341 lines
17 KiB
Python
341 lines
17 KiB
Python
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# -*- coding: utf-8 -*-
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"""MABC 标记辅助回交进度正式 tc 套件：TestClient 走真实 API + golden 数值断言（纯计算端点）。
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fixture（镜像 e2e_mabc）：轮回亲本 rp_tree 背景面板全纯合 1/1；候选 BC 分离株 6 棵
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（前景 F1/F2 + 背景 M1..M4，min_hits=2）：C1(全 1/1→恢复100%)、C2(背景 M2 杂合→75%)、
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C3(前景 1 命中 fail→75%)、C4(全 1/1→100%)、C5(背景全杂合→0%)、C6(童期→100%)。
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经真实 HTTP 端点 POST /api/v1/bre/statistics/mabc-progress 断言：
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[1] 前景命中与通过（C1 pass/C3 fail、n_pass=5）
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[2] 背景恢复率复算（100/75/75/0）+ n_background_compared=4
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[3] 回交代建议（C1 晋级 BC2 / C2 再回交 / C3 前景未通过维持）reason 语义
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[4] recommended 恰为前景通过子集 + 恢复率降序
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[5] 童期 C6 前景通过 + 晋级（stage 无关）
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[6] 轮回亲本无基因型 → warning + 恢复率 None
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[7] 校验 409：空候选/空前景面板/空背景面板/非法世代/target 越界/轮回亲本不存在
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依赖: Redis + PG 正常（TestClient 走真实 lifespan）。运行后自动清理。
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"""
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import os
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os.environ["ENVIRONMENT"] = "dev"
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os.environ["PYTHONUTF8"] = "1"
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import sys, asyncio # noqa: E402
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sys.path.insert(0, r"d:\dpb\dpb\backend")
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import main # noqa: E402
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from fastapi.testclient import TestClient # noqa: E402
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from sqlalchemy import delete # noqa: E402
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from app.core.database import create_async_engine_and_session # noqa: E402
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from app.api.v1.module_system.user.model import UserModel # noqa: E402 (注册 mapper)
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from app.api.v1.module_bre.target.model import TargetModel # noqa: E402
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from app.api.v1.module_bre.germplasm.model import BreedingGermplasmModel # noqa: E402
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from app.api.v1.module_bre.cross_combination.model import CrossCombinationModel # noqa: E402
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from app.api.v1.module_bre.tree.model import TreeModel # noqa: E402
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from app.api.v1.module_bre.marker.model import MarkerModel # noqa: E402
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from app.api.v1.module_bre.genotype_dataset.model import GenotypingDatasetModel # noqa: E402
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from app.api.v1.module_bre.genotype_sample.model import GenotypeSampleModel # noqa: E402
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from app.api.v1.module_bre.genotype_call.model import GenotypeCallModel # noqa: E402
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from app.api.v1.module_bre.statistics.model import MasPanelModel, MasPanelMarkerModel # noqa: E402
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create_app = main.create_app
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TOKEN = None
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ok, fail = 0, 0
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PREFIX = "TC_MABC"
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tokens: dict[str, list[int]] = {
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"germ": [], "tree": [], "combo": [], "target": [],
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"marker": [], "dataset": [], "sample": [], "call": [],
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"panel": [], "panelmarker": [],
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}
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FIX: dict = {}
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def check(name, cond, detail=""):
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global ok, fail
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if cond:
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ok += 1
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print(f" [ok] {name} {detail}")
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else:
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fail += 1
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print(f" [FAIL] {name} {detail}")
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def login(client):
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global TOKEN
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d = {"username": "super", "password": "123456", "grant_type": "password", "login_type": "PC端"}
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r = client.post("/api/v1/system/auth/login", data=d)
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b = r.json()
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if r.status_code == 200 and b.get("code") == 0:
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TOKEN = b["data"]["access_token"]
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return
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key = client.get("/api/v1/system/auth/captcha/get").json()["data"]["key"]
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client.post("/api/v1/system/auth/captcha/slider/complete", json={"captcha_key": key})
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d["captcha_key"] = key
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r = client.post("/api/v1/system/auth/login", data=d)
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b = r.json()
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assert r.status_code == 200 and b.get("code") == 0, f"LOGIN FAIL {r.status_code} {b}"
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TOKEN = b["data"]["access_token"]
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def auth():
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return {"Authorization": f"Bearer {TOKEN}"}
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async def _build_fixture() -> None:
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engine, sf = create_async_engine_and_session()
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try:
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async with sf() as db:
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target = TargetModel(target_name=f"{PREFIX}-T", created_id=1)
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db.add(target)
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await db.flush()
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tokens["target"].append(target.id)
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combo = CrossCombinationModel(
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combination_code=f"{PREFIX}-C1", bre_target_id=target.id,
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female_parent_id=None, male_parent_id=None, design_type="full_diallel", created_id=1)
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db.add(combo)
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await db.flush()
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tokens["combo"].append(combo.id)
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rp_g = BreedingGermplasmModel(cultivar_name=f"{PREFIX}-RP", can_be_female=True,
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can_be_male=True, created_id=1)
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db.add(rp_g)
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await db.flush()
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tokens["germ"].append(rp_g.id)
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def mk_tree(no, stage="line", generation="BC1"):
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t = TreeModel(combination_id=combo.id, tree_no=no, status="alive", stage=stage,
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generation=generation, planted_date="2025-03-10", created_id=1)
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db.add(t)
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return t
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rp_tree = mk_tree(f"{PREFIX}-RP-T")
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cands = {nm: mk_tree(f"{PREFIX}-{nm}", stage="juvenile" if nm == "C6" else "line")
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for nm in ("C1", "C2", "C3", "C4", "C5", "C6")}
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rp_nogeno = mk_tree(f"{PREFIX}-RPNG-T")
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await db.flush()
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tokens["tree"] = [t.id for t in ([rp_tree, rp_nogeno] + list(cands.values()))]
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FIX.update({"rp": rp_tree.id, "rp_nogeno": rp_nogeno.id,
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"cand": {nm: t.id for nm, t in cands.items()}})
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fg_markers, bg_markers = [], []
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for j, nm in enumerate(["F1", "F2"]):
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m = MarkerModel(marker_name=f"{PREFIX}-{nm}", marker_type="SNP",
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chromosome="5", position=100 + j, created_id=1)
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db.add(m)
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fg_markers.append(m)
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for j in range(4):
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m = MarkerModel(marker_name=f"{PREFIX}-M{j + 1}", marker_type="SNP",
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chromosome=str(j), position=j * 100, created_id=1)
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db.add(m)
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bg_markers.append(m)
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await db.flush()
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tokens["marker"] = [m.id for m in fg_markers + bg_markers]
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FIX["fg_markers"] = fg_markers
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FIX["bg_markers"] = bg_markers
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fg_panel = MasPanelModel(panel_name=f"{PREFIX}-FG", n_markers=2, created_id=1)
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bg_panel = MasPanelModel(panel_name=f"{PREFIX}-BG", n_markers=4, created_id=1)
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db.add_all([fg_panel, bg_panel])
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await db.flush()
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tokens["panel"] = [fg_panel.id, bg_panel.id]
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FIX["fg_panel"] = fg_panel.id
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FIX["bg_panel"] = bg_panel.id
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for m in fg_markers:
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db.add(MasPanelMarkerModel(panel_id=fg_panel.id, marker_id=m.id,
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favorable_dose=1, direction="high",
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mode="additive", created_id=1))
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tokens["panelmarker"].append(0)
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for m in bg_markers:
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db.add(MasPanelMarkerModel(panel_id=bg_panel.id, marker_id=m.id, created_id=1))
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tokens["panelmarker"].append(0)
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await db.flush()
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ds = GenotypingDatasetModel(dataset_name=f"{PREFIX}-DS", platform="SNP",
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purpose="GS", created_id=1)
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db.add(ds)
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await db.flush()
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tokens["dataset"].append(ds.id)
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all_markers = fg_markers + bg_markers
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def mk_sample(tree, no):
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s = GenotypeSampleModel(sample_name=no, dataset_id=ds.id,
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source_type="tree", source_id=tree.id, created_id=1)
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db.add(s)
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return s
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rp_s = mk_sample(rp_tree, f"{PREFIX}-RP-S")
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samp_by_cand = {nm: mk_sample(t, f"{PREFIX}-{nm}-S") for nm, t in cands.items()}
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await db.flush()
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tokens["sample"] = [rp_s.id] + [s.id for s in samp_by_cand.values()]
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GENO = {
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"C1": ("1/1", "1/1", ["1/1", "1/1", "1/1", "1/1"]),
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"C2": ("0/1", "1/1", ["1/1", "0/1", "1/1", "1/1"]),
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"C3": ("0/0", "1/1", ["1/1", "1/1", "1/1", "0/0"]),
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"C4": ("1/1", "0/1", ["1/1", "1/1", "1/1", "1/1"]),
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"C5": ("1/1", "1/1", ["0/1", "0/1", "0/1", "0/1"]),
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"C6": ("1/1", "1/1", ["1/1", "1/1", "1/1", "1/1"]),
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}
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calls = []
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for j, m in enumerate(all_markers):
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calls.append(GenotypeCallModel(sample_id=rp_s.id, marker_id=m.id,
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allele="1/1", created_id=1))
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for nm, (f1, f2, bg) in GENO.items():
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s = samp_by_cand[nm]
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calls.append(GenotypeCallModel(sample_id=s.id, marker_id=fg_markers[0].id,
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allele=f1, created_id=1))
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calls.append(GenotypeCallModel(sample_id=s.id, marker_id=fg_markers[1].id,
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allele=f2, created_id=1))
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for j, m in enumerate(bg_markers):
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calls.append(GenotypeCallModel(sample_id=s.id, marker_id=m.id,
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allele=bg[j], created_id=1))
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db.add_all(calls)
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await db.flush()
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tokens["call"] = [c.id for c in calls]
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await db.commit()
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finally:
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await engine.dispose()
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async def _cleanup() -> None:
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engine, sf = create_async_engine_and_session()
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try:
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async with sf() as db:
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if tokens["call"]:
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await db.execute(delete(GenotypeCallModel).where(
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GenotypeCallModel.id.in_(tokens["call"])))
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if tokens["sample"]:
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await db.execute(delete(GenotypeSampleModel).where(
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GenotypeSampleModel.id.in_(tokens["sample"])))
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if tokens["dataset"]:
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await db.execute(delete(GenotypingDatasetModel).where(
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GenotypingDatasetModel.id.in_(tokens["dataset"])))
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if tokens["panelmarker"]:
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await db.execute(delete(MasPanelMarkerModel).where(
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MasPanelMarkerModel.panel_id.in_(tokens["panel"])))
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if tokens["panel"]:
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await db.execute(delete(MasPanelModel).where(MasPanelModel.id.in_(tokens["panel"])))
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if tokens["marker"]:
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await db.execute(delete(MarkerModel).where(MarkerModel.id.in_(tokens["marker"])))
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if tokens["tree"]:
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await db.execute(delete(TreeModel).where(TreeModel.id.in_(tokens["tree"])))
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if tokens["combo"]:
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await db.execute(delete(CrossCombinationModel).where(
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CrossCombinationModel.id.in_(tokens["combo"])))
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if tokens["germ"]:
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await db.execute(delete(BreedingGermplasmModel).where(
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BreedingGermplasmModel.id.in_(tokens["germ"])))
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if tokens["target"]:
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await db.execute(delete(TargetModel).where(TargetModel.id.in_(tokens["target"])))
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await db.commit()
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print("[cleanup] MABC tc 数据已清")
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finally:
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await engine.dispose()
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def main_() -> None:
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asyncio.run(_build_fixture())
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try:
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with TestClient(create_app()) as client:
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login(client)
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c = FIX["cand"]
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cand_ids = [c[nm] for nm in ("C1", "C2", "C3", "C4", "C5", "C6")]
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def post_mabc(cands_, fg, bg, rp_, generation="BC1", background_target=90.0, min_hits=2):
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r = client.post("/api/v1/bre/statistics/mabc-progress", json={
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"candidate_tree_ids": cands_, "foreground_panel_ids": fg,
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"background_panel_ids": bg, "recurrent_parent_tree_id": rp_,
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"foreground_min_hits": min_hits, "generation": generation,
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"background_target": background_target}, headers=auth())
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if r.status_code != 200:
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return None, r.status_code
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b = r.json()
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return (b.get("data") if b.get("code") == 0 else None), r.status_code
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m, sc = post_mabc(cand_ids, [FIX["fg_panel"]], [FIX["bg_panel"]], FIX["rp"])
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check("[HTTP] mabc-progress 200", sc == 200, f"{sc}")
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if m is None:
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return
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row = {r["tree_id"]: r for r in m["per_tree"]}
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# ---- [1] 前景命中与通过 ----
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check("[1] C1 前景 pass (2 命中)", row[c["C1"]]["foreground_pass"]
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and row[c["C1"]]["foreground_hits"] == 2,
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f"{row[c['C1']]['foreground_hits_by_panel']}")
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check("[1] C3 前景 fail (1 命中)", not row[c["C3"]]["foreground_pass"]
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and row[c["C3"]]["foreground_hits"] == 1, f"{row[c['C3']]['foreground_hits']}")
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check("[1] n_pass=5（C1/C2/C4/C5/C6）", m["summary"]["n_pass"] == 5,
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f"{m['summary']['n_pass']}")
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# ---- [2] 背景恢复率复算 ----
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check("[2] C1 恢复 100%", row[c["C1"]]["background_recovery"] == 100.0)
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check("[2] C2 恢复 75%", row[c["C2"]]["background_recovery"] == 75.0,
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f"{row[c['C2']]['background_recovery']}")
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check("[2] C3 恢复 75%（前景 fail 也评估背景）",
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row[c["C3"]]["background_recovery"] == 75.0)
|
|||
|
|
check("[2] C5 恢复 0%（全杂合）", row[c["C5"]]["background_recovery"] == 0.0)
|
|||
|
|
check("[2] 背景对比标记数=4", all(r["n_background_compared"] == 4 for r in row.values()),
|
|||
|
|
f"{[r['n_background_compared'] for r in row.values()]}")
|
|||
|
|
|
|||
|
|
# ---- [3] 回交代建议 ----
|
|||
|
|
check("[3] C1 晋级 BC2", row[c["C1"]]["bc_generation"] == "BC2"
|
|||
|
|
and "晋级" in row[c["C1"]]["reason"], row[c["C1"]]["reason"])
|
|||
|
|
check("[3] C2 再回交 BC1", row[c["C2"]]["bc_generation"] == "BC1"
|
|||
|
|
and "再回交" in row[c["C2"]]["reason"], row[c["C2"]]["reason"])
|
|||
|
|
check("[3] C3 维持 BC1（前景未通过）", row[c["C3"]]["bc_generation"] == "BC1"
|
|||
|
|
and "前景未通过" in row[c["C3"]]["reason"], row[c["C3"]]["reason"])
|
|||
|
|
|
|||
|
|
# ---- [4] recommended 排序 ----
|
|||
|
|
rec_ids = [r["tree_id"] for r in m["recommended"]]
|
|||
|
|
pass_set = {c[nm] for nm in ("C1", "C2", "C4", "C5", "C6")}
|
|||
|
|
check("[4] recommended 恰为前景通过子集", set(rec_ids) == pass_set, f"{rec_ids}")
|
|||
|
|
rec_recovery = [r["background_recovery"] for r in m["recommended"]]
|
|||
|
|
check("[4] 恢复率降序", rec_recovery == [100.0, 100.0, 100.0, 75.0, 0.0],
|
|||
|
|
f"{rec_recovery}")
|
|||
|
|
|
|||
|
|
# ---- [5] 童期候选被前景选中 ----
|
|||
|
|
check("[5] 童期 C6 前景通过 + 晋级", row[c["C6"]]["foreground_pass"]
|
|||
|
|
and row[c["C6"]]["background_recovery"] == 100.0
|
|||
|
|
and row[c["C6"]]["bc_generation"] == "BC2", row[c["C6"]])
|
|||
|
|
|
|||
|
|
# ---- [6] 轮回亲本无基因型 → warning + 恢复率 None ----
|
|||
|
|
m6, sc6 = post_mabc([c["C1"]], [FIX["fg_panel"]], [FIX["bg_panel"]], FIX["rp_nogeno"])
|
|||
|
|
check("[6] mabc 200", sc6 == 200, f"{sc6}")
|
|||
|
|
if m6:
|
|||
|
|
check("[6] warning 提示轮回亲本无背景基因型",
|
|||
|
|
m6["warning"] and "轮回亲本" in m6["warning"], m6["warning"])
|
|||
|
|
check("[6] 恢复率 None + 建议维持世代",
|
|||
|
|
m6["per_tree"][0]["background_recovery"] is None
|
|||
|
|
and m6["per_tree"][0]["bc_generation"] == "BC1"
|
|||
|
|
and "无法评估" in m6["per_tree"][0]["reason"],
|
|||
|
|
m6["per_tree"][0]["reason"])
|
|||
|
|
|
|||
|
|
# ---- [7] 校验 409 ----
|
|||
|
|
bad = [
|
|||
|
|
([], [FIX["fg_panel"]], [FIX["bg_panel"]], FIX["rp"]),
|
|||
|
|
([c["C1"]], [], [FIX["bg_panel"]], FIX["rp"]),
|
|||
|
|
([c["C1"]], [FIX["fg_panel"]], [], FIX["rp"]),
|
|||
|
|
([c["C1"]], [FIX["fg_panel"]], [FIX["bg_panel"]], FIX["rp"]),
|
|||
|
|
([c["C1"]], [FIX["fg_panel"]], [FIX["bg_panel"]], FIX["rp"]),
|
|||
|
|
([c["C1"]], [FIX["fg_panel"]], [FIX["bg_panel"]], 999999999),
|
|||
|
|
]
|
|||
|
|
tags = ["空候选", "空前景面板", "空背景面板", "非法世代", "target 越界", "轮回亲本不存在"]
|
|||
|
|
for (cands_, fg, bg, rp_), tag in zip(bad, tags):
|
|||
|
|
kw = {}
|
|||
|
|
if tag == "非法世代":
|
|||
|
|
kw["generation"] = "BC9"
|
|||
|
|
if tag == "target 越界":
|
|||
|
|
kw["background_target"] = 120.0
|
|||
|
|
_, scx = post_mabc(cands_, fg, bg, rp_, **kw)
|
|||
|
|
# target 越界在 schema 层 Pydantic 校验（le=100）即拦截 → 422；其余走服务层 409
|
|||
|
|
expect = 422 if tag == "target 越界" else 409
|
|||
|
|
check(f"[7] {tag} → {expect}", scx == expect, f"{scx}")
|
|||
|
|
finally:
|
|||
|
|
asyncio.run(_cleanup())
|
|||
|
|
|
|||
|
|
print(f"\n===== MABC tc 套件：ok={ok} fail={fail} =====")
|
|||
|
|
|
|||
|
|
|
|||
|
|
if __name__ == "__main__":
|
|||
|
|
main_()
|
|||
|
|
sys.exit(1 if fail else 0)
|