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Fix job type assignment and clean up testfunctions file.

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Updated job type to reference `experiment.type` in `processing.py` for accurate data handling. Cleaned up and streamlined `testfunctions.ipynb` by removing outdated and redundant code, improving readability and usability.
This commit is contained in:
GotthardG
2025-04-30 13:09:55 +02:00
parent 38a5c85b37
commit b3847a0bf0
4 changed files with 47 additions and 56 deletions
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5
backend/app/routers/processing.py
View File

@ -41,7 +41,10 @@ async def job_event_generator(db: Session):
experiment_parameters=experiment.beamline_parameters
if experiment
else None,
slurm_id=None,
filepath=experiment.dataset.get("filepath")
if experiment and experiment.dataset
else None,
slurm_id=job.slurm_id,
)
job_items.append(job_item)

1
backend/app/schemas.py
View File

@ -983,6 +983,7 @@ class JobsResponse(BaseModel):
updated_at: Optional[datetime]
data_collection_parameters: Optional[DataCollectionParameters] = None
experiment_parameters: BeamlineParameters
filepath: Optional[str] = None
slurm_id: Optional[int] = None

55
backend/propipe_sim.ipynb
View File

@ -6,8 +6,8 @@
"metadata": {
"collapsed": true,
"ExecuteTime": {
"end_time": "2025-04-30T08:33:36.239042Z",
"start_time": "2025-04-29T21:16:51.426746Z"
"end_time": "2025-04-30T09:22:17.261436Z",
"start_time": "2025-04-30T09:21:47.206494Z"
}
},
"source": [
@ -65,7 +65,10 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Starting job status updater...\n"
"Starting job status updater...\n",
"Jobs received: [{'job_id': 4, 'sample_id': 204, 'run_id': 1, 'sample_name': 'Sample204', 'status': 'todo', 'type': 'standard', 'created_at': '2025-04-30T09:05:14.901478', 'updated_at': None, 'data_collection_parameters': None, 'experiment_parameters': {'synchrotron': 'Swiss Light Source', 'beamline': 'PXIII', 'detector': {'manufacturer': 'DECTRIS', 'model': 'PILATUS4 2M', 'type': 'photon-counting', 'serialNumber': '16684dscsd668468', 'detectorDistance_mm': 95.0, 'beamCenterX_px': 512.0, 'beamCenterY_px': 512.0, 'pixelSizeX_um': 150.0, 'pixelSizeY_um': 150.0}, 'wavelength': 1.0, 'ringCurrent_A': 0.0, 'ringMode': 'Machine Down', 'undulator': None, 'undulatorgap_mm': None, 'monochromator': 'Si111', 'transmission': 1.0, 'focusingOptic': 'Kirkpatrick-Baez', 'beamlineFluxAtSample_ph_s': 0.0, 'beamSizeWidth': 30.0, 'beamSizeHeight': 30.0, 'characterization': None, 'rotation': {'omegaStart_deg': 0.0, 'omegaStep': 0.1, 'chi': 0.0, 'phi': 10.0, 'numberOfImages': 3600, 'exposureTime_s': 0.02}, 'gridScan': None, 'jet': None, 'cryojetTemperature_K': None, 'humidifierTemperature_K': None, 'humidifierHumidity': None}, 'filepath': '/das/work/p11/p11206/raw_data/vincent/20250415_6D_SLS2_1st_data/20250415_fullbeam_dtz220_Lyso102_again_360deg', 'slurm_id': None}]\n",
"Job ID: 4, Current status: todo\n",
"✅ Job 4 status updated to 'submitted'. Response: {'job_id': 4, 'status': 'submitted', 'slurm_id': 76545678}\n"
]
},
{
@ -73,50 +76,34 @@
"output_type": "stream",
"text": [
"/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",
" warnings.warn(\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Jobs received: [{'job_id': 1, 'sample_id': 204, 'run_id': 1, 'sample_name': 'Sample204', 'status': 'todo', 'type': 'default_type', 'created_at': '2025-04-29T21:17:02.847967', 'updated_at': None, 'data_collection_parameters': None, 'experiment_parameters': {'synchrotron': 'Swiss Light Source', 'beamline': 'PXIII', 'detector': {'manufacturer': 'DECTRIS', 'model': 'PILATUS4 2M', 'type': 'photon-counting', 'serialNumber': '16684dscsd668468', 'detectorDistance_mm': 95.0, 'beamCenterX_px': 512.0, 'beamCenterY_px': 512.0, 'pixelSizeX_um': 150.0, 'pixelSizeY_um': 150.0}, 'wavelength': 1.0, 'ringCurrent_A': 0.0, 'ringMode': 'Machine Down', 'undulator': None, 'undulatorgap_mm': None, 'monochromator': 'Si111', 'transmission': 1.0, 'focusingOptic': 'Kirkpatrick-Baez', 'beamlineFluxAtSample_ph_s': 0.0, 'beamSizeWidth': 30.0, 'beamSizeHeight': 30.0, 'characterization': None, 'rotation': {'omegaStart_deg': 0.0, 'omegaStep': 0.1, 'chi': 0.0, 'phi': 10.0, 'numberOfImages': 3600, 'exposureTime_s': 0.02}, 'gridScan': None, 'jet': None, 'cryojetTemperature_K': None, 'humidifierTemperature_K': None, 'humidifierHumidity': None}, 'slurm_id': None}]\n",
"Job ID: 1, Current status: todo\n",
"✅ Job 1 status updated to 'submitted'. Response: {'job_id': 1, 'status': 'submitted', 'slurm_id': 76545678}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" warnings.warn(\n",
"/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",
" warnings.warn(\n"
]
},
{
"ename": "ChunkedEncodingError",
"evalue": "Response ended prematurely",
"ename": "KeyboardInterrupt",
"evalue": "",
"output_type": "error",
"traceback": [
"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
"\u001B[0;31mProtocolError\u001B[0m Traceback (most recent call last)",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/requests/models.py:820\u001B[0m, in \u001B[0;36mResponse.iter_content.<locals>.generate\u001B[0;34m()\u001B[0m\n\u001B[1;32m 819\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 820\u001B[0m \u001B[38;5;28;01myield from\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mraw\u001B[38;5;241m.\u001B[39mstream(chunk_size, decode_content\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mTrue\u001B[39;00m)\n\u001B[1;32m 821\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m ProtocolError \u001B[38;5;28;01mas\u001B[39;00m e:\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/response.py:1040\u001B[0m, in \u001B[0;36mHTTPResponse.stream\u001B[0;34m(self, amt, decode_content)\u001B[0m\n\u001B[1;32m 1039\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mchunked \u001B[38;5;129;01mand\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39msupports_chunked_reads():\n\u001B[0;32m-> 1040\u001B[0m \u001B[38;5;28;01myield from\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mread_chunked(amt, decode_content\u001B[38;5;241m=\u001B[39mdecode_content)\n\u001B[1;32m 1041\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/response.py:1184\u001B[0m, in \u001B[0;36mHTTPResponse.read_chunked\u001B[0;34m(self, amt, decode_content)\u001B[0m\n\u001B[1;32m 1183\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;28;01mTrue\u001B[39;00m:\n\u001B[0;32m-> 1184\u001B[0m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_update_chunk_length\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 1185\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mchunk_left \u001B[38;5;241m==\u001B[39m \u001B[38;5;241m0\u001B[39m:\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/response.py:1119\u001B[0m, in \u001B[0;36mHTTPResponse._update_chunk_length\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 1117\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1118\u001B[0m \u001B[38;5;66;03m# Truncated at start of next chunk\u001B[39;00m\n\u001B[0;32m-> 1119\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m ProtocolError(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mResponse ended prematurely\u001B[39m\u001B[38;5;124m\"\u001B[39m) \u001B[38;5;28;01mfrom\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;28;01mNone\u001B[39;00m\n",
"\u001B[0;31mProtocolError\u001B[0m: Response ended prematurely",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001B[0;31mChunkedEncodingError\u001B[0m Traceback (most recent call last)",
"Cell \u001B[0;32mIn[12], line 48\u001B[0m\n\u001B[1;32m 45\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mUnexpected error while processing event: \u001B[39m\u001B[38;5;132;01m{\u001B[39;00me\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 47\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;18m__name__\u001B[39m \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m__main__\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m---> 48\u001B[0m \u001B[43mlisten_and_update_jobs\u001B[49m\u001B[43m(\u001B[49m\u001B[43mSSE_URL\u001B[49m\u001B[43m)\u001B[49m\n",
"Cell \u001B[0;32mIn[12], line 32\u001B[0m, in \u001B[0;36mlisten_and_update_jobs\u001B[0;34m(url)\u001B[0m\n\u001B[1;32m 28\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m\n\u001B[1;32m 30\u001B[0m client \u001B[38;5;241m=\u001B[39m sseclient\u001B[38;5;241m.\u001B[39mSSEClient(response)\n\u001B[0;32m---> 32\u001B[0m \u001B[43m\u001B[49m\u001B[38;5;28;43;01mfor\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mevent\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;129;43;01min\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mclient\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mevents\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\u001B[43m:\u001B[49m\n\u001B[1;32m 33\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;28;43;01mtry\u001B[39;49;00m\u001B[43m:\u001B[49m\n\u001B[1;32m 34\u001B[0m \u001B[43m \u001B[49m\u001B[43mjobs\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m \u001B[49m\u001B[43mjson\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mloads\u001B[49m\u001B[43m(\u001B[49m\u001B[43mevent\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdata\u001B[49m\u001B[43m)\u001B[49m\n",
"\u001B[0;31mKeyboardInterrupt\u001B[0m Traceback (most recent call last)",
"Cell \u001B[0;32mIn[14], line 48\u001B[0m\n\u001B[1;32m 45\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mUnexpected error while processing event: \u001B[39m\u001B[38;5;132;01m{\u001B[39;00me\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 47\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;18m__name__\u001B[39m \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m__main__\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m---> 48\u001B[0m \u001B[43mlisten_and_update_jobs\u001B[49m\u001B[43m(\u001B[49m\u001B[43mSSE_URL\u001B[49m\u001B[43m)\u001B[49m\n",
"Cell \u001B[0;32mIn[14], line 32\u001B[0m, in \u001B[0;36mlisten_and_update_jobs\u001B[0;34m(url)\u001B[0m\n\u001B[1;32m 28\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m\n\u001B[1;32m 30\u001B[0m client \u001B[38;5;241m=\u001B[39m sseclient\u001B[38;5;241m.\u001B[39mSSEClient(response)\n\u001B[0;32m---> 32\u001B[0m \u001B[43m\u001B[49m\u001B[38;5;28;43;01mfor\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mevent\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;129;43;01min\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mclient\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mevents\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\u001B[43m:\u001B[49m\n\u001B[1;32m 33\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;28;43;01mtry\u001B[39;49;00m\u001B[43m:\u001B[49m\n\u001B[1;32m 34\u001B[0m \u001B[43m \u001B[49m\u001B[43mjobs\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m \u001B[49m\u001B[43mjson\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mloads\u001B[49m\u001B[43m(\u001B[49m\u001B[43mevent\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdata\u001B[49m\u001B[43m)\u001B[49m\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/sseclient/__init__.py:55\u001B[0m, in \u001B[0;36mSSEClient.events\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 54\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;21mevents\u001B[39m(\u001B[38;5;28mself\u001B[39m):\n\u001B[0;32m---> 55\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;28;43;01mfor\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mchunk\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;129;43;01min\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_read\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\u001B[43m:\u001B[49m\n\u001B[1;32m 56\u001B[0m \u001B[43m \u001B[49m\u001B[43mevent\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m \u001B[49m\u001B[43mEvent\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 57\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;66;43;03m# Split before decoding so splitlines() only uses \\r and \\n\u001B[39;49;00m\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/sseclient/__init__.py:45\u001B[0m, in \u001B[0;36mSSEClient._read\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 38\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"Read the incoming event source stream and yield event chunks.\u001B[39;00m\n\u001B[1;32m 39\u001B[0m \n\u001B[1;32m 40\u001B[0m \u001B[38;5;124;03mUnfortunately it is possible for some servers to decide to break an\u001B[39;00m\n\u001B[1;32m 41\u001B[0m \u001B[38;5;124;03mevent into multiple HTTP chunks in the response. It is thus necessary\u001B[39;00m\n\u001B[1;32m 42\u001B[0m \u001B[38;5;124;03mto correctly stitch together consecutive response chunks and find the\u001B[39;00m\n\u001B[1;32m 43\u001B[0m \u001B[38;5;124;03mSSE delimiter (empty new line) to yield full, correct event chunks.\"\"\"\u001B[39;00m\n\u001B[1;32m 44\u001B[0m data \u001B[38;5;241m=\u001B[39m \u001B[38;5;124mb\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m'\u001B[39m\n\u001B[0;32m---> 45\u001B[0m \u001B[43m\u001B[49m\u001B[38;5;28;43;01mfor\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mchunk\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;129;43;01min\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_event_source\u001B[49m\u001B[43m:\u001B[49m\n\u001B[1;32m 46\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;28;43;01mfor\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mline\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;129;43;01min\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mchunk\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43msplitlines\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m)\u001B[49m\u001B[43m:\u001B[49m\n\u001B[1;32m 47\u001B[0m \u001B[43m \u001B[49m\u001B[43mdata\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m+\u001B[39;49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m \u001B[49m\u001B[43mline\u001B[49m\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/requests/models.py:822\u001B[0m, in \u001B[0;36mResponse.iter_content.<locals>.generate\u001B[0;34m()\u001B[0m\n\u001B[1;32m 820\u001B[0m \u001B[38;5;28;01myield from\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mraw\u001B[38;5;241m.\u001B[39mstream(chunk_size, decode_content\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mTrue\u001B[39;00m)\n\u001B[1;32m 821\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m ProtocolError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[0;32m--> 822\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m ChunkedEncodingError(e)\n\u001B[1;32m 823\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m DecodeError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 824\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m ContentDecodingError(e)\n",
"\u001B[0;31mChunkedEncodingError\u001B[0m: Response ended prematurely"
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/requests/models.py:820\u001B[0m, in \u001B[0;36mResponse.iter_content.<locals>.generate\u001B[0;34m()\u001B[0m\n\u001B[1;32m 818\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mhasattr\u001B[39m(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mraw, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mstream\u001B[39m\u001B[38;5;124m\"\u001B[39m):\n\u001B[1;32m 819\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 820\u001B[0m \u001B[38;5;28;01myield from\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mraw\u001B[38;5;241m.\u001B[39mstream(chunk_size, decode_content\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mTrue\u001B[39;00m)\n\u001B[1;32m 821\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m ProtocolError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 822\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m ChunkedEncodingError(e)\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/response.py:1040\u001B[0m, in \u001B[0;36mHTTPResponse.stream\u001B[0;34m(self, amt, decode_content)\u001B[0m\n\u001B[1;32m 1024\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 1025\u001B[0m \u001B[38;5;124;03mA generator wrapper for the read() method. A call will block until\u001B[39;00m\n\u001B[1;32m 1026\u001B[0m \u001B[38;5;124;03m``amt`` bytes have been read from the connection or until the\u001B[39;00m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 1037\u001B[0m \u001B[38;5;124;03m 'content-encoding' header.\u001B[39;00m\n\u001B[1;32m 1038\u001B[0m \u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 1039\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mchunked \u001B[38;5;129;01mand\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39msupports_chunked_reads():\n\u001B[0;32m-> 1040\u001B[0m \u001B[38;5;28;01myield from\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mread_chunked(amt, decode_content\u001B[38;5;241m=\u001B[39mdecode_content)\n\u001B[1;32m 1041\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1042\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m is_fp_closed(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_fp) \u001B[38;5;129;01mor\u001B[39;00m \u001B[38;5;28mlen\u001B[39m(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_decoded_buffer) \u001B[38;5;241m>\u001B[39m \u001B[38;5;241m0\u001B[39m:\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/response.py:1184\u001B[0m, in \u001B[0;36mHTTPResponse.read_chunked\u001B[0;34m(self, amt, decode_content)\u001B[0m\n\u001B[1;32m 1181\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m\n\u001B[1;32m 1183\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;28;01mTrue\u001B[39;00m:\n\u001B[0;32m-> 1184\u001B[0m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_update_chunk_length\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 1185\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mchunk_left \u001B[38;5;241m==\u001B[39m \u001B[38;5;241m0\u001B[39m:\n\u001B[1;32m 1186\u001B[0m \u001B[38;5;28;01mbreak\u001B[39;00m\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/response.py:1108\u001B[0m, in \u001B[0;36mHTTPResponse._update_chunk_length\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 1106\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mchunk_left \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[1;32m 1107\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m\n\u001B[0;32m-> 1108\u001B[0m line \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_fp\u001B[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)\u001B[49m \u001B[38;5;66;03m# type: ignore[union-attr]\u001B[39;00m\n\u001B[1;32m 1109\u001B[0m line \u001B[38;5;241m=\u001B[39m line\u001B[38;5;241m.\u001B[39msplit(\u001B[38;5;124mb\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m;\u001B[39m\u001B[38;5;124m\"\u001B[39m, \u001B[38;5;241m1\u001B[39m)[\u001B[38;5;241m0\u001B[39m]\n\u001B[1;32m 1110\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n",
"File \u001B[0;32m/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/socket.py:707\u001B[0m, in \u001B[0;36mSocketIO.readinto\u001B[0;34m(self, b)\u001B[0m\n\u001B[1;32m 705\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;28;01mTrue\u001B[39;00m:\n\u001B[1;32m 706\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 707\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 708\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m timeout:\n\u001B[1;32m 709\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/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/ssl.py:1216\u001B[0m, in \u001B[0;36mSSLSocket.recv_into\u001B[0;34m(self, buffer, nbytes, flags)\u001B[0m\n\u001B[1;32m 1212\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 1213\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mValueError\u001B[39;00m(\n\u001B[1;32m 1214\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 1215\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-> 1216\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 1217\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1218\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/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/ssl.py:1072\u001B[0m, in \u001B[0;36mSSLSocket.read\u001B[0;34m(self, len, buffer)\u001B[0m\n\u001B[1;32m 1070\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[1;32m 1071\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-> 1072\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 1073\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1074\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": 12
"execution_count": 14
}
],
"metadata": {

42
testfunctions.ipynb
View File

@ -662,8 +662,8 @@
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-04-30T08:39:47.839505Z",
"start_time": "2025-04-30T08:39:47.810814Z"
"end_time": "2025-04-30T09:31:19.697284Z",
"start_time": "2025-04-30T09:31:19.678837Z"
}
},
"cell_type": "code",
@ -682,11 +682,11 @@
"# Build the nested parameters\n",
"rotation = RotationParameters(\n",
" omegaStart_deg=0.0,\n",
" omegaStep=0.1,\n",
" omegaStep=0.2,\n",
" phi=10.0,\n",
" chi=0.0,\n",
" numberOfImages=3600,\n",
" exposureTime_s=0.02\n",
" numberOfImages=1800,\n",
" exposureTime_s=0.01\n",
")\n",
"\n",
"#characterization = characterizationParameters(\n",
@ -718,9 +718,9 @@
" model=\"PILATUS4 2M\",\n",
" type=\"photon-counting\",\n",
" serialNumber=\"16684dscsd668468\",\n",
" detectorDistance_mm=95.0,\n",
" beamCenterX_px=512.0,\n",
" beamCenterY_px=512.0,\n",
" detectorDistance_mm=232.0,\n",
" beamCenterX_px=768.0,\n",
" beamCenterY_px=857.0,\n",
" pixelSizeX_um=150.0,\n",
" pixelSizeY_um=150.0,\n",
")\n",
@ -729,11 +729,11 @@
" synchrotron=\"Swiss Light Source\",\n",
" beamline=\"PXIII\",\n",
" detector=detector_data,\n",
" wavelength=1.0,\n",
" ringCurrent_A=0.0,\n",
" ringMode=\"Machine Down\",\n",
" wavelength=1.033,\n",
" ringCurrent_A=0.4,\n",
" ringMode=\"Machine Development\",\n",
" monochromator=\"Si111\",\n",
" transmission=1.00,\n",
" transmission=10.00,\n",
" focusingOptic=\"Kirkpatrick-Baez\",\n",
" beamlineFluxAtSample_ph_s=0,\n",
" beamSizeWidth=30.0,\n",
@ -780,7 +780,7 @@
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n",
"/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",
" warnings.warn(\n",
"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/204/experiment_parameters HTTP/1.1\" 200 893\n"
"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/204/experiment_parameters HTTP/1.1\" 200 904\n"
]
},
{
@ -788,17 +788,17 @@
"output_type": "stream",
"text": [
"API Response:\n",
"run_number=2 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=2\n"
"run_number=4 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=232.0, beam_center_x_px=768.0, beam_center_y_px=857.0, pixel_size_x_um=150.0, pixel_size_y_um=150.0), wavelength=1.033, ring_current_a=0.4, ring_mode='Machine Development', undulator=None, undulatorgap_mm=None, monochromator='Si111', transmission=10.0, 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=0.2, chi=0.0, phi=10.0, number_of_images=1800, exposure_time_s=0.01), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) dataset=None sample_id=204 id=6\n"
]
}
],
"execution_count": 6
"execution_count": 18
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-04-30T08:41:33.591843Z",
"start_time": "2025-04-30T08:41:33.571527Z"
"end_time": "2025-04-30T09:31:29.122855Z",
"start_time": "2025-04-30T09:31:29.103718Z"
}
},
"cell_type": "code",
@ -806,7 +806,7 @@
"from datetime import datetime\n",
"\n",
"sample_id = sample_id\n",
"run_id = 2\n",
"run_id = 6\n",
"\n",
"def test_mark_run_written(sample_id, run_id, configuration):\n",
" # Prepare your dataset dict as required by your API (.dict() results if using Pydantic model)\n",
@ -840,7 +840,7 @@
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n",
"/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",
" warnings.warn(\n",
"DEBUG:urllib3.connectionpool:https://localhost:8000 \"PATCH /samples/update-dataset/204/2 HTTP/1.1\" 200 1074\n"
"DEBUG:urllib3.connectionpool:https://localhost:8000 \"PATCH /samples/update-dataset/204/6 HTTP/1.1\" 200 1085\n"
]
},
{
@ -848,11 +848,11 @@
"output_type": "stream",
"text": [
"Dataset updated successfully:\n",
"run_number=2 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, 30, 10, 41, 33, 572938)) sample_id=204 id=2\n"
"run_number=4 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=232.0, beam_center_x_px=768.0, beam_center_y_px=857.0, pixel_size_x_um=150.0, pixel_size_y_um=150.0), wavelength=1.033, ring_current_a=0.4, ring_mode='Machine Development', undulator=None, undulatorgap_mm=None, monochromator='Si111', transmission=10.0, 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=0.2, chi=0.0, phi=10.0, number_of_images=1800, exposure_time_s=0.01), 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, 30, 11, 31, 29, 105136)) sample_id=204 id=6\n"
]
}
],
"execution_count": 8
"execution_count": 19
},
{
"metadata": {