more type fixes

Author: mr-c

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -1425,7 +1425,7 @@ def traverse_CommandLineTool(
                     new_clt_step = copy.copy(
                         step
                     )  # a deepcopy would be convenient, but params2.cwl gives it problems
-                    new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
+                    new_clt_step.id = new_clt_step.id.split("#")[-1]
                     new_clt_step.run = copy.copy(step.run)
                     new_clt_step.run.id = None
                     remove_JSReq(new_clt_step.run, skip_command_line1)

cwl_utils/cwl_v1_1_expression_refactor.py

@@ -1425,7 +1425,7 @@ def traverse_CommandLineTool(
                     new_clt_step = copy.copy(
                         step
                     )  # a deepcopy would be convenient, but params2.cwl gives it problems
-                    new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
+                    new_clt_step.id = new_clt_step.id.split("#")[-1]
                     new_clt_step.run = copy.copy(step.run)
                     new_clt_step.run.id = None
                     remove_JSReq(new_clt_step.run, skip_command_line1)

cwl_utils/cwl_v1_2_expression_refactor.py

@@ -696,7 +696,7 @@ def process_workflow_inputs_and_outputs(
                 )
                 target_type = copy.deepcopy(param2.type_)
                 if isinstance(target_type, cwl.OutputArraySchema):
-                    target_type.name = None
+                    target_type.name = ""
                 target = cwl.WorkflowInputParameter(id=None, type_=target_type)
                 if not isinstance(param2.outputSource, list):
                     sources = param2.outputSource.split("#")[-1]
@@ -1520,7 +1520,7 @@ def traverse_CommandLineTool(
                     new_clt_step = copy.copy(
                         step
                     )  # a deepcopy would be convenient, but params2.cwl gives it problems
-                    new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
+                    new_clt_step.id = new_clt_step.id.split("#")[-1]
                     new_clt_step.run = copy.copy(step.run)
                     new_clt_step.run.id = None
                     remove_JSReq(new_clt_step.run, skip_command_line1)

cwl_utils/parser/cwl_v1_0_utils.py

@@ -214,7 +214,7 @@ def check_all_types(
             for src in srcs_of_sink:
                 check_result = check_types(
                     type_dict[cast(str, src.id)],
-                    type_dict[cast(str, sink.id)],
+                    type_dict[sink.id],
                     linkMerge,
                     getattr(sink, "valueFrom", None),
                 )
@@ -312,6 +312,7 @@ def load_inputfile(
         baseuri = cwl.file_uri(os.getcwd()) + "/"
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions()
+
     result, metadata = _inputfile_load(
         doc,
         baseuri,
@@ -380,10 +381,7 @@ def type_for_step_input(
     cwl_utils.parser.utils.convert_stdstreams_to_files(step_run)
     if step_run and step_run.inputs:
         for step_input in step_run.inputs:
-            if (
-                cast(str, step_input.id).split("#")[-1]
-                == cast(str, in_.id).split("#")[-1]
-            ):
+            if cast(str, step_input.id).split("#")[-1] == in_.id.split("#")[-1]:
                 input_type = step_input.type_
                 if step.scatter is not None and in_.id in aslist(step.scatter):
                     input_type = cwl.ArraySchema(items=input_type, type_="array")

cwl_utils/parser/cwl_v1_1_utils.py

@@ -214,7 +214,7 @@ def check_all_types(
             for src in srcs_of_sink:
                 check_result = check_types(
                     type_dict[cast(str, src.id)],
-                    type_dict[cast(str, sink.id)],
+                    type_dict[sink.id],
                     linkMerge,
                     getattr(sink, "valueFrom", None),
                 )
@@ -397,10 +397,7 @@ def type_for_step_input(
     cwl_utils.parser.utils.convert_stdstreams_to_files(step_run)
     if step_run and step_run.inputs:
         for step_input in step_run.inputs:
-            if (
-                cast(str, step_input.id).split("#")[-1]
-                == cast(str, in_.id).split("#")[-1]
-            ):
+            if cast(str, step_input.id).split("#")[-1] == in_.id.split("#")[-1]:
                 input_type = step_input.type_
                 if step.scatter is not None and in_.id in aslist(step.scatter):
                     input_type = cwl.ArraySchema(items=input_type, type_="array")

cwl_utils/parser/cwl_v1_2_utils.py

@@ -264,7 +264,7 @@ def check_all_types(
                     )
                 if _is_conditional_step(param_to_step, parm_id):
                     src_typ = aslist(type_dict[src_dict[parm_id].id])
-                    snk_typ = type_dict[cast(str, sink.id)]
+                    snk_typ = type_dict[sink.id]
                     if "null" not in src_typ:
                         src_typ = ["null"] + cast(list[Any], src_typ)
                     if (
@@ -288,7 +288,7 @@ def check_all_types(
             for src in srcs_of_sink:
                 check_result = check_types(
                     type_dict[cast(str, src.id)],
-                    type_dict[cast(str, sink.id)],
+                    type_dict[sink.id],
                     linkMerge,
                     getattr(sink, "valueFrom", None),
                 )
@@ -411,6 +411,7 @@ def load_inputfile(
         baseuri = cwl.file_uri(os.getcwd()) + "/"
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions()
+
     result, metadata = _inputfile_load(
         doc,
         baseuri,
@@ -479,10 +480,7 @@ def type_for_step_input(
     cwl_utils.parser.utils.convert_stdstreams_to_files(step_run)
     if step_run and step_run.inputs:
         for step_input in step_run.inputs:
-            if (
-                cast(str, step_input.id).split("#")[-1]
-                == cast(str, in_.id).split("#")[-1]
-            ):
+            if cast(str, step_input.id).split("#")[-1] == in_.id.split("#")[-1]:
                 input_type = step_input.type_
                 if step.scatter is not None and in_.id in aslist(step.scatter):
                     input_type = cwl.ArraySchema(items=input_type, type_="array")