From 04fb306624b4f1b45124378146e3be93e80c93c8 Mon Sep 17 00:00:00 2001 From: admin Date: Tue, 15 Sep 2026 23:22:06 +0800 Subject: [PATCH] =?UTF-8?q?fix(bioflow):=20=E5=86=85=E6=A0=B8=E6=A0=91?= =?UTF-8?q?=E8=BF=90=E8=A1=8C=E6=97=B6=E6=8C=82=E8=BD=BD=E2=80=94=E2=80=94?= =?UTF-8?q?=E9=9D=9E=20gf=20=E9=98=B6=E6=AE=B5=E9=95=9C=E5=83=8F=E7=BC=BA?= =?UTF-8?q?=20cli=20=E6=A8=A1=E5=9D=97?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - 8 个阶段镜像中仅 bioflow-gf 内置 /bioflow-kernel,其余 7 个 (rnaseq/wgs/gfpy/rnar/rde/pan/interproscan) 执行时 No module named cli - 服务端统一 -v kernel_dir:/bioflow-kernel:ro + -w /bioflow-kernel, 全部镜像可用,免重建 7 个镜像 - config 新增 kernel_dir/container_kernel_dir(env 可覆盖) - 337 用例全绿 Co-Authored-By: Claude Fable 5 --- bioflow_service/app/config.py | 8 ++++++++ bioflow_service/app/services/bioflow/kernel.py | 8 ++++++++ bioflow_service/tests/test_kernel.py | 14 ++++++++++++++ 3 files changed, 30 insertions(+) diff --git a/bioflow_service/app/config.py b/bioflow_service/app/config.py index ceb17fa..aa41bcc 100644 --- a/bioflow_service/app/config.py +++ b/bioflow_service/app/config.py @@ -35,6 +35,10 @@ class Settings(BaseSettings): # ---- 阶段→镜像映射（A1 交付物，仓库内 bioflow_kernel/stage_image_map.json）---- image_map_path: str = "bioflow_kernel/stage_image_map.json" + # 内核树：运行时只读挂载进执行容器（-v kernel:/bioflow-kernel:ro + -w） + # 除 bioflow-gf 外其余镜像未内置内核，挂载后全部阶段镜像统一可用 + kernel_dir: str = "bioflow_kernel" + container_kernel_dir: str = "/bioflow-kernel" # ---- 数据与任务目录 ---- data_root: str = "bioflow_data" # 生信数据根（hmm/rag_db 等，只读挂载进容器） @@ -125,6 +129,10 @@ class Settings(BaseSettings): def data_root_abs(self) -> str: return _resolve_root(self.data_root) + @property + def kernel_dir_abs(self) -> str: + return _resolve_root(self.kernel_dir) + @property def jobs_dir_abs(self) -> str: return _resolve_root(self.jobs_dir) diff --git a/bioflow_service/app/services/bioflow/kernel.py b/bioflow_service/app/services/bioflow/kernel.py index 550dd29..b10bca2 100644 --- a/bioflow_service/app/services/bioflow/kernel.py +++ b/bioflow_service/app/services/bioflow/kernel.py @@ -72,6 +72,8 @@ class KernelConfig: cpu_allow: str = "4,8,16,32" memory_allow: str = "16g,32g,64g" extra_mounts: list[str] = field(default_factory=list) # 登记路径只读挂载(src==dst) + kernel_dir: str = "" # 内核树宿主路径(运行时挂载进容器) + container_kernel_dir: str = "/bioflow-kernel" # 容器内内核树路径 class Kernel: @@ -145,6 +147,10 @@ class Kernel: # 登记路径只读挂载（src==dst，容器内原路径直接可见；登记时已过黑名单） for m in (extra_mounts or self.cfg.extra_mounts): cmd += ["-v", f"{m}:{m}:ro"] + # 内核树运行时挂载（除 bioflow-gf 外其余镜像未内置内核，统一走挂载） + if self.cfg.kernel_dir: + cmd += ["-v", f"{self.cfg.kernel_dir}:{self.cfg.container_kernel_dir}:ro"] + cmd += ["-w", self.cfg.container_kernel_dir] eff_cpu = cpu or str(params.get("cpu") or "") eff_memory = memory or str(params.get("memory") or "") cmd += ["--cpus", self._safe_cpu(eff_cpu or self.cfg.default_cpus)] @@ -286,6 +292,8 @@ def _default_kernel_config() -> KernelConfig: stage_timeout_sec=s.stage_timeout_sec, log_tail_lines=s.log_tail_lines, bba_env=s.bba_env, + kernel_dir=s.kernel_dir_abs, + container_kernel_dir=s.container_kernel_dir, ) diff --git a/bioflow_service/tests/test_kernel.py b/bioflow_service/tests/test_kernel.py index 9fa72ab..b2d6ab4 100644 --- a/bioflow_service/tests/test_kernel.py +++ b/bioflow_service/tests/test_kernel.py @@ -75,6 +75,20 @@ def test_build_command_extra_mounts(kernel, tmp_path): assert f"{m}:{m}:ro" in cmd +def test_build_command_kernel_dir_mount(tmp_path): + """内核树运行时挂载：-v kernel:/bioflow-kernel:ro + -w /bioflow-kernel。""" + from app.services.bioflow.kernel import Kernel, KernelConfig, ImageMap + cfg = KernelConfig(host_uid=1234, kernel_dir=str(tmp_path / "kernel"), + container_kernel_dir="/bioflow-kernel", + data_root=str(tmp_path / "data")) + img = ImageMap(images={"gf": {"docker_tag": "bioflow-gf"}}, + stages={"identify": {"image": "gf", "module": "cli.run_identify"}}) + k = Kernel(img, cfg) + cmd = k.build_command("identify", tmp_path / "in", tmp_path / "ws") + assert f"{tmp_path}/kernel:/bioflow-kernel:ro" in cmd + assert "-w" in cmd and "/bioflow-kernel" in cmd + + def test_build_command_params(kernel, tmp_path): cmd = kernel.build_command("identify", tmp_path / "in", tmp_path / "ws", {"prefix": "Ft.SPL", "required_pfams": "PF03110",