array outputs

giannisdoukas · Apr 2, 2020 · 4f64972 · 4f64972
1 parent 85aa142
commit 4f64972
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Showing 5 changed files with 130 additions and 12 deletions.
diff --git a/cwlkernel/CWLKernel.py b/cwlkernel/CWLKernel.py
@@ -207,13 +207,21 @@ def _execute_workflow(self, code) -> Optional[Exception]:
         logger.debug(f'\texecution results: {run_id}, {results}, {stdout}, {stderr}, {exception}')
         output_directory_for_that_run = str(run_id)
         for output in results:
-            logger.info(f'output result: {results}')
-            results[output]['id'] = output
-            self._results_manager.append_files(
-                [results[output]['location']],
-                output_directory_for_that_run,
-                metadata=results[output]
-            )
+            if isinstance(results[output], list):
+                for i, output_i in enumerate(results[output]):
+                    results[output][i]['id'] = f'{output}_{i+1}'
+                    self._results_manager.append_files(
+                        [results[output][i]['location']],
+                        output_directory_for_that_run,
+                        metadata=results[output][i]
+                    )
+            else:
+                results[output]['id'] = output
+                self._results_manager.append_files(
+                    [results[output]['location']],
+                    output_directory_for_that_run,
+                    metadata=results[output]
+                )
         self.send_response(
             self.iopub_socket,
             'display_data',

diff --git a/examples/array_outputs.ipynb b/examples/array_outputs.ipynb
@@ -11,9 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## [Array Outputs](https://www.commonwl.org/user_guide/10-array-outputs/index.html)\n",
-    "\n",
-    "Not supported yet"
+    "## [Array Outputs](https://www.commonwl.org/user_guide/10-array-outputs/index.html)"
    ]
   },
   {
@@ -38,9 +36,50 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/json": {
+       "output": [
+        {
+         "basename": "baz.txt",
+         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+         "class": "File",
+         "http://commonwl.org/cwltool#generation": 0,
+         "id": "output_1",
+         "location": "file:///private/tmp/CWLKERNEL_DATA/runtime_data/baz.txt",
+         "nameext": ".txt",
+         "nameroot": "baz",
+         "size": 0
+        },
+        {
+         "basename": "foo.txt",
+         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+         "class": "File",
+         "http://commonwl.org/cwltool#generation": 0,
+         "id": "output_2",
+         "location": "file:///private/tmp/CWLKERNEL_DATA/runtime_data/foo.txt",
+         "nameext": ".txt",
+         "nameroot": "foo",
+         "size": 0
+        }
+       ]
+      },
+      "text/plain": [
+       "<IPython.core.display.JSON object>"
+      ]
+     },
+     "metadata": {
+      "application/json": {
+       "expanded": false,
+       "root": "root"
+      }
+     },
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "#!/usr/bin/env cwl-runner\n",
     "\n",
@@ -62,6 +101,33 @@
     "    outputBinding:\n",
     "      glob: \"*.txt\""
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<ul>\n",
+       "\t<li><a href=\"file:///private/tmp/CWLKERNEL_DATA/results/d79b3512-f8b5-4f59-b3c0-40834c9dc58a/baz.txt\" target=\"_empty\">/private/tmp/CWLKERNEL_DATA/results/d79b3512-f8b5-4f59-b3c0-40834c9dc58a/baz.txt</a></li>\n",
+       "\t<li><a href=\"file:///private/tmp/CWLKERNEL_DATA/results/d79b3512-f8b5-4f59-b3c0-40834c9dc58a/foo.txt\" target=\"_empty\">/private/tmp/CWLKERNEL_DATA/results/d79b3512-f8b5-4f59-b3c0-40834c9dc58a/foo.txt</a></li>\n",
+       "</ul>"
+      ]
+     },
+     "metadata": {
+      "application/json": {
+       "expanded": false,
+       "root": "root"
+      }
+     },
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "% data"
+   ]
   }
  ],
  "metadata": {

diff --git a/tests/cwl/array-outputs.cwl b/tests/cwl/array-outputs.cwl
@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: touch
+inputs:
+  touchfiles:
+    type:
+      type: array
+      items: string
+    inputBinding:
+      position: 1
+outputs:
+  output:
+    type:
+      type: array
+      items: File
+    outputBinding:
+      glob: "*.txt"
diff --git a/tests/input_data/array-outputs-job.yml b/tests/input_data/array-outputs-job.yml
@@ -0,0 +1,5 @@
+touchfiles:
+  - foo.txt
+  - bar.dat
+  - baz.txt
+
diff --git a/tests/test_CWLKernel.py b/tests/test_CWLKernel.py
@@ -282,5 +282,25 @@ def test_display_json_output_after_execution(self):
             responses[1][0]
         )
 
+
+    def test_array_output(self):
+        from cwlkernel.CWLKernel import CWLKernel
+        kernel = CWLKernel()
+        # cancel send_response
+        kernel.send_response = lambda *args, **kwargs: None
+        with open(os.sep.join([self.data_directory, 'array-outputs-job.yml'])) as f:
+            data = f.read()
+        with open(os.sep.join([self.cwl_directory, 'array-outputs.cwl'])) as f:
+            workflow_str = f.read()
+        self.assertDictEqual(
+            {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}},
+            kernel.do_execute(data)
+        )
+        self.assertDictEqual(
+            {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}},
+            kernel.do_execute(workflow_str)
+        )
+
+
     if __name__ == '__main__':
         unittest.main()