Add dataset, slurm_id, and FAILED status to models
Enhanced the models with new fields: a dataset field for Experiment Parameters and a slurm_id for Jobs. Introduced a FAILED status for the JobStatus enum. Updated functionality to handle datasets and trigger job creation based on dataset status.
This commit is contained in:
GotthardG
@ -3,8 +3,8 @@
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T11:59:40.825956Z",
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"start_time": "2025-04-29T11:59:40.822492Z"
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"end_time": "2025-04-29T20:17:17.478562Z",
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"start_time": "2025-04-29T20:17:16.842590Z"
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"cell_type": "code",
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@ -43,12 +43,12 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"0.1.1a1\n",
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"0.1.1a2\n",
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"https://localhost:8000\n"
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]
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}
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],
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"execution_count": 31
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"execution_count": 1
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},
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{
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"metadata": {},
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@ -427,21 +427,21 @@
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T12:00:18.905592Z",
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"start_time": "2025-04-29T12:00:18.903773Z"
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"end_time": "2025-04-29T20:17:43.335654Z",
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"start_time": "2025-04-29T20:17:43.333828Z"
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}
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},
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"cell_type": "code",
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"source": "sample_id = 250",
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"source": "sample_id = 230",
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"id": "54d4d46ca558e7b9",
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"outputs": [],
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"execution_count": 32
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"execution_count": 2
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},
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T12:00:20.537319Z",
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"start_time": "2025-04-29T12:00:20.510157Z"
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"end_time": "2025-04-29T20:17:46.414835Z",
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"start_time": "2025-04-29T20:17:46.379138Z"
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}
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},
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"cell_type": "code",
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@ -493,7 +493,7 @@
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"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n",
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"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1103: InsecureRequestWarning: Unverified HTTPS request is being made to host 'localhost'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
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" warnings.warn(\n",
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/250/events HTTP/1.1\" 200 412\n"
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/230/events HTTP/1.1\" 200 413\n"
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]
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},
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{
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@ -503,9 +503,9 @@
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"Payload being sent to API:\n",
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"{\"event_type\":\"Collecting\"}\n",
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"API response:\n",
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"('id', 250)\n",
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"('sample_name', 'Sample250')\n",
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"('position', 9)\n",
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"('id', 230)\n",
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"('sample_name', 'Sample230')\n",
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"('position', 16)\n",
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"('puck_id', 30)\n",
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"('crystalname', None)\n",
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"('proteinname', None)\n",
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@ -513,19 +513,22 @@
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"('priority', None)\n",
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"('comments', None)\n",
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"('data_collection_parameters', None)\n",
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"('events', [SampleEventResponse(event_type='Mounting', id=490, sample_id=250, timestamp=datetime.datetime(2025, 4, 28, 13, 42)), SampleEventResponse(event_type='Collecting', id=491, sample_id=250, timestamp=datetime.datetime(2025, 4, 29, 12, 0, 20, 528955))])\n",
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"('events', [SampleEventResponse(event_type='Mounting', id=453, sample_id=230, timestamp=datetime.datetime(2025, 4, 28, 13, 22)), SampleEventResponse(event_type='Collecting', id=454, sample_id=230, timestamp=datetime.datetime(2025, 4, 29, 20, 17, 46, 405264))])\n",
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"('mount_count', 0)\n",
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"('unmount_count', 0)\n"
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]
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}
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],
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"execution_count": 33
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"execution_count": 3
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},
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{
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"metadata": {},
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T14:27:46.730515Z",
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"start_time": "2025-04-29T14:27:46.622922Z"
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}
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},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"### not working\n",
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"with aareDBclient.ApiClient(configuration) as api_client:\n",
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@ -541,13 +544,27 @@
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" except ApiException as e:\n",
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" print(\"Exception when calling get_last_sample_event: %s\\n\" % e)\n"
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],
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"id": "f1d171700d6cf7fe"
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"id": "f1d171700d6cf7fe",
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"outputs": [
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{
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"ename": "AttributeError",
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"evalue": "'SamplesApi' object has no attribute 'get_last_sample_event_samples_samples_sample_id_events_last_get'",
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"output_type": "error",
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"traceback": [
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"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
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"\u001B[0;31mAttributeError\u001B[0m Traceback (most recent call last)",
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"Cell \u001B[0;32mIn[48], line 8\u001B[0m\n\u001B[1;32m 4\u001B[0m api_instance \u001B[38;5;241m=\u001B[39m aareDBclient\u001B[38;5;241m.\u001B[39mSamplesApi(api_client)\n\u001B[1;32m 6\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[1;32m 7\u001B[0m \u001B[38;5;66;03m# Get the last sample event\u001B[39;00m\n\u001B[0;32m----> 8\u001B[0m last_event_response \u001B[38;5;241m=\u001B[39m \u001B[43mapi_instance\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget_last_sample_event_samples_samples_sample_id_events_last_get\u001B[49m(\u001B[38;5;241m27\u001B[39m)\n\u001B[1;32m 9\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mThe response of get_last_sample_event:\u001B[39m\u001B[38;5;130;01m\\n\u001B[39;00m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 10\u001B[0m pprint(last_event_response)\n",
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"\u001B[0;31mAttributeError\u001B[0m: 'SamplesApi' object has no attribute 'get_last_sample_event_samples_samples_sample_id_events_last_get'"
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]
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}
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],
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"execution_count": 48
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},
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T12:21:22.613961Z",
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"start_time": "2025-04-29T12:21:22.585856Z"
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"end_time": "2025-04-29T20:17:52.059793Z",
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"start_time": "2025-04-29T20:17:51.939047Z"
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}
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},
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"cell_type": "code",
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@ -618,7 +635,7 @@
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"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): 127.0.0.1:8000\n",
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"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1103: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
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" warnings.warn(\n",
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"DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/250/upload-images HTTP/1.1\" 200 204\n"
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"DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/230/upload-images HTTP/1.1\" 200 205\n"
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]
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},
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{
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@ -628,11 +645,11 @@
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"Uploading after_dc.jpeg.jpg...\n",
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"API Response for after_dc.jpeg.jpg:\n",
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"200\n",
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"{'pgroup': 'p20003', 'sample_id': 250, 'sample_event_id': 492, 'filepath': 'images/p20003/2025-04-29/Dewar Five/PKK007/9/Collecting_2025-04-29_12-00-30/after_dc.jpeg.jpg', 'status': 'active', 'comment': None, 'id': 2}\n"
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"{'pgroup': 'p20003', 'sample_id': 230, 'sample_event_id': 454, 'filepath': 'images/p20003/2025-04-29/Dewar Five/PKK007/16/Collecting_2025-04-29_20-17-46/after_dc.jpeg.jpg', 'status': 'active', 'comment': None, 'id': 1}\n"
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]
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}
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],
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"execution_count": 36
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"execution_count": 4
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},
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{
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"metadata": {},
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@ -645,8 +662,8 @@
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T12:21:30.879657Z",
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"start_time": "2025-04-29T12:21:30.855622Z"
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"end_time": "2025-04-29T20:17:56.494919Z",
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"start_time": "2025-04-29T20:17:56.469538Z"
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}
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},
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"cell_type": "code",
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@ -761,7 +778,7 @@
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"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n",
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"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1103: InsecureRequestWarning: Unverified HTTPS request is being made to host 'localhost'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
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" warnings.warn(\n",
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/250/experiment_parameters HTTP/1.1\" 200 860\n"
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/230/experiment_parameters HTTP/1.1\" 200 875\n"
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]
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},
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{
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@ -769,11 +786,71 @@
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"output_type": "stream",
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"text": [
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"API Response:\n",
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"run_number=2 beamline_parameters=BeamlineParameters(synchrotron='Swiss Light Source', beamline='PXIII', detector=Detector(manufacturer='DECTRIS', model='PILATUS4 2M', type='photon-counting', serial_number='16684dscsd668468', detector_distance_mm=95.0, beam_center_x_px=512.0, beam_center_y_px=512.0, pixel_size_x_um=150.0, pixel_size_y_um=150.0), wavelength=1.0, ring_current_a=0.0, ring_mode='Machine Down', undulator=None, undulatorgap_mm=None, monochromator='Si111', transmission=1.0, focusing_optic='Kirkpatrick-Baez', beamline_flux_at_sample_ph_s=0.0, beam_size_width=30.0, beam_size_height=30.0, characterization=None, rotation=RotationParameters(omega_start_deg=0.0, omega_step=0.1, chi=0.0, phi=10.0, number_of_images=3600, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) sample_id=250 id=2\n"
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"run_number=1 beamline_parameters=BeamlineParameters(synchrotron='Swiss Light Source', beamline='PXIII', detector=Detector(manufacturer='DECTRIS', model='PILATUS4 2M', type='photon-counting', serial_number='16684dscsd668468', detector_distance_mm=95.0, beam_center_x_px=512.0, beam_center_y_px=512.0, pixel_size_x_um=150.0, pixel_size_y_um=150.0), wavelength=1.0, ring_current_a=0.0, ring_mode='Machine Down', undulator=None, undulatorgap_mm=None, monochromator='Si111', transmission=1.0, focusing_optic='Kirkpatrick-Baez', beamline_flux_at_sample_ph_s=0.0, beam_size_width=30.0, beam_size_height=30.0, characterization=None, rotation=RotationParameters(omega_start_deg=0.0, omega_step=0.1, chi=0.0, phi=10.0, number_of_images=3600, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) dataset=None sample_id=230 id=1\n"
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]
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}
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],
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"execution_count": 37
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"execution_count": 5
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},
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T20:29:27.657874Z",
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"start_time": "2025-04-29T20:29:27.623737Z"
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}
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},
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"cell_type": "code",
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"source": [
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"from datetime import datetime\n",
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"\n",
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"sample_id = sample_id\n",
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"run_id = 1\n",
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"\n",
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"def test_mark_run_written(sample_id, run_id, configuration):\n",
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" # Prepare your dataset dict as required by your API (.dict() results if using Pydantic model)\n",
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" dataset_payload = {\n",
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" \"filepath\": \"/das/work/p11/p11206/raw_data/vincent/20250415_6D_SLS2_1st_data/20250415_fullbeam_dtz220_Lyso102_again_360deg\",\n",
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" \"status\": \"written\",\n",
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" \"written_at\": datetime.now().isoformat()\n",
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" }\n",
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"\n",
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" # The API method and argument names may differ if autogenerated — adjust accordingly\n",
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" with aareDBclient.ApiClient(configuration) as api_client:\n",
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" api_instance = aareDBclient.SamplesApi(api_client)\n",
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" try:\n",
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" api_response = api_instance.update_dataset_for_experiment_run(\n",
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" sample_id=sample_id, run_id=run_id, datasets=dataset_payload\n",
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" )\n",
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" print(\"Dataset updated successfully:\")\n",
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" print(api_response)\n",
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" except ApiException as e:\n",
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" print(f\"API call failed: {e}\")\n",
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"\n",
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"# Usage example (replace with your actual IDs and configuration):\n",
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"test_mark_run_written(sample_id, run_id, configuration)"
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],
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"id": "77793ecd843c1ef3",
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n",
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"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1103: InsecureRequestWarning: Unverified HTTPS request is being made to host 'localhost'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
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" warnings.warn(\n",
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"PATCH /samples/update-dataset/230/1 HTTP/1.1\" 200 1056\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Dataset updated successfully:\n",
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"run_number=1 beamline_parameters=BeamlineParameters(synchrotron='Swiss Light Source', beamline='PXIII', detector=Detector(manufacturer='DECTRIS', model='PILATUS4 2M', type='photon-counting', serial_number='16684dscsd668468', detector_distance_mm=95.0, beam_center_x_px=512.0, beam_center_y_px=512.0, pixel_size_x_um=150.0, pixel_size_y_um=150.0), wavelength=1.0, ring_current_a=0.0, ring_mode='Machine Down', undulator=None, undulatorgap_mm=None, monochromator='Si111', transmission=1.0, focusing_optic='Kirkpatrick-Baez', beamline_flux_at_sample_ph_s=0.0, beam_size_width=30.0, beam_size_height=30.0, characterization=None, rotation=RotationParameters(omega_start_deg=0.0, omega_step=0.1, chi=0.0, phi=10.0, number_of_images=3600, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) dataset=Datasets(filepath='/das/work/p11/p11206/raw_data/vincent/20250415_6D_SLS2_1st_data/20250415_fullbeam_dtz220_Lyso102_again_360deg', status='written', written_at=datetime.datetime(2025, 4, 29, 22, 29, 27, 626524)) sample_id=230 id=1\n"
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]
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}
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],
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"execution_count": 13
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},
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{
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"metadata": {
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