gotthard_g/aaredb
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
aaredb/testfunctions.ipynb
GotthardG 4328b84795 Add beamtime relationships and enhance sample handling 
This commit adds relationships to link Pucks and Samples to Beamtime in the models, enabling better data association. Includes changes to assign beamtime IDs during data generation and updates in API response models for improved data loading. Removed redundant code in testfunctions.ipynb to clean up the notebook.
2025-05-06 11:28:36 +02:00

1130 lines
62 KiB
Plaintext
Raw Blame History

{
"cells": [
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:24:28.514707Z",
"start_time": "2025-05-05T13:24:27.932416Z"
}
},
"cell_type": "code",
"source": [
"import json\n",
"import requests\n",
"#from nbclient.client import timestamp\n",
"\n",
"import backend.aareDBclient as aareDBclient\n",
"from aareDBclient.rest import ApiException\n",
"from pprint import pprint\n",
"\n",
"from app.schemas import characterizationParameters, ResultCreate, BeamtimeCreate\n",
"\n",
"#from app.data.data import sample\n",
"\n",
"#from aareDBclient import SamplesApi, ShipmentsApi, PucksApi\n",
"#from aareDBclient.models import SampleEventCreate, SetTellPosition\n",
"#from examples.examples import api_response\n",
"\n",
"print(aareDBclient.__version__)\n",
"\n",
"configuration = aareDBclient.Configuration(\n",
" #host = \"https://mx-aare-test.psi.ch:1492\"\n",
" host = \"https://localhost:8000\"\n",
")\n",
"\n",
"# 1. Get the token\n",
"login_resp = requests.post(\n",
" \"https://localhost:8000/auth/token/login\",\n",
" data={\"username\": \"testuser\", \"password\": \"testpass\"},\n",
" verify=False # Only for self-signed/dev certs!\n",
")\n",
"\n",
"token = login_resp.json()[\"access_token\"]\n",
"\n",
"print(configuration.host)\n",
"\n",
"configuration.verify_ssl = False # Disable SSL verification\n",
"#print(dir(SamplesApi))"
],
"id": "3b7c27697a4d5c83",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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 /auth/token/login HTTP/1.1\" 200 233\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.1.1a2\n",
"https://localhost:8000\n"
]
}
],
"execution_count": 1
},
{
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"## Fetch all Shipments, list corresponding dewars and pucks\n",
"\n",
"from datetime import date, datetime\n",
"from aareDBclient import ShipmentsApi, SamplesApi, GridScanParamers\n",
"from aareDBclient.models import Shipment\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" api_instance = aareDBclient.ShipmentsApi(api_client)\n",
"\n",
" try:\n",
" # Fetch all shipments\n",
" all_shipments_response = api_instance.fetch_shipments_shipments_get()\n",
"\n",
" # Print shipment names and their associated puck names\n",
" for shipment in all_shipments_response:\n",
" print(f\"Shipment ID: {shipment.id}, Shipment Name: {shipment.shipment_name}\")\n",
" if hasattr(shipment, 'dewars') and shipment.dewars: # Ensure 'dewars' exists\n",
" for dewar in shipment.dewars:\n",
" print(f\" Dewar ID: {dewar.id}, Dewar Name: {dewar.dewar_name}, Dewar Unique ID: {dewar.unique_id} \")\n",
"\n",
" if hasattr(dewar, 'pucks') and dewar.pucks: # Ensure 'pucks' exists\n",
" for puck in dewar.pucks:\n",
" print(f\" Puck ID: {puck.id}, Puck Name: {puck.puck_name}\")\n",
" else:\n",
" print(\" No pucks found in this dewar.\")\n",
" else:\n",
" print(\" No dewars found in this shipment.\")\n",
"\n",
" except ApiException as e:\n",
" print(f\"Exception when calling ShipmentsApi->fetch_shipments_shipments_get: {e}\")\n"
],
"id": "4955b858f2cef93e"
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-02-25T15:47:34.956061Z",
"start_time": "2025-02-25T15:47:34.941372Z"
}
},
"cell_type": "code",
"source": [
"from datetime import date\n",
"from aareDBclient import LogisticsApi\n",
"from aareDBclient.models import LogisticsEventCreate # Import required model\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" api_instance = aareDBclient.LogisticsApi(api_client)\n",
"\n",
" try:\n",
" # Create payload using the required model\n",
" logistics_event_create = LogisticsEventCreate(\n",
" dewar_qr_code='923db239427869be',\n",
" location_qr_code='A2-X06SA',\n",
" transaction_type='incoming',\n",
" timestamp=date.today() # Adjust if the API expects datetime\n",
" )\n",
"\n",
" # Pass the payload to the API function\n",
" api_response = api_instance.scan_dewar_logistics_dewar_scan_post(\n",
" logistics_event_create=logistics_event_create # Pass as an object\n",
" )\n",
" print(\"API Response:\", api_response)\n",
"\n",
" except ApiException as e:\n",
" print(f\"Exception when calling LogisticsApi->scan_dewar_logistics_dewar_scan_post: {e}\")\n",
"\n",
" try:\n",
" # Create payload using the required model\n",
" logistics_event_create = LogisticsEventCreate(\n",
" dewar_qr_code='923db239427869be',\n",
" location_qr_code='A2-X06SA',\n",
" transaction_type='refill',\n",
" timestamp=date.today() # Adjust if the API expects datetime\n",
" )\n",
"\n",
" # Pass the payload to the API function\n",
" api_response = api_instance.scan_dewar_logistics_dewar_scan_post(\n",
" logistics_event_create=logistics_event_create # Pass as an object\n",
" )\n",
" print(\"API Response:\", api_response)\n",
"\n",
" except ApiException as e:\n",
" print(f\"Exception when calling LogisticsApi->scan_dewar_logistics_dewar_scan_post: {e}\")\n",
"\n",
" try:\n",
" # Create payload using the required model\n",
" logistics_event_create = LogisticsEventCreate(\n",
" dewar_qr_code='923db239427869be',\n",
" location_qr_code='X06DA-Beamline',\n",
" transaction_type='beamline',\n",
" timestamp=date.today() # Adjust if the API expects datetime\n",
" )\n",
"\n",
" # Pass the payload to the API function\n",
" api_response = api_instance.scan_dewar_logistics_dewar_scan_post(\n",
" logistics_event_create=logistics_event_create # Pass as an object\n",
" )\n",
" print(\"API Response:\", api_response)\n",
"\n",
" except ApiException as e:\n",
" print(f\"Exception when calling LogisticsApi->scan_dewar_logistics_dewar_scan_post: {e}\")\n"
],
"id": "8fd3638bffaecd23",
"outputs": [
{
"ename": "TypeError",
"evalue": "ApiClient.call_api() got an unexpected keyword argument 'path_params'",
"output_type": "error",
"traceback": [
"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
"\u001B[0;31mTypeError\u001B[0m Traceback (most recent call last)",
"Cell \u001B[0;32mIn[43], line 19\u001B[0m\n\u001B[1;32m 15\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[1;32m 16\u001B[0m \u001B[38;5;28;01mwith\u001B[39;00m \u001B[38;5;28mopen\u001B[39m(file_path, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mrb\u001B[39m\u001B[38;5;124m\"\u001B[39m) \u001B[38;5;28;01mas\u001B[39;00m file_data:\n\u001B[1;32m 17\u001B[0m \u001B[38;5;66;03m# Use the low-level call_api method; note that the files parameter here is\u001B[39;00m\n\u001B[1;32m 18\u001B[0m \u001B[38;5;66;03m# a dictionary with key matching the FastAPI parameter name.\u001B[39;00m\n\u001B[0;32m---> 19\u001B[0m response \u001B[38;5;241m=\u001B[39m \u001B[43mapi_client\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mcall_api\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 20\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;124;43mf\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43m/\u001B[39;49m\u001B[38;5;132;43;01m{\u001B[39;49;00m\u001B[43msample_id\u001B[49m\u001B[38;5;132;43;01m}\u001B[39;49;00m\u001B[38;5;124;43m/upload_images\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m,\u001B[49m\n\u001B[1;32m 21\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mPOST\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m,\u001B[49m\n\u001B[1;32m 22\u001B[0m \u001B[43m \u001B[49m\u001B[43mpath_params\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m{\u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43msample_id\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m:\u001B[49m\u001B[43m \u001B[49m\u001B[43msample_id\u001B[49m\u001B[43m}\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 23\u001B[0m \u001B[43m \u001B[49m\u001B[43mfiles\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m{\u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43muploaded_file\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m:\u001B[49m\u001B[43m \u001B[49m\u001B[43m(\u001B[49m\u001B[43mfilename\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mfile_data\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mmime_type\u001B[49m\u001B[43m)\u001B[49m\u001B[43m}\u001B[49m\n\u001B[1;32m 24\u001B[0m \u001B[43m \u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 25\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mAPI Response:\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 26\u001B[0m \u001B[38;5;28mprint\u001B[39m(response)\n",
"\u001B[0;31mTypeError\u001B[0m: ApiClient.call_api() got an unexpected keyword argument 'path_params'"
]
}
],
"execution_count": 43
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-04-28T14:36:56.694422Z",
"start_time": "2025-04-28T14:36:56.656426Z"
}
},
"cell_type": "code",
"source": [
"# Get a list of pucks that are \"at the beamline\"\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" # Create an instance of the API class\n",
" api_instance = aareDBclient.PucksApi(api_client)\n",
" get_pucks_at_beamline = aareDBclient.PucksApi(api_client)\n",
"\n",
" try:\n",
" # Create Return Address\n",
" api_response = api_instance.get_pucks_by_slot_pucks_slot_slot_identifier_get(slot_identifier='X06DA')\n",
" print(\"The response of PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get:\\n\")\n",
" pprint(api_response)\n",
"\n",
" except ApiException as e:\n",
" print(\"Exception when calling PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get: %s\\n\" % e)"
],
"id": "9cf3457093751b61",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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:1097: 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 \"GET /pucks/slot/X06DA HTTP/1.1\" 200 693\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"The response of PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get:\n",
"\n",
"[PuckWithTellPosition(id=27, puck_name='PKK004', puck_type='Unipuck', puck_location_in_dewar=4, dewar_id=5, dewar_name='Dewar Five', pgroup='p20003', samples=None, tell_position=None),\n",
" PuckWithTellPosition(id=28, puck_name='PKK005', puck_type='Unipuck', puck_location_in_dewar=5, dewar_id=5, dewar_name='Dewar Five', pgroup='p20003', samples=None, tell_position=None),\n",
" PuckWithTellPosition(id=29, puck_name='PKK006', puck_type='Unipuck', puck_location_in_dewar=6, dewar_id=5, dewar_name='Dewar Five', pgroup='p20003', samples=None, tell_position=None),\n",
" PuckWithTellPosition(id=30, puck_name='PKK007', puck_type='Unipuck', puck_location_in_dewar=7, dewar_id=5, dewar_name='Dewar Five', pgroup='p20003', samples=None, tell_position=None)]\n"
]
}
],
"execution_count": 3
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-04-28T14:37:09.989924Z",
"start_time": "2025-04-28T14:37:09.960196Z"
}
},
"cell_type": "code",
"source": [
"from aareDBclient import SetTellPosition, SetTellPositionRequest\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" # Create an instance of the API class\n",
" api_instance = aareDBclient.PucksApi(api_client)\n",
"\n",
" # Payload with SetTellPosition objects\n",
" payload = SetTellPositionRequest(\n",
" tell=\"X06DA\",\n",
" #pucks=[\n",
" # SetTellPosition(puck_name='PSIMX074', segment='B', puck_in_segment=1),\n",
" # SetTellPosition(puck_name='PSIMX080', segment='B', puck_in_segment=2),\n",
" # SetTellPosition(puck_name='PSIMX081', segment='C', puck_in_segment=3),\n",
" # SetTellPosition(puck_name='PSIMX084', segment='C', puck_in_segment=4),\n",
" # SetTellPosition(puck_name='PSIMX104', segment='E', puck_in_segment=5),\n",
" # SetTellPosition(puck_name='PSIMX107', segment='E', puck_in_segment=1),\n",
" # SetTellPosition(puck_name='PSIMX117', segment='F', puck_in_segment=2),\n",
" #]\n",
" #pucks=[\n",
" # SetTellPosition(puck_name='PSIMX074', segment='F', puck_in_segment=1),\n",
" # SetTellPosition(puck_name='PSIMX080', segment='F', puck_in_segment=2),\n",
" # SetTellPosition(puck_name='PSIMX107', segment='A', puck_in_segment=1),\n",
" # SetTellPosition(puck_name='PSIMX117', segment='A', puck_in_segment=2),\n",
" #]\n",
" pucks=[\n",
" SetTellPosition(puck_name='PKK006', segment='F', puck_in_segment=1),\n",
" SetTellPosition(puck_name='PKK005', segment='F', puck_in_segment=2),\n",
" SetTellPosition(puck_name='PKK007', segment='A', puck_in_segment=1),\n",
" SetTellPosition(puck_name='PKK004', segment='A', puck_in_segment=2),\n",
" ]\n",
" #pucks = []\n",
" )\n",
"\n",
" # Call the PUT method to update the tell_position\n",
" try:\n",
" api_response = api_instance.set_tell_positions_pucks_set_tell_positions_put(\n",
" set_tell_position_request=payload\n",
" ) # Pass the entire payload as a single parameter\n",
"\n",
" print(\"The response of PucksApi->pucks_puck_id_tell_position_put:\\n\")\n",
" pprint(api_response)\n",
"\n",
" except Exception as e:\n",
" print(f\"Exception when calling PucksApi: {e}\")\n"
],
"id": "37e3eac6760150ee",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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:1097: 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 \"PUT /pucks/set-tell-positions HTTP/1.1\" 200 601\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"The response of PucksApi->pucks_puck_id_tell_position_put:\n",
"\n",
"[{'message': 'Tell position updated successfully.',\n",
" 'new_position': 'F1',\n",
" 'previous_position': None,\n",
" 'puck_name': 'PKK006',\n",
" 'status': 'updated',\n",
" 'tell': 'X06DA'},\n",
" {'message': 'Tell position updated successfully.',\n",
" 'new_position': 'F2',\n",
" 'previous_position': None,\n",
" 'puck_name': 'PKK005',\n",
" 'status': 'updated',\n",
" 'tell': 'X06DA'},\n",
" {'message': 'Tell position updated successfully.',\n",
" 'new_position': 'A1',\n",
" 'previous_position': None,\n",
" 'puck_name': 'PKK007',\n",
" 'status': 'updated',\n",
" 'tell': 'X06DA'},\n",
" {'message': 'Tell position updated successfully.',\n",
" 'new_position': 'A2',\n",
" 'previous_position': None,\n",
" 'puck_name': 'PKK004',\n",
" 'status': 'updated',\n",
" 'tell': 'X06DA'}]\n"
]
}
],
"execution_count": 4
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-04-28T14:37:23.148869Z",
"start_time": "2025-04-28T14:37:23.115094Z"
}
},
"cell_type": "code",
"source": [
"# Get puck_id puck_name sample_id sample_name of pucks in the tell\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" # Create an instance of the API class\n",
" api_instance = aareDBclient.PucksApi(api_client)\n",
"\n",
" # GET request: Fetch all pucks in the tell\n",
" try:\n",
" # Call the API method to fetch pucks\n",
" all_pucks_response = api_instance.get_pucks_with_tell_position_pucks_with_tell_position_get(tell='X06DA')\n",
"\n",
" # Debug response structure by printing it in JSON format\n",
" formatted_response = json.dumps(\n",
" [p.to_dict() for p in all_pucks_response], # Assuming the API response can be converted to dicts\n",
" indent=4 # Use indentation for readability\n",
" )\n",
" #print(\"The response of PucksApi->get_all_pucks_in_tell (formatted):\\n\")\n",
" #print(formatted_response)\n",
"\n",
" # Iterate through each puck and print information\n",
" for p in all_pucks_response:\n",
" print(f\"Puck ID: {p.id}, Puck Name: {p.puck_name}\")\n",
"\n",
" ## Check if the puck has any samples\n",
" if hasattr(p, 'samples') and p.samples: # Ensure 'samples' attribute exists and is not empty\n",
" for sample in p.samples:\n",
" print(f\" Sample ID: {sample.id}, Sample Name: {sample.sample_name}, Position: {sample.position}, Mount count: {sample.mount_count}\")\n",
" else:\n",
" print(\" No samples found in this puck.\")\n",
"\n",
" except ApiException as e:\n",
" print(\"Exception when calling PucksApi->get_all_pucks_in_tell: %s\\n\" % e)"
],
"id": "51578d944878db6a",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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:1097: 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 \"GET /pucks/with-tell-position?tell=X06DA HTTP/1.1\" 200 7592\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Puck ID: 29, Puck Name: PKK006\n",
" Sample ID: 268, Sample Name: Sample268, Position: 13, Mount count: 0\n",
" Sample ID: 265, Sample Name: Sample265, Position: 3, Mount count: 0\n",
" Sample ID: 266, Sample Name: Sample266, Position: 4, Mount count: 0\n",
" Sample ID: 269, Sample Name: Sample269, Position: 16, Mount count: 0\n",
" Sample ID: 267, Sample Name: Sample267, Position: 6, Mount count: 0\n",
"Puck ID: 30, Puck Name: PKK007\n",
" Sample ID: 276, Sample Name: Sample276, Position: 15, Mount count: 0\n",
" Sample ID: 270, Sample Name: Sample270, Position: 1, Mount count: 0\n",
" Sample ID: 274, Sample Name: Sample274, Position: 6, Mount count: 0\n",
" Sample ID: 277, Sample Name: Sample277, Position: 16, Mount count: 0\n",
" Sample ID: 273, Sample Name: Sample273, Position: 5, Mount count: 0\n",
" Sample ID: 271, Sample Name: Sample271, Position: 2, Mount count: 0\n",
" Sample ID: 275, Sample Name: Sample275, Position: 7, Mount count: 0\n",
" Sample ID: 272, Sample Name: Sample272, Position: 4, Mount count: 0\n",
"Puck ID: 28, Puck Name: PKK005\n",
" Sample ID: 264, Sample Name: Sample264, Position: 11, Mount count: 0\n",
" Sample ID: 261, Sample Name: Sample261, Position: 6, Mount count: 0\n",
" Sample ID: 262, Sample Name: Sample262, Position: 7, Mount count: 0\n",
" Sample ID: 260, Sample Name: Sample260, Position: 5, Mount count: 0\n",
" Sample ID: 263, Sample Name: Sample263, Position: 9, Mount count: 0\n",
"Puck ID: 27, Puck Name: PKK004\n",
" Sample ID: 251, Sample Name: Sample251, Position: 3, Mount count: 0\n",
" Sample ID: 253, Sample Name: Sample253, Position: 7, Mount count: 0\n",
" Sample ID: 252, Sample Name: Sample252, Position: 4, Mount count: 0\n",
" Sample ID: 255, Sample Name: Sample255, Position: 9, Mount count: 0\n",
" Sample ID: 250, Sample Name: Sample250, Position: 2, Mount count: 0\n",
" Sample ID: 254, Sample Name: Sample254, Position: 8, Mount count: 0\n",
" Sample ID: 258, Sample Name: Sample258, Position: 14, Mount count: 0\n",
" Sample ID: 256, Sample Name: Sample256, Position: 12, Mount count: 0\n",
" Sample ID: 249, Sample Name: Sample249, Position: 1, Mount count: 0\n",
" Sample ID: 257, Sample Name: Sample257, Position: 13, Mount count: 0\n",
" Sample ID: 259, Sample Name: Sample259, Position: 16, Mount count: 0\n"
]
}
],
"execution_count": 5
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:31:12.902282Z",
"start_time": "2025-05-05T13:31:12.900432Z"
}
},
"cell_type": "code",
"source": "sample_id = 277",
"id": "54d4d46ca558e7b9",
"outputs": [],
"execution_count": 7
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:31:16.752616Z",
"start_time": "2025-05-05T13:31:16.720296Z"
}
},
"cell_type": "code",
"source": [
"from aareDBclient import SampleEventCreate\n",
"\n",
"# Create an event for a sample\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" # Instance of the API client\n",
" api_instance = aareDBclient.SamplesApi(api_client)\n",
" #sample_id=293\n",
" try:\n",
" # Define the payload with only `event_type`\n",
" sample_event_create = SampleEventCreate(\n",
" sample_id=sample_id,\n",
" #event_type=\"Centering\" # Valid event type\n",
" event_type=\"Collecting\" # Valid event type\n",
" )\n",
"\n",
" # Debug the payload before sending\n",
" print(\"Payload being sent to API:\")\n",
" print(sample_event_create.json()) # Ensure it matches `SampleEventCreate`\n",
"\n",
" # Call the API\n",
" api_response = api_instance.create_sample_event_samples_samples_sample_id_events_post(\n",
" sample_id=sample_id, # Ensure this matches a valid sample ID in the database\n",
" sample_event_create=sample_event_create\n",
" )\n",
"\n",
" print(\"API response:\")\n",
" #pprint(api_response)\n",
"\n",
" for p in api_response:\n",
" print(p)\n",
"\n",
" except ApiException as e:\n",
" print(\"Exception when calling post_sample_event:\")\n",
" print(f\"Status Code: {e.status}\")\n",
" if e.body:\n",
" print(f\"Error Details: {e.body}\")\n"
],
"id": "4a0665f92756b486",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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/277/events HTTP/1.1\" 200 413\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Payload being sent to API:\n",
"{\"event_type\":\"Collecting\"}\n",
"API response:\n",
"('id', 277)\n",
"('sample_name', 'Sample277')\n",
"('position', 15)\n",
"('puck_id', 30)\n",
"('crystalname', None)\n",
"('proteinname', None)\n",
"('positioninpuck', None)\n",
"('priority', None)\n",
"('comments', None)\n",
"('data_collection_parameters', None)\n",
"('events', [SampleEventResponse(event_type='Mounting', id=533, sample_id=277, timestamp=datetime.datetime(2025, 5, 4, 14, 9)), SampleEventResponse(event_type='Collecting', id=534, sample_id=277, timestamp=datetime.datetime(2025, 5, 5, 13, 31, 16, 741949))])\n",
"('mount_count', 0)\n",
"('unmount_count', 0)\n"
]
}
],
"execution_count": 8
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-04-29T14:27:46.730515Z",
"start_time": "2025-04-29T14:27:46.622922Z"
}
},
"cell_type": "code",
"source": [
"### not working\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" # Create an instance of the Samples API class\n",
" api_instance = aareDBclient.SamplesApi(api_client)\n",
"\n",
" try:\n",
" # Get the last sample event\n",
" last_event_response = api_instance.get_last_sample_event_samples_samples_sample_id_events_last_get(27)\n",
" print(\"The response of get_last_sample_event:\\n\")\n",
" pprint(last_event_response)\n",
"\n",
" except ApiException as e:\n",
" print(\"Exception when calling get_last_sample_event: %s\\n\" % e)\n"
],
"id": "f1d171700d6cf7fe",
"outputs": [
{
"ename": "AttributeError",
"evalue": "'SamplesApi' object has no attribute 'get_last_sample_event_samples_samples_sample_id_events_last_get'",
"output_type": "error",
"traceback": [
"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
"\u001B[0;31mAttributeError\u001B[0m Traceback (most recent call last)",
"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",
"\u001B[0;31mAttributeError\u001B[0m: 'SamplesApi' object has no attribute 'get_last_sample_event_samples_samples_sample_id_events_last_get'"
]
}
],
"execution_count": 48
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:31:21.833174Z",
"start_time": "2025-05-05T13:31:21.791711Z"
}
},
"cell_type": "code",
"source": [
"# Post multiple images to the sample database\n",
"\n",
"import os\n",
"import mimetypes\n",
"import requests\n",
"\n",
"# List of file paths to the images you want to upload\n",
"#file_paths = [\n",
"# \"backend/tests/sample_image/0_200.jpg\",\n",
"# \"backend/tests/sample_image/90_200.jpg\",\n",
"# \"backend/tests/sample_image/0_700.jpg\",\n",
"# \"backend/tests/sample_image/90_700.jpg\",\n",
"#]\n",
"\n",
"#file_paths = [\"backend/tests/sample_image/mount.jpeg.jpg\"]\n",
"\n",
"#file_paths = [\n",
"# \"backend/tests/sample_image/bb_raster_90.jpg\"\n",
"#]\n",
"\n",
"file_paths = [\"backend/tests/sample_image/after_dc.jpeg.jpg\"]\n",
"\n",
"\n",
"\n",
"# Base URL for the upload endpoint\n",
"url = f\"https://127.0.0.1:8000/samples/{sample_id}/upload-images\"\n",
"\n",
"# Iterate through each file and upload it\n",
"for file_path in file_paths:\n",
" # Determine file name and MIME type\n",
" filename = os.path.basename(file_path)\n",
" mime_type, _ = mimetypes.guess_type(file_path)\n",
" if mime_type is None:\n",
" mime_type = \"application/octet-stream\"\n",
"\n",
" # Open the file for uploading\n",
" with open(file_path, \"rb\") as file_data:\n",
" files = {\n",
" # Use key \"uploaded_file\" as required by your API\n",
" \"uploaded_file\": (filename, file_data, mime_type)\n",
" }\n",
" headers = {\n",
" \"accept\": \"application/json\"\n",
" }\n",
"\n",
" # Send the POST request\n",
" print(f\"Uploading {filename}...\")\n",
" response = requests.post(url, headers=headers, files=files, verify=False)\n",
"\n",
" # Check the API response\n",
" print(f\"API Response for {filename}:\")\n",
" print(response.status_code)\n",
" try:\n",
" print(response.json())\n",
" except Exception:\n",
" print(response.text)\n"
],
"id": "11f62976d2e7d9b1",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): 127.0.0.1:8000\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 '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",
"DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/277/upload-images HTTP/1.1\" 200 205\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Uploading after_dc.jpeg.jpg...\n",
"API Response for after_dc.jpeg.jpg:\n",
"200\n",
"{'pgroup': 'p20003', 'sample_id': 277, 'sample_event_id': 534, 'filepath': 'images/p20003/2025-05-05/Dewar Five/PKK007/15/Collecting_2025-05-05_13-31-16/after_dc.jpeg.jpg', 'status': 'active', 'comment': None, 'id': 1}\n"
]
}
],
"execution_count": 9
},
{
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": "help(api_instance.upload_sample_images_samples_samples_sample_id_upload_images_post)",
"id": "cb1b99e6327fff84"
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:34:32.164108Z",
"start_time": "2025-05-05T13:34:32.130230Z"
}
},
"cell_type": "code",
"source": [
"# post experiment results to sample database\n",
"\n",
"from aareDBclient.models import (\n",
" ExperimentParametersCreate,\n",
" RotationParameters,\n",
" BeamlineParameters,\n",
" GridScanParamers,\n",
" Detector\n",
")\n",
"\n",
"\n",
"# Build the nested parameters\n",
"rotation = RotationParameters(\n",
" omegaStart_deg=0.0,\n",
" omegaStep=0.2,\n",
" phi=10.0,\n",
" chi=0.0,\n",
" numberOfImages=1800,\n",
" exposureTime_s=0.01\n",
")\n",
"\n",
"#characterization = characterizationParameters(\n",
"# omegaStart_deg=0.0,\n",
"# omegaStep=90.0,\n",
"# oscillation_deg=1.0,\n",
"# phi=10.0,\n",
"# chi=0.0,\n",
"# numberOfImages=4,\n",
"# exposureTime_s=0.02\n",
"#)\n",
"\n",
"#gridscan = GridScanParamers(\n",
"# xStart=90.0,\n",
"# xStep=0.1,\n",
"# yStart=0.0,\n",
"# yStep= 0.1,\n",
"# zStart=0.0,\n",
"# zStep=0.0,\n",
"# numberOfImages=4600,\n",
"# exposureTime_s=0.001\n",
"#)\n",
"\n",
"# If your client code requires you to build a detector model,\n",
"# you can either use a Detector model or pass a dictionary.\n",
"# Here we pass a dictionary.\n",
"detector_data = Detector(\n",
" manufacturer=\"DECTRIS\",\n",
" model=\"PILATUS4 2M\",\n",
" type=\"photon-counting\",\n",
" serialNumber=\"16684dscsd668468\",\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",
"\n",
"beamline_params = BeamlineParameters(\n",
" synchrotron=\"Swiss Light Source\",\n",
" beamline=\"PXIII\",\n",
" detector=detector_data,\n",
" wavelength=1.033,\n",
" ringCurrent_A=0.4,\n",
" ringMode=\"Machine Development\",\n",
" monochromator=\"Si111\",\n",
" transmission=10.00,\n",
" focusingOptic=\"Kirkpatrick-Baez\",\n",
" beamlineFluxAtSample_ph_s=0,\n",
" beamSizeWidth=30.0,\n",
" beamSizeHeight=30.0,\n",
" #characterization=characterization\n",
" rotation=rotation # Optional nested parameter\n",
" #gridScan=gridscan\n",
" # gridScan and jet are optional and can be added similarly\n",
")\n",
"\n",
"# Prepare the experiment parameters payload.\n",
"# Note that the run_number will be set on the server side, so you can leave\n",
"# it out or set it to a dummy value if your client model requires it.\n",
"experiment_params_payload = ExperimentParametersCreate(\n",
" # run_number can be omitted/ignored if computed on the server\n",
" type=\"standard\",\n",
" beamline_parameters=beamline_params,\n",
" sample_id=sample_id # change sample_id to an existing sample in your database\n",
")\n",
"\n",
"# Now, use the API instance to send the POST request\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" api_instance = aareDBclient.SamplesApi(api_client)\n",
"\n",
" try:\n",
" # Call the endpoint. The endpoint path expects the sample_id.\n",
" api_response = api_instance.create_experiment_parameters_for_sample(\n",
" sample_id=experiment_params_payload.sample_id,\n",
" experiment_parameters_create=experiment_params_payload\n",
")\n",
"\n",
" print(\"API Response:\")\n",
" print(api_response)\n",
" except ApiException as e:\n",
" print(\"Exception when calling ExperimentParametersApi->create_experiment_parameters_for_sample:\")\n",
" print(e)\n"
],
"id": "421ba0710f29a5fa",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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/277/experiment_parameters HTTP/1.1\" 200 904\n"
]
},
{
"name": "stdout",
"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=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=277 id=2\n"
]
}
],
"execution_count": 13
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:34:49.891432Z",
"start_time": "2025-05-05T13:34:49.872697Z"
}
},
"cell_type": "code",
"source": [
"from datetime import datetime\n",
"\n",
"sample_id = sample_id\n",
"run_id = 2\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",
" dataset_payload = {\n",
" \"filepath\": \"/das/work/p11/p11206/raw_data/vincent/20250415_6D_SLS2_1st_data/20250415_fullbeam_dtz220_Lyso102_again_360deg\",\n",
" \"status\": \"written\",\n",
" \"written_at\": datetime.now().isoformat()\n",
" }\n",
"\n",
" # The API method and argument names may differ if autogenerated — adjust accordingly\n",
" with aareDBclient.ApiClient(configuration) as api_client:\n",
" api_instance = aareDBclient.SamplesApi(api_client)\n",
" try:\n",
" api_response = api_instance.update_dataset_for_experiment_run(\n",
" sample_id=sample_id, run_id=run_id, datasets=dataset_payload\n",
" )\n",
" print(\"Dataset updated successfully:\")\n",
" print(api_response)\n",
" except ApiException as e:\n",
" print(f\"API call failed: {e}\")\n",
"\n",
"# Usage example (replace with your actual IDs and configuration):\n",
"test_mark_run_written(sample_id, run_id, configuration)"
],
"id": "77793ecd843c1ef3",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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/277/2 HTTP/1.1\" 200 1085\n"
]
},
{
"name": "stdout",
"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=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, 5, 5, 15, 34, 49, 874526)) sample_id=277 id=2\n"
]
}
],
"execution_count": 15
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T14:38:32.418132Z",
"start_time": "2025-05-05T14:38:32.370685Z"
}
},
"cell_type": "code",
"source": [
"from app.schemas import CurvePoint\n",
"# %%\n",
"from app.schemas import ResultCreate, Results\n",
"from pprint import pprint\n",
"import random\n",
"import math\n",
"import aareDBclient\n",
"from aareDBclient.rest import ApiException\n",
"\n",
"# Your actual sample and experiment IDs\n",
"sample_id = sample_id # Replace with valid IDs\n",
"status = \"successful\"\n",
"run_id = 2 # Replace with valid run_id\n",
"\n",
"# Function to generate list of CurvePoint (resolution, value pairs)\n",
"def logarithmic_decay_curve(length, min_res=4.0, max_res=1.0, max_value=1.0, min_value=0.0, noise=0.005, decimals=3):\n",
" resolutions = sorted([round(random.uniform(min_res, max_res), decimals) for _ in range(length)], reverse=True) # Reverse order\n",
"\n",
" curve = []\n",
" for res in resolutions:\n",
" # Exponential-like decay: Higher resolution (small number) -> value ~1, Lower resolution (big number) -> value ~0\n",
" decay_factor = (res - max_res) / (min_res - max_res) # Normalize res to [0,1]\n",
" value = max_value - ( math.exp(- 20 * decay_factor ) ) # Exponential decay\n",
"\n",
" # Add small random noise for realism\n",
" noise_value = random.uniform(-noise, noise)\n",
" value = min(max(value + noise_value, min_value), max_value) # Clamp between min_value and max_value\n",
"\n",
" curve.append(CurvePoint(resolution=res, value=round(value, decimals)))\n",
"\n",
" return curve\n",
"\n",
"# Create random Results payload\n",
"results_data = Results(\n",
" pipeline=\"autoproc\",\n",
" status=status,\n",
" resolution=round(random.uniform(1.0, 4.0), 2),\n",
" unit_cell=f\"{random.uniform(20, 120):.2f}, {random.uniform(20, 120):.2f}, \"\n",
" f\"{random.uniform(20, 120):.2f}, {random.uniform(60, 120):.2f}, \"\n",
" f\"{random.uniform(60, 120):.2f}, {random.uniform(60, 120):.2f}\",\n",
" spacegroup=random.choice(['P212121', 'C2', 'P1', 'P21', 'P21212', 'P41212']),\n",
" rmerge=round(random.uniform(0.02, 0.10), 3),\n",
" rmeas=round(random.uniform(0.02, 0.15), 3),\n",
" isig=round(random.uniform(1.0, 30.0), 2),\n",
" cc=logarithmic_decay_curve(100), # List of CurvePoint for CC curve\n",
" cchalf=logarithmic_decay_curve(100), # List of CurvePoint for CC(1/2) curve\n",
" completeness=round(random.uniform(85.0, 100.0), 2),\n",
" multiplicity=round(random.uniform(1.0, 10.0), 2),\n",
" nobs=random.randint(10000, 500000),\n",
" total_refl=random.randint(5000, 250000),\n",
" unique_refl=random.randint(5000, 100000),\n",
" comments=\"Random auto-generated test entry\"\n",
")\n",
"\n",
"payload = ResultCreate(sample_id=sample_id, run_id=run_id, result=results_data, status=status)\n",
"\n",
"# correct serialization, passing exact required dict structure\n",
"payload_dict = {\n",
" \"sample_id\": sample_id,\n",
" \"run_id\": run_id,\n",
" \"status\": status,\n",
" \"result\": results_data.model_dump(),\n",
"}\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" api_instance = aareDBclient.SamplesApi(api_client)\n",
"\n",
" try:\n",
" api_response = api_instance.create_result(\n",
" result_create=payload_dict\n",
" )\n",
"\n",
" print(\"API call successful:\")\n",
" pprint(api_response)\n",
"\n",
" except ApiException as e:\n",
" print(f\"API call failed: {e}\")\n"
],
"id": "3e3974d5df795c32",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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/processing-results HTTP/1.1\" 200 7213\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"API call successful:\n",
"ResultResponse(id=5, status='successful', sample_id=277, run_id=2, result=Results(pipeline='autoproc', resolution=1.4, unit_cell='108.05, 108.47, 84.95, 78.67, 102.50, 78.68', spacegroup='P1', rmerge=0.033, rmeas=0.049, isig=3.77, cc=[CurvePoint(resolution=3.982, value=0.995), CurvePoint(resolution=3.944, value=0.998), CurvePoint(resolution=3.937, value=0.996), CurvePoint(resolution=3.87, value=0.999), CurvePoint(resolution=3.85, value=1.0), CurvePoint(resolution=3.841, value=1.0), CurvePoint(resolution=3.827, value=1.0), CurvePoint(resolution=3.775, value=1.0), CurvePoint(resolution=3.719, value=0.996), CurvePoint(resolution=3.718, value=0.998), CurvePoint(resolution=3.711, value=1.0), CurvePoint(resolution=3.688, value=0.998), CurvePoint(resolution=3.684, value=0.997), CurvePoint(resolution=3.679, value=0.998), CurvePoint(resolution=3.53, value=1.0), CurvePoint(resolution=3.518, value=0.999), CurvePoint(resolution=3.493, value=0.997), CurvePoint(resolution=3.456, value=1.0), CurvePoint(resolution=3.443, value=0.998), CurvePoint(resolution=3.416, value=1.0), CurvePoint(resolution=3.368, value=1.0), CurvePoint(resolution=3.334, value=1.0), CurvePoint(resolution=3.32, value=1.0), CurvePoint(resolution=3.287, value=1.0), CurvePoint(resolution=3.278, value=0.995), CurvePoint(resolution=3.26, value=0.999), CurvePoint(resolution=3.247, value=1.0), CurvePoint(resolution=3.225, value=0.995), CurvePoint(resolution=3.173, value=0.996), CurvePoint(resolution=3.17, value=0.998), CurvePoint(resolution=3.155, value=1.0), CurvePoint(resolution=3.019, value=1.0), CurvePoint(resolution=3.007, value=0.997), CurvePoint(resolution=3.005, value=1.0), CurvePoint(resolution=2.962, value=0.999), CurvePoint(resolution=2.954, value=1.0), CurvePoint(resolution=2.939, value=1.0), CurvePoint(resolution=2.935, value=1.0), CurvePoint(resolution=2.935, value=1.0), CurvePoint(resolution=2.93, value=1.0), CurvePoint(resolution=2.903, value=1.0), CurvePoint(resolution=2.889, value=0.997), CurvePoint(resolution=2.851, value=1.0), CurvePoint(resolution=2.721, value=1.0), CurvePoint(resolution=2.705, value=0.999), CurvePoint(resolution=2.671, value=0.997), CurvePoint(resolution=2.639, value=0.996), CurvePoint(resolution=2.536, value=1.0), CurvePoint(resolution=2.529, value=1.0), CurvePoint(resolution=2.509, value=1.0), CurvePoint(resolution=2.501, value=0.997), CurvePoint(resolution=2.485, value=0.998), CurvePoint(resolution=2.458, value=1.0), CurvePoint(resolution=2.454, value=1.0), CurvePoint(resolution=2.452, value=1.0), CurvePoint(resolution=2.438, value=0.998), CurvePoint(resolution=2.435, value=1.0), CurvePoint(resolution=2.402, value=1.0), CurvePoint(resolution=2.354, value=0.999), CurvePoint(resolution=2.345, value=1.0), CurvePoint(resolution=2.334, value=0.997), CurvePoint(resolution=2.331, value=1.0), CurvePoint(resolution=2.255, value=0.999), CurvePoint(resolution=2.229, value=1.0), CurvePoint(resolution=2.186, value=1.0), CurvePoint(resolution=2.128, value=1.0), CurvePoint(resolution=2.08, value=1.0), CurvePoint(resolution=2.004, value=0.999), CurvePoint(resolution=1.991, value=0.997), CurvePoint(resolution=1.981, value=0.997), CurvePoint(resolution=1.966, value=1.0), CurvePoint(resolution=1.951, value=0.996), CurvePoint(resolution=1.926, value=0.997), CurvePoint(resolution=1.915, value=0.996), CurvePoint(resolution=1.904, value=0.995), CurvePoint(resolution=1.889, value=0.994), CurvePoint(resolution=1.872, value=1.0), CurvePoint(resolution=1.825, value=0.995), CurvePoint(resolution=1.818, value=0.999), CurvePoint(resolution=1.811, value=0.991), CurvePoint(resolution=1.791, value=0.994), CurvePoint(resolution=1.722, value=0.992), CurvePoint(resolution=1.702, value=0.991), CurvePoint(resolution=1.696, value=0.993), CurvePoint(resolution=1.665, value=0.985), CurvePoint(resolution=1.648, value=0.987), CurvePoint(resolution=1.519, value=0.969), CurvePoint(resolution=1.467, value=0.954), CurvePoint(resolution=1.394, value=0.931), CurvePoint(resolution=1.365, value=0.914), CurvePoint(resolution=1.351, value=0.905), CurvePoint(resolution=1.338, value=0.895), CurvePoint(resolution=1.278, value=0.847), CurvePoint(resolution=1.233, value=0.79), CurvePoint(resolution=1.191, value=0.723), CurvePoint(resolution=1.187, value=0.715), CurvePoint(resolution=1.114, value=0.534), CurvePoint(resolution=1.107, value=0.514), CurvePoint(resolution=1.084, value=0.434), CurvePoint(resolution=1.038, value=0.229)], cchalf=[CurvePoint(resolution=3.994, value=0.999), CurvePoint(resolution=3.994, value=0.996), CurvePoint(resolution=3.986, value=1.0), CurvePoint(resolution=3.929, value=1.0), CurvePoint(resolution=3.926, value=1.0), CurvePoint(resolution=3.892, value=0.996), CurvePoint(resolution=3.797, value=1.0), CurvePoint(resolution=3.784, value=0.999), CurvePoint(resolution=3.7, value=0.998), CurvePoint(resolution=3.694, value=1.0), CurvePoint(resolution=3.66, value=0.998), CurvePoint(resolution=3.645, value=0.999), CurvePoint(resolution=3.601, value=1.0), CurvePoint(resolution=3.581, value=0.996), CurvePoint(resolution=3.555, value=1.0), CurvePoint(resolution=3.421, value=1.0), CurvePoint(resolution=3.421, value=1.0), CurvePoint(resolution=3.365, value=1.0), CurvePoint(resolution=3.339, value=0.999), CurvePoint(resolution=3.271, value=0.999), CurvePoint(resolution=3.261, value=1.0), CurvePoint(resolution=3.252, value=0.996), CurvePoint(resolution=3.22, value=0.995), CurvePoint(resolution=3.205, value=0.996), CurvePoint(resolution=3.179, value=0.999), CurvePoint(resolution=3.116, value=0.996), CurvePoint(resolution=3.073, value=0.998), CurvePoint(resolution=3.012, value=0.999), CurvePoint(resolution=2.999, value=0.999), CurvePoint(resolution=2.985, value=1.0), CurvePoint(resolution=2.98, value=1.0), CurvePoint(resolution=2.976, value=1.0), CurvePoint(resolution=2.927, value=0.996), CurvePoint(resolution=2.911, value=0.996), CurvePoint(resolution=2.855, value=1.0), CurvePoint(resolution=2.831, value=1.0), CurvePoint(resolution=2.827, value=1.0), CurvePoint(resolution=2.785, value=0.996), CurvePoint(resolution=2.778, value=0.999), CurvePoint(resolution=2.753, value=0.998), CurvePoint(resolution=2.716, value=1.0), CurvePoint(resolution=2.691, value=1.0), CurvePoint(resolution=2.677, value=0.995), CurvePoint(resolution=2.659, value=0.998), CurvePoint(resolution=2.646, value=1.0), CurvePoint(resolution=2.626, value=1.0), CurvePoint(resolution=2.532, value=0.996), CurvePoint(resolution=2.508, value=1.0), CurvePoint(resolution=2.507, value=0.999), CurvePoint(resolution=2.446, value=0.997), CurvePoint(resolution=2.439, value=0.997), CurvePoint(resolution=2.409, value=1.0), CurvePoint(resolution=2.404, value=0.995), CurvePoint(resolution=2.346, value=1.0), CurvePoint(resolution=2.332, value=1.0), CurvePoint(resolution=2.328, value=0.996), CurvePoint(resolution=2.309, value=0.996), CurvePoint(resolution=2.27, value=1.0), CurvePoint(resolution=2.193, value=0.997), CurvePoint(resolution=2.148, value=1.0), CurvePoint(resolution=2.143, value=1.0), CurvePoint(resolution=2.123, value=0.995), CurvePoint(resolution=2.109, value=1.0), CurvePoint(resolution=2.099, value=1.0), CurvePoint(resolution=2.051, value=1.0), CurvePoint(resolution=2.036, value=0.999), CurvePoint(resolution=2.035, value=0.995), CurvePoint(resolution=2.033, value=0.999), CurvePoint(resolution=1.996, value=1.0), CurvePoint(resolution=1.99, value=1.0), CurvePoint(resolution=1.988, value=1.0), CurvePoint(resolution=1.977, value=0.994), CurvePoint(resolution=1.934, value=0.997), CurvePoint(resolution=1.898, value=1.0), CurvePoint(resolution=1.856, value=0.994), CurvePoint(resolution=1.808, value=0.994), CurvePoint(resolution=1.755, value=0.993), CurvePoint(resolution=1.743, value=0.998), CurvePoint(resolution=1.735, value=0.991), CurvePoint(resolution=1.701, value=0.987), CurvePoint(resolution=1.687, value=0.992), CurvePoint(resolution=1.561, value=0.98), CurvePoint(resolution=1.538, value=0.975), CurvePoint(resolution=1.533, value=0.974), CurvePoint(resolution=1.456, value=0.956), CurvePoint(resolution=1.452, value=0.948), CurvePoint(resolution=1.419, value=0.938), CurvePoint(resolution=1.404, value=0.935), CurvePoint(resolution=1.371, value=0.919), CurvePoint(resolution=1.346, value=0.902), CurvePoint(resolution=1.315, value=0.876), CurvePoint(resolution=1.286, value=0.848), CurvePoint(resolution=1.266, value=0.833), CurvePoint(resolution=1.212, value=0.753), CurvePoint(resolution=1.21, value=0.75), CurvePoint(resolution=1.175, value=0.692), CurvePoint(resolution=1.172, value=0.678), CurvePoint(resolution=1.156, value=0.649), CurvePoint(resolution=1.147, value=0.625), CurvePoint(resolution=1.109, value=0.517)], completeness=97.29, multiplicity=5.3, nobs=189003, total_refl=140823, unique_refl=44561, comments='Random auto-generated test entry'))\n"
]
}
],
"execution_count": 27
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:24:47.091043Z",
"start_time": "2025-05-05T13:24:47.082140Z"
}
},
"cell_type": "code",
"source": [
"# get experiment results to sample database\n",
"\n",
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" # Create an instance of the API class\n",
" api_instance = aareDBclient.SamplesApi(api_client)\n",
"\n",
" # GET request: Fetch all pucks in the tell\n",
" try:\n",
" # Call the API method to fetch pucks\n",
" all_results_response = api_instance.get_sample_results_samples_results_get(active_pgroup=\"p20003\")\n",
" pprint(all_results_response)\n",
" ## Debug response structure by printing it in JSON format\n",
" #formatted_response = json.dumps(\n",
" # [p.to_dict() for p in all_results_response], # Assuming the API response can be converted to dicts\n",
" # indent=4 # Use indentation for readability\n",
" #)\n",
" #print(\"The response of PucksApi->get_all_pucks_in_tell (formatted):\\n\")\n",
" #print(formatted_response)\n",
"\n",
" ## Iterate through each puck and print information\n",
" #for p in all_results_response:\n",
" # print(f\"Puck ID: {p.id}, Puck Name: {p.puck_name}\")\n",
" #\n",
" # ## Check if the puck has any samples\n",
" # if hasattr(p, 'samples') and p.samples: # Ensure 'samples' attribute exists and is not empty\n",
" # for sample in p.samples:\n",
" # print(f\" Sample ID: {sample.id}, Sample Name: {sample.sample_name}, Position: {sample.position}, Mount count: {sample.mount_count}\")\n",
" # else:\n",
" # print(\" No samples found in this puck.\")\n",
" #\n",
" except ApiException as e:\n",
" print(\"Exception when calling PucksApi->get_all_pucks_in_tell: %s\\n\" % e)"
],
"id": "6079a4f10102e906",
"outputs": [
{
"ename": "AttributeError",
"evalue": "'SamplesApi' object has no attribute 'get_sample_results_samples_results_get'",
"output_type": "error",
"traceback": [
"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
"\u001B[0;31mAttributeError\u001B[0m Traceback (most recent call last)",
"Cell \u001B[0;32mIn[4], line 10\u001B[0m\n\u001B[1;32m 7\u001B[0m \u001B[38;5;66;03m# GET request: Fetch all pucks in the tell\u001B[39;00m\n\u001B[1;32m 8\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[1;32m 9\u001B[0m \u001B[38;5;66;03m# Call the API method to fetch pucks\u001B[39;00m\n\u001B[0;32m---> 10\u001B[0m all_results_response \u001B[38;5;241m=\u001B[39m \u001B[43mapi_instance\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget_sample_results_samples_results_get\u001B[49m(active_pgroup\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mp20003\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 11\u001B[0m pprint(all_results_response)\n\u001B[1;32m 12\u001B[0m \u001B[38;5;66;03m## Debug response structure by printing it in JSON format\u001B[39;00m\n\u001B[1;32m 13\u001B[0m \u001B[38;5;66;03m#formatted_response = json.dumps(\u001B[39;00m\n\u001B[1;32m 14\u001B[0m \u001B[38;5;66;03m# [p.to_dict() for p in all_results_response], # Assuming the API response can be converted to dicts\u001B[39;00m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 29\u001B[0m \u001B[38;5;66;03m# print(\" No samples found in this puck.\")\u001B[39;00m\n\u001B[1;32m 30\u001B[0m \u001B[38;5;66;03m#\u001B[39;00m\n",
"\u001B[0;31mAttributeError\u001B[0m: 'SamplesApi' object has no attribute 'get_sample_results_samples_results_get'"
]
}
],
"execution_count": 4
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-05-05T13:39:17.528508Z",
"start_time": "2025-05-05T13:39:17.496188Z"
}
},
"cell_type": "code",
"source": [
"with aareDBclient.ApiClient(configuration) as api_client:\n",
" api_client.default_headers[\"Authorization\"] = f\"Bearer {token}\"\n",
" api_instance = aareDBclient.BeamtimesApi(api_client)\n",
"\n",
"\n",
" payload = BeamtimeCreate(\n",
" pgroups = \"p20003\",\n",
" shift = \"morning\",\n",
" beamtime_name = \"unscheduled beamtime\",\n",
" beamline = \"X06DA\",\n",
" start_date = \"2025-05-05\",\n",
" end_date = \"2025-05-05\",\n",
" status = \"unscheduled\",\n",
" comments = \"unscheduled beamtime created by test functions\",\n",
" proposal_id = 1,\n",
" local_contact_id= 1\n",
" )\n",
"\n",
" try:\n",
" api_response = api_instance.create_beamtime_protected_beamtimes_post(payload.dict())\n",
" pprint(api_response)\n",
"\n",
" print(\"The response of BeamtimesApi->beamtime_create:\\n\")\n",
" pprint(api_response)\n",
"\n",
" except Exception as e:\n",
" print(f\"Exception when calling BeamtimesApi: {e}\")\n"
],
"id": "deff7388a205e169",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"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 /protected/beamtimes/ HTTP/1.1\" 400 66\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Exception when calling BeamtimesApi: (400)\n",
"Reason: Bad Request\n",
"HTTP response headers: HTTPHeaderDict({'date': 'Mon, 05 May 2025 13:39:16 GMT', 'server': 'uvicorn', 'content-length': '66', 'content-type': 'application/json'})\n",
"HTTP response body: {\"detail\":\"A beamtime for this pgroup/shift/date already exists.\"}\n",
"\n"
]
}
],
"execution_count": 18
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
Reference in New Issue View Git Blame Copy Permalink