iomgaa
bceb01e8fa
按任务书 01 实现 delivery、library、answers、runs（快照部分）、build 五个模块， scripts/build.py、scripts/scan_library.py 与 config/build.yaml（decode_codes: false）。 交付包整表检查 T1–T4、映射表检查 T5、逐例检查 C01–C13，一例遇到第一项不过即整例跳过。 与任务书原文的出入： - C04 报告表名随视频名配对（负责人 2026-10-16 定）。 - 按两轮独立审阅加严 C11（更多换行符、比例号冒号）、C12（同义词与词根）、 C13（空格、周岁、中文数字、繁体）；泄露扫描做 NFKC；关键图只接受能保真重编码的 PNG； YAML 配置拒绝重复键和空路径。 - import-linter 第 1 条拆成互不依赖与不引用其他 cadx 模块两条。 文档：结构.md 第五、六、八部分按实际更新；新增 guides/装配两个库.md；WORK_LOG 更新。 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
421 lines
16 KiB
Python
421 lines
16 KiB
Python
"""逐例检查 C01–C13：只让一例违反一项，这一例跳过、记对检查编号，其余病例照常通过。
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预期值照任务书 01 第二部分「单个病例的问题」的文字写。
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"""
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import shutil
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from pathlib import Path
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from cadx.delivery import DeliveryResult, read_delivery
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from cadx.delivery._text import conclusion_headings
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from fake_delivery import (
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CLINICAL_PATH,
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DIAGNOSIS_COLUMN,
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MR_PATH,
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MR_TEXT,
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SAMPLE_CODE_MAPS,
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ULTRASOUND_HEADER,
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ULTRASOUND_PATH,
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ULTRASOUND_TEXT,
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FakeDelivery,
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make_delivery,
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)
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def _read(
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tmp_path: Path, delivery: FakeDelivery, code_maps: dict[str, dict[int, str]] | None
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) -> DeliveryResult:
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return read_delivery(delivery.write(tmp_path / "delivery"), code_maps)
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def _assert_only_skipped(result: DeliveryResult, case: str, check: str, total: int) -> None:
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assert [(s.case, s.check) for s in result.skipped] == [(case, check)]
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passed = [f"{n:03d}" for n in range(1, total + 1) if f"{n:03d}" != case]
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assert [c.case_no for c in result.cases] == passed
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assert result.total_cases == total
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def test_all_pass(tmp_path: Path) -> None:
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result = _read(tmp_path, make_delivery(4), None)
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assert [c.case_no for c in result.cases] == ["001", "002", "003", "004"]
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assert result.skipped == ()
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assert result.unrecognized_rows == 0
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def test_c01_unrecognized_clinical_id_is_its_own_row_and_case_missing(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(2).clinical["Case_ID"] = "P2" # 临床表要求 P 加三位数字
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result = _read(tmp_path, delivery, None)
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# 第 1 行是表头，病例 2 在第 3 行；同一个病人因此在 C03（缺在临床表）再记一条。
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assert [(s.case, s.check) for s in result.skipped] == [
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(f"{CLINICAL_PATH} 第 3 行", "C01"),
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("002", "C03"),
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]
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assert result.unrecognized_rows == 1
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assert result.total_cases == 4
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assert [c.case_no for c in result.cases] == ["001", "003", "004"]
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def test_c01_float_report_id_is_unrecognized(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(3).mr["患者ID"] = 3.5 # 浮点不是认得出的写法
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result = _read(tmp_path, delivery, None)
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assert [(s.case, s.check) for s in result.skipped] == [
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(f"{MR_PATH} 第 4 行", "C01"),
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("003", "C03"),
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]
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def test_c01_report_ids_accept_int_and_zero_padded_strings(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).ultrasound["患者ID"] = 1
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delivery.case(2).mr["患者ID"] = "002"
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delivery.case(2).ultrasound["患者ID"] = "02"
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result = _read(tmp_path, delivery, None)
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assert result.skipped == ()
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assert len(result.cases) == 3
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def test_c02_duplicate_id_in_one_table(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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duplicate = delivery.case(2).mr
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delivery.extra_rows[MR_PATH].append([duplicate[h] for h in delivery.headers[MR_PATH]])
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C02", 4)
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def test_c03_case_directory_missing(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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root = delivery.write(tmp_path / "delivery")
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shutil.rmtree(root / "CEUS_agent" / "003")
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_assert_only_skipped(read_delivery(root, None), "003", "C03", 4)
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def test_c04_missing_key_image(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(4).dir_files.remove("U004_key.png")
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_assert_only_skipped(_read(tmp_path, delivery, None), "004", "C04", 4)
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def test_c04_extra_file(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).dir_files.append("U001.mp4") # 两个视频共四个文件
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_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C04", 3)
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def test_c04_roi2_video_with_roi2_report_passes(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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assert delivery.case(2).dir_files == ["U002_key.png", "U002_roi2.mp4", "U002_roi2_report.xlsx"]
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assert _read(tmp_path, delivery, None).skipped == ()
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def test_c04_plain_video_with_plain_report_passes(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(3).dir_files = ["U003_key.png", "U003.mp4", "U003_report.xlsx"]
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result = _read(tmp_path, delivery, None)
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assert result.skipped == ()
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assert len(result.cases) == 3
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def test_c04_roi2_video_with_plain_report_is_skipped(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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# 文件名被 gitleaks 的通用密钥规则误报，不是密钥。
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delivery.case(1).dir_files = [
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"U001_key.png",
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"U001_roi2.mp4", # gitleaks:allow
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"U001_report.xlsx",
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]
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_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C04", 3)
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def test_c04_plain_video_with_roi2_report_is_skipped(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(2).dir_files = ["U002_key.png", "U002.mp4", "U002_roi2_report.xlsx"]
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C04", 3)
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def test_c06_reads_plain_report_when_paired_with_plain_video(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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case = delivery.case(3)
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case.dir_files = ["U003_key.png", "U003.mp4", "U003_report.xlsx"]
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row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
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row[-1] = ULTRASOUND_TEXT + "补充一句。"
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case.case_report_rows = [list(ULTRASOUND_HEADER), row]
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_assert_only_skipped(_read(tmp_path, delivery, None), "003", "C06", 3)
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def test_c05_video_id_mismatch(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(2).ultrasound["CEUS视频ID"] = "U003"
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C05", 4)
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def test_c06_case_report_cell_differs(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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case = delivery.case(3)
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row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
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row[-1] = ULTRASOUND_TEXT + "补充一句。"
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case.case_report_rows = [list(ULTRASOUND_HEADER), row]
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result = _read(tmp_path, delivery, None)
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_assert_only_skipped(result, "003", "C06", 4)
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assert result.skipped[0].columns == ("超声描述",)
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def test_c06_case_report_cell_type_differs(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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case = delivery.case(1)
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row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
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row[0] = 1 # 汇总表里是字符串 "1"
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case.case_report_rows = [list(ULTRASOUND_HEADER), row]
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_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C06", 3)
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def test_c06_case_report_wrong_sheet(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(2).case_report_sheet = "Sheet2"
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C06", 3)
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def test_c06_case_report_two_data_rows(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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case = delivery.case(2)
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row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
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case.case_report_rows = [list(ULTRASOUND_HEADER), row, row]
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C06", 3)
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def test_c07_bool_sex_is_not_an_int(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).clinical["Sex"] = True # bool 是 int 的子类，不能当作 1
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_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C07", 3)
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def test_c01_bool_report_id_is_unrecognized(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).ultrasound["患者ID"] = True
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result = _read(tmp_path, delivery, None)
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assert [(s.case, s.check) for s in result.skipped] == [
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(f"{ULTRASOUND_PATH} 第 2 行", "C01"),
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("001", "C03"),
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]
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def test_c07_sex_out_of_range(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(1).clinical["Sex"] = 3
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_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C07", 4)
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def test_c07_non_integer_age(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(2).clinical["Age"] = 32.5
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C07", 3)
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def test_c07_symptom_empty(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(2).clinical["Symptom_Fever"] = None
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C07", 3)
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def test_c07_lab_only_one_column_empty(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(2).clinical["CA199"] = None # 档位列仍是 0
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result = _read(tmp_path, delivery, None)
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_assert_only_skipped(result, "002", "C07", 4)
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assert set(result.skipped[0].columns) == {"CA199", "CA199_Level"}
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def test_c07_lab_both_empty_is_fine(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).clinical["TBil"] = None
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delivery.case(1).clinical["TBil_Level"] = None
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assert _read(tmp_path, delivery, None).skipped == ()
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def test_c07_value_missing_from_code_map(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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maps = {**SAMPLE_CODE_MAPS, "Hx_Alcohol": {0: "否"}} # 映射表里没有 1
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delivery.case(2).clinical["Hx_Alcohol"] = 1
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_assert_only_skipped(_read(tmp_path, delivery, maps), "002", "C07", 3)
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def test_c08_ultrasound_sex_invalid(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(4).ultrasound["性别"] = "M"
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_assert_only_skipped(_read(tmp_path, delivery, None), "004", "C08", 4)
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def test_c08_negative_bolus_time(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(3).ultrasound["推注开始时间s"] = -1
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_assert_only_skipped(_read(tmp_path, delivery, None), "003", "C08", 3)
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def test_c08_empty_description(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).ultrasound["超声描述"] = None
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_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C08", 3)
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def test_c09_mr_age_not_number_plus_sui(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(3).mr["年龄"] = "33"
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_assert_only_skipped(_read(tmp_path, delivery, None), "003", "C09", 4)
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def test_c09_mr_diagnosis_out_of_range(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(2).mr[DIAGNOSIS_COLUMN] = 5
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C09", 3)
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def test_c10_diagnosis_mismatch(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(1).clinical["Diagnosis"] = 2 # 两张报告表仍是 1
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result = _read(tmp_path, delivery, None)
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_assert_only_skipped(result, "001", "C10", 4)
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assert result.skipped[0].columns == ("诊断",)
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def test_c10_age_mismatch(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(2).mr["年龄"] = "99岁"
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result = _read(tmp_path, delivery, None)
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_assert_only_skipped(result, "002", "C10", 4)
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assert result.skipped[0].columns == ("年龄",)
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def test_c10_sex_mismatch_between_reports(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(3).mr["性别"] = "男" if delivery.case(3).ultrasound["性别"] == "女" else "女"
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result = _read(tmp_path, delivery, None)
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_assert_only_skipped(result, "003", "C10", 4)
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assert result.skipped[0].columns == ("性别",)
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def test_c10_clinical_sex_compared_only_when_decoding(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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case = delivery.case(2)
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case.clinical["Sex"] = 1 if case.clinical["Sex"] == 2 else 2 # 报告表的性别不变
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undecoded = _read(tmp_path / "a", delivery, None)
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assert undecoded.skipped == ()
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assert undecoded.uncompared == ("临床性别未比对",)
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decoded = _read(tmp_path / "b", delivery, SAMPLE_CODE_MAPS)
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_assert_only_skipped(decoded, "002", "C10", 3)
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assert decoded.uncompared == ()
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def test_c11_heading_at_start_with_fullwidth_colon(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(2).ultrasound["超声描述"] = "结论：胰体部囊性病灶。" + ULTRASOUND_TEXT
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_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C11", 4)
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def test_c11_heading_after_newline(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(3).mr["MR描述"] = MR_TEXT + "\n印象 : 胰体部囊性病灶。"
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result = _read(tmp_path, delivery, None)
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_assert_only_skipped(result, "003", "C11", 4)
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assert result.skipped[0].columns == ("MR描述",)
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def test_c11_heading_mid_text_is_not_a_failure(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).ultrasound["超声描述"] = "胰体部见一无回声区。造影提示：囊壁呈等增强。"
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result = _read(tmp_path, delivery, None)
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assert result.skipped == ()
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assert len(result.cases) == 3
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def test_c12_subtype_name_fullwidth_lowercase(tmp_path: Path) -> None:
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delivery = make_delivery(4)
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delivery.case(4).mr["MR描述"] = MR_TEXT + "形态类似ｉｐｍｎ。"
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_assert_only_skipped(_read(tmp_path, delivery, None), "004", "C12", 4)
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def test_c12_chinese_subtype_name(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).ultrasound["超声描述"] = ULTRASOUND_TEXT + "符合浆液性囊腺瘤表现。"
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_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C12", 3)
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def test_c11_heading_after_vertical_tab_or_form_feed() -> None:
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# xlsx（XML）里写不进 \x0b、\x0c，openpyxl 拒绝生成，所以直接测规则函数。
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for separator in ("\x0b", "\x0c"):
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text = MR_TEXT + separator + "诊断：胰体部囊性病灶。"
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assert [k for k, _ in conclusion_headings(text)] == ["诊断"]
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def test_c11_heading_after_unicode_line_separator(tmp_path: Path) -> None:
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for i, separator in enumerate(("\x85", "\u2028", "\u2029")):
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delivery = make_delivery(3)
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delivery.case(2).mr["MR描述"] = MR_TEXT + separator + "诊断：胰体部囊性病灶。"
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_assert_only_skipped(_read(tmp_path / str(i), delivery, None), "002", "C11", 3)
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def test_c11_ratio_sign_as_colon(tmp_path: Path) -> None:
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delivery = make_delivery(3)
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delivery.case(1).ultrasound["超声描述"] = "超声提示∶胰体部囊性病灶。" + ULTRASOUND_TEXT
|
||
result = _read(tmp_path, delivery, None)
|
||
_assert_only_skipped(result, "001", "C11", 3)
|
||
assert '"关键词": "超声提示"' in result.skipped[0].value_json
|
||
|
||
|
||
def test_c12_new_subtype_terms(tmp_path: Path) -> None:
|
||
terms = (
|
||
"SPT",
|
||
"ｓｐｔｐ",
|
||
"IPMT",
|
||
"导管内乳头",
|
||
"实性假乳头",
|
||
"黏液囊性",
|
||
"粘液囊性",
|
||
"囊腺瘤",
|
||
"浆液性微囊",
|
||
)
|
||
for i, term in enumerate(terms):
|
||
delivery = make_delivery(3)
|
||
delivery.case(3).ultrasound["超声描述"] = ULTRASOUND_TEXT + f"形态与{term}相似。"
|
||
_assert_only_skipped(_read(tmp_path / str(i), delivery, None), "003", "C12", 3)
|
||
|
||
|
||
def test_c12_serous_alone_is_fine(tmp_path: Path) -> None:
|
||
delivery = make_delivery(3)
|
||
delivery.case(1).ultrasound["超声描述"] = ULTRASOUND_TEXT + "囊液呈浆液性。"
|
||
assert _read(tmp_path, delivery, None).skipped == ()
|
||
|
||
|
||
def test_c13_age_in_report(tmp_path: Path) -> None:
|
||
delivery = make_delivery(4)
|
||
delivery.case(1).ultrasound["超声描述"] = "患者４５岁。" + ULTRASOUND_TEXT
|
||
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C13", 4)
|
||
|
||
|
||
def test_c13_age_variants(tmp_path: Path) -> None:
|
||
for i, age in enumerate(("四十五岁", "45 岁", "6周岁", "三十歲", "１２周岁")):
|
||
delivery = make_delivery(3)
|
||
delivery.case(2).mr["MR描述"] = f"患者{age}。" + MR_TEXT
|
||
_assert_only_skipped(_read(tmp_path / str(i), delivery, None), "002", "C13", 3)
|
||
|
||
|
||
def test_c13_sex_character_in_report(tmp_path: Path) -> None:
|
||
delivery = make_delivery(3)
|
||
delivery.case(3).mr["MR描述"] = "女性患者。" + MR_TEXT
|
||
_assert_only_skipped(_read(tmp_path, delivery, None), "003", "C13", 3)
|
||
|
||
|
||
def test_only_first_failing_check_is_recorded(tmp_path: Path) -> None:
|
||
delivery = make_delivery(3)
|
||
delivery.case(2).ultrasound["性别"] = "M" # C08
|
||
delivery.case(2).mr["年龄"] = "99岁" # C10
|
||
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C08", 3)
|
||
|
||
|
||
def test_skip_record_names_file_and_column(tmp_path: Path) -> None:
|
||
delivery = make_delivery(3)
|
||
delivery.case(2).ultrasound["推注开始时间s"] = 2.5
|
||
record = _read(tmp_path, delivery, None).skipped[0]
|
||
assert record.files == (ULTRASOUND_PATH,)
|
||
assert record.columns == ("推注开始时间s",)
|
||
assert record.value_json == '{"推注开始时间s": 2.5}'
|