Refine event types and update related models and logic
Standardized event types with stricter validation using `Literal`. Adjusted related data and logic to align with new types, including changes to PGROUP assignments, event timeline increments, and schema updates. Cleaned up unused code and clarified database initialization behavior.
This commit is contained in:
GotthardG
@ -3,8 +3,8 @@
|
||||
{
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2025-03-04T09:22:38.371102Z",
|
||||
"start_time": "2025-03-04T09:22:37.939673Z"
|
||||
"end_time": "2025-03-11T15:04:51.407218Z",
|
||||
"start_time": "2025-03-11T15:04:51.403058Z"
|
||||
}
|
||||
},
|
||||
"cell_type": "code",
|
||||
@ -41,12 +41,12 @@
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"0.1.0a24\n",
|
||||
"0.1.0a25\n",
|
||||
"https://127.0.0.1:8000\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"execution_count": 1
|
||||
"execution_count": 48
|
||||
},
|
||||
{
|
||||
"metadata": {},
|
||||
@ -328,8 +328,8 @@
|
||||
{
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2025-03-03T10:06:39.979358Z",
|
||||
"start_time": "2025-03-03T10:06:39.957359Z"
|
||||
"end_time": "2025-03-07T12:40:09.769132Z",
|
||||
"start_time": "2025-03-07T12:40:09.752103Z"
|
||||
}
|
||||
},
|
||||
"cell_type": "code",
|
||||
@ -369,48 +369,6 @@
|
||||
],
|
||||
"id": "51578d944878db6a",
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"Puck ID: 6, Puck Name: PUCK006\n",
|
||||
" Sample ID: 44, Sample Name: Sample044, Position: 2, Mount count: 1\n",
|
||||
" Sample ID: 45, Sample Name: Sample045, Position: 3, Mount count: 0\n",
|
||||
" Sample ID: 46, Sample Name: Sample046, Position: 4, Mount count: 0\n",
|
||||
" Sample ID: 47, Sample Name: Sample047, Position: 5, Mount count: 1\n",
|
||||
"Puck ID: 3, Puck Name: PUCK003\n",
|
||||
" Sample ID: 24, Sample Name: Sample024, Position: 1, Mount count: 0\n",
|
||||
" Sample ID: 25, Sample Name: Sample025, Position: 5, Mount count: 1\n",
|
||||
" Sample ID: 26, Sample Name: Sample026, Position: 8, Mount count: 1\n",
|
||||
" Sample ID: 27, Sample Name: Sample027, Position: 11, Mount count: 1\n",
|
||||
" Sample ID: 28, Sample Name: Sample028, Position: 12, Mount count: 1\n",
|
||||
"Puck ID: 2, Puck Name: PUCK002\n",
|
||||
" Sample ID: 17, Sample Name: Sample017, Position: 4, Mount count: 1\n",
|
||||
" Sample ID: 18, Sample Name: Sample018, Position: 5, Mount count: 0\n",
|
||||
" Sample ID: 19, Sample Name: Sample019, Position: 7, Mount count: 1\n",
|
||||
" Sample ID: 20, Sample Name: Sample020, Position: 10, Mount count: 0\n",
|
||||
" Sample ID: 21, Sample Name: Sample021, Position: 11, Mount count: 1\n",
|
||||
" Sample ID: 22, Sample Name: Sample022, Position: 13, Mount count: 0\n",
|
||||
" Sample ID: 23, Sample Name: Sample023, Position: 16, Mount count: 1\n",
|
||||
"Puck ID: 1, Puck Name: PUCK-001\n",
|
||||
" Sample ID: 1, Sample Name: Sample001, Position: 1, Mount count: 1\n",
|
||||
" Sample ID: 2, Sample Name: Sample002, Position: 2, Mount count: 1\n",
|
||||
" Sample ID: 3, Sample Name: Sample003, Position: 3, Mount count: 0\n",
|
||||
" Sample ID: 4, Sample Name: Sample004, Position: 4, Mount count: 0\n",
|
||||
" Sample ID: 5, Sample Name: Sample005, Position: 5, Mount count: 0\n",
|
||||
" Sample ID: 6, Sample Name: Sample006, Position: 6, Mount count: 1\n",
|
||||
" Sample ID: 7, Sample Name: Sample007, Position: 7, Mount count: 0\n",
|
||||
" Sample ID: 8, Sample Name: Sample008, Position: 8, Mount count: 1\n",
|
||||
" Sample ID: 9, Sample Name: Sample009, Position: 9, Mount count: 1\n",
|
||||
" Sample ID: 10, Sample Name: Sample010, Position: 10, Mount count: 1\n",
|
||||
" Sample ID: 11, Sample Name: Sample011, Position: 11, Mount count: 1\n",
|
||||
" Sample ID: 12, Sample Name: Sample012, Position: 12, Mount count: 1\n",
|
||||
" Sample ID: 13, Sample Name: Sample013, Position: 13, Mount count: 0\n",
|
||||
" Sample ID: 14, Sample Name: Sample014, Position: 14, Mount count: 1\n",
|
||||
" Sample ID: 15, Sample Name: Sample015, Position: 15, Mount count: 0\n",
|
||||
" Sample ID: 16, Sample Name: Sample016, Position: 16, Mount count: 1\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "stderr",
|
||||
"output_type": "stream",
|
||||
@ -420,13 +378,13 @@
|
||||
]
|
||||
}
|
||||
],
|
||||
"execution_count": 3
|
||||
"execution_count": 2
|
||||
},
|
||||
{
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2025-02-26T12:05:03.257159Z",
|
||||
"start_time": "2025-02-26T12:05:03.232846Z"
|
||||
"end_time": "2025-03-07T20:50:06.182786Z",
|
||||
"start_time": "2025-03-07T20:50:06.165153Z"
|
||||
}
|
||||
},
|
||||
"cell_type": "code",
|
||||
@ -438,12 +396,12 @@
|
||||
"with aareDBclient.ApiClient(configuration) as api_client:\n",
|
||||
" # Instance of the API client\n",
|
||||
" api_instance = aareDBclient.SamplesApi(api_client)\n",
|
||||
"\n",
|
||||
" sample_id=258\n",
|
||||
" try:\n",
|
||||
" # Define the payload with only `event_type`\n",
|
||||
" sample_event_create = SampleEventCreate(\n",
|
||||
" sample_id=16,\n",
|
||||
" event_type=\"Mounted\" # Valid event type\n",
|
||||
" sample_id=sample_id,\n",
|
||||
" event_type=\"Centering\" # Valid event type\n",
|
||||
" )\n",
|
||||
"\n",
|
||||
" # Debug the payload before sending\n",
|
||||
@ -452,7 +410,7 @@
|
||||
"\n",
|
||||
" # Call the API\n",
|
||||
" api_response = api_instance.create_sample_event_samples_samples_sample_id_events_post(\n",
|
||||
" sample_id=16, # Ensure this matches a valid sample ID in the database\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",
|
||||
@ -475,20 +433,20 @@
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"Payload being sent to API:\n",
|
||||
"{\"event_type\":\"Mounted\"}\n",
|
||||
"{\"event_type\":\"Centering\"}\n",
|
||||
"API response:\n",
|
||||
"('id', 16)\n",
|
||||
"('sample_name', 'Sample016')\n",
|
||||
"('position', 16)\n",
|
||||
"('puck_id', 1)\n",
|
||||
"('id', 258)\n",
|
||||
"('sample_name', 'Sample258')\n",
|
||||
"('position', 14)\n",
|
||||
"('puck_id', 26)\n",
|
||||
"('crystalname', None)\n",
|
||||
"('proteinname', None)\n",
|
||||
"('positioninpuck', None)\n",
|
||||
"('priority', None)\n",
|
||||
"('comments', None)\n",
|
||||
"('data_collection_parameters', None)\n",
|
||||
"('events', [SampleEventResponse(id=399, sample_id=16, event_type='Mounted', timestamp=datetime.datetime(2025, 2, 26, 13, 5, 3))])\n",
|
||||
"('mount_count', 1)\n",
|
||||
"('events', [SampleEventResponse(id=492, sample_id=258, event_type='Mounting', timestamp=datetime.datetime(2025, 3, 6, 13, 50)), SampleEventResponse(id=493, sample_id=258, event_type='Unmounting', timestamp=datetime.datetime(2025, 3, 6, 13, 50, 50)), SampleEventResponse(id=573, sample_id=258, event_type='Centering', timestamp=datetime.datetime(2025, 3, 7, 21, 50, 6))])\n",
|
||||
"('mount_count', 0)\n",
|
||||
"('unmount_count', 0)\n"
|
||||
]
|
||||
},
|
||||
@ -501,7 +459,7 @@
|
||||
]
|
||||
}
|
||||
],
|
||||
"execution_count": 80
|
||||
"execution_count": 46
|
||||
},
|
||||
{
|
||||
"metadata": {},
|
||||
@ -528,52 +486,64 @@
|
||||
{
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2025-02-26T16:15:33.052345Z",
|
||||
"start_time": "2025-02-26T16:15:33.022632Z"
|
||||
"end_time": "2025-03-07T20:51:14.203996Z",
|
||||
"start_time": "2025-03-07T20:51:14.134135Z"
|
||||
}
|
||||
},
|
||||
"cell_type": "code",
|
||||
"source": [
|
||||
"# post images to sample database\n",
|
||||
"# Post multiple images to the sample database\n",
|
||||
"\n",
|
||||
"import os\n",
|
||||
"import mimetypes\n",
|
||||
"import requests\n",
|
||||
"\n",
|
||||
"# File path to the image\n",
|
||||
"file_path = \"backend/tests/sample_image/IMG_1942.jpg\"\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",
|
||||
"# 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",
|
||||
"\n",
|
||||
"# Sample ID (ensure this exists on your backend)\n",
|
||||
"sample_id = 16\n",
|
||||
"sample_id = 299\n",
|
||||
"\n",
|
||||
"# Build the URL for the upload endpoint.\n",
|
||||
"# Base URL for the upload endpoint\n",
|
||||
"url = f\"https://127.0.0.1:8000/samples/{sample_id}/upload-images\"\n",
|
||||
"\n",
|
||||
"# Open the file and construct the files dictionary\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",
|
||||
" comment = \"before loop centering\"\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",
|
||||
" # Set verify=False to bypass certificate verification (only use in development)\n",
|
||||
" response = requests.post(url, headers=headers, files=files, verify=False)\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",
|
||||
"# Check the API response\n",
|
||||
"print(\"API Response:\")\n",
|
||||
"print(response.status_code)\n",
|
||||
"try:\n",
|
||||
" print(response.json())\n",
|
||||
"except Exception:\n",
|
||||
" print(response.text)\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": [
|
||||
@ -581,21 +551,40 @@
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"API Response:\n",
|
||||
"Uploading 0_200.jpg...\n",
|
||||
"API Response for 0_200.jpg:\n",
|
||||
"200\n",
|
||||
"{'pgroup': 'p20001', 'sample_id': 16, 'filepath': 'images/p20001/2025-02-26/Dewar One/PUCK-001/16/IMG_1942.jpg', 'status': 'active', 'comment': None, 'id': 4}\n"
|
||||
"{'pgroup': 'p20003', 'sample_id': 299, 'sample_event_id': 572, 'filepath': 'images/p20003/2025-03-07/Dewar Five/PKK007/16/Mounting_2025-03-06_14-31-00/0_200.jpg', 'status': 'active', 'comment': None, 'id': 2}\n",
|
||||
"Uploading 90_200.jpg...\n",
|
||||
"API Response for 90_200.jpg:\n",
|
||||
"200\n",
|
||||
"{'pgroup': 'p20003', 'sample_id': 299, 'sample_event_id': 572, 'filepath': 'images/p20003/2025-03-07/Dewar Five/PKK007/16/Mounting_2025-03-06_14-31-00/90_200.jpg', 'status': 'active', 'comment': None, 'id': 3}\n",
|
||||
"Uploading 0_700.jpg...\n",
|
||||
"API Response for 0_700.jpg:\n",
|
||||
"200\n",
|
||||
"{'pgroup': 'p20003', 'sample_id': 299, 'sample_event_id': 572, 'filepath': 'images/p20003/2025-03-07/Dewar Five/PKK007/16/Mounting_2025-03-06_14-31-00/0_700.jpg', 'status': 'active', 'comment': None, 'id': 4}\n",
|
||||
"Uploading 90_700.jpg...\n",
|
||||
"API Response for 90_700.jpg:\n",
|
||||
"200\n",
|
||||
"{'pgroup': 'p20003', 'sample_id': 299, 'sample_event_id': 572, 'filepath': 'images/p20003/2025-03-07/Dewar Five/PKK007/16/Mounting_2025-03-06_14-31-00/90_700.jpg', 'status': 'active', 'comment': None, 'id': 5}\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "stderr",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"/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 '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",
|
||||
"/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 '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",
|
||||
"/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 '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",
|
||||
"/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 '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"
|
||||
]
|
||||
}
|
||||
],
|
||||
"execution_count": 89
|
||||
"execution_count": 47
|
||||
},
|
||||
{
|
||||
"metadata": {},
|
||||
@ -608,8 +597,8 @@
|
||||
{
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2025-03-04T09:17:34.613556Z",
|
||||
"start_time": "2025-03-04T09:17:34.599367Z"
|
||||
"end_time": "2025-03-11T15:05:58.348843Z",
|
||||
"start_time": "2025-03-11T15:05:58.331240Z"
|
||||
}
|
||||
},
|
||||
"cell_type": "code",
|
||||
@ -624,27 +613,27 @@
|
||||
")\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"## Build the nested parameters\n",
|
||||
"#rotation = RotationParameters(\n",
|
||||
"# omegaStart_deg=0.0,\n",
|
||||
"# omegaStep=90.0,\n",
|
||||
"# phi=10.0,\n",
|
||||
"# chi=0.0,\n",
|
||||
"# numberOfImages=4,\n",
|
||||
"# exposureTime_s=0.02\n",
|
||||
"#)\n",
|
||||
"\n",
|
||||
"gridscan = GridScanParamers(\n",
|
||||
" xStart=0.0,\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",
|
||||
"# Build the nested parameters\n",
|
||||
"rotation = RotationParameters(\n",
|
||||
" omegaStart_deg=0.0,\n",
|
||||
" omegaStep=90.0,\n",
|
||||
" phi=10.0,\n",
|
||||
" chi=0.0,\n",
|
||||
" numberOfImages=4,\n",
|
||||
" exposureTime_s=0.02\n",
|
||||
")\n",
|
||||
"\n",
|
||||
"#gridscan = GridScanParamers(\n",
|
||||
"# xStart=0.0,\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",
|
||||
@ -673,8 +662,8 @@
|
||||
" beamlineFluxAtSample_ph_s=0,\n",
|
||||
" beamSizeWidth=30.0,\n",
|
||||
" beamSizeHeight=30.0,\n",
|
||||
"# rotation=rotation # Optional nested parameter\n",
|
||||
" gridScan=gridscan\n",
|
||||
" rotation=rotation # Optional nested parameter\n",
|
||||
" #gridScan=gridscan\n",
|
||||
" # gridScan and jet are optional and can be added similarly\n",
|
||||
")\n",
|
||||
"\n",
|
||||
@ -684,7 +673,7 @@
|
||||
"experiment_params_payload = ExperimentParametersCreate(\n",
|
||||
" # run_number can be omitted/ignored if computed on the server\n",
|
||||
" beamline_parameters=beamline_params,\n",
|
||||
" sample_id=15 # change sample_id to an existing sample in your database\n",
|
||||
" sample_id=299 # change sample_id to an existing sample in your database\n",
|
||||
")\n",
|
||||
"\n",
|
||||
"# Now, use the API instance to send the POST request\n",
|
||||
@ -711,7 +700,7 @@
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"API Response:\n",
|
||||
"run_number=3 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, rotation=None, grid_scan=GridScanParamers(x_start=0.0, x_step=0.1, y_start=0.0, y_step=0.1, z_start=0.0, z_step=0.0, number_of_images=4600, exposure_time_s=0.001), jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) sample_id=15 id=10\n"
|
||||
"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, rotation=RotationParameters(omega_start_deg=0.0, omega_step=90.0, chi=0.0, phi=10.0, number_of_images=4, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) sample_id=299 id=1\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -723,7 +712,7 @@
|
||||
]
|
||||
}
|
||||
],
|
||||
"execution_count": 12
|
||||
"execution_count": 49
|
||||
},
|
||||
{
|
||||
"metadata": {
|
||||
|
||||
Reference in New Issue
Block a user