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Add dataset, slurm_id, and FAILED status to models

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Enhanced the models with new fields: a dataset field for Experiment Parameters and a slurm_id for Jobs. Introduced a FAILED status for the JobStatus enum. Updated functionality to handle datasets and trigger job creation based on dataset status.
This commit is contained in:
GotthardG
2025-04-29 22:52:36 +02:00
parent 9af2e84f9e
commit 57de665c7b
8 changed files with 202 additions and 55 deletions
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3
backend/app/models.py
View File

@ -273,6 +273,7 @@ class ExperimentParameters(Base):
id = Column(Integer, primary_key=True, index=True, autoincrement=True)
run_number = Column(Integer, nullable=False)
beamline_parameters = Column(JSON, nullable=True)
dataset = Column(JSON, nullable=True)
sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
@ -311,6 +312,7 @@ class JobStatus(str, enum.Enum):
TODO = "todo"
SUBMITTED = "submitted"
DONE = "done"
FAILED = "failed"
class Jobs(Base):
@ -323,3 +325,4 @@ class Jobs(Base):
experiment_parameters = relationship(ExperimentParameters)
created_at = Column(DateTime, server_default=func.now())
updated_at = Column(DateTime, onupdate=func.now())
slurm_id = Column(Integer, nullable=True)

8
backend/app/routers/processing.py
View File

@ -41,6 +41,7 @@ async def job_event_generator(db: Session):
experiment_parameters=experiment.beamline_parameters
if experiment
else None,
slurm_id=None,
)
job_items.append(job_item)
@ -75,13 +76,14 @@ def update_jobs_status(payload: JobsUpdate, db: Session = Depends(get_db)):
# Update the status
job.status = payload.status
job.slurm_id = payload.slurm_id
# Optionally update 'updated_at'
from sqlalchemy import func
from datetime import datetime
job.updated_at = func.now()
job.updated_at = datetime.now()
db.commit()
db.refresh(job)
# Return the updated job's info as response
return JobsUpdate(job_id=job.id, status=job.status)
return JobsUpdate(job_id=job.id, status=job.status, slurm_id=job.slurm_id)

63
backend/app/routers/sample.py
View File

@ -1,4 +1,5 @@
from fastapi import APIRouter, HTTPException, Depends, UploadFile, File, Form
from fastapi.encoders import jsonable_encoder
from sqlalchemy.orm import Session
from pathlib import Path
from typing import List
@ -18,6 +19,7 @@ from app.schemas import (
ResultResponse,
ResultCreate,
Results as ProcessingResults,
Datasets,
)
from app.models import (
Puck as PuckModel,
@ -350,19 +352,60 @@ def create_experiment_parameters_for_sample(
db.add(new_event)
db.commit()
new_job = JobModel(
sample_id=sample_id,
run_id=new_exp.id,
experiment_parameters=new_exp, # not sure yet
status=JobStatus.TODO,
)
db.add(new_job)
db.commit()
db.refresh(new_job)
return new_exp
@router.patch(
"/update-dataset/{sample_id}/{run_id}",
response_model=ExperimentParametersRead,
operation_id="update_dataset_for_experiment_run",
)
def update_experiment_run_dataset(
sample_id: int,
run_id: int,
dataset: Datasets,
db: Session = Depends(get_db),
):
# Find the run for this sample and run_id
exp = (
db.query(ExperimentParametersModel)
.filter(
ExperimentParametersModel.sample_id == sample_id,
ExperimentParametersModel.id == run_id,
)
.first()
)
if not exp:
raise HTTPException(
status_code=404,
detail="ExperimentParameters (run) not found for this sample",
)
exp.dataset = jsonable_encoder(dataset)
db.commit()
db.refresh(exp)
# Only create a job if status is "written" and job does not exist yet
if dataset.status == "written":
job_exists = (
db.query(JobModel)
.filter(JobModel.sample_id == sample_id, JobModel.run_id == run_id)
.first()
)
if not job_exists:
new_job = JobModel(
sample_id=sample_id,
run_id=run_id,
experiment_parameters=exp, # adjust this line as appropriate
status=JobStatus.TODO,
)
db.add(new_job)
db.commit()
db.refresh(new_job)
return exp
@router.post(
"/processing-results", response_model=ResultResponse, operation_id="create_result"
)

16
backend/app/schemas.py
View File

@ -898,9 +898,16 @@ class BeamlineParameters(BaseModel):
# beamstopDiameter_mm: Optional[float] = None
class Datasets(BaseModel):
filepath: str
status: str
written_at: datetime
class ExperimentParametersBase(BaseModel):
run_number: int
beamline_parameters: Optional[BeamlineParameters] = None
dataset: Optional[Datasets] = None
sample_id: int
@ -915,6 +922,12 @@ class ExperimentParametersRead(ExperimentParametersBase):
from_attributes = True
class ExperimentParametersUpdate(BaseModel):
run_number: int
dataset: Optional[Datasets]
sample_id: int
class SampleResult(BaseModel):
sample_id: int
sample_name: str
@ -952,6 +965,7 @@ class JobsCreate(BaseModel):
created_at: datetime
updated_at: datetime
experiment_parameters: BeamlineParameters
slurm_id: Optional[int] = None
class Config:
from_attributes = True
@ -968,8 +982,10 @@ class JobsResponse(BaseModel):
updated_at: Optional[datetime]
data_collection_parameters: Optional[DataCollectionParameters] = None
experiment_parameters: BeamlineParameters
slurm_id: Optional[int] = None
class JobsUpdate(BaseModel):
job_id: int
status: str
slurm_id: int

4
backend/main.py
View File

@ -154,8 +154,8 @@ async def lifespan(app: FastAPI):
load_slots_data(db)
else: # dev or test environments
print(f"{environment.capitalize()} environment: Regenerating database.")
Base.metadata.drop_all(bind=engine)
Base.metadata.create_all(bind=engine)
# Base.metadata.drop_all(bind=engine)
# Base.metadata.create_all(bind=engine)
# from sqlalchemy.engine import reflection
# from app.models import ExperimentParameters # adjust the import as needed
# inspector = reflection.Inspector.from_engine(engine)

24
backend/propipe_sim.ipynb
View File

@ -9,7 +9,7 @@
"is_executing": true
},
"ExecuteTime": {
"start_time": "2025-04-29T12:21:15.813326Z"
"start_time": "2025-04-29T20:30:28.354331Z"
}
},
"source": [
@ -20,10 +20,11 @@
"SSE_URL = \"https://127.0.0.1:8000/processing/jobs/stream\"\n",
"UPDATE_URL = \"https://127.0.0.1:8000/processing/jobs/update_status\"\n",
"\n",
"def submit_job_update(job_id, status):\n",
"def submit_job_update(job_id, status, slurm_id):\n",
" payload = {\n",
" \"job_id\": job_id,\n",
" \"status\": status\n",
" \"status\": status,\n",
" \"slurm_id\": slurm_id,\n",
" }\n",
" try:\n",
" response = requests.post(UPDATE_URL, json=payload, verify=False)\n",
@ -48,11 +49,11 @@
" jobs = json.loads(event.data)\n",
" print(f\"Jobs received: {jobs}\")\n",
"\n",
" #for job in jobs:\n",
" # job_id = job.get(\"job_id\")\n",
" # print(f\"Job ID: {job_id}, Current status: {job.get('status')}\")\n",
" # # Immediately update status to \"submitted\"\n",
" # submit_job_update(job_id, \"submitted\")\n",
" for job in jobs:\n",
" job_id = job.get(\"job_id\")\n",
" print(f\"Job ID: {job_id}, Current status: {job.get('status')}\")\n",
" # Immediately update status to \"submitted\"\n",
" submit_job_update(job_id, \"submitted\", 76545678)\n",
" except json.JSONDecodeError as e:\n",
" print(f\"Error decoding event data: {e}\")\n",
" except Exception as e:\n",
@ -66,13 +67,18 @@
"name": "stdout",
"output_type": "stream",
"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",
"output_type": "stream",
"text": [
"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1103: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
" warnings.warn(\n",
"/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"
]

2
backend/pyproject.toml
View File

@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "aareDB"
version = "0.1.1a1"
version = "0.1.1a2"
description = "Backend for next gen sample management system"
authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}]
license = {text = "MIT"}