update to worker for simularium io fix

compose_worker/.CONTAINER_VERSION

@@ -1 +1 @@
-1.2.1
+1.2.2

compose_worker/io_worker.py

@@ -114,7 +114,7 @@ async def save_uploaded_file(uploaded_file: UploadFile | str, save_dest: str) ->
             file.write(contents)
     # case: is a string
     else:
-        with open(uploaded_file, 'r') as fp:
+        with open(filename, 'r') as fp:
             contents = fp.read()
         with open(file_path, 'w') as f:
             f.write(contents)

compose_worker/test.ipynb

@@ -191,13 +191,83 @@
    ],
    "execution_count": 14
   },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-16T16:27:53.329449Z",
+     "start_time": "2024-08-16T16:27:53.324343Z"
+    }
+   },
+   "cell_type": "code",
+   "source": "job = {'status': 'PENDING', 'job_id': 'files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11', 'timestamp': '2024-08-16 16:09:28.578099', 'path': 'uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelout.txt', 'filename': 'simulation', 'box_size': 10.0}",
+   "id": "e28c150926800fd6",
+   "outputs": [],
+   "execution_count": 1
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-16T16:27:55.662239Z",
+     "start_time": "2024-08-16T16:27:53.525441Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "from workers import FilesWorker\n",
+    "\n",
+    "worker = FilesWorker(job)"
+   ],
+   "id": "436b54da8b148037",
+   "outputs": [],
+   "execution_count": 2
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-16T16:27:59.482241Z",
+     "start_time": "2024-08-16T16:27:55.663211Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "from asyncio import run \n",
+    "\n",
+    "await worker.run()"
+   ],
+   "id": "49e481a5ae875ac2",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/yy/8crj8x7x5_3b86f0js6_0bn00000gr/T/tmp4fkcjh7t/modelout.txt\n",
+      "Reading Smoldyn Data -------------\n",
+      "Filtering: translation -------------\n",
+      "Converting Trajectory Data to JSON -------------\n",
+      "Writing JSON -------------\n",
+      "saved to /var/folders/yy/8crj8x7x5_3b86f0js6_0bn00000gr/T/tmp4fkcjh7t/modelouttxt-simulation.simularium\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "{'results': {'results_file': 'uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelouttxt-simulation.simularium'}}"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "execution_count": 3
+  },
   {
    "metadata": {},
    "cell_type": "code",
    "outputs": [],
    "execution_count": null,
    "source": "",
-   "id": "e28c150926800fd6"
+   "id": "9920ec3288a1bd56"
   }
  ],
  "metadata": {

compose_worker/workers.py

@@ -478,8 +478,8 @@ async def run(self):
         if input_path is not None:
             # download the input file
             dest = tempfile.mkdtemp()
-            local_input_path = await download_file(source_blob_path=input_path, bucket_name=BUCKET_NAME, out_dir=dest)
-
+            local_input_path = download_file(source_blob_path=input_path, bucket_name=BUCKET_NAME, out_dir=dest)
+            print(local_input_path)
             # case: is a smoldyn output file and thus a simularium job
             if input_path.endswith('.txt'):
                 await self._run_simularium(job_id=job_id, input_path=local_input_path, dest=dest)
@@ -493,6 +493,8 @@ async def _run_simularium(self, job_id: str, input_path: str, dest: str):
         results_file = result.get('simularium_file')
         uploaded_file_location = None
         if results_file is not None:
+            if not results_file.endswith('.simularium'):
+                results_file += '.simularium'
             uploaded_file_location = await write_uploaded_file(job_id=job_id, bucket_name=BUCKET_NAME, uploaded_file=results_file, extension='.simularium')
 
         self.job_result['results'] = {'results_file': uploaded_file_location}