__init__.py

@@ -21,30 +21,12 @@
 InputParameter = Union[
     cwl_v1_0.InputParameter, cwl_v1_1.InputParameter, cwl_v1_2.InputParameter
 ]
-"""Type union for a CWL v1.x InputParameter object."""
-InputArraySchema = Union[
-    cwl_v1_0.InputArraySchema,
-    cwl_v1_1.InputArraySchema,
-    cwl_v1_2.InputArraySchema,
-]
-"""Type union for a CWL v1.x InputArraySchema object."""
-InputEnumSchema = Union[
-    cwl_v1_0.InputEnumSchema,
-    cwl_v1_1.InputEnumSchema,
-    cwl_v1_2.InputEnumSchema,
-]
 """Type union for a CWL v1.x InputEnumSchema object."""
 InputRecordField = Union[
     cwl_v1_0.InputRecordField,
     cwl_v1_1.InputRecordField,
     cwl_v1_2.InputRecordField,
 ]
-"""Type union for a CWL v1.x InputRecordField object."""
-InputRecordSchema = Union[
-    cwl_v1_0.InputRecordSchema,
-    cwl_v1_1.InputRecordSchema,
-    cwl_v1_2.InputRecordSchema,
-]
 """Type union for a CWL v1.x InputRecordSchema object."""
 OutputParameter = Union[
     cwl_v1_0.OutputParameter, cwl_v1_1.OutputParameter, cwl_v1_2.OutputParameter

cwl_utils/utils.py

@@ -11,7 +11,7 @@
 from collections.abc import MutableMapping, MutableSequence
 from copy import deepcopy
 from io import StringIO
-from typing import Any, Optional, Union
+from typing import Any, Optional, Union, Dict, List
 
 from ruamel.yaml.main import YAML
 from ruamel.yaml.parser import ParserError

tests/test_inputs_schema_gen.py

@@ -79,7 +79,7 @@ def test_cwl_inputs_to_jsonschema(test_param: Dict[str, str]) -> None:
 
 
 def test_cwl_inputs_to_jsonschema_fails() -> None:
-    """Compare tool schema of param 1 against input schema of param 2"""
+    """Compare tool schema of param 1 against input schema of param 2."""
     tool_url = TEST_PARAMS[0]["tool_url"]
     input_url = TEST_PARAMS[3]["input_url"]