fix optionals

Author: giannisdoukas

ipython2cwl/cwltoolextractor.py

@@ -11,6 +11,7 @@
 import astor
 import nbconvert
 import yaml
+from astor.string_repr import pretty_string
 from nbformat.notebooknode import NotebookNode
 
 from .iotypes import CWLFilePathInput, CWLBooleanInput, CWLIntInput, CWLStringInput, CWLFilePathOutput
@@ -78,7 +79,7 @@ def visit_AnnAssign(self, node):
             if annotation in self.input_type_mapper:
                 mapper = self.input_type_mapper[annotation]
                 self.extracted_nodes.append(
-                    (node, mapper[0], mapper[1], True, True, False)
+                    (node, mapper[0], mapper[1], not mapper[0].endswith('?'), True, False)
                 )
                 return None
 
@@ -176,18 +177,24 @@ def _wrap_script_to_method(cls, tree, variables) -> str:
         main_function = ast.parse(main_template_code)
         [node for node in main_function.body if isinstance(node, ast.FunctionDef) and node.name == 'main'][0] \
             .body = tree.body
-        return astor.to_source(main_function)
+        return astor.to_source(
+            main_function,
+            pretty_string=lambda s, embedded, current_line, uni: pretty_string(s, embedded, current_line, uni, max_line=500)
+        )
 
     @classmethod
     def __get_add_arguments__(cls, variables):
         args = []
         for variable in variables:
             is_array = variable.cwl_typeof.endswith('[]')
+            is_optional = variable.cwl_typeof.endswith('?')
             arg: str = f'parser.add_argument("--{variable.name}", '
             arg += f'type={variable.argparse_typeof}, '
             arg += f'required={variable.required}, '
             if is_array:
                 arg += f'nargs="+", '
+            if is_optional:
+                arg += f'default=None, '
             arg = arg.strip()
             arg += ')'
             args.append(arg)

tests/simple.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "import pandas as pd\n",
-    "from typing import List\n",
+    "from typing import List, Optional\n",
     "import matplotlib\n",
     "from ipython2cwl.iotypes import CWLFilePathInput, CWLFilePathOutput, CWLStringInput"
    ]
@@ -19,7 +19,8 @@
    "outputs": [],
    "source": [
     "dataset: CWLFilePathInput = './data/data.csv'\n",
-    "messages: List[CWLStringInput] = ['hello', 'world']"
+    "messages: List[CWLStringInput] = ['hello', 'world']\n",
+    "optional_message: Optional[CWLStringInput] = \"Hello from optional\""
    ]
   },
   {
@@ -60,6 +61,16 @@
     "with open(messages_filename, 'w') as f:\n",
     "    f.write(' '.join(messages))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if optional_message is not None:\n",
+    "    print(optional_message)"
+   ]
   }
  ],
  "metadata": {

tests/test_ipython2cwl_from_repo.py

@@ -40,7 +40,9 @@ def test_docker_build(self):
         docker_client = docker.from_env()
         script = docker_client.containers.run(dockerfile_image_id, '/app/cwl/bin/simple', entrypoint='/bin/cat')
         self.assertIn('fig.figure.savefig(after_transform_data)', script.decode())
-        messages_array_arg_line = ast.parse([line.strip() for line in script.decode().splitlines() if '--messages' in line][-1])
+        messages_array_arg_line = ast.parse(
+            [line.strip() for line in script.decode().splitlines() if '--messages' in line][-1]
+        )
         self.assertEqual(
             '+',  # nargs = '+'
             [k.value.s for k in messages_array_arg_line.body[0].value.keywords if k.arg == 'nargs'][0]
@@ -49,6 +51,19 @@ def test_docker_build(self):
             'str',  # type = 'str'
             [k.value.id for k in messages_array_arg_line.body[0].value.keywords if k.arg == 'type'][0]
         )
+
+        script_tree = ast.parse(script.decode())
+        optional_expression = [x for x in script_tree.body[-1].body if
+                               isinstance(x, ast.Expr) and isinstance(x.value, ast.Call) and len(x.value.args) > 0 and
+                               x.value.args[0].s == '--optional_message'][0]
+        self.assertEqual(
+            False,
+            [k.value for k in optional_expression.value.keywords if k.arg == 'required'][0].value
+        )
+        self.assertEqual(
+            None,
+            [k.value for k in optional_expression.value.keywords if k.arg == 'default'][0].value
+        )
         self.assertDictEqual(
             {
                 'cwlVersion': "v1.1",
@@ -70,6 +85,12 @@ def test_docker_build(self):
                         'inputBinding': {
                             'prefix': '--messages'
                         }
+                    },
+                    'optional_message': {
+                        'type': 'string?',
+                        'inputBinding': {
+                            'prefix': '--optional_message'
+                        }
                     }
                 },
                 'outputs': {