add magics commands

cwlkernel/CWLKernel.py

@@ -211,6 +211,9 @@ def do_complete(self, code: str, cursor_pos: int):
         self.log.debug(f'suggestions: {suggestions["matches"]}')
         return {**suggestions, 'status': 'ok'}
 
+    def send_text_to_stdout(self, text: str):
+        self.send_response(self.iopub_socket, 'stream', {'name': 'stdout', 'text': text})
+
 
 if __name__ == '__main__':
     from ipykernel.kernelapp import IPKernelApp

cwlkernel/kernel_magics.py

@@ -1,3 +1,4 @@
+import argparse
 import json
 import os
 import random
@@ -104,7 +105,15 @@ def execute(kernel: CWLKernel, execute_argument_string: str):
 
 
 @CWLKernel.register_magic
-def display_data(kernel: CWLKernel, data_name: str):
+def display_data(kernel: CWLKernel, data_name: str) -> None:
+    """
+    Display the data generated by workflow.
+    Usage % display_data [data id]
+
+    @param kernel: the kernel instance
+    @param data_name: the data id
+    @return None
+    """
     if not isinstance(data_name, str) or len(data_name.split()) == 0:
         kernel._send_error_response(
             'ERROR: you must select an output to display. Correct format:\n % display_data [output name]'
@@ -245,6 +254,9 @@ def logs(kernel: CWLKernel, limit=None):
 
 @CWLKernel.register_magic
 def data(kernel: CWLKernel, *args):
+    """
+    Display all the data which are registered in the kernel session.
+    """
     data = "<ul>\n" + '\n'.join(
         [f'\t<li><a href="file://{d}" target="_empty">{d}</a></li>' for d in kernel.get_past_results()]) + "\n</ul>"
     kernel.send_response(
@@ -286,8 +298,35 @@ def viewTool(kernel: CWLKernel, workflow_id: str):
 
 
 @CWLKernel.register_magic
-def magics(kernel: CWLKernel, *args):
-    kernel._send_json_response(list(kernel._magic_commands.keys()))
+def magics(kernel: CWLKernel, arg: str):
+    arg = arg.split()
+    parser = argparse.ArgumentParser()
+    parser.add_argument('magic', default=None, nargs='?')
+    arg = parser.parse_args(arg)
+    if arg.magic is None:
+        commands = ['\t- ' + cmd for cmd in kernel._magic_commands.keys()]
+        commands.sort()
+        commands = os.linesep.join(commands)
+        kernel.send_text_to_stdout(
+            f'List of Available Magic commands\n{commands}'
+        )
+    else:
+        try:
+            full_doc: str = globals()[arg.magic].__doc__.splitlines()
+            doc = []
+            for line_number, line in enumerate(full_doc):
+                line = line.strip()
+                if line.startswith('@'):
+                    break
+                elif len(line) > 0:
+                    doc.append(line)
+            doc = os.linesep.join(doc)
+
+            kernel.send_text_to_stdout(doc)
+        except Exception:
+            kernel.send_text_to_stdout(
+                'The function does not provide documentation'
+            )
 
 
 # import user's magic commands

examples/introduction.ipynb

@@ -52,7 +52,7 @@
    "source": [
     "#!/usr/bin/env cwl-runner\n",
     "\n",
-    "cwlVersion: v1.0\n",
+    "cwlVersion: v1.1\n",
     "class: CommandLineTool\n",
     "baseCommand: echo\n",
     "id: echo\n",
@@ -89,19 +89,20 @@
      "data": {
       "application/json": {
        "example_output": {
-        "basename": "f811c63eed22dec4eec6f02280820eabf16fa779",
+        "basename": "2e0a23bee9af60260156f18c56053610387aefc3",
         "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
         "class": "File",
         "http://commonwl.org/cwltool#generation": 0,
         "id": "example_output",
-        "location": "file:///private/tmp/CWLKERNEL_DATA/runtime_data/f811c63eed22dec4eec6f02280820eabf16fa779",
+        "location": "file:///private/tmp/CWLKERNEL_DATA/fde9200f-dffd-4493-9ff5-03ea5f0cd4dd/runtime_data/2e0a23bee9af60260156f18c56053610387aefc3",
         "nameext": "",
-        "nameroot": "f811c63eed22dec4eec6f02280820eabf16fa779",
+        "nameroot": "2e0a23bee9af60260156f18c56053610387aefc3",
+        "result_counter": 0,
         "size": 13
        }
       },
       "text/plain": [
-       "<IPython.core.display.JSON object>"
+       "{\"example_output\": {\"location\": \"file:///private/tmp/CWLKERNEL_DATA/fde9200f-dffd-4493-9ff5-03ea5f0cd4dd/runtime_data/2e0a23bee9af60260156f18c56053610387aefc3\", \"basename\": \"2e0a23bee9af60260156f18c56053610387aefc3\", \"nameroot\": \"2e0a23bee9af60260156f18c56053610387aefc3\", \"nameext\": \"\", \"class\": \"File\", \"checksum\": \"sha1$47a013e660d408619d894b20806b1d5086aab03b\", \"size\": 13, \"http://commonwl.org/cwltool#generation\": 0, \"id\": \"example_output\", \"result_counter\": 0}}"
       ]
      },
      "metadata": {
@@ -122,6 +123,58 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "List of Available Magic commands\n",
+      "\t- data\n",
+      "\t- display_data\n",
+      "\t- display_data_csv\n",
+      "\t- display_data_image\n",
+      "\t- execute\n",
+      "\t- githubImport\n",
+      "\t- logs\n",
+      "\t- magics\n",
+      "\t- newWorkflow\n",
+      "\t- newWorkflowAddInput\n",
+      "\t- newWorkflowAddOutputSource\n",
+      "\t- newWorkflowAddStep\n",
+      "\t- newWorkflowAddStepIn\n",
+      "\t- newWorkflowBuild\n",
+      "\t- sample_csv\n",
+      "\t- snippet\n",
+      "\t- viewTool"
+     ]
+    }
+   ],
+   "source": [
+    "% magics"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Display the data generated by workflow.\n",
+      "Usage % display_data [data id]"
+     ]
+    }
+   ],
+   "source": [
+    "% magics display_data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",

tests/test_CWLKernel.py

@@ -835,6 +835,38 @@ def test_import_users_magic_commands(self):
         )
         os.environ.pop('CWLKERNEL_MAGIC_COMMANDS_DIRECTORY')
 
+    def test_magics_magic_command(self):
+        kernel = CWLKernel()
+        # cancel send_response
+        responses = []
+        kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs))
+
+        commands = [f'\t- {cmd}' for cmd in kernel._magic_commands.keys()]
+        commands.sort()
+
+
+        self.assertDictEqual(
+            {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}},
+            kernel.do_execute(f"""% magics""")
+        )
+        self.assertEqual(
+            'List of Available Magic commands\n' + os.linesep.join(commands),
+            responses[-1][0][2]['text']
+        )
+
+        self.assertDictEqual(
+            {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}},
+            kernel.do_execute(f"""% magics data""")
+        )
+        from cwlkernel.kernel_magics import data as data_magic_command
+        import inspect
+        self.assertEqual(
+            inspect.getdoc(data_magic_command),
+            responses[-1][0][2]['text']
+        )
+        self.assertIn(' '.join('Display all the data which are registered in the kernel session.'.split()),
+                      ' '.join(responses[-1][0][2]['text'].split()))
+
 
 if __name__ == '__main__':
     unittest.main()