85 lines
2.8 KiB
Python
85 lines
2.8 KiB
Python
"""tests/test_catalog.py —— 阶段目录（映射表驱动 + 参数 schema + 前置补全）。"""
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from __future__ import annotations
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import pytest
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pytestmark = pytest.mark.bioflow_unit
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def test_stage_names(catalog):
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names = catalog.stage_names()
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assert "identify" in names
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assert "phylogeny" in names
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assert len(names) >= 7
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def test_has_and_get(catalog):
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assert catalog.has("identify")
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assert not catalog.has("fake_stage_xyz")
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entry = catalog.get("identify")
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assert entry.name == "identify"
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assert entry.image == "bioflow-gf"
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assert entry.module == "cli.run_identify"
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assert entry.executable is True
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assert entry.description == "基因家族鉴定"
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assert entry.estimated_time == 5
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assert entry.to_dict()["image"] == "bioflow-gf"
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def test_params_schema(catalog):
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entry = catalog.get("identify")
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assert entry.params
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for p in entry.params:
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assert {"name", "type", "default", "source", "help"} <= set(p.keys())
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names = {p["name"] for p in entry.params}
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assert "cpu" in names and "required_pfams" in names
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def test_inputs_outputs(catalog):
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entry = catalog.get("identify")
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assert any(i["name"] == "protein_fasta" for i in entry.inputs)
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assert any(o["name"] == "final_members" for o in entry.outputs)
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# 下游阶段通用跨阶段输入
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entry2 = catalog.get("phylogeny")
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assert entry2.inputs
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def test_family_chain(catalog):
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chain = catalog.family_chain()
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assert chain[0] == "genome_prepare"
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assert "identify" in chain
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assert len(chain) == 5 # 测试映射表的 family_chain
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def test_validate_chain(catalog):
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assert catalog.validate_chain(["identify", "phylogeny"]) == []
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assert catalog.validate_chain(["fake_stage_xyz"]) == ["fake_stage_xyz"]
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def test_auto_fill_prerequisites(catalog):
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"""FR-BIO-003：前置补全 + 拓扑排序（依赖在前）。"""
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ordered, added = catalog.auto_fill_prerequisites(["motif", "phylogeny"])
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assert "identify" in ordered
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assert ordered.index("identify") < ordered.index("phylogeny")
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assert ordered.index("phylogeny") < ordered.index("motif")
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assert "identify" in added # 明示补全
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def test_topo_order():
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from app.services.bioflow.catalog import topo_order
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# reference_classification 依赖 identify/phylogeny/motif/structure/domain/combo
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ordered = topo_order(["reference_classification", "identify"])
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assert ordered[0] == "identify"
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assert ordered[-1] == "reference_classification"
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def test_note_passthrough(catalog):
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entry = catalog.get("expression")
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assert entry.note.startswith("跨环境")
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assert entry.to_dict()["note"] == entry.note
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def test_dependencies(catalog):
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assert "identify" in catalog.dependencies("phylogeny")
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assert catalog.dependencies("identify") == []
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