Initial commit: BtToxin Pipeline project structure

backend/app/api/v1/jobs.py

@@ -0,0 +1,98 @@
+"""任务管理 API"""
+from fastapi import APIRouter, Depends, HTTPException, UploadFile, File
+from sqlalchemy.orm import Session
+from typing import List
+from pathlib import Path
+import uuid
+import shutil
+
+from ...database import get_db
+from ...models.job import Job, JobStatus
+from ...schemas.job import JobResponse
+from ...workers.tasks import run_bttoxin_analysis
+from ...config import settings
+
+router = APIRouter()
+
+UPLOAD_DIR = Path(settings.UPLOAD_DIR)
+RESULTS_DIR = Path(settings.RESULTS_DIR)
+UPLOAD_DIR.mkdir(exist_ok=True)
+RESULTS_DIR.mkdir(exist_ok=True)
+
+@router.post("/create", response_model=JobResponse)
+async def create_job(
+    files: List[UploadFile] = File(...),
+    sequence_type: str = "nucl",
+    scaf_suffix: str = ".fna",
+    threads: int = 4,
+    db: Session = Depends(get_db)
+):
+    """创建新任务"""
+    job_id = str(uuid.uuid4())
+
+    job_input_dir = UPLOAD_DIR / job_id
+    job_output_dir = RESULTS_DIR / job_id
+    job_input_dir.mkdir(parents=True)
+    job_output_dir.mkdir(parents=True)
+
+    uploaded_files = []
+    for file in files:
+        file_path = job_input_dir / file.filename
+        with open(file_path, "wb") as buffer:
+            shutil.copyfileobj(file.file, buffer)
+        uploaded_files.append(file.filename)
+
+    job = Job(
+        id=job_id,
+        status=JobStatus.PENDING,
+        input_files=uploaded_files,
+        sequence_type=sequence_type,
+        scaf_suffix=scaf_suffix,
+        threads=threads
+    )
+
+    db.add(job)
+    db.commit()
+    db.refresh(job)
+
+    task = run_bttoxin_analysis.delay(
+        job_id=job_id,
+        input_dir=str(job_input_dir),
+        output_dir=str(job_output_dir),
+        sequence_type=sequence_type,
+        scaf_suffix=scaf_suffix,
+        threads=threads
+    )
+
+    job.celery_task_id = task.id
+    db.commit()
+
+    return job
+
+@router.get("/{job_id}", response_model=JobResponse)
+async def get_job(job_id: str, db: Session = Depends(get_db)):
+    """获取任务详情"""
+    job = db.query(Job).filter(Job.id == job_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Job not found")
+    return job
+
+@router.get("/{job_id}/progress")
+async def get_job_progress(job_id: str, db: Session = Depends(get_db)):
+    """获取任务进度"""
+    job = db.query(Job).filter(Job.id == job_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Job not found")
+
+    if job.celery_task_id:
+        from ...core.celery_app import celery_app
+        task = celery_app.AsyncResult(job.celery_task_id)
+
+        return {
+            'job_id': job_id,
+            'status': job.status,
+            'celery_state': task.state,
+            'progress': task.info if task.state == 'PROGRESS' else None
+        }
+
+    return {'job_id': job_id, 'status': job.status}