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debug: set Vina timeout to 60s for testing timeout mechanism
Browse files
bioai-platform/backend/app/tools/docking.py
CHANGED
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@@ -33,7 +33,7 @@ async def _run_vina_with_timeout(
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timeout=timeout + 30,
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)
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except subprocess.TimeoutExpired:
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-
raise asyncio.TimeoutError(f"Vina timed out after {timeout}s")
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with open(stdout_path, "wb") as f:
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f.write(r.stdout or b"")
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with open(stderr_path, "wb") as f:
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@@ -613,13 +613,13 @@ class DockingTool(BaseTool):
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"--num_modes", "3"],
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stdout_path=vina_stdout,
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stderr_path=vina_stderr,
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-
timeout=
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)
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with open(vina_stderr, "r") as f:
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stderr_str = f.read()
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except asyncio.TimeoutError:
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logger.error("Vina timed out after
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return {"error": "Docking timed out after
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except Exception as exc:
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logger.exception("Vina subprocess failed to start")
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return {"error": f"Vina execution failed: {exc}"}
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timeout=timeout + 30,
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)
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except subprocess.TimeoutExpired:
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+
raise asyncio.TimeoutError(f"Vina timed out after {timeout}s (subprocess)")
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with open(stdout_path, "wb") as f:
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f.write(r.stdout or b"")
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with open(stderr_path, "wb") as f:
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"--num_modes", "3"],
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stdout_path=vina_stdout,
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stderr_path=vina_stderr,
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timeout=60,
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)
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with open(vina_stderr, "r") as f:
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stderr_str = f.read()
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except asyncio.TimeoutError:
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logger.error("Vina timed out after 60s")
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return {"error": "Docking timed out after 60 seconds"}
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except Exception as exc:
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logger.exception("Vina subprocess failed to start")
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return {"error": f"Vina execution failed: {exc}"}
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