diff --git a/demos/bio_check_demo.ipynb b/demos/bio_check_demo.ipynb index ce2880880..1b6dca7ac 100644 --- a/demos/bio_check_demo.ipynb +++ b/demos/bio_check_demo.ipynb @@ -3,8 +3,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T17:21:18.539794Z", - "start_time": "2024-07-31T17:21:18.534606Z" + "end_time": "2024-07-31T17:42:03.949867Z", + "start_time": "2024-07-31T17:42:03.945957Z" } }, "cell_type": "code", @@ -24,8 +24,8 @@ "metadata": { "collapsed": true, "ExecuteTime": { - "end_time": "2024-07-31T17:21:19.278526Z", - "start_time": "2024-07-31T17:21:19.235578Z" + "end_time": "2024-07-31T17:42:03.984099Z", + "start_time": "2024-07-31T17:42:03.950698Z" } }, "source": [ @@ -38,8 +38,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T17:20:12.336832Z", - "start_time": "2024-07-31T17:20:12.334406Z" + "end_time": "2024-07-31T17:42:04.671301Z", + "start_time": "2024-07-31T17:42:04.668827Z" } }, "cell_type": "code", @@ -60,8 +60,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T17:20:13.149311Z", - "start_time": "2024-07-31T17:20:12.776540Z" + "end_time": "2024-07-31T17:42:05.568338Z", + "start_time": "2024-07-31T17:42:05.325893Z" } }, "cell_type": "code", @@ -81,8 +81,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:19:33.025683Z", - "start_time": "2024-07-31T16:19:33.023469Z" + "end_time": "2024-07-31T17:42:06.758616Z", + "start_time": "2024-07-31T17:42:06.756109Z" } }, "cell_type": "code", @@ -117,8 +117,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T15:05:23.896365Z", - "start_time": "2024-07-31T15:05:23.547982Z" + "end_time": "2024-07-31T17:42:11.489742Z", + "start_time": "2024-07-31T17:42:11.140734Z" } }, "cell_type": "code", @@ -134,8 +134,8 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T15:05:25.111602Z", - "start_time": "2024-07-31T15:05:25.106056Z" + "end_time": "2024-07-31T17:42:11.986584Z", + "start_time": "2024-07-31T17:42:11.983501Z" } }, "cell_type": "code", @@ -158,21 +158,29 @@ { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:06:28.207698Z", - "start_time": "2024-07-31T16:06:27.297660Z" + "end_time": "2024-07-31T17:42:19.496507Z", + "start_time": "2024-07-31T17:42:18.019930Z" } }, "cell_type": "code", "source": "submission_2 = verify.verify_omex(omex_filepath=omex_fp, comparison_id=comparison_id, truth=report_fp)", "id": "c9fc32addb37cd52", - "outputs": [], - "execution_count": 6 + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Selection list: None\n" + ] + } + ], + "execution_count": 8 }, { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:06:30.022047Z", - "start_time": "2024-07-31T16:06:30.016806Z" + "end_time": "2024-07-31T17:42:24.423638Z", + "start_time": "2024-07-31T17:42:24.420866Z" } }, "cell_type": "code", @@ -182,11 +190,11 @@ { "data": { "text/plain": [ - "{'job_id': 'utc_comparison_313c3504-1246-4cc6-b31d-56587e20b3e6',\n", + "{'job_id': 'utc_comparison_01936049-81b2-4ee2-9b05-472cd45a8e46',\n", " 'status': 'PENDING',\n", - " 'timestamp': '2024-07-31 16:06:28.041043',\n", + " 'timestamp': '2024-07-31 17:42:18.467037',\n", " 'comparison_id': 'utc_comparison',\n", - " 'omex_path': 'uploads/utc_comparison_313c3504-1246-4cc6-b31d-56587e20b3e6/Elowitz-Nature-2000-Repressilator.omex',\n", + " 'path': 'uploads/utc_comparison_01936049-81b2-4ee2-9b05-472cd45a8e46/Elowitz-Nature-2000-Repressilator.omex',\n", " 'simulators': ['amici', 'copasi', 'tellurium'],\n", " 'ground_truth_report_path': None,\n", " 'include_output': True,\n", @@ -195,18 +203,18 @@ " 'selection_list': None}" ] }, - "execution_count": 7, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], - "execution_count": 7 + "execution_count": 9 }, { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:07:51.280921Z", - "start_time": "2024-07-31T16:07:51.036139Z" + "end_time": "2024-07-31T17:42:30.126860Z", + "start_time": "2024-07-31T17:42:29.880843Z" } }, "cell_type": "code", @@ -222,25 +230,25 @@ { "data": { "text/plain": [ - "{'content': {'job_id': 'utc_comparison_313c3504-1246-4cc6-b31d-56587e20b3e6',\n", + "{'content': {'job_id': 'utc_comparison_01936049-81b2-4ee2-9b05-472cd45a8e46',\n", " 'status': 'IN_PROGRESS',\n", - " 'timestamp': '2024-07-31 16:06:28.259823',\n", + " 'timestamp': '2024-07-31 17:42:19.492427',\n", " 'comparison_id': 'utc_comparison',\n", - " 'worker_id': 'bfb015a5-6bd1-42a4-8aac-f5856914f1a5'}}" + " 'worker_id': 'ac8a23ef-d810-4a07-9222-2e096adf0ad4'}}" ] }, - "execution_count": 8, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], - "execution_count": 8 + "execution_count": 10 }, { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:08:15.801005Z", - "start_time": "2024-07-31T16:08:15.475270Z" + "end_time": "2024-07-31T17:42:31.067779Z", + "start_time": "2024-07-31T17:42:30.836497Z" } }, "cell_type": "code", @@ -254,38 +262,38 @@ { "data": { "text/plain": [ - "{'content': {'job_id': 'utc_comparison_313c3504-1246-4cc6-b31d-56587e20b3e6',\n", + "{'content': {'job_id': 'utc_comparison_01936049-81b2-4ee2-9b05-472cd45a8e46',\n", " 'status': 'IN_PROGRESS',\n", - " 'timestamp': '2024-07-31 16:06:28.259823',\n", + " 'timestamp': '2024-07-31 17:42:19.492427',\n", " 'comparison_id': 'utc_comparison',\n", - " 'worker_id': 'bfb015a5-6bd1-42a4-8aac-f5856914f1a5'}}" + " 'worker_id': 'ac8a23ef-d810-4a07-9222-2e096adf0ad4'}}" ] }, - "execution_count": 9, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], - "execution_count": 9 + "execution_count": 11 }, { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:12:03.316184Z", - "start_time": "2024-07-31T16:12:02.906385Z" + "end_time": "2024-07-31T17:42:31.951209Z", + "start_time": "2024-07-31T17:42:31.699988Z" } }, "cell_type": "code", "source": "output = verify.get_verify_output(omex_job_id)", "id": "b58badbdd12f1861", "outputs": [], - "execution_count": 15 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"{'job_id': 'utc_comparison_173edc57-4e5b-4d99-bcb1-b92b97a8cad4',\n", + "{'job_id': 'utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9',\n", " 'status': 'PENDING',\n", - " 'timestamp': '2024-07-31 16:19:48.574680',\n", + " 'timestamp': '2024-07-31 17:42:39.985493',\n", " 'comparison_id': 'utc_comparison',\n", - " 'omex_path': 'uploads/utc_comparison_173edc57-4e5b-4d99-bcb1-b92b97a8cad4/Elowitz-Nature-2000-Repressilator.omex',\n", + " 'path': 'uploads/utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9/Elowitz-Nature-2000-Repressilator.omex',\n", " 'simulators': ['amici', 'copasi', 'tellurium'],\n", " 'ground_truth_report_path': None,\n", " 'include_output': True,\n", @@ -11286,31 +368,31 @@ " 'selection_list': None}" ] }, - "execution_count": 7, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], - "execution_count": 7 + "execution_count": 15 }, { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:18:24.674523Z", - "start_time": "2024-07-31T16:18:24.437184Z" + "end_time": "2024-07-31T17:42:43.020303Z", + "start_time": "2024-07-31T17:42:42.724286Z" } }, "cell_type": "code", "source": "output2 = verify.get_verify_output(submission_3['job_id'])", "id": "31df26bf5a752f4", "outputs": [], - "execution_count": 10 + "execution_count": 16 }, { "metadata": { "ExecuteTime": { - "end_time": "2024-07-31T16:18:25.471175Z", - "start_time": "2024-07-31T16:18:25.468331Z" + "end_time": "2024-07-31T17:42:44.262672Z", + "start_time": "2024-07-31T17:42:44.258541Z" } }, "cell_type": "code", @@ -11321,11 +403,11 @@ "data": { "text/plain": [ "{'content': {'status': 'PENDING',\n", - " 'job_id': 'utc_comparison_0340b5f6-2c02-4b9c-897e-52d440be7bef',\n", - " 'omex_path': 'uploads/utc_comparison_0340b5f6-2c02-4b9c-897e-52d440be7bef/Elowitz-Nature-2000-Repressilator.omex',\n", + " 'job_id': 'utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9',\n", + " 'path': 'uploads/utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9/Elowitz-Nature-2000-Repressilator.omex',\n", " 'simulators': ['amici', 'copasi', 'tellurium'],\n", " 'comparison_id': 'utc_comparison',\n", - " 'timestamp': '2024-07-31 16:16:24.487428',\n", + " 'timestamp': '2024-07-31 17:42:39.985493',\n", " 'ground_truth_report_path': None,\n", " 'include_outputs': True,\n", " 'rTol': None,\n", @@ -11333,12 +415,127 @@ " 'selection_list': None}}" ] }, - "execution_count": 11, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } ], - "execution_count": 11 + "execution_count": 17 + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2024-07-31T17:46:35.833181Z", + "start_time": "2024-07-31T17:44:05.404298Z" + } + }, + "cell_type": "code", + "source": [ + "output = None \n", + "while isinstance(output, type(None)):\n", + " output2 = verify.get_verify_output(submission_3['job_id'])\n", + " if output2['content']['status'] == \"COMPLETED\":\n", + " output = output2" + ], + "id": "f788b67be0804bb", + "outputs": [ + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", + "\u001B[0;31mKeyboardInterrupt\u001B[0m Traceback (most recent call last)", + "Cell \u001B[0;32mIn[19], line 3\u001B[0m\n\u001B[1;32m 1\u001B[0m output \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mNone\u001B[39;00m \n\u001B[1;32m 2\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(output, \u001B[38;5;28mtype\u001B[39m(\u001B[38;5;28;01mNone\u001B[39;00m)):\n\u001B[0;32m----> 3\u001B[0m output2 \u001B[38;5;241m=\u001B[39m \u001B[43mverify\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget_verify_output\u001B[49m\u001B[43m(\u001B[49m\u001B[43msubmission_3\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43mjob_id\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 4\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m output2[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcontent\u001B[39m\u001B[38;5;124m'\u001B[39m][\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mstatus\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mCOMPLETED\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 5\u001B[0m output \u001B[38;5;241m=\u001B[39m output2\n", + "File \u001B[0;32m~/Desktop/repos/bio-check/demos/../bio_check/verifier.py:168\u001B[0m, in \u001B[0;36mVerifier.get_verify_output\u001B[0;34m(self, job_id)\u001B[0m\n\u001B[1;32m 165\u001B[0m headers \u001B[38;5;241m=\u001B[39m {\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mAccept\u001B[39m\u001B[38;5;124m'\u001B[39m: \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mapplication/json\u001B[39m\u001B[38;5;124m'\u001B[39m}\n\u001B[1;32m 167\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 168\u001B[0m response \u001B[38;5;241m=\u001B[39m \u001B[43mrequests\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget\u001B[49m\u001B[43m(\u001B[49m\u001B[43mendpoint\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mheaders\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mheaders\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 169\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_check_response(response)\n\u001B[1;32m 170\u001B[0m data \u001B[38;5;241m=\u001B[39m response\u001B[38;5;241m.\u001B[39mjson()\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/requests/api.py:73\u001B[0m, in \u001B[0;36mget\u001B[0;34m(url, params, **kwargs)\u001B[0m\n\u001B[1;32m 62\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mget\u001B[39m(url, params\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mNone\u001B[39;00m, \u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mkwargs):\n\u001B[1;32m 63\u001B[0m \u001B[38;5;250m \u001B[39m\u001B[38;5;124mr\u001B[39m\u001B[38;5;124;03m\"\"\"Sends a GET request.\u001B[39;00m\n\u001B[1;32m 64\u001B[0m \n\u001B[1;32m 65\u001B[0m \u001B[38;5;124;03m :param url: URL for the new :class:`Request` object.\u001B[39;00m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 70\u001B[0m \u001B[38;5;124;03m :rtype: requests.Response\u001B[39;00m\n\u001B[1;32m 71\u001B[0m \u001B[38;5;124;03m \"\"\"\u001B[39;00m\n\u001B[0;32m---> 73\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mrequest\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mget\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43murl\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mparams\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mparams\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/requests/api.py:59\u001B[0m, in \u001B[0;36mrequest\u001B[0;34m(method, url, **kwargs)\u001B[0m\n\u001B[1;32m 55\u001B[0m \u001B[38;5;66;03m# By using the 'with' statement we are sure the session is closed, thus we\u001B[39;00m\n\u001B[1;32m 56\u001B[0m \u001B[38;5;66;03m# avoid leaving sockets open which can trigger a ResourceWarning in some\u001B[39;00m\n\u001B[1;32m 57\u001B[0m \u001B[38;5;66;03m# cases, and look like a memory leak in others.\u001B[39;00m\n\u001B[1;32m 58\u001B[0m \u001B[38;5;28;01mwith\u001B[39;00m sessions\u001B[38;5;241m.\u001B[39mSession() \u001B[38;5;28;01mas\u001B[39;00m session:\n\u001B[0;32m---> 59\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43msession\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mrequest\u001B[49m\u001B[43m(\u001B[49m\u001B[43mmethod\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mmethod\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43murl\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43murl\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/requests/sessions.py:589\u001B[0m, in \u001B[0;36mSession.request\u001B[0;34m(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)\u001B[0m\n\u001B[1;32m 584\u001B[0m send_kwargs \u001B[38;5;241m=\u001B[39m {\n\u001B[1;32m 585\u001B[0m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mtimeout\u001B[39m\u001B[38;5;124m\"\u001B[39m: timeout,\n\u001B[1;32m 586\u001B[0m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mallow_redirects\u001B[39m\u001B[38;5;124m\"\u001B[39m: allow_redirects,\n\u001B[1;32m 587\u001B[0m }\n\u001B[1;32m 588\u001B[0m send_kwargs\u001B[38;5;241m.\u001B[39mupdate(settings)\n\u001B[0;32m--> 589\u001B[0m resp \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43msend\u001B[49m\u001B[43m(\u001B[49m\u001B[43mprep\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43msend_kwargs\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 591\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m resp\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/requests/sessions.py:703\u001B[0m, in \u001B[0;36mSession.send\u001B[0;34m(self, request, **kwargs)\u001B[0m\n\u001B[1;32m 700\u001B[0m start \u001B[38;5;241m=\u001B[39m preferred_clock()\n\u001B[1;32m 702\u001B[0m \u001B[38;5;66;03m# Send the request\u001B[39;00m\n\u001B[0;32m--> 703\u001B[0m r \u001B[38;5;241m=\u001B[39m \u001B[43madapter\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43msend\u001B[49m\u001B[43m(\u001B[49m\u001B[43mrequest\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 705\u001B[0m \u001B[38;5;66;03m# Total elapsed time of the request (approximately)\u001B[39;00m\n\u001B[1;32m 706\u001B[0m elapsed \u001B[38;5;241m=\u001B[39m preferred_clock() \u001B[38;5;241m-\u001B[39m start\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/requests/adapters.py:667\u001B[0m, in \u001B[0;36mHTTPAdapter.send\u001B[0;34m(self, request, stream, timeout, verify, cert, proxies)\u001B[0m\n\u001B[1;32m 664\u001B[0m timeout \u001B[38;5;241m=\u001B[39m TimeoutSauce(connect\u001B[38;5;241m=\u001B[39mtimeout, read\u001B[38;5;241m=\u001B[39mtimeout)\n\u001B[1;32m 666\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 667\u001B[0m resp \u001B[38;5;241m=\u001B[39m \u001B[43mconn\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43murlopen\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 668\u001B[0m \u001B[43m \u001B[49m\u001B[43mmethod\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mrequest\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mmethod\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 669\u001B[0m \u001B[43m \u001B[49m\u001B[43murl\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43murl\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 670\u001B[0m \u001B[43m \u001B[49m\u001B[43mbody\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mrequest\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mbody\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 671\u001B[0m \u001B[43m \u001B[49m\u001B[43mheaders\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mrequest\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mheaders\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 672\u001B[0m \u001B[43m \u001B[49m\u001B[43mredirect\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m,\u001B[49m\n\u001B[1;32m 673\u001B[0m \u001B[43m \u001B[49m\u001B[43massert_same_host\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m,\u001B[49m\n\u001B[1;32m 674\u001B[0m \u001B[43m \u001B[49m\u001B[43mpreload_content\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m,\u001B[49m\n\u001B[1;32m 675\u001B[0m \u001B[43m \u001B[49m\u001B[43mdecode_content\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m,\u001B[49m\n\u001B[1;32m 676\u001B[0m \u001B[43m \u001B[49m\u001B[43mretries\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mmax_retries\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 677\u001B[0m \u001B[43m \u001B[49m\u001B[43mtimeout\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mtimeout\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 678\u001B[0m \u001B[43m \u001B[49m\u001B[43mchunked\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mchunked\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 679\u001B[0m \u001B[43m \u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 681\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m (ProtocolError, \u001B[38;5;167;01mOSError\u001B[39;00m) \u001B[38;5;28;01mas\u001B[39;00m err:\n\u001B[1;32m 682\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mConnectionError\u001B[39;00m(err, request\u001B[38;5;241m=\u001B[39mrequest)\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/urllib3/connectionpool.py:715\u001B[0m, in \u001B[0;36mHTTPConnectionPool.urlopen\u001B[0;34m(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)\u001B[0m\n\u001B[1;32m 712\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_prepare_proxy(conn)\n\u001B[1;32m 714\u001B[0m \u001B[38;5;66;03m# Make the request on the httplib connection object.\u001B[39;00m\n\u001B[0;32m--> 715\u001B[0m httplib_response \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_make_request\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 716\u001B[0m \u001B[43m \u001B[49m\u001B[43mconn\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 717\u001B[0m \u001B[43m \u001B[49m\u001B[43mmethod\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 718\u001B[0m \u001B[43m \u001B[49m\u001B[43murl\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 719\u001B[0m \u001B[43m \u001B[49m\u001B[43mtimeout\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mtimeout_obj\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 720\u001B[0m \u001B[43m \u001B[49m\u001B[43mbody\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mbody\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 721\u001B[0m \u001B[43m \u001B[49m\u001B[43mheaders\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mheaders\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 722\u001B[0m \u001B[43m \u001B[49m\u001B[43mchunked\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mchunked\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 723\u001B[0m \u001B[43m\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 725\u001B[0m \u001B[38;5;66;03m# If we're going to release the connection in ``finally:``, then\u001B[39;00m\n\u001B[1;32m 726\u001B[0m \u001B[38;5;66;03m# the response doesn't need to know about the connection. Otherwise\u001B[39;00m\n\u001B[1;32m 727\u001B[0m \u001B[38;5;66;03m# it will also try to release it and we'll have a double-release\u001B[39;00m\n\u001B[1;32m 728\u001B[0m \u001B[38;5;66;03m# mess.\u001B[39;00m\n\u001B[1;32m 729\u001B[0m response_conn \u001B[38;5;241m=\u001B[39m conn \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m release_conn \u001B[38;5;28;01melse\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/urllib3/connectionpool.py:467\u001B[0m, in \u001B[0;36mHTTPConnectionPool._make_request\u001B[0;34m(self, conn, method, url, timeout, chunked, **httplib_request_kw)\u001B[0m\n\u001B[1;32m 462\u001B[0m httplib_response \u001B[38;5;241m=\u001B[39m conn\u001B[38;5;241m.\u001B[39mgetresponse()\n\u001B[1;32m 463\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mBaseException\u001B[39;00m \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 464\u001B[0m \u001B[38;5;66;03m# Remove the TypeError from the exception chain in\u001B[39;00m\n\u001B[1;32m 465\u001B[0m \u001B[38;5;66;03m# Python 3 (including for exceptions like SystemExit).\u001B[39;00m\n\u001B[1;32m 466\u001B[0m \u001B[38;5;66;03m# Otherwise it looks like a bug in the code.\u001B[39;00m\n\u001B[0;32m--> 467\u001B[0m \u001B[43msix\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mraise_from\u001B[49m\u001B[43m(\u001B[49m\u001B[43me\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;28;43;01mNone\u001B[39;49;00m\u001B[43m)\u001B[49m\n\u001B[1;32m 468\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m (SocketTimeout, BaseSSLError, SocketError) \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 469\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_raise_timeout(err\u001B[38;5;241m=\u001B[39me, url\u001B[38;5;241m=\u001B[39murl, timeout_value\u001B[38;5;241m=\u001B[39mread_timeout)\n", + "File \u001B[0;32m:3\u001B[0m, in \u001B[0;36mraise_from\u001B[0;34m(value, from_value)\u001B[0m\n", + "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/bio-check-lb7k8x6F-py3.9/lib/python3.9/site-packages/urllib3/connectionpool.py:462\u001B[0m, in \u001B[0;36mHTTPConnectionPool._make_request\u001B[0;34m(self, conn, method, url, timeout, chunked, **httplib_request_kw)\u001B[0m\n\u001B[1;32m 459\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mTypeError\u001B[39;00m:\n\u001B[1;32m 460\u001B[0m \u001B[38;5;66;03m# Python 3\u001B[39;00m\n\u001B[1;32m 461\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 462\u001B[0m httplib_response \u001B[38;5;241m=\u001B[39m \u001B[43mconn\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mgetresponse\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 463\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mBaseException\u001B[39;00m \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 464\u001B[0m \u001B[38;5;66;03m# Remove the TypeError from the exception chain in\u001B[39;00m\n\u001B[1;32m 465\u001B[0m \u001B[38;5;66;03m# Python 3 (including for exceptions like SystemExit).\u001B[39;00m\n\u001B[1;32m 466\u001B[0m \u001B[38;5;66;03m# Otherwise it looks like a bug in the code.\u001B[39;00m\n\u001B[1;32m 467\u001B[0m six\u001B[38;5;241m.\u001B[39mraise_from(e, \u001B[38;5;28;01mNone\u001B[39;00m)\n", + "File \u001B[0;32m/opt/homebrew/Cellar/python@3.9/3.9.19/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py:1377\u001B[0m, in \u001B[0;36mHTTPConnection.getresponse\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 1375\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[1;32m 1376\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m-> 1377\u001B[0m \u001B[43mresponse\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mbegin\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 1378\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mConnectionError\u001B[39;00m:\n\u001B[1;32m 1379\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mclose()\n", + "File \u001B[0;32m/opt/homebrew/Cellar/python@3.9/3.9.19/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py:320\u001B[0m, in \u001B[0;36mHTTPResponse.begin\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 318\u001B[0m \u001B[38;5;66;03m# read until we get a non-100 response\u001B[39;00m\n\u001B[1;32m 319\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;28;01mTrue\u001B[39;00m:\n\u001B[0;32m--> 320\u001B[0m version, status, reason \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_read_status\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 321\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m status \u001B[38;5;241m!=\u001B[39m CONTINUE:\n\u001B[1;32m 322\u001B[0m \u001B[38;5;28;01mbreak\u001B[39;00m\n", + "File \u001B[0;32m/opt/homebrew/Cellar/python@3.9/3.9.19/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py:281\u001B[0m, in \u001B[0;36mHTTPResponse._read_status\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 280\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m_read_status\u001B[39m(\u001B[38;5;28mself\u001B[39m):\n\u001B[0;32m--> 281\u001B[0m line \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mstr\u001B[39m(\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mfp\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mreadline\u001B[49m\u001B[43m(\u001B[49m\u001B[43m_MAXLINE\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m+\u001B[39;49m\u001B[43m \u001B[49m\u001B[38;5;241;43m1\u001B[39;49m\u001B[43m)\u001B[49m, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124miso-8859-1\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 282\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mlen\u001B[39m(line) \u001B[38;5;241m>\u001B[39m _MAXLINE:\n\u001B[1;32m 283\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m LineTooLong(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mstatus line\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n", + "File \u001B[0;32m/opt/homebrew/Cellar/python@3.9/3.9.19/Frameworks/Python.framework/Versions/3.9/lib/python3.9/socket.py:704\u001B[0m, in \u001B[0;36mSocketIO.readinto\u001B[0;34m(self, b)\u001B[0m\n\u001B[1;32m 702\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;28;01mTrue\u001B[39;00m:\n\u001B[1;32m 703\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 704\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_sock\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mrecv_into\u001B[49m\u001B[43m(\u001B[49m\u001B[43mb\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 705\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m timeout:\n\u001B[1;32m 706\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_timeout_occurred \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mTrue\u001B[39;00m\n", + "File \u001B[0;32m/opt/homebrew/Cellar/python@3.9/3.9.19/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py:1275\u001B[0m, in \u001B[0;36mSSLSocket.recv_into\u001B[0;34m(self, buffer, nbytes, flags)\u001B[0m\n\u001B[1;32m 1271\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m flags \u001B[38;5;241m!=\u001B[39m \u001B[38;5;241m0\u001B[39m:\n\u001B[1;32m 1272\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mValueError\u001B[39;00m(\n\u001B[1;32m 1273\u001B[0m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mnon-zero flags not allowed in calls to recv_into() on \u001B[39m\u001B[38;5;132;01m%s\u001B[39;00m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;241m%\u001B[39m\n\u001B[1;32m 1274\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m\u001B[38;5;18m__class__\u001B[39m)\n\u001B[0;32m-> 1275\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mread\u001B[49m\u001B[43m(\u001B[49m\u001B[43mnbytes\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mbuffer\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 1276\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1277\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28msuper\u001B[39m()\u001B[38;5;241m.\u001B[39mrecv_into(buffer, nbytes, flags)\n", + "File \u001B[0;32m/opt/homebrew/Cellar/python@3.9/3.9.19/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py:1133\u001B[0m, in \u001B[0;36mSSLSocket.read\u001B[0;34m(self, len, buffer)\u001B[0m\n\u001B[1;32m 1131\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[1;32m 1132\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m buffer \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m:\n\u001B[0;32m-> 1133\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_sslobj\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mread\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mlen\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mbuffer\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 1134\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1135\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_sslobj\u001B[38;5;241m.\u001B[39mread(\u001B[38;5;28mlen\u001B[39m)\n", + "\u001B[0;31mKeyboardInterrupt\u001B[0m: " + ] + } + ], + "execution_count": 19 + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2024-07-31T17:46:46.122487Z", + "start_time": "2024-07-31T17:46:45.864511Z" + } + }, + "cell_type": "code", + "source": "verify.get_verify_output(submission_3['job_id'])", + "id": "cdf50bb88a07944e", + "outputs": [ + { + "data": { + "text/plain": [ + "{'content': {'status': 'PENDING',\n", + " 'job_id': 'utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9',\n", + " 'path': 'uploads/utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9/Elowitz-Nature-2000-Repressilator.omex',\n", + " 'simulators': ['amici', 'copasi', 'tellurium'],\n", + " 'comparison_id': 'utc_comparison',\n", + " 'timestamp': '2024-07-31 17:42:39.985493',\n", + " 'ground_truth_report_path': None,\n", + " 'include_outputs': True,\n", + " 'rTol': None,\n", + " 'aTol': None,\n", + " 'selection_list': None}}" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "execution_count": 20 + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2024-07-31T17:46:48.155312Z", + "start_time": "2024-07-31T17:46:47.888445Z" + } + }, + "cell_type": "code", + "source": "verify.get_verify_output(submission_3['job_id'])", + "id": "1124535b0a55db0c", + "outputs": [ + { + "data": { + "text/plain": [ + "{'content': {'status': 'PENDING',\n", + " 'job_id': 'utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9',\n", + " 'path': 'uploads/utc_comparison_d8389eed-bce2-47d8-894c-9d7519dbc2b9/Elowitz-Nature-2000-Repressilator.omex',\n", + " 'simulators': ['amici', 'copasi', 'tellurium'],\n", + " 'comparison_id': 'utc_comparison',\n", + " 'timestamp': '2024-07-31 17:42:39.985493',\n", + " 'ground_truth_report_path': None,\n", + " 'include_outputs': True,\n", + " 'rTol': None,\n", + " 'aTol': None,\n", + " 'selection_list': None}}" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "execution_count": 21 }, { "metadata": {}, @@ -11346,7 +543,7 @@ "outputs": [], "execution_count": null, "source": "", - "id": "f788b67be0804bb" + "id": "fb9b64137a58ad30" } ], "metadata": {