Refactor: Unified pipeline execution, simplified UI, and fixed Docker config

- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency.
- Backend: Changed output format to ZIP and added auto-cleanup of intermediate files.
- Backend: Fixed language parameter passing in API and tasks.
- Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views.
- Frontend: Implemented simulated progress bar for better UX.
- Frontend: Restored One-click load button and added result file structure documentation.
- Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml.
- Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.

backend/app/api/v1/examples.py

@@ -0,0 +1,60 @@
+from fastapi import APIRouter, HTTPException
+from fastapi.responses import FileResponse
+from pathlib import Path
+import os
+
+router = APIRouter()
+
+# Define the path to examples relative to this file
+# This file: backend/app/api/v1/examples.py
+# Root: backend/app/api/v1/../../../../.. = root (where Data/ is)
+# But in Docker, backend/ is at /app/backend and Data/ is at /app/Data
+# So we need to go up 5 levels to get to /app (or project root)
+
+current_file = Path(__file__).resolve()
+# Go up 5 levels: v1 -> api -> app -> backend -> root
+PROJECT_ROOT = current_file.parent.parent.parent.parent.parent
+EXAMPLES_DIR = PROJECT_ROOT / "Data" / "examples"
+
+@router.get("/")
+async def list_examples():
+    """List available example files"""
+    if not EXAMPLES_DIR.exists():
+        return []
+
+    files = []
+    # Sort files to ensure consistent order (e.g. C15.fna, then 97-27.fna)
+    # Actually just grab all .fna files
+    if EXAMPLES_DIR.exists():
+        for f in sorted(EXAMPLES_DIR.glob("*.fna")):
+            files.append({
+                "name": f.name,
+                "size": f.stat().st_size
+            })
+    return files
+
+@router.get("/{filename}")
+async def get_example(filename: str):
+    """Get an example file content"""
+    file_path = EXAMPLES_DIR / filename
+
+    # Ensure directory exists
+    if not EXAMPLES_DIR.exists():
+         raise HTTPException(status_code=404, detail="Examples directory not found")
+
+    # Security check to prevent path traversal
+    try:
+        if not file_path.resolve().is_relative_to(EXAMPLES_DIR.resolve()):
+             raise HTTPException(status_code=403, detail="Access denied")
+    except ValueError:
+        # Can happen if paths are on different drives or completely messed up
+        raise HTTPException(status_code=403, detail="Access denied")
+
+    if not file_path.exists() or not file_path.is_file():
+        raise HTTPException(status_code=404, detail="File not found")
+
+    return FileResponse(
+        path=file_path,
+        filename=filename,
+        media_type="application/octet-stream"
+    )

backend/app/api/v1/jobs.py

@@ -31,8 +31,7 @@ async def create_job(
     min_coverage: float = Form(0.6),
     allow_unknown_families: bool = Form(False),
     require_index_hit: bool = Form(True),
-    crispr_fusion: bool = Form(False),
-    crispr_weight: float = Form(0.0),
+    lang: str = Form("zh"),
     db: Session = Depends(get_db),
     i18n: I18n = Depends(get_i18n)
 ):
@@ -48,6 +47,7 @@ async def create_job(
         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
+        lang: 报告语言 (zh/en)
     """
     # 验证文件类型
     allowed_extensions = {".fna", ".fa", ".fasta", ".faa"}
@@ -91,8 +91,6 @@ async def create_job(
         min_coverage=int(min_coverage * 100),
         allow_unknown_families=int(allow_unknown_families),
         require_index_hit=int(require_index_hit),
-        crispr_fusion=int(crispr_fusion),
-        crispr_weight=int(crispr_weight * 100),
     )
 
     db.add(job)
@@ -111,8 +109,7 @@ async def create_job(
         min_coverage=min_coverage,
         allow_unknown_families=allow_unknown_families,
         require_index_hit=require_index_hit,
-        crispr_fusion=crispr_fusion,
-        crispr_weight=crispr_weight,
+        lang=lang,
     )
 
     job.celery_task_id = task.id

backend/app/api/v1/results.py

@@ -1,11 +1,12 @@
 """结果下载 API"""
 from fastapi import APIRouter, HTTPException, Response, Depends
-from fastapi.responses import FileResponse
+from fastapi.responses import FileResponse, JSONResponse
 from sqlalchemy.orm import Session
 from pathlib import Path
 import tarfile
 import io
 import shutil
+import json
 
 from ...database import get_db
 from ...models.job import Job, JobStatus
@@ -53,6 +54,39 @@ async def download_results(job_id: str, db: Session = Depends(get_db), i18n: I18
     )
 
 
+@router.get("/{job_id}/crispr")
+async def get_crispr_results(job_id: str, db: Session = Depends(get_db), i18n: I18n = Depends(get_i18n)):
+    """获取 CRISPR 分析结果"""
+    job = db.query(Job).filter(Job.id == job_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail=i18n.t("job_not_found"))
+
+    if not job.crispr_fusion:
+        # 即使没启用，如果用户请求了，我们也可以返回一个提示或者空数据，但400可能更合适
+        # 或者仅仅返回空对象
+        return {"status": "disabled", "message": "CRISPR analysis disabled"}
+
+    job_output_dir = RESULTS_DIR / job_id
+
+    # 优先返回融合分析结果
+    fusion_file = job_output_dir / "crispr" / "fusion_analysis.json"
+    if fusion_file.exists():
+        with open(fusion_file) as f:
+            return json.load(f)
+
+    # 其次返回检测结果
+    detect_file = job_output_dir / "crispr" / "results.json"
+    if detect_file.exists():
+         with open(detect_file) as f:
+            return json.load(f)
+
+    # 如果任务已完成但文件不存在
+    if job.status == JobStatus.COMPLETED:
+        return {"status": "empty", "message": "No CRISPR elements detected"}
+
+    return {"status": "pending", "message": "Analysis in progress"}
+
+
 @router.delete("/{job_id}")
 async def delete_job(job_id: str, db: Session = Depends(get_db), i18n: I18n = Depends(get_i18n)):
     """删除任务及其结果"""
@@ -60,6 +94,18 @@ async def delete_job(job_id: str, db: Session = Depends(get_db), i18n: I18n = De
     if not job:
         raise HTTPException(status_code=404, detail=i18n.t("job_not_found"))
 
+    # 如果任务正在运行或排队，尝试取消 Celery 任务
+    if job.status in [JobStatus.PENDING, JobStatus.QUEUED, JobStatus.RUNNING] and job.celery_task_id:
+        try:
+            from ...core.celery_app import celery_app
+            celery_app.control.revoke(job.celery_task_id, terminate=True)
+            # 标记为已取消 (虽然后面马上删除了，但为了逻辑完整性)
+            job.status = JobStatus.FAILED
+            job.error_message = "Task cancelled by user"
+            db.commit()
+        except Exception as e:
+            print(f"Failed to revoke task {job.celery_task_id}: {e}")
+
     # 删除磁盘上的文件
     job_input_dir = Path(settings.UPLOAD_DIR) / job_id
     job_output_dir = RESULTS_DIR / job_id