Add 'type' field to ExperimentParametersModel
This commit introduces a new 'type' field in the ExperimentParametersModel schema and updates the associated code in `sample.py` to include this field during object creation. Additionally, unnecessary lines and redundant code in `testfunctions.ipynb` have been removed for better readability and maintainability.
This commit is contained in:
GotthardG
@ -3,8 +3,8 @@
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"cell_type": "code",
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@ -48,7 +48,7 @@
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"execution_count": 1
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"execution_count": 3
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"metadata": {},
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@ -427,21 +427,21 @@
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"metadata": {
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"end_time": "2025-04-29T21:15:51.203912Z",
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"start_time": "2025-04-29T21:15:51.200888Z"
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}
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},
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"cell_type": "code",
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"source": "sample_id = 230",
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"source": "sample_id = 204",
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"id": "54d4d46ca558e7b9",
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"outputs": [],
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"execution_count": 2
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"execution_count": 1
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},
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T20:17:46.414835Z",
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"start_time": "2025-04-29T20:17:46.379138Z"
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"end_time": "2025-04-29T20:57:41.460728Z",
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"start_time": "2025-04-29T20:57:41.399620Z"
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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/230/events HTTP/1.1\" 200 413\n"
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/204/events HTTP/1.1\" 200 413\n"
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]
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},
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{
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@ -503,8 +503,8 @@
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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', 230)\n",
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"('sample_name', 'Sample230')\n",
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"('id', 204)\n",
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"('sample_name', 'Sample204')\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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@ -513,13 +513,13 @@
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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=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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"('events', [SampleEventResponse(event_type='Mounting', id=396, sample_id=204, timestamp=datetime.datetime(2025, 4, 28, 12, 56)), SampleEventResponse(event_type='Collecting', id=397, sample_id=204, timestamp=datetime.datetime(2025, 4, 29, 20, 57, 41, 453326))])\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": 3
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"execution_count": 15
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},
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{
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"metadata": {
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@ -563,8 +563,8 @@
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{
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"metadata": {
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"ExecuteTime": {
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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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"end_time": "2025-04-29T20:57:47.969390Z",
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"start_time": "2025-04-29T20:57:47.936166Z"
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}
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},
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"cell_type": "code",
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@ -635,7 +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/230/upload-images HTTP/1.1\" 200 205\n"
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"DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/204/upload-images HTTP/1.1\" 200 205\n"
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]
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},
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{
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@ -645,11 +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': 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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"{'pgroup': 'p20003', 'sample_id': 204, 'sample_event_id': 397, 'filepath': 'images/p20003/2025-04-29/Dewar Five/PKK007/16/Collecting_2025-04-29_20-57-41/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": 4
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"execution_count": 16
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},
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{
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"metadata": {},
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@ -662,8 +662,8 @@
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-04-29T20:17:56.494919Z",
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"start_time": "2025-04-29T20:17:56.469538Z"
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"end_time": "2025-04-29T21:16:26.759058Z",
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"start_time": "2025-04-29T21:16:26.727172Z"
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}
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},
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"cell_type": "code",
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@ -674,7 +674,8 @@
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" ExperimentParametersCreate,\n",
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" RotationParameters,\n",
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" BeamlineParameters,\n",
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" GridScanParamers\n",
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" GridScanParamers,\n",
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" Detector\n",
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")\n",
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"\n",
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"\n",
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@ -712,17 +713,17 @@
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"# If your client code requires you to build a detector model,\n",
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"# you can either use a Detector model or pass a dictionary.\n",
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"# Here we pass a dictionary.\n",
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"detector_data = {\n",
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" \"manufacturer\": \"DECTRIS\",\n",
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" \"model\": \"PILATUS4 2M\",\n",
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" \"type\": \"photon-counting\",\n",
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" \"serialNumber\": \"16684dscsd668468\",\n",
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" \"detectorDistance_mm\": 95.0,\n",
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" \"beamCenterX_px\": 512.0,\n",
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" \"beamCenterY_px\": 512.0,\n",
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" \"pixelSizeX_um\": 150.0,\n",
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" \"pixelSizeY_um\": 150.0,\n",
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"}\n",
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"detector_data = Detector(\n",
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" manufacturer=\"DECTRIS\",\n",
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" model=\"PILATUS4 2M\",\n",
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" type=\"photon-counting\",\n",
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" serialNumber=\"16684dscsd668468\",\n",
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" detectorDistance_mm=95.0,\n",
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" beamCenterX_px=512.0,\n",
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" beamCenterY_px=512.0,\n",
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" pixelSizeX_um=150.0,\n",
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" pixelSizeY_um=150.0,\n",
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")\n",
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"\n",
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"beamline_params = BeamlineParameters(\n",
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" synchrotron=\"Swiss Light Source\",\n",
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@ -748,6 +749,7 @@
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"# it out or set it to a dummy value if your client model requires it.\n",
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"experiment_params_payload = ExperimentParametersCreate(\n",
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" # run_number can be omitted/ignored if computed on the server\n",
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" type=\"standard\",\n",
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" beamline_parameters=beamline_params,\n",
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" sample_id=sample_id # change sample_id to an existing sample in your database\n",
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")\n",
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@ -778,7 +780,7 @@
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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/230/experiment_parameters HTTP/1.1\" 200 875\n"
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/204/experiment_parameters HTTP/1.1\" 200 893\n"
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]
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},
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{
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@ -786,17 +788,17 @@
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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=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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"run_number=1 type='standard' 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=204 id=1\n"
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]
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}
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],
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"execution_count": 5
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"execution_count": 4
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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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"end_time": "2025-04-29T21:17:02.855772Z",
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"start_time": "2025-04-29T21:17:02.821634Z"
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}
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},
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"cell_type": "code",
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@ -838,7 +840,7 @@
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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 \"PATCH /samples/update-dataset/230/1 HTTP/1.1\" 200 1056\n"
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"DEBUG:urllib3.connectionpool:https://localhost:8000 \"PATCH /samples/update-dataset/204/1 HTTP/1.1\" 200 1074\n"
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]
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},
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{
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@ -846,11 +848,11 @@
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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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"run_number=1 type='standard' 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, 23, 17, 2, 823503)) sample_id=204 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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"execution_count": 5
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},
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{
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"metadata": {
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