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Add 'type' field to ExperimentParametersModel

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This commit introduces a new 'type' field in the ExperimentParametersModel schema and updates the associated code in `sample.py` to include this field during object creation. Additionally, unnecessary lines and redundant code in `testfunctions.ipynb` have been removed for better readability and maintainability.
This commit is contained in:
GotthardG
2025-04-29 23:17:53 +02:00
parent 57de665c7b
commit 58dcaf892f
5 changed files with 48 additions and 48 deletions
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1
backend/app/models.py
View File

@ -272,6 +272,7 @@ class ExperimentParameters(Base):
__tablename__ = "experiment_parameters" __tablename__ = "experiment_parameters"
id = Column(Integer, primary_key=True, index=True, autoincrement=True) id = Column(Integer, primary_key=True, index=True, autoincrement=True)
run_number = Column(Integer, nullable=False) run_number = Column(Integer, nullable=False)
type = Column(String(255), nullable=False)
beamline_parameters = Column(JSON, nullable=True) beamline_parameters = Column(JSON, nullable=True)
dataset = Column(JSON, nullable=True) dataset = Column(JSON, nullable=True)
sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False) sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)

1
backend/app/routers/sample.py
View File

@ -334,6 +334,7 @@ def create_experiment_parameters_for_sample(
# stored as JSON. # stored as JSON.
new_exp = ExperimentParametersModel( new_exp = ExperimentParametersModel(
run_number=new_run_number, run_number=new_run_number,
type=exp_params.type,
beamline_parameters=exp_params.beamline_parameters.dict() beamline_parameters=exp_params.beamline_parameters.dict()
if exp_params.beamline_parameters if exp_params.beamline_parameters
else None, else None,

1
backend/app/schemas.py
View File

@ -906,6 +906,7 @@ class Datasets(BaseModel):
class ExperimentParametersBase(BaseModel): class ExperimentParametersBase(BaseModel):
run_number: int run_number: int
type: str
beamline_parameters: Optional[BeamlineParameters] = None beamline_parameters: Optional[BeamlineParameters] = None
dataset: Optional[Datasets] = None dataset: Optional[Datasets] = None
sample_id: int sample_id: int

9
backend/propipe_sim.ipynb
View File

@ -9,7 +9,7 @@
"is_executing": true "is_executing": true
}, },
"ExecuteTime": { "ExecuteTime": {
"start_time": "2025-04-29T20:30:28.354331Z" "start_time": "2025-04-29T21:16:51.426746Z"
} }
}, },
"source": [ "source": [
@ -67,18 +67,13 @@
"name": "stdout", "name": "stdout",
"output_type": "stream", "output_type": "stream",
"text": [ "text": [
"Starting job status updater...\n", "Starting job status updater...\n"
"Jobs received: [{'job_id': 1, 'sample_id': 230, 'run_id': 1, 'sample_name': 'Sample230', 'status': 'todo', 'type': 'default_type', 'created_at': '2025-04-29T20:25:20.888394', '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", "name": "stderr",
"output_type": "stream", "output_type": "stream",
"text": [ "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",
"/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", "/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" " warnings.warn(\n"
] ]

84
testfunctions.ipynb
View File

@ -3,8 +3,8 @@
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-04-29T20:17:17.478562Z", "end_time": "2025-04-29T21:16:17.176129Z",
"start_time": "2025-04-29T20:17:16.842590Z" "start_time": "2025-04-29T21:16:17.104720Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -48,7 +48,7 @@
] ]
} }
], ],
"execution_count": 1 "execution_count": 3
}, },
{ {
"metadata": {}, "metadata": {},
@ -427,21 +427,21 @@
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-04-29T20:17:43.335654Z", "end_time": "2025-04-29T21:15:51.203912Z",
"start_time": "2025-04-29T20:17:43.333828Z" "start_time": "2025-04-29T21:15:51.200888Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
"source": "sample_id = 230", "source": "sample_id = 204",
"id": "54d4d46ca558e7b9", "id": "54d4d46ca558e7b9",
"outputs": [], "outputs": [],
"execution_count": 2 "execution_count": 1
}, },
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-04-29T20:17:46.414835Z", "end_time": "2025-04-29T20:57:41.460728Z",
"start_time": "2025-04-29T20:17:46.379138Z" "start_time": "2025-04-29T20:57:41.399620Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -493,7 +493,7 @@
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n", "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", "/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", " warnings.warn(\n",
"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/230/events HTTP/1.1\" 200 413\n" "DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/204/events HTTP/1.1\" 200 413\n"
] ]
}, },
{ {
@ -503,8 +503,8 @@
"Payload being sent to API:\n", "Payload being sent to API:\n",
"{\"event_type\":\"Collecting\"}\n", "{\"event_type\":\"Collecting\"}\n",
"API response:\n", "API response:\n",
"('id', 230)\n", "('id', 204)\n",
"('sample_name', 'Sample230')\n", "('sample_name', 'Sample204')\n",
"('position', 16)\n", "('position', 16)\n",
"('puck_id', 30)\n", "('puck_id', 30)\n",
"('crystalname', None)\n", "('crystalname', None)\n",
@ -513,13 +513,13 @@
"('priority', None)\n", "('priority', None)\n",
"('comments', None)\n", "('comments', None)\n",
"('data_collection_parameters', None)\n", "('data_collection_parameters', None)\n",
"('events', [SampleEventResponse(event_type='Mounting', id=453, sample_id=230, timestamp=datetime.datetime(2025, 4, 28, 13, 22)), SampleEventResponse(event_type='Collecting', id=454, sample_id=230, timestamp=datetime.datetime(2025, 4, 29, 20, 17, 46, 405264))])\n", "('events', [SampleEventResponse(event_type='Mounting', id=396, sample_id=204, timestamp=datetime.datetime(2025, 4, 28, 12, 56)), SampleEventResponse(event_type='Collecting', id=397, sample_id=204, timestamp=datetime.datetime(2025, 4, 29, 20, 57, 41, 453326))])\n",
"('mount_count', 0)\n", "('mount_count', 0)\n",
"('unmount_count', 0)\n" "('unmount_count', 0)\n"
] ]
} }
], ],
"execution_count": 3 "execution_count": 15
}, },
{ {
"metadata": { "metadata": {
@ -563,8 +563,8 @@
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-04-29T20:17:52.059793Z", "end_time": "2025-04-29T20:57:47.969390Z",
"start_time": "2025-04-29T20:17:51.939047Z" "start_time": "2025-04-29T20:57:47.936166Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -635,7 +635,7 @@
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): 127.0.0.1:8000\n", "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", "/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", " warnings.warn(\n",
"DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/230/upload-images HTTP/1.1\" 200 205\n" "DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/204/upload-images HTTP/1.1\" 200 205\n"
] ]
}, },
{ {
@ -645,11 +645,11 @@
"Uploading after_dc.jpeg.jpg...\n", "Uploading after_dc.jpeg.jpg...\n",
"API Response for after_dc.jpeg.jpg:\n", "API Response for after_dc.jpeg.jpg:\n",
"200\n", "200\n",
"{'pgroup': 'p20003', 'sample_id': 230, 'sample_event_id': 454, 'filepath': 'images/p20003/2025-04-29/Dewar Five/PKK007/16/Collecting_2025-04-29_20-17-46/after_dc.jpeg.jpg', 'status': 'active', 'comment': None, 'id': 1}\n" "{'pgroup': 'p20003', 'sample_id': 204, 'sample_event_id': 397, 'filepath': 'images/p20003/2025-04-29/Dewar Five/PKK007/16/Collecting_2025-04-29_20-57-41/after_dc.jpeg.jpg', 'status': 'active', 'comment': None, 'id': 1}\n"
] ]
} }
], ],
"execution_count": 4 "execution_count": 16
}, },
{ {
"metadata": {}, "metadata": {},
@ -662,8 +662,8 @@
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-04-29T20:17:56.494919Z", "end_time": "2025-04-29T21:16:26.759058Z",
"start_time": "2025-04-29T20:17:56.469538Z" "start_time": "2025-04-29T21:16:26.727172Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -674,7 +674,8 @@
" ExperimentParametersCreate,\n", " ExperimentParametersCreate,\n",
" RotationParameters,\n", " RotationParameters,\n",
" BeamlineParameters,\n", " BeamlineParameters,\n",
" GridScanParamers\n", " GridScanParamers,\n",
" Detector\n",
")\n", ")\n",
"\n", "\n",
"\n", "\n",
@ -712,17 +713,17 @@
"# If your client code requires you to build a detector model,\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", "# you can either use a Detector model or pass a dictionary.\n",
"# Here we pass a dictionary.\n", "# Here we pass a dictionary.\n",
"detector_data = {\n", "detector_data = Detector(\n",
" \"manufacturer\": \"DECTRIS\",\n", " manufacturer=\"DECTRIS\",\n",
" \"model\": \"PILATUS4 2M\",\n", " model=\"PILATUS4 2M\",\n",
" \"type\": \"photon-counting\",\n", " type=\"photon-counting\",\n",
" \"serialNumber\": \"16684dscsd668468\",\n", " serialNumber=\"16684dscsd668468\",\n",
" \"detectorDistance_mm\": 95.0,\n", " detectorDistance_mm=95.0,\n",
" \"beamCenterX_px\": 512.0,\n", " beamCenterX_px=512.0,\n",
" \"beamCenterY_px\": 512.0,\n", " beamCenterY_px=512.0,\n",
" \"pixelSizeX_um\": 150.0,\n", " pixelSizeX_um=150.0,\n",
" \"pixelSizeY_um\": 150.0,\n", " pixelSizeY_um=150.0,\n",
"}\n", ")\n",
"\n", "\n",
"beamline_params = BeamlineParameters(\n", "beamline_params = BeamlineParameters(\n",
" synchrotron=\"Swiss Light Source\",\n", " synchrotron=\"Swiss Light Source\",\n",
@ -748,6 +749,7 @@
"# it out or set it to a dummy value if your client model requires it.\n", "# it out or set it to a dummy value if your client model requires it.\n",
"experiment_params_payload = ExperimentParametersCreate(\n", "experiment_params_payload = ExperimentParametersCreate(\n",
" # run_number can be omitted/ignored if computed on the server\n", " # run_number can be omitted/ignored if computed on the server\n",
" type=\"standard\",\n",
" beamline_parameters=beamline_params,\n", " beamline_parameters=beamline_params,\n",
" sample_id=sample_id # change sample_id to an existing sample in your database\n", " sample_id=sample_id # change sample_id to an existing sample in your database\n",
")\n", ")\n",
@ -778,7 +780,7 @@
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n", "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", "/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", " warnings.warn(\n",
"DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/230/experiment_parameters HTTP/1.1\" 200 875\n" "DEBUG:urllib3.connectionpool:https://localhost:8000 \"POST /samples/samples/204/experiment_parameters HTTP/1.1\" 200 893\n"
] ]
}, },
{ {
@ -786,17 +788,17 @@
"output_type": "stream", "output_type": "stream",
"text": [ "text": [
"API Response:\n", "API Response:\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, characterization=None, rotation=RotationParameters(omega_start_deg=0.0, omega_step=0.1, chi=0.0, phi=10.0, number_of_images=3600, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) dataset=None sample_id=230 id=1\n" "run_number=1 type='standard' beamline_parameters=BeamlineParameters(synchrotron='Swiss Light Source', beamline='PXIII', detector=Detector(manufacturer='DECTRIS', model='PILATUS4 2M', type='photon-counting', serial_number='16684dscsd668468', detector_distance_mm=95.0, beam_center_x_px=512.0, beam_center_y_px=512.0, pixel_size_x_um=150.0, pixel_size_y_um=150.0), wavelength=1.0, ring_current_a=0.0, ring_mode='Machine Down', undulator=None, undulatorgap_mm=None, monochromator='Si111', transmission=1.0, focusing_optic='Kirkpatrick-Baez', beamline_flux_at_sample_ph_s=0.0, beam_size_width=30.0, beam_size_height=30.0, characterization=None, rotation=RotationParameters(omega_start_deg=0.0, omega_step=0.1, chi=0.0, phi=10.0, number_of_images=3600, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) dataset=None sample_id=204 id=1\n"
] ]
} }
], ],
"execution_count": 5 "execution_count": 4
}, },
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-04-29T20:29:27.657874Z", "end_time": "2025-04-29T21:17:02.855772Z",
"start_time": "2025-04-29T20:29:27.623737Z" "start_time": "2025-04-29T21:17:02.821634Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -838,7 +840,7 @@
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): localhost:8000\n", "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", "/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", " warnings.warn(\n",
"DEBUG:urllib3.connectionpool:https://localhost:8000 \"PATCH /samples/update-dataset/230/1 HTTP/1.1\" 200 1056\n" "DEBUG:urllib3.connectionpool:https://localhost:8000 \"PATCH /samples/update-dataset/204/1 HTTP/1.1\" 200 1074\n"
] ]
}, },
{ {
@ -846,11 +848,11 @@
"output_type": "stream", "output_type": "stream",
"text": [ "text": [
"Dataset updated successfully:\n", "Dataset updated successfully:\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, characterization=None, rotation=RotationParameters(omega_start_deg=0.0, omega_step=0.1, chi=0.0, phi=10.0, number_of_images=3600, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) dataset=Datasets(filepath='/das/work/p11/p11206/raw_data/vincent/20250415_6D_SLS2_1st_data/20250415_fullbeam_dtz220_Lyso102_again_360deg', status='written', written_at=datetime.datetime(2025, 4, 29, 22, 29, 27, 626524)) sample_id=230 id=1\n" "run_number=1 type='standard' beamline_parameters=BeamlineParameters(synchrotron='Swiss Light Source', beamline='PXIII', detector=Detector(manufacturer='DECTRIS', model='PILATUS4 2M', type='photon-counting', serial_number='16684dscsd668468', detector_distance_mm=95.0, beam_center_x_px=512.0, beam_center_y_px=512.0, pixel_size_x_um=150.0, pixel_size_y_um=150.0), wavelength=1.0, ring_current_a=0.0, ring_mode='Machine Down', undulator=None, undulatorgap_mm=None, monochromator='Si111', transmission=1.0, focusing_optic='Kirkpatrick-Baez', beamline_flux_at_sample_ph_s=0.0, beam_size_width=30.0, beam_size_height=30.0, characterization=None, rotation=RotationParameters(omega_start_deg=0.0, omega_step=0.1, chi=0.0, phi=10.0, number_of_images=3600, exposure_time_s=0.02), grid_scan=None, jet=None, cryojet_temperature_k=None, humidifier_temperature_k=None, humidifier_humidity=None) dataset=Datasets(filepath='/das/work/p11/p11206/raw_data/vincent/20250415_6D_SLS2_1st_data/20250415_fullbeam_dtz220_Lyso102_again_360deg', status='written', written_at=datetime.datetime(2025, 4, 29, 23, 17, 2, 823503)) sample_id=204 id=1\n"
] ]
} }
], ],
"execution_count": 13 "execution_count": 5
}, },
{ {
"metadata": { "metadata": {