Fix Optional-Lists

.gitignore

@@ -246,3 +246,4 @@ tmp.py
 /html/
 cwlbuild
 /tests/repo-like/result.yaml
+/tests/repo-like/messages.txt

README.md

@@ -42,4 +42,4 @@ jupyter repo2cwl https://github.com/giannisdoukas/cwl-annotated-jupyter-notebook
 
 ### Docs
 
-[https://ipython2cwl.readthedocs.io/](https://readthedocs.org/projects/ipython2cwl/badge/?version=latest)
+[https://ipython2cwl.readthedocs.io/](https://ipython2cwl.readthedocs.io/en/latest/)

ipython2cwl/cwltoolextractor.py

@@ -22,27 +22,35 @@
     SETUP_TEMPLATE = f.read()
 
 
-# TODO: does not support recursion if main function exists
+# TODO: check if supports recursion if main function exists
 
 class AnnotatedVariablesExtractor(ast.NodeTransformer):
     input_type_mapper = {
-        CWLFilePathInput.__name__: (
+        (CWLFilePathInput.__name__,): (
             'File',
             'pathlib.Path',
         ),
-        CWLBooleanInput.__name__: (
+        (CWLBooleanInput.__name__,): (
             'boolean',
             'lambda flag: flag.upper() == "TRUE"',
         ),
-        CWLIntInput.__name__: (
+        (CWLIntInput.__name__,): (
             'int',
             'int',
         ),
-        CWLStringInput.__name__: (
+        (CWLStringInput.__name__,): (
             'string',
             'str',
         ),
     }
+    input_type_mapper = {**input_type_mapper, **{
+        ('List', *(t for t in types_names)): (types[0] + "[]", types[1])
+        for types_names, types in input_type_mapper.items()
+    }, **{
+        ('Optional', *(t for t in types_names)): (types[0] + "?", types[1])
+        for types_names, types in input_type_mapper.items()
+    }}
+
     output_type_mapper = {
         CWLFilePathOutput.__name__
     }
@@ -51,30 +59,29 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.extracted_nodes = []
 
+    def __get_annotation__(self, type_annotation):
+        annotation = None
+        if isinstance(type_annotation, ast.Name):
+            annotation = (type_annotation.id,)
+        elif isinstance(type_annotation, ast.Str):
+            annotation = (type_annotation.s,)
+            ann_expr = ast.parse(type_annotation.s.strip()).body[0]
+            if hasattr(ann_expr, 'value') and isinstance(ann_expr.value, ast.Subscript):
+                annotation = self.__get_annotation__(ann_expr.value)
+        elif isinstance(type_annotation, ast.Subscript):
+            annotation = (type_annotation.value.id, *self.__get_annotation__(type_annotation.slice.value))
+        return annotation
+
     def visit_AnnAssign(self, node):
         try:
-            if (isinstance(node.annotation, ast.Name) and node.annotation.id in self.input_type_mapper) or \
-                    (isinstance(node.annotation, ast.Str) and node.annotation.s in self.input_type_mapper):
-                mapper = self.input_type_mapper[node.annotation.id]
+            annotation = self.__get_annotation__(node.annotation)
+            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
-            elif isinstance(node.annotation, ast.Subscript):
-                if node.annotation.value.id == "Optional" \
-                        and node.annotation.slice.value.id in self.input_type_mapper:
-                    mapper = self.input_type_mapper[node.annotation.slice.value.id]
-                    self.extracted_nodes.append(
-                        (node, mapper[0] + '?', mapper[1], False, True, False)
-                    )
-                    return None
-                elif node.annotation.value.id == "List" \
-                        and node.annotation.slice.value.id in self.input_type_mapper:
-                    mapper = self.input_type_mapper[node.annotation.slice.value.id]
-                    self.extracted_nodes.append(
-                        (node, mapper[0] + '[]', mapper[1], True, True, False)
-                    )
-                    return None
+
             elif (isinstance(node.annotation, ast.Name) and node.annotation.id in self.output_type_mapper) or \
                     (isinstance(node.annotation, ast.Str) and node.annotation.s in self.output_type_mapper):
                 self.extracted_nodes.append(
@@ -87,7 +94,7 @@ def visit_AnnAssign(self, node):
                     targets=[node.target],
                     value=node.value
                 )
-        except AttributeError:
+        except Exception:
             pass
         return node
 
@@ -152,6 +159,7 @@ def from_jupyter_notebook_node(cls, node: NotebookNode) -> 'AnnotatedIPython2CWL
 
     @classmethod
     def _wrap_script_to_method(cls, tree, variables) -> str:
+        add_args = cls.__get_add_arguments__([v for v in variables if v.is_input])
         main_template_code = os.linesep.join([
             f"def main({','.join([v.name for v in variables if v.is_input])}):",
             "\tpass",
@@ -160,19 +168,34 @@ def _wrap_script_to_method(cls, tree, variables) -> str:
                 "import argparse",
                 'import pathlib',
                 "parser = argparse.ArgumentParser()",
-                *[f'parser.add_argument("--{variable.name}", '
-                  f'type={variable.argparse_typeof}, '
-                  f'required={variable.required})'
-                  for variable in variables],
+                *add_args,
                 "args = parser.parse_args()",
-                f"main({','.join([f'{v.name}=args.{v.name}' for v in variables if v.is_input])})"
+                f"main({','.join([f'{v.name}=args.{v.name} ' for v in variables if v.is_input])})"
             ]],
         ])
         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)
 
+    @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)
+        return args
+
     def cwl_command_line_tool(self, docker_image_id: str = 'jn2cwl:latest') -> Dict:
         """
         Creates the description of the CWL Command Line Tool.

tests/repo-like/example1.ipynb

@@ -2,30 +2,24 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ipython2cwl.iotypes import CWLFilePathInput, CWLFilePathOutput\n",
-    "import yaml"
+    "from ipython2cwl.iotypes import CWLFilePathInput, CWLStringInput, CWLFilePathOutput\n",
+    "from typing import List\n",
+    "import yaml\n",
+    "import os"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{'entry1': 1, 'entry2': 'foo', 'entry3': 'bar'}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "datafilename: CWLFilePathInput = 'data.yaml'\n",
-    "\n",
+    "messages: List[CWLStringInput] = ['hello', 'world']\n",
     "with open(datafilename) as fd: \n",
     "    data = yaml.safe_load(fd)\n",
     "print(data)"
@@ -42,13 +36,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "results_filename: CWLFilePathOutput = 'result.yaml'\n",
     "with open(results_filename, 'w') as fd:\n",
-    "    yaml.safe_dump(data, fd)"
+    "    yaml.safe_dump(data, fd)\n",
+    "messages_outputs: CWLFilePathOutput = 'messages.txt'\n",
+    "with open(messages_outputs, 'w') as f:\n",
+    "    f.write(' '.join(messages))"
    ]
   }
  ],

tests/repo-like/requirements.txt

@@ -1,2 +1 @@
-PyYAML==5.3.1
-ipython2cwl==0.0.1
+PyYAML==5.3.1

tests/simple.ipynb

@@ -2,27 +2,30 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import pandas as pd\n",
+    "from typing import List, Optional\n",
     "import matplotlib\n",
-    "from ipython2cwl.iotypes import CWLFilePathInput, CWLFilePathOutput"
+    "from ipython2cwl.iotypes import CWLFilePathInput, CWLFilePathOutput, CWLStringInput"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset: CWLFilePathInput = 'example.csv'"
+    "dataset: CWLFilePathInput = './data/data.csv'\n",
+    "messages: List[CWLStringInput] = ['hello', 'world']\n",
+    "optional_message: Optional[CWLStringInput] = \"Hello from optional\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -36,17 +39,38 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "# transform data\n",
-    "data.sort_values(by='Random B', ascending=False, inplace=True, ignore_index=True)\n",
+    "data.sort_values(by='Y', ascending=False, inplace=True, ignore_index=True)\n",
     "fig = data.plot()\n",
     "\n",
     "after_transform_data: CWLFilePathOutput = 'new_data.png'\n",
     "fig.figure.savefig(after_transform_data)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "messages_filename = 'messages.txt'\n",
+    "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_cwltool.py → tests/test_cwltoolextractor.py

@@ -328,3 +328,52 @@ def test_AnnotatedIPython2CWLToolConverter_exclamation_mark_command(self):
         exec(new_script_without_magics)
         locals()['main']('original\n!ls -l')
         self.assertEqual('original\n!ls -l', globals()['printed_message'])
+
+    def test_AnnotatedIPython2CWLToolConverter_optional_array_input(self):
+        s1 = os.linesep.join([
+            'x1: CWLBooleanInput = True',
+        ])
+        s2 = os.linesep.join([
+            'x1: "CWLBooleanInput" = True',
+        ])
+        # all variables must be the same
+        self.assertEqual(
+            AnnotatedIPython2CWLToolConverter(s1)._variables[0],
+            AnnotatedIPython2CWLToolConverter(s2)._variables[0],
+        )
+
+        s1 = os.linesep.join([
+            'x1: Optional[CWLBooleanInput] = True',
+        ])
+        s2 = os.linesep.join([
+            'x1: "Optional[CWLBooleanInput]" = True',
+        ])
+        s3 = os.linesep.join([
+            'x1: Optional["CWLBooleanInput"] = True',
+        ])
+        # all variables must be the same
+        self.assertEqual(
+            AnnotatedIPython2CWLToolConverter(s1)._variables[0],
+            AnnotatedIPython2CWLToolConverter(s2)._variables[0],
+        )
+        self.assertEqual(
+            AnnotatedIPython2CWLToolConverter(s1)._variables[0],
+            AnnotatedIPython2CWLToolConverter(s3)._variables[0],
+        )
+
+        # test that does not crash
+        self.assertListEqual([], AnnotatedIPython2CWLToolConverter(os.linesep.join([
+            'x1: RandomHint = True'
+        ]))._variables)
+        self.assertListEqual([], AnnotatedIPython2CWLToolConverter(os.linesep.join([
+            'x1: List[RandomHint] = True'
+        ]))._variables)
+        self.assertListEqual([], AnnotatedIPython2CWLToolConverter(os.linesep.join([
+            'x1: List["RandomHint"] = True'
+        ]))._variables)
+        self.assertListEqual([], AnnotatedIPython2CWLToolConverter(os.linesep.join([
+            'x1: "List[List[Union[RandomHint, Foo]]]" = True'
+        ]))._variables)
+        self.assertListEqual([], AnnotatedIPython2CWLToolConverter(os.linesep.join([
+            'x1: "RANDOM CHARACTERS!!!!!!" = True'
+        ]))._variables)