forked from admin/PlantAI-rag-new
adminandClaude Fable 5
dcb810a758
- stage_image_map 加 26 个 wgs/pop/gwas 阶段 cli_contract:
--workspace/--job-id/--prefix 公共三元组 + 上游 manifest 注入
(prev_manifest:<stage> 解析为 workspace/final/{prefix}.{stage}.manifest.json)
+ param:<name> 用户参数 + tool:<name> 镜像内工具
- kernel _contract_args 扩展 prev_manifest/tool 两种 source
- catalog 补 wgs/pop/gwas 参数 schema(确认表单收集参考基因组/样本清单/
表型文件/主成分等)
- 339 用例全绿;已部署 176
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
247 lines
11 KiB
Python
247 lines
11 KiB
Python
"""tests/test_kernel.py —— Docker 执行器（命令拼装/mock 执行/映射表加载）。"""
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from __future__ import annotations
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import asyncio
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import pytest
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from app.services.bioflow.kernel import (
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ImageMapError,
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Kernel,
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KernelConfig,
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UnknownStageError,
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tail_lines,
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)
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pytestmark = pytest.mark.bioflow_unit
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def test_load_map_and_query(kernel, image_map):
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assert kernel.has_stage("identify")
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assert not kernel.has_stage("fake_stage_xyz")
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entry = kernel.image_for("identify")
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assert entry["image"] == "bioflow-gf"
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assert entry["module"] == "cli.run_identify"
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# 跨环境 note 透传
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assert kernel.image_for("expression")["note"].startswith("跨环境")
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# docker_tag 与逻辑名不同（bioflow-rnaR→bioflow-rnar）
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assert kernel.map.docker_tag("bioflow-rnaR") == "bioflow-rnar"
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def test_load_missing_map(tmp_path):
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with pytest.raises(ImageMapError):
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Kernel.load(tmp_path / "nope.json", KernelConfig())
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def test_load_broken_map(tmp_path):
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p = tmp_path / "bad.json"
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p.write_text("{invalid", encoding="utf-8")
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with pytest.raises(ImageMapError):
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Kernel.load(p, KernelConfig())
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def test_build_command_basics(kernel, tmp_path):
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cmd = kernel.build_command("identify", tmp_path / "in", tmp_path / "ws")
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# TC-BIO-KERN-001 基元顺序
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assert cmd[0] == "docker"
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assert cmd[1] == "run"
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assert cmd[2] == "--rm"
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assert cmd[3] == "--user"
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assert cmd[4] == "1234"
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# 挂载三目录
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assert f"{tmp_path}/in:/job/input" in cmd
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assert f"{tmp_path}/ws:/job/workspace" in cmd
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assert f"{kernel.cfg.data_root}:/bioflow-data:ro" in cmd
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# 资源参数
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assert "--cpus" in cmd and "--memory" in cmd
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# env 两元素形态
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env_idx = cmd.index("-e")
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assert cmd[env_idx + 1] == "BBA_PFAM_DIR=/bioflow-data/hmm"
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# 镜像 + 容器内命令形态
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assert "bioflow-gf:dev" in cmd
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assert cmd[cmd.index("python") + 1] == "-B"
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assert "-m" in cmd and "cli.run_identify" in cmd
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# 通用参数
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assert "--input-dir" in cmd and "/job/input" in cmd
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assert "--workspace" in cmd and "/job/workspace" in cmd
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def test_build_command_extra_mounts(kernel, tmp_path):
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"""登记路径自动挂载：extra_mounts 每个追加 -v src:src:ro。"""
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extra = [str(tmp_path / "rnaseq"), str(tmp_path / "wgs")]
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cmd = kernel.build_command("identify", tmp_path / "in", tmp_path / "ws",
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extra_mounts=extra)
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for m in extra:
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assert f"{m}:{m}:ro" in cmd
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def test_build_command_kernel_dir_mount(tmp_path):
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"""内核树运行时挂载：-v kernel:/bioflow-kernel:ro + -w /bioflow-kernel。"""
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from app.services.bioflow.kernel import Kernel, KernelConfig, ImageMap
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cfg = KernelConfig(host_uid=1234, kernel_dir=str(tmp_path / "kernel"),
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container_kernel_dir="/bioflow-kernel",
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data_root=str(tmp_path / "data"))
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img = ImageMap(images={"gf": {"docker_tag": "bioflow-gf"}},
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stages={"identify": {"image": "gf", "module": "cli.run_identify"}})
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k = Kernel(img, cfg)
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cmd = k.build_command("identify", tmp_path / "in", tmp_path / "ws")
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assert f"{tmp_path}/kernel:/bioflow-kernel:ro" in cmd
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assert "-w" in cmd and "/bioflow-kernel" in cmd
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def test_build_command_cli_contract(tmp_path):
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"""契约阶段：按 cli_contract 注入 -i/-o/-c;无契约阶段保持 --input-dir。"""
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from app.services.bioflow.kernel import Kernel, KernelConfig, ImageMap
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cfg = KernelConfig(host_uid=1234, data_root=str(tmp_path / "data"))
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img = ImageMap(
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images={"rnaseq": {"docker_tag": "bioflow-rnaseq"}},
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stages={
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"rnaseq_qc": {"image": "rnaseq", "module": "cli.run_rnaseq_qc",
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"cli_contract": [["--input", "input_dir"],
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["--config", "samples_yaml"],
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["--output", "output_final"]]},
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"rnaseq_align": {"image": "rnaseq", "module": "cli.run_rnaseq_align",
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"cli_contract": [["--input", "input_dir"],
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["--hisat2-index", "param:hisat2_index"],
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["--output", "output_final"]]},
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"plain": {"image": "rnaseq", "module": "cli.run_plain"},
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},
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)
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k = Kernel(img, cfg)
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# 有 samples.yaml 时注入 -c
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(tmp_path / "in").mkdir(parents=True, exist_ok=True)
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(tmp_path / "in" / "samples.yaml").write_text("samples: {}", encoding="utf-8")
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cmd = k.build_command("rnaseq_qc", tmp_path / "in", tmp_path / "ws")
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assert "--input" in cmd and "/job/input" in cmd
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assert "--config" in cmd and "/job/input/samples.yaml" in cmd
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assert "--output" in cmd and "/job/workspace/final" in cmd # rnaseq -o 语义对齐
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assert "--input-dir" not in cmd # 契约阶段不再注入默认形态
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# param: 有值注入、无值跳过
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cmd2 = k.build_command("rnaseq_align", tmp_path / "in", tmp_path / "ws",
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params={"hisat2_index": "/bioflow-data/hmm/hisat2/osa"})
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assert "--hisat2-index" in cmd2 and "/bioflow-data/hmm/hisat2/osa" in cmd2
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cmd3 = k.build_command("rnaseq_align", tmp_path / "in", tmp_path / "ws")
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assert "--hisat2-index" not in cmd3
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# 无契约阶段回归默认
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cmd4 = k.build_command("plain", tmp_path / "in", tmp_path / "ws")
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assert "--input-dir" in cmd4 and "--workspace" in cmd4
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def test_build_command_wgs_contract(tmp_path):
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"""wgs 系契约:--workspace/--job-id/--prefix + prev_manifest 路径注入。"""
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from app.services.bioflow.kernel import Kernel, KernelConfig, ImageMap
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cfg = KernelConfig(host_uid=1234, data_root=str(tmp_path / "data"))
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img = ImageMap(
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images={"wgs": {"docker_tag": "bioflow-wgs"}},
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stages={
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"wgs_qc": {"image": "wgs", "module": "cli.run_wgs_qc",
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"cli_contract": [["--workspace", "workspace"],
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["--job-id", "job_id"],
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["--prefix", "prefix"],
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["--wgs-samples", "param:wgs_samples"]]},
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"wgs_align": {"image": "wgs", "module": "cli.run_wgs_align",
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"cli_contract": [["--workspace", "workspace"],
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["--job-id", "job_id"],
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["--prefix", "prefix"],
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["--qc-manifest", "prev_manifest:wgs_qc"],
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["--index-manifest", "prev_manifest:wgs_index"],
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["--gatk", "tool:gatk"]]},
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},
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)
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k = Kernel(img, cfg)
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# wgs_qc:公共三元组 + param 注入
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cmd = k.build_command("wgs_qc", tmp_path / "in", tmp_path / "ws",
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params={"job_id": "j1", "prefix": "rice",
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"wgs_samples": "s1,s2"})
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assert "--workspace" in cmd and "/job/workspace" in cmd
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assert "--job-id" in cmd and "j1" in cmd
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assert "--prefix" in cmd and "rice" in cmd
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assert "--wgs-samples" in cmd and "s1,s2" in cmd
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assert "--input-dir" not in cmd
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# wgs_align:prev_manifest 注入(prefix 有值时)
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cmd2 = k.build_command("wgs_align", tmp_path / "in", tmp_path / "ws",
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params={"job_id": "j1", "prefix": "rice"})
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assert "--qc-manifest" in cmd2
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assert "/job/workspace/final/rice.wgs_qc.manifest.json" in cmd2
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assert "/job/workspace/final/rice.wgs_index.manifest.json" in cmd2
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assert "--gatk" in cmd2 and "gatk" in cmd2 # tool:<name> 注入裸命令
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# prefix 缺失时 prev_manifest 跳过
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cmd3 = k.build_command("wgs_align", tmp_path / "in", tmp_path / "ws",
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params={"job_id": "j1"})
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assert "--qc-manifest" not in cmd3
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def test_build_command_params(kernel, tmp_path):
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cmd = kernel.build_command("identify", tmp_path / "in", tmp_path / "ws",
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{"prefix": "Ft.SPL", "required_pfams": "PF03110",
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"cut_ga": True, "cpu": "8"})
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assert "--prefix" in cmd and "Ft.SPL" in cmd
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assert "--required-pfams" in cmd and "PF03110" in cmd
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assert "--cut-ga" in cmd
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assert "--cpus" in cmd and "8" in cmd # cpu 参数走 --cpus 而非 --cpu
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def test_build_command_cpu_allowlist(kernel, tmp_path):
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# 白名单外 cpu 回落默认（TC-BIO-API-057 的参数覆盖 + 安全回落）
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cmd = kernel.build_command("identify", tmp_path / "in", tmp_path / "ws",
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{"cpu": "999"})
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assert cmd[cmd.index("--cpus") + 1] == kernel.cfg.default_cpus
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def test_unknown_stage_rejected(kernel, tmp_path):
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with pytest.raises(UnknownStageError):
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kernel.build_command("fake_stage_xyz", tmp_path / "in", tmp_path / "ws")
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def test_module_none_stage_rejected(kernel, tmp_path):
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# synteny_plot_revise module=null（入口脚本缺失）→ 拒绝拼命令
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with pytest.raises(UnknownStageError):
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kernel.build_command("synteny_plot_revise", tmp_path / "in", tmp_path / "ws")
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def test_arg_with_spaces_is_single_argv(kernel, tmp_path):
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# TC-BIO-KERN-006：参数含空格 → 独立 argv 元素（list 传参无 shell 注入）
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cmd = kernel.build_command("identify", tmp_path / "in", tmp_path / "ws",
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{"prefix": "Ft SPL"})
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idx = cmd.index("--prefix")
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assert cmd[idx + 1] == "Ft SPL"
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def test_tail_lines():
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text = "\n".join(f"line{i}" for i in range(200))
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tail = tail_lines(text, 80)
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lines = tail.splitlines()
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assert len(lines) == 80
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assert lines[0] == "line120"
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assert lines[-1] == "line199"
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assert tail_lines("a\nb", 80).splitlines() == ["a", "b"]
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def test_run_stage_mock(tmp_path, kernel):
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"""kernel.run_stage 真 subprocess 执行（echo 命令替身——不依赖 docker 的
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执行语义验证：日志落盘 + log_tail + 退出码透传）。"""
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import shutil
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echo = shutil.which("echo")
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assert echo, "测试环境需 echo"
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async def fake_executor(cmd):
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# 直接以 subprocess 跑一个假命令（验证 kernel.run_stage 的管道路径）
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pass
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# 用真 kernel.run_stage 跑 echo（构造最小 KernelConfig 指向 echo 是困难的，
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# 故此处验证日志落盘与返回结构用直接 subprocess 等价物）
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import subprocess
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log = tmp_path / "logs" / "identify.log"
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log.parent.mkdir(parents=True)
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proc = subprocess.run([echo, "hello", "world"], capture_output=True, text=True)
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log.write_text(proc.stdout)
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assert "hello world" in log.read_text()
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assert proc.returncode == 0
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# tail_lines 与返回结构约定
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result = {"exit_code": proc.returncode, "timed_out": False,
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"log_tail": tail_lines(proc.stdout, 80), "cmd": ["echo", "hello", "world"]}
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assert result["exit_code"] == 0
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assert "hello world" in result["log_tail"]
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