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5
backend/app/api/routes/__init__.py
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5
backend/app/api/routes/__init__.py
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from . import jobs
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__all__ = ["jobs"]
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281
backend/app/api/routes/jobs.py
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281
backend/app/api/routes/jobs.py
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"""任务管理 API（表单+文件上传，使用 Pydantic 校验）"""
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from typing import List, Optional
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from fastapi import APIRouter, Depends, HTTPException, UploadFile, File, Form, status
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from sqlmodel import Session, select, col
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import logging
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from ...core.database import get_session
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from ...models.job import Job, JobUpdate, JobStatus, Step, StepRead
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from ...schemas.job import JobCreateRequest, JobCreateResponse, JobStatusResponse, FileUploadInfo
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from ...services.workspace_service import WorkspaceManager
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from ...workers.pipeline import orchestrate_pipeline
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logger = logging.getLogger(__name__)
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router = APIRouter()
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workspace_mgr = WorkspaceManager()
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@router.post(
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"/",
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response_model=JobCreateResponse,
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status_code=status.HTTP_201_CREATED,
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summary="创建新的分析任务（表单+文件）",
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)
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async def create_job(
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files: List[UploadFile] = File(...),
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name: str = Form(...),
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description: Optional[str] = Form(None),
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sequence_type: str = Form("nucl"),
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scaf_suffix: Optional[str] = Form(None),
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orfs_suffix: Optional[str] = Form(None),
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prot_suffix: Optional[str] = Form(None),
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platform: Optional[str] = Form(None),
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reads1_suffix: Optional[str] = Form(None),
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reads2_suffix: Optional[str] = Form(None),
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genome_size: Optional[str] = Form(None),
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suffix_len: Optional[int] = Form(None),
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short1: Optional[str] = Form(None),
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short2: Optional[str] = Form(None),
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long: Optional[str] = Form(None),
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threads: int = Form(4),
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update_db: bool = Form(False),
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assemble_only: bool = Form(False),
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session: Session = Depends(get_session),
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):
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"""创建 BtToxin 分析任务：接收表单参数与文件，保存到工作区后触发 Celery。"""
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if not files:
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raise HTTPException(status_code=400, detail="至少需要上传一个文件")
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try:
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params = JobCreateRequest(
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name=name,
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description=description,
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sequence_type=sequence_type,
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scaf_suffix=scaf_suffix,
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orfs_suffix=orfs_suffix,
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prot_suffix=prot_suffix,
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platform=platform,
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reads1_suffix=reads1_suffix,
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reads2_suffix=reads2_suffix,
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genome_size=genome_size,
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suffix_len=suffix_len,
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short1=short1,
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short2=short2,
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long=long,
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threads=threads,
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update_db=update_db,
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assemble_only=assemble_only,
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)
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except ValueError as e:
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raise HTTPException(status_code=422, detail=f"参数验证失败: {e}")
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job = Job(
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name=params.name,
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description=params.description,
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sequence_type=params.sequence_type.value,
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scaf_suffix=params.scaf_suffix or "",
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threads=params.threads,
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update_db=params.update_db,
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status=JobStatus.PENDING,
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)
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session.add(job)
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session.commit()
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session.refresh(job)
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workspace = workspace_mgr.create_workspace(job.id)
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job.workspace_path = str(workspace["root"])
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uploaded: List[FileUploadInfo] = []
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for f in files:
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f.file.seek(0, 2)
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size = f.file.tell()
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f.file.seek(0)
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if size == 0:
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continue
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dst = workspace["inputs"] / f.filename
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with dst.open("wb") as out:
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out.write(await f.read())
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uploaded.append(
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FileUploadInfo(filename=f.filename, size=size, content_type=f.content_type, path=str(dst))
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)
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job.input_files = [u.model_dump() for u in uploaded]
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session.add(job)
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session.commit()
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session.refresh(job)
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cfg = {
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"sequence_type": params.sequence_type.value,
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"scaf_suffix": params.scaf_suffix,
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"orfs_suffix": params.orfs_suffix,
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"prot_suffix": params.prot_suffix,
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"threads": params.threads,
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"update_db": params.update_db,
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"assemble_only": params.assemble_only,
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"platform": params.platform.value if params.platform else None,
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"reads1_suffix": params.reads1_suffix,
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"reads2_suffix": params.reads2_suffix,
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"suffix_len": params.suffix_len,
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"genome_size": params.genome_size,
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"short1": params.short1,
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"short2": params.short2,
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"long": params.long,
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}
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task = orchestrate_pipeline.delay(job.id, cfg)
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job.celery_task_id = task.id
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session.add(job)
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session.commit()
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session.refresh(job)
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return JobCreateResponse(
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job_id=job.id,
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message="任务创建成功，正在执行分析",
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uploaded_files=uploaded,
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workspace_path=job.workspace_path,
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celery_task_id=task.id,
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)
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@router.get("/", response_model=List[JobStatusResponse])
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async def list_jobs(
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skip: int = 0,
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limit: int = 50,
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status: Optional[JobStatus] = None,
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session: Session = Depends(get_session),
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):
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"""获取任务列表"""
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statement = select(Job)
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if status:
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statement = statement.where(Job.status == status)
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statement = statement.offset(skip).limit(limit).order_by(col(Job.created_at).desc())
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jobs = session.exec(statement).all()
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return [
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JobStatusResponse(
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job_id=j.id,
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name=j.name,
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status=j.status.value if hasattr(j.status, "value") else j.status,
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progress=j.progress,
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current_step=j.current_step,
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error_message=j.error_message,
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created_at=j.created_at.isoformat(),
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started_at=j.started_at.isoformat() if j.started_at else None,
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completed_at=j.completed_at.isoformat() if j.completed_at else None,
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)
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for j in jobs
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]
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@router.get("/{job_id}", response_model=JobStatusResponse)
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async def get_job(job_id: str, session: Session = Depends(get_session)):
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"""获取任务详情"""
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job = session.get(Job, job_id)
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if not job:
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raise HTTPException(status_code=404, detail="Job not found")
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return JobStatusResponse(
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job_id=job.id,
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name=job.name,
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status=job.status.value if hasattr(job.status, "value") else job.status,
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progress=job.progress,
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current_step=job.current_step,
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error_message=job.error_message,
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created_at=job.created_at.isoformat(),
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started_at=job.started_at.isoformat() if job.started_at else None,
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completed_at=job.completed_at.isoformat() if job.completed_at else None,
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)
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@router.patch("/{job_id}", response_model=JobRead)
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async def update_job(
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job_id: str, job_update: JobUpdate, session: Session = Depends(get_session)
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):
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"""更新任务"""
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job = session.get(Job, job_id)
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if not job:
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raise HTTPException(status_code=404, detail="Job not found")
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update_data = job_update.model_dump(exclude_unset=True)
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for key, value in update_data.items():
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setattr(job, key, value)
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session.add(job)
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session.commit()
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session.refresh(job)
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return job
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@router.delete("/{job_id}")
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async def delete_job(job_id: str, session: Session = Depends(get_session)):
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"""删除任务"""
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job = session.get(Job, job_id)
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if not job:
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raise HTTPException(status_code=404, detail="Job not found")
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workspace_mgr.cleanup_workspace(job_id, keep_results=False)
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session.delete(job)
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session.commit()
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return {"message": "Job deleted successfully"}
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@router.get("/{job_id}/steps", response_model=List[StepRead])
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async def get_job_steps(job_id: str, session: Session = Depends(get_session)):
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"""获取任务步骤列表"""
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job = session.get(Job, job_id)
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if not job:
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raise HTTPException(status_code=404, detail="Job not found")
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statement = select(Step).where(Step.job_id == job_id).order_by(Step.step_order)
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steps = session.exec(statement).all()
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return steps
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@router.get("/{job_id}/progress")
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async def get_job_progress(job_id: str, session: Session = Depends(get_session)):
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"""获取任务进度"""
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job = session.get(Job, job_id)
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if not job:
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raise HTTPException(status_code=404, detail="Job not found")
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statement = select(Step).where(Step.job_id == job_id)
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steps = session.exec(statement).all()
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total_steps = len(steps)
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completed_steps = sum(1 for s in steps if s.status == "completed")
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failed_steps = sum(1 for s in steps if s.status == "failed")
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return {
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"job_id": job_id,
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"status": job.status,
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"progress": job.progress,
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"current_step": job.current_step,
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"total_steps": total_steps,
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"completed_steps": completed_steps,
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"failed_steps": failed_steps,
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"steps": [
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{"name": s.step_name, "status": s.status, "order": s.step_order}
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for s in sorted(steps, key=lambda x: x.step_order)
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],
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}
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