port some functions from isinstance to match 1/n

Author: Vasu Jaganath

src/sophios/run_local.py

@@ -9,7 +9,7 @@
 import shutil
 import platform
 import traceback
-from typing import Dict, List, Optional
+from typing import List, Optional
 from datetime import datetime
 
 try:
@@ -413,20 +413,23 @@ def stage_input_files(yml_inputs: Yaml, root_yml_dir_abs: Path,
         FileNotFoundError: If throw and it any of the input files do not exist.
     """
     for key, val in yml_inputs.items():
-        if isinstance(val, Dict) and val.get('class', '') == 'File':
-            path = root_yml_dir_abs / Path(val['path'])
-            if not path.exists() and throw:
-                # raise FileNotFoundError(f'Error! {path} does not exist!')
-                print(f'Error! {path} does not exist!')
-                sys.exit(1)
-
-            relpath = Path('autogenerated/') if relative_run_path else Path('.')
-            pathauto = relpath / Path(val['path'])  # .name # NOTE: Use .name ?
-            pathauto.parent.mkdir(parents=True, exist_ok=True)
-
-            if path != pathauto:
-                cmd = ['cp', str(path), str(pathauto)]
-                proc = sub.run(cmd, check=False)
+        match val:
+            case {'class': 'File', **rest_of_val}:
+                path = root_yml_dir_abs / Path(val['path'])
+                if not path.exists() and throw:
+                    # raise FileNotFoundError(f'Error! {path} does not exist!')
+                    print(f'Error! {path} does not exist!')
+                    sys.exit(1)
+
+                relpath = Path('autogenerated/') if relative_run_path else Path('.')
+                pathauto = relpath / Path(val['path'])  # .name # NOTE: Use .name ?
+                pathauto.parent.mkdir(parents=True, exist_ok=True)
+
+                if path != pathauto:
+                    cmd = ['cp', str(path), str(pathauto)]
+                    _ = sub.run(cmd, check=False)
+            case _:
+                pass
 
 
 def cwltool_main() -> int:

src/sophios/utils_cwl.py

@@ -229,15 +229,19 @@ def canonicalize_type(type_obj: Any) -> Any:
     Returns:
         Any: The JSON canonical normal form associated with type_obj
     """
-    if isinstance(type_obj, str):
-        if len(type_obj) >= 1 and type_obj[-1:] == '?':
-            return ['null', canonicalize_type(type_obj[:-1])]
-        if len(type_obj) >= 2 and type_obj[-2:] == '[]':
-            return {'type': 'array', 'items': canonicalize_type(type_obj[:-2])}
-    if isinstance(type_obj, Dict):
-        if type_obj.get('type') == 'array':
-            return {**type_obj, 'items': canonicalize_type(type_obj['items'])}
-    return type_obj
+    match type_obj:
+        case str() as str_obj:
+            if len(str_obj) >= 1 and str_obj[-1:] == '?':
+                return ['null', canonicalize_type(str_obj[:-1])]
+            if len(str_obj) >= 2 and str_obj[-2:] == '[]':
+                return {'type': 'array', 'items': canonicalize_type(str_obj[:-2])}
+            return str_obj
+        case dict() as dict_obj:
+            if dict_obj.get('type') == 'array':
+                return {**dict_obj, 'items': canonicalize_type(dict_obj['items'])}
+            return dict_obj
+        case _:
+            return type_obj
 
 
 def canonicalize_steps_list(steps: Yaml) -> List[Yaml]: