feat: 装配两个库（不含 CEUS 结果）
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>
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## 当前目标
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## 当前目标
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骨架已完成；整体架构已和负责人讨论定稿（`research-wiki/design/0002`、`explanation/结构.md`）。下一步是写第 2 步「装配两个库（不含 CEUS）」的任务书 `research-wiki/任务书/01-装配两个库.md`。
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第 2 步「装配两个库（不含 CEUS）」已按任务书 01 实现，等监督者验收。之后是第 3 步 CEUS 定量或会诊口径讨论（`结构.md` 第七部分）。
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## 已完成
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## 已完成
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- 2026-10-15/16 深读旧项目三条线（CEUS 算法、资料与答案隔离、会诊与评价），两位中立评审独立评了存储与迁移方案；结论落成 design 0002 与重写的 `结构.md`。待定的研究问题记在 `research-wiki/待定问题/`。
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- 2026-10-15/16 深读旧项目三条线（CEUS 算法、资料与答案隔离、会诊与评价），两位中立评审独立评了存储与迁移方案；结论落成 design 0002 与重写的 `结构.md`。待定的研究问题记在 `research-wiki/待定问题/`。
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- 2026-10-16 任务书 01 装配两个库：delivery、library、answers、runs（快照）、build 五个模块，`scripts/build.py`、`scripts/scan_library.py`、`config/build.yaml`，91 条测试，`make check` 通过（6 条导入契约）。两轮独立审阅的会悄悄漏答案的意见已修（C11–C13 加严、泄露扫描 NFKC、关键图只收能保真重编码的 PNG、YAML 拒绝重复键）。真实 40 例：40 例中 34 例进库，跳过 6 例全为 C10（跨表不一致，与 `待定问题/04` 一致），复核清单 2 条，泄露扫描命中 0；构建号与提交号见提交说明和本次汇报。使用说明 `guides/装配两个库.md`。
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## 未完成
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## 未完成
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- `结构.md` 按负责人要求对照 ClinDB 的 `结构.md` 重写后，重写版还没再过一轮「硕士生阅读」（design 0002 与上一版结构文档过过）。
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- `结构.md` 按负责人要求对照 ClinDB 的 `结构.md` 重写后，重写版还没再过一轮「硕士生阅读」（design 0002 与上一版结构文档过过）。
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- 负责人 2026-10-16：先做第 2 步装配两个库；配置每段一份（`config/<段>.yaml`），编码解码是可选开关、映射表单独一份配置；交付资料检查一例有一项不过就整例跳过并记录，「都是遇到整个病例跳过，让医生核对去吧」；化名对照存进答案库。已写进 `结构.md`（框架图、第五部分「配置」）和 `AGENTS.md`「错误怎么处理」。
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- 负责人 2026-10-16：先做第 2 步装配两个库；配置每段一份（`config/<段>.yaml`），编码解码是可选开关、映射表单独一份配置；交付资料检查一例有一项不过就整例跳过并记录，「都是遇到整个病例跳过，让医生核对去吧」；化名对照存进答案库。已写进 `结构.md`（框架图、第五部分「配置」）和 `AGENTS.md`「错误怎么处理」。
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- 负责人 2026-10-16 定 C04：报告表名随视频名配对（`U<号>_roi2.mp4` 配 `U<号>_roi2_report.xlsx`，`U<号>.mp4` 配 `U<号>_report.xlsx`），绿框版那一例因此进库。任务书 01 原文只认前一种，未改任务书。
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## 下一步
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## 下一步
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- 任务书 01「装配两个库」已写好（`research-wiki/任务书/01-装配两个库.md`），交负责人另开会话执行，本会话验收。
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- 监督者验收任务书 01。
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- 待负责人定：关键图格式不合要求时整次停下还是整例跳过；化名种子在 git 里，拿到种子可反推进库病例的病例号先后（专家拿不到种子）；含「造影提示：」的那份超声描述所在病例被 C10 跳过，故不在复核清单里。
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- 向临床方要编码映射表（性别、诊断、症状、既往史、化验档位）。
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- 向临床方要编码映射表（性别、诊断、症状、既往史、化验档位）。
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- 把 `待定问题/04`（6 例跨表不一致）、`待定问题/06`（1 份超声描述中段的「造影提示：」）转给医生；06 定之前的构建不做正式会诊。
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- 把 `待定问题/04`（6 例跨表不一致）、`待定问题/06`（1 份超声描述中段的「造影提示：」）转给医生；06 定之前的构建不做正式会诊。
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- 等临床方交付 40 例的医生标注工作簿（含造影剂到达时间和注射时间）。
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- 等临床方交付 40 例的医生标注工作簿（含造影剂到达时间和注射时间）。
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# 装配两个库（scripts/build.py）的配置。字段定义与校验见 src/cadx/build/_config.py，
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# 每个字段必填；相对路径相对仓库根目录解析。
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delivery_dir: data/交付包_20260908_40例
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library_root: library
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answers_root: answers
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# 生成化名的随机种子。
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alias_seed: 20261016
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# 编码列是否按映射表解码。映射表还没向临床方拿到，先不解码，code_maps 必须是 null。
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decode_codes: false
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code_maps: null
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version = "0.0.0"
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version = "0.0.0"
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description = "胰腺囊性肿瘤多模态会诊诊断的研究代码"
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description = "胰腺囊性肿瘤多模态会诊诊断的研究代码"
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requires-python = ">=3.12"
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requires-python = ">=3.12"
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dependencies = []
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dependencies = [
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"openpyxl>=3.1.5",
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"pillow>=12.3.0",
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"pydantic>=2.14.1",
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"pyyaml>=6.0.3",
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]
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[dependency-groups]
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[dependency-groups]
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dev = [
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dev = [
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"pytest>=8.3",
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"pytest>=8.3",
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"import-linter>=2.1",
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"import-linter>=2.1",
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"pre-commit>=4.0",
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"pre-commit>=4.0",
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"types-pyyaml>=6.0.12.20260906",
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"types-openpyxl>=3.1.5.20260827",
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]
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]
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[build-system]
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[build-system]
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typeCheckingMode = "strict"
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typeCheckingMode = "strict"
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venvPath = "."
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venvPath = "."
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venv = ".venv"
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venv = ".venv"
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extraPaths = ["tests"]
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[tool.pytest.ini_options]
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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testpaths = ["tests"]
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# 测试辅助（假交付包生成器）放在 tests/ 下，按普通模块导入。
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pythonpath = ["tests"]
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addopts = "--strict-markers --import-mode=importlib"
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addopts = "--strict-markers --import-mode=importlib"
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markers = [
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markers = [
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"live: 真实模型调用，花钱，需要 .env 里的密钥",
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"live: 真实模型调用，花钱，需要 .env 里的密钥",
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]
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]
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# 导入边界。改契约先改 research-wiki/explanation/结构.md，再改这里；
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# 导入边界。改契约先改 research-wiki/explanation/结构.md，再改这里；
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# 不靠 ignore_imports 让违规通过。规划中的契约见结构.md 第四节，模块落地时随任务书加入。
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# 不靠 ignore_imports 让违规通过。规划中的契约见结构.md 第五部分，模块落地时随任务书加入。
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[tool.importlinter]
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[tool.importlinter]
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root_packages = ["cadx"]
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root_packages = ["cadx"]
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include_external_packages = true
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include_external_packages = true
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type = "forbidden"
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type = "forbidden"
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source_modules = ["cadx"]
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source_modules = ["cadx"]
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forbidden_modules = ["torch", "sam2"]
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forbidden_modules = ["torch", "sam2"]
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[[tool.importlinter.contracts]]
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# 结构.md 第三部分依赖表：外部层与格式层的模块不依赖其他 cadx 模块。
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name = "delivery、library、answers、runs 互不依赖"
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type = "independence"
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modules = ["cadx.delivery", "cadx.library", "cadx.answers", "cadx.runs"]
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[[tool.importlinter.contracts]]
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# 同上，依赖表的另一半：它们也不引用上层和其余规划中的模块（独立契约只管它们之间）。
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name = "delivery、library、answers、runs 不引用其他 cadx 模块"
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type = "forbidden"
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source_modules = ["cadx.delivery", "cadx.library", "cadx.answers", "cadx.runs"]
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forbidden_modules = [
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"cadx.build", "cadx.ceus", "cadx.segment", "cadx.llm", "cadx.ledger",
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"cadx.consult", "cadx.evaluate", "cadx.verdicts",
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]
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[[tool.importlinter.contracts]]
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# 结构.md 第三部分依赖表：build 只依赖 delivery、library、answers、runs（ceus 落地时加入）。
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name = "build 只引用 delivery、library、answers、runs"
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type = "forbidden"
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source_modules = ["cadx.build"]
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forbidden_modules = [
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"cadx.ceus", "cadx.segment", "cadx.llm", "cadx.ledger",
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"cadx.consult", "cadx.evaluate", "cadx.verdicts",
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]
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allow_indirect_imports = true
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[[tool.importlinter.contracts]]
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# 结构.md 第五部分：交付包的 Excel 只有 delivery 碰。
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name = "只有 delivery 引用 openpyxl"
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type = "forbidden"
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source_modules = ["cadx.library", "cadx.answers", "cadx.runs", "cadx.build"]
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forbidden_modules = ["openpyxl"]
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allow_indirect_imports = true
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[[tool.importlinter.contracts]]
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# 结构.md 第五部分：写资料库的图片（去掉元数据）只有 library 碰。
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name = "只有 library 引用 PIL"
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type = "forbidden"
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source_modules = ["cadx.delivery", "cadx.answers", "cadx.runs", "cadx.build"]
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forbidden_modules = ["PIL"]
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allow_indirect_imports = true
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@@ -98,7 +98,7 @@ work/ 中间文件 ─────────► ② 装配两个库
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| 层 | 模块 | 藏住的决定 | 旧项目里的对应内容 |
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| 层 | 模块 | 藏住的决定 | 旧项目里的对应内容 |
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| --- | --- | --- | --- |
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| --- | --- | --- | --- |
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| 入口 | `scripts/`（不在包内） | 人怎么操作：每段一个脚本（`ceus_quant`、`build`、`consult`、`evaluate`），另有一个按顺序调用四段的总入口；读配置文件，把模块装配起来 | `debugs/t1_local_debug.py`、`debugs/tic_lognormal_replay.py` |
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| 入口 | `scripts/`（不在包内） | 人怎么操作：每段一个脚本（`ceus_quant`、`build`、`consult`、`evaluate`），另有一个按顺序调用四段的总入口；读配置文件，把模块装配起来 | `debugs/t1_local_debug.py`、`debugs/tic_lognormal_replay.py` |
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| 组织 | build | 两个库怎么装配：每一路放哪些内容（可见性的唯一决定处）、化名怎么取、病例顺序怎么打乱、清单记什么。全项目只有它同时碰得到原始资料和答案 | `app/domain/input_readers.py`、`ingestion*.py` 的装配部分 |
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| 组织 | build | 两个库怎么装配：每一路放哪些内容（可见性的唯一决定处）、化名怎么取（化名随机，资料库按化名排序，顺序就与交付顺序无关）、清单记什么。全项目只有它同时碰得到原始资料和答案 | `app/domain/input_readers.py`、`ingestion*.py` 的装配部分 |
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| 组织 | consult | 会诊怎么进行：几个专家、谁先说、后发言的看得到前面的什么、什么时候结束；「调一次模型」的统一入口（先存请求、记开始、调用、存回复、记结束）也在这里 | 没有 |
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| 组织 | consult | 会诊怎么进行：几个专家、谁先说、后发言的看得到前面的什么、什么时候结束；「调一次模型」的统一入口（先存请求、记开始、调用、存回复、记结束）也在这里 | 没有 |
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| 组织 | evaluate | 评价口径：指标、统计方法、字段级对照怎么计分 | 没有（`core/eval` 已删） |
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| 组织 | evaluate | 评价口径：指标、统计方法、字段级对照怎么计分 | 没有（`core/eval` 已删） |
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| 格式 | library | 给专家的资料库的目录布局、文件格式和读取；按路分别读出，一路一个对象 | `app/domain/input_packages.py` 的数据形状 |
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| 格式 | library | 给专家的资料库的目录布局、文件格式和读取；按路分别读出，一路一个对象 | `app/domain/input_packages.py` 的数据形状 |
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@@ -137,7 +137,7 @@ work/ 中间文件 ─────────► ② 装配两个库
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### 几条边界
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### 几条边界
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- **专家能看见什么，只在 build 一处决定。** build 按白名单把每路允许的内容写进 `library/`，此外任何模块都不挑选给专家的材料。consult 只拿到某一次构建的路径，经 library 按路读出；它不依赖 delivery、answers、build，读原始资料和答案的代码对它来说根本不存在。报告的「印象 / 结论」段（医生写的诊断倾向）由 delivery 认出、由 build 剔除，`library/` 里只有「所见」描述。
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- **专家能看见什么，只在 build 一处决定。** build 按白名单把每路允许的内容写进 `library/`，此外任何模块都不挑选给专家的材料。consult 只拿到某一次构建的路径，经 library 按路读出；它不依赖 delivery、answers、build，读原始资料和答案的代码对它来说根本不存在。报告的「印象 / 结论」段（医生写的诊断倾向）由 delivery 认出、由 build 剔除，`library/` 里只有「所见」描述。
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- **交付资料的检查不过，整例跳过。** delivery 逐例检查（编号、文件、取值、跨表是否一致，具体检查项在装配两个库的任务书里列），build 把没过的病例整例跳过：资料库和答案库的病理诊断里都没有它，答案库的跳过清单写明它没过哪一项、涉及哪个文件哪一列。一例遇到第一项不过就不再往下查，清单上每例只记一项。整张表读不了时整次构建停下。规则见 `AGENTS.md`「错误怎么处理」。
|
- **交付资料的检查不过，整例跳过。** delivery 逐例检查（编号、文件、取值、跨表是否一致；检查项 C01–C13 的速查表见 `../guides/装配两个库.md`，规则以 `src/cadx/delivery/_cases.py`、`_text.py` 为准），build 把没过的病例整例跳过：资料库和答案库的病理诊断里都没有它，答案库的跳过清单写明它没过哪一项、涉及哪个文件哪一列。一例遇到第一项不过就不再往下查，清单上每例只记一项。整张表读不了时整次构建停下。规则见 `AGENTS.md`「错误怎么处理」。
|
||||||
- **三路互相隔开。** 每个专家的提示词只用自己那一路的对象拼。consult 里拼某一路提示词的函数只接收那一路的对象，不接收整个病例。这是研究设计本身：模拟各科医生各看各的检查结果，再在会诊时交换意见。会诊时一路能看到另一路的什么，由 consult 的会诊流程决定，在会诊的任务书里定。
|
- **三路互相隔开。** 每个专家的提示词只用自己那一路的对象拼。consult 里拼某一路提示词的函数只接收那一路的对象，不接收整个病例。这是研究设计本身：模拟各科医生各看各的检查结果，再在会诊时交换意见。会诊时一路能看到另一路的什么，由 consult 的会诊流程决定，在会诊的任务书里定。
|
||||||
- **我们自己调模型只有一个入口：consult 的「调一次模型」。** 它按固定顺序做五步：把完整请求存进账本的大块存储、写「调用开始」、经 llm 调用、把完整回复存进大块存储、写「调用结束」。llm 只管调用，不写账本，所以任何一次模型调用都绕不开登记。中断后重启时，从账本找出开始了没结束的调用，记为「状态未知」，不重做已有结果的调用。做重复运行（同一病例、同一专家调多次，测一致性）时，每一次都恰好登记一次。
|
- **我们自己调模型只有一个入口：consult 的「调一次模型」。** 它按固定顺序做五步：把完整请求存进账本的大块存储、写「调用开始」、经 llm 调用、把完整回复存进大块存储、写「调用结束」。llm 只管调用，不写账本，所以任何一次模型调用都绕不开登记。中断后重启时，从账本找出开始了没结束的调用，记为「状态未知」，不重做已有结果的调用。做重复运行（同一病例、同一专家调多次，测一致性）时，每一次都恰好登记一次。
|
||||||
- **CEUS 算法不知道分割模型是谁，也不管中间文件放哪。** ceus 接收视频路径、参数和分割结果，交出曲线、拟合、关键帧和指标；中间文件写在哪、按什么复用，由 `scripts/ceus_quant.py` 决定（目前只有它一个使用者，出现第二个使用者再收进模块）。segment 只管「给提示、出逐帧掩码」，不认识分屏和绿框。
|
- **CEUS 算法不知道分割模型是谁，也不管中间文件放哪。** ceus 接收视频路径、参数和分割结果，交出曲线、拟合、关键帧和指标；中间文件写在哪、按什么复用，由 `scripts/ceus_quant.py` 决定（目前只有它一个使用者，出现第二个使用者再收进模块）。segment 只管「给提示、出逐帧掩码」，不认识分屏和绿框。
|
||||||
@@ -156,6 +156,7 @@ library/<构建号>/
|
|||||||
cases/<化名>/
|
cases/<化名>/
|
||||||
clinical/clinical.json 临床那一路
|
clinical/clinical.json 临床那一路
|
||||||
ultrasound/ 超声那一路：report.txt、key.png、keyframes/*.png、tic.json
|
ultrasound/ 超声那一路：report.txt、key.png、keyframes/*.png、tic.json
|
||||||
|
（后两项等 CEUS 定量落地后由 build 加入，目前只有前两项）
|
||||||
mr/report.txt MR 那一路
|
mr/report.txt MR 那一路
|
||||||
```
|
```
|
||||||
|
|
||||||
@@ -172,7 +173,7 @@ library/<构建号>/
|
|||||||
|
|
||||||
性别、年龄只给临床一路：医院在两份报告工作簿里也复制了这两列，但影像两路先看到它们会被人口学先验带偏（旧项目 design 0026 决定三）。
|
性别、年龄只给临床一路：医院在两份报告工作簿里也复制了这两列，但影像两路先看到它们会被人口学先验带偏（旧项目 design 0026 决定三）。
|
||||||
|
|
||||||
病例用化名，目录顺序打乱：交付文件名里带病例号（如 `U001_roi2.mp4`），行序可能和诊断有关。图片写入时去掉文件元数据。构建完不再修改；要改就做一次新构建。
|
病例用化名，目录和清单按化名排序：交付文件名里带病例号（如 `U001_roi2.mp4`），行序可能和诊断有关；化名是按种子随机抽的 4 位小写字母加数字，按它排序后的顺序与交付顺序无关。图片写入时去掉文件元数据。构建完不再修改；要改就做一次新构建。
|
||||||
|
|
||||||
### 标准答案库（`answers/<构建号>/`）
|
### 标准答案库（`answers/<构建号>/`）
|
||||||
|
|
||||||
@@ -241,8 +242,8 @@ X 是超声报告工作簿的「推注开始时间s」，含义是视频第 0
|
|||||||
|
|
||||||
| 文件 | 给谁用 | 内容 |
|
| 文件 | 给谁用 | 内容 |
|
||||||
| --- | --- | --- |
|
| --- | --- | --- |
|
||||||
| `build.yaml` | `scripts/build.py` | 交付包位置、两个库的输出位置、化名与打乱顺序的随机种子、编码解码开关与映射表位置 |
|
| `build.yaml` | `scripts/build.py` | `delivery_dir`（交付包位置）、`library_root`、`answers_root`（两个库的上级目录）、`alias_seed`（生成化名的随机种子）、`decode_codes`（编码解码开关）、`code_maps`（映射表位置或 null）；字段定义和校验在 `src/cadx/build/_config.py`，逐项说明见 `../guides/装配两个库.md` |
|
||||||
| `code_maps.yaml` | build（经 `build.yaml` 引用） | 编码映射表：交付包里每个用数字编码的列，每个数字代表什么（如性别的 1、2） |
|
| `code_maps.yaml` | build（经 `build.yaml` 引用） | 编码映射表：交付包里每个用数字编码的列，每个数字代表什么（如性别的 1、2）。还没向临床方拿到，尚未建 |
|
||||||
| `ceus.yaml` | `scripts/ceus_quant.py` | CEUS 定量的全部参数，每个参数用注释写明出处 |
|
| `ceus.yaml` | `scripts/ceus_quant.py` | CEUS 定量的全部参数，每个参数用注释写明出处 |
|
||||||
| `consult.yaml` | `scripts/consult.py` | 会诊的实验配置与模型用途 |
|
| `consult.yaml` | `scripts/consult.py` | 会诊的实验配置与模型用途 |
|
||||||
| `evaluate.yaml` | `scripts/evaluate.py` | 评价的指标与统计设置 |
|
| `evaluate.yaml` | `scripts/evaluate.py` | 评价的指标与统计设置 |
|
||||||
@@ -259,11 +260,16 @@ X 是超声报告工作簿的「推注开始时间s」，含义是视频第 0
|
|||||||
|
|
||||||
文件格式：数组用 npz（读取时 `allow_pickle=False`，pickle 读取时会执行任意代码），每例的标量和摘要用 json，跨病例的表用 csv，图用 png。缺失值写 null，不写 NaN 或 0：0 是合法的测量值，NaN 在 json 里不合法。
|
文件格式：数组用 npz（读取时 `allow_pickle=False`，pickle 读取时会执行任意代码），每例的标量和摘要用 json，跨病例的表用 csv，图用 png。缺失值写 null，不写 NaN 或 0：0 是合法的测量值，NaN 在 json 里不合法。
|
||||||
|
|
||||||
导入边界用 import-linter 检查，写进 `make check`。契约在 `pyproject.toml`，检查范围是 `src/cadx`，**不含 `scripts/` 和 `tests/`**。下面只列契约实际强制的，没有的保护不写：
|
导入边界用 import-linter 检查，写进 `make check`。契约在 `pyproject.toml`，检查范围是 `src/cadx`，**不含 `scripts/` 和 `tests/`**。下面只列契约实际强制的（共 6 条），没有的保护不写：
|
||||||
|
|
||||||
- `cadx` 不引用 `torch`、`sam2`。
|
- `cadx` 不引用 `torch`、`sam2`。
|
||||||
|
- delivery、library、answers、runs 互不引用。
|
||||||
|
- delivery、library、answers、runs 不引用其他 `cadx` 模块（build 和规划中的各模块）。
|
||||||
|
- build 不引用 delivery、library、answers、runs 以外的 `cadx` 模块（ceus 落地时放行）。
|
||||||
|
- 只有 delivery 引用 `openpyxl`（交付包的 Excel 只有它碰）。
|
||||||
|
- 只有 library 引用 `PIL`（写资料库的图片时去掉元数据）。
|
||||||
|
|
||||||
第三部分的依赖表和下面几条外部库独占，随模块落地逐条写成契约（import-linter 只能检查已经存在的模块）：只有 delivery 引用 `openpyxl`；只有 library 引用 `PIL`（写资料库的图片时去掉元数据）；只有 segment 引用 `torch`、`sam2`；只有 llm 引用 `polygateway`；只有 ledger 引用 `sqlite3`。
|
第三部分依赖表的其余部分和下面几条外部库独占，随模块落地逐条写成契约（import-linter 只能检查已经存在的模块）：只有 segment 引用 `torch`、`sam2`（落地时把上面第一条改成放行 segment）；只有 llm 引用 `polygateway`；只有 ledger 引用 `sqlite3`。
|
||||||
|
|
||||||
契约管不到的，不要当成机器守住了：
|
契约管不到的，不要当成机器守住了：
|
||||||
|
|
||||||
@@ -283,17 +289,17 @@ Python 环境用 uv；安装与检查命令见 `../guides/开发环境.md`。
|
|||||||
| --- | --- | --- | --- |
|
| --- | --- | --- | --- |
|
||||||
| ceus | 6000–7500（基本照搬旧算法，去掉只为产品层服务的部分） | — | `ceus_roi/` 除 `service.py` 7330，`video_decoder.py` 135 |
|
| ceus | 6000–7500（基本照搬旧算法，去掉只为产品层服务的部分） | — | `ceus_roi/` 除 `service.py` 7330，`video_decoder.py` 135 |
|
||||||
| segment | 150–300 | — | `medsam2_local_track.py` 240 |
|
| segment | 150–300 | — | `medsam2_local_track.py` 240 |
|
||||||
| delivery | 400–700 | — | `clinical.py` 266、`modalities.py` 522、`workbook.py` 99、`delivery.py` 134，共 1021，其中入库与数据库部分不迁 |
|
| delivery | 400–700 | 733 | `clinical.py` 266、`modalities.py` 522、`workbook.py` 99、`delivery.py` 134，共 1021，其中入库与数据库部分不迁 |
|
||||||
| library | 150–300 | — | `input_packages.py` 104 |
|
| library | 150–300 | 300 | `input_packages.py` 104 |
|
||||||
| answers | 100–200 | — | — |
|
| answers | 100–200 | 201 | — |
|
||||||
| verdicts | 100–200 | — | — |
|
| verdicts | 100–200 | — | — |
|
||||||
| build | 300–500 | — | `input_readers.py` 329 的装配部分 |
|
| build | 300–500 | 307 | `input_readers.py` 329 的装配部分 |
|
||||||
| llm | 200–450 | — | ClinDB `llm/` 415 |
|
| llm | 200–450 | — | ClinDB `llm/` 415 |
|
||||||
| ledger | 200–300 | — | ClinDB `ledger/` 274 |
|
| ledger | 200–300 | — | ClinDB `ledger/` 274 |
|
||||||
| runs | 100–250 | — | — |
|
| runs | 100–250 | 86（只含快照部分） | — |
|
||||||
| consult | 500–1000（会诊口径定后重估） | — | — |
|
| consult | 500–1000（会诊口径定后重估） | — | — |
|
||||||
| evaluate | 300–600（评价口径定后重估） | — | 已删的 `core/eval` 622 |
|
| evaluate | 300–600（评价口径定后重估） | — | 已删的 `core/eval` 622 |
|
||||||
| scripts/ 每个 | ≤ 300 | — | `t1_local_debug.py` 762、`tic_lognormal_replay.py` 627 |
|
| scripts/ 每个 | ≤ 300 | `build.py` 37、`scan_library.py` 88 | `t1_local_debug.py` 762、`tic_lognormal_replay.py` 627 |
|
||||||
|
|
||||||
---
|
---
|
||||||
|
|
||||||
@@ -311,4 +317,54 @@ Python 环境用 uv；安装与检查命令见 `../guides/开发环境.md`。
|
|||||||
|
|
||||||
## 八、各模块对外的函数与类型
|
## 八、各模块对外的函数与类型
|
||||||
|
|
||||||
写到哪个模块时，再把它对外的函数和类型补在这里。
|
写到哪个模块时，再把它对外的函数和类型补在这里。以各子包 `__init__.py` 导出的为准；参数和字段的细节看代码的 docstring。
|
||||||
|
|
||||||
|
### delivery（`src/cadx/delivery/`）
|
||||||
|
|
||||||
|
- `read_delivery(delivery_dir, code_maps)`：读交付包，做整张表的检查 T1–T4 和逐例检查 C01–C13，交出 `DeliveryResult`；`code_maps` 为 None 表示不解码。
|
||||||
|
- `DeliveryResult`：一次读取的结果：通过的病例（按病例号排序）、跳过记录、病例总数、认不出编号的行数、因没有映射表而没比对的项。
|
||||||
|
- `CaseRecord`：一个检查全部通过的病例：三位病例号、视频号、临床一路的 22 列、超声描述、MR 描述、关键图路径、三张表的诊断编码。
|
||||||
|
- `DiagnosisCodes`：一例在临床表、超声表、MR 表里各自的诊断编码（C10 保证三者相等）。
|
||||||
|
- `SkipRecord`：一条跳过记录：病例号（认不出编号时是「文件 第 N 行」或「病例目录 名字」）、检查编号、检查说明、涉及的文件和列、涉及值的 JSON 字符串。
|
||||||
|
- `DeliveryError`：整张表读不了（T1–T4）时抛出，消息以检查编号开头，整次构建停下。
|
||||||
|
- `CODED_COLUMNS`：用数字编码、需要映射表才知道含义的 17 项列名，映射表必须恰好覆盖它们。
|
||||||
|
- `CodeMaps`：映射表的类型，「列名 → {数字 → 含义}」。
|
||||||
|
- `SKIPPED_NOTE`：跳过清单的说明句（每例只记第一项没过的检查），写进答案库清单并在终端打印。
|
||||||
|
- `review_sentences(text)`：报告文字里含「考虑」「可能」「倾向」「提示」的句子，每句一条（命中的词，句子），用来生成复核清单。
|
||||||
|
|
||||||
|
### library（`src/cadx/library/`）
|
||||||
|
|
||||||
|
- `write_library(build_dir, build_id, git_commit, git_clean, config_sha256, codes_decoded, uncompared, ceus_source, cases)`：把一次构建的各例三路内容写进一个已存在的空目录，关键图去掉附加数据重新编码，最后写 `manifest.json`。
|
||||||
|
- `LibraryCase`：要写进资料库的一例：化名、临床一路的字段、超声描述、关键图源文件、MR 描述。
|
||||||
|
- `list_aliases(build_dir)`：一次构建的全部化名（按化名排序）。
|
||||||
|
- `read_clinical(build_dir, alias)`、`read_ultrasound(build_dir, alias)`、`read_mr(build_dir, alias)`：按路读出一例，读时核对 SHA-256，拒绝 `.partial` 目录。
|
||||||
|
- `ClinicalRoute`：临床一路：是否已解码、22 列字段。
|
||||||
|
- `UltrasoundRoute`：超声一路：报告「所见」原文、关键图路径。
|
||||||
|
- `MrRoute`：MR 一路：报告「所见」原文。
|
||||||
|
- `scan_for_leaks(build_dir, forbidden_strings, forbidden_keys)`：在构建目录的全部 `.txt`、`.json` 里找禁止的字符串（NFKC 归一、不分大小写、按子串）和禁止的 JSON 键名，返回命中列表。
|
||||||
|
- `LeakHit`：一处命中：文件（相对构建目录）、类别（「字符串」或「键名」）、命中的词。
|
||||||
|
|
||||||
|
### answers（`src/cadx/answers/`）
|
||||||
|
|
||||||
|
- `write_answers(answers_dir, build_id, skipped_note, aliases, diagnoses, skipped, reviews)`：写 `aliases.csv`、`diagnoses.csv`、`skipped.csv`、`review.csv`，再给目录里全部文件（含 `snapshot/`）算 SHA-256 写进 `manifest.json`。
|
||||||
|
- `AliasRow`：化名、三位病例号、视频号。
|
||||||
|
- `DiagnosisRow`：化名、病例号、三张表的诊断编码、诊断名（不解码时为 None）。
|
||||||
|
- `SkippedRow`：跳过清单的一行，字段同 `SkipRecord`。
|
||||||
|
- `ReviewRow`：复核清单的一行：化名、路（「超声」或「MR」）、命中的词、所在句子。
|
||||||
|
- `read_aliases(answers_dir)`、`read_diagnoses(answers_dir)`：评价用的读取，读时核对 SHA-256 和表头，拒绝 `.partial` 目录。
|
||||||
|
|
||||||
|
### runs（`src/cadx/runs/`，目前只有快照部分）
|
||||||
|
|
||||||
|
- `read_git_state(repo_root)`：读出完整和短提交号、工作区是否干净（含未跟踪文件）、`git diff HEAD` 输出的 SHA-256。
|
||||||
|
- `GitState`：上面这四项。
|
||||||
|
- `make_build_id(now, git)`：构建号 `YYYYMMDD-HHMMSS-<git 短哈希>`，工作区不干净时末尾加 `-dirty`。
|
||||||
|
- `write_snapshot(snapshot_dir, build_id, git, started_at, finished_at, uv_lock, configs)`：新建快照目录，复制配置原文并写 `snapshot.json`（构建号、git 状态、Python 版本、`uv.lock` 哈希、起止时间、各配置的哈希）。
|
||||||
|
|
||||||
|
### build（`src/cadx/build/`）
|
||||||
|
|
||||||
|
- `run_build(config_path, repo_root, now)`：完整做一次构建：读配置和映射表、读交付包、取化名、先写进 `.partial` 目录再改名，交出 `BuildSummary`。
|
||||||
|
- `BuildSummary`：供终端打印的计数：构建号、两个库的路径、病例总数、进库数、跳过数、认不出编号的行数、按检查编号分的跳过数、复核清单条数、跳过清单说明句。
|
||||||
|
- `BuildConfig`：`build.yaml` 的字段定义（pydantic，字段必填、不许多写、读入后不可改）。
|
||||||
|
- `load_build_config(path, repo_root)`：读并校验 `build.yaml`，相对路径按仓库根目录解析。
|
||||||
|
- `load_code_maps(path)`：读映射表并做 T5（恰好覆盖 17 项，性别映射到「男」「女」，诊断映射到四个亚型缩写）。
|
||||||
|
- `make_aliases(case_nos, seed)`：病例号排序后依次抽 4 位化名，同种子同病例得到同样的化名。
|
||||||
|
|||||||
@@ -0,0 +1,212 @@
|
|||||||
|
# 装配两个库
|
||||||
|
|
||||||
|
读者：要跑一次「装配两个库」、或者要把跳过清单交给医生的人。这一步读入医院的交付包，逐例检查，把检查全部通过的病例写成两个库：给 AI 专家看的**资料库**（`library/`）和只给评价用的**标准答案库**（`answers/`）。它在整条流水线里的位置见 `../explanation/结构.md` 第二部分；为什么这样设计见 `../任务书/01-装配两个库.md` 和 `../design/0002-四段流水线与两个库.md`。
|
||||||
|
|
||||||
|
## 先认识几个词
|
||||||
|
|
||||||
|
- **四类胰腺囊性肿瘤**：IPMN（导管内乳头状黏液性肿瘤）、SPN（实性假乳头状肿瘤）、MCN（黏液性囊性肿瘤）、SCN（浆液性囊性肿瘤）。项目要专家判断病灶属于哪一类，所以资料库里出现这些名字就等于泄露答案。
|
||||||
|
- **金标准**：术后或穿刺的病理结论，交付表里叫「病理类型」或 `Diagnosis`，用 1–4 的数字记。
|
||||||
|
- **CEUS、MR**：CEUS 是超声造影视频（往静脉打造影剂后录的超声）；MR 是磁共振检查，本项目只有它的文字报告。这一步不处理 CEUS 视频，只检查它在不在。
|
||||||
|
- **交付包**：临床方交来的一批原始资料，目前是 `data/交付包_20260908_40例/`：三张汇总表（临床工作簿、超声报告、MR 报告）和每例一个病例目录（关键图、CEUS 视频、单例报告表）。
|
||||||
|
- **单例报告表**：每个病例目录里的一份 Excel，只有一行，列与超声汇总表相同（7 列）。它和汇总表重复，用来核对两份是否一致。
|
||||||
|
- **所见、结论段**：一份影像报告通常分「所见」（描述看到了什么）和「印象 / 结论」（医生的诊断倾向）。交付包的报告文字只有所见，这一步检查里面没有混进结论段（C11）。
|
||||||
|
- **`roi2`**：交付视频文件名里的版本标记，表示视频上带医生画的病灶框（ROI，感兴趣区）。
|
||||||
|
- **推注开始时间**：超声表的一列，单位秒，表示视频第 0 秒时造影剂已经推注（注射）了多少秒。以后 CEUS 定量（从视频里算亮度曲线、挑关键帧、算灌注指标的那一步）要用，这一步只检查它是非负整数，不放进资料库。
|
||||||
|
- **档位**：临床表每项化验除原值外还有一个 `*_Level` 列，取 0/1，看起来是正常/异常，未经临床方确认。
|
||||||
|
- **三路**：临床、超声、MR。每个 AI 专家只看自己那一路（`AGENTS.md` 硬性约束 2）。
|
||||||
|
- **构建**：跑一次 `scripts/build.py`，产出一对同号的 `library/<构建号>/` 和 `answers/<构建号>/`。构建完不再改，要改就重新构建。
|
||||||
|
- **化名**：资料库里代替病例号的 4 位随机名字（小写字母加数字；36 的 4 次方约 168 万种，几十例足够，抽到重复的或含亚型缩写的就重抽）。真实病例号会暴露交付顺序，而交付表是按诊断分组录入的，顺序本身带着答案（`AGENTS.md` 硬性约束 1）。
|
||||||
|
- **编码列**：交付包里用数字表示类别的列，如性别 1/2、症状 0/1。数字代表什么交付包没写，要向临床方要**映射表**。
|
||||||
|
- **结论段**：报告里医生写诊断倾向的那一段（「印象：」「提示：」之类），接近答案，不能给专家。
|
||||||
|
- **NFKC**：Unicode 的一种归一化，把全角字母、数字、标点转成半角。文字检查都先做它，全角写法就绕不过去。
|
||||||
|
|
||||||
|
## 一、改配置
|
||||||
|
|
||||||
|
配置是 `config/build.yaml`，进 git。字段定义和校验在 `src/cadx/build/_config.py` 的 `BuildConfig`：每个字段必填，没有默认值；多写一个字段、拼错字段名、同一层出现重复的键都直接报错；除路径以外不做类型转换（例如 `alias_seed` 写成 `"7"` 会报错）。这样配置写错时构建停在第一步，而不是用一个没人知道的值跑完（`AGENTS.md`「不设默认值」）。
|
||||||
|
|
||||||
|
| 字段 | 类型 | 含义 |
|
||||||
|
| --- | --- | --- |
|
||||||
|
| `delivery_dir` | 路径 | 交付包目录 |
|
||||||
|
| `library_root` | 路径 | 资料库的上级目录，每次构建在它下面新建 `<构建号>/` |
|
||||||
|
| `answers_root` | 路径 | 答案库的上级目录，同上 |
|
||||||
|
| `alias_seed` | 整数 | 生成化名的随机种子。同一个种子、同一批通过的病例，得到同样的化名 |
|
||||||
|
| `decode_codes` | true / false | 编码列是否按映射表解码 |
|
||||||
|
| `code_maps` | 路径或 null | 映射表位置 |
|
||||||
|
|
||||||
|
相对路径**相对仓库根目录**解析，不相对配置文件所在目录，也不相对你敲命令时所在的目录。路径不能写空串（空串会变成当前目录）。
|
||||||
|
|
||||||
|
### decode_codes 与 code_maps 要配套
|
||||||
|
|
||||||
|
- `decode_codes: false` 时 `code_maps` 必须是 `null`。编码列按原始数字写进资料库，`clinical.json` 里 `codes_decoded` 为 false；答案库 `diagnoses.csv` 的「诊断名」一栏留空；临床表的性别（1/2）没法和报告表的「男」「女」比对，资料库清单的 `uncompared` 里写明「临床性别未比对」。
|
||||||
|
- `decode_codes: true` 时 `code_maps` 必须是映射表的路径。
|
||||||
|
- 配错（true 配 null，或 false 配路径）读配置时就报错。
|
||||||
|
|
||||||
|
为什么做成开关：映射表还没从临床方拿到，不能编造含义；先用 false 跑通，映射表到位后改成 true 重新构建一次（负责人 2026-10-16：解码做成可选开关，映射表是独立的配置文件）。诊断编码和其他编码列一样归这个开关管；诊断不进资料库，所以开关对诊断只影响答案库。
|
||||||
|
|
||||||
|
### 映射表的格式
|
||||||
|
|
||||||
|
映射表目前**还没有**（`config/code_maps.yaml` 尚未建）。拿到后按下面的格式写：每个编码列一项，列名映射到「数字 → 含义」。
|
||||||
|
|
||||||
|
```yaml
|
||||||
|
Sex: {1: ..., 2: ...}
|
||||||
|
Symptom_Pain: {0: ..., 1: ...}
|
||||||
|
```
|
||||||
|
|
||||||
|
- 键必须是整数（不加引号），含义必须是字符串。YAML 会把不加引号的 `yes`、`no`、`on`、`off` 读成布尔值，含义一律加引号最稳；读成布尔值时会报错，不会悄悄通过。
|
||||||
|
- 需要映射的 17 项列名是 `src/cadx/delivery/_shape.py` 里的 `CODED_COLUMNS`（性别、诊断、5 个症状、5 项既往史、5 项化验的档位列）。其中 `Diagnosis` 一项同时管临床表的 `Diagnosis` 列和两张报告表的「病理类型」列，三列编码相同。名单放在 delivery，是因为「哪些列是编码列」是交付包形状的一部分。
|
||||||
|
- 映射表在构建开始时检查（检查编号 T5，代码在 `src/cadx/build/_config.py` 的 `load_code_maps`）：必须恰好覆盖这 17 项，多一项少一项都整次构建停下；`Sex` 的含义必须恰好是「男」「女」，才能和报告表的性别比对；`Diagnosis` 的含义必须恰好是 `IPMN`、`SPN`、`MCN`、`SCN`，评价要拿它和专家的结论比。
|
||||||
|
- 解码时，某一例出现映射表里没有的值，这一例按 C07（临床表）或 C08、C09（报告表的诊断）跳过。
|
||||||
|
|
||||||
|
## 二、怎么跑
|
||||||
|
|
||||||
|
```bash
|
||||||
|
uv run python scripts/build.py --config config/build.yaml
|
||||||
|
```
|
||||||
|
|
||||||
|
脚本只接收 `--config` 一个参数，不能在命令行单独改某个参数，这次用了什么参数只看配置文件就知道（`结构.md` 第五部分「配置」）。
|
||||||
|
|
||||||
|
终端只打印计数：构建号、两个库的路径、病例总数、进库病例数、跳过病例数、认不出编号的行数、按检查编号分的跳过数、复核清单条数、跳过清单的说明句。不打印病例号和任何资料内容，终端输出可以贴进汇报。
|
||||||
|
|
||||||
|
跑完建议再做一次泄露扫描：
|
||||||
|
|
||||||
|
```bash
|
||||||
|
uv run python scripts/scan_library.py --library library/<构建号> --answers answers/<构建号>
|
||||||
|
```
|
||||||
|
|
||||||
|
它从答案库读出这次构建的真实病例号和视频号，加上脚本里独立写的亚型名、诊断列名、交付文件名词表，扫资料库的全部 `.txt`、`.json`（不扫 PNG：PNG 的附加数据在写入时已经去掉，像素上烧录的信息栏按 `AGENTS.md` 硬性约束 3 不遮蔽，文字扫描也查不了像素），并检查 JSON 里有没有 `diagnosis`、`label`、`gold`、`pathology`、`name`、`row` 这类键名。只输出命中的条数和类别，不输出命中的内容；全部为 0 才说明资料库里没有这些东西。两个目录的构建号不同时直接报错。词表在脚本里另写一份、不取自 delivery 的常量，是为了让扫描不依赖被检查的代码本身：delivery 漏了一个词，扫描还能查出来。这个脚本同时读两个库，所以只能放在 `scripts/`，不能进 `src/cadx`（会诊代码不许碰答案库）。
|
||||||
|
|
||||||
|
## 三、产物在哪
|
||||||
|
|
||||||
|
### 构建号
|
||||||
|
|
||||||
|
`YYYYMMDD-HHMMSS-<git 短哈希>`，时间是本地时间（代码在 `src/cadx/runs/_snapshot.py` 的 `make_build_id`）。工作区有未提交的改动（含未跟踪的文件）时末尾加 `-dirty`。不干净的工作区照样允许构建，但如实记下：带 `-dirty` 的构建，代码不能只凭提交号复现，快照里另记了 `git diff HEAD` 输出的哈希。要写进论文的构建，应在干净的工作区上跑。
|
||||||
|
|
||||||
|
### 资料库 `library/<构建号>/`
|
||||||
|
|
||||||
|
```
|
||||||
|
manifest.json
|
||||||
|
cases/<化名>/
|
||||||
|
clinical/clinical.json
|
||||||
|
ultrasound/report.txt
|
||||||
|
ultrasound/key.png
|
||||||
|
mr/report.txt
|
||||||
|
```
|
||||||
|
|
||||||
|
| 文件 | 内容 |
|
||||||
|
| --- | --- |
|
||||||
|
| `manifest.json` | 构建号、git 提交号、工作区是否干净、配置文件（解码时含映射表）的 SHA-256、`codes_decoded`、`uncompared`（没比对的项）、`ceus_source`（所用 CEUS 结果的来源，这一步是 null）、化名列表（按化名排序）、每个文件的相对路径和 SHA-256。不含真实病例号、交付文件名和诊断 |
|
||||||
|
| `clinical.json` | `{"codes_decoded": ..., "fields": {列名: 值}}`。字段是临床表去掉编号和诊断后的 22 列：性别、年龄、5 个症状、5 项既往史、5 项化验的原值和档位。没测的化验写 null |
|
||||||
|
| `ultrasound/report.txt` | 超声报告的「所见」原文，UTF-8，不加标题 |
|
||||||
|
| `ultrasound/key.png` | 医生截的超声关键图，只保留像素和颜色模式重新编码，不带文本块、EXIF、ICC 等附加数据（附加数据里可能有文件名、时间等线索）。超声帧上烧录的信息栏不遮蔽（`AGENTS.md` 硬性约束 3） |
|
||||||
|
| `mr/report.txt` | MR 报告的「所见」原文 |
|
||||||
|
|
||||||
|
性别、年龄只在临床一路：两份报告表里医院也复制了这两列，但影像两路先看到会被人口学先验带偏（`结构.md` 第四部分）。以后 CEUS 定量落地，超声一路再加关键帧和灌注指标。
|
||||||
|
|
||||||
|
读资料库要经 `cadx.library` 的 `read_clinical`、`read_ultrasound`、`read_mr`：读时逐个核对文件的 SHA-256 与清单一致，被改过就报错。
|
||||||
|
|
||||||
|
### 答案库 `answers/<构建号>/`
|
||||||
|
|
||||||
|
```
|
||||||
|
manifest.json
|
||||||
|
snapshot/
|
||||||
|
snapshot.json
|
||||||
|
build.yaml
|
||||||
|
code_maps.yaml （只在 decode_codes 为 true 时有）
|
||||||
|
aliases.csv
|
||||||
|
diagnoses.csv
|
||||||
|
skipped.csv
|
||||||
|
review.csv
|
||||||
|
```
|
||||||
|
|
||||||
|
| 文件 | 内容 |
|
||||||
|
| --- | --- |
|
||||||
|
| `manifest.json` | 构建号、跳过清单的说明句（`skipped_note`）、本目录其余全部文件（含 `snapshot/` 下的）的 SHA-256 |
|
||||||
|
| `snapshot/snapshot.json` | 构建号、完整 git 提交号、工作区是否干净、`git diff HEAD` 的 SHA-256、Python 版本、`uv.lock` 的 SHA-256、开始和结束时间、各配置文件的 SHA-256 |
|
||||||
|
| `snapshot/build.yaml` 等 | 这次所用配置的原文副本。配置文件以后改了，这次构建用的是什么仍然查得到 |
|
||||||
|
| `aliases.csv` | 化名、三位病例号、视频号（`U` 加病例号）。会诊产物只用化名，评价靠这张表接回真实病例；CEUS 定量的结果按视频号接回 |
|
||||||
|
| `diagnoses.csv` | 化名、病例号、临床表、超声表、MR 表各自的诊断编码、诊断名（不解码时留空）。三张表各存一份，用哪一份算分由评价决定（进库病例已过 C10，三份相同；分开存是为了保留各表原值，评价口径不必在装配时定） |
|
||||||
|
| `skipped.csv` | 跳过清单，见第四节 |
|
||||||
|
| `review.csv` | 复核清单，见第五节 |
|
||||||
|
|
||||||
|
CSV 用带 BOM 的 UTF-8（文件开头有一个不可见的标记），医生用 Excel 直接打开不会乱码。
|
||||||
|
|
||||||
|
### `.partial` 是什么
|
||||||
|
|
||||||
|
两个库先写进 `<根目录>/<构建号>.partial/`，全部写完、清单算完后再改名成 `<构建号>/`：先改答案库，最后改资料库。所以：
|
||||||
|
|
||||||
|
- **资料库的 `<构建号>/` 出现，才算这次构建完成。** 会诊只读资料库，读取函数也拒绝名字以 `.partial` 结尾的目录，没写完的构建不会被用上。
|
||||||
|
- 看到 `.partial` 目录，说明那次构建中途出错。目前已知的一种是某张关键图的格式（位深、颜色类型、透明色）不能逐像素保真重编码：这本是只落在一例上的问题，但现在的代码让整次构建停下，而不是跳过这一例。它不会被自动删除，留着给人查原因；查完由人决定删不删。
|
||||||
|
- 只有答案库的 `<构建号>/`、没有同号的资料库，同样是没完成的构建。
|
||||||
|
- 配置、映射表或整张表的检查（T1–T5）不过时，构建在建目录之前就停下，不留任何目录。
|
||||||
|
- 目标目录已经存在时报错，不覆盖。构建号带到秒，正常不会重名。
|
||||||
|
|
||||||
|
## 四、跳过清单怎么看
|
||||||
|
|
||||||
|
### 规则
|
||||||
|
|
||||||
|
交付资料里的问题分两种（`AGENTS.md`「错误怎么处理」）：
|
||||||
|
|
||||||
|
- **整张表的问题**（T1–T5）：一例也读不出来，整次构建停下，报错信息以检查编号开头，写明哪个文件哪一项不符。
|
||||||
|
- **只落在某一个病例上的问题**（C01–C13）：跳过这一整例，接着处理下一例，在 `skipped.csv` 里记一行。这一例不进资料库，也不进答案库的 `aliases.csv`、`diagnoses.csv`。
|
||||||
|
|
||||||
|
先对三张表的每一行和每个病例目录做 C01（编号认不认得出）；认得出的，再逐例按 C02 到 C13 的顺序检查，**遇到第一项没过就停下**，清单上每例只记这一项（C01 记的是认不出的那一行，不算某一例，见下文）。后面的检查没做过，不代表没问题：医生改好这一项后，重新构建时它可能卡在后面某一项。这句说明写在答案库 `manifest.json` 的 `skipped_note` 里，终端也会打印；CSV 文件开头不能加注释行，所以没写在 `skipped.csv` 里。为什么整例跳过而不是停下整次构建：负责人 2026-10-16「都是遇到整个病例跳过，让医生核对去吧」。评价时要报告跳过了几例、各因为什么。
|
||||||
|
|
||||||
|
### skipped.csv 的列
|
||||||
|
|
||||||
|
| 列 | 含义 |
|
||||||
|
| --- | --- |
|
||||||
|
| 病例 | 三位病例号。C01（编号认不出）的行不知道是哪个病人，写成「表的路径 第 N 行」（N 是 Excel 行号，第 1 行是表头）；病例目录名不在 1–999 之间时写成「病例目录 目录名」 |
|
||||||
|
| 检查编号 | C01–C13 |
|
||||||
|
| 检查说明 | 这项检查的一句话说明 |
|
||||||
|
| 文件 | 涉及的文件，相对交付包根目录，多个用「; 」隔开 |
|
||||||
|
| 列 | 涉及的列，多个用「; 」隔开；不涉及具体列（如目录里的文件不对）时为空 |
|
||||||
|
| 涉及值 | JSON 字符串：不合规的原值、对不上的各表的值、命中的词和所在句子等，供医生核对 |
|
||||||
|
|
||||||
|
C01 的行不计入病例数，也不计入终端的「跳过病例」，单独算在「认不出编号的行」里；「按检查编号分的跳过数」里的 C01 就是这些行。同一个病人如果在某张表里编号写坏了，他在 C01 记一条（那一行），又会因为「缺在那张表」在 C03 再记一条，这是预期的。
|
||||||
|
|
||||||
|
### 检查编号速查
|
||||||
|
|
||||||
|
规则细节以代码为准：T1–T4 在 `src/cadx/delivery/_tables.py`，T5 在 `src/cadx/build/_config.py`，C01–C10 在 `src/cadx/delivery/_cases.py`，C11–C13 的词表和正则在 `src/cadx/delivery/_text.py`，表名、工作表名、表头在 `src/cadx/delivery/_shape.py`。每条规则为什么这样定见任务书 `../任务书/01-装配两个库.md` 第二部分。
|
||||||
|
|
||||||
|
| 编号 | 查什么 | 不过时 |
|
||||||
|
| --- | --- | --- |
|
||||||
|
| T1 | 三张汇总表都存在 | 整次构建停下 |
|
||||||
|
| T2 | 每张汇总表恰好有约定的那一个工作表 | 整次构建停下 |
|
||||||
|
| T3 | 表头与约定一字不差（含诊断列名里写的编码含义） | 整次构建停下 |
|
||||||
|
| T4 | 三个子目录里没有多余的文件：临床、MR 目录只有自己那张汇总表；超声目录只有超声汇总表和三位数字命名的病例目录 | 整次构建停下 |
|
||||||
|
| T5 | 解码时映射表恰好覆盖 17 项，性别、诊断的含义合规（见第一节） | 整次构建停下 |
|
||||||
|
| C01 | 编号认得出：临床表是 `P` 加三位数字，两张报告表是补零或不补零的纯数字，病例目录是三位数字；规范化后在 1–999 之间 | 记一行，不计入病例数 |
|
||||||
|
| C02 | 同一张表里这个编号只出现一次 | 跳过这一例 |
|
||||||
|
| C03 | 三张表和病例目录里都有这一例 | 跳过这一例 |
|
||||||
|
| C04 | 病例目录恰好三个文件：`U<号>_key.png`，加一对配套的视频和单例报告表：`U<号>_roi2.mp4` 配 `U<号>_roi2_report.xlsx`，或 `U<号>.mp4` 配 `U<号>_report.xlsx`；混搭不过（负责人 2026-10-16 定）：单例报告表的名字随视频名配对，不配套时说不清这份报告属于哪个版本的视频，交医生确认 | 跳过这一例 |
|
||||||
|
| C05 | 超声表的「CEUS视频ID」是 `U<号>`，与病例号一致 | 跳过这一例 |
|
||||||
|
| C06 | 单例报告表的工作表、表头正确，恰好 1 行数据，7 格与超声汇总表对应行逐格相等（类型也要相同） | 跳过这一例 |
|
||||||
|
| C07 | 临床表取值：性别、年龄、诊断、症状、既往史的取值范围；化验原值和档位要么都空（没测），要么都有值；解码时编码列的值在映射表里 | 跳过这一例 |
|
||||||
|
| C08 | 超声表取值：性别「男」或「女」、年龄形如「数字岁」、诊断 1–4（解码时还要在映射表里）、推注开始时间是非负整数、超声描述非空 | 跳过这一例 |
|
||||||
|
| C09 | MR 表取值：性别、年龄、诊断同 C08，MR 描述非空 | 跳过这一例 |
|
||||||
|
| C10 | 跨表一致：诊断三张表两两相等；年龄三张表相等（报告表去掉「岁」后和临床表的数字比）；性别超声表与 MR 表相等，解码时临床表的性别也要相等 | 跳过这一例 |
|
||||||
|
| C11 | 报告文字里没有结论段标题：段首（全文开头或换行之后）出现「印象」「结论」「提示」等关键词加冒号 | 跳过这一例 |
|
||||||
|
| C12 | 报告文字里没有亚型名（缩写、中文名及其常见变体） | 跳过这一例 |
|
||||||
|
| C13 | 报告文字里没有人口学信息：没有「数字岁」，没有「男」「女」两个字 | 跳过这一例 |
|
||||||
|
|
||||||
|
几点说明：
|
||||||
|
|
||||||
|
- 类型按 Excel 读出的原样判断，不做转换：要求整数的格读出 `45.0` 也不过，字符串不去首尾空格。录入时的这类小毛病可能对应真的录错，不替医生猜。
|
||||||
|
- C10 是负责人点名要的：同一个人在不同表里本应一样的值对不上，大概率是录入错误，要拿去找医生改。`待定问题/04` 记了 40 例里已知的跨表不一致。
|
||||||
|
- C11 只认段首的标题。正文中段出现「提示：」这类写法不算不过，这一例照常进库，但它会出现在复核清单里；这种中段的提示该不该给专家，等 `../待定问题/06-超声描述中段的造影提示.md` 定。在那之前，不能用构建做正式会诊。
|
||||||
|
- C12 不查单独出现的「浆液性」「黏液性」：它们在描述囊液性状时是正常用语。
|
||||||
|
- C13 禁单字「男」「女」：描述病灶用不到这两个字，出现了多半是写了患者性别，影像两路不该看到。
|
||||||
|
|
||||||
|
## 五、review.csv 是什么
|
||||||
|
|
||||||
|
复核清单：进库病例的超声描述、MR 描述里，含「考虑」「可能」「倾向」「提示」任一词的句子，每句一行（化名、路、命中的词、所在句子）。句子按「。」和「;」切（先做 NFKC，全角分号变成半角）。只扫进库的病例，跳过的病例不在这里。
|
||||||
|
|
||||||
|
这些词不带冒号时不算检查不过，因为它们也常用来描述影像所见；但它们可能引出医生的诊断倾向，所以列出来由负责人过目，决定要不要改规则或问医生。这里用化名而不是病例号，过目时如需对回病例，查同目录的 `aliases.csv`。
|
||||||
|
|
||||||
|
## 六、交给医生之前
|
||||||
|
|
||||||
|
- **`answers/` 里有真实病例号和报告原句**（`skipped.csv` 的涉及值、`review.csv` 的句子、`aliases.csv`、`diagnoses.csv`），只在本机，不进 git（`.gitignore` 和 pre-commit 两道拦截）。不能贴进文档、提交说明、Linear 评论或发给外部模型服务（`AGENTS.md` 硬性约束 3）。交给医生核对要走负责人认可的渠道，由负责人转交。
|
||||||
|
- 交给医生的通常只有 `skipped.csv`，说明里带上 `skipped_note` 那句话：每例只记第一项没过的检查。
|
||||||
|
- 不要把 `diagnoses.csv` 和资料库放在同一个地方给任何会诊代码或模型读（`AGENTS.md` 硬性约束 1）。
|
||||||
|
- 汇报、终端输出、日志里只写计数和检查编号，不写病例号和资料内容。
|
||||||
|
- 医生改好交付资料后，重新构建一次，得到新的构建号；旧的构建目录不删、不改（`AGENTS.md`「两档标准」：运行产物只追加）。
|
||||||
@@ -0,0 +1,37 @@
|
|||||||
|
"""装配两个库：读交付包，写出一对同号的资料库与答案库。
|
||||||
|
|
||||||
|
用法：uv run python scripts/build.py --config config/build.yaml
|
||||||
|
终端只打印计数，不打印病例号和资料内容。
|
||||||
|
"""
|
||||||
|
|
||||||
|
import argparse
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
from cadx.build import run_build
|
||||||
|
|
||||||
|
REPO_ROOT = Path(__file__).resolve().parents[1]
|
||||||
|
|
||||||
|
|
||||||
|
def main() -> None:
|
||||||
|
parser = argparse.ArgumentParser(description="装配给专家的资料库和标准答案库")
|
||||||
|
parser.add_argument("--config", type=Path, required=True, help="build.yaml 的路径")
|
||||||
|
config: Path = parser.parse_args().config
|
||||||
|
|
||||||
|
summary = run_build(config, REPO_ROOT, datetime.now().astimezone())
|
||||||
|
|
||||||
|
print(f"构建号：{summary.build_id}")
|
||||||
|
print(f"资料库：{summary.library_dir}")
|
||||||
|
print(f"答案库：{summary.answers_dir}")
|
||||||
|
print(f"病例总数：{summary.total_cases}")
|
||||||
|
print(f"进库病例：{summary.passed_cases}")
|
||||||
|
print(f"跳过病例：{summary.skipped_cases}")
|
||||||
|
print(f"认不出编号的行：{summary.unrecognized_rows}")
|
||||||
|
by_check = "，".join(f"{check} {n}" for check, n in summary.skipped_by_check.items())
|
||||||
|
print(f"按检查编号分的跳过数：{by_check or '无'}")
|
||||||
|
print(f"复核清单条数：{summary.review_rows}")
|
||||||
|
print(f"跳过清单说明：{summary.skipped_note}")
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
main()
|
||||||
@@ -0,0 +1,88 @@
|
|||||||
|
"""泄露扫描：查一次构建的资料库里有没有真实病例号、交付文件名、亚型名、诊断列名。
|
||||||
|
|
||||||
|
用法：uv run python scripts/scan_library.py --library library/<构建号> --answers answers/<构建号>
|
||||||
|
病例号和视频号从答案库读；亚型名、列名、文件名的词表在本脚本里独立写，不取自 delivery。
|
||||||
|
只输出命中的条数和类别，不输出命中的内容。这个脚本同时读两个库，只能放在 scripts/。
|
||||||
|
"""
|
||||||
|
|
||||||
|
import argparse
|
||||||
|
from collections import Counter
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
from cadx.answers import read_aliases
|
||||||
|
from cadx.library import scan_for_leaks
|
||||||
|
|
||||||
|
SUBTYPE_NAMES = (
|
||||||
|
"IPMN",
|
||||||
|
"IPMT",
|
||||||
|
"SPN",
|
||||||
|
"SPT",
|
||||||
|
"SPTP",
|
||||||
|
"MCN",
|
||||||
|
"SCN",
|
||||||
|
"导管内乳头状黏液性肿瘤",
|
||||||
|
"导管内乳头状",
|
||||||
|
"导管内乳头",
|
||||||
|
"实性假乳头状",
|
||||||
|
"实性假乳头",
|
||||||
|
"黏液性囊性肿瘤",
|
||||||
|
"黏液性囊",
|
||||||
|
"粘液性囊",
|
||||||
|
"黏液囊性",
|
||||||
|
"粘液囊性",
|
||||||
|
"浆液性囊性肿瘤",
|
||||||
|
"浆液性囊",
|
||||||
|
"浆液性微囊",
|
||||||
|
"囊腺瘤",
|
||||||
|
)
|
||||||
|
COLUMN_NAMES = (
|
||||||
|
"Case_ID",
|
||||||
|
"Diagnosis",
|
||||||
|
"病理类型",
|
||||||
|
"病理类型（1 IPMN，2 SPN，3 MCN，4 SCN）",
|
||||||
|
"患者ID",
|
||||||
|
"CEUS视频ID",
|
||||||
|
"推注开始时间",
|
||||||
|
)
|
||||||
|
DELIVERY_FILE_NAMES = (
|
||||||
|
"临床工作簿_40例.xlsx",
|
||||||
|
"超声报告文本_40例.xlsx",
|
||||||
|
"MR报告文本_40例.xlsx",
|
||||||
|
"Clinical_agent",
|
||||||
|
"CEUS_agent",
|
||||||
|
"MR_agent",
|
||||||
|
)
|
||||||
|
FORBIDDEN_KEYS = ("diagnosis", "label", "gold", "pathology", "name", "row")
|
||||||
|
|
||||||
|
|
||||||
|
def main() -> None:
|
||||||
|
parser = argparse.ArgumentParser(description="扫描资料库里的泄露")
|
||||||
|
parser.add_argument("--library", type=Path, required=True, help="资料库的构建目录")
|
||||||
|
parser.add_argument("--answers", type=Path, required=True, help="同一构建号的答案库目录")
|
||||||
|
args = parser.parse_args()
|
||||||
|
library: Path = args.library
|
||||||
|
answers: Path = args.answers
|
||||||
|
if library.name != answers.name:
|
||||||
|
raise SystemExit(f"两个目录的构建号不同：{library.name} 与 {answers.name}")
|
||||||
|
|
||||||
|
categories: dict[str, str] = {}
|
||||||
|
for row in read_aliases(answers):
|
||||||
|
categories[f"P{row.case_no}"] = "病例号"
|
||||||
|
categories[row.video_id] = "视频号"
|
||||||
|
for suffix in ("_key.png", "_roi2.mp4", ".mp4", "_roi2_report.xlsx", "_report.xlsx"):
|
||||||
|
categories[f"{row.video_id}{suffix}"] = "交付文件名"
|
||||||
|
categories.update(dict.fromkeys(DELIVERY_FILE_NAMES, "交付文件名"))
|
||||||
|
categories.update(dict.fromkeys(SUBTYPE_NAMES, "亚型名"))
|
||||||
|
categories.update(dict.fromkeys(COLUMN_NAMES, "列名"))
|
||||||
|
|
||||||
|
hits = scan_for_leaks(library, list(categories), FORBIDDEN_KEYS)
|
||||||
|
counts = Counter("键名" if hit.kind == "键名" else categories[hit.term] for hit in hits)
|
||||||
|
print(f"扫描的病例数：{len(read_aliases(answers))}")
|
||||||
|
print(f"禁止的字符串：{len(categories)} 个；禁止的键名：{len(FORBIDDEN_KEYS)} 个")
|
||||||
|
print(f"命中总数：{len(hits)}")
|
||||||
|
for category in ("病例号", "视频号", "交付文件名", "亚型名", "列名", "键名"):
|
||||||
|
print(f" {category}：{counts[category]}")
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
main()
|
||||||
@@ -0,0 +1,24 @@
|
|||||||
|
"""answers：标准答案库的目录布局、文件格式、写入和评价要用的读取。
|
||||||
|
|
||||||
|
拒绝读取名字以 `.partial` 结尾的目录；读时核对清单里的 SHA-256。
|
||||||
|
"""
|
||||||
|
|
||||||
|
from cadx.answers._files import (
|
||||||
|
AliasRow,
|
||||||
|
DiagnosisRow,
|
||||||
|
ReviewRow,
|
||||||
|
SkippedRow,
|
||||||
|
read_aliases,
|
||||||
|
read_diagnoses,
|
||||||
|
write_answers,
|
||||||
|
)
|
||||||
|
|
||||||
|
__all__ = [
|
||||||
|
"AliasRow",
|
||||||
|
"DiagnosisRow",
|
||||||
|
"ReviewRow",
|
||||||
|
"SkippedRow",
|
||||||
|
"read_aliases",
|
||||||
|
"read_diagnoses",
|
||||||
|
"write_answers",
|
||||||
|
]
|
||||||
@@ -0,0 +1,177 @@
|
|||||||
|
"""标准答案库的目录布局、写入和读取。
|
||||||
|
|
||||||
|
```
|
||||||
|
<构建目录>/
|
||||||
|
manifest.json 构建号、跳过清单的说明、本目录其余全部文件的 SHA-256
|
||||||
|
snapshot/ 运行快照（由 runs 写，先于本模块写入）
|
||||||
|
aliases.csv 化名、病例号、视频号
|
||||||
|
diagnoses.csv 化名、病例号、三张表的诊断编码、诊断名
|
||||||
|
skipped.csv 没进资料库的病例和第一项没过的检查
|
||||||
|
review.csv 进库病例报告里含复核措辞的句子
|
||||||
|
```
|
||||||
|
|
||||||
|
CSV 用带 BOM 的 UTF-8，医生用 Excel 直接打开不乱码。
|
||||||
|
"""
|
||||||
|
|
||||||
|
import csv
|
||||||
|
import hashlib
|
||||||
|
import json
|
||||||
|
from collections.abc import Sequence
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from pathlib import Path
|
||||||
|
from typing import Any, cast
|
||||||
|
|
||||||
|
MANIFEST = "manifest.json"
|
||||||
|
_ENCODING = "utf-8-sig"
|
||||||
|
_JOIN = "; "
|
||||||
|
|
||||||
|
ALIASES_HEADER = ("化名", "病例号", "视频号")
|
||||||
|
DIAGNOSES_HEADER = ("化名", "病例号", "临床表诊断编码", "超声表诊断编码", "MR表诊断编码", "诊断名")
|
||||||
|
SKIPPED_HEADER = ("病例", "检查编号", "检查说明", "文件", "列", "涉及值")
|
||||||
|
REVIEW_HEADER = ("化名", "路", "命中的词", "所在句子")
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class AliasRow:
|
||||||
|
"""化名与真实病例号、视频号的对照。"""
|
||||||
|
|
||||||
|
alias: str
|
||||||
|
case_no: str
|
||||||
|
video_id: str
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class DiagnosisRow:
|
||||||
|
"""一例的金标准：三张表各自的诊断编码，解码后的诊断名（不解码时为 None）。"""
|
||||||
|
|
||||||
|
alias: str
|
||||||
|
case_no: str
|
||||||
|
clinical_code: int
|
||||||
|
ultrasound_code: int
|
||||||
|
mr_code: int
|
||||||
|
name: str | None
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class SkippedRow:
|
||||||
|
"""跳过清单的一行。`case` 是病例号，或认不出编号时的「文件 第 N 行」。"""
|
||||||
|
|
||||||
|
case: str
|
||||||
|
check: str
|
||||||
|
description: str
|
||||||
|
files: tuple[str, ...]
|
||||||
|
columns: tuple[str, ...]
|
||||||
|
value_json: str
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class ReviewRow:
|
||||||
|
"""复核清单的一行：`route` 是「超声」或「MR」。"""
|
||||||
|
|
||||||
|
alias: str
|
||||||
|
route: str
|
||||||
|
words: str
|
||||||
|
sentence: str
|
||||||
|
|
||||||
|
|
||||||
|
def _sha256(path: Path) -> str:
|
||||||
|
return hashlib.sha256(path.read_bytes()).hexdigest()
|
||||||
|
|
||||||
|
|
||||||
|
def _write_csv(path: Path, header: tuple[str, ...], rows: Sequence[Sequence[object]]) -> None:
|
||||||
|
with path.open("w", encoding=_ENCODING, newline="") as handle:
|
||||||
|
writer = csv.writer(handle)
|
||||||
|
writer.writerow(header)
|
||||||
|
writer.writerows(rows)
|
||||||
|
|
||||||
|
|
||||||
|
def write_answers(
|
||||||
|
answers_dir: Path,
|
||||||
|
build_id: str,
|
||||||
|
skipped_note: str,
|
||||||
|
aliases: Sequence[AliasRow],
|
||||||
|
diagnoses: Sequence[DiagnosisRow],
|
||||||
|
skipped: Sequence[SkippedRow],
|
||||||
|
reviews: Sequence[ReviewRow],
|
||||||
|
) -> None:
|
||||||
|
"""写四张表，再给目录里全部文件（含已写好的 snapshot/）算 SHA-256 写进清单。"""
|
||||||
|
_write_csv(
|
||||||
|
answers_dir / "aliases.csv",
|
||||||
|
ALIASES_HEADER,
|
||||||
|
[(r.alias, r.case_no, r.video_id) for r in aliases],
|
||||||
|
)
|
||||||
|
_write_csv(
|
||||||
|
answers_dir / "diagnoses.csv",
|
||||||
|
DIAGNOSES_HEADER,
|
||||||
|
[
|
||||||
|
(r.alias, r.case_no, r.clinical_code, r.ultrasound_code, r.mr_code, r.name or "")
|
||||||
|
for r in diagnoses
|
||||||
|
],
|
||||||
|
)
|
||||||
|
_write_csv(
|
||||||
|
answers_dir / "skipped.csv",
|
||||||
|
SKIPPED_HEADER,
|
||||||
|
[
|
||||||
|
(
|
||||||
|
r.case,
|
||||||
|
r.check,
|
||||||
|
r.description,
|
||||||
|
_JOIN.join(r.files),
|
||||||
|
_JOIN.join(r.columns),
|
||||||
|
r.value_json,
|
||||||
|
)
|
||||||
|
for r in skipped
|
||||||
|
],
|
||||||
|
)
|
||||||
|
_write_csv(
|
||||||
|
answers_dir / "review.csv",
|
||||||
|
REVIEW_HEADER,
|
||||||
|
[(r.alias, r.route, r.words, r.sentence) for r in reviews],
|
||||||
|
)
|
||||||
|
files = {
|
||||||
|
p.relative_to(answers_dir).as_posix(): _sha256(p)
|
||||||
|
for p in sorted(answers_dir.rglob("*"))
|
||||||
|
if p.is_file()
|
||||||
|
}
|
||||||
|
manifest = {"build_id": build_id, "skipped_note": skipped_note, "files": files}
|
||||||
|
(answers_dir / MANIFEST).write_text(
|
||||||
|
json.dumps(manifest, ensure_ascii=False, indent=2) + "\n", encoding="utf-8"
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def _read_csv(answers_dir: Path, name: str, header: tuple[str, ...]) -> list[list[str]]:
|
||||||
|
if answers_dir.name.endswith(".partial"):
|
||||||
|
raise ValueError(f"{answers_dir} 是没写完的构建（.partial），不能读")
|
||||||
|
manifest = cast(
|
||||||
|
dict[str, Any], json.loads((answers_dir / MANIFEST).read_text(encoding="utf-8"))
|
||||||
|
)
|
||||||
|
path = answers_dir / name
|
||||||
|
if _sha256(path) != manifest["files"][name]:
|
||||||
|
raise ValueError(f"{name} 的 SHA-256 与清单不一致，答案库被改动过")
|
||||||
|
with path.open(encoding=_ENCODING, newline="") as handle:
|
||||||
|
rows = list(csv.reader(handle))
|
||||||
|
if tuple(rows[0]) != header:
|
||||||
|
raise ValueError(f"{name} 的表头与约定不一致")
|
||||||
|
return rows[1:]
|
||||||
|
|
||||||
|
|
||||||
|
def read_aliases(answers_dir: Path) -> tuple[AliasRow, ...]:
|
||||||
|
"""读化名对照。"""
|
||||||
|
rows = _read_csv(answers_dir, "aliases.csv", ALIASES_HEADER)
|
||||||
|
return tuple(AliasRow(alias=a, case_no=c, video_id=v) for a, c, v in rows)
|
||||||
|
|
||||||
|
|
||||||
|
def read_diagnoses(answers_dir: Path) -> tuple[DiagnosisRow, ...]:
|
||||||
|
"""读金标准。诊断名一栏为空表示构建时没有解码。"""
|
||||||
|
rows = _read_csv(answers_dir, "diagnoses.csv", DIAGNOSES_HEADER)
|
||||||
|
return tuple(
|
||||||
|
DiagnosisRow(
|
||||||
|
alias=alias,
|
||||||
|
case_no=case_no,
|
||||||
|
clinical_code=int(clinical),
|
||||||
|
ultrasound_code=int(ultrasound),
|
||||||
|
mr_code=int(mr),
|
||||||
|
name=name or None,
|
||||||
|
)
|
||||||
|
for alias, case_no, clinical, ultrasound, mr, name in rows
|
||||||
|
)
|
||||||
@@ -0,0 +1,13 @@
|
|||||||
|
"""build：装配两个库。可见性（每一路放什么）、化名、清单内容只在这里决定。"""
|
||||||
|
|
||||||
|
from cadx.build._assemble import BuildSummary, make_aliases, run_build
|
||||||
|
from cadx.build._config import BuildConfig, load_build_config, load_code_maps
|
||||||
|
|
||||||
|
__all__ = [
|
||||||
|
"BuildConfig",
|
||||||
|
"BuildSummary",
|
||||||
|
"load_build_config",
|
||||||
|
"load_code_maps",
|
||||||
|
"make_aliases",
|
||||||
|
"run_build",
|
||||||
|
]
|
||||||
@@ -0,0 +1,198 @@
|
|||||||
|
"""装配一次构建：决定每一路放什么、化名怎么取，写出资料库和答案库。
|
||||||
|
|
||||||
|
全项目只有这里同时碰得到原始资料和答案。
|
||||||
|
"""
|
||||||
|
|
||||||
|
import hashlib
|
||||||
|
import random
|
||||||
|
import string
|
||||||
|
from collections import Counter
|
||||||
|
from collections.abc import Sequence
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
from typing import cast
|
||||||
|
|
||||||
|
from cadx.answers import AliasRow, DiagnosisRow, ReviewRow, SkippedRow, write_answers
|
||||||
|
from cadx.build._config import load_build_config, load_code_maps
|
||||||
|
from cadx.delivery import (
|
||||||
|
CODED_COLUMNS,
|
||||||
|
SKIPPED_NOTE,
|
||||||
|
CaseRecord,
|
||||||
|
CodeMaps,
|
||||||
|
read_delivery,
|
||||||
|
review_sentences,
|
||||||
|
)
|
||||||
|
from cadx.library import LibraryCase, write_library
|
||||||
|
from cadx.runs import make_build_id, read_git_state, write_snapshot
|
||||||
|
|
||||||
|
ALIAS_ALPHABET = string.ascii_lowercase + string.digits
|
||||||
|
ALIAS_LENGTH = 4
|
||||||
|
# 化名里出现亚型缩写会被泄露扫描（不分大小写）误报，抽到就重抽。
|
||||||
|
_ALIAS_BANNED = ("ipmn", "spn", "mcn", "scn")
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class BuildSummary:
|
||||||
|
"""一次构建的计数，供终端打印；不含病例号和资料内容。"""
|
||||||
|
|
||||||
|
build_id: str
|
||||||
|
library_dir: Path
|
||||||
|
answers_dir: Path
|
||||||
|
total_cases: int
|
||||||
|
passed_cases: int
|
||||||
|
skipped_cases: int
|
||||||
|
unrecognized_rows: int
|
||||||
|
skipped_by_check: dict[str, int]
|
||||||
|
review_rows: int
|
||||||
|
skipped_note: str
|
||||||
|
|
||||||
|
|
||||||
|
def make_aliases(case_nos: Sequence[str], seed: int) -> dict[str, str]:
|
||||||
|
"""按病例号排序后依次抽化名：同一个种子、同一批病例得到同样的化名。"""
|
||||||
|
rng = random.Random(seed) # noqa: S311 化名只需可复现，不需要密码学强度
|
||||||
|
aliases: dict[str, str] = {}
|
||||||
|
for case_no in sorted(case_nos):
|
||||||
|
while True:
|
||||||
|
alias = "".join(rng.choice(ALIAS_ALPHABET) for _ in range(ALIAS_LENGTH))
|
||||||
|
if alias not in aliases.values() and not any(b in alias for b in _ALIAS_BANNED):
|
||||||
|
break
|
||||||
|
aliases[case_no] = alias
|
||||||
|
return aliases
|
||||||
|
|
||||||
|
|
||||||
|
def _clinical_fields(
|
||||||
|
case: CaseRecord, code_maps: CodeMaps | None
|
||||||
|
) -> dict[str, str | int | float | None]:
|
||||||
|
"""临床一路的 22 列；解码时编码列写映射表里的含义，没测的化验保持 None。"""
|
||||||
|
if code_maps is None:
|
||||||
|
return dict(case.clinical)
|
||||||
|
return {
|
||||||
|
column: code_maps[column][cast(int, value)]
|
||||||
|
if column in CODED_COLUMNS and value is not None
|
||||||
|
else value
|
||||||
|
for column, value in case.clinical.items()
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def _sha256(path: Path) -> str:
|
||||||
|
return hashlib.sha256(path.read_bytes()).hexdigest()
|
||||||
|
|
||||||
|
|
||||||
|
def _rename(partial: Path, final: Path) -> None:
|
||||||
|
# POSIX 的 rename 会悄悄覆盖空目录，所以改名前再查一次。
|
||||||
|
if final.exists():
|
||||||
|
raise FileExistsError(f"{final} 已存在，不覆盖")
|
||||||
|
partial.rename(final)
|
||||||
|
|
||||||
|
|
||||||
|
def run_build(config_path: Path, repo_root: Path, now: datetime) -> BuildSummary:
|
||||||
|
"""读配置和交付包，装配一对同号的资料库与答案库。`now` 是本地时间，定构建号。"""
|
||||||
|
config = load_build_config(config_path, repo_root)
|
||||||
|
code_maps = load_code_maps(config.code_maps) if config.code_maps is not None else None
|
||||||
|
delivery = read_delivery(config.delivery_dir, code_maps)
|
||||||
|
|
||||||
|
git = read_git_state(repo_root)
|
||||||
|
build_id = make_build_id(now, git)
|
||||||
|
library_dir = config.library_root / build_id
|
||||||
|
answers_dir = config.answers_root / build_id
|
||||||
|
library_partial = config.library_root / f"{build_id}.partial"
|
||||||
|
answers_partial = config.answers_root / f"{build_id}.partial"
|
||||||
|
for final in (library_dir, answers_dir):
|
||||||
|
if final.exists():
|
||||||
|
raise FileExistsError(f"{final} 已存在，不覆盖")
|
||||||
|
for partial in (library_partial, answers_partial):
|
||||||
|
partial.mkdir(parents=True, exist_ok=False)
|
||||||
|
|
||||||
|
aliases = make_aliases([case.case_no for case in delivery.cases], config.alias_seed)
|
||||||
|
by_alias = sorted(delivery.cases, key=lambda case: aliases[case.case_no])
|
||||||
|
|
||||||
|
configs = {"build.yaml": config_path}
|
||||||
|
if config.code_maps is not None:
|
||||||
|
configs["code_maps.yaml"] = config.code_maps
|
||||||
|
write_library(
|
||||||
|
build_dir=library_partial,
|
||||||
|
build_id=build_id,
|
||||||
|
git_commit=git.commit,
|
||||||
|
git_clean=git.clean,
|
||||||
|
config_sha256={name: _sha256(path) for name, path in configs.items()},
|
||||||
|
codes_decoded=code_maps is not None,
|
||||||
|
uncompared=delivery.uncompared,
|
||||||
|
ceus_source=None,
|
||||||
|
cases=[
|
||||||
|
LibraryCase(
|
||||||
|
alias=aliases[case.case_no],
|
||||||
|
clinical_fields=_clinical_fields(case, code_maps),
|
||||||
|
ultrasound_report=case.ultrasound_report,
|
||||||
|
key_image_source=case.key_image,
|
||||||
|
mr_report=case.mr_report,
|
||||||
|
)
|
||||||
|
for case in by_alias
|
||||||
|
],
|
||||||
|
)
|
||||||
|
|
||||||
|
reviews = [
|
||||||
|
ReviewRow(alias=aliases[case.case_no], route=route, words=words, sentence=sentence)
|
||||||
|
for case in by_alias
|
||||||
|
for route, text in (("超声", case.ultrasound_report), ("MR", case.mr_report))
|
||||||
|
for words, sentence in review_sentences(text)
|
||||||
|
]
|
||||||
|
write_snapshot(
|
||||||
|
snapshot_dir=answers_partial / "snapshot",
|
||||||
|
build_id=build_id,
|
||||||
|
git=git,
|
||||||
|
started_at=now,
|
||||||
|
finished_at=datetime.now().astimezone(),
|
||||||
|
uv_lock=repo_root / "uv.lock",
|
||||||
|
configs=configs,
|
||||||
|
)
|
||||||
|
write_answers(
|
||||||
|
answers_dir=answers_partial,
|
||||||
|
build_id=build_id,
|
||||||
|
skipped_note=SKIPPED_NOTE,
|
||||||
|
aliases=[
|
||||||
|
AliasRow(alias=aliases[c.case_no], case_no=c.case_no, video_id=c.video_id)
|
||||||
|
for c in delivery.cases
|
||||||
|
],
|
||||||
|
diagnoses=[
|
||||||
|
DiagnosisRow(
|
||||||
|
alias=aliases[c.case_no],
|
||||||
|
case_no=c.case_no,
|
||||||
|
clinical_code=c.diagnosis.clinical,
|
||||||
|
ultrasound_code=c.diagnosis.ultrasound,
|
||||||
|
mr_code=c.diagnosis.mr,
|
||||||
|
name=None if code_maps is None else code_maps["Diagnosis"][c.diagnosis.clinical],
|
||||||
|
)
|
||||||
|
for c in delivery.cases
|
||||||
|
],
|
||||||
|
skipped=[
|
||||||
|
SkippedRow(
|
||||||
|
case=s.case,
|
||||||
|
check=s.check,
|
||||||
|
description=s.description,
|
||||||
|
files=s.files,
|
||||||
|
columns=s.columns,
|
||||||
|
value_json=s.value_json,
|
||||||
|
)
|
||||||
|
for s in delivery.skipped
|
||||||
|
],
|
||||||
|
reviews=reviews,
|
||||||
|
)
|
||||||
|
|
||||||
|
# 先改答案库，最后改资料库：资料库的 <构建号>/ 出现才算构建完成。
|
||||||
|
_rename(answers_partial, answers_dir)
|
||||||
|
_rename(library_partial, library_dir)
|
||||||
|
|
||||||
|
by_check = Counter(s.check for s in delivery.skipped)
|
||||||
|
return BuildSummary(
|
||||||
|
build_id=build_id,
|
||||||
|
library_dir=library_dir,
|
||||||
|
answers_dir=answers_dir,
|
||||||
|
total_cases=delivery.total_cases,
|
||||||
|
passed_cases=len(delivery.cases),
|
||||||
|
skipped_cases=len(delivery.skipped) - delivery.unrecognized_rows,
|
||||||
|
unrecognized_rows=delivery.unrecognized_rows,
|
||||||
|
skipped_by_check=dict(sorted(by_check.items())),
|
||||||
|
review_rows=len(reviews),
|
||||||
|
skipped_note=SKIPPED_NOTE,
|
||||||
|
)
|
||||||
@@ -0,0 +1,96 @@
|
|||||||
|
"""`config/build.yaml` 与编码映射表的字段定义和校验（含 T5）。"""
|
||||||
|
|
||||||
|
from collections.abc import Hashable
|
||||||
|
from pathlib import Path
|
||||||
|
from typing import Annotated, Any, Self
|
||||||
|
|
||||||
|
import yaml
|
||||||
|
from pydantic import BaseModel, BeforeValidator, ConfigDict, Field, TypeAdapter, model_validator
|
||||||
|
|
||||||
|
from cadx.delivery import CODED_COLUMNS, CodeMaps
|
||||||
|
|
||||||
|
|
||||||
|
def _reject_empty_path(value: object) -> object:
|
||||||
|
# Path("") 会变成 "."（当前目录），空串在转换前就拦下。
|
||||||
|
if value == "":
|
||||||
|
raise ValueError("路径不能是空串")
|
||||||
|
return value
|
||||||
|
|
||||||
|
|
||||||
|
# YAML 里的路径是字符串；路径字段是唯一允许从字符串转换类型的地方。
|
||||||
|
type _PathField = Annotated[Path, Field(strict=False), BeforeValidator(_reject_empty_path)]
|
||||||
|
|
||||||
|
|
||||||
|
class _UniqueKeyLoader(yaml.SafeLoader):
|
||||||
|
"""同一层出现重复键就报错：PyYAML 默认让后一个悄悄覆盖前一个。"""
|
||||||
|
|
||||||
|
# 签名（含 deep 的默认值）照抄 PyYAML 的基类方法，覆盖时必须一致。
|
||||||
|
def construct_mapping(self, node: yaml.MappingNode, deep: bool = False) -> dict[Hashable, Any]:
|
||||||
|
seen: set[Hashable] = set()
|
||||||
|
for key_node, _ in node.value:
|
||||||
|
key = self.construct_object(key_node, deep=deep) # pyright: ignore[reportUnknownMemberType]
|
||||||
|
if key in seen:
|
||||||
|
raise ValueError(f"YAML 第 {key_node.start_mark.line + 1} 行重复的键：{key!r}")
|
||||||
|
seen.add(key)
|
||||||
|
return super().construct_mapping(node, deep=deep)
|
||||||
|
|
||||||
|
|
||||||
|
def _load_yaml(path: Path) -> object:
|
||||||
|
return yaml.load(path.read_text(encoding="utf-8"), Loader=_UniqueKeyLoader) # noqa: S506 _UniqueKeyLoader 继承 SafeLoader
|
||||||
|
|
||||||
|
|
||||||
|
SUBTYPES = frozenset({"IPMN", "SPN", "MCN", "SCN"})
|
||||||
|
SEXES = frozenset({"男", "女"})
|
||||||
|
|
||||||
|
|
||||||
|
class BuildConfig(BaseModel):
|
||||||
|
"""装配两个库的配置。每个字段必填；相对路径相对仓库根目录解析。"""
|
||||||
|
|
||||||
|
model_config = ConfigDict(strict=True, extra="forbid", frozen=True)
|
||||||
|
|
||||||
|
delivery_dir: _PathField
|
||||||
|
library_root: _PathField
|
||||||
|
answers_root: _PathField
|
||||||
|
alias_seed: int
|
||||||
|
decode_codes: bool
|
||||||
|
code_maps: Annotated[Path | None, Field(strict=False), BeforeValidator(_reject_empty_path)]
|
||||||
|
|
||||||
|
@model_validator(mode="after")
|
||||||
|
def _code_maps_match_switch(self) -> Self:
|
||||||
|
if self.decode_codes and self.code_maps is None:
|
||||||
|
raise ValueError("decode_codes 为 true 时 code_maps 必须是映射表路径")
|
||||||
|
if not self.decode_codes and self.code_maps is not None:
|
||||||
|
raise ValueError("decode_codes 为 false 时 code_maps 必须是 null")
|
||||||
|
return self
|
||||||
|
|
||||||
|
|
||||||
|
def load_build_config(path: Path, repo_root: Path) -> BuildConfig:
|
||||||
|
"""读并校验 `build.yaml`，把相对路径换成 `repo_root` 下的绝对路径。"""
|
||||||
|
config = BuildConfig.model_validate(_load_yaml(path))
|
||||||
|
return config.model_copy(
|
||||||
|
update={
|
||||||
|
"delivery_dir": repo_root / config.delivery_dir,
|
||||||
|
"library_root": repo_root / config.library_root,
|
||||||
|
"answers_root": repo_root / config.answers_root,
|
||||||
|
"code_maps": None if config.code_maps is None else repo_root / config.code_maps,
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
_CODE_MAPS = TypeAdapter(dict[str, dict[int, str]], config=ConfigDict(strict=True))
|
||||||
|
|
||||||
|
|
||||||
|
def load_code_maps(path: Path) -> CodeMaps:
|
||||||
|
"""读映射表并做 T5：恰好覆盖全部编码列，性别映射到「男」「女」，诊断映射到四个亚型缩写。"""
|
||||||
|
maps = _CODE_MAPS.validate_python(_load_yaml(path))
|
||||||
|
if set(maps) != set(CODED_COLUMNS):
|
||||||
|
extra = sorted(set(maps) - set(CODED_COLUMNS))
|
||||||
|
missing = sorted(set(CODED_COLUMNS) - set(maps))
|
||||||
|
raise ValueError(
|
||||||
|
f"T5 映射表应恰好覆盖 {len(CODED_COLUMNS)} 项编码列：多了 {extra}，缺 {missing}"
|
||||||
|
)
|
||||||
|
for column, expected in (("Sex", SEXES), ("Diagnosis", SUBTYPES)):
|
||||||
|
values = list(maps[column].values())
|
||||||
|
if len(values) != len(expected) or frozenset(values) != expected:
|
||||||
|
raise ValueError(f"T5 映射表的 {column} 应恰好映射到 {sorted(expected)}")
|
||||||
|
return maps
|
||||||
@@ -0,0 +1,31 @@
|
|||||||
|
"""delivery：读 40 例交付包、逐例检查。只读，不决定谁能看见什么。
|
||||||
|
|
||||||
|
整张表的问题（T1–T4）抛 `DeliveryError`，整次构建停下；单个病例的问题（C01–C13）
|
||||||
|
跳过整例，记一条 `SkipRecord`。
|
||||||
|
"""
|
||||||
|
|
||||||
|
from cadx.delivery._cases import (
|
||||||
|
SKIPPED_NOTE,
|
||||||
|
CaseRecord,
|
||||||
|
CodeMaps,
|
||||||
|
DeliveryResult,
|
||||||
|
DiagnosisCodes,
|
||||||
|
SkipRecord,
|
||||||
|
read_delivery,
|
||||||
|
)
|
||||||
|
from cadx.delivery._shape import CODED_COLUMNS
|
||||||
|
from cadx.delivery._tables import DeliveryError
|
||||||
|
from cadx.delivery._text import review_sentences
|
||||||
|
|
||||||
|
__all__ = [
|
||||||
|
"CODED_COLUMNS",
|
||||||
|
"SKIPPED_NOTE",
|
||||||
|
"CaseRecord",
|
||||||
|
"CodeMaps",
|
||||||
|
"DeliveryError",
|
||||||
|
"DeliveryResult",
|
||||||
|
"DiagnosisCodes",
|
||||||
|
"SkipRecord",
|
||||||
|
"read_delivery",
|
||||||
|
"review_sentences",
|
||||||
|
]
|
||||||
@@ -0,0 +1,412 @@
|
|||||||
|
"""逐例检查 C01–C13，交出通过的病例和跳过记录。
|
||||||
|
|
||||||
|
一例遇到第一项不过的检查就跳过整例，后面的检查不再做（`AGENTS.md`「错误怎么处理」）。
|
||||||
|
类型按 openpyxl 读出的 Python 类型判断，不做转换：要求整数的格读出 `45.0` 也不过，
|
||||||
|
字符串不去首尾空格。
|
||||||
|
"""
|
||||||
|
|
||||||
|
import json
|
||||||
|
import re
|
||||||
|
from collections.abc import Callable, Mapping
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from pathlib import Path
|
||||||
|
from typing import TypeGuard, cast
|
||||||
|
|
||||||
|
from cadx.delivery import _text
|
||||||
|
from cadx.delivery._shape import (
|
||||||
|
CASE_REPORT_SHEET,
|
||||||
|
CLINICAL,
|
||||||
|
CLINICAL_ROUTE_COLUMNS,
|
||||||
|
CODED_COLUMNS,
|
||||||
|
DIAGNOSIS_HEADER,
|
||||||
|
HISTORY_COLUMNS,
|
||||||
|
LAB_PAIRS,
|
||||||
|
MR,
|
||||||
|
SUMMARY_TABLES,
|
||||||
|
SYMPTOM_COLUMNS,
|
||||||
|
ULTRASOUND,
|
||||||
|
TableShape,
|
||||||
|
case_dir_path,
|
||||||
|
video_id,
|
||||||
|
)
|
||||||
|
from cadx.delivery._tables import Cell, Row, open_workbook, read_tables
|
||||||
|
|
||||||
|
type CodeMaps = Mapping[str, Mapping[int, str]]
|
||||||
|
|
||||||
|
CHECK_DESCRIPTIONS = {
|
||||||
|
"C01": "编号能规范化",
|
||||||
|
"C02": "同一张表里这个编号只出现一次",
|
||||||
|
"C03": "三张表和病例目录里都有这一例",
|
||||||
|
"C04": "病例目录恰好有关键图、视频、与视频名配对的单例报告表三个文件",
|
||||||
|
"C05": "超声表的 CEUS视频ID 与病例号一致",
|
||||||
|
"C06": "单例报告表与超声汇总表对应行一致",
|
||||||
|
"C07": "临床表取值合规",
|
||||||
|
"C08": "超声表取值合规",
|
||||||
|
"C09": "MR 表取值合规",
|
||||||
|
"C10": "跨表一致（诊断、年龄、性别）",
|
||||||
|
"C11": "报告文字里没有结论段标题",
|
||||||
|
"C12": "报告文字里没有亚型名",
|
||||||
|
"C13": "报告文字里没有人口学信息",
|
||||||
|
}
|
||||||
|
|
||||||
|
SKIPPED_NOTE = "每例只记第一项没过的检查：遇到它就跳过整例，后面的检查没有做过，不代表没有问题。"
|
||||||
|
|
||||||
|
UNCOMPARED_CLINICAL_SEX = "临床性别未比对"
|
||||||
|
|
||||||
|
_CLINICAL_ID = re.compile(r"P([0-9]{3})")
|
||||||
|
_REPORT_ID = re.compile(r"[0-9]+")
|
||||||
|
_REPORT_AGE = re.compile(r"[0-9]+岁")
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class DiagnosisCodes:
|
||||||
|
"""三张表各自的诊断编码（C10 保证三者相等）。"""
|
||||||
|
|
||||||
|
clinical: int
|
||||||
|
ultrasound: int
|
||||||
|
mr: int
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class CaseRecord:
|
||||||
|
"""一个检查全部通过的病例读到的内容。"""
|
||||||
|
|
||||||
|
case_no: str # 三位补零
|
||||||
|
video_id: str
|
||||||
|
clinical: Mapping[str, int | float | None] # 临床表除 Case_ID、Diagnosis 外的 22 列
|
||||||
|
ultrasound_report: str
|
||||||
|
mr_report: str
|
||||||
|
key_image: Path
|
||||||
|
diagnosis: DiagnosisCodes
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class SkipRecord:
|
||||||
|
"""一条跳过记录。`case` 是三位病例号，C01 认不出编号时是「文件 第 N 行」。"""
|
||||||
|
|
||||||
|
case: str
|
||||||
|
check: str
|
||||||
|
description: str
|
||||||
|
files: tuple[str, ...]
|
||||||
|
columns: tuple[str, ...]
|
||||||
|
value_json: str
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class DeliveryResult:
|
||||||
|
"""读一次交付包的结果。"""
|
||||||
|
|
||||||
|
cases: tuple[CaseRecord, ...] # 按病例号排序
|
||||||
|
skipped: tuple[SkipRecord, ...]
|
||||||
|
total_cases: int # 三张表和病例目录里认得出的病例号的并集大小
|
||||||
|
unrecognized_rows: int # C01 认不出编号的行数，不计入病例数
|
||||||
|
uncompared: tuple[str, ...] # 因为没有映射表而没比对的项
|
||||||
|
|
||||||
|
|
||||||
|
def _skip(
|
||||||
|
case: str, check: str, files: tuple[str, ...], columns: tuple[str, ...], value: object
|
||||||
|
) -> SkipRecord:
|
||||||
|
# 涉及值可能是 openpyxl 读出的任何类型（如日期），JSON 表示不了的按 repr 写，供医生核对。
|
||||||
|
return SkipRecord(
|
||||||
|
case=case,
|
||||||
|
check=check,
|
||||||
|
description=CHECK_DESCRIPTIONS[check],
|
||||||
|
files=files,
|
||||||
|
columns=columns,
|
||||||
|
value_json=json.dumps(value, ensure_ascii=False, default=repr),
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def _is_int(value: Cell) -> TypeGuard[int]:
|
||||||
|
return type(value) is int # bool 是 int 的子类，要排除
|
||||||
|
|
||||||
|
|
||||||
|
def _is_number(value: Cell) -> TypeGuard[int | float]:
|
||||||
|
return type(value) in (int, float)
|
||||||
|
|
||||||
|
|
||||||
|
def _in_range(value: Cell, low: int, high: int) -> bool:
|
||||||
|
return _is_int(value) and low <= value <= high
|
||||||
|
|
||||||
|
|
||||||
|
def _normalize_id(table: TableShape, raw: Cell) -> str | None:
|
||||||
|
"""C01：认得出就返回三位病例号，认不出返回 None。"""
|
||||||
|
number: int | None = None
|
||||||
|
if table is CLINICAL:
|
||||||
|
if isinstance(raw, str) and (m := _CLINICAL_ID.fullmatch(raw)):
|
||||||
|
number = int(m.group(1))
|
||||||
|
elif isinstance(raw, str) and _REPORT_ID.fullmatch(raw):
|
||||||
|
number = int(raw)
|
||||||
|
elif _is_int(raw):
|
||||||
|
number = raw
|
||||||
|
if number is None or not 1 <= number <= 999:
|
||||||
|
return None
|
||||||
|
return f"{number:03d}"
|
||||||
|
|
||||||
|
|
||||||
|
def _index_rows(
|
||||||
|
rows: dict[TableShape, list[Row]], case_dirs: list[str]
|
||||||
|
) -> tuple[dict[TableShape, dict[str, list[Row]]], set[str], list[SkipRecord]]:
|
||||||
|
index: dict[TableShape, dict[str, list[Row]]] = {}
|
||||||
|
unrecognized: list[SkipRecord] = []
|
||||||
|
for table in SUMMARY_TABLES:
|
||||||
|
index[table] = {}
|
||||||
|
for row in rows[table]:
|
||||||
|
raw = row.cells[table.id_column]
|
||||||
|
case_no = _normalize_id(table, raw)
|
||||||
|
if case_no is None:
|
||||||
|
unrecognized.append(
|
||||||
|
_skip(
|
||||||
|
f"{table.path} 第 {row.number} 行",
|
||||||
|
"C01",
|
||||||
|
(table.path,),
|
||||||
|
(table.id_column,),
|
||||||
|
{"原始写法": raw, "行号": row.number},
|
||||||
|
)
|
||||||
|
)
|
||||||
|
continue
|
||||||
|
index[table].setdefault(case_no, []).append(row)
|
||||||
|
dirs: set[str] = set()
|
||||||
|
for name in case_dirs:
|
||||||
|
if not 1 <= int(name) <= 999:
|
||||||
|
unrecognized.append(
|
||||||
|
_skip(f"病例目录 {name}", "C01", (case_dir_path(name),), (), {"目录名": name})
|
||||||
|
)
|
||||||
|
continue
|
||||||
|
dirs.add(name)
|
||||||
|
return index, dirs, unrecognized
|
||||||
|
|
||||||
|
|
||||||
|
# 单例报告表的名字随视频名配对：带 roi2 标记的视频配带 roi2 的报告，反之亦然（负责人 2026-10-16）。
|
||||||
|
_VIDEO_REPORT_PAIRS = (("_roi2.mp4", "_roi2_report.xlsx"), (".mp4", "_report.xlsx"))
|
||||||
|
|
||||||
|
|
||||||
|
def _check_case_dir(case_no: str, folder: Path) -> str | SkipRecord:
|
||||||
|
"""C04：通过时返回这一例单例报告表的文件名。"""
|
||||||
|
u = video_id(case_no)
|
||||||
|
names = sorted(p.name for p in folder.iterdir())
|
||||||
|
for video, report in _VIDEO_REPORT_PAIRS:
|
||||||
|
if names == sorted((f"{u}_key.png", f"{u}{video}", f"{u}{report}")):
|
||||||
|
return f"{u}{report}"
|
||||||
|
return _skip(case_no, "C04", (case_dir_path(case_no),), (), {"文件": names})
|
||||||
|
|
||||||
|
|
||||||
|
def _check_case_report(case_no: str, path: Path, summary: Row, rel: str) -> SkipRecord | None:
|
||||||
|
"""C06：单例报告表与超声汇总表那一行逐格相等（类型也要相同）。"""
|
||||||
|
sheets = open_workbook(path)
|
||||||
|
if sheets.names != (CASE_REPORT_SHEET,):
|
||||||
|
return _skip(case_no, "C06", (rel,), (), {"工作表": list(sheets.names)})
|
||||||
|
if not sheets.rows or sheets.rows[0] != ULTRASOUND.header:
|
||||||
|
return _skip(case_no, "C06", (rel,), (), {"表头": "与超声汇总表不一致"})
|
||||||
|
if len(sheets.rows) != 2:
|
||||||
|
return _skip(case_no, "C06", (rel,), (), {"数据行数": len(sheets.rows) - 1})
|
||||||
|
diffs = {
|
||||||
|
column: {"单例报告表": mine, "超声汇总表": summary.cells[column]}
|
||||||
|
for column, mine in zip(ULTRASOUND.header, sheets.rows[1], strict=True)
|
||||||
|
if not (type(mine) is type(summary.cells[column]) and mine == summary.cells[column])
|
||||||
|
}
|
||||||
|
if diffs:
|
||||||
|
return _skip(case_no, "C06", (rel, ULTRASOUND.path), tuple(diffs), diffs)
|
||||||
|
return None
|
||||||
|
|
||||||
|
|
||||||
|
def _clinical_violations(cells: dict[str, Cell], code_maps: CodeMaps | None) -> dict[str, Cell]:
|
||||||
|
"""C07：返回不合规的列和值。"""
|
||||||
|
bad: dict[str, Cell] = {}
|
||||||
|
if not _in_range(cells["Sex"], 1, 2):
|
||||||
|
bad["Sex"] = cells["Sex"]
|
||||||
|
if not (_is_int(cells["Age"]) and cells["Age"] > 0):
|
||||||
|
bad["Age"] = cells["Age"]
|
||||||
|
if not _in_range(cells["Diagnosis"], 1, 4):
|
||||||
|
bad["Diagnosis"] = cells["Diagnosis"]
|
||||||
|
for column in (*SYMPTOM_COLUMNS, *HISTORY_COLUMNS):
|
||||||
|
if not _in_range(cells[column], 0, 1):
|
||||||
|
bad[column] = cells[column]
|
||||||
|
for raw_column, level_column in LAB_PAIRS:
|
||||||
|
raw, level = cells[raw_column], cells[level_column]
|
||||||
|
if raw is None and level is None:
|
||||||
|
continue
|
||||||
|
if not (_is_number(raw) and _in_range(level, 0, 1)):
|
||||||
|
bad[raw_column], bad[level_column] = raw, level
|
||||||
|
if code_maps is not None:
|
||||||
|
for column in CODED_COLUMNS:
|
||||||
|
value = cells[column]
|
||||||
|
if value is not None and not (_is_int(value) and value in code_maps[column]):
|
||||||
|
bad[column] = value
|
||||||
|
return bad
|
||||||
|
|
||||||
|
|
||||||
|
def _report_violations(
|
||||||
|
cells: dict[str, Cell], text_column: str, code_maps: CodeMaps | None
|
||||||
|
) -> dict[str, Cell]:
|
||||||
|
"""C08 / C09 共同的部分：性别、年龄、诊断、描述文字。"""
|
||||||
|
bad: dict[str, Cell] = {}
|
||||||
|
if cells["性别"] not in ("男", "女"):
|
||||||
|
bad["性别"] = cells["性别"]
|
||||||
|
age = cells["年龄"]
|
||||||
|
if not (isinstance(age, str) and _REPORT_AGE.fullmatch(age)):
|
||||||
|
bad["年龄"] = age
|
||||||
|
diagnosis = cells[DIAGNOSIS_HEADER]
|
||||||
|
if not _in_range(diagnosis, 1, 4) or (
|
||||||
|
code_maps is not None and diagnosis not in code_maps["Diagnosis"]
|
||||||
|
):
|
||||||
|
bad[DIAGNOSIS_HEADER] = diagnosis
|
||||||
|
text = cells[text_column]
|
||||||
|
if not (isinstance(text, str) and text):
|
||||||
|
bad[text_column] = text
|
||||||
|
return bad
|
||||||
|
|
||||||
|
|
||||||
|
def _report_age(cells: dict[str, Cell]) -> int:
|
||||||
|
return int(cast(str, cells["年龄"]).removesuffix("岁"))
|
||||||
|
|
||||||
|
|
||||||
|
def _cross_table(
|
||||||
|
clinical: dict[str, Cell],
|
||||||
|
ultrasound: dict[str, Cell],
|
||||||
|
mr: dict[str, Cell],
|
||||||
|
code_maps: CodeMaps | None,
|
||||||
|
) -> dict[str, dict[str, Cell]]:
|
||||||
|
"""C10：返回对不上的字段和各表的值。"""
|
||||||
|
bad: dict[str, dict[str, Cell]] = {}
|
||||||
|
diagnoses = (clinical["Diagnosis"], ultrasound[DIAGNOSIS_HEADER], mr[DIAGNOSIS_HEADER])
|
||||||
|
if len(set(diagnoses)) != 1:
|
||||||
|
bad["诊断"] = dict(zip(("临床表", "超声表", "MR 表"), diagnoses, strict=True))
|
||||||
|
ages = (clinical["Age"], _report_age(ultrasound), _report_age(mr))
|
||||||
|
if len(set(ages)) != 1:
|
||||||
|
bad["年龄"] = {"临床表": clinical["Age"], "超声表": ultrasound["年龄"], "MR 表": mr["年龄"]}
|
||||||
|
sexes = {"超声表": ultrasound["性别"], "MR 表": mr["性别"]}
|
||||||
|
if code_maps is not None:
|
||||||
|
sexes["临床表（解码后）"] = code_maps["Sex"][cast(int, clinical["Sex"])]
|
||||||
|
if len(set(sexes.values())) != 1:
|
||||||
|
bad["性别"] = sexes
|
||||||
|
return bad
|
||||||
|
|
||||||
|
|
||||||
|
def _text_hits(
|
||||||
|
case_no: str, check: str, reports: dict[TableShape, str], find: Callable[[str], list[object]]
|
||||||
|
) -> SkipRecord | None:
|
||||||
|
"""C11–C13 共同的部分：两份报告文字各查一遍，命中的都记下。"""
|
||||||
|
text_columns = {ULTRASOUND: "超声描述", MR: "MR描述"}
|
||||||
|
hits = {table: found for table, text in reports.items() if (found := find(text))}
|
||||||
|
if not hits:
|
||||||
|
return None
|
||||||
|
return _skip(
|
||||||
|
case_no,
|
||||||
|
check,
|
||||||
|
tuple(table.path for table in hits),
|
||||||
|
tuple(text_columns[table] for table in hits),
|
||||||
|
{text_columns[table]: found for table, found in hits.items()},
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def _headings(text: str) -> list[object]:
|
||||||
|
return [{"关键词": k, "句子": s} for k, s in _text.conclusion_headings(text)]
|
||||||
|
|
||||||
|
|
||||||
|
def _subtypes(text: str) -> list[object]:
|
||||||
|
return list(_text.subtype_terms(text))
|
||||||
|
|
||||||
|
|
||||||
|
def _demographics(text: str) -> list[object]:
|
||||||
|
return list(_text.demographic_terms(text))
|
||||||
|
|
||||||
|
|
||||||
|
def _check_case(
|
||||||
|
case_no: str,
|
||||||
|
delivery_dir: Path,
|
||||||
|
index: dict[TableShape, dict[str, list[Row]]],
|
||||||
|
dirs: set[str],
|
||||||
|
code_maps: CodeMaps | None,
|
||||||
|
) -> CaseRecord | SkipRecord:
|
||||||
|
"""按 C02–C13 的顺序检查一例，遇到第一项不过就返回它的跳过记录。"""
|
||||||
|
for table in SUMMARY_TABLES:
|
||||||
|
found = index[table].get(case_no, [])
|
||||||
|
if len(found) > 1:
|
||||||
|
numbers = [row.number for row in found]
|
||||||
|
return _skip(case_no, "C02", (table.path,), (table.id_column,), {"行号": numbers})
|
||||||
|
|
||||||
|
missing = [table.path for table in SUMMARY_TABLES if case_no not in index[table]]
|
||||||
|
if case_no not in dirs:
|
||||||
|
missing.append(case_dir_path(case_no) + "/")
|
||||||
|
if missing:
|
||||||
|
return _skip(case_no, "C03", tuple(missing), (), {"缺在": missing})
|
||||||
|
|
||||||
|
clinical, ultrasound, mr = (index[table][case_no][0].cells for table in SUMMARY_TABLES)
|
||||||
|
folder = delivery_dir / case_dir_path(case_no)
|
||||||
|
u = video_id(case_no)
|
||||||
|
|
||||||
|
report_name = _check_case_dir(case_no, folder)
|
||||||
|
if isinstance(report_name, SkipRecord):
|
||||||
|
return report_name
|
||||||
|
|
||||||
|
if ultrasound["CEUS视频ID"] != u:
|
||||||
|
value = {"CEUS视频ID": ultrasound["CEUS视频ID"], "病例号": case_no}
|
||||||
|
return _skip(case_no, "C05", (ULTRASOUND.path,), ("CEUS视频ID",), value)
|
||||||
|
|
||||||
|
report_rel = f"{case_dir_path(case_no)}/{report_name}"
|
||||||
|
summary_row = index[ULTRASOUND][case_no][0]
|
||||||
|
report_path = delivery_dir / report_rel
|
||||||
|
if (skip := _check_case_report(case_no, report_path, summary_row, report_rel)) is not None:
|
||||||
|
return skip
|
||||||
|
|
||||||
|
if bad := _clinical_violations(clinical, code_maps):
|
||||||
|
return _skip(case_no, "C07", (CLINICAL.path,), tuple(bad), bad)
|
||||||
|
bad = _report_violations(ultrasound, "超声描述", code_maps)
|
||||||
|
bolus = ultrasound["推注开始时间s"]
|
||||||
|
if not (_is_int(bolus) and bolus >= 0):
|
||||||
|
bad["推注开始时间s"] = bolus
|
||||||
|
if bad:
|
||||||
|
return _skip(case_no, "C08", (ULTRASOUND.path,), tuple(bad), bad)
|
||||||
|
if bad := _report_violations(mr, "MR描述", code_maps):
|
||||||
|
return _skip(case_no, "C09", (MR.path,), tuple(bad), bad)
|
||||||
|
if mismatched := _cross_table(clinical, ultrasound, mr, code_maps):
|
||||||
|
files = tuple(table.path for table in SUMMARY_TABLES)
|
||||||
|
return _skip(case_no, "C10", files, tuple(mismatched), mismatched)
|
||||||
|
|
||||||
|
# C08、C09 已保证两份描述是非空字符串。
|
||||||
|
reports = {ULTRASOUND: cast(str, ultrasound["超声描述"]), MR: cast(str, mr["MR描述"])}
|
||||||
|
for check, find in (("C11", _headings), ("C12", _subtypes), ("C13", _demographics)):
|
||||||
|
if (skip := _text_hits(case_no, check, reports, find)) is not None:
|
||||||
|
return skip
|
||||||
|
|
||||||
|
# C07 已保证临床各列是整数、浮点数或空；C07–C10 已保证三个诊断是相等的整数。
|
||||||
|
return CaseRecord(
|
||||||
|
case_no=case_no,
|
||||||
|
video_id=u,
|
||||||
|
clinical={c: cast(int | float | None, clinical[c]) for c in CLINICAL_ROUTE_COLUMNS},
|
||||||
|
ultrasound_report=reports[ULTRASOUND],
|
||||||
|
mr_report=reports[MR],
|
||||||
|
key_image=folder / f"{u}_key.png",
|
||||||
|
diagnosis=DiagnosisCodes(
|
||||||
|
clinical=cast(int, clinical["Diagnosis"]),
|
||||||
|
ultrasound=cast(int, ultrasound[DIAGNOSIS_HEADER]),
|
||||||
|
mr=cast(int, mr[DIAGNOSIS_HEADER]),
|
||||||
|
),
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def read_delivery(delivery_dir: Path, code_maps: CodeMaps | None) -> DeliveryResult:
|
||||||
|
"""读交付包并逐例检查。
|
||||||
|
|
||||||
|
`code_maps` 为 None 表示不解码：编码列只查取值范围，不查是否在映射表里，
|
||||||
|
临床表的性别不和报告表比对。整张表的问题抛 `DeliveryError`。
|
||||||
|
"""
|
||||||
|
rows, case_dirs = read_tables(delivery_dir)
|
||||||
|
index, dirs, skipped = _index_rows(rows, case_dirs)
|
||||||
|
unrecognized = len(skipped)
|
||||||
|
all_cases = sorted(dirs.union(*(index[table].keys() for table in SUMMARY_TABLES)))
|
||||||
|
cases: list[CaseRecord] = []
|
||||||
|
for case_no in all_cases:
|
||||||
|
outcome = _check_case(case_no, delivery_dir, index, dirs, code_maps)
|
||||||
|
if isinstance(outcome, SkipRecord):
|
||||||
|
skipped.append(outcome)
|
||||||
|
else:
|
||||||
|
cases.append(outcome)
|
||||||
|
return DeliveryResult(
|
||||||
|
cases=tuple(cases),
|
||||||
|
skipped=tuple(skipped),
|
||||||
|
total_cases=len(all_cases),
|
||||||
|
unrecognized_rows=unrecognized,
|
||||||
|
uncompared=() if code_maps is not None else (UNCOMPARED_CLINICAL_SEX,),
|
||||||
|
)
|
||||||
@@ -0,0 +1,104 @@
|
|||||||
|
"""交付包的形状：目录、文件名、工作表名、表头、编码列名单。
|
||||||
|
|
||||||
|
全部按 40 例交付包（`data/交付包_20260908_40例/`）写死；交付方式变了就改这里，不做兼容。
|
||||||
|
"""
|
||||||
|
|
||||||
|
from dataclasses import dataclass
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class TableShape:
|
||||||
|
"""一张汇总表的形状。"""
|
||||||
|
|
||||||
|
path: str # 相对交付包根目录
|
||||||
|
sheet: str
|
||||||
|
header: tuple[str, ...]
|
||||||
|
id_column: str
|
||||||
|
|
||||||
|
|
||||||
|
DIAGNOSIS_HEADER = "病理类型（1 IPMN，2 SPN，3 MCN，4 SCN）"
|
||||||
|
|
||||||
|
SYMPTOM_COLUMNS = (
|
||||||
|
"Symptom_Pain",
|
||||||
|
"Symptom_Jaundice",
|
||||||
|
"Symptom_WeightLoss",
|
||||||
|
"Symptom_Fever",
|
||||||
|
"Symptom_Asymptomatic",
|
||||||
|
)
|
||||||
|
HISTORY_COLUMNS = (
|
||||||
|
"Hx_Pancreatitis",
|
||||||
|
"Hx_Alcohol",
|
||||||
|
"Hx_Gallstones",
|
||||||
|
"Hx_Malignancy",
|
||||||
|
"Hx_Family_PC",
|
||||||
|
)
|
||||||
|
# 化验原值列与档位列成对出现。
|
||||||
|
LAB_PAIRS = (
|
||||||
|
("CA199", "CA199_Level"),
|
||||||
|
("CEA", "CEA_Level"),
|
||||||
|
("Amylase", "Amylase_Level"),
|
||||||
|
("Lipase", "Lipase_Level"),
|
||||||
|
("TBil", "TBil_Level"),
|
||||||
|
)
|
||||||
|
|
||||||
|
CLINICAL = TableShape(
|
||||||
|
path="Clinical_agent/临床工作簿_40例.xlsx",
|
||||||
|
sheet="Sheet",
|
||||||
|
header=(
|
||||||
|
"Case_ID",
|
||||||
|
"Sex",
|
||||||
|
"Age",
|
||||||
|
"Diagnosis",
|
||||||
|
*SYMPTOM_COLUMNS,
|
||||||
|
*HISTORY_COLUMNS,
|
||||||
|
*(column for pair in LAB_PAIRS for column in pair),
|
||||||
|
),
|
||||||
|
id_column="Case_ID",
|
||||||
|
)
|
||||||
|
ULTRASOUND = TableShape(
|
||||||
|
path="CEUS_agent/超声报告文本_40例.xlsx",
|
||||||
|
sheet="超声报告",
|
||||||
|
header=(
|
||||||
|
"患者ID",
|
||||||
|
"CEUS视频ID",
|
||||||
|
"性别",
|
||||||
|
"年龄",
|
||||||
|
DIAGNOSIS_HEADER,
|
||||||
|
"推注开始时间s",
|
||||||
|
"超声描述",
|
||||||
|
),
|
||||||
|
id_column="患者ID",
|
||||||
|
)
|
||||||
|
MR = TableShape(
|
||||||
|
path="MR_agent/MR报告文本_40例.xlsx",
|
||||||
|
sheet="MR报告",
|
||||||
|
header=("患者ID", "性别", "年龄", DIAGNOSIS_HEADER, "MR描述"),
|
||||||
|
id_column="患者ID",
|
||||||
|
)
|
||||||
|
SUMMARY_TABLES = (CLINICAL, ULTRASOUND, MR)
|
||||||
|
|
||||||
|
# 病例目录里的单例报告表：工作表名固定，表头与超声汇总表相同。
|
||||||
|
CASE_REPORT_SHEET = "Sheet1"
|
||||||
|
|
||||||
|
# 临床一路拿到的列：临床表去掉编号和诊断。
|
||||||
|
CLINICAL_ROUTE_COLUMNS = tuple(c for c in CLINICAL.header if c not in ("Case_ID", "Diagnosis"))
|
||||||
|
|
||||||
|
# 用数字编码、需要映射表才知道含义的列。`Diagnosis` 同时管临床表的 `Diagnosis`
|
||||||
|
# 和两张报告表的诊断列，三列编码相同。
|
||||||
|
CODED_COLUMNS = (
|
||||||
|
"Sex",
|
||||||
|
"Diagnosis",
|
||||||
|
*SYMPTOM_COLUMNS,
|
||||||
|
*HISTORY_COLUMNS,
|
||||||
|
*(level for _, level in LAB_PAIRS),
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def case_dir_path(case_no: str) -> str:
|
||||||
|
"""病例目录相对交付包根目录的路径。"""
|
||||||
|
return f"CEUS_agent/{case_no}"
|
||||||
|
|
||||||
|
|
||||||
|
def video_id(case_no: str) -> str:
|
||||||
|
"""病例号对应的视频号（`U` 加三位病例号）。"""
|
||||||
|
return f"U{case_no}"
|
||||||
@@ -0,0 +1,84 @@
|
|||||||
|
"""读工作簿；整张表的检查 T1–T4，不过就整次构建停下。"""
|
||||||
|
|
||||||
|
import re
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
import openpyxl
|
||||||
|
|
||||||
|
from cadx.delivery._shape import CLINICAL, MR, SUMMARY_TABLES, ULTRASOUND, TableShape
|
||||||
|
|
||||||
|
# 单元格按 openpyxl 读出的原样保留，不做类型转换；类型检查在各条 C 检查里做。
|
||||||
|
type Cell = object
|
||||||
|
|
||||||
|
CASE_DIR_NAME = re.compile(r"[0-9]{3}")
|
||||||
|
|
||||||
|
|
||||||
|
class DeliveryError(Exception):
|
||||||
|
"""整张表读不了：交付方式变了，一例也读不出来。消息以检查编号开头。"""
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class Row:
|
||||||
|
"""汇总表的一行：Excel 行号与「列名 → 单元格」。"""
|
||||||
|
|
||||||
|
number: int
|
||||||
|
cells: dict[str, Cell]
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class Sheets:
|
||||||
|
"""一个工作簿：全部工作表名，以及第一张表逐行的单元格（第 1 行是表头）。"""
|
||||||
|
|
||||||
|
names: tuple[str, ...]
|
||||||
|
rows: tuple[tuple[Cell, ...], ...]
|
||||||
|
|
||||||
|
|
||||||
|
def open_workbook(path: Path) -> Sheets:
|
||||||
|
"""读出工作簿的工作表名和第一张工作表的全部行。"""
|
||||||
|
workbook = openpyxl.load_workbook(path, read_only=True, data_only=True)
|
||||||
|
names = tuple(workbook.sheetnames)
|
||||||
|
rows = tuple(tuple(row) for row in workbook.worksheets[0].iter_rows(values_only=True))
|
||||||
|
workbook.close()
|
||||||
|
return Sheets(names=names, rows=rows)
|
||||||
|
|
||||||
|
|
||||||
|
def _read_summary(delivery_dir: Path, table: TableShape) -> list[Row]:
|
||||||
|
sheets = open_workbook(delivery_dir / table.path)
|
||||||
|
if sheets.names != (table.sheet,):
|
||||||
|
raise DeliveryError(
|
||||||
|
f"T2 {table.path} 的工作表应恰好是 [{table.sheet}]，实际 {sheets.names}"
|
||||||
|
)
|
||||||
|
if not sheets.rows or sheets.rows[0] != table.header:
|
||||||
|
raise DeliveryError(f"T3 {table.path} 第 1 行表头与约定不一致")
|
||||||
|
return [
|
||||||
|
Row(number=number, cells=dict(zip(table.header, values, strict=True)))
|
||||||
|
for number, values in enumerate(sheets.rows[1:], start=2)
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
def _check_layout(delivery_dir: Path) -> list[str]:
|
||||||
|
"""T4：三个子目录里没有多余的东西。返回病例目录名（按名排序）。"""
|
||||||
|
for table in (CLINICAL, MR):
|
||||||
|
folder = (delivery_dir / table.path).parent
|
||||||
|
names = sorted(p.name for p in folder.iterdir())
|
||||||
|
if names != [Path(table.path).name]:
|
||||||
|
raise DeliveryError(f"T4 {folder.name}/ 下应只有 {Path(table.path).name}，实际 {names}")
|
||||||
|
ceus = (delivery_dir / ULTRASOUND.path).parent
|
||||||
|
case_dirs: list[str] = []
|
||||||
|
for entry in sorted(ceus.iterdir()):
|
||||||
|
if entry.name == Path(ULTRASOUND.path).name:
|
||||||
|
continue
|
||||||
|
if not (entry.is_dir() and CASE_DIR_NAME.fullmatch(entry.name)):
|
||||||
|
raise DeliveryError(f"T4 {ceus.name}/ 下有不认识的条目 {entry.name}")
|
||||||
|
case_dirs.append(entry.name)
|
||||||
|
return case_dirs
|
||||||
|
|
||||||
|
|
||||||
|
def read_tables(delivery_dir: Path) -> tuple[dict[TableShape, list[Row]], list[str]]:
|
||||||
|
"""依次做 T1–T4，交出三张汇总表的数据行和病例目录名。"""
|
||||||
|
for table in SUMMARY_TABLES:
|
||||||
|
if not (delivery_dir / table.path).is_file():
|
||||||
|
raise DeliveryError(f"T1 缺汇总表 {table.path}")
|
||||||
|
rows = {table: _read_summary(delivery_dir, table) for table in SUMMARY_TABLES}
|
||||||
|
return rows, _check_layout(delivery_dir)
|
||||||
@@ -0,0 +1,102 @@
|
|||||||
|
"""报告文字的规则：结论段标题、亚型名、人口学信息、复核用的措辞。
|
||||||
|
|
||||||
|
都先做 NFKC 归一（全角字母、数字、标点转半角），这样全角写法绕不过去。
|
||||||
|
"""
|
||||||
|
|
||||||
|
import re
|
||||||
|
import unicodedata
|
||||||
|
|
||||||
|
# 结论段标题的关键词。长的写在前面，正则按顺序尝试，命中「超声提示」时不会只报「提示」。
|
||||||
|
CONCLUSION_KEYWORDS = (
|
||||||
|
"超声提示",
|
||||||
|
"超声诊断",
|
||||||
|
"影像学诊断",
|
||||||
|
"检查结论",
|
||||||
|
"诊断意见",
|
||||||
|
"印象",
|
||||||
|
"结论",
|
||||||
|
"诊断",
|
||||||
|
"意见",
|
||||||
|
"提示",
|
||||||
|
)
|
||||||
|
# 段首 = 全文开头或换行之后；沿用旧代码，允许标题前有空格或制表符缩进。
|
||||||
|
# 换行认 str.splitlines 认的全部行边界（含 \x0b、\x0c、\x85、U+2028、U+2029），
|
||||||
|
# 冒号除 NFKC 后的「:」外也认比例号「∶」（U+2236，NFKC 不把它转成冒号）。
|
||||||
|
_LINE_BREAKS = "\r\n\x0b\x0c\x1c\x1d\x1e\x85\u2028\u2029"
|
||||||
|
_CONCLUSION_HEADING = re.compile(
|
||||||
|
rf"(?:^|(?<=[{_LINE_BREAKS}]))[ \t]*(" + "|".join(CONCLUSION_KEYWORDS) + r")\s*[:∶]"
|
||||||
|
)
|
||||||
|
|
||||||
|
# 归一并转大写后按子串查。「浆液性」「黏液性」单独出现是描述囊液的正常用语，不查。
|
||||||
|
# 词根覆盖了更长的写法（「SPT」覆盖「SPTP」，「导管内乳头」覆盖「导管内乳头状」），长的不再单列。
|
||||||
|
SUBTYPE_TERMS = (
|
||||||
|
"IPMN",
|
||||||
|
"IPMT",
|
||||||
|
"SPN",
|
||||||
|
"SPT",
|
||||||
|
"MCN",
|
||||||
|
"SCN",
|
||||||
|
"导管内乳头",
|
||||||
|
"实性假乳头",
|
||||||
|
"黏液性囊",
|
||||||
|
"粘液性囊",
|
||||||
|
"黏液囊性",
|
||||||
|
"粘液囊性",
|
||||||
|
"浆液性囊",
|
||||||
|
"浆液性微囊",
|
||||||
|
"囊腺瘤",
|
||||||
|
)
|
||||||
|
|
||||||
|
# 阿拉伯数字或中文数字，可带「周」，简繁「岁」都认。
|
||||||
|
_AGE = re.compile(r"[0-9一二三四五六七八九十百]+\s*周?[岁歲]")
|
||||||
|
SEX_CHARACTERS = ("男", "女")
|
||||||
|
|
||||||
|
# 不带冒号出现时不算检查不过，只列进复核清单。
|
||||||
|
REVIEW_WORDS = ("考虑", "可能", "倾向", "提示")
|
||||||
|
|
||||||
|
_SENTENCE = re.compile(r"[^。;]+")
|
||||||
|
|
||||||
|
|
||||||
|
def normalize(text: str) -> str:
|
||||||
|
"""NFKC 归一。"""
|
||||||
|
return unicodedata.normalize("NFKC", text)
|
||||||
|
|
||||||
|
|
||||||
|
def _sentence_at(normalized: str, position: int) -> str:
|
||||||
|
for match in _SENTENCE.finditer(normalized):
|
||||||
|
if match.start() <= position < match.end():
|
||||||
|
return match.group()
|
||||||
|
raise ValueError(f"位置 {position} 不在任何句子里（落在分隔符上）")
|
||||||
|
|
||||||
|
|
||||||
|
def conclusion_headings(text: str) -> list[tuple[str, str]]:
|
||||||
|
"""段首的结论段标题：每处命中给出（关键词，所在句子）。"""
|
||||||
|
normalized = normalize(text)
|
||||||
|
return [
|
||||||
|
(m.group(1), _sentence_at(normalized, m.start(1)))
|
||||||
|
for m in _CONCLUSION_HEADING.finditer(normalized)
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
def subtype_terms(text: str) -> list[str]:
|
||||||
|
"""报告文字里出现的亚型名。"""
|
||||||
|
upper = normalize(text).upper()
|
||||||
|
return [term for term in SUBTYPE_TERMS if term in upper]
|
||||||
|
|
||||||
|
|
||||||
|
def demographic_terms(text: str) -> list[str]:
|
||||||
|
"""报告文字里出现的「数字岁」和性别字。"""
|
||||||
|
normalized = normalize(text)
|
||||||
|
ages = [m.group() for m in _AGE.finditer(normalized)]
|
||||||
|
return ages + [ch for ch in SEX_CHARACTERS if ch in normalized]
|
||||||
|
|
||||||
|
|
||||||
|
def review_sentences(text: str) -> list[tuple[str, str]]:
|
||||||
|
"""含复核措辞的句子：每句一条（命中的词用「、」连接，句子）。按「。」「;」切句。"""
|
||||||
|
found: list[tuple[str, str]] = []
|
||||||
|
for match in _SENTENCE.finditer(normalize(text)):
|
||||||
|
sentence = match.group()
|
||||||
|
words = [w for w in REVIEW_WORDS if w in sentence]
|
||||||
|
if words:
|
||||||
|
found.append(("、".join(words), sentence))
|
||||||
|
return found
|
||||||
@@ -0,0 +1,30 @@
|
|||||||
|
"""library：给专家的资料库的目录布局、文件格式、写入和按路读取。
|
||||||
|
|
||||||
|
拒绝读取名字以 `.partial` 结尾的目录；读每个文件时核对清单里的 SHA-256。
|
||||||
|
"""
|
||||||
|
|
||||||
|
from cadx.library._read import (
|
||||||
|
ClinicalRoute,
|
||||||
|
MrRoute,
|
||||||
|
UltrasoundRoute,
|
||||||
|
list_aliases,
|
||||||
|
read_clinical,
|
||||||
|
read_mr,
|
||||||
|
read_ultrasound,
|
||||||
|
)
|
||||||
|
from cadx.library._scan import LeakHit, scan_for_leaks
|
||||||
|
from cadx.library._write import LibraryCase, write_library
|
||||||
|
|
||||||
|
__all__ = [
|
||||||
|
"ClinicalRoute",
|
||||||
|
"LeakHit",
|
||||||
|
"LibraryCase",
|
||||||
|
"MrRoute",
|
||||||
|
"UltrasoundRoute",
|
||||||
|
"list_aliases",
|
||||||
|
"read_clinical",
|
||||||
|
"read_mr",
|
||||||
|
"read_ultrasound",
|
||||||
|
"scan_for_leaks",
|
||||||
|
"write_library",
|
||||||
|
]
|
||||||
@@ -0,0 +1,83 @@
|
|||||||
|
"""按路读出资料库，读时核对清单里的 SHA-256。"""
|
||||||
|
|
||||||
|
import json
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from pathlib import Path
|
||||||
|
from typing import Any, cast
|
||||||
|
|
||||||
|
from cadx.library._write import (
|
||||||
|
CLINICAL_JSON,
|
||||||
|
KEY_IMAGE,
|
||||||
|
MANIFEST,
|
||||||
|
MR_REPORT,
|
||||||
|
ULTRASOUND_REPORT,
|
||||||
|
case_file,
|
||||||
|
sha256_file,
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class ClinicalRoute:
|
||||||
|
"""临床一路：性别、年龄、症状、既往史、化验。"""
|
||||||
|
|
||||||
|
codes_decoded: bool
|
||||||
|
fields: dict[str, str | int | float | None]
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class UltrasoundRoute:
|
||||||
|
"""超声一路：报告「所见」原文和医生截的关键图（给路径）。"""
|
||||||
|
|
||||||
|
report: str
|
||||||
|
key_image: Path
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class MrRoute:
|
||||||
|
"""MR 一路：报告「所见」原文。"""
|
||||||
|
|
||||||
|
report: str
|
||||||
|
|
||||||
|
|
||||||
|
def _manifest(build_dir: Path) -> dict[str, Any]:
|
||||||
|
if build_dir.name.endswith(".partial"):
|
||||||
|
raise ValueError(f"{build_dir} 是没写完的构建（.partial），不能读")
|
||||||
|
return cast(dict[str, Any], json.loads((build_dir / MANIFEST).read_text(encoding="utf-8")))
|
||||||
|
|
||||||
|
|
||||||
|
def _verified(build_dir: Path, alias: str, relative: str) -> Path:
|
||||||
|
manifest = _manifest(build_dir)
|
||||||
|
if alias not in manifest["aliases"]:
|
||||||
|
raise ValueError(f"构建 {build_dir.name} 里没有化名 {alias}")
|
||||||
|
key = case_file(alias, relative)
|
||||||
|
path = build_dir / key
|
||||||
|
if sha256_file(path) != manifest["files"][key]:
|
||||||
|
raise ValueError(f"{key} 的 SHA-256 与清单不一致，资料库被改动过")
|
||||||
|
return path
|
||||||
|
|
||||||
|
|
||||||
|
def _text(path: Path) -> str:
|
||||||
|
# 按字节解码，不做换行转换，读出的就是写进去的原文。
|
||||||
|
return path.read_bytes().decode("utf-8")
|
||||||
|
|
||||||
|
|
||||||
|
def list_aliases(build_dir: Path) -> tuple[str, ...]:
|
||||||
|
"""一次构建的全部化名（按化名排序）。"""
|
||||||
|
return tuple(_manifest(build_dir)["aliases"])
|
||||||
|
|
||||||
|
|
||||||
|
def read_clinical(build_dir: Path, alias: str) -> ClinicalRoute:
|
||||||
|
"""读一例的临床一路。"""
|
||||||
|
content = json.loads(_text(_verified(build_dir, alias, CLINICAL_JSON)))
|
||||||
|
return ClinicalRoute(codes_decoded=content["codes_decoded"], fields=content["fields"])
|
||||||
|
|
||||||
|
|
||||||
|
def read_ultrasound(build_dir: Path, alias: str) -> UltrasoundRoute:
|
||||||
|
"""读一例的超声一路。"""
|
||||||
|
report = _text(_verified(build_dir, alias, ULTRASOUND_REPORT))
|
||||||
|
return UltrasoundRoute(report=report, key_image=_verified(build_dir, alias, KEY_IMAGE))
|
||||||
|
|
||||||
|
|
||||||
|
def read_mr(build_dir: Path, alias: str) -> MrRoute:
|
||||||
|
"""读一例的 MR 一路。"""
|
||||||
|
return MrRoute(report=_text(_verified(build_dir, alias, MR_REPORT)))
|
||||||
@@ -0,0 +1,68 @@
|
|||||||
|
"""泄露扫描：在一次构建的文字文件里找不该出现的字符串和 JSON 键名。"""
|
||||||
|
|
||||||
|
import json
|
||||||
|
import unicodedata
|
||||||
|
from collections.abc import Sequence
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from pathlib import Path
|
||||||
|
from typing import cast
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class LeakHit:
|
||||||
|
"""一处命中。`kind` 是「字符串」或「键名」。"""
|
||||||
|
|
||||||
|
file: str # 相对构建目录
|
||||||
|
kind: str
|
||||||
|
term: str
|
||||||
|
|
||||||
|
|
||||||
|
def _fold(text: str) -> str:
|
||||||
|
"""NFKC 再 casefold：全角、大小写写法都按同一个词比。"""
|
||||||
|
return unicodedata.normalize("NFKC", text).casefold()
|
||||||
|
|
||||||
|
|
||||||
|
def _json_keys_and_strings(node: object, keys: list[str], strings: list[str]) -> None:
|
||||||
|
# json.loads 出来的对象：dict 的键都是字符串。
|
||||||
|
if isinstance(node, dict):
|
||||||
|
for key, value in cast(dict[str, object], node).items():
|
||||||
|
keys.append(key)
|
||||||
|
_json_keys_and_strings(value, keys, strings)
|
||||||
|
elif isinstance(node, list):
|
||||||
|
for item in cast(list[object], node):
|
||||||
|
_json_keys_and_strings(item, keys, strings)
|
||||||
|
elif isinstance(node, str):
|
||||||
|
strings.append(node)
|
||||||
|
|
||||||
|
|
||||||
|
def scan_for_leaks(
|
||||||
|
build_dir: Path, forbidden_strings: Sequence[str], forbidden_keys: Sequence[str]
|
||||||
|
) -> list[LeakHit]:
|
||||||
|
"""扫构建目录下全部 `.txt`、`.json`（含清单），不扫 PNG。
|
||||||
|
|
||||||
|
字符串做 NFKC 并 casefold 后按子串比较；JSON 文件除原文外还扫解析后的键和字符串值，
|
||||||
|
这样以 `\\uXXXX` 转义写出的中文也查得到。键名按整个键名、不分大小写比较。
|
||||||
|
"""
|
||||||
|
hits: list[LeakHit] = []
|
||||||
|
banned_keys = {key.casefold() for key in forbidden_keys}
|
||||||
|
paths = sorted(p for p in build_dir.rglob("*") if p.suffix in (".txt", ".json"))
|
||||||
|
for path in paths:
|
||||||
|
relative = path.relative_to(build_dir).as_posix()
|
||||||
|
text = path.read_bytes().decode("utf-8")
|
||||||
|
haystacks = [text]
|
||||||
|
if path.suffix == ".json":
|
||||||
|
keys: list[str] = []
|
||||||
|
_json_keys_and_strings(json.loads(text), keys, haystacks)
|
||||||
|
hits.extend(
|
||||||
|
LeakHit(relative, "键名", key)
|
||||||
|
for key in sorted(set(keys))
|
||||||
|
if key.casefold() in banned_keys
|
||||||
|
)
|
||||||
|
haystacks.extend(keys)
|
||||||
|
folded = [_fold(h) for h in haystacks]
|
||||||
|
hits.extend(
|
||||||
|
LeakHit(relative, "字符串", term)
|
||||||
|
for term in forbidden_strings
|
||||||
|
if any(_fold(term) in h for h in folded)
|
||||||
|
)
|
||||||
|
return hits
|
||||||
@@ -0,0 +1,119 @@
|
|||||||
|
"""资料库的目录布局与写入。
|
||||||
|
|
||||||
|
```
|
||||||
|
<构建目录>/
|
||||||
|
manifest.json
|
||||||
|
cases/<化名>/clinical/clinical.json
|
||||||
|
cases/<化名>/ultrasound/report.txt
|
||||||
|
cases/<化名>/ultrasound/key.png
|
||||||
|
cases/<化名>/mr/report.txt
|
||||||
|
```
|
||||||
|
"""
|
||||||
|
|
||||||
|
import hashlib
|
||||||
|
import json
|
||||||
|
from collections.abc import Mapping, Sequence
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
from PIL import Image
|
||||||
|
|
||||||
|
MANIFEST = "manifest.json"
|
||||||
|
CLINICAL_JSON = "clinical/clinical.json"
|
||||||
|
ULTRASOUND_REPORT = "ultrasound/report.txt"
|
||||||
|
KEY_IMAGE = "ultrasound/key.png"
|
||||||
|
MR_REPORT = "mr/report.txt"
|
||||||
|
|
||||||
|
_PNG_SIGNATURE = b"\x89PNG\r\n\x1a\n"
|
||||||
|
# 能逐像素保真重编码的 (位深, PNG 颜色类型)：8 位的灰度、RGB、灰度加透明、RGBA，以及 1 位灰度。
|
||||||
|
# 16 位图 Pillow 读 RGB 时会悄悄降成 8 位；调色板图按像素重编码会丢调色板。40 例都是 8 位 RGB。
|
||||||
|
_FAITHFUL = frozenset({(8, 0), (8, 2), (8, 4), (8, 6), (1, 0)})
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class LibraryCase:
|
||||||
|
"""要写进资料库的一例：三路各自的内容。"""
|
||||||
|
|
||||||
|
alias: str
|
||||||
|
clinical_fields: Mapping[str, str | int | float | None]
|
||||||
|
ultrasound_report: str
|
||||||
|
key_image_source: Path
|
||||||
|
mr_report: str
|
||||||
|
|
||||||
|
|
||||||
|
def case_file(alias: str, relative: str) -> str:
|
||||||
|
"""病例文件相对构建目录的路径。"""
|
||||||
|
return f"cases/{alias}/{relative}"
|
||||||
|
|
||||||
|
|
||||||
|
def sha256_file(path: Path) -> str:
|
||||||
|
"""文件内容的 SHA-256。"""
|
||||||
|
return hashlib.sha256(path.read_bytes()).hexdigest()
|
||||||
|
|
||||||
|
|
||||||
|
def _write_json(path: Path, content: object) -> None:
|
||||||
|
# ensure_ascii=False：中文原样写出，泄露扫描按子串才查得到。
|
||||||
|
path.write_text(json.dumps(content, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
|
||||||
|
|
||||||
|
|
||||||
|
def _write_clean_png(source: Path, target: Path) -> None:
|
||||||
|
"""只保留像素和颜色模式重新编码：文本块、EXIF、ICC 等附加数据都不带过去。
|
||||||
|
|
||||||
|
不能逐像素保真的图（非 PNG、位深或颜色类型不在 `_FAITHFUL` 里、带 tRNS 透明色）报错停下，
|
||||||
|
不悄悄降位或丢透明。
|
||||||
|
"""
|
||||||
|
header = source.read_bytes()[:26]
|
||||||
|
if header[:8] != _PNG_SIGNATURE or header[12:16] != b"IHDR":
|
||||||
|
raise ValueError(f"关键图不是 PNG：{source}")
|
||||||
|
bit_depth, color_type = header[24], header[25]
|
||||||
|
if (bit_depth, color_type) not in _FAITHFUL:
|
||||||
|
raise ValueError(
|
||||||
|
f"关键图位深 {bit_depth}、颜色类型 {color_type} 不能逐像素保真重编码：{source}"
|
||||||
|
)
|
||||||
|
with Image.open(source) as image:
|
||||||
|
if "transparency" in image.info:
|
||||||
|
raise ValueError(f"关键图带 tRNS 透明色，重编码会丢透明：{source}")
|
||||||
|
clean = Image.frombytes(image.mode, image.size, image.tobytes())
|
||||||
|
clean.save(target, format="PNG")
|
||||||
|
|
||||||
|
|
||||||
|
def write_library(
|
||||||
|
build_dir: Path,
|
||||||
|
build_id: str,
|
||||||
|
git_commit: str,
|
||||||
|
git_clean: bool,
|
||||||
|
config_sha256: Mapping[str, str],
|
||||||
|
codes_decoded: bool,
|
||||||
|
uncompared: Sequence[str],
|
||||||
|
ceus_source: str | None,
|
||||||
|
cases: Sequence[LibraryCase],
|
||||||
|
) -> None:
|
||||||
|
"""把一次构建写进已经存在的空目录 `build_dir`，最后写清单。"""
|
||||||
|
files: dict[str, str] = {}
|
||||||
|
for case in cases:
|
||||||
|
case_dir = build_dir / "cases" / case.alias
|
||||||
|
for relative in (CLINICAL_JSON, ULTRASOUND_REPORT, MR_REPORT):
|
||||||
|
(case_dir / relative).parent.mkdir(parents=True, exist_ok=True)
|
||||||
|
_write_json(
|
||||||
|
case_dir / CLINICAL_JSON,
|
||||||
|
{"codes_decoded": codes_decoded, "fields": dict(case.clinical_fields)},
|
||||||
|
)
|
||||||
|
(case_dir / ULTRASOUND_REPORT).write_text(case.ultrasound_report, encoding="utf-8")
|
||||||
|
_write_clean_png(case.key_image_source, case_dir / KEY_IMAGE)
|
||||||
|
(case_dir / MR_REPORT).write_text(case.mr_report, encoding="utf-8")
|
||||||
|
for relative in (CLINICAL_JSON, ULTRASOUND_REPORT, KEY_IMAGE, MR_REPORT):
|
||||||
|
files[case_file(case.alias, relative)] = sha256_file(case_dir / relative)
|
||||||
|
_write_json(
|
||||||
|
build_dir / MANIFEST,
|
||||||
|
{
|
||||||
|
"build_id": build_id,
|
||||||
|
"git_commit": git_commit,
|
||||||
|
"git_clean": git_clean,
|
||||||
|
"config_sha256": dict(config_sha256),
|
||||||
|
"codes_decoded": codes_decoded,
|
||||||
|
"uncompared": list(uncompared),
|
||||||
|
"ceus_source": ceus_source,
|
||||||
|
"aliases": sorted(case.alias for case in cases),
|
||||||
|
"files": dict(sorted(files.items())),
|
||||||
|
},
|
||||||
|
)
|
||||||
@@ -0,0 +1,5 @@
|
|||||||
|
"""runs：构建号怎么取、运行快照记什么。会诊运行目录等会诊那一步再加。"""
|
||||||
|
|
||||||
|
from cadx.runs._snapshot import GitState, make_build_id, read_git_state, write_snapshot
|
||||||
|
|
||||||
|
__all__ = ["GitState", "make_build_id", "read_git_state", "write_snapshot"]
|
||||||
@@ -0,0 +1,81 @@
|
|||||||
|
"""构建号与运行快照：一次构建用的是哪份代码、哪份配置、哪个环境。"""
|
||||||
|
|
||||||
|
import hashlib
|
||||||
|
import json
|
||||||
|
import shutil
|
||||||
|
import subprocess
|
||||||
|
import sys
|
||||||
|
from collections.abc import Mapping
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass(frozen=True)
|
||||||
|
class GitState:
|
||||||
|
"""仓库当前的提交和工作区状态。"""
|
||||||
|
|
||||||
|
commit: str
|
||||||
|
short_commit: str
|
||||||
|
clean: bool # `git status --porcelain` 为空（含未跟踪文件）
|
||||||
|
diff_sha256: str # `git diff HEAD` 输出的 SHA-256
|
||||||
|
|
||||||
|
|
||||||
|
def _git(repo_root: Path, *args: str) -> bytes:
|
||||||
|
git = shutil.which("git")
|
||||||
|
if git is None:
|
||||||
|
raise RuntimeError("找不到 git，无法记录构建用的代码版本")
|
||||||
|
return subprocess.run( # noqa: S603 参数是写死的 git 子命令，不含外部输入
|
||||||
|
[git, *args], cwd=repo_root, check=True, capture_output=True
|
||||||
|
).stdout
|
||||||
|
|
||||||
|
|
||||||
|
def read_git_state(repo_root: Path) -> GitState:
|
||||||
|
"""读出 `repo_root` 所在仓库的提交号、是否干净、未提交改动的哈希。"""
|
||||||
|
return GitState(
|
||||||
|
commit=_git(repo_root, "rev-parse", "HEAD").decode().strip(),
|
||||||
|
short_commit=_git(repo_root, "rev-parse", "--short", "HEAD").decode().strip(),
|
||||||
|
clean=_git(repo_root, "status", "--porcelain").strip() == b"",
|
||||||
|
diff_sha256=hashlib.sha256(_git(repo_root, "diff", "HEAD")).hexdigest(),
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def make_build_id(now: datetime, git: GitState) -> str:
|
||||||
|
"""`YYYYMMDD-HHMMSS-<git 短哈希>`，工作区不干净时末尾加 `-dirty`。`now` 用本地时间。"""
|
||||||
|
build_id = f"{now:%Y%m%d-%H%M%S}-{git.short_commit}"
|
||||||
|
return build_id if git.clean else f"{build_id}-dirty"
|
||||||
|
|
||||||
|
|
||||||
|
def _sha256(path: Path) -> str:
|
||||||
|
return hashlib.sha256(path.read_bytes()).hexdigest()
|
||||||
|
|
||||||
|
|
||||||
|
def write_snapshot(
|
||||||
|
snapshot_dir: Path,
|
||||||
|
build_id: str,
|
||||||
|
git: GitState,
|
||||||
|
started_at: datetime,
|
||||||
|
finished_at: datetime,
|
||||||
|
uv_lock: Path,
|
||||||
|
configs: Mapping[str, Path],
|
||||||
|
) -> None:
|
||||||
|
"""建 `snapshot_dir`，写 snapshot.json，并把 `configs`（快照里的文件名 → 原文件）原样复制进去。"""
|
||||||
|
snapshot_dir.mkdir(exist_ok=False)
|
||||||
|
copied: dict[str, str] = {}
|
||||||
|
for name, source in configs.items():
|
||||||
|
shutil.copyfile(source, snapshot_dir / name)
|
||||||
|
copied[name] = _sha256(snapshot_dir / name)
|
||||||
|
snapshot = {
|
||||||
|
"build_id": build_id,
|
||||||
|
"git_commit": git.commit,
|
||||||
|
"git_clean": git.clean,
|
||||||
|
"git_diff_head_sha256": git.diff_sha256,
|
||||||
|
"python_version": sys.version,
|
||||||
|
"uv_lock_sha256": _sha256(uv_lock),
|
||||||
|
"started_at": started_at.isoformat(),
|
||||||
|
"finished_at": finished_at.isoformat(),
|
||||||
|
"config_sha256": copied,
|
||||||
|
}
|
||||||
|
(snapshot_dir / "snapshot.json").write_text(
|
||||||
|
json.dumps(snapshot, ensure_ascii=False, indent=2) + "\n", encoding="utf-8"
|
||||||
|
)
|
||||||
@@ -0,0 +1,267 @@
|
|||||||
|
"""测试用假交付包：形状照 40 例交付包写（表头、工作表名、目录结构），内容全部编造。
|
||||||
|
|
||||||
|
这里的表头和文件名是按任务书 01 第二部分的表格独立写的，不取自 delivery 的常量，
|
||||||
|
这样 delivery 的常量写错时测试能发现。各条测试在 `FakeDelivery` 上改出要测的情况，再 `write`。
|
||||||
|
"""
|
||||||
|
|
||||||
|
from collections.abc import Sequence
|
||||||
|
from dataclasses import dataclass, field
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
from typing import Any, cast
|
||||||
|
|
||||||
|
import openpyxl
|
||||||
|
import yaml
|
||||||
|
from PIL import Image, PngImagePlugin
|
||||||
|
|
||||||
|
from cadx.build import BuildSummary, run_build
|
||||||
|
|
||||||
|
REPO_ROOT = Path(__file__).resolve().parents[1]
|
||||||
|
|
||||||
|
DIAGNOSIS_COLUMN = "病理类型（1 IPMN，2 SPN，3 MCN，4 SCN）"
|
||||||
|
CLINICAL_HEADER = [
|
||||||
|
"Case_ID",
|
||||||
|
"Sex",
|
||||||
|
"Age",
|
||||||
|
"Diagnosis",
|
||||||
|
"Symptom_Pain",
|
||||||
|
"Symptom_Jaundice",
|
||||||
|
"Symptom_WeightLoss",
|
||||||
|
"Symptom_Fever",
|
||||||
|
"Symptom_Asymptomatic",
|
||||||
|
"Hx_Pancreatitis",
|
||||||
|
"Hx_Alcohol",
|
||||||
|
"Hx_Gallstones",
|
||||||
|
"Hx_Malignancy",
|
||||||
|
"Hx_Family_PC",
|
||||||
|
"CA199",
|
||||||
|
"CA199_Level",
|
||||||
|
"CEA",
|
||||||
|
"CEA_Level",
|
||||||
|
"Amylase",
|
||||||
|
"Amylase_Level",
|
||||||
|
"Lipase",
|
||||||
|
"Lipase_Level",
|
||||||
|
"TBil",
|
||||||
|
"TBil_Level",
|
||||||
|
]
|
||||||
|
ULTRASOUND_HEADER = [
|
||||||
|
"患者ID",
|
||||||
|
"CEUS视频ID",
|
||||||
|
"性别",
|
||||||
|
"年龄",
|
||||||
|
DIAGNOSIS_COLUMN,
|
||||||
|
"推注开始时间s",
|
||||||
|
"超声描述",
|
||||||
|
]
|
||||||
|
MR_HEADER = ["患者ID", "性别", "年龄", DIAGNOSIS_COLUMN, "MR描述"]
|
||||||
|
|
||||||
|
CLINICAL_PATH = "Clinical_agent/临床工作簿_40例.xlsx"
|
||||||
|
ULTRASOUND_PATH = "CEUS_agent/超声报告文本_40例.xlsx"
|
||||||
|
MR_PATH = "MR_agent/MR报告文本_40例.xlsx"
|
||||||
|
|
||||||
|
# 编造的报告文字：不含亚型名、结论段标题、性别字、「数字岁」和复核措辞。
|
||||||
|
ULTRASOUND_TEXT = "胰体部见一无回声区，边界清晰，壁薄。造影后囊壁呈等增强，内部未见增强。"
|
||||||
|
MR_TEXT = "胰体部见一类圆形长T2信号灶，边界清楚，内见细分隔；增强后分隔轻度强化。"
|
||||||
|
|
||||||
|
# 测试用的样例映射表：含义是编的，只用来验证解码路径。
|
||||||
|
SAMPLE_CODE_MAPS: dict[str, dict[int, str]] = {
|
||||||
|
"Sex": {1: "男", 2: "女"},
|
||||||
|
"Diagnosis": {1: "IPMN", 2: "SPN", 3: "MCN", 4: "SCN"},
|
||||||
|
**{
|
||||||
|
column: {0: "否", 1: "是"}
|
||||||
|
for column in (
|
||||||
|
"Symptom_Pain",
|
||||||
|
"Symptom_Jaundice",
|
||||||
|
"Symptom_WeightLoss",
|
||||||
|
"Symptom_Fever",
|
||||||
|
"Symptom_Asymptomatic",
|
||||||
|
"Hx_Pancreatitis",
|
||||||
|
"Hx_Alcohol",
|
||||||
|
"Hx_Gallstones",
|
||||||
|
"Hx_Malignancy",
|
||||||
|
"Hx_Family_PC",
|
||||||
|
)
|
||||||
|
},
|
||||||
|
**{
|
||||||
|
column: {0: "正常", 1: "异常"}
|
||||||
|
for column in ("CA199_Level", "CEA_Level", "Amylase_Level", "Lipase_Level", "TBil_Level")
|
||||||
|
},
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass
|
||||||
|
class FakeCase:
|
||||||
|
"""一例：三张表各一行，病例目录里的文件名和单例报告表的行。"""
|
||||||
|
|
||||||
|
number: int
|
||||||
|
clinical: dict[str, object]
|
||||||
|
ultrasound: dict[str, object]
|
||||||
|
mr: dict[str, object]
|
||||||
|
dir_files: list[str]
|
||||||
|
# None 表示单例报告表照抄超声汇总表那一行。
|
||||||
|
case_report_rows: list[list[object]] | None = None
|
||||||
|
case_report_sheet: str = "Sheet1"
|
||||||
|
|
||||||
|
@property
|
||||||
|
def no(self) -> str:
|
||||||
|
return f"{self.number:03d}"
|
||||||
|
|
||||||
|
|
||||||
|
def make_case(number: int) -> FakeCase:
|
||||||
|
"""一例全部检查都能通过的病例。诊断按病例号轮转 1–4。"""
|
||||||
|
no = f"{number:03d}"
|
||||||
|
sex = 1 + number % 2
|
||||||
|
age = 30 + number
|
||||||
|
diagnosis = 1 + (number - 1) % 4
|
||||||
|
clinical: dict[str, object] = dict.fromkeys(CLINICAL_HEADER, 0)
|
||||||
|
clinical.update(
|
||||||
|
{
|
||||||
|
"Case_ID": f"P{no}",
|
||||||
|
"Sex": sex,
|
||||||
|
"Age": age,
|
||||||
|
"Diagnosis": diagnosis,
|
||||||
|
"Symptom_Pain": 1,
|
||||||
|
"CA199": 12.5,
|
||||||
|
"CA199_Level": 0,
|
||||||
|
"CEA": 3,
|
||||||
|
"CEA_Level": 1,
|
||||||
|
"Amylase": None,
|
||||||
|
"Amylase_Level": None,
|
||||||
|
"Lipase": None,
|
||||||
|
"Lipase_Level": None,
|
||||||
|
"TBil": 10.2,
|
||||||
|
"TBil_Level": 0,
|
||||||
|
}
|
||||||
|
)
|
||||||
|
sex_text = {1: "男", 2: "女"}[sex]
|
||||||
|
ultrasound: dict[str, object] = {
|
||||||
|
"患者ID": str(number),
|
||||||
|
"CEUS视频ID": f"U{no}",
|
||||||
|
"性别": sex_text,
|
||||||
|
"年龄": f"{age}岁",
|
||||||
|
DIAGNOSIS_COLUMN: diagnosis,
|
||||||
|
"推注开始时间s": 5,
|
||||||
|
"超声描述": ULTRASOUND_TEXT,
|
||||||
|
}
|
||||||
|
mr: dict[str, object] = {
|
||||||
|
"患者ID": str(number),
|
||||||
|
"性别": sex_text,
|
||||||
|
"年龄": f"{age}岁",
|
||||||
|
DIAGNOSIS_COLUMN: diagnosis,
|
||||||
|
"MR描述": MR_TEXT,
|
||||||
|
}
|
||||||
|
files = [f"U{no}_key.png", f"U{no}_roi2.mp4", f"U{no}_roi2_report.xlsx"]
|
||||||
|
return FakeCase(number, clinical, ultrasound, mr, files)
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass
|
||||||
|
class FakeDelivery:
|
||||||
|
"""一个假交付包。`extra_rows` 是附加在汇总表末尾的整行（测试编号认不出的行）。"""
|
||||||
|
|
||||||
|
cases: list[FakeCase]
|
||||||
|
sheet_names: dict[str, str] = field(
|
||||||
|
default_factory=lambda: {
|
||||||
|
CLINICAL_PATH: "Sheet",
|
||||||
|
ULTRASOUND_PATH: "超声报告",
|
||||||
|
MR_PATH: "MR报告",
|
||||||
|
}
|
||||||
|
)
|
||||||
|
headers: dict[str, list[str]] = field(
|
||||||
|
default_factory=lambda: {
|
||||||
|
CLINICAL_PATH: list(CLINICAL_HEADER),
|
||||||
|
ULTRASOUND_PATH: list(ULTRASOUND_HEADER),
|
||||||
|
MR_PATH: list(MR_HEADER),
|
||||||
|
}
|
||||||
|
)
|
||||||
|
extra_rows: dict[str, list[list[object]]] = field(
|
||||||
|
default_factory=lambda: {CLINICAL_PATH: [], ULTRASOUND_PATH: [], MR_PATH: []}
|
||||||
|
)
|
||||||
|
|
||||||
|
def case(self, number: int) -> FakeCase:
|
||||||
|
return next(c for c in self.cases if c.number == number)
|
||||||
|
|
||||||
|
def write(self, root: Path) -> Path:
|
||||||
|
tables = {
|
||||||
|
CLINICAL_PATH: [c.clinical for c in self.cases],
|
||||||
|
ULTRASOUND_PATH: [c.ultrasound for c in self.cases],
|
||||||
|
MR_PATH: [c.mr for c in self.cases],
|
||||||
|
}
|
||||||
|
for path, rows in tables.items():
|
||||||
|
header = self.headers[path]
|
||||||
|
values = [[row.get(h) for h in header] for row in rows]
|
||||||
|
_write_workbook(
|
||||||
|
root / path, self.sheet_names[path], [header, *values, *self.extra_rows[path]]
|
||||||
|
)
|
||||||
|
for case in self.cases:
|
||||||
|
folder = root / "CEUS_agent" / case.no
|
||||||
|
folder.mkdir(parents=True, exist_ok=True)
|
||||||
|
for name in case.dir_files:
|
||||||
|
if name.endswith(".png"):
|
||||||
|
_write_png(folder / name, case.number)
|
||||||
|
elif name.endswith(".xlsx"):
|
||||||
|
row = [case.ultrasound.get(h) for h in ULTRASOUND_HEADER]
|
||||||
|
rows = case.case_report_rows or [list(ULTRASOUND_HEADER), row]
|
||||||
|
_write_workbook(folder / name, case.case_report_sheet, rows)
|
||||||
|
else:
|
||||||
|
(folder / name).write_bytes(b"not a real video")
|
||||||
|
(root / "交付说明_40例_20260908.md").write_text("说明不读", encoding="utf-8")
|
||||||
|
return root
|
||||||
|
|
||||||
|
|
||||||
|
def make_delivery(count: int) -> FakeDelivery:
|
||||||
|
"""病例号 1..count、全部能通过检查的假交付包。"""
|
||||||
|
return FakeDelivery(cases=[make_case(n) for n in range(1, count + 1)])
|
||||||
|
|
||||||
|
|
||||||
|
def _write_workbook(path: Path, sheet: str, rows: Sequence[Sequence[object]]) -> None:
|
||||||
|
path.parent.mkdir(parents=True, exist_ok=True)
|
||||||
|
workbook = openpyxl.Workbook()
|
||||||
|
worksheet = workbook.active
|
||||||
|
assert worksheet is not None
|
||||||
|
worksheet.title = sheet
|
||||||
|
for row in rows:
|
||||||
|
# 假数据里的值都是 openpyxl 认得的单元格类型（字符串、数字、None）。
|
||||||
|
worksheet.append(cast("list[Any]", list(row)))
|
||||||
|
workbook.save(path)
|
||||||
|
|
||||||
|
|
||||||
|
def _write_png(path: Path, number: int) -> None:
|
||||||
|
pixels = bytes(v for i in range(24) for v in (number * 10 % 256, i * 10, 255 - i * 10))
|
||||||
|
image = Image.frombytes("RGB", (6, 4), pixels)
|
||||||
|
info = PngImagePlugin.PngInfo()
|
||||||
|
info.add_text("PatientName", "should-not-survive")
|
||||||
|
image.save(path, format="PNG", pnginfo=info)
|
||||||
|
|
||||||
|
|
||||||
|
def write_config(
|
||||||
|
tmp_path: Path, delivery_dir: Path, seed: int, code_maps: dict[str, dict[int, str]] | None
|
||||||
|
) -> Path:
|
||||||
|
"""在 tmp_path 写一份 build.yaml（路径都写绝对路径）；给了映射表就同时写 code_maps.yaml。"""
|
||||||
|
maps_path = None
|
||||||
|
if code_maps is not None:
|
||||||
|
maps_path = tmp_path / "code_maps.yaml"
|
||||||
|
maps_path.write_text(yaml.safe_dump(code_maps, allow_unicode=True), encoding="utf-8")
|
||||||
|
config = {
|
||||||
|
"delivery_dir": str(delivery_dir),
|
||||||
|
"library_root": str(tmp_path / "library"),
|
||||||
|
"answers_root": str(tmp_path / "answers"),
|
||||||
|
"alias_seed": seed,
|
||||||
|
"decode_codes": code_maps is not None,
|
||||||
|
"code_maps": None if maps_path is None else str(maps_path),
|
||||||
|
}
|
||||||
|
path = tmp_path / "build.yaml"
|
||||||
|
path.write_text(yaml.safe_dump(config, allow_unicode=True), encoding="utf-8")
|
||||||
|
return path
|
||||||
|
|
||||||
|
|
||||||
|
def build(
|
||||||
|
tmp_path: Path,
|
||||||
|
delivery: FakeDelivery,
|
||||||
|
seed: int,
|
||||||
|
code_maps: dict[str, dict[int, str]] | None,
|
||||||
|
now: datetime,
|
||||||
|
) -> BuildSummary:
|
||||||
|
"""写出假交付包和配置，跑一次构建。"""
|
||||||
|
delivery_dir = delivery.write(tmp_path / "delivery")
|
||||||
|
return run_build(write_config(tmp_path, delivery_dir, seed, code_maps), REPO_ROOT, now)
|
||||||
@@ -0,0 +1,352 @@
|
|||||||
|
"""构建产物：可见性、泄露扫描、化名、解码开关、关键图、清单与读取、不覆盖、答案库内容。"""
|
||||||
|
|
||||||
|
import csv
|
||||||
|
import json
|
||||||
|
import re
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
import pytest
|
||||||
|
from PIL import Image
|
||||||
|
|
||||||
|
from cadx.answers import read_aliases, read_diagnoses
|
||||||
|
from cadx.build import make_aliases, run_build
|
||||||
|
from cadx.library import (
|
||||||
|
list_aliases,
|
||||||
|
read_clinical,
|
||||||
|
read_mr,
|
||||||
|
read_ultrasound,
|
||||||
|
scan_for_leaks,
|
||||||
|
)
|
||||||
|
from fake_delivery import (
|
||||||
|
CLINICAL_HEADER,
|
||||||
|
MR_TEXT,
|
||||||
|
REPO_ROOT,
|
||||||
|
SAMPLE_CODE_MAPS,
|
||||||
|
ULTRASOUND_TEXT,
|
||||||
|
build,
|
||||||
|
make_delivery,
|
||||||
|
write_config,
|
||||||
|
)
|
||||||
|
|
||||||
|
NOW = datetime(2026, 10, 16, 9, 30, 0).astimezone()
|
||||||
|
|
||||||
|
# 独立写的泄露词表，不取自 delivery 的常量。
|
||||||
|
SUBTYPES = (
|
||||||
|
"IPMN",
|
||||||
|
"SPN",
|
||||||
|
"MCN",
|
||||||
|
"SCN",
|
||||||
|
"导管内乳头状黏液性肿瘤",
|
||||||
|
"实性假乳头状瘤",
|
||||||
|
"黏液性囊性肿瘤",
|
||||||
|
"浆液性囊性肿瘤",
|
||||||
|
"浆液性囊腺瘤",
|
||||||
|
)
|
||||||
|
DIAGNOSIS_COLUMNS = ("病理类型（1 IPMN，2 SPN，3 MCN，4 SCN）", "病理类型", "Diagnosis", "Case_ID")
|
||||||
|
DELIVERY_FILE_NAMES = ("临床工作簿_40例.xlsx", "超声报告文本_40例.xlsx", "MR报告文本_40例.xlsx")
|
||||||
|
FORBIDDEN_KEYS = ("diagnosis", "label", "gold", "pathology", "name", "row")
|
||||||
|
|
||||||
|
|
||||||
|
def _forbidden_strings(case_nos: list[str]) -> list[str]:
|
||||||
|
per_case = [
|
||||||
|
term
|
||||||
|
for no in case_nos
|
||||||
|
for term in (
|
||||||
|
f"P{no}",
|
||||||
|
f"U{no}",
|
||||||
|
f"U{no}_key.png",
|
||||||
|
f"U{no}_roi2.mp4",
|
||||||
|
f"U{no}_roi2_report.xlsx",
|
||||||
|
)
|
||||||
|
]
|
||||||
|
return [*per_case, *DELIVERY_FILE_NAMES, *SUBTYPES, *DIAGNOSIS_COLUMNS]
|
||||||
|
|
||||||
|
|
||||||
|
def _case_dirs(library_dir: Path) -> list[Path]:
|
||||||
|
return sorted((library_dir / "cases").iterdir())
|
||||||
|
|
||||||
|
|
||||||
|
def test_visibility_sex_and_age_only_in_clinical_route(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
summary = build(tmp_path, delivery, 1, SAMPLE_CODE_MAPS, NOW)
|
||||||
|
clinical_names = [*CLINICAL_HEADER, "男", "女", "岁"]
|
||||||
|
for case_dir in _case_dirs(summary.library_dir):
|
||||||
|
files = sorted(p.relative_to(case_dir).as_posix() for p in case_dir.rglob("*.*"))
|
||||||
|
assert files == [
|
||||||
|
"clinical/clinical.json",
|
||||||
|
"mr/report.txt",
|
||||||
|
"ultrasound/key.png",
|
||||||
|
"ultrasound/report.txt",
|
||||||
|
]
|
||||||
|
clinical = json.loads((case_dir / "clinical/clinical.json").read_text(encoding="utf-8"))
|
||||||
|
assert set(clinical["fields"]) == set(CLINICAL_HEADER) - {"Case_ID", "Diagnosis"}
|
||||||
|
for report in ("ultrasound/report.txt", "mr/report.txt"):
|
||||||
|
text = (case_dir / report).read_text(encoding="utf-8")
|
||||||
|
assert [name for name in clinical_names if name in text] == []
|
||||||
|
ages = {f"{30 + n}" for n in range(1, 5)}
|
||||||
|
for alias in list_aliases(summary.library_dir):
|
||||||
|
assert str(read_clinical(summary.library_dir, alias).fields["Age"]) in ages
|
||||||
|
assert read_ultrasound(summary.library_dir, alias).report == ULTRASOUND_TEXT
|
||||||
|
assert read_mr(summary.library_dir, alias).report == MR_TEXT
|
||||||
|
|
||||||
|
|
||||||
|
def test_leak_scan_finds_nothing_in_clean_build(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(4), 1, None, NOW)
|
||||||
|
case_nos = [f"{n:03d}" for n in range(1, 5)]
|
||||||
|
hits = scan_for_leaks(summary.library_dir, _forbidden_strings(case_nos), FORBIDDEN_KEYS)
|
||||||
|
assert hits == []
|
||||||
|
|
||||||
|
|
||||||
|
def test_leak_scan_detects_planted_leaks(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(3), 1, None, NOW)
|
||||||
|
case_dir = _case_dirs(summary.library_dir)[0]
|
||||||
|
(case_dir / "mr/report.txt").write_text(MR_TEXT + "见 P002 。", encoding="utf-8")
|
||||||
|
(case_dir / "ultrasound/note.json").write_text('{"Label": "x"}', encoding="utf-8")
|
||||||
|
(case_dir / "clinical/extra.json").write_text(
|
||||||
|
'{"k": "\\u6d46\\u6db2\\u6027\\u56ca\\u6027\\u80bf\\u7624"}', encoding="utf-8"
|
||||||
|
)
|
||||||
|
hits = scan_for_leaks(summary.library_dir, _forbidden_strings(["002"]), FORBIDDEN_KEYS)
|
||||||
|
found = {(Path(h.file).name, h.kind, h.term) for h in hits}
|
||||||
|
assert found == {
|
||||||
|
("report.txt", "字符串", "P002"),
|
||||||
|
("note.json", "键名", "Label"),
|
||||||
|
("extra.json", "字符串", "浆液性囊性肿瘤"),
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def test_leak_scan_normalizes_fullwidth_and_case(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(2), 1, None, NOW)
|
||||||
|
case_dir = _case_dirs(summary.library_dir)[0]
|
||||||
|
leaked = MR_TEXT + "形态似ｉｐｍｎ，见ｐ００２。"
|
||||||
|
(case_dir / "mr/report.txt").write_text(leaked, encoding="utf-8")
|
||||||
|
hits = scan_for_leaks(summary.library_dir, ["IPMN", "P002", "Ｕ００２"], FORBIDDEN_KEYS)
|
||||||
|
assert {(Path(h.file).name, h.term) for h in hits} == {
|
||||||
|
("report.txt", "IPMN"),
|
||||||
|
("report.txt", "P002"),
|
||||||
|
}
|
||||||
|
(case_dir / "mr/report.txt").write_text(MR_TEXT + "U002", encoding="utf-8")
|
||||||
|
hits = scan_for_leaks(summary.library_dir, ["Ｕ００２"], FORBIDDEN_KEYS)
|
||||||
|
assert [(Path(h.file).name, h.term) for h in hits] == [("report.txt", "Ｕ００２")]
|
||||||
|
|
||||||
|
|
||||||
|
def test_aliases_are_reproducible_and_well_formed(tmp_path: Path) -> None:
|
||||||
|
first = build(tmp_path / "a", make_delivery(5), 11, None, NOW)
|
||||||
|
second = build(tmp_path / "b", make_delivery(5), 11, None, NOW)
|
||||||
|
other = build(tmp_path / "c", make_delivery(5), 12, None, NOW)
|
||||||
|
aliases = list_aliases(first.library_dir)
|
||||||
|
assert aliases == list_aliases(second.library_dir)
|
||||||
|
assert aliases != list_aliases(other.library_dir)
|
||||||
|
assert len(set(aliases)) == 5
|
||||||
|
assert all(re.fullmatch(r"[a-z0-9]{4}", a) for a in aliases)
|
||||||
|
|
||||||
|
|
||||||
|
def test_aliases_avoid_subtype_substrings_and_repeats() -> None:
|
||||||
|
case_nos = [f"{n:03d}" for n in range(1, 1000)]
|
||||||
|
aliases = make_aliases(case_nos, 3)
|
||||||
|
assert len(set(aliases.values())) == 999
|
||||||
|
banned = ("ipmn", "spn", "mcn", "scn")
|
||||||
|
assert [a for a in aliases.values() if any(b in a for b in banned)] == []
|
||||||
|
|
||||||
|
|
||||||
|
def test_alias_order_does_not_depend_on_input_order() -> None:
|
||||||
|
case_nos = ["003", "001", "002"]
|
||||||
|
assert make_aliases(case_nos, 5) == make_aliases(sorted(case_nos), 5)
|
||||||
|
|
||||||
|
|
||||||
|
def test_decode_off_keeps_raw_numbers(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(3), 1, None, NOW)
|
||||||
|
for alias in list_aliases(summary.library_dir):
|
||||||
|
clinical = read_clinical(summary.library_dir, alias)
|
||||||
|
assert clinical.codes_decoded is False
|
||||||
|
assert clinical.fields["Sex"] in (1, 2)
|
||||||
|
assert clinical.fields["Symptom_Pain"] == 1
|
||||||
|
assert clinical.fields["CEA_Level"] == 1
|
||||||
|
assert [d.name for d in read_diagnoses(summary.answers_dir)] == [None, None, None]
|
||||||
|
manifest = json.loads((summary.library_dir / "manifest.json").read_text(encoding="utf-8"))
|
||||||
|
assert manifest["codes_decoded"] is False
|
||||||
|
assert manifest["uncompared"] == ["临床性别未比对"]
|
||||||
|
|
||||||
|
|
||||||
|
def test_decode_on_uses_code_maps(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(3), 1, SAMPLE_CODE_MAPS, NOW)
|
||||||
|
by_case = {row.case_no: row.alias for row in read_aliases(summary.answers_dir)}
|
||||||
|
# 假交付包：病例 n 的性别编码是 1 + n % 2，诊断编码是 1 + (n - 1) % 4。
|
||||||
|
expected_sex = {"001": "女", "002": "男", "003": "女"}
|
||||||
|
for case_no, alias in by_case.items():
|
||||||
|
clinical = read_clinical(summary.library_dir, alias)
|
||||||
|
assert clinical.codes_decoded is True
|
||||||
|
assert clinical.fields["Sex"] == expected_sex[case_no]
|
||||||
|
assert clinical.fields["Symptom_Pain"] == "是"
|
||||||
|
assert clinical.fields["CEA_Level"] == "异常"
|
||||||
|
assert clinical.fields["Amylase_Level"] is None
|
||||||
|
assert clinical.fields["Age"] == 30 + int(case_no)
|
||||||
|
names = {d.case_no: d.name for d in read_diagnoses(summary.answers_dir)}
|
||||||
|
assert names == {"001": "IPMN", "002": "SPN", "003": "MCN"}
|
||||||
|
|
||||||
|
|
||||||
|
def test_key_image_pixels_kept_and_text_chunk_dropped(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(2), 1, None, NOW)
|
||||||
|
by_case = {row.case_no: row.alias for row in read_aliases(summary.answers_dir)}
|
||||||
|
for case_no, alias in by_case.items():
|
||||||
|
source = tmp_path / "delivery" / "CEUS_agent" / case_no / f"U{case_no}_key.png"
|
||||||
|
with Image.open(source) as original:
|
||||||
|
assert original.info.get("PatientName") == "should-not-survive"
|
||||||
|
original_mode, original_pixels = original.mode, original.tobytes()
|
||||||
|
copied = read_ultrasound(summary.library_dir, alias).key_image
|
||||||
|
with Image.open(copied) as image:
|
||||||
|
assert image.mode == original_mode
|
||||||
|
assert image.tobytes() == original_pixels
|
||||||
|
assert "PatientName" not in image.info
|
||||||
|
assert _png_chunks(copied.read_bytes()) == ["IHDR", "IDAT", "IEND"]
|
||||||
|
|
||||||
|
|
||||||
|
def _png_chunks(data: bytes) -> list[str]:
|
||||||
|
"""按 PNG 格式逐块读出块类型（8 字节签名后：4 字节长度、4 字节类型、数据、4 字节 CRC）。"""
|
||||||
|
chunks: list[str] = []
|
||||||
|
offset = 8
|
||||||
|
while offset < len(data):
|
||||||
|
length = int.from_bytes(data[offset : offset + 4], "big")
|
||||||
|
chunks.append(data[offset + 4 : offset + 8].decode("ascii"))
|
||||||
|
offset += 12 + length
|
||||||
|
return chunks
|
||||||
|
|
||||||
|
|
||||||
|
def _build_with_key_image(tmp_path: Path, image: Image.Image) -> None:
|
||||||
|
root = make_delivery(2).write(tmp_path / "delivery")
|
||||||
|
image.save(root / "CEUS_agent" / "002" / "U002_key.png", format="PNG")
|
||||||
|
run_build(write_config(tmp_path, root, 1, None), REPO_ROOT, NOW)
|
||||||
|
|
||||||
|
|
||||||
|
def test_key_image_16_bit_source_stops_build(tmp_path: Path) -> None:
|
||||||
|
image = Image.new("I;16", (4, 4))
|
||||||
|
with pytest.raises(ValueError, match=r"U002_key\.png"):
|
||||||
|
_build_with_key_image(tmp_path, image)
|
||||||
|
assert not (tmp_path / "library" / f"{NOW:%Y%m%d-%H%M%S}").exists()
|
||||||
|
assert [p for p in (tmp_path / "library").iterdir() if not p.name.endswith(".partial")] == []
|
||||||
|
|
||||||
|
|
||||||
|
def test_key_image_with_transparency_stops_build(tmp_path: Path) -> None:
|
||||||
|
image = Image.new("RGB", (4, 4))
|
||||||
|
image.info["transparency"] = (0, 0, 0)
|
||||||
|
with pytest.raises(ValueError, match=r"U002_key\.png"):
|
||||||
|
_build_with_key_image(tmp_path, image)
|
||||||
|
|
||||||
|
|
||||||
|
def test_key_image_palette_source_stops_build(tmp_path: Path) -> None:
|
||||||
|
with pytest.raises(ValueError, match=r"U002_key\.png"):
|
||||||
|
_build_with_key_image(tmp_path, Image.new("P", (4, 4)))
|
||||||
|
|
||||||
|
|
||||||
|
def test_key_image_one_bit_kept_as_is(tmp_path: Path) -> None:
|
||||||
|
source = Image.frombytes("1", (8, 2), bytes([0b10110010, 0b01001101]))
|
||||||
|
_build_with_key_image(tmp_path, source)
|
||||||
|
library_root = tmp_path / "library"
|
||||||
|
(library_dir,) = list(library_root.iterdir())
|
||||||
|
by_case = {r.case_no: r.alias for r in read_aliases(tmp_path / "answers" / library_dir.name)}
|
||||||
|
copied = read_ultrasound(library_dir, by_case["002"]).key_image
|
||||||
|
with Image.open(copied) as image:
|
||||||
|
assert image.mode == "1"
|
||||||
|
assert image.tobytes() == source.tobytes()
|
||||||
|
assert _png_chunks(copied.read_bytes()) == ["IHDR", "IDAT", "IEND"]
|
||||||
|
|
||||||
|
|
||||||
|
def test_library_read_rejects_modified_file(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(2), 1, None, NOW)
|
||||||
|
alias = list_aliases(summary.library_dir)[0]
|
||||||
|
report = summary.library_dir / "cases" / alias / "mr" / "report.txt"
|
||||||
|
report.write_text(MR_TEXT + "改", encoding="utf-8")
|
||||||
|
with pytest.raises(ValueError, match="SHA-256"):
|
||||||
|
read_mr(summary.library_dir, alias)
|
||||||
|
|
||||||
|
|
||||||
|
def test_library_read_rejects_partial_directory(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(2), 1, None, NOW)
|
||||||
|
partial = summary.library_dir.with_name(summary.library_dir.name + ".partial")
|
||||||
|
summary.library_dir.rename(partial)
|
||||||
|
with pytest.raises(ValueError, match="partial"):
|
||||||
|
list_aliases(partial)
|
||||||
|
|
||||||
|
|
||||||
|
def test_answers_read_rejects_modified_file(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(2), 1, None, NOW)
|
||||||
|
path = summary.answers_dir / "diagnoses.csv"
|
||||||
|
path.write_text(path.read_text(encoding="utf-8-sig") + "x\n", encoding="utf-8-sig")
|
||||||
|
with pytest.raises(ValueError, match="SHA-256"):
|
||||||
|
read_diagnoses(summary.answers_dir)
|
||||||
|
|
||||||
|
|
||||||
|
def test_existing_build_directory_is_not_overwritten(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(2), 1, None, NOW)
|
||||||
|
manifest = (summary.library_dir / "manifest.json").read_bytes()
|
||||||
|
with pytest.raises(FileExistsError):
|
||||||
|
build(tmp_path, make_delivery(3), 1, None, NOW) # 同一时刻、同一提交 → 同一构建号
|
||||||
|
assert (summary.library_dir / "manifest.json").read_bytes() == manifest
|
||||||
|
assert len(list_aliases(summary.library_dir)) == 2
|
||||||
|
|
||||||
|
|
||||||
|
def _csv_rows(path: Path) -> list[list[str]]:
|
||||||
|
with path.open(encoding="utf-8-sig", newline="") as handle:
|
||||||
|
return list(csv.reader(handle))
|
||||||
|
|
||||||
|
|
||||||
|
def test_answers_contents(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(3).mr["年龄"] = "99岁" # C10
|
||||||
|
delivery.case(1).ultrasound["超声描述"] = "胰体部见无回声区。考虑囊性病灶;边界清。"
|
||||||
|
summary = build(tmp_path, delivery, 1, None, NOW)
|
||||||
|
|
||||||
|
assert summary.total_cases == 4
|
||||||
|
assert summary.passed_cases == 3
|
||||||
|
assert summary.skipped_cases == 1
|
||||||
|
assert summary.skipped_by_check == {"C10": 1}
|
||||||
|
assert summary.review_rows == 1
|
||||||
|
|
||||||
|
skipped = _csv_rows(summary.answers_dir / "skipped.csv")
|
||||||
|
assert skipped[0] == ["病例", "检查编号", "检查说明", "文件", "列", "涉及值"]
|
||||||
|
assert [row[:2] for row in skipped[1:]] == [["003", "C10"]]
|
||||||
|
assert json.loads(skipped[1][5])["年龄"]["MR 表"] == "99岁"
|
||||||
|
|
||||||
|
review = _csv_rows(summary.answers_dir / "review.csv")
|
||||||
|
alias_of_1 = {r.case_no: r.alias for r in read_aliases(summary.answers_dir)}["001"]
|
||||||
|
assert review[1:] == [[alias_of_1, "超声", "考虑", "考虑囊性病灶"]]
|
||||||
|
|
||||||
|
assert [r.case_no for r in read_aliases(summary.answers_dir)] == ["001", "002", "004"]
|
||||||
|
assert [r.video_id for r in read_aliases(summary.answers_dir)] == ["U001", "U002", "U004"]
|
||||||
|
codes = [
|
||||||
|
(d.clinical_code, d.ultrasound_code, d.mr_code) for d in read_diagnoses(summary.answers_dir)
|
||||||
|
]
|
||||||
|
assert codes == [(1, 1, 1), (2, 2, 2), (4, 4, 4)]
|
||||||
|
|
||||||
|
manifest = json.loads((summary.answers_dir / "manifest.json").read_text(encoding="utf-8"))
|
||||||
|
assert manifest["build_id"] == summary.build_id
|
||||||
|
assert "不代表没有问题" in manifest["skipped_note"]
|
||||||
|
assert sorted(manifest["files"]) == [
|
||||||
|
"aliases.csv",
|
||||||
|
"diagnoses.csv",
|
||||||
|
"review.csv",
|
||||||
|
"skipped.csv",
|
||||||
|
"snapshot/build.yaml",
|
||||||
|
"snapshot/snapshot.json",
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
def test_snapshot_records_config_and_git(tmp_path: Path) -> None:
|
||||||
|
summary = build(tmp_path, make_delivery(2), 1, SAMPLE_CODE_MAPS, NOW)
|
||||||
|
snapshot_dir = summary.answers_dir / "snapshot"
|
||||||
|
assert (snapshot_dir / "build.yaml").read_bytes() == (tmp_path / "build.yaml").read_bytes()
|
||||||
|
assert (snapshot_dir / "code_maps.yaml").read_bytes() == (
|
||||||
|
tmp_path / "code_maps.yaml"
|
||||||
|
).read_bytes()
|
||||||
|
snapshot = json.loads((snapshot_dir / "snapshot.json").read_text(encoding="utf-8"))
|
||||||
|
assert snapshot["build_id"] == summary.build_id
|
||||||
|
assert re.fullmatch(r"[0-9a-f]{40}", snapshot["git_commit"])
|
||||||
|
assert summary.build_id.startswith("20261016-093000-" + snapshot["git_commit"][:7])
|
||||||
|
assert summary.build_id.endswith("-dirty") == (snapshot["git_clean"] is False)
|
||||||
|
assert set(snapshot["config_sha256"]) == {"build.yaml", "code_maps.yaml"}
|
||||||
|
library_manifest = json.loads(
|
||||||
|
(summary.library_dir / "manifest.json").read_text(encoding="utf-8")
|
||||||
|
)
|
||||||
|
assert library_manifest["config_sha256"] == snapshot["config_sha256"]
|
||||||
|
assert library_manifest["ceus_source"] is None
|
||||||
|
assert library_manifest["aliases"] == sorted(library_manifest["aliases"])
|
||||||
@@ -0,0 +1,187 @@
|
|||||||
|
"""整张表的问题 T1–T5 与配置错误：整次构建停下，两个库下不留完成的构建目录。"""
|
||||||
|
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
import pytest
|
||||||
|
from pydantic import ValidationError
|
||||||
|
|
||||||
|
from cadx.build import load_build_config, load_code_maps, run_build
|
||||||
|
from cadx.delivery import DeliveryError
|
||||||
|
from fake_delivery import (
|
||||||
|
CLINICAL_PATH,
|
||||||
|
MR_PATH,
|
||||||
|
REPO_ROOT,
|
||||||
|
SAMPLE_CODE_MAPS,
|
||||||
|
ULTRASOUND_PATH,
|
||||||
|
make_delivery,
|
||||||
|
write_config,
|
||||||
|
)
|
||||||
|
|
||||||
|
NOW = datetime(2026, 10, 16, 9, 0, 0).astimezone()
|
||||||
|
|
||||||
|
|
||||||
|
def _assert_no_finished_build(tmp_path: Path) -> None:
|
||||||
|
for root in (tmp_path / "library", tmp_path / "answers"):
|
||||||
|
if root.exists():
|
||||||
|
assert all(p.name.endswith(".partial") for p in root.iterdir())
|
||||||
|
|
||||||
|
|
||||||
|
def _run(tmp_path: Path, root: Path, code_maps: dict[str, dict[int, str]] | None) -> None:
|
||||||
|
run_build(write_config(tmp_path, root, 7, code_maps), REPO_ROOT, NOW)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t1_missing_summary_table(tmp_path: Path) -> None:
|
||||||
|
root = make_delivery(3).write(tmp_path / "delivery")
|
||||||
|
(root / MR_PATH).unlink()
|
||||||
|
with pytest.raises(DeliveryError, match=r"^T1"):
|
||||||
|
_run(tmp_path, root, None)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t2_wrong_sheet_name(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.sheet_names[ULTRASOUND_PATH] = "Sheet1"
|
||||||
|
root = delivery.write(tmp_path / "delivery")
|
||||||
|
with pytest.raises(DeliveryError, match=r"^T2"):
|
||||||
|
_run(tmp_path, root, None)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t3_header_differs(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.headers[MR_PATH][3] = "病理类型" # 诊断列名里写的编码含义丢了
|
||||||
|
root = delivery.write(tmp_path / "delivery")
|
||||||
|
with pytest.raises(DeliveryError, match=r"^T3"):
|
||||||
|
_run(tmp_path, root, None)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t4_extra_file_in_clinical_folder(tmp_path: Path) -> None:
|
||||||
|
root = make_delivery(3).write(tmp_path / "delivery")
|
||||||
|
(root / CLINICAL_PATH).with_name("备注.txt").write_text("x", encoding="utf-8")
|
||||||
|
with pytest.raises(DeliveryError, match=r"^T4"):
|
||||||
|
_run(tmp_path, root, None)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t4_unexpected_entry_in_ceus_folder(tmp_path: Path) -> None:
|
||||||
|
root = make_delivery(3).write(tmp_path / "delivery")
|
||||||
|
(root / "CEUS_agent" / "41").mkdir() # 不是三位数字
|
||||||
|
with pytest.raises(DeliveryError, match=r"^T4"):
|
||||||
|
_run(tmp_path, root, None)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t5_code_maps_missing_a_column(tmp_path: Path) -> None:
|
||||||
|
root = make_delivery(3).write(tmp_path / "delivery")
|
||||||
|
maps = {k: v for k, v in SAMPLE_CODE_MAPS.items() if k != "TBil_Level"}
|
||||||
|
with pytest.raises(ValueError, match=r"^T5"):
|
||||||
|
_run(tmp_path, root, maps)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t5_code_maps_extra_column(tmp_path: Path) -> None:
|
||||||
|
root = make_delivery(3).write(tmp_path / "delivery")
|
||||||
|
maps = {**SAMPLE_CODE_MAPS, "Age": {1: "一"}}
|
||||||
|
with pytest.raises(ValueError, match=r"^T5"):
|
||||||
|
_run(tmp_path, root, maps)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t5_sex_must_map_to_chinese_characters(tmp_path: Path) -> None:
|
||||||
|
root = make_delivery(3).write(tmp_path / "delivery")
|
||||||
|
maps = {**SAMPLE_CODE_MAPS, "Sex": {1: "M", 2: "F"}}
|
||||||
|
with pytest.raises(ValueError, match=r"^T5"):
|
||||||
|
_run(tmp_path, root, maps)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_t5_diagnosis_must_map_to_four_subtypes(tmp_path: Path) -> None:
|
||||||
|
root = make_delivery(3).write(tmp_path / "delivery")
|
||||||
|
maps = {**SAMPLE_CODE_MAPS, "Diagnosis": {1: "IPMN", 2: "SPN", 3: "MCN", 4: "MCN"}}
|
||||||
|
with pytest.raises(ValueError, match=r"^T5"):
|
||||||
|
_run(tmp_path, root, maps)
|
||||||
|
_assert_no_finished_build(tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def _write_yaml(tmp_path: Path, body: str) -> Path:
|
||||||
|
path = tmp_path / "build.yaml"
|
||||||
|
path.write_text(body, encoding="utf-8")
|
||||||
|
return path
|
||||||
|
|
||||||
|
|
||||||
|
_BASE = "delivery_dir: d\nlibrary_root: l\nanswers_root: a\nalias_seed: 1\n"
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_decode_true_needs_code_maps(tmp_path: Path) -> None:
|
||||||
|
path = _write_yaml(tmp_path, _BASE + "decode_codes: true\ncode_maps: null\n")
|
||||||
|
with pytest.raises(ValidationError):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_decode_false_needs_null_code_maps(tmp_path: Path) -> None:
|
||||||
|
path = _write_yaml(tmp_path, _BASE + "decode_codes: false\ncode_maps: maps.yaml\n")
|
||||||
|
with pytest.raises(ValidationError):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_field_missing(tmp_path: Path) -> None:
|
||||||
|
path = _write_yaml(tmp_path, _BASE + "decode_codes: false\n")
|
||||||
|
with pytest.raises(ValidationError):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_extra_field(tmp_path: Path) -> None:
|
||||||
|
path = _write_yaml(tmp_path, _BASE + "decode_codes: false\ncode_maps: null\nseed: 2\n")
|
||||||
|
with pytest.raises(ValidationError):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_seed_must_be_int_not_string(tmp_path: Path) -> None:
|
||||||
|
body = _BASE.replace("alias_seed: 1", "alias_seed: '1'")
|
||||||
|
path = _write_yaml(tmp_path, body + "decode_codes: false\ncode_maps: null\n")
|
||||||
|
with pytest.raises(ValidationError):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_relative_paths_resolve_against_repo_root(tmp_path: Path) -> None:
|
||||||
|
path = _write_yaml(tmp_path, _BASE + "decode_codes: false\ncode_maps: null\n")
|
||||||
|
config = load_build_config(path, Path("/repo"))
|
||||||
|
assert config.delivery_dir == Path("/repo/d")
|
||||||
|
assert config.library_root == Path("/repo/l")
|
||||||
|
assert config.answers_root == Path("/repo/a")
|
||||||
|
assert config.code_maps is None
|
||||||
|
|
||||||
|
|
||||||
|
def test_committed_config_is_valid() -> None:
|
||||||
|
config = load_build_config(REPO_ROOT / "config" / "build.yaml", REPO_ROOT)
|
||||||
|
assert config.decode_codes is False
|
||||||
|
assert config.code_maps is None
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_duplicate_key(tmp_path: Path) -> None:
|
||||||
|
body = _BASE + "decode_codes: false\ncode_maps: null\nalias_seed: 2\n"
|
||||||
|
path = _write_yaml(tmp_path, body)
|
||||||
|
with pytest.raises(ValueError, match="重复的键"):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_empty_path(tmp_path: Path) -> None:
|
||||||
|
body = _BASE.replace("delivery_dir: d", "delivery_dir: ''")
|
||||||
|
path = _write_yaml(tmp_path, body + "decode_codes: false\ncode_maps: null\n")
|
||||||
|
with pytest.raises(ValidationError, match="空串"):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_config_empty_code_maps_path(tmp_path: Path) -> None:
|
||||||
|
path = _write_yaml(tmp_path, _BASE + "decode_codes: true\ncode_maps: ''\n")
|
||||||
|
with pytest.raises(ValidationError, match="空串"):
|
||||||
|
load_build_config(path, tmp_path)
|
||||||
|
|
||||||
|
|
||||||
|
def test_code_maps_duplicate_key(tmp_path: Path) -> None:
|
||||||
|
path = tmp_path / "code_maps.yaml"
|
||||||
|
path.write_text("Sex: {1: 男, 1: 女}\n", encoding="utf-8")
|
||||||
|
with pytest.raises(ValueError, match="重复的键"):
|
||||||
|
load_code_maps(path)
|
||||||
@@ -0,0 +1,420 @@
|
|||||||
|
"""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。
|
||||||
|
|
||||||
|
预期值照任务书 01 第二部分「单个病例的问题」的文字写。
|
||||||
|
"""
|
||||||
|
|
||||||
|
import shutil
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
from cadx.delivery import DeliveryResult, read_delivery
|
||||||
|
from cadx.delivery._text import conclusion_headings
|
||||||
|
from fake_delivery import (
|
||||||
|
CLINICAL_PATH,
|
||||||
|
DIAGNOSIS_COLUMN,
|
||||||
|
MR_PATH,
|
||||||
|
MR_TEXT,
|
||||||
|
SAMPLE_CODE_MAPS,
|
||||||
|
ULTRASOUND_HEADER,
|
||||||
|
ULTRASOUND_PATH,
|
||||||
|
ULTRASOUND_TEXT,
|
||||||
|
FakeDelivery,
|
||||||
|
make_delivery,
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def _read(
|
||||||
|
tmp_path: Path, delivery: FakeDelivery, code_maps: dict[str, dict[int, str]] | None
|
||||||
|
) -> DeliveryResult:
|
||||||
|
return read_delivery(delivery.write(tmp_path / "delivery"), code_maps)
|
||||||
|
|
||||||
|
|
||||||
|
def _assert_only_skipped(result: DeliveryResult, case: str, check: str, total: int) -> None:
|
||||||
|
assert [(s.case, s.check) for s in result.skipped] == [(case, check)]
|
||||||
|
passed = [f"{n:03d}" for n in range(1, total + 1) if f"{n:03d}" != case]
|
||||||
|
assert [c.case_no for c in result.cases] == passed
|
||||||
|
assert result.total_cases == total
|
||||||
|
|
||||||
|
|
||||||
|
def test_all_pass(tmp_path: Path) -> None:
|
||||||
|
result = _read(tmp_path, make_delivery(4), None)
|
||||||
|
assert [c.case_no for c in result.cases] == ["001", "002", "003", "004"]
|
||||||
|
assert result.skipped == ()
|
||||||
|
assert result.unrecognized_rows == 0
|
||||||
|
|
||||||
|
|
||||||
|
def test_c01_unrecognized_clinical_id_is_its_own_row_and_case_missing(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(2).clinical["Case_ID"] = "P2" # 临床表要求 P 加三位数字
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
# 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。
|
||||||
|
assert [(s.case, s.check) for s in result.skipped] == [
|
||||||
|
(f"{CLINICAL_PATH} 第 3 行", "C01"),
|
||||||
|
("002", "C03"),
|
||||||
|
]
|
||||||
|
assert result.unrecognized_rows == 1
|
||||||
|
assert result.total_cases == 4
|
||||||
|
assert [c.case_no for c in result.cases] == ["001", "003", "004"]
|
||||||
|
|
||||||
|
|
||||||
|
def test_c01_float_report_id_is_unrecognized(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(3).mr["患者ID"] = 3.5 # 浮点不是认得出的写法
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
assert [(s.case, s.check) for s in result.skipped] == [
|
||||||
|
(f"{MR_PATH} 第 4 行", "C01"),
|
||||||
|
("003", "C03"),
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
def test_c01_report_ids_accept_int_and_zero_padded_strings(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(1).ultrasound["患者ID"] = 1
|
||||||
|
delivery.case(2).mr["患者ID"] = "002"
|
||||||
|
delivery.case(2).ultrasound["患者ID"] = "02"
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
assert result.skipped == ()
|
||||||
|
assert len(result.cases) == 3
|
||||||
|
|
||||||
|
|
||||||
|
def test_c02_duplicate_id_in_one_table(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
duplicate = delivery.case(2).mr
|
||||||
|
delivery.extra_rows[MR_PATH].append([duplicate[h] for h in delivery.headers[MR_PATH]])
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C02", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c03_case_directory_missing(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
root = delivery.write(tmp_path / "delivery")
|
||||||
|
shutil.rmtree(root / "CEUS_agent" / "003")
|
||||||
|
_assert_only_skipped(read_delivery(root, None), "003", "C03", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c04_missing_key_image(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(4).dir_files.remove("U004_key.png")
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "004", "C04", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c04_extra_file(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(1).dir_files.append("U001.mp4") # 两个视频共四个文件
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C04", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c04_roi2_video_with_roi2_report_passes(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
assert delivery.case(2).dir_files == ["U002_key.png", "U002_roi2.mp4", "U002_roi2_report.xlsx"]
|
||||||
|
assert _read(tmp_path, delivery, None).skipped == ()
|
||||||
|
|
||||||
|
|
||||||
|
def test_c04_plain_video_with_plain_report_passes(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(3).dir_files = ["U003_key.png", "U003.mp4", "U003_report.xlsx"]
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
assert result.skipped == ()
|
||||||
|
assert len(result.cases) == 3
|
||||||
|
|
||||||
|
|
||||||
|
def test_c04_roi2_video_with_plain_report_is_skipped(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
# 文件名被 gitleaks 的通用密钥规则误报，不是密钥。
|
||||||
|
delivery.case(1).dir_files = [
|
||||||
|
"U001_key.png",
|
||||||
|
"U001_roi2.mp4", # gitleaks:allow
|
||||||
|
"U001_report.xlsx",
|
||||||
|
]
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C04", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c04_plain_video_with_roi2_report_is_skipped(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(2).dir_files = ["U002_key.png", "U002.mp4", "U002_roi2_report.xlsx"]
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C04", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c06_reads_plain_report_when_paired_with_plain_video(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
case = delivery.case(3)
|
||||||
|
case.dir_files = ["U003_key.png", "U003.mp4", "U003_report.xlsx"]
|
||||||
|
row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
|
||||||
|
row[-1] = ULTRASOUND_TEXT + "补充一句。"
|
||||||
|
case.case_report_rows = [list(ULTRASOUND_HEADER), row]
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "003", "C06", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c05_video_id_mismatch(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(2).ultrasound["CEUS视频ID"] = "U003"
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C05", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c06_case_report_cell_differs(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
case = delivery.case(3)
|
||||||
|
row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
|
||||||
|
row[-1] = ULTRASOUND_TEXT + "补充一句。"
|
||||||
|
case.case_report_rows = [list(ULTRASOUND_HEADER), row]
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
_assert_only_skipped(result, "003", "C06", 4)
|
||||||
|
assert result.skipped[0].columns == ("超声描述",)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c06_case_report_cell_type_differs(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
case = delivery.case(1)
|
||||||
|
row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
|
||||||
|
row[0] = 1 # 汇总表里是字符串 "1"
|
||||||
|
case.case_report_rows = [list(ULTRASOUND_HEADER), row]
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C06", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c06_case_report_wrong_sheet(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(2).case_report_sheet = "Sheet2"
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C06", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c06_case_report_two_data_rows(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
case = delivery.case(2)
|
||||||
|
row = [case.ultrasound[h] for h in ULTRASOUND_HEADER]
|
||||||
|
case.case_report_rows = [list(ULTRASOUND_HEADER), row, row]
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C06", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c07_bool_sex_is_not_an_int(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(1).clinical["Sex"] = True # bool 是 int 的子类，不能当作 1
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C07", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c01_bool_report_id_is_unrecognized(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(1).ultrasound["患者ID"] = True
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
assert [(s.case, s.check) for s in result.skipped] == [
|
||||||
|
(f"{ULTRASOUND_PATH} 第 2 行", "C01"),
|
||||||
|
("001", "C03"),
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
def test_c07_sex_out_of_range(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(1).clinical["Sex"] = 3
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C07", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c07_non_integer_age(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(2).clinical["Age"] = 32.5
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C07", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c07_symptom_empty(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(2).clinical["Symptom_Fever"] = None
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C07", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c07_lab_only_one_column_empty(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(2).clinical["CA199"] = None # 档位列仍是 0
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
_assert_only_skipped(result, "002", "C07", 4)
|
||||||
|
assert set(result.skipped[0].columns) == {"CA199", "CA199_Level"}
|
||||||
|
|
||||||
|
|
||||||
|
def test_c07_lab_both_empty_is_fine(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(1).clinical["TBil"] = None
|
||||||
|
delivery.case(1).clinical["TBil_Level"] = None
|
||||||
|
assert _read(tmp_path, delivery, None).skipped == ()
|
||||||
|
|
||||||
|
|
||||||
|
def test_c07_value_missing_from_code_map(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
maps = {**SAMPLE_CODE_MAPS, "Hx_Alcohol": {0: "否"}} # 映射表里没有 1
|
||||||
|
delivery.case(2).clinical["Hx_Alcohol"] = 1
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, maps), "002", "C07", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c08_ultrasound_sex_invalid(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(4).ultrasound["性别"] = "M"
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "004", "C08", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c08_negative_bolus_time(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(3).ultrasound["推注开始时间s"] = -1
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "003", "C08", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c08_empty_description(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(1).ultrasound["超声描述"] = None
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C08", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c09_mr_age_not_number_plus_sui(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(3).mr["年龄"] = "33"
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "003", "C09", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c09_mr_diagnosis_out_of_range(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(2).mr[DIAGNOSIS_COLUMN] = 5
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C09", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c10_diagnosis_mismatch(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(1).clinical["Diagnosis"] = 2 # 两张报告表仍是 1
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
_assert_only_skipped(result, "001", "C10", 4)
|
||||||
|
assert result.skipped[0].columns == ("诊断",)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c10_age_mismatch(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(2).mr["年龄"] = "99岁"
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
_assert_only_skipped(result, "002", "C10", 4)
|
||||||
|
assert result.skipped[0].columns == ("年龄",)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c10_sex_mismatch_between_reports(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(3).mr["性别"] = "男" if delivery.case(3).ultrasound["性别"] == "女" else "女"
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
_assert_only_skipped(result, "003", "C10", 4)
|
||||||
|
assert result.skipped[0].columns == ("性别",)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c10_clinical_sex_compared_only_when_decoding(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
case = delivery.case(2)
|
||||||
|
case.clinical["Sex"] = 1 if case.clinical["Sex"] == 2 else 2 # 报告表的性别不变
|
||||||
|
undecoded = _read(tmp_path / "a", delivery, None)
|
||||||
|
assert undecoded.skipped == ()
|
||||||
|
assert undecoded.uncompared == ("临床性别未比对",)
|
||||||
|
decoded = _read(tmp_path / "b", delivery, SAMPLE_CODE_MAPS)
|
||||||
|
_assert_only_skipped(decoded, "002", "C10", 3)
|
||||||
|
assert decoded.uncompared == ()
|
||||||
|
|
||||||
|
|
||||||
|
def test_c11_heading_at_start_with_fullwidth_colon(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(2).ultrasound["超声描述"] = "结论：胰体部囊性病灶。" + ULTRASOUND_TEXT
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "002", "C11", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c11_heading_after_newline(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(3).mr["MR描述"] = MR_TEXT + "\n印象 : 胰体部囊性病灶。"
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
_assert_only_skipped(result, "003", "C11", 4)
|
||||||
|
assert result.skipped[0].columns == ("MR描述",)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c11_heading_mid_text_is_not_a_failure(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
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。"
|
||||||
|
result = _read(tmp_path, delivery, None)
|
||||||
|
assert result.skipped == ()
|
||||||
|
assert len(result.cases) == 3
|
||||||
|
|
||||||
|
|
||||||
|
def test_c12_subtype_name_fullwidth_lowercase(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(4)
|
||||||
|
delivery.case(4).mr["MR描述"] = MR_TEXT + "形态类似ｉｐｍｎ。"
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "004", "C12", 4)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c12_chinese_subtype_name(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(1).ultrasound["超声描述"] = ULTRASOUND_TEXT + "符合浆液性囊腺瘤表现。"
|
||||||
|
_assert_only_skipped(_read(tmp_path, delivery, None), "001", "C12", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c11_heading_after_vertical_tab_or_form_feed() -> None:
|
||||||
|
# xlsx（XML）里写不进 \x0b、\x0c，openpyxl 拒绝生成，所以直接测规则函数。
|
||||||
|
for separator in ("\x0b", "\x0c"):
|
||||||
|
text = MR_TEXT + separator + "诊断：胰体部囊性病灶。"
|
||||||
|
assert [k for k, _ in conclusion_headings(text)] == ["诊断"]
|
||||||
|
|
||||||
|
|
||||||
|
def test_c11_heading_after_unicode_line_separator(tmp_path: Path) -> None:
|
||||||
|
for i, separator in enumerate(("\x85", "\u2028", "\u2029")):
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
delivery.case(2).mr["MR描述"] = MR_TEXT + separator + "诊断：胰体部囊性病灶。"
|
||||||
|
_assert_only_skipped(_read(tmp_path / str(i), delivery, None), "002", "C11", 3)
|
||||||
|
|
||||||
|
|
||||||
|
def test_c11_ratio_sign_as_colon(tmp_path: Path) -> None:
|
||||||
|
delivery = make_delivery(3)
|
||||||
|
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}'
|
||||||
@@ -2,10 +2,25 @@ version = 1
|
|||||||
revision = 2
|
revision = 2
|
||||||
requires-python = ">=3.12"
|
requires-python = ">=3.12"
|
||||||
|
|
||||||
|
[[package]]
|
||||||
|
name = "annotated-types"
|
||||||
|
version = "0.8.0"
|
||||||
|
source = { registry = "https://pypi.org/simple" }
|
||||||
|
sdist = { url = "https://files.pythonhosted.org/packages/5f/56/a8120250d128bed162cd73c76d45f6ef9991f3e068f62a8ee060afa3104a/annotated_types-0.8.0.tar.gz", hash = "sha256:13b2beaad985e05e2d6407ee4c4f35590b11f8d693a258a561055cac8f64cab7", size = 15893, upload-time = "2026-07-23T20:16:13.995Z" }
|
||||||
|
wheels = [
|
||||||
|
{ url = "https://files.pythonhosted.org/packages/99/91/8acff4f5e50511b911bbccb72b8628a49c68ce14148cd9f6431094859a90/annotated_types-0.8.0-py3-none-any.whl", hash = "sha256:f072f4d804ea359e4eaf198b1af7a8b0943881a87f31bb764f8bf219bb9419e0", size = 13427, upload-time = "2026-07-23T20:16:12.938Z" },
|
||||||
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "cadx"
|
name = "cadx"
|
||||||
version = "0.0.0"
|
version = "0.0.0"
|
||||||
source = { editable = "." }
|
source = { editable = "." }
|
||||||
|
dependencies = [
|
||||||
|
{ name = "openpyxl" },
|
||||||
|
{ name = "pillow" },
|
||||||
|
{ name = "pydantic" },
|
||||||
|
{ name = "pyyaml" },
|
||||||
|
]
|
||||||
|
|
||||||
[package.dev-dependencies]
|
[package.dev-dependencies]
|
||||||
dev = [
|
dev = [
|
||||||
@@ -14,9 +29,17 @@ dev = [
|
|||||||
{ name = "pyright" },
|
{ name = "pyright" },
|
||||||
{ name = "pytest" },
|
{ name = "pytest" },
|
||||||
{ name = "ruff" },
|
{ name = "ruff" },
|
||||||
|
{ name = "types-openpyxl" },
|
||||||
|
{ name = "types-pyyaml" },
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.metadata]
|
[package.metadata]
|
||||||
|
requires-dist = [
|
||||||
|
{ name = "openpyxl", specifier = ">=3.1.5" },
|
||||||
|
{ name = "pillow", specifier = ">=12.3.0" },
|
||||||
|
{ name = "pydantic", specifier = ">=2.14.1" },
|
||||||
|
{ name = "pyyaml", specifier = ">=6.0.3" },
|
||||||
|
]
|
||||||
|
|
||||||
[package.metadata.requires-dev]
|
[package.metadata.requires-dev]
|
||||||
dev = [
|
dev = [
|
||||||
@@ -25,6 +48,8 @@ dev = [
|
|||||||
{ name = "pyright", specifier = ">=1.1.380" },
|
{ name = "pyright", specifier = ">=1.1.380" },
|
||||||
{ name = "pytest", specifier = ">=8.3" },
|
{ name = "pytest", specifier = ">=8.3" },
|
||||||
{ name = "ruff", specifier = ">=0.6" },
|
{ name = "ruff", specifier = ">=0.6" },
|
||||||
|
{ name = "types-openpyxl", specifier = ">=3.1.5.20260827" },
|
||||||
|
{ name = "types-pyyaml", specifier = ">=6.0.12.20260906" },
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
@@ -63,6 +88,15 @@ wheels = [
|
|||||||
{ url = "https://files.pythonhosted.org/packages/02/08/9c41fb51ab5b43eb21674aff13df270e8ba6c4b29c8624e328dc7a9482af/distlib-0.4.3-py2.py3-none-any.whl", hash = "sha256:4b0ce306c966eb73bc3a7b6abad017c556dadd92c44701562cd528ac7fde4d5b", size = 470628, upload-time = "2026-06-12T08:04:50.506Z" },
|
{ url = "https://files.pythonhosted.org/packages/02/08/9c41fb51ab5b43eb21674aff13df270e8ba6c4b29c8624e328dc7a9482af/distlib-0.4.3-py2.py3-none-any.whl", hash = "sha256:4b0ce306c966eb73bc3a7b6abad017c556dadd92c44701562cd528ac7fde4d5b", size = 470628, upload-time = "2026-06-12T08:04:50.506Z" },
|
||||||
]
|
]
|
||||||
|
|
||||||
|
[[package]]
|
||||||
|
name = "et-xmlfile"
|
||||||
|
version = "2.0.0"
|
||||||
|
source = { registry = "https://pypi.org/simple" }
|
||||||
|
sdist = { url = "https://files.pythonhosted.org/packages/d3/38/af70d7ab1ae9d4da450eeec1fa3918940a5fafb9055e934af8d6eb0c2313/et_xmlfile-2.0.0.tar.gz", hash = "sha256:dab3f4764309081ce75662649be815c4c9081e88f0837825f90fd28317d4da54", size = 17234, upload-time = "2024-10-25T17:25:40.039Z" }
|
||||||
|
wheels = [
|
||||||
|
{ url = "https://files.pythonhosted.org/packages/c1/8b/5fe2cc11fee489817272089c4203e679c63b570a5aaeb18d852ae3cbba6a/et_xmlfile-2.0.0-py3-none-any.whl", hash = "sha256:7a91720bc756843502c3b7504c77b8fe44217c85c537d85037f0f536151b2caa", size = 18059, upload-time = "2024-10-25T17:25:39.051Z" },
|
||||||
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "filelock"
|
name = "filelock"
|
||||||
version = "4.2.0"
|
version = "4.2.0"
|
||||||
@@ -215,6 +249,18 @@ wheels = [
|
|||||||
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||||||
|
{ url = "https://files.pythonhosted.org/packages/15/c0/fc0644b7ddcfb969e95845837143cb5173ddd6e06ee4ba5fc493cd9329b7/types_pyyaml-6.0.12.20260906-py3-none-any.whl", hash = "sha256:bca893ff0d51df5c9053137d5d0e6ccd36e939a196356f1d5c16372422f5137b", size = 21282, upload-time = "2026-09-06T06:35:34.372Z" },
|
||||||
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "typing-extensions"
|
name = "typing-extensions"
|
||||||
version = "4.16.0"
|
version = "4.16.0"
|
||||||
@@ -401,6 +657,18 @@ wheels = [
|
|||||||
{ url = "https://files.pythonhosted.org/packages/49/d3/b8441a820a491ddfc024b0b0cf0393375b75ea13866d9c66727e54c2fc80/typing_extensions-4.16.0-py3-none-any.whl", hash = "sha256:481caa481374e813c1b176ada14e97f1f67a4539ce9cfeb3f350d78d6370c2e8", size = 45571, upload-time = "2026-07-02T08:40:04.659Z" },
|
{ url = "https://files.pythonhosted.org/packages/49/d3/b8441a820a491ddfc024b0b0cf0393375b75ea13866d9c66727e54c2fc80/typing_extensions-4.16.0-py3-none-any.whl", hash = "sha256:481caa481374e813c1b176ada14e97f1f67a4539ce9cfeb3f350d78d6370c2e8", size = 45571, upload-time = "2026-07-02T08:40:04.659Z" },
|
||||||
]
|
]
|
||||||
|
|
||||||
|
[[package]]
|
||||||
|
name = "typing-inspection"
|
||||||
|
version = "0.4.4"
|
||||||
|
source = { registry = "https://pypi.org/simple" }
|
||||||
|
dependencies = [
|
||||||
|
{ name = "typing-extensions" },
|
||||||
|
]
|
||||||
|
sdist = { url = "https://files.pythonhosted.org/packages/a3/26/b09b8010994eccc3c09092e6b34058f36a460eea2d4c3e8b910c695975a0/typing_inspection-0.4.4.tar.gz", hash = "sha256:547274fa6b0a561ccf549cc9524b999a578e737d015d8709d021f9d0d13bea47", size = 76928, upload-time = "2026-08-12T12:37:25.997Z" }
|
||||||
|
wheels = [
|
||||||
|
{ url = "https://files.pythonhosted.org/packages/67/81/4add07e5172b7ac40d8ed5ff580409a7801a4fe26d529bdd915401dabfbe/typing_inspection-0.4.4-py3-none-any.whl", hash = "sha256:65b8397ba37ccbce054456aaccddfc91e6e3083c92824df348d96ca832f3f147", size = 14750, upload-time = "2026-08-12T12:37:24.648Z" },
|
||||||
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "virtualenv"
|
name = "virtualenv"
|
||||||
version = "21.14.8"
|
version = "21.14.8"
|
||||||
|
|||||||
Reference in New Issue
Block a user