first add

backend/app/workers/__init__.py

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+
+

backend/app/workers/pipeline.py

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+from datetime import datetime
+from pathlib import Path
+from sqlmodel import Session, select
+
+from . import __init__  # noqa: F401
+from ..core.celery_app import celery_app
+from ..core.database import SessionLocal
+from ..models.job import Job, Step, StepStatus, JobStatus
+from .steps.run_digger import run_bttoxin_digger
+
+
+def _with_session():
+    return SessionLocal()
+
+
+def _update_job(session: Session, job: Job, **changes) -> None:
+    for k, v in changes.items():
+        setattr(job, k, v)
+    session.add(job)
+    session.commit()
+    session.refresh(job)
+
+
+def _create_or_get_step(session: Session, job_id: str, step_name: str, order: int) -> Step:
+    step = session.exec(select(Step).where(Step.job_id == job_id, Step.step_name == step_name)).first()
+    if step is None:
+        step = Step(job_id=job_id, step_name=step_name, step_order=order, status=StepStatus.PENDING)
+        session.add(step)
+        session.commit()
+        session.refresh(step)
+    return step
+
+
+@celery_app.task(name="pipeline.orchestrate")
+def orchestrate_pipeline(job_id: str, config: dict) -> dict:
+    with _with_session() as session:
+        job = session.get(Job, job_id)
+        if job is None:
+            return {"error": "job not found", "job_id": job_id}
+
+        _update_job(
+            session,
+            job,
+            status=JobStatus.RUNNING,
+            started_at=datetime.utcnow(),
+            current_step="run_digger",
+            progress=0,
+        )
+
+        # Step 1: run_digger
+        step = _create_or_get_step(session, job_id, "run_digger", 1)
+        step.status = StepStatus.RUNNING
+        step.started_at = datetime.utcnow()
+        session.add(step)
+        session.commit()
+        session.refresh(step)
+
+        try:
+            ws_root = Path(job.workspace_path or ".")
+            result = run_bttoxin_digger(
+                workspace_root=ws_root,
+                threads=job.threads,
+                sequence_type=job.sequence_type,
+                scaf_suffix=job.scaf_suffix,
+                update_db=job.update_db,
+            )
+
+            step.status = StepStatus.COMPLETED
+            step.completed_at = datetime.utcnow()
+            step.result_data = {"results_dir": result["results_dir"]}
+            session.add(step)
+            session.commit()
+            session.refresh(step)
+
+            _update_job(session, job, progress=100, status=JobStatus.COMPLETED, completed_at=datetime.utcnow())
+            return {"job_id": job_id, "ok": True, "step": "run_digger", "result": result}
+
+        except Exception as exc:  # 仅顶层捕获，记录失败
+            step.status = StepStatus.FAILED
+            step.error_message = str(exc)
+            step.completed_at = datetime.utcnow()
+            session.add(step)
+            session.commit()
+
+            _update_job(session, job, status=JobStatus.FAILED, error_message=str(exc))
+            return {"job_id": job_id, "ok": False, "error": str(exc)}
+
+

backend/app/workers/steps/run_digger.py

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+from __future__ import annotations
+
+from pathlib import Path
+from typing import Dict
+from ...services.docker_service import DockerRunner
+
+
+def run_bttoxin_digger(workspace_root: Path, threads: int, sequence_type: str, scaf_suffix: str, update_db: bool) -> Dict:
+    runner = DockerRunner()
+
+    inputs_dir = workspace_root / "inputs"
+    results_dir = workspace_root / "results"
+    results_dir.mkdir(parents=True, exist_ok=True)
+
+    # 示例命令：根据实际 BtToxin_Digger CLI 调整
+    command = [
+        "BtToxin_Digger",
+        "--threads", str(threads),
+        "--seq_type", sequence_type,
+        "--scaf_suffix", scaf_suffix,
+        "--input", str(inputs_dir),
+        "--outdir", str(results_dir),
+    ]
+    if update_db:
+        command += ["--update_db"]
+
+    logs = runner.run(
+        image=None,
+        command=command,
+        workdir=Path("/work"),
+        mounts={
+            workspace_root: "/work",
+        },
+        env=None,
+        platform=None,
+        detach=False,
+        remove=True,
+    )
+
+    return {
+        "command": command,
+        "logs": logs,
+        "results_dir": str(results_dir),
+    }
+
+