fix re-serializing 'string' input and general array input

src/sophios/compiler.py

@@ -4,7 +4,7 @@
 import os
 from pathlib import Path
 import sys
-from typing import Dict, List
+from typing import Dict, List, Any
 
 import graphviz
 from mergedeep import merge, Strategy
@@ -861,10 +861,8 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
         steps_list.append(step_i_copy)
     yaml_tree.update({'steps': steps_list})  # steps_list ?
 
-    # Dump the workflow inputs to a separate yml file.
-    yaml_inputs: WorkflowInputsFile = {}
-    for key, in_dict in inputs_file_workflow.items():
-        new_keyval: WorkflowInputsFile = {}
+    def populate_scalar_val(in_dict: dict) -> Any:
+        newval: Any = ()
         if 'File' == in_dict['type']:
             # path = Path(in_dict['value']).name # NOTE: Use .name ?
             newval = {'class': 'File', 'path': in_dict['value']}
@@ -878,15 +876,28 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                         print(f'Choosing {in_format[0]}')
                     in_format = in_format[0]
                 newval['format'] = in_format
-            new_keyval = {key: newval}
         elif 'Directory' == in_dict['type']:
             newval = {'class': 'Directory', 'location': in_dict['value']}
-            new_keyval = {key: newval}
+        elif 'string' == in_dict['type'] or 'string?' == in_dict['type']:
+            # We cannot store string values as a dict, so use type: ignore
+            newval = str(in_dict['value'])
         # TODO: Check for all valid types?
         else:
-            # We cannot store string values as a dict, so use type: ignore
-            arg_val = in_dict['value']
-            new_keyval = {key: arg_val}
+            newval = in_dict['value']
+        return newval
+
+    # Dump the workflow inputs to a separate yml file.
+    yaml_inputs: WorkflowInputsFile = {}
+    for key, in_dict in inputs_file_workflow.items():
+        new_keyval: WorkflowInputsFile = {}
+        if isinstance(in_dict['type'], dict) and 'array' == in_dict['type']['type']:
+            val_list = []
+            for val in in_dict['value']:
+                val_list.append(populate_scalar_val(
+                    {'type': in_dict['type']['items'], 'value': val, 'format': in_dict.get('format')}))
+            new_keyval = {key: val_list}
+        else:
+            new_keyval = {key: populate_scalar_val(in_dict)}
         # else:
         #    raise Exception(f"Error! Unknown type: {in_dict['type']}")
         yaml_inputs.update(new_keyval)