feat(backend): add missing API endpoints, concurrency control, and queue management\n\n- Add /api/v1/tasks router for task management\n- Add DELETE endpoint for task deletion\n- Add GET /download endpoint for result bundling (tar.gz)\n- Add GET /queue endpoint for queue position queries\n- Create ConcurrencyManager service with Redis Semaphore (16 concurrent limit)\n- Add QUEUED status to JobStatus enum\n- Update Job model with queue_position, current_stage, progress_percent fields\n- Add scoring parameters (min_identity, min_coverage, etc.) to jobs API\n- Implement pipeline stages: digger -> shoter -> plots -> bundle\n- Add update_queue_positions Celery task for periodic queue updates\n- Clean up duplicate code in main.py\n\nCo-Authored-By: Claude <noreply@anthropic.com>

backend/app/api/v1/__init__.py

@@ -0,0 +1,4 @@
+"""API v1 路由"""
+from . import jobs, upload, results, tasks
+
+__all__ = ["jobs", "upload", "results", "tasks"]

backend/app/api/v1/jobs.py

@@ -1,7 +1,7 @@
 """任务管理 API"""
-from fastapi import APIRouter, Depends, HTTPException, UploadFile, File
+from fastapi import APIRouter, Depends, HTTPException, UploadFile, File, Form
 from sqlalchemy.orm import Session
-from typing import List
+from typing import List, Optional
 from pathlib import Path
 import uuid
 import shutil
@@ -9,7 +9,7 @@ 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 ...workers.tasks import run_bttoxin_analysis, update_queue_positions
 from ...config import settings
 
 router = APIRouter()
@@ -19,21 +19,55 @@ 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,
+    sequence_type: str = Form("nucl"),
+    scaf_suffix: str = Form(".fna"),
+    threads: int = Form(4),
+    min_identity: float = Form(0.8),
+    min_coverage: float = Form(0.6),
+    allow_unknown_families: bool = Form(False),
+    require_index_hit: bool = Form(True),
     db: Session = Depends(get_db)
 ):
-    """创建新任务"""
+    """
+    创建新分析任务
+
+    Args:
+        files: 上传的文件列表（单文件）
+        sequence_type: 序列类型 (nucl=核酸, prot=蛋白)
+        scaf_suffix: 文件后缀
+        threads: 线程数
+        min_identity: 最小相似度 (0-1)
+        min_coverage: 最小覆盖度 (0-1)
+        allow_unknown_families: 是否允许未知家族
+        require_index_hit: 是否要求索引命中
+    """
+    # 验证文件类型
+    allowed_extensions = {".fna", ".fa", ".fasta", ".faa"}
+    for file in files:
+        ext = Path(file.filename).suffix.lower()
+        if ext not in allowed_extensions:
+            raise HTTPException(
+                status_code=400,
+                detail=f"Invalid file extension: {ext}. Allowed: {', '.join(allowed_extensions)}"
+            )
+
+    # 限制单文件上传
+    if len(files) != 1:
+        raise HTTPException(
+            status_code=400,
+            detail="Only one file allowed per task"
+        )
+
     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)
+    job_input_dir.mkdir(parents=True, exist_ok=True)
+    job_output_dir.mkdir(parents=True, exist_ok=True)
 
     uploaded_files = []
     for file in files:
@@ -48,20 +82,29 @@ async def create_job(
         input_files=uploaded_files,
         sequence_type=sequence_type,
         scaf_suffix=scaf_suffix,
-        threads=threads
+        threads=threads,
+        min_identity=int(min_identity * 100),  # 存储为百分比
+        min_coverage=int(min_coverage * 100),
+        allow_unknown_families=int(allow_unknown_families),
+        require_index_hit=int(require_index_hit),
     )
 
     db.add(job)
     db.commit()
     db.refresh(job)
 
+    # 启动 Celery 任务
     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
+        threads=threads,
+        min_identity=min_identity,
+        min_coverage=min_coverage,
+        allow_unknown_families=allow_unknown_families,
+        require_index_hit=require_index_hit,
     )
 
     job.celery_task_id = task.id
@@ -69,6 +112,7 @@ async def create_job(
 
     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"""
@@ -77,6 +121,7 @@ async def get_job(job_id: str, db: Session = Depends(get_db)):
         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"""
@@ -84,15 +129,26 @@ async def get_job_progress(job_id: str, db: Session = Depends(get_db)):
     if not job:
         raise HTTPException(status_code=404, detail="Job not found")
 
+    result = {
+        'job_id': job_id,
+        'status': job.status.value if isinstance(job.status, JobStatus) else job.status,
+        'current_stage': job.current_stage,
+        'progress_percent': job.progress_percent,
+        'queue_position': job.queue_position,
+    }
+
     if job.celery_task_id:
         from ...core.celery_app import celery_app
         task = celery_app.AsyncResult(job.celery_task_id)
+        result['celery_state'] = task.state
+        if task.state == 'PROGRESS':
+            result['celery_info'] = task.info
 
-        return {
-            'job_id': job_id,
-            'status': job.status,
-            'celery_state': task.state,
-            'progress': task.info if task.state == 'PROGRESS' else None
-        }
+    return result
 
-    return {'job_id': job_id, 'status': job.status}
+
+@router.post("/update-queue-positions")
+async def trigger_queue_update(db: Session = Depends(get_db)):
+    """手动触发队列位置更新"""
+    task = update_queue_positions.delay()
+    return {"message": "Queue update triggered", "task_id": task.id}

backend/app/api/v1/results.py

@@ -1,8 +1,76 @@
-"""结果查询 API"""
-from fastapi import APIRouter
+"""结果下载 API"""
+from fastapi import APIRouter, HTTPException, Response
+from fastapi.responses import FileResponse
+from sqlalchemy.orm import Session
+from pathlib import Path
+import tarfile
+import io
+import shutil
+
+from ...database import get_db
+from ...models.job import Job, JobStatus
+from ...config import settings
 
 router = APIRouter()
 
-@router.get("/")
-async def results_info():
-    return {"message": "Results endpoint"}
+RESULTS_DIR = Path(settings.RESULTS_DIR)
+
+
+@router.get("/{job_id}/download")
+async def download_results(job_id: str, db: Session = Depends(get_db)):
+    """下载任务结果（打包为 .tar.gz）"""
+    job = db.query(Job).filter(Job.id == job_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Job not found")
+
+    if job.status != JobStatus.COMPLETED:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Job not completed. Current status: {job.status}"
+        )
+
+    job_output_dir = RESULTS_DIR / job_id
+    if not job_output_dir.exists():
+        raise HTTPException(status_code=404, detail="Results not found on disk")
+
+    # 创建 tar.gz 文件到内存
+    tar_buffer = io.BytesIO()
+    with tarfile.open(fileobj=tar_buffer, mode="w:gz") as tar:
+        for file_path in job_output_dir.rglob("*"):
+            if file_path.is_file():
+                arcname = file_path.relative_to(job_output_dir)
+                tar.add(file_path, arcname=arcname)
+
+    tar_buffer.seek(0)
+
+    return Response(
+        content=tar_buffer.read(),
+        media_type="application/gzip",
+        headers={
+            "Content-Disposition": f"attachment; filename=bttoxin_{job_id}.tar.gz"
+        }
+    )
+
+
+@router.delete("/{job_id}")
+async def delete_job(job_id: str, db: Session = Depends(get_db)):
+    """删除任务及其结果"""
+    job = db.query(Job).filter(Job.id == job_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Job not found")
+
+    # 删除磁盘上的文件
+    job_input_dir = Path(settings.UPLOAD_DIR) / job_id
+    job_output_dir = RESULTS_DIR / job_id
+
+    if job_input_dir.exists():
+        shutil.rmtree(job_input_dir)
+
+    if job_output_dir.exists():
+        shutil.rmtree(job_output_dir)
+
+    # 删除数据库记录
+    db.delete(job)
+    db.commit()
+
+    return {"message": f"Job {job_id} deleted successfully"}

backend/app/api/v1/tasks.py

@@ -0,0 +1,70 @@
+"""任务管理 API - 兼容 /api/v1/tasks 路径"""
+from fastapi import APIRouter, Depends, HTTPException
+from sqlalchemy.orm import Session
+from typing import List
+from pathlib import Path
+from pydantic import BaseModel
+
+from ...database import get_db
+from ...models.job import Job, JobStatus
+from ...schemas.job import JobResponse
+from ...config import settings
+
+router = APIRouter()
+
+
+class TaskCreateRequest(BaseModel):
+    """任务创建请求"""
+    files: List[str]  # 文件名列表
+    sequence_type: str = "nucl"
+    min_identity: float = 0.8
+    min_coverage: float = 0.6
+    allow_unknown_families: bool = False
+    require_index_hit: bool = True
+
+
+class QueuePosition(BaseModel):
+    """队列位置信息"""
+    position: int
+    estimated_wait_minutes: int = None
+
+
+@router.post("/", response_model=JobResponse)
+async def create_task(request: TaskCreateRequest, db: Session = Depends(get_db)):
+    """创建新任务（兼容前端）"""
+    # 暂时复用 jobs 逻辑
+    # TODO: 实现完整的文件上传和处理
+    raise HTTPException(status_code=501, detail="Use POST /api/v1/jobs/create for now")
+
+
+@router.get("/{task_id}", response_model=JobResponse)
+async def get_task(task_id: str, db: Session = Depends(get_db)):
+    """获取任务状态"""
+    job = db.query(Job).filter(Job.id == task_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Task not found")
+    return job
+
+
+@router.get("/{task_id}/queue")
+async def get_queue_position(task_id: str, db: Session = Depends(get_db)):
+    """获取排队位置"""
+    job = db.query(Job).filter(Job.id == task_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Task not found")
+
+    if job.status not in [JobStatus.PENDING, JobStatus.QUEUED]:
+        return {"position": 0, "message": "Task is not in queue"}
+
+    # 计算排队位置
+    ahead_jobs = db.query(Job).filter(
+        Job.id != task_id,
+        Job.status.in_([JobStatus.PENDING, JobStatus.QUEUED]),
+        Job.created_at < job.created_at
+    ).count()
+
+    position = ahead_jobs + 1
+    # 假设每个任务约5分钟
+    estimated_wait = position * 5
+
+    return QueuePosition(position=position, estimated_wait_minutes=estimated_wait)