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Author SHA1 Message Date
codex-bot a3b677bdf2 Add verified PostgreSQL migration and shared research queries
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2026-11-07 02:09:19 +08:00
Zayden-Jung 029e73cafe Merge pull request '补齐 ACM MM、MLSys 范围并接入官方摘要与发表身份' (#12) from codex/multimedia-mlsys into main
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Reviewed-on: #12
2026-11-06 16:15:16 +00:00
Zayden-Jung 2e95e91f5e Merge pull request '逐条审计 arXiv 类别完整性及来源证据' (#10) from codex/arxiv-tag-audit into main
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Reviewed-on: #10
2026-11-06 16:15:09 +00:00
Zayden-Jung a58b96341a Merge pull request '修正 ICML 多轨道分类并保留既有投稿与决定历史' (#11) from codex/pmlr-track-scope into main
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Reviewed-on: #11
2026-11-06 16:15:04 +00:00
codex-bot 9a279f2eae Handle MLSys year-labelled proceedings and bridge retained publisher evidence
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2026-11-06 22:58:50 +08:00
codex-bot 25cc5b865b Preserve unspecified MM tracks and validate MLSys identities at the shared boundary
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2026-11-06 22:49:41 +08:00
codex-bot c9b0cfa857 Bound arXiv tag audit batches by primary key instead of sorting the source
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2026-11-06 22:41:43 +08:00
codex-bot a65edc6b9d Add ACM Multimedia scope and MLSys metadata with shared publication identities
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2026-11-06 22:39:55 +08:00
codex-bot 4e0e3f0ce8 Migrate existing PMLR submission tracks with atomic provenance checks
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2026-11-06 22:15:56 +08:00
codex-bot 17bdaa77fb Resolve mixed ICML PMLR tracks from verified official programs
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2026-11-06 22:12:08 +08:00
codex-bot bfa7fe2e94 Merge remote-tracking branch 'origin/main' into codex/arxiv-tag-audit
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# Conflicts:
#	paper_atlas/cli.py
2026-11-06 21:51:29 +08:00
codex-bot d712a4fbed Audit every arXiv record category and evidence owner after repair
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2026-11-06 21:43:50 +08:00
Zayden-Jung 0fbcaf4ec7 Merge pull request '核验 ICLR 2020 真实投稿身份并修复旧版论文链接' (#9) from codex/iclr-legacy-identities into main
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Reviewed-on: #9
2026-11-06 13:29:08 +00:00
Zayden-Jung c199ed3c1d Merge pull request '补齐其他会议公开拒稿采集及投稿历史核验' (#8) from codex/public-rejections into main
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Reviewed-on: #8
2026-11-06 13:28:59 +00:00
codex-bot 4d17231f1f Verify ICLR 2020 legacy forum identities before importing submission history
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2026-11-06 21:19:10 +08:00
42 changed files with 2459 additions and 79 deletions
+8 -2
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@@ -30,11 +30,16 @@ jobs:
if len(candidates)!=1:
raise SystemExit('Unexpected repository archive layout')
src = candidates[0].parent
subprocess.run(['python3','-B','-m','unittest','discover','-s','tests','-t','.','-v'],cwd=src,check=True)
# Build and installation checks run only on the approved remote runner.
venv = root / 'venv'
subprocess.run(['python3','-B','-m','venv','--system-site-packages',str(venv)],check=True)
python = str(venv / 'bin/python')
subprocess.run([python,'-B','-m','pip','install','--only-binary=:all:','--no-compile','psycopg[binary]==3.3.8'],check=True)
testenv = os.environ.copy()
service_file = pathlib.Path('/etc/paper-atlas/pg_service.conf')
if service_file.is_file():
testenv.update(PGSERVICEFILE=str(service_file),PAPER_ATLAS_TEST_PG_SERVICE='foundry-research')
subprocess.run([python,'-B','-m','unittest','discover','-s','tests','-t','.','-v'],cwd=src,env=testenv,check=True)
wheels = root / 'wheels'
subprocess.run([python,'-B','-m','pip','wheel','--no-deps','--wheel-dir',str(wheels),str(src)],check=True)
wheel, = wheels.glob('paper_atlas-*.whl')
@@ -43,7 +48,8 @@ jobs:
outside.mkdir()
subprocess.run([str(venv/'bin/paper-atlas'),'--help'],cwd=outside,check=True)
subprocess.run([python,'-I','-B','-m','paper_atlas','collect','cvf','--help'],cwd=outside,check=True)
smoke = "from paper_atlas.db.store import Store; from paper_atlas.config import DEFAULT_REGISTRY; import json; assert len(json.loads(DEFAULT_REGISTRY.read_text())['venues'])==41; s=Store('installed.sqlite'); s.conn.close()"
subprocess.run([python,'-I','-B','-m','paper_atlas','maintain','postgres','--help'],cwd=outside,check=True)
smoke = "from paper_atlas.db.store import Store; from paper_atlas.config import DEFAULT_REGISTRY; import json; assert {'COLM','MM','MLSys'} <= {v['acronym'] for v in json.loads(DEFAULT_REGISTRY.read_text())['venues']}; s=Store('installed.sqlite'); s.conn.close()"
subprocess.run([python,'-I','-B','-c',smoke],cwd=outside,check=True)
subprocess.run([python,'-I','-B','-m','paper_atlas','query','--db','installed.sqlite','--stats'],cwd=outside,check=True)
PY
+9 -6
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@@ -2,9 +2,9 @@
**长期维护、按需运行的论文元数据与公开投稿历史工具。**
Paper Atlas 将 arXiv、AI 会议论文集及公开投稿决定整理到可追溯的 SQLite 数据库中,用于查询和后续研究分析。它按批次运行,不需要常驻 Web 服务;采集标题、摘要、标识、标签及决定证据,不下载论文全文。
Paper Atlas 将 arXiv、AI 会议论文集及公开投稿决定整理到可追溯的数据库中,用于查询和后续研究分析。生产数据使用 PostgreSQL,支持从既有 SQLite 索引完整迁移;SQLite 保留离线核验和小型样本用途。它按批次运行,不需要常驻 Web 服务;采集标题、摘要、标识、标签及决定证据,不下载论文全文。
项目仍在建设中。候选范围包含 41 个会议,尚未完成全部历史数据和最终去重复核。实际进度以数据库、来源清单和覆盖报告为准,而不是仓库文件数量。
项目仍在建设中。候选范围包含 43 个会议(含 ACM MM、MLSys),尚未完成全部历史数据和最终去重复核。实际进度以数据库、来源清单和覆盖报告为准,而不是仓库文件数量。
## 项目结构
@@ -14,6 +14,7 @@ paper_atlas/
collectors/ 各来源采集与目录盘点
ingestion/ 导入、身份回填与单写入协调
db/ 数据模型、身份解析与 SQL schema
postgres/ PostgreSQL 迁移、原生全文索引和只读连接
audits/ 来源核验和覆盖报告
io/ 网络、快照下载、HTML 与 Git 元数据读取
resources/ 候选会议目录
@@ -30,7 +31,7 @@ pyproject.toml 包元数据、依赖和命令注册
```sh
python3 -m venv .venv
.venv/bin/python -m pip install .
.venv/bin/python -m pip install '.[postgres]'
source .venv/bin/activate
paper-atlas --help
```
@@ -41,13 +42,13 @@ paper-atlas --help
```sh
# 查看当前入库量;不同平台记录数不等于独立论文数
paper-atlas query --db /data/paper-index/papers.sqlite --stats
PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas query --pg-service foundry-research --stats
# 查询标题与摘要
paper-atlas query --db /data/paper-index/papers.sqlite --query '"language model"'
PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas query --pg-service foundry-research --query '"language model"'
# 查看一篇论文的来源、标签和所有已知投稿历史
paper-atlas query --db /data/paper-index/papers.sqlite --paper 123
PGSERVICEFILE=/etc/paper-atlas/pg_service.conf paper-atlas query --pg-service foundry-research --paper 123
# 列出全部目标会议,包括尚未入库的项目
paper-atlas coverage --db /data/paper-index/papers.sqlite \
@@ -60,6 +61,8 @@ paper-atlas collect colm --cache /data/paper-index/raw/http-cache \
`paper-atlas collect --help` 查看来源;`paper-atlas import --help` 查看导入方式。完整批次步骤见[使用指南](docs/usage.md)。
共享实例名为 `foundry-postgres`,数据位于 `foundry_data` 库的 `research` schema;其他项目可按权限复用同一组表。库名通过 libpq service 配置、schema 通过 search_path 或 `--pg-schema` 指定,不写死在查询中。PostgreSQL 凭据放在服务器权限为 `0600` 的 libpq service 文件中;命令行只使用服务名称。`paper-atlas maintain postgres --help` 提供迁移入口:先完整核验 21 张业务表,再发布目标 schema。SQLite FTS5 内部表由 PostgreSQL GIN 索引替代。切换后 SQLite 为备份,不能继续用旧导入器写入它;后续生产导入须适配 PostgreSQL,不能把 SQLite 更新当作生产更新。
## 数据如何组织
- **论文和投稿分开。** 一篇论文可以多次投稿;某次被拒、后来在其他会议录用,两段历史都保留。
+49
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@@ -16,6 +16,8 @@
- [ACL Anthology 权威 XML 与 API](https://aclanthology.org/info/development/)
- [NeurIPS](https://proceedings.neurips.cc/)
- [COLM](https://proceedings.colm.cc/)
- [MLSys](https://proceedings.mlsys.org/)
- [ACM Multimedia 历史目录](https://dblp.org/db/conf/mm/index.html)
- [CVF](https://openaccess.thecvf.com/)
- [ECVA](https://www.ecva.net/papers.php)
- [IJCAI](https://www.ijcai.org/all_proceedings/)
@@ -29,6 +31,7 @@
| 机器学习、理论 | NeurIPS、ICML、ICLR、COLM、COLT、AISTATS、UAI、CLeaR | OpenReview、PMLR、NeurIPS、COLM 官方论文集 |
| 自然语言 | ACL、EMNLP、NAACL、EACL、COLING、CoNLL | ACL Anthology |
| 视觉 | CVPR、ICCV、ECCV | CVF、ECVA |
| 多模态与机器学习系统 | ACM MM、MLSys | ACM / DBLP、MLSys 官方论文集 |
| 综合 AI | AAAI、IJCAI、ECAI | 官方论文集、DBLP |
| 检索与数据 | KDD、SIGIR、WWW、WSDM、RecSys、CIKM、ICDM、SDM、ECML-PKDD | 官方出版方、DBLP,具体年份入口待逐项登记 |
| 机器人 | ICRA、IROS、RSS、CoRL | 官方论文集、PMLR、DBLP |
@@ -38,6 +41,23 @@
这些是领域覆盖候选,不构成统一排名,也不能据此声称已全部入库。逐年目录以真实举办届次和正式出版清单为准:双年会议不补造不存在的年份;主会、Findings、workshop 分开。`edition_sources` 保存实际采集状态,不能用候选名单代替覆盖率报告。
## ACM MM 与 MLSys
会议注册表包含 `MM`(别名 `ACMMM`、`ACM MM`)和 `MLSys`。MLSys 官方根目录目前列出 2019–2026 年的 8 卷,直接采集每篇标题、摘要、公开作者和引用元数据:
```sh
paper-atlas collect mlsys --cache /data/paper-index/raw/http-cache \
--out /data/paper-index/collected/mlsys
```
每年清单核对官方声明数量,缺摘要标为 partial;未知现代轨道、空目录或读取失败不能记为成功。`SysML 2019` 归于同一 MLSys 系列并保留别名。2018 年官方说明接受的投稿为 non-archival,论文集从 2019 年开始;不拼造 2018 年归档卷,也不把未出现在论文集中的投稿判为拒稿。参见 [2018 年官方说明](https://mlsys.org/Conferences/2018/)。
MLSys 老式 `/paper/<year>/hash/…` 与新式 `/paper_files/paper/<year>/hash/…` 链接规范为同一个 `publication_mlsys` 标识,也支持 2023 年实际使用的 `-Abstract-mlsys2023.html` 及对应年份标签;标签年份必须与目录年份一致。DBLP 和官方摘要源共用它,避免同一发表记录成为两个论文实体或两次投稿。只从自身出版社链接提取,不从摘要参考文献提取,也不把发表标识用于合并某次拒稿尝试。共享投稿身份入口要求 MLSys 源具有有效的同年出版社身份,缺失或错年的文件不能生成投稿事件;旧版 DBLP 整理文件可利用已保留的唯一自身出版社链接补得此身份,不需要丢弃来源或依靠标题猜测。
ACM MM 使用固定 DBLP 原始快照和已核验的 proceedings crossref 盘点历史,主会 `ACM Multimedia`、历史编号分卷与同系列 workshop 分开。主会卷也包含 Doctoral Symposium、Reproducibility Companion Papers、Tutorials 等章节(参见 [2025 年目录](https://dblp.org/db/conf/mm/mm2025.html)),而原始 XML 不含逐篇章节,所以这类记录暂标 `proceedings_unspecified`,不能整卷当作 regular 主轨道;后续需逐篇目录证据补齐。旧版候选 JSONL 没有 `mm` / `mlsys` 家族,不能用它假装覆盖新增会议;应从已经下载并校验的原始 XML 重新筛选这两个会议,保留完整扫描数量、卷证据与遗漏原因。DBLP 没有摘要,后续须通过 DOI、真实 forum 等独立标识关联官方或公开元数据,不能将书目导入成功表述为摘要已齐全。
公开拒稿镜像的 `acmmm` 家族映射到 `MM`,只接受明确的负面状态,继续保留镜像与原始签名决定的区别。现有固定 OpenReview 镜像只含 ACM MM 2024 的录用记录,没有据此证明其他年份没有公开拒稿;[2025 年官方 CFP](https://acmmm2025.org/call-for-papers/) 仅说明审稿期间不公开,不能外推为会后永不公开。
## 官方会议元数据采集
```sh
@@ -253,6 +273,25 @@ python3 -B -m paper_atlas query --db /data/paper-index/papers.sqlite \
只将 Conference 来源的论文视为 ICLR 主会录用,排除 Blog 和期刊转会展示,并在审计清单保存排除计数。2020/2021 旧数据允许依据官方主会 paper program 形成录用证据;无 forum ID 时保留 program 身份和匹配候选,不伪造标识。历史年度返回 404 会登记 unavailable,未来未发表届次登记 not_yet_published,其他访问或解析失败登记 blocked;这些状态都不能宣称该年已覆盖。
ICLR 2020 的现代程序 JSON 没有真实 forum 链接,数字 event ID 也不能拼接为旧版海报地址。该年未核验身份的记录先使用官方 Papers 索引地址。旧版官方页面实际引用的 [papers.json](https://iclr.cc/virtual_2020/papers.json) 提供 687 个 forum;可用固定大小及 SHA-256 校验的副本进行独立身份核对:
```sh
paper-atlas download --url https://iclr.cc/virtual_2020/papers.json \
--output /data/paper-index/raw/iclr-2020-legacy-papers.json \
--expected-bytes 391687 \
--sha256 2405f2da6e2641fa600762f7d7cdf7c9d27f4d0ae65799168f3aee46036d30d2
paper-atlas audit iclr-legacy \
--program /data/paper-index/collected/iclr-program-2020-main.jsonl \
--snapshot /data/paper-index/collected/openreview-snapshot-2020-main.jsonl \
--legacy /data/paper-index/raw/iclr-2020-legacy-papers.json \
--out /data/paper-index/collected/iclr-2020-verified
```
核对同时要求同届公开录用、唯一投稿编号和官方 forum 清单一致;编号只是候选关联,还必须有独立的标题/摘要/公开作者证据。旧版作者缩写或姓名格式差异不会放宽全库作者匹配规则。一篇 Explain Your Move 有三个来源中的三种标题,使用逐个核对的精确标题组合及至少两名共同公开作者作例外,不启用通用模糊标题合并。
输出保留原 `2020/program-编号` 来源 ID、标题、摘要和作者,补充真实 forum、核验证据和旧版官方海报 URL。它不写数据库,也不修改输入文件。先在维护锁下使用输出的 `iclr-2020-backfill-queue.json` 给已有程序投稿回填身份,再导入核验后的程序文件与原始投稿快照;这样补充拒稿不会把已有录用事件再建一次。`iclr-2020-snapshot-queue.json` 和审计报告均记录待用文件的哈希,合并前仍须复核。
主题、关键词使用 `iclr_program:topic`、`iclr_program:keyword` 命名空间。通用导入器按源记录刷新标签证据,保留同一论文其他源记录及 `custom:*` 标签。每年的 JSONL、manifest、`iclr-program-year-status.json` 和 `iclr-program-last-run.json` 保存实际范围、独立展示数、主会展示数、论文数、缺失摘要与缺失 forum 数。录用程序不能提供拒稿全集,公开投稿及拒稿补充仍需独立来源。
### CVF / ECVA 视觉会议元数据
@@ -281,3 +320,13 @@ paper-atlas collect cvf --cache /data/paper-index/raw/http-cache \
```
parser_version 2 的清单还保存实际遍历的 index_urls、入口错误及缺失摘要页面。补采结果经过清单与身份核验后才导入,不能因重试任务启动就标记缺口已解决。
## PMLR 中的 ICML 多轨道论文
ICML 2024 起的一个 PMLR 卷可以同时包含研究主轨道与 Position Paper,不能把整卷都标为 `main`。采集器 v3 按轨道输出 `pmlr-v<VOLUME>-main.jsonl`、`pmlr-v<VOLUME>-position.jsonl` 及各自 manifest;卷级 `pmlr-v<VOLUME>.inventory.json` 和目录清单的 `files` 数组列出实际文件。导入队列应展开 `files`,不能假定每卷只有一个 `file`。
2025、2026 年通过出版社元数据的真实 OpenReview forum ID,匹配官方完整节目单中的 `Conference` / `Position_Paper_Track` 来源组;忽略负编号生成的口头报告副本,遇到冲突、缺少身份或未匹配的发表记录停止发布结果。每条记录保存节目单 URL、SHA-256、事件 ID、关联身份及轨道证据。
2024 年的官方节目单把两轨都放在 `Conference`,但提供 PMLR 论文自链接。该年仅采用组织方在 [2025 Position CFP](https://icml.cc/Conferences/2025/CallForPositionPapers) 明确链接的 [2024 Position 论文标题筛选](https://icml.cc/virtual/2024/papers.html?filter=titles&search=position%3A) 规则;同时保存规则页面的哈希。这个规则不用于其他会议或年份。官方节目单将 `guyard24a` 链接误写为 `theo24a`:只对这条已核查的映射额外要求标题精确一致、至少两名公开作者重合,不进行全库模糊匹配。
导入与身份回填拒绝 ICML 2024 起 parser_version<3 或没有官方轨道证据的旧文件。已有主库中的错误轨道需要在独占维护锁内迁移原投稿事件、保留决定与来源关联;仅重新导入拆分文件会留下旧的主轨道事件,不能作为修复方式。完成迁移前,不把新文件直接导入现有库。
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@@ -1,5 +1,31 @@
# 运行维护与数据核验
## PostgreSQL 迁移
共享实例的容器名为 `foundry-postgres`,底层镜像为 `postgres:17-alpine`;Compose 服务名仍为 `postgres`。数据库和 schema 是可配置的逻辑边界,表按研究数据域组织,不按调用项目复制。其他项目可获授 `research` 的 USAGE 及必要表权限,复用相同论文 ID 和表。未来换库只更新 libpq service;换 schema 可更新角色 search_path 或查询的 `--pg-schema`。
复用已确认的现有实例,在共享 `foundry_data` 数据库按数据域使用 `research` schema 和专用角色,不修改其他业务库。安装、测试和构建在已批准的 `ces-control:host` 执行环境运行。libpq service 文件由服务器提供,权限必须为 `0600`,不得放进仓库或带密码的命令行参数。
冻结 SQLite 写入,确认维护进程实际结束、WAL 已清空;采集到独立文件不修改索引。迁移持有源维护锁和目标 advisory lock,还须确保没有绕过协调器的旧版手工写入。
```sh
export PGSERVICEFILE=/etc/paper-atlas/pg_service.conf
paper-atlas maintain postgres \
--db /data/paper-index/papers.sqlite --pg-service foundry-research \
--storage-path /var/lib/docker/volumes/endoleap-dev_postgres/_data \
--min-free-gib 8 --out /data/paper-index/collected/postgres-migration.json
```
全部 21 张业务表保留原 ID、原始 JSON 文本、NULL、来源、投稿、决定、标签出处和合并记录。`sqlite_sequence` 用于重设 PostgreSQL identity 序列,并考虑已合并的历史 ID,避免复用;SQLite FTS5 shadow 表根据完整标题/摘要重建为原生 GIN 索引,不逐字复制引擎文件。
先 COPY 到独立暂存 schema,每张表提交和记录哈希。中断后以同一命令、同一报告路径恢复,必须仍是**完全相同的未变更快照**。不同输入、已发布目标、未清空 WAL、新的未知业务表都会拒绝覆盖;恢复只会清空本次运行尚未完成且尚未发布的暂存表。保留错误现场,不盲目从头复制。
发布前逐表按主键完整回读,比较数量及逐行 SHA-256;建立并验证所有主键、唯一约束、CHECK 和外键,重设序列、建立 GIN 并 ANALYZE。全部通过后原子重命名为 `research` schema,报告才为 `complete`。`copying`、`prepared`、部分表通过或 CI 通过均不代表生产迁移完成,也不替代原任务最后的实体去重和会议覆盖审计。
发布后核对 PostgreSQL 的统计、全文检索、论文详情,以及 reject 后另会 accept 的历史。确认后保留 SQLite 只读备份,并在旁保存 `<SQLite路径>.postgresql-cutover.json`,记录报告路径、源哈希、目标 service/schema;新版本旧写入入口见此标记会拒绝写入。标记不含密码。后续导入适配属于下一阶段,不可继续更新 SQLite 后声称 PostgreSQL 已同步。
远程集成测试通过 `PAPER_ATLAS_TEST_PG_SERVICE` 显式指定,使用随机前缀 schema 并仅清理自己的 fixture;没有该配置时会跳过,应另外报告“未运行”,不能用 SQLite 测试代替 PostgreSQL 验证。
代码以固定 commit 部署,已经启动的任务继续使用其原版本。目录重构不要求迁移数据库,也不更改已有 JSONL 和 manifest 格式。
## arXiv 原始编号与类别证据
@@ -20,6 +46,20 @@ paper-atlas maintain arxiv-tags --db /data/paper-index/papers.sqlite \
修复使用同一维护锁,分批提交并保存断点,保留 `custom:*` 和其他来源证据;失败后确认原因已解决,再增加 `--resume` 从上次提交位置继续。完成报告不能作为重新扫描的断点,重新核验应指定新报告。源审计和标签修复均保留 8 GiB 空闲空间,不能代替所有来源入库后的实体、投稿去重与完整性检查。
修复结束后还须核对每条 arXiv 来源记录的类别集合,不能只看旧证据键是否清零。下面的只读审计比较来源 metadata 中的类别、所属论文实体和逐记录证据键,同时检查没有合法 arXiv 来源的类别行:
```sh
paper-atlas audit arxiv-tags --db /data/paper-index/papers.sqlite \
--repair-report /data/paper-index/collected/arxiv-tag-repair.json \
--out /data/paper-index/collected/arxiv-tag-coverage-audit.json
```
审计持有共享维护锁;修复或其他协调写入尚未结束时会拒绝运行。提供修复报告时,还会核对其已完成状态、数据库路径和固定来源范围。审计以一致的只读快照分批读取,记录完整扫描数量、缺失/多余证据、错误论文归属、残留旧键及少量异常样例,不修改主库。
来源记录按整数主键区间读取,避免 SQLite 误选按 external_id 排列的来源索引、每批重新排序整个来源;其他来源交错在编号区间内时仍按 source_id 过滤。类别证据继续使用 source_record_id 索引批量读取。完整核验范围不因查询优化缩小。
只有全量记录核对完毕且无差异时才标记 `passed`;存在差异为 `failed` 并返回非零退出码,解析或执行中断为 `error`。运行中的报告不能作为完成证明。重新核验须使用新输出路径,不能覆盖已有报告;该检查不替代最后的实体去重、外键、SQLite 与全文索引核验。
## 长期维护与更新
1. 每次采集先核对来源、许可、可访问性、空闲空间和现有运行批次。保持低并发,遵守来源限流、重试与人机验证要求。
@@ -47,3 +87,18 @@ paper-atlas coverage --db /data/paper-index/papers.sqlite \
manifest 和采集器状态清单用于确认文件是否齐全及是否缺摘要;`ingest_runs` 和协调器日志用于确认主库导入是否成功。官方程序、书目目录和公开投稿快照分别保留,未出现在某份清单不等于被拒稿;第三方快照也不能代表平台当前全量状态。代码测试成功不能代替最终全库去重、完整性和逐届覆盖核验。
当前代码与合并状态以 [Pull Requests](https://gitea.entroia.com/Zayden-Jung/paper-atlas/pulls) 为准;CI 结果以对应提交的 Actions 检查为准。工作分支交付后等待用户手动合并。合并代码不自动部署、不自动启动采集,也不代表数据批次已完成。
## 修正已有 PMLR 投稿的轨道
先用采集器 v3 把 ICML 多轨道卷采集到新目录,保留旧文件。以下命令默认只读生成迁移计划;`--inventory` 可重复指定,以完整卷为单位核对,不能只提供 Position 子集:
```sh
paper-atlas maintain pmlr-tracks --db /data/paper-index/papers.sqlite \
--inventory /data/paper-index/collected/pmlr-tracks-v3/pmlr-v235.inventory.json \
--inventory /data/paper-index/collected/pmlr-tracks-v3/pmlr-v267.inventory.json \
--inventory /data/paper-index/collected/pmlr-tracks-v3/pmlr-v306.inventory.json \
--out /data/paper-index/collected/pmlr-track-plan.json
```
检查报告后,在同一命令添加 `--apply` 并使用新的 `--out` 路径执行迁移。计划使用共享维护锁,实际迁移使用独占锁;已有 arXiv 类别修复或其他写入运行时会拒绝启动,不会停止或重启它们。一次事务内核对整个来源集合、原始题目/摘要/作者、forum 身份、已有事件及目标冲突,更新原投稿的 edition 和身份归属,回填官方轨道出处及逐轨道覆盖数,最后复查轨道与外键后提交。论文、来源、投稿、决定的 ID 及决定观察均保留,不重新创建事件、不做实体合并、不改论文正文元数据或标签。
报告记录每个迁移事件的旧 edition、原身份、完整决定观察及新轨道证据。`planned` 是未执行的计划;`complete` 才表示事务已提交;`error` 表示执行失败。若进程在提交前后中断而报告停在 `prepared`,先对照主库和报告核查,不根据日志缺失自行重启任务。新路径重跑会重新核对当前数据库,已正确的轨道不会再次迁移。共享多个来源、重复目标事件或冲突决定会停止迁移,需另行核对,不能直接删掉其中一条。
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@@ -2,6 +2,22 @@
先在已确认的远程环境安装项目,使用 `paper-atlas`。从源码运行时,将命令前缀替换为 `python3 -B -m paper_atlas`,其余参数相同。数据目录位于仓库外。
## PostgreSQL 查询
在远程环境安装 `.[postgres]`,通过权限为 `0600` 的 libpq service 文件连接,不把密码放入 URL、命令行或仓库。
```sh
export PGSERVICEFILE=/etc/paper-atlas/pg_service.conf
paper-atlas query --pg-service foundry-research --stats
paper-atlas query --pg-service foundry-research --query '"language model"' --tag arxiv:category=cs.CL
paper-atlas query --pg-service foundry-research --status rejected --outcome accepted --limit 20
paper-atlas query --pg-service foundry-research --paper 123
```
使用只读一致性事务,支持论文 ID、会议别名、年份、轨道、标签、最新决定和跨会议录用筛选。全文检索使用 PostgreSQL `websearch_to_tsquery('english', ...)`,支持引号短语、`OR` 和减号排除;与 SQLite FTS5 的语法及分词结果不完全相同。JSON 来源列保留原始文本,SQL 分析时可用 `metadata_json::jsonb`、`authors_json::jsonb`。
迁移与切换见[运行维护](operations.md#postgresql-迁移)。下述 SQLite 导入命令仅用于未切换的索引或独立样本;切换后的生产源拒绝旧写入。尚未适配的覆盖审计可只读检查冻结备份,不能当作 PostgreSQL 当前状态。
## 1. 下载固定快照
`paper-atlas download --help` 说明大小、校验和与续传参数。各来源的固定版本与具体命令见[数据源说明](data-sources.md)。下载成功只表示原始文件已核验。
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@@ -0,0 +1,143 @@
"""Compare every arXiv record's category evidence with retained source metadata."""
import argparse
from collections import defaultdict
from contextlib import closing
import fcntl
import json
from pathlib import Path
import sqlite3
from paper_atlas.db.submissions import timestamp
def save(path, state):
part = path.with_suffix('.part')
part.write_text(json.dumps(state, ensure_ascii=False, indent=2) + '\n')
part.replace(path)
def audit(db, out, repair_report=None, batch_size=500):
db, out = Path(db).resolve(), Path(out).resolve()
if not db.is_file():
raise ValueError('Existing database required')
if not 1 <= batch_size <= 500:
raise ValueError('Batch size must be between 1 and 500')
if out == db or repair_report and out == Path(repair_report).resolve():
raise ValueError('Audit output must preserve its inputs')
out.parent.mkdir(parents=True, exist_ok=True)
with Path(str(db) + '.maintenance.lock').open('a') as maintenance, Path(str(out) + '.lock').open('a') as output_lock:
# A partial repair is not a useful full-category audit. This also keeps
# cooperating maintenance writers out for the entire read-only snapshot.
fcntl.flock(maintenance, fcntl.LOCK_SH | fcntl.LOCK_NB)
fcntl.flock(output_lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
if out.exists():
raise ValueError('Audit report exists; select a new output path')
with closing(sqlite3.connect(db.as_uri() + '?mode=ro', uri=True)) as c:
c.execute('PRAGMA cache_size=-32768')
c.execute('BEGIN')
source = c.execute("SELECT id FROM sources WHERE name='arxiv'").fetchone()
if source is None:
raise ValueError('No imported arXiv source')
total, maximum = c.execute('SELECT count(*),COALESCE(max(id),0) FROM source_records WHERE source_id=?', source).fetchone()
if not total:
raise ValueError('No imported arXiv records')
scope = {'db': str(db), 'source_id': source[0], 'source_record_count': total,
'maximum_source_record_id': maximum}
if repair_report:
repair = json.loads(Path(repair_report).read_text())
if repair.get('status') != 'complete' or repair.get('records_refreshed') != total:
raise ValueError('Category repair has not completed this source inventory')
if any(repair.get(key) != value for key, value in scope.items()):
raise ValueError('Repair report belongs to a different source inventory')
state = {**scope, 'started_at': timestamp(), 'status': 'running', 'records_checked': 0,
'last_record_id': 0, 'expected_evidence': 0, 'actual_evidence': 0,
'records_with_mismatches': 0, 'missing_evidence': 0, 'unexpected_evidence': 0,
'legacy_evidence': 0, 'examples': [], 'repair_report': str(Path(repair_report).resolve()) if repair_report else None}
save(out, state)
try:
while True:
# The (source_id,external_id) index orders by external ID,
# so choosing it sorts the entire source again per batch.
# This fixed ID interval must use the integer primary key.
records = c.execute('''SELECT id,external_id,paper_id,metadata_json FROM source_records NOT INDEXED
WHERE source_id=? AND id>? AND id<=? ORDER BY id LIMIT ?''',
(source[0], state['last_record_id'], maximum, batch_size)).fetchall()
if not records:
break
ids = [row[0] for row in records]
actual = defaultdict(set)
for record, paper, category, evidence in c.execute('''SELECT pt.source_record_id,pt.paper_id,t.value,pt.evidence_key
FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id WHERE t.namespace='arxiv:category'
AND pt.source_record_id IN (''' + ','.join('?' for _ in ids) + ')', ids):
actual[record].add((category, paper, evidence))
state['legacy_evidence'] += evidence == 'arxiv:categories'
for record, external, paper, payload in records:
metadata = json.loads(payload)
if not isinstance(metadata, dict):
raise ValueError('arXiv source metadata must be an object')
categories = metadata.get('categories')
if categories is None:
categories = ''
if not isinstance(categories, str):
raise ValueError('arXiv source categories must be text')
evidence_key = f'arxiv:record:{record}:tags'
expected = {(category, paper, evidence_key) for category in categories.split()}
found = actual[record]
missing, unexpected = expected - found, found - expected
state['expected_evidence'] += len(expected)
state['actual_evidence'] += len(found)
state['missing_evidence'] += len(missing)
state['unexpected_evidence'] += len(unexpected)
if missing or unexpected:
state['records_with_mismatches'] += 1
if len(state['examples']) < 20:
state['examples'].append({'record_id': record, 'external_id': external,
'paper_id': paper, 'missing': sorted(missing), 'unexpected': sorted(unexpected)})
state['records_checked'] += 1
state['last_record_id'] = ids[-1]
if state['records_checked'] % 10000 < len(records):
save(out, state)
print(json.dumps({k: state[k] for k in ('status', 'records_checked', 'source_record_count', 'records_with_mismatches')}), flush=True)
if state['records_checked'] != total:
raise ValueError('Audited record count differs from the fixed source inventory')
# Every category row must also have an arXiv source-record owner.
# The full namespace total catches orphan and wrong-source evidence
# that cannot appear in the per-record traversal above.
all_evidence = c.execute("SELECT count(*) FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id WHERE t.namespace='arxiv:category'").fetchone()[0]
unscoped = all_evidence - state['actual_evidence']
if unscoped < 0:
raise ValueError('Category evidence totals are inconsistent')
state.update(namespace_evidence=all_evidence, evidence_without_arxiv_record=unscoped)
if unscoped:
state['unscoped_examples'] = [dict(zip(('paper_id', 'category', 'source_record_id', 'evidence_key'), row))
for row in c.execute('''SELECT pt.paper_id,t.value,pt.source_record_id,pt.evidence_key
FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id
LEFT JOIN source_records r ON r.id=pt.source_record_id
WHERE t.namespace='arxiv:category' AND (r.source_id IS NULL OR r.source_id<>?) LIMIT 20''', source)]
passed = not state['records_with_mismatches'] and not unscoped
state.update(status='passed' if passed else 'failed', finished_at=timestamp(),
note='Full per-record category, canonical paper and evidence-key equality. '
'Read-only; not a global paper deduplication or full database-integrity audit.')
save(out, state)
except BaseException as error:
state.update(status='error', error=str(error), finished_at=timestamp())
save(out, state)
raise
print(json.dumps(state), flush=True)
return state
def main(argv=None, *, prog=None):
parser = argparse.ArgumentParser(prog=prog)
parser.add_argument('--db', required=True)
parser.add_argument('--out', required=True)
parser.add_argument('--repair-report')
parser.add_argument('--batch-size', type=int, default=500)
args = parser.parse_args(argv)
result = audit(args.db, args.out, args.repair_report, args.batch_size)
if result['status'] != 'passed':
raise SystemExit('arXiv category evidence audit failed; inspect the report')
if __name__ == '__main__':
main()
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@@ -0,0 +1,172 @@
"""Reconcile the 2020 program with independently identified official papers."""
import argparse
from collections import Counter, defaultdict
import copy
import fcntl
import hashlib
import json
from pathlib import Path
import re
import tempfile
from paper_atlas.audits.iclr import load
from paper_atlas.db.store import author_keys, normalized
from paper_atlas.db.submissions import timestamp
LEGACY_URL = 'https://iclr.cc/virtual_2020/papers.json'
LEGACY_SHA256 = '2405f2da6e2641fa600762f7d7cdf7c9d27f4d0ae65799168f3aee46036d30d2'
LEGACY_BYTES = 391687
EXPECTED = 687
# This one paper has three documented titles across the pinned official legacy
# list, current official program, and public submission snapshot. The exception
# also requires independent public-author agreement; it is not fuzzy matching.
REVIEWED_TITLE_VARIANT = {
'forum': 'SJgzLkBKPB',
'program': 'Explain Your Move: Understanding Agent Actions Using Salient and Relevant Feature Attribution',
'legacy': 'Explain Your Move: Understanding Agent Actions Using Focused Feature Saliency',
'snapshot': 'Explain Your Move: Understanding Agent Actions Using Specific and Relevant Feature Attribution',
}
def reconcile(program, snapshot, legacy):
by_number = defaultdict(list)
for row in snapshot.values():
by_number[row['metadata'].get('source_submission_number')].append(row)
legacy_by_forum = {}
for note in legacy:
forum = note.get('forum')
content = note.get('content') or {}
if not isinstance(forum, str) or not re.fullmatch(r'[A-Za-z0-9_-]+', forum):
raise ValueError('Invalid legacy forum identity')
if note.get('id') != forum or content.get('iclr_id') != forum or forum in legacy_by_forum:
raise ValueError('Conflicting or repeated official legacy forum')
if not isinstance(content.get('title'), str) or not content['title'].strip() or not isinstance(content.get('authors'), list):
raise ValueError('Legacy paper lacks title or public authors')
legacy_by_forum[forum] = content
if len(program) != len(legacy_by_forum):
raise ValueError('Official program and legacy inventories differ')
title_counts = Counter(normalized(row['title']) for row in legacy_by_forum.values())
enriched = []
assigned = set()
numbers = set()
evidence_counts = Counter()
for original in program:
if any(original.get(k) != v for k, v in {'source': 'iclr_program', 'venue': 'ICLR', 'year': 2020, 'track': 'main', 'status': 'accepted'}.items()):
raise ValueError('Program record is outside the accepted 2020 main track')
metadata = original.get('metadata') or {}
number = metadata.get('program_source_id')
if metadata.get('program_identity_type') != 'submission' or type(number) is not int or number <= 0 or number in numbers:
raise ValueError('Missing or repeated program submission number')
numbers.add(number)
candidates = by_number[number]
if len(candidates) != 1:
raise ValueError('Submission number is absent or ambiguous in the public snapshot')
submission = candidates[0]
forum = submission['identifiers']['openreview']
if submission['status'] != 'accepted' or forum not in legacy_by_forum or forum in assigned:
raise ValueError('Snapshot acceptance and official forum inventory do not agree')
content = legacy_by_forum[forum]
shared_legacy = len(author_keys(original['authors']) & author_keys(content['authors']))
shared_snapshot = len(author_keys(original['authors']) & author_keys(submission['authors']))
checks = {'legacy_title': normalized(original['title']) == normalized(content['title']),
'snapshot_title': normalized(original['title']) == normalized(submission['title']),
'snapshot_abstract': bool(original.get('abstract')) and original['abstract'].strip() == (submission.get('abstract') or '').strip(),
'two_snapshot_authors': shared_snapshot >= 2}
independent_snapshot = sum(checks[k] for k in ('snapshot_title', 'snapshot_abstract', 'two_snapshot_authors')) >= 2
checks['legacy_title_unique'] = title_counts[normalized(content['title'])] == 1
independent_legacy = checks['legacy_title'] and checks['legacy_title_unique'] and shared_legacy >= 1
reviewed_variant = (forum == REVIEWED_TITLE_VARIANT['forum']
and normalized(original['title']) == normalized(REVIEWED_TITLE_VARIANT['program'])
and normalized(content['title']) == normalized(REVIEWED_TITLE_VARIANT['legacy'])
and normalized(submission['title']) == normalized(REVIEWED_TITLE_VARIANT['snapshot'])
and shared_legacy >= 2 and shared_snapshot >= 2)
if not (independent_snapshot or independent_legacy or reviewed_variant):
raise ValueError('Submission number alone cannot establish forum identity: ' + original['external_id'])
own = original.get('identifiers') or {}
if own.get('openreview') not in (None, forum):
raise ValueError('Existing program forum conflicts with independent evidence')
row = copy.deepcopy(original)
row['identifiers'] = {**own, 'openreview': forum}
row['url'] = 'https://iclr.cc/virtual_2020/poster_' + forum + '.html'
row['metadata'].update(identity_state='forum', program_submission_number_verified=True,
program_identity_verification={'method': 'official_legacy_and_public_submission_crosscheck',
'legacy_url': LEGACY_URL, 'legacy_sha256': LEGACY_SHA256,
'original_program_url': original['url'], 'legacy_forum': forum,
'checks': checks, 'shared_legacy_authors': shared_legacy,
'shared_snapshot_authors': shared_snapshot, 'reviewed_title_variant': reviewed_variant})
enriched.append(row)
assigned.add(forum)
evidence_counts.update({'independent_snapshot': int(independent_snapshot),
'independent_legacy': int(independent_legacy),
'reviewed_title_variant': int(reviewed_variant)})
if assigned != legacy_by_forum.keys():
raise ValueError('Unmatched official legacy forum identities remain')
if assigned != {forum for forum, row in snapshot.items() if row['status'] == 'accepted'}:
raise ValueError('Accepted snapshot forum inventory differs from the official program')
return enriched, dict(evidence_counts)
def audit(program_path, snapshot_path, legacy_path, out):
program_path, snapshot_path, legacy_path = map(lambda p: Path(p).resolve(), (program_path, snapshot_path, legacy_path))
raw = legacy_path.read_bytes()
if len(raw) != LEGACY_BYTES or hashlib.sha256(raw).hexdigest() != LEGACY_SHA256:
raise ValueError('Official legacy snapshot checksum mismatch')
legacy = json.loads(raw)
if not isinstance(legacy, list) or len(legacy) != EXPECTED:
raise ValueError('Official legacy count mismatch')
manifest = json.loads(program_path.with_suffix('.manifest.json').read_text())
if manifest.get('parser_version', 0) < 2 or any(manifest.get(k) != v for k, v in {'source': 'iclr_program', 'venue': 'ICLR', 'year': 2020, 'track': 'main', 'count': EXPECTED}.items()):
raise ValueError('Invalid collected program inventory')
program_bytes = program_path.read_bytes()
program = [json.loads(line) for line in program_bytes.splitlines()]
if len(program) != EXPECTED or len({r['external_id'] for r in program}) != EXPECTED:
raise ValueError('Program count or source identity mismatch')
snapshot, snapshot_manifest, snapshot_sha = load(snapshot_path, 'openreview_snapshot', 2020)
rows, checks = reconcile(program, snapshot, legacy)
out = Path(out).resolve()
if out / 'iclr-program-2020-main.jsonl' in (program_path, snapshot_path, legacy_path):
raise ValueError('Output must preserve the original input files')
out.mkdir(parents=True, exist_ok=True)
with (out / 'iclr-legacy.lock').open('a') as lock:
fcntl.flock(lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
if (out / 'iclr-2020-identity-audit.json').exists():
raise ValueError('Completed identity audit exists; choose a new output directory')
with tempfile.TemporaryDirectory(prefix='.iclr-legacy-', dir=out) as temporary:
stage = Path(temporary)
path = stage / 'iclr-program-2020-main.jsonl'
path.write_text(''.join(json.dumps(row, ensure_ascii=False) + '\n' for row in rows))
digest = hashlib.sha256(path.read_bytes()).hexdigest()
manifest.update(parser_version=3, file=str(out / path.name), file_sha256=digest,
missing_forum_count=0, legacy_identity_sha256=LEGACY_SHA256)
path.with_suffix('.manifest.json').write_text(json.dumps(manifest, indent=2) + '\n')
backfill = {'files': [str(out / path.name)], 'file_sha256': {str(out / path.name): digest}}
snapshots = {'files': [str(snapshot_path)], 'file_sha256': {str(snapshot_path): snapshot_sha}}
result = {'year': 2020, 'checked_at': timestamp(), 'program_records': len(rows),
'snapshot_records': len(snapshot), 'snapshot_status_counts': snapshot_manifest['submission_status_counts'],
'legacy_url': LEGACY_URL, 'legacy_sha256': LEGACY_SHA256,
'program_input_sha256': hashlib.sha256(program_bytes).hexdigest(),
'corroboration_counts': checks, 'backfill_queue': backfill, 'snapshot_files': snapshots,
'note': 'No database writes. Backfill existing program identities before importing the snapshot; source IDs, titles and abstracts are preserved.'}
(stage / 'iclr-2020-backfill-queue.json').write_text(json.dumps(backfill, indent=2) + '\n')
(stage / 'iclr-2020-snapshot-queue.json').write_text(json.dumps(snapshots, indent=2) + '\n')
report = stage / 'iclr-2020-identity-audit.json'
report.write_text(json.dumps(result, ensure_ascii=False, indent=2) + '\n')
for child in sorted(stage.iterdir(), key=lambda child: child == report):
child.replace(out / child.name)
print(json.dumps(result), flush=True)
return result
def main(argv=None, *, prog=None):
parser = argparse.ArgumentParser(prog=prog)
parser.add_argument('--program', required=True)
parser.add_argument('--snapshot', required=True)
parser.add_argument('--legacy', required=True)
parser.add_argument('--out', required=True)
args = parser.parse_args(argv)
audit(args.program, args.snapshot, args.legacy, args.out)
if __name__ == '__main__':
main()
+5
View File
@@ -18,6 +18,7 @@ COMMANDS = {
('collect','peerread'): ('paper_atlas.collectors.peerread', {}, 'PeerRead 历史决定补充'),
('collect','colm'): ('paper_atlas.collectors.proceedings', {'source':'colm'}, 'COLM 官方论文集'),
('collect','neurips'): ('paper_atlas.collectors.proceedings', {'source':'neurips'}, 'NeurIPS 官方论文集'),
('collect','mlsys'): ('paper_atlas.collectors.proceedings', {'source':'mlsys'}, 'MLSys 官方历年标题与摘要'),
('collect','cvf'): ('paper_atlas.collectors.vision', {'source':'cvf'}, 'CVPR / ICCV 官方开放目录'),
('collect','ecva'): ('paper_atlas.collectors.vision', {'source':'ecva'}, 'ECCV 官方开放目录'),
('collect','dblp'): ('paper_atlas.collectors.dblp_records', {}, '核对并整理 DBLP 历史发表记录'),
@@ -27,8 +28,12 @@ COMMANDS = {
('maintain','merge'): ('paper_atlas.ingestion.maintenance', {}, '协调单写入合并与恢复'),
('maintain','backfill'): ('paper_atlas.ingestion.backfill', {}, '回填既有投稿的来源身份'),
('maintain','arxiv-tags'): ('paper_atlas.ingestion.arxiv_tags', {}, '恢复逐来源记录的 arXiv 类别证据'),
('maintain','pmlr-tracks'): ('paper_atlas.ingestion.pmlr_tracks', {}, '核对并迁移既有 PMLR 投稿轨道'),
('maintain','postgres'): ('paper_atlas.postgres.migration', {}, '迁移 SQLite 完整业务数据并核验 PostgreSQL'),
('audit','iclr'): ('paper_atlas.audits.iclr', {}, '核对 ICLR 快照与同届官方程序'),
('audit','iclr-legacy'): ('paper_atlas.audits.iclr_legacy', {}, '独立核验 ICLR 2020 旧目录投稿身份'),
('audit','arxiv'): ('paper_atlas.audits.arxiv', {}, '核验 arXiv 原始编号、重复行与 ZIP 完整性'),
('audit','arxiv-tags'): ('paper_atlas.audits.arxiv_tags', {}, '逐记录核验 arXiv 类别及出处完整性'),
('audit','public-openreview'): ('paper_atlas.audits.public_openreview', {}, '核对公开负面决定与已有投稿历史'),
}
+1 -1
View File
@@ -20,7 +20,7 @@ DTD_MD5='96e4283e71886dec2173718957293648'
DTD_NAMES={'dblp.dtd','dblp-2023-06-28.dtd'}
RELEASE='https://doi.org/10.4230/dblp.xml.2026-11-01'
# Broad discovery candidates, including historical names; not a venue mapping.
FAMILIES=set('nips icml iclr colm colt aistats uai clear acl emnlp naacl eacl coling conll cvpr iccv eccv aaai ijcai ecai kdd sigir www wsdm recsys cikm icdm sdm ecml pkdd ecmlpkdd icra iros rss corl aips icaps kr atal aamas icassp interspeech eurospeech icslp ismir miccai fat facct lrec'.split())
FAMILIES=set('nips icml iclr colm colt aistats uai clear acl emnlp naacl eacl coling conll cvpr iccv eccv aaai ijcai ecai kdd sigir www wsdm recsys cikm icdm sdm ecml pkdd ecmlpkdd icra iros rss corl aips icaps kr atal aamas icassp interspeech eurospeech icslp ismir miccai fat facct lrec mm mlsys'.split())
def records(archive,dtd_bytes):
+15 -3
View File
@@ -17,6 +17,7 @@ from paper_atlas.collectors.dblp import XML_SHA,DTD_MD5,RELEASE,records
from paper_atlas.collectors.dblp_scope import scope
from paper_atlas.db.submissions import timestamp
from paper_atlas.io.snapshots import digest_file
from paper_atlas.io.publication_ids import mlsys_id
AS_OF='2026-11-01T00:00:00.000Z'
MATERIAL_PART=r'(?:title(?: page)?|preface|foreword|editorial|front\s?matter|back\s?matter|(?:table of )?contents|(?:author |subject )?index|contributors|(?:conference |program |organizing |steering )?committee|conference organization|reviewers)'
@@ -36,8 +37,10 @@ def material_reason(title,authors,key,year,track):
def identifiers(fields):
dois=set();arxiv=set();forums=set()
dois=set();arxiv=set();forums=set();mlsys=set()
for link in fields.get('ee',[]):
if own_mlsys := mlsys_id(link):
mlsys.add(own_mlsys)
parsed=urlsplit(link);path=unquote(parsed.path)
doi=None
if parsed.netloc in ('doi.org','dx.doi.org','doi.ieeecomputersociety.org'):doi=path.lstrip('/')
@@ -57,9 +60,10 @@ def identifiers(fields):
if match:arxiv.add(re.sub(r'v\d+$','',match[1]))
publications={doi for doi in dois if not doi.startswith('10.48550/arxiv.')}
own={}
for scheme,values in (('doi',publications),('arxiv',arxiv),('openreview',forums)):
groups=(('doi',publications),('arxiv',arxiv),('openreview',forums),('publication_mlsys',mlsys))
for scheme,values in groups:
if len(values)==1:own[scheme]=next(iter(values))
ambiguous={scheme:sorted(values) for scheme,values in (('doi',publications),('arxiv',arxiv),('openreview',forums)) if len(values)>1}
ambiguous={scheme:sorted(values) for scheme,values in groups if len(values)>1}
return own,ambiguous
@@ -84,6 +88,8 @@ def normalize_row(row,volumes,targets,include_workshops=False,through_year=2026)
'scope_rule':edition['rule'],'author_names_raw':fields.get('author',[]),'publtype':row.get('publtype'),
'bibliography':{key:value for key,value in fields.items() if key in ('booktitle','year','ee','url','pages','volume','number','publisher','series','isbn')},
'ambiguous_identifiers':ambiguous,'publication_evidence':'inproceedings bibliography; not an original decision note'}
if edition.get('track_scope_note'):
metadata['track_scope_note']=edition['track_scope_note']
flagged=bool(re.search(r'\b(?:withdrawn|retracted)\b',row.get('publtype') or '',re.I))
result={'source':'dblp','external_id':row['key'],'url':'https://dblp.org/rec/'+row['key']+'.html',
'title':title,'abstract':None,'authors':authors,'identifiers':own,
@@ -110,6 +116,12 @@ def collect(catalogue,out,venues=None,candidates=None,archive=None,dtd=None,incl
allowed={row['acronym'].casefold():row['acronym'] for row in json.loads(DEFAULT_REGISTRY.read_text())['venues']}
if venues and set(name.casefold() for name in venues)-allowed.keys():raise ValueError('Unknown registry venue')
targets={allowed[name.casefold()] for name in venues} if venues else set(allowed.values())
if candidates:
families = manifest.get('candidate_family_counts', {})
missing = [venue for venue, family in [('MM', 'mm'), ('MLSys', 'mlsys')]
if venue in targets and not families.get(family)]
if missing:
raise ValueError('Candidate file predates requested families ' + ', '.join(missing) + '; use the original --archive')
out=Path(out);out.mkdir(parents=True,exist_ok=True)
with (out/'dblp.normalize.lock').open('a') as lock:
fcntl.flock(lock,fcntl.LOCK_EX|fcntl.LOCK_NB)
+12 -2
View File
@@ -33,6 +33,8 @@ BOOKS = {
'interspeech':[('INTERSPEECH','INTERSPEECH',[]),('EUROSPEECH','EUROSPEECH',['INTERSPEECH']),('ICSLP','ICSLP',['INTERSPEECH']),('ECST','ECST',['INTERSPEECH'])],
'ismir':[('ISMIR','ISMIR',[])], 'miccai':[('MICCAI','MICCAI',[])],
'fat':[('FAccT','FAccT',[]),('FAT*','FAccT',[]),('FAT','FAccT',[])],
'mm':[('ACM Multimedia','MM',['ACMMM','ACM MM'])],
'mlsys':[('MLSys','MLSys',[]),('SysML','MLSys',['SysML'])],
}
@@ -45,6 +47,7 @@ def scope(row,volume,through_year=2026):
if not volume:return None,'missing_proceedings'
title=' '.join(volume['fields'].get('title',[]))
if family=='clear2' and 'causal learning and reasoning' not in title.casefold():return None,'ambiguous_venue_name'
if family=='mlsys' and 'machine learning and systems' not in title.casefold():return None,'ambiguous_venue_name'
matched=None
for base,venue,aliases in BOOKS[family]:
match=re.fullmatch(re.escape(base)+r'(?:\s+\((.*)\)|\s+(.*)|,\s*(Vol\.\s*\d+))?',book,re.I)
@@ -67,6 +70,7 @@ def scope(row,volume,through_year=2026):
if year%100!=int(short[1]):return None,'unverified_edition_year'
year_basis='unique explicit event year in proceedings title, corroborated by two-digit proceedings key'
if year>through_year:return None,'future_edition'
if venue=='MLSys' and year<2019:return None,'nonarchival_predecessor'
bibliographic=fields.get('year',[])
if len(bibliographic)!=1 or not re.fullmatch(r'\d{4}',bibliographic[0]):return None,'ambiguous_bibliographic_year'
if int(bibliographic[0])!=year and not re.search(r'\b'+str(year)+r'\b',title):return None,'unverified_year_difference'
@@ -92,5 +96,11 @@ def scope(row,volume,through_year=2026):
elif suffix.casefold() in ('poster','posters') and venue not in ('ICLR','ACL','EMNLP','NAACL','EACL','COLING','CoNLL'):track='poster'
if venue=='AAAI+IAAI':track='proceedings_unspecified'
if venue=='AAMAS' and year<2002:return None,'predecessor_not_aamas'
return {'venue':venue,'venue_aliases':aliases,'year':year,'track':track,'bibliographic_year':int(bibliographic[0]),
'rule':family+':'+base,'proceedings_title':title,'edition_year_basis':year_basis},None
result = {'venue':venue,'venue_aliases':aliases,'year':year,'track':track,'bibliographic_year':int(bibliographic[0]),
'rule':family+':'+base,'proceedings_title':title,'edition_year_basis':year_basis}
if venue=='MM' and track=='main':
# A main MM volume also includes doctoral, tutorials, companion papers
# and other sections. DBLP XML omits the per-paper TOC section.
result['track']='proceedings_unspecified'
result['track_scope_note']='Main proceedings volume; per-paper section is absent from the bibliography. Do not infer a regular research track.'
return result,None
+4
View File
@@ -141,6 +141,10 @@ def parse_program(data, abstracts, year, index_url):
external = f'{year}/{forum}' if forum else f'{year}/program-{identity[1]}'
missing_identity += not bool(forum)
page = urljoin(ROOT, primary.get('virtualsite_url') or f'/virtual/{year}/{str(primary.get("eventtype", "Poster")).lower()}/{primary["id"]}')
if year == 2020 and not primary.get('virtualsite_url'):
# Numeric modern event IDs do not identify legacy poster pages.
# The independently verified forum bridge supplies the paper URL.
page = index_url
topics = sorted({str(row['topic']).strip() for row in group if row.get('topic')})
keywords = sorted({str(keyword).strip() for row in group for keyword in row.get('keywords', []) if keyword})
records.append({'source': SOURCE, 'external_id': external, 'url': page,
+80 -45
View File
@@ -1,5 +1,7 @@
"""Collect official PMLR metadata, never the PDFs linked by the metadata."""
import argparse
from collections import defaultdict
import hashlib
from paper_atlas.config import DEFAULT_REGISTRY
import io
import json
@@ -8,6 +10,7 @@ import os
import subprocess
import tarfile
import time
import tempfile
from pathlib import Path
import yaml
@@ -37,6 +40,7 @@ def venue_key(shortname):
from paper_atlas.io.http import fetch
from paper_atlas.collectors.pmlr_tracks import collect_track_evidence, record_track
def metadata_texts(volume,cache):
@@ -98,57 +102,88 @@ def collect_volume(volume,cache,out,allowed=None):
track = 'workshop' if 'workshop' in title.lower() else 'main'
path = Path(out)/f'pmlr-v{volume}.jsonl'
path.parent.mkdir(parents=True,exist_ok=True)
part = path.with_suffix('.part')
mixed_icml = venue == 'ICML' and year >= 2024
mapping, track_program = collect_track_evidence(year, cache) if mixed_icml else ({}, None)
records = {}
duplicate_posts = 0
with part.open('w') as output:
for member_name,content in metadata_texts(volume,cache):
parts = re.split(r'(?m)^---\s*$',content,maxsplit=2)
if len(parts)<3 or parts[0].strip():
raise RuntimeError('Missing YAML frontmatter: '+member_name)
row = load_metadata(parts[1])
if row.get('layout') not in ('inproceedings','article'):
continue
if not row.get('title'):
raise ValueError('Paper metadata has no title: '+member_name)
if not row.get('id'):
raise ValueError('Paper metadata has no publication ID: '+member_name)
external = f"v{volume}/{row['id']}"
ids = {}
for key in ('doi','openreview','arxiv'):
value = row.get(key)
if value:
value = str(value)
if key=='arxiv':
value = re.sub(r'^https?://arxiv.org/(abs|pdf)/','',value).removesuffix('.pdf')
if key=='openreview':
value = value.split('id=')[-1].split('&')[0]
ids[key] = value
record = {'source':'pmlr','external_id':external,'url':f"https://proceedings.mlr.press/v{volume}/{row.get('id')}.html",'title':row['title'],'abstract':row.get('abstract'),'authors':row.get('author',[]),'identifiers':ids,'venue':venue,'year':year,'track':track,'status':'accepted','list_url':f'https://proceedings.mlr.press/v{volume}/','metadata':{key:row[key] for key in ('id','volume','date','page','doi','openreview','arxiv','publisher') if key in row}}
version={'path':member_name,'date':row.get('date')}
if external in records:
previous=records[external]
if ({k:v for k,v in previous.items() if k!='metadata'} != {k:v for k,v in record.items() if k!='metadata'}
or {k:v for k,v in previous['metadata'].items() if k not in ('date','source_versions')} != {k:v for k,v in record['metadata'].items() if k!='date'}):
raise ValueError('Conflicting metadata posts share a publication ID: '+external)
previous['metadata']['source_versions'].append(version)
if str(row.get('date') or '')>str(previous['metadata'].get('date') or ''):
previous['metadata']['date']=row['date']
duplicate_posts+=1
continue
record['metadata']['source_versions']=[version]
records[external]=record
for record in records.values():
output.write(json.dumps(record,ensure_ascii=False,default=str)+'\n')
for member_name,content in metadata_texts(volume,cache):
parts = re.split(r'(?m)^---\s*$',content,maxsplit=2)
if len(parts)<3 or parts[0].strip():
raise RuntimeError('Missing YAML frontmatter: '+member_name)
row = load_metadata(parts[1])
if row.get('layout') not in ('inproceedings','article'):
continue
if not row.get('title'):
raise ValueError('Paper metadata has no title: '+member_name)
if not row.get('id'):
raise ValueError('Paper metadata has no publication ID: '+member_name)
external = f"v{volume}/{row['id']}"
ids = {}
for key in ('doi','openreview','arxiv'):
value = row.get(key)
if value:
value = str(value)
if key=='arxiv':
value = re.sub(r'^https?://arxiv.org/(abs|pdf)/','',value).removesuffix('.pdf')
if key=='openreview':
value = value.split('id=')[-1].split('&')[0]
ids[key] = value
record = {'source':'pmlr','external_id':external,'url':f"https://proceedings.mlr.press/v{volume}/{row.get('id')}.html",'title':row['title'],'abstract':row.get('abstract'),'authors':row.get('author',[]),'identifiers':ids,'venue':venue,'year':year,'track':track,'status':'accepted','list_url':f'https://proceedings.mlr.press/v{volume}/','metadata':{key:row[key] for key in ('id','volume','date','page','doi','openreview','arxiv','publisher') if key in row}}
version={'path':member_name,'date':row.get('date')}
if external in records:
previous=records[external]
if ({k:v for k,v in previous.items() if k!='metadata'} != {k:v for k,v in record.items() if k!='metadata'}
or {k:v for k,v in previous['metadata'].items() if k not in ('date','source_versions')} != {k:v for k,v in record['metadata'].items() if k!='date'}):
raise ValueError('Conflicting metadata posts share a publication ID: '+external)
previous['metadata']['source_versions'].append(version)
if str(row.get('date') or '')>str(previous['metadata'].get('date') or ''):
previous['metadata']['date']=row['date']
duplicate_posts+=1
continue
record['metadata']['source_versions']=[version]
records[external]=record
count=len(records)
missing_abstracts=sum(not (record.get('abstract') or '').strip() for record in records.values())
if count==0:
part.unlink(missing_ok=True)
raise RuntimeError('No papers parsed; refusing an empty successful collection')
part.replace(path)
result = {'source':'pmlr','parser_version':2,'venue':venue,'year':year,'track':track,'volume':volume,'count':count,'metadata_post_count':count+duplicate_posts,'duplicate_post_count':duplicate_posts,'missing_abstract_count':missing_abstracts,'list_url':f'https://proceedings.mlr.press/v{volume}/','file':str(path),'status':'partial' if missing_abstracts else 'collected'}
path.with_suffix('.manifest.json').write_text(json.dumps(result,indent=2))
print(json.dumps(result),flush=True)
grouped = defaultdict(list)
for record in records.values():
if mixed_icml:
record_track(record, mapping, track_program)
grouped[record['track']].append(record)
# Parse and verify the entire volume before replacing any published output.
manifests = []
with tempfile.TemporaryDirectory(prefix=f'.pmlr-v{volume}-', dir=path.parent) as temporary:
stage = Path(temporary)
for current_track, rows in sorted(grouped.items()):
filename = f'pmlr-v{volume}-{current_track}.jsonl' if mixed_icml else path.name
output = stage / filename
output.write_text(''.join(json.dumps(row, ensure_ascii=False, default=str)+'\n' for row in rows))
absent = sum(not (row.get('abstract') or '').strip() for row in rows)
manifest = {'source': 'pmlr', 'parser_version': 3, 'venue': venue, 'year': year,
'track': current_track, 'volume': volume, 'count': len(rows),
'missing_abstract_count': absent, 'list_url': f'https://proceedings.mlr.press/v{volume}/',
'file': str(path.parent / filename), 'file_sha256': hashlib.sha256(output.read_bytes()).hexdigest(),
'status': 'partial' if absent else 'collected'}
if track_program:
manifest['track_program'] = track_program
output.with_suffix('.manifest.json').write_text(json.dumps(manifest, indent=2)+'\n')
manifests.append(manifest)
result = {'source': 'pmlr', 'parser_version': 3, 'venue': venue, 'year': year,
'track': next(iter(grouped)) if len(grouped) == 1 else 'mixed', 'volume': volume,
'count': count, 'metadata_post_count': count + duplicate_posts,
'duplicate_post_count': duplicate_posts, 'missing_abstract_count': missing_abstracts,
'list_url': f'https://proceedings.mlr.press/v{volume}/', 'files': manifests,
'status': 'partial' if missing_abstracts else 'collected'}
if len(manifests) == 1:
result['file'] = manifests[0]['file']
if track_program:
result['track_program'] = track_program
inventory = stage / f'pmlr-v{volume}.inventory.json'
inventory.write_text(json.dumps(result, indent=2)+'\n')
for child in sorted(stage.iterdir(), key=lambda child: child == inventory):
child.replace(path.parent / child.name)
print(json.dumps(result), flush=True)
return result
+140
View File
@@ -0,0 +1,140 @@
"""Resolve mixed ICML proceedings tracks from the official paper program."""
from collections import Counter
import hashlib
import json
import re
from urllib.parse import parse_qs, urlsplit
from paper_atlas.collectors.iclr import identifiers, source_number
from paper_atlas.db.store import author_keys, normalized
from paper_atlas.io.html import Document, clean
from paper_atlas.io.http import fetch
POSITION_LIST_POLICY = 'https://icml.cc/Conferences/2025/CallForPositionPapers'
PUBLISHER_LINK_ALIASES = {'v235/theo24a': 'v235/guyard24a'}
def position_list_policy(data):
"""The organizers explicitly link this title filter as the 2024 position list."""
for node in Document(data.decode()).root.walk():
if node.tag != 'a' or clean(node.text()).casefold() != 'position papers':
continue
url = node.attrs.get('href', '')
parsed = urlsplit(url)
query = parse_qs(parsed.query)
if (parsed.netloc in ('', 'icml.cc') and parsed.path == '/virtual/2024/papers.html'
and query.get('filter') == ['titles'] and query.get('search') == ['position:']):
return {'url': POSITION_LIST_POLICY, 'sha256': hashlib.sha256(data).hexdigest(),
'position_list_url': 'https://icml.cc' + parsed.path + '?' + parsed.query}
raise ValueError('Official policy no longer identifies the 2024 position-paper title list')
def program_tracks(data, year, policy=None):
program = json.loads(data)
events = program.get('results') if isinstance(program, dict) else None
if (not isinstance(events, list) or program.get('count') != len(events)
or program.get('next') or program.get('previous')):
raise ValueError('Official ICML program must be a complete counted event list')
if len({str(row['id']) for row in events}) != len(events):
raise ValueError('Repeated event identity in official ICML program')
if year == 2024 and policy is None:
raise ValueError('The 2024 position-list policy is required')
mapping = {}
excluded = Counter()
for row in events:
number = source_number(row)
if number is not None and number < 0:
excluded['synthetic_oral_event'] += 1
continue
parsed = urlsplit(row.get('sourceurl') or '')
group = parse_qs(parsed.query).get('id', [])
groups = {f'ICML.cc/{year}/Conference': 'main',
f'ICML.cc/{year}/Position_Paper_Track': 'position'}
if (parsed.netloc != 'openreview.net' or parsed.path != '/group'
or len(group) != 1 or group[0] not in groups):
excluded['other_source'] += 1
continue
if not str(row.get('decision') or '').casefold().startswith('accept'):
raise ValueError('Non-accepted event in official ICML paper program')
if year == 2024:
# The 2024 program flattens both tracks into Conference and links
# PMLR publication IDs instead of forums. Use only this year-specific,
# organizer-endorsed list rule, never a global title heuristic.
link = urlsplit(row.get('paper_pdf_url') or '')
if link.netloc != 'proceedings.mlr.press' or not re.fullmatch(r'/v\d+/[^/]+\.html', link.path):
raise ValueError('2024 ICML paper has no publisher self-link')
key = ('pmlr', link.path.lstrip('/').removesuffix('.html'))
track = 'position' if re.match(r'^Position(?: Paper)?:', row.get('name') or '', re.I) else 'main'
kind = 'official_2024_position_list'
else:
forum = identifiers(row).get('openreview')
if not forum:
raise ValueError('ICML paper has no real OpenReview self-identity')
key = ('openreview', forum)
track, kind = groups[group[0]], 'official_openreview_track_group'
evidence = {'track': track, 'kind': kind, 'event_ids': [row['id']],
'source_group': group[0], 'program_title': row.get('name')}
if key[0] == 'pmlr' and key[1] in PUBLISHER_LINK_ALIASES:
evidence['publisher_link_alias'] = key[1]
evidence['_authors'] = [author['fullname'] for author in row.get('authors', [])]
key = ('pmlr', PUBLISHER_LINK_ALIASES[key[1]])
if key in mapping:
if mapping[key]['track'] != track:
raise ValueError('One paper identity has conflicting official tracks')
mapping[key]['event_ids'].append(row['id'])
else:
mapping[key] = evidence
if not mapping:
raise ValueError('Official ICML program contains no supported paper identities')
return mapping, {'event_count': len(events), 'paper_identity_count': len(mapping),
'excluded_events': dict(excluded)}
def collect_track_evidence(year, cache):
url = f'https://icml.cc/static/virtual/data/icml-{year}-orals-posters.json'
data = fetch(url, cache)
policy = position_list_policy(fetch(POSITION_LIST_POLICY, cache)) if year == 2024 else None
mapping, inventory = program_tracks(data, year, policy)
provenance = {'url': url, 'sha256': hashlib.sha256(data).hexdigest(), **inventory}
if policy:
provenance['position_list_policy'] = policy
return mapping, provenance
def record_track(record, mapping, provenance):
key = ('pmlr', record['external_id']) if record['year'] == 2024 else ('openreview', record['identifiers'].get('openreview'))
if key not in mapping:
raise ValueError('Published ICML paper is absent from the verified official track inventory: ' + record['external_id'])
evidence = {**mapping[key], 'identity_scheme': key[0], 'identity_value': key[1],
'program_url': provenance['url'], 'program_sha256': provenance['sha256']}
if 'publisher_link_alias' in evidence:
overlap = author_keys(record.get('authors', [])) & author_keys(evidence.pop('_authors', []))
if normalized(record['title']) != normalized(evidence['program_title']) or len(overlap) < 2:
raise ValueError('Reviewed publisher-link alias lacks exact title and independent author corroboration')
evidence['corroborating_author_count'] = len(overlap)
if 'position_list_policy' in provenance:
evidence['position_list_policy'] = provenance['position_list_policy']
record['track'] = evidence['track']
record['metadata']['track_evidence'] = evidence
def require_track_manifest(manifest):
if (manifest.get('source') == 'pmlr' and str(manifest.get('venue', '')).upper() == 'ICML'
and int(manifest.get('year', 0)) >= 2024
and (manifest.get('parser_version', 0) < 3 or not manifest.get('track_program'))):
raise ValueError('Recollect mixed ICML PMLR proceedings with parser_version>=3 and official track evidence')
def require_track_record(row, manifest):
require_track_manifest({**manifest, **{key: row.get(key) for key in ('source', 'venue', 'year')}})
if manifest.get('track_program'):
evidence = row.get('metadata', {}).get('track_evidence', {})
program = manifest['track_program']
if (evidence.get('track') != row.get('track') or evidence.get('program_url') != program.get('url')
or evidence.get('program_sha256') != program.get('sha256')
or not evidence.get('event_ids') or evidence.get('identity_scheme') not in ('pmlr', 'openreview')):
raise ValueError('PMLR record differs from its official track evidence')
own = row['external_id'] if evidence['identity_scheme'] == 'pmlr' else row.get('identifiers', {}).get('openreview')
if not own or evidence.get('identity_value') != own:
raise ValueError('PMLR track evidence belongs to a different paper identity')
+26 -4
View File
@@ -1,4 +1,4 @@
"""Collect COLM/NeurIPS official abstract pages without downloading PDFs."""
"""Collect COLM, NeurIPS and MLSys official metadata without downloading PDFs."""
import argparse
import json
import re
@@ -8,8 +8,11 @@ from pathlib import Path
from urllib.parse import urljoin,urlsplit
from paper_atlas.io.http import fetch
from paper_atlas.io.publication_ids import mlsys_id
ROOTS={'colm':'https://proceedings.colm.cc/','neurips':'https://proceedings.neurips.cc/'}
ROOTS={'colm':'https://proceedings.colm.cc/','neurips':'https://proceedings.neurips.cc/',
'mlsys':'https://proceedings.mlsys.org/'}
VENUES={'colm':'COLM','neurips':'NeurIPS','mlsys':'MLSys'}
from paper_atlas.io.html import Document,Node,clean
@@ -72,6 +75,22 @@ def parse_paper(html,url,source,year,index_url):
track_text=' '.join(clean(n.text()) for n in nodes if 'paper-track' in n.attrs.get('class','').split())
track=track_key(track_text or url)
identifiers={}
if source == 'mlsys':
if year < 2019:
raise ValueError('SysML 2018 was non-archival; official proceedings begin in 2019')
own = mlsys_id(url)
if not own or int(own.split('/')[0]) != year:
raise ValueError('MLSys paper URL does not identify this publication year')
identifiers['publication_mlsys'] = own
if track_text:
explicit = {'conference': 'main', 'main track': 'main', 'research track': 'main',
'industry track': 'industry', 'industrial track': 'industry',
'mlsys' + str(year): 'main'}
if track_text.casefold() not in explicit:
raise ValueError('Unclassified official MLSys track: ' + track_text)
track = explicit[track_text.casefold()]
elif year >= 2025 and not url.endswith('-Abstract-Conference.html'):
raise ValueError('Modern MLSys paper lacks an explicit conference track')
if meta['citation_doi']:
identifiers['doi']=meta['citation_doi'][0]
action_nodes=[]
@@ -90,8 +109,11 @@ def parse_paper(html,url,source,year,index_url):
from urllib.parse import parse_qs
forum=parse_qs(parsed.query).get('id')
if forum: identifiers['openreview']=forum[0]
venue='COLM' if source=='colm' else 'NeurIPS'
return {'source':source,'external_id':urlsplit(url).path,'url':url,'title':clean(title),'abstract':abstract,'authors':authors,'identifiers':identifiers,'venue':venue,'year':year,'track':track,'status':'accepted','raw_decision':'listed in official proceedings','list_url':index_url,'metadata':{'citation':dict(meta),'publication_state':'pre-proceedings' if 'pre-proceedings' in html.lower() else 'proceedings'}}
venue=VENUES[source]
result = {'source':source,'external_id':urlsplit(url).path,'url':url,'title':clean(title),'abstract':abstract,'authors':authors,'identifiers':identifiers,'venue':venue,'year':year,'track':track,'status':'accepted','raw_decision':'listed in official proceedings','list_url':index_url,'metadata':{'citation':dict(meta),'publication_state':'pre-proceedings' if 'pre-proceedings' in html.lower() else 'proceedings'}}
if source == 'mlsys' and year == 2019:
result['venue_aliases'] = ['SysML']
return result
def discover(source,cache):
+1 -1
View File
@@ -85,7 +85,7 @@ def normalize(row, family, year, provenance, include_workshops=False):
if prefixed and (prefixed[1].casefold() != ('neurips' if family == 'nips' else family) or int(prefixed[2]) != year):
raise ValueError('Status label conflicts with source conference year')
allowed = {v['acronym'].casefold(): v['acronym'] for v in json.loads(DEFAULT_REGISTRY.read_text())['venues']}
venue = allowed.get('neurips' if family == 'nips' else family)
venue = allowed.get({'nips': 'neurips', 'acmmm': 'mm'}.get(family, family))
if venue is None:
return None, 'unmapped_venue'
title = row.get('title')
+8
View File
@@ -0,0 +1,8 @@
"""Prevent legacy writers from diverging after an explicit PostgreSQL cutover."""
from pathlib import Path
def require_sqlite_writable(path):
marker = Path(str(Path(path).resolve()) + '.postgresql-cutover.json')
if marker.exists():
raise RuntimeError('This SQLite source was cut over to PostgreSQL; use the configured PostgreSQL database. Marker: ' + str(marker))
+2
View File
@@ -6,6 +6,7 @@ import sqlite3
import unicodedata
from pathlib import Path
from paper_atlas.db.submissions import attach_submission,migrate_sources,write_decision
from paper_atlas.db.backend import require_sqlite_writable
def normalized(value):
@@ -29,6 +30,7 @@ def author_keys(authors):
class Store:
def __init__(self,path):
require_sqlite_writable(path)
self.conn = sqlite3.connect(path,timeout=60)
self.conn.executescript(files('paper_atlas.db').joinpath('schema.sql').read_text())
self.conn.execute('PRAGMA synchronous=NORMAL')
+20 -1
View File
@@ -1,9 +1,10 @@
"""Canonical submission events with independent source and decision evidence."""
from datetime import datetime, timezone
import re
from paper_atlas.io.publication_ids import mlsys_id
PUBLICATIONS={'pmlr','acl_anthology','colm','neurips','cvf','ecva','dblp'}
PUBLICATIONS={'pmlr','acl_anthology','colm','neurips','mlsys','cvf','ecva','dblp'}
def timestamp(value=None):
@@ -15,11 +16,26 @@ def timestamp(value=None):
def identities_for_row(row):
identities=list(row.get('submission_identifiers') or [])
own=row.get('identifiers') or {}
if row['source']=='mlsys':
value=own.get('publication_mlsys')
if (not isinstance(value,str) or not re.fullmatch(str(row['year'])+r'/[a-f0-9]{32}',value)
or row['venue']!='MLSys'):
raise ValueError('Invalid authoritative MLSys publisher identity')
if own.get('openreview'):
identities.append({'scheme':'openreview','value':own['openreview']})
if row['source'] in PUBLICATIONS and row.get('status')=='accepted' and own.get('doi'):
doi=re.sub(r'^https?://(?:dx\.)?doi\.org/','',str(own['doi']),flags=re.I).strip().lower()
if re.fullmatch(r'10\.\d{4,9}/\S+',doi):identities.append({'scheme':'publication_doi','value':doi})
publication_mlsys = own.get('publication_mlsys')
if not publication_mlsys and row['source']=='dblp' and row['venue']=='MLSys':
# Older normalized DBLP files retain their own publisher links even
# when a newly supported historical URL label was not yet parsed.
links = (row.get('metadata') or {}).get('bibliography', {}).get('ee', [])
candidates = {identity for link in links if (identity := mlsys_id(link))}
if len(candidates)==1:
publication_mlsys = candidates.pop()
if row['source'] in PUBLICATIONS and row.get('status')=='accepted' and publication_mlsys:
identities.append({'scheme':'publication_mlsys','value':publication_mlsys})
meta=row.get('metadata') or {}
if row['source']=='iclr_program' and row['venue']=='ICLR' and meta.get('program_identity_type')=='submission' and meta.get('program_submission_number_verified') is True:
identities.append({'scheme':'iclr_number','value':str(meta['program_source_id'])})
@@ -30,6 +46,9 @@ def identities_for_row(row):
valid=re.fullmatch(r'[A-Za-z0-9_-]+',value) and not re.match(r'20\d{2}-Oral-',value)
elif scheme=='iclr_number':valid=re.fullmatch(r'[1-9]\d*',value) and row['venue']=='ICLR'
elif scheme=='publication_doi':valid=re.fullmatch(r'10\.\d{4,9}/\S+',value)
elif scheme=='publication_mlsys':
valid=(re.fullmatch(str(row['year'])+r'/[a-f0-9]{32}',value)
and row['venue']=='MLSys' and row['source'] in PUBLICATIONS and row.get('status')=='accepted')
else:valid=False
if not valid:raise ValueError('Invalid authoritative submission identity')
result.add((scheme,value))
+2
View File
@@ -18,6 +18,8 @@ def save(path,state):
def repair(db,out,resume=False,batch_size=1000):
db=Path(db).resolve();out=Path(out).resolve()
from paper_atlas.db.backend import require_sqlite_writable
require_sqlite_writable(db)
if not db.is_file():raise ValueError('Existing database required')
if batch_size<1 or batch_size>10000:raise ValueError('Batch size must be between 1 and 10000')
out.parent.mkdir(parents=True,exist_ok=True)
+3
View File
@@ -6,6 +6,7 @@ from pathlib import Path
from paper_atlas.db.store import Store
from paper_atlas.db.submissions import attach_submission,identities_for_row
from paper_atlas.collectors.pmlr_tracks import require_track_manifest, require_track_record
def queue_files(path):
@@ -21,6 +22,7 @@ def queue_files(path):
def backfill(db,files):
for filename in files:
manifest=json.loads(Path(filename).with_suffix('.manifest.json').read_text())
require_track_manifest(manifest)
if manifest['source'] in ('colm','neurips','iclr_program') and manifest.get('parser_version',0)<2:
raise ValueError('Recollect old parser output before submission evidence backfill')
store=Store(db);c=store.conn;count=0
@@ -35,6 +37,7 @@ def backfill(db,files):
seen.add(row['external_id'])
if any(row.get(key)!=manifest.get(key) for key in ('source','venue','year','track')):
raise ValueError('Evidence row differs from edition manifest')
require_track_record(row, manifest)
record=c.execute('SELECT r.id,r.paper_id,r.metadata_json FROM source_records r JOIN sources s ON s.id=r.source_id WHERE s.name=? AND r.external_id=?',(row['source'],row['external_id'])).fetchone()
edition=c.execute('SELECT e.id FROM editions e JOIN venues v ON v.id=e.venue_id WHERE v.acronym=? COLLATE NOCASE AND e.year=? AND e.track=?',(row['venue'],row['year'],row['track'])).fetchone()
if not record or not edition:raise ValueError('Evidence backfill requires an already imported record and edition')
+2
View File
@@ -15,6 +15,7 @@ from pathlib import Path
from paper_atlas.ingestion.records import ingest_file
from paper_atlas.db.store import Store
from paper_atlas.ingestion.backfill import backfill,queue_files
from paper_atlas.db.backend import require_sqlite_writable
UNIT='paper-atlas-arxiv-import.service'
@@ -25,6 +26,7 @@ def property_value(name):
def merge_locked(db,archive,files,backfill_queue=None):
require_sqlite_writable(db)
# Validate inputs before stopping the existing writer.
for filename in files:
path=Path(filename)
+203
View File
@@ -0,0 +1,203 @@
"""Move existing PMLR submission events to verified tracks without reimporting."""
import argparse
from contextlib import closing
import fcntl
import hashlib
import json
from pathlib import Path
import sqlite3
from paper_atlas.collectors.pmlr_tracks import require_track_manifest, require_track_record
from paper_atlas.db.submissions import identities_for_row, timestamp
def save(path, result):
part = path.with_suffix('.part')
part.write_text(json.dumps(result, ensure_ascii=False, indent=2) + '\n')
part.replace(path)
def load_inventories(paths):
scopes, seen, forums = [], set(), set()
for filename in paths:
path = Path(filename).resolve()
inventory = json.loads(path.read_text())
require_track_manifest(inventory)
if inventory.get('source') != 'pmlr' or inventory.get('venue') != 'ICML' or inventory.get('year', 0) < 2024:
raise ValueError('Only verified modern ICML PMLR volumes may be reclassified')
if not inventory.get('count') or not inventory.get('files'):
raise ValueError('A nonempty complete publication inventory is required')
rows, manifests = [], []
tracks = set()
for manifest in inventory['files']:
require_track_manifest(manifest)
if any(manifest.get(key) != inventory.get(key) for key in ('source', 'venue', 'year', 'volume', 'track_program')):
raise ValueError('Track manifest differs from volume inventory')
if manifest['track'] not in ('main', 'position') or manifest['track'] in tracks:
raise ValueError('Invalid or repeated track in volume inventory')
tracks.add(manifest['track'])
data = Path(manifest['file']).read_bytes()
if hashlib.sha256(data).hexdigest() != manifest.get('file_sha256'):
raise ValueError('Track file differs from its verified inventory')
chunk = [json.loads(line) for line in data.splitlines()]
if not chunk or len(chunk) != manifest['count']:
raise ValueError('Track inventory count mismatch')
for row in chunk:
if any(row.get(key) != manifest.get(key) for key in ('source', 'venue', 'year', 'track')):
raise ValueError('Record differs from its track manifest')
if not row['external_id'].startswith('v' + str(inventory['volume']) + '/') or row['status'] != 'accepted':
raise ValueError('Record is outside the accepted publication scope')
if row['external_id'] in seen:
raise ValueError('Repeated publication in reclassification inventory')
seen.add(row['external_id'])
require_track_record(row, manifest)
own_forum = row.get('identifiers', {}).get('openreview')
if not own_forum or (row['year'], own_forum) in forums:
raise ValueError('Missing or repeated forum identity in one ICML edition')
forums.add((row['year'], own_forum))
rows.extend(chunk); manifests.append(manifest)
if len(rows) != inventory['count']:
raise ValueError('Volume count differs from its track files')
scopes.append({'path': str(path), 'sha256': hashlib.sha256(path.read_bytes()).hexdigest(),
'inventory': inventory, 'manifests': manifests, 'rows': rows})
if not scopes:
raise ValueError('At least one complete volume inventory is required')
return scopes
def plan(c, scopes):
updates, changes = [], []
for scope in scopes:
volume = scope['inventory']['volume']
source_rows = c.execute('''SELECT r.id,r.external_id FROM source_records r JOIN sources src ON src.id=r.source_id
WHERE src.name='pmlr' AND r.external_id LIKE ?''', ('v' + str(volume) + '/%',)).fetchall()
if {r[1] for r in source_rows} != {r['external_id'] for r in scope['rows']}:
raise ValueError('Existing PMLR volume differs from the complete audited publication inventory')
for row in scope['rows']:
record = c.execute('''SELECT r.id,r.paper_id,r.title,r.abstract,r.authors_json,r.metadata_json FROM source_records r
JOIN sources src ON src.id=r.source_id WHERE src.name='pmlr' AND r.external_id=?''', (row['external_id'],)).fetchone()
if (record[2] != row['title'] or record[3] != row.get('abstract')
or json.loads(record[4]) != row.get('authors', [])):
raise ValueError('Reclassification must preserve existing publisher text and authors: ' + row['external_id'])
metadata = json.loads(record[5])
forum = str(metadata.get('openreview') or (metadata.get('record_identifiers') or {}).get('openreview') or '')
forum = forum.split('id=')[-1].split('&')[0]
if not forum or forum != row['identifiers'].get('openreview'):
raise ValueError('Publisher forum identity differs from retained source metadata')
events = c.execute('''SELECT s.id,s.paper_id,s.edition_id,e.venue_id,e.year,e.track,v.acronym,s.source_record_id,s.source_submission_id
FROM submission_sources ss JOIN submissions s ON s.id=ss.submission_id JOIN editions e ON e.id=s.edition_id
JOIN venues v ON v.id=e.venue_id WHERE ss.source_record_id=? AND ss.source_submission_id=?''',
(record[0], row['external_id'])).fetchall()
if len(events) != 1:
raise ValueError('Publication must have exactly one existing submission event')
event = events[0]
sid, paper, old_edition, venue, year, old_track, acronym, owner, external = event
if paper != record[1] or year != row['year'] or acronym.upper() != 'ICML' or old_track not in ('main', 'position'):
raise ValueError('Existing submission is outside this publication scope')
identities = c.execute('SELECT scheme,value FROM submission_identifiers WHERE submission_id=? ORDER BY scheme,value', (sid,)).fetchall()
own = identities_for_row(row)
if {value for scheme, value in identities if scheme == 'openreview'} - {forum}:
raise ValueError('Existing event has a conflicting forum identity')
target = c.execute('SELECT id FROM editions WHERE venue_id=? AND year=? AND track=?', (venue, year, row['track'])).fetchone()
if target:
for scheme, value in sorted(set(identities) | set(own)):
collision = c.execute('SELECT submission_id FROM submission_identifiers WHERE edition_id=? AND scheme=? AND value=?', (target[0], scheme, value)).fetchone()
if collision and collision[0] != sid:
raise ValueError('Target track already has another event for this identity; reconcile sources before moving')
if c.execute('SELECT 1 FROM submissions WHERE source_record_id=? AND source_submission_id=? AND edition_id=? AND id<>?', (owner, external, target[0], sid)).fetchone():
raise ValueError('Target track already has this publication event')
if old_track != row['track']:
links = c.execute('SELECT source_record_id,source_submission_id FROM submission_sources WHERE submission_id=?', (sid,)).fetchall()
if links != [(record[0], row['external_id'])] or owner != record[0] or external != row['external_id']:
raise ValueError('Moving an event shared by multiple sources requires a separate reconciliation')
decisions = c.execute('SELECT id,status,raw_value,evidence_url,observed_at,decision_date FROM decisions WHERE submission_id=? ORDER BY id', (sid,)).fetchall()
if not decisions or any(d[1] != 'accepted' for d in decisions):
raise ValueError('Moving a publication with conflicting decision history requires reconciliation')
changes.append({'submission_id': sid, 'source_record_id': record[0], 'external_id': row['external_id'],
'paper_id': paper, 'from_edition_id': old_edition, 'from_track': old_track,
'to_track': row['track'], 'year': year, 'before_identifiers': identities,
'before_decisions': decisions, 'track_evidence': row['metadata']['track_evidence']})
updates.append((row, record, event, own))
return updates, changes
def reclassify(db, inventories, out, apply=False):
db, out = Path(db).resolve(), Path(out).resolve()
if apply:
from paper_atlas.db.backend import require_sqlite_writable
require_sqlite_writable(db)
if not db.is_file() or out == db:
raise ValueError('Existing database and distinct report path required')
scopes = load_inventories(inventories)
inputs = {Path(scope['path']) for scope in scopes}
inputs.update(Path(m['file']).resolve() for scope in scopes for m in scope['manifests'])
inputs.update(Path(m['file']).with_suffix('.manifest.json').resolve() for scope in scopes for m in scope['manifests'])
if out in inputs:
raise ValueError('Report must preserve evidence inputs')
out.parent.mkdir(parents=True, exist_ok=True)
with Path(str(db) + '.maintenance.lock').open('a') as lock, Path(str(out) + '.lock').open('a') as output_lock:
fcntl.flock(lock, (fcntl.LOCK_EX if apply else fcntl.LOCK_SH) | fcntl.LOCK_NB)
fcntl.flock(output_lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
if out.exists():
raise ValueError('Reclassification report exists; use a new path')
mode = 'rw' if apply else 'ro'
with closing(sqlite3.connect(db.as_uri() + '?mode=' + mode, uri=True)) as c:
c.execute('PRAGMA foreign_keys=ON'); c.execute('PRAGMA cache_size=-32768')
c.execute('BEGIN IMMEDIATE' if apply else 'BEGIN')
updates, changes = plan(c, scopes)
result = {'status': 'planned', 'db': str(db), 'started_at': timestamp(),
'records_verified': len(updates), 'events_to_move': len(changes), 'changes': changes,
'inputs': [{key: scope[key] for key in ('path', 'sha256')} for scope in scopes],
'note': 'Preserves paper/source/submission/decision IDs and all decision observations; no entity merges or text reimport.'}
save(out, result)
if not apply:
return result
try:
for row, record, event, own in updates:
sid, _, old_edition, venue, year, old_track, _, _, _ = event
c.execute('INSERT OR IGNORE INTO editions(venue_id,year,track) VALUES(?,?,?)', (venue, year, row['track']))
target = c.execute('SELECT id FROM editions WHERE venue_id=? AND year=? AND track=?', (venue, year, row['track'])).fetchone()[0]
if target != old_edition:
c.execute('UPDATE submission_identifiers SET edition_id=? WHERE submission_id=?', (target, sid))
c.execute('UPDATE submissions SET edition_id=? WHERE id=?', (target, sid))
for scheme, value in own:
c.execute('INSERT OR IGNORE INTO submission_identifiers VALUES(?,?,?,?)', (target, scheme, value, sid))
metadata = json.loads(record[5]); metadata.update(row['metadata'])
c.execute('UPDATE source_records SET metadata_json=? WHERE id=?', (json.dumps(metadata, ensure_ascii=False), record[0]))
for scope in scopes:
for m in scope['manifests']:
edition = c.execute('SELECT e.id FROM editions e JOIN venues v ON v.id=e.venue_id WHERE v.acronym=? COLLATE NOCASE AND e.year=? AND e.track=?', ('ICML', m['year'], m['track'])).fetchone()[0]
source = c.execute("SELECT id FROM sources WHERE name='pmlr'").fetchone()[0]
c.execute('''INSERT INTO edition_sources(edition_id,source_id,list_url,status,expected_count,imported_count,last_success_at)
VALUES(?,?,?,?,?,?,?) ON CONFLICT(edition_id,source_id,list_url) DO UPDATE SET status=excluded.status,
expected_count=excluded.expected_count,imported_count=excluded.imported_count,last_success_at=excluded.last_success_at,last_error=NULL''',
(edition, source, m['list_url'], 'partial' if m.get('missing_abstract_count') or m.get('status') == 'partial' else 'complete', m['count'], m['count'], timestamp()))
_, remaining = plan(c, scopes)
if remaining:
raise ValueError('Post-migration track comparison still has mismatches')
print(json.dumps({'stage': 'checking_foreign_keys', 'events_moved': len(changes)}), flush=True)
if c.execute('PRAGMA foreign_key_check').fetchone():
raise ValueError('Foreign key violations after track reclassification')
result.update(status='prepared', events_moved=len(changes))
save(out, result)
c.commit()
except BaseException as error:
c.rollback(); result.update(status='error', error=str(error)); save(out, result); raise
result.update(status='complete', finished_at=timestamp())
save(out, result)
return result
def main(argv=None, *, prog=None):
parser = argparse.ArgumentParser(prog=prog)
parser.add_argument('--db', required=True)
parser.add_argument('--inventory', action='append', required=True)
parser.add_argument('--out', required=True)
parser.add_argument('--apply', action='store_true', help='Apply the verified migration under an exclusive maintenance lock')
args = parser.parse_args(argv)
result = reclassify(args.db, args.inventory, args.out, args.apply)
print(json.dumps({key: value for key, value in result.items() if key != 'changes'}), flush=True)
if __name__ == '__main__':
main()
+3
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@@ -6,12 +6,14 @@ from pathlib import Path
from paper_atlas.db.store import Store
from paper_atlas.db.submissions import identities_for_row,timestamp
from paper_atlas.collectors.pmlr_tracks import require_track_manifest, require_track_record
def ingest_file(db,path):
path = Path(path)
manifest_path = path.with_suffix('.manifest.json')
manifest = json.loads(manifest_path.read_text()) if manifest_path.exists() else {}
require_track_manifest(manifest)
if manifest.get('source') in ('colm','neurips') and manifest.get('parser_version',0)<2:
raise ValueError('Recollect proceedings with parser_version>=2 before identity matching')
if manifest.get('source')=='iclr_program' and manifest.get('parser_version',0)<2:
@@ -36,6 +38,7 @@ def ingest_file(db,path):
raise ValueError('Source differs from manifest')
if any(key in manifest and manifest[key]!=row[key] for key in ('venue','year','track')):
raise ValueError('Conference edition differs from manifest')
require_track_record(row, manifest)
external = row['external_id']
if external in seen:
raise ValueError('Duplicate external ID in one collected file: '+external)
+13
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@@ -0,0 +1,13 @@
"""Stable identities from publisher-owned metadata self-links."""
import re
from urllib.parse import urlsplit
def mlsys_id(url):
parsed = urlsplit(url)
if parsed.scheme not in ('https', 'http') or parsed.netloc != 'proceedings.mlsys.org':
return None
match = re.fullmatch(r'/paper(?:_files/paper)?/((?:19|20)\d{2})/hash/([a-f0-9]{32})-Abstract(?:-(?:Conference|mlsys(20\d{2})))?\.html', parsed.path)
if not match or match[3] and match[3] != match[1]:
return None
return match[1] + '/' + match[2]
+1
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@@ -0,0 +1 @@
"""PostgreSQL migration and read access for the paper index."""
+83
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@@ -0,0 +1,83 @@
"""Libpq service connections; credentials never belong in CLI arguments."""
from collections.abc import Mapping
import re
SEARCH_VECTOR = "to_tsvector('english'::regconfig,coalesce(title,'') || ' ' || coalesce(abstract,''))"
def driver():
try:
import psycopg
except ImportError as error:
raise RuntimeError('Install paper-atlas[postgres] on the approved remote runner') from error
return psycopg
def connect(service, *, readonly=False):
if not re.fullmatch(r'[A-Za-z0-9_-]+', service):
raise ValueError('Use a libpq service name, never a password or connection URL')
connection = driver().connect(service=service, connect_timeout=15, autocommit=True,
application_name='paper-atlas')
connection.execute("SET timezone='UTC'")
connection.execute("SET lock_timeout='5s'")
connection.execute("SET work_mem='2MB'")
connection.execute("SET maintenance_work_mem='16MB'")
connection.execute('SET max_parallel_workers_per_gather=0')
connection.execute('SET max_parallel_maintenance_workers=0')
if readonly:
connection.execute('BEGIN ISOLATION LEVEL REPEATABLE READ READ ONLY')
return connection
class Row(Mapping):
"""The small mapping/positional interface used by existing query output."""
def __init__(self, columns, values):
self.columns, self.values = columns, values
def __getitem__(self, key):
return self.values[key if isinstance(key, int) else self.columns.index(key)]
def __iter__(self):
return iter(self.columns)
def __len__(self):
return len(self.columns)
def row_factory(cursor):
columns = [column.name for column in cursor.description] if cursor.description else []
return lambda values: Row(columns, values)
class ReadConnection:
postgres = True
def __init__(self, service, schema=None):
if schema is not None and not re.fullmatch(r'[a-z][a-z0-9_]{0,35}', schema):
raise ValueError('Invalid schema name')
self.connection = connect(service, readonly=True)
from paper_atlas.postgres.schema import quote
if schema is not None:
self.connection.execute('SET LOCAL search_path TO ' + quote(schema) + ',pg_catalog')
self.connection.row_factory = row_factory
if not self.has_table('papers'):
self.close()
raise RuntimeError('PostgreSQL publication is not ready in the configured search_path')
def execute(self, query, params=()):
# All caller SQL is static; user values are always bound parameters.
if 'sqlite_master' in query:
match = re.search(r"name='([a-z_]+)'", query)
if not match or match[1] not in ('decision_sources', 'submission_sources', 'venue_aliases'):
raise ValueError('Unsupported legacy table lookup')
return self.connection.execute('''SELECT 1 FROM information_schema.tables
WHERE table_schema=current_schema() AND table_name=%s''',
(match[1],))
return self.connection.execute(query.replace('?', '%s'), params)
def has_table(self, name):
return bool(self.connection.execute('''SELECT 1 FROM information_schema.tables
WHERE table_schema=current_schema() AND table_name=%s''', (name,)).fetchone())
def close(self):
self.connection.close()
+232
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@@ -0,0 +1,232 @@
"""Resumable, unpublished COPY followed by complete ordered content verification."""
import argparse
from contextlib import closing
import fcntl
import hashlib
import json
from pathlib import Path
import re
import shutil
import sqlite3
import uuid
import zlib
from paper_atlas.db.submissions import timestamp
from paper_atlas.postgres.client import connect, SEARCH_VECTOR
from paper_atlas.postgres.schema import TABLES, inspect, fingerprint, quote, select_sql, table_sql
def digest_file(path):
digest = hashlib.sha256()
with path.open('rb') as stream:
while block := stream.read(8 * 1024 ** 2):
digest.update(block)
return digest.hexdigest()
def update_hash(digest, row):
# Raw JSON columns remain text: whitespace, escapes and source evidence survive.
data = json.dumps(tuple(row), ensure_ascii=False, separators=(',', ':')).encode()
digest.update(len(data).to_bytes(8, 'big')); digest.update(data)
def save(path, result):
path.parent.mkdir(parents=True, exist_ok=True)
part = path.with_suffix(path.suffix + '.part')
part.write_text(json.dumps(result, ensure_ascii=False, indent=2) + '\n')
part.replace(path)
def free_space(path, minimum):
if path and shutil.disk_usage(path).free < minimum * 1024 ** 3:
raise RuntimeError('Migration storage headroom fell below the configured minimum')
def qualify(schema, table):
return quote(schema) + '.' + quote(table)
def add_constraints(pg, stage, plan):
def constraint(table, name, clause):
exists = pg.execute('''SELECT 1 FROM pg_constraint co JOIN pg_class cl ON cl.oid=co.conrelid
JOIN pg_namespace ns ON ns.oid=cl.relnamespace WHERE ns.nspname=%s AND cl.relname=%s AND co.conname=%s''',
(stage, table, name)).fetchone()
if not exists:
pg.execute('ALTER TABLE ' + qualify(stage, table) + ' ADD CONSTRAINT ' + quote(name) + ' ' + clause)
for table, spec in plan.items():
constraint(table, table + '_pkey', 'PRIMARY KEY (' + ','.join(map(quote, spec['pk'])) + ')')
for number, index in enumerate(spec['indexes']):
if index['origin'] == 'u':
constraint(table, table + '_unique_' + str(number), 'UNIQUE (' + ','.join(quote(n) for n, desc in index['terms']) + ')')
else:
terms = ','.join(quote(n) + (' DESC' if desc else '') for n, desc in index['terms'])
pg.execute('CREATE ' + ('UNIQUE ' if index['unique'] else '') + 'INDEX IF NOT EXISTS ' +
quote(index['name']) + ' ON ' + qualify(stage, table) + '(' + terms + ')')
for table, spec in plan.items():
for number, fk in enumerate(spec['foreign_keys']):
clause = ('FOREIGN KEY (' + ','.join(map(quote, fk['columns'])) + ') REFERENCES ' +
qualify(stage, fk['table']) + '(' + ','.join(map(quote, fk['references'])) + ') NOT VALID')
constraint(table, table + '_fk_' + str(number), clause)
for number, check in enumerate(spec['checks']):
constraint(table, table + '_check_' + str(number), 'CHECK (' + check + ') NOT VALID')
constraints = pg.execute('''SELECT cl.relname,co.conname FROM pg_constraint co
JOIN pg_class cl ON cl.oid=co.conrelid JOIN pg_namespace ns ON ns.oid=cl.relnamespace
WHERE ns.nspname=%s AND NOT co.convalidated ORDER BY cl.relname,co.conname''', (stage,)).fetchall()
for table, name in constraints:
pg.execute('ALTER TABLE ' + qualify(stage, table) + ' VALIDATE CONSTRAINT ' + quote(name))
def sequences(pg, source, stage, plan):
old = dict(source.execute('SELECT name,seq FROM sqlite_sequence'))
history = {'papers': ('paper_merges', 'former_paper_id'),
'submissions': ('submission_merges', 'former_submission_id'),
'decisions': ('decision_merges', 'former_decision_id')}
result = {}
for table, spec in plan.items():
if spec['pk'] != ['id']:
continue
value = max(source.execute('SELECT coalesce(max(id),0) FROM ' + quote(table)).fetchone()[0], old.get(table, 0))
if table in history:
audit, column = history[table]
value = max(value, source.execute('SELECT coalesce(max(' + quote(column) + '),0) FROM ' + quote(audit)).fetchone()[0])
sequence = pg.execute('SELECT pg_get_serial_sequence(%s,%s)', (qualify(stage, table), 'id')).fetchone()[0]
pg.execute('SELECT setval(%s,%s,%s)', (sequence, max(value, 1), value > 0))
result[table] = value
return result
def migrate(db, service, out, *, schema='research', storage_path=None, min_free_gib=8):
if not re.fullmatch(r'[a-z][a-z0-9_]{0,35}', schema):
raise ValueError('Use a short lowercase target schema name')
db, out = Path(db).resolve(), Path(out).resolve()
if not db.is_file() or out == db:
raise ValueError('Existing source and a distinct report are required')
if out.exists() and json.loads(out.read_text()).get('status') == 'complete':
raise ValueError('Completed report must be preserved')
free_space(storage_path, min_free_gib)
control = schema + '_migration'
report = {'status': 'preflight', 'source': str(db), 'service': service, 'schema': schema,
'started_at': timestamp(), 'tables': {}, 'scope': 'All 21 business tables; FTS5 internals rebuilt as native PostgreSQL GIN.'}
with Path(str(db) + '.maintenance.lock').open('a') as lock:
fcntl.flock(lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
if Path(str(db) + '-wal').exists() and Path(str(db) + '-wal').stat().st_size:
raise ValueError('Freeze writers and checkpoint SQLite WAL before migrating')
with closing(sqlite3.connect(db.as_uri() + '?mode=ro', uri=True)) as source, closing(connect(service)) as pg:
source.execute('PRAGMA query_only=ON'); source.execute('PRAGMA cache_size=-16384'); source.execute('BEGIN')
plan = inspect(source)
stat = db.stat()
identity = {'file_sha256': digest_file(db), 'bytes': stat.st_size, 'mtime_ns': stat.st_mtime_ns,
'schema_sha256': fingerprint(plan)}
report['source_identity'] = identity
advisory = zlib.crc32(schema.encode()) & 0x7fffffff
if not pg.execute('SELECT pg_try_advisory_lock(%s,%s)', (615173, advisory)).fetchone()[0]:
raise RuntimeError('Another migration holds the target lock')
if pg.execute('SELECT 1 FROM pg_namespace WHERE nspname=%s', (schema,)).fetchone():
raise ValueError('Target schema already exists; published data will never be overwritten')
pg.execute('CREATE SCHEMA IF NOT EXISTS ' + quote(control))
pg.execute('CREATE TABLE IF NOT EXISTS ' + qualify(control, 'run') +
'(id INTEGER PRIMARY KEY CHECK(id=1), source_json TEXT NOT NULL, stage TEXT NOT NULL, status TEXT NOT NULL)')
pg.execute('CREATE TABLE IF NOT EXISTS ' + qualify(control, 'tables') +
'(name TEXT PRIMARY KEY, rows BIGINT NOT NULL, sha256 TEXT NOT NULL, verified BOOLEAN NOT NULL DEFAULT false)')
run = pg.execute('SELECT source_json,stage,status FROM ' + qualify(control, 'run') + ' WHERE id=1').fetchone()
if run:
if json.loads(run[0]) != identity or run[2] == 'complete':
raise ValueError('Resume requires the exact same unpublished SQLite snapshot')
stage = run[1]
else:
stage = schema + '_stage_' + uuid.uuid4().hex[:12]
with pg.transaction():
pg.execute('CREATE SCHEMA ' + quote(stage))
for table, spec in plan.items():
pg.execute(table_sql(stage, table, spec))
pg.execute('INSERT INTO ' + qualify(control, 'run') + ' VALUES(1,%s,%s,%s)',
(json.dumps(identity, sort_keys=True), stage, 'copying'))
report.update(status='copying', stage=stage); save(out, report)
try:
for table, spec in plan.items():
free_space(storage_path, min_free_gib)
previous = pg.execute('SELECT rows,sha256 FROM ' + qualify(control, 'tables') + ' WHERE name=%s', (table,)).fetchone()
if previous:
rows, digest = previous
else:
digest = hashlib.sha256(); rows = 0
with pg.transaction():
# Only this run's unpublished, incomplete table can be reset.
pg.execute('TRUNCATE ' + qualify(stage, table))
columns = ','.join(quote(c['name']) for c in spec['columns'])
with pg.cursor().copy('COPY ' + qualify(stage, table) + '(' + columns + ') FROM STDIN') as copy:
for row in source.execute(select_sql(None, table, spec)):
copy.write_row(row); update_hash(digest, row); rows += 1
if rows % 10000 == 0:
free_space(storage_path, min_free_gib)
if rows % 100000 == 0:
print(json.dumps({'stage': 'copying', 'table': table, 'rows': rows}), flush=True)
digest = digest.hexdigest()
pg.execute('INSERT INTO ' + qualify(control, 'tables') + '(name,rows,sha256) VALUES(%s,%s,%s)', (table, rows, digest))
report['tables'][table] = {'source_rows': rows, 'source_sha256': digest}
save(out, report)
print(json.dumps({'stage': 'copied', 'table': table, 'rows': rows}), flush=True)
report['status'] = 'validating_constraints'; save(out, report)
add_constraints(pg, stage, plan)
report['sequences'] = sequences(pg, source, stage, plan)
report['status'] = 'verifying_contents'; save(out, report)
for table, spec in plan.items():
digest = hashlib.sha256(); rows = 0
with pg.transaction(), pg.cursor(name='verify_' + table) as cursor:
cursor.itersize = 512
cursor.execute(select_sql(stage, table, spec))
for row in cursor:
update_hash(digest, row); rows += 1
entry = report['tables'][table]
entry.update(target_rows=rows, target_sha256=digest.hexdigest())
if rows != entry['source_rows'] or digest.hexdigest() != entry['source_sha256']:
raise ValueError('Complete content verification failed for ' + table)
pg.execute('UPDATE ' + qualify(control, 'tables') + ' SET verified=true WHERE name=%s', (table,))
save(out, report)
print(json.dumps({'stage': 'verified', 'table': table, 'rows': rows}), flush=True)
report['status'] = 'building_search_index'; save(out, report)
free_space(storage_path, min_free_gib)
pg.execute('CREATE INDEX IF NOT EXISTS papers_search_gin ON ' + qualify(stage, 'papers') + ' USING gin (' + SEARCH_VECTOR + ')')
search = pg.execute('''SELECT am.amname,i.indisvalid,i.indisready,t.relname
FROM pg_index i JOIN pg_class ix ON ix.oid=i.indexrelid
JOIN pg_class t ON t.oid=i.indrelid JOIN pg_namespace ns ON ns.oid=ix.relnamespace
JOIN pg_am am ON am.oid=ix.relam WHERE ns.nspname=%s AND ix.relname='papers_search_gin' ''', (stage,)).fetchone()
if search != ('gin', True, True, 'papers'):
raise ValueError('Native full-text index is not valid and ready')
for table in TABLES:
pg.execute('ANALYZE ' + qualify(stage, table))
invalid = pg.execute('''SELECT count(*) FROM pg_constraint co JOIN pg_class cl ON cl.oid=co.conrelid
JOIN pg_namespace ns ON ns.oid=cl.relnamespace WHERE ns.nspname=%s AND NOT co.convalidated''', (stage,)).fetchone()[0]
if invalid:
raise ValueError('Unvalidated constraints remain')
if (db.stat().st_size, db.stat().st_mtime_ns) != (identity['bytes'], identity['mtime_ns']):
raise ValueError('Source changed during migration')
if Path(str(db) + '-wal').exists() and Path(str(db) + '-wal').stat().st_size:
raise ValueError('A source writer committed during migration')
report.update(status='prepared', foreign_keys='all_validated', checks='all_validated', native_search_index=True)
save(out, report)
with pg.transaction():
pg.execute('ALTER SCHEMA ' + quote(stage) + ' RENAME TO ' + quote(schema))
pg.execute('UPDATE ' + qualify(control, 'run') + " SET status='complete' WHERE id=1")
report.update(status='complete', finished_at=timestamp())
save(out, report)
return report
except BaseException as error:
report.update(status='error', error_type=type(error).__name__, error=str(error), failed_at=timestamp())
save(out, report)
raise
def main(argv=None, *, prog=None):
parser = argparse.ArgumentParser(prog=prog)
parser.add_argument('--db', required=True, help='Frozen SQLite source')
parser.add_argument('--pg-service', required=True, help='Protected libpq service name')
parser.add_argument('--schema', default='research')
parser.add_argument('--out', required=True)
parser.add_argument('--storage-path', help='Target filesystem path for free-space checks')
parser.add_argument('--min-free-gib', type=float, default=8)
args = parser.parse_args(argv)
result = migrate(args.db, args.pg_service, args.out, schema=args.schema,
storage_path=args.storage_path, min_free_gib=args.min_free_gib)
print(json.dumps(result, ensure_ascii=False), flush=True)
+120
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@@ -0,0 +1,120 @@
"""Inspect the complete business schema; rebuild SQLite engine internals natively."""
import hashlib
import json
import re
TABLES = ('sources', 'papers', 'identifiers', 'source_records', 'venues', 'editions',
'venue_aliases', 'edition_sources', 'submissions', 'decisions',
'submission_sources', 'submission_identifiers', 'decision_sources',
'submission_merges', 'decision_merges', 'schema_migrations', 'tags',
'paper_tags', 'match_candidates', 'paper_merges', 'ingest_runs')
CHECKS = {
'venues': ["venue_type IN ('conference','journal','review_platform')"],
'edition_sources': ["status IN ('pending','running','complete','partial','blocked','unavailable','not_yet_published')"],
'decisions': ["status IN ('accepted','rejected','desk_rejected','withdrawn','under_review','unknown')"],
'match_candidates': ["status IN ('pending','merged','distinct')"],
}
TYPES = {'INTEGER': 'BIGINT', 'TEXT': 'TEXT COLLATE "C"', 'REAL': 'DOUBLE PRECISION'}
def checks_in(ddl):
result = []
for match in re.finditer(r'\bCHECK\s*\(', ddl, re.I):
start = position = match.end()
depth, quoted = 1, False
while position < len(ddl) and depth:
char = ddl[position]
if char == "'":
if quoted and position + 1 < len(ddl) and ddl[position + 1] == "'":
position += 2; continue
quoted = not quoted
elif not quoted:
depth += (char == '(') - (char == ')')
position += 1
if depth:
raise ValueError('Unclosed CHECK constraint')
result.append(ddl[start:position - 1])
return result
def normalize_check(expression):
# Normalize SQL layout/keywords, retaining case and spaces inside literals.
tokens = re.findall(r"'(?:[^']|'')*'|[^']+", expression)
return ''.join(token if token.startswith("'") else re.sub(r'\s+', '', token).lower() for token in tokens)
def quote(name):
return '"' + name.replace('"', '""') + '"'
def inspect(connection):
business = {name for schema, name, kind, *_ in connection.execute('PRAGMA table_list')
if schema == 'main' and kind == 'table' and not name.startswith('sqlite_')}
if business != set(TABLES):
raise ValueError('Unexpected business tables: ' + repr(sorted(business ^ set(TABLES))))
result = {}
for table in TABLES:
columns = [{'name': r[1], 'type': r[2].upper(), 'notnull': bool(r[3]),
'default': r[4], 'pk': r[5]}
for r in connection.execute('PRAGMA table_info(' + quote(table) + ')')]
if any(c['type'] not in TYPES for c in columns):
raise ValueError('Unsupported storage type in ' + table)
pk = [c['name'] for c in sorted(columns, key=lambda c: c['pk']) if c['pk']]
if not pk:
raise ValueError('A deterministic primary key is required for ' + table)
indexes = []
for row in connection.execute('PRAGMA index_list(' + quote(table) + ')'):
if row[3] == 'pk':
continue
if row[4]:
raise ValueError('Partial indexes require explicit migration support')
terms = [(r[2], bool(r[3]), r[4]) for r in connection.execute('PRAGMA index_xinfo(' + quote(row[1]) + ')') if r[5]]
if any(name is None or coll != 'BINARY' for name, desc, coll in terms):
raise ValueError('Unsupported expression or collation in ' + table)
indexes.append({'name': row[1], 'unique': bool(row[2]), 'origin': row[3],
'terms': [(name, desc) for name, desc, coll in terms]})
fks = {}
for row in connection.execute('PRAGMA foreign_key_list(' + quote(table) + ')'):
if row[5:7] != ('NO ACTION', 'NO ACTION'):
raise ValueError('Unsupported foreign key actions')
fk = fks.setdefault(row[0], {'table': row[2], 'columns': [], 'references': []})
fk['columns'].append(row[3]); fk['references'].append(row[4])
ddl = connection.execute("SELECT sql FROM sqlite_schema WHERE type='table' AND name=?", (table,)).fetchone()[0]
checks = CHECKS.get(table, [])
if sorted(map(normalize_check, checks_in(ddl))) != sorted(map(normalize_check, checks)):
raise ValueError('Unrecognized CHECK constraint in ' + table)
result[table] = {'columns': columns, 'pk': pk, 'indexes': indexes,
'foreign_keys': list(fks.values()), 'checks': checks}
return result
def fingerprint(plan):
return hashlib.sha256(json.dumps(plan, sort_keys=True, separators=(',', ':')).encode()).hexdigest()
def default_sql(value):
if value is None:
return ''
if value.upper() == 'CURRENT_TIMESTAMP':
return " DEFAULT to_char(CURRENT_TIMESTAMP AT TIME ZONE 'UTC','YYYY-MM-DD\"T\"HH24:MI:SS.MS\"Z\"')"
if re.fullmatch(r'-?\d+|\'(?:[^\']|\'\')*\'', value):
return ' DEFAULT ' + value
raise ValueError('Unsupported column default')
def table_sql(schema, table, spec):
columns = []
for column in spec['columns']:
generated = column['name'] == 'id' and spec['pk'] == ['id'] and column['type'] == 'INTEGER'
value = quote(column['name']) + ' ' + TYPES[column['type']]
value += ' GENERATED BY DEFAULT AS IDENTITY' if generated else default_sql(column['default'])
if column['notnull']:
value += ' NOT NULL'
columns.append(value)
return 'CREATE TABLE ' + quote(schema) + '.' + quote(table) + '(' + ','.join(columns) + ')'
def select_sql(schema, table, spec):
prefix = quote(schema) + '.' if schema else ''
return ('SELECT ' + ','.join(quote(c['name']) for c in spec['columns']) +
' FROM ' + prefix + quote(table) + ' ORDER BY ' + ','.join(quote(c) for c in spec['pk']))
+22 -8
View File
@@ -23,8 +23,11 @@ def known_acceptances(conn,paper):
def main(argv=None, *, prog=None):
parser = argparse.ArgumentParser(prog=prog)
parser.add_argument('--db', required=True)
parser.add_argument('--query', help='SQLite FTS5 query over title and abstract')
database = parser.add_mutually_exclusive_group(required=True)
database.add_argument('--db', help='SQLite file')
database.add_argument('--pg-service', help='Protected libpq service; credentials stay outside CLI arguments')
parser.add_argument('--pg-schema', help='Optional PostgreSQL schema override; otherwise use the configured search_path')
parser.add_argument('--query', help='Title/abstract search: FTS5 for SQLite, web-search syntax for PostgreSQL')
parser.add_argument('--paper',type=int,help='Paper ID; include sources, tags and submission history')
parser.add_argument('--tag', help='Filter as namespace=value, e.g. arxiv:category=cs.AI')
parser.add_argument('--venue', help='Conference acronym')
@@ -35,9 +38,15 @@ def main(argv=None, *, prog=None):
parser.add_argument('--limit', type=int, default=20)
parser.add_argument('--stats', action='store_true')
args = parser.parse_args(argv)
conn = sqlite3.connect(Path(args.db).resolve().as_uri()+'?mode=ro', uri=True)
conn.row_factory = sqlite3.Row
conn.execute('BEGIN') # One consistent read snapshot while ingestion continues.
if args.pg_schema and not args.pg_service:
parser.error('--pg-schema requires --pg-service')
if args.pg_service:
from paper_atlas.postgres.client import ReadConnection
conn = ReadConnection(args.pg_service, schema=args.pg_schema) if args.pg_schema else ReadConnection(args.pg_service)
else:
conn = sqlite3.connect(Path(args.db).resolve().as_uri()+'?mode=ro', uri=True)
conn.row_factory = sqlite3.Row
conn.execute('BEGIN') # One consistent read snapshot while ingestion continues.
if args.stats:
result = {name:conn.execute('SELECT count(*) FROM '+name).fetchone()[0] for name in ('papers','source_records','submissions','decisions','tags','match_candidates')}
result['records_by_source'] = [dict(r) for r in conn.execute('SELECT s.name,count(r.id) AS imported_records FROM sources s LEFT JOIN source_records r ON r.source_id=s.id GROUP BY s.id ORDER BY s.name')]
@@ -53,7 +62,12 @@ def main(argv=None, *, prog=None):
if args.paper is not None:
where.append('p.id=?'); params.append(args.paper)
if args.query:
where.append('p.id IN (SELECT rowid FROM papers_fts WHERE papers_fts MATCH ?)'); params.append(args.query)
if args.pg_service:
from paper_atlas.postgres.client import SEARCH_VECTOR
where.append('p.id IN (SELECT id FROM papers WHERE '+SEARCH_VECTOR+" @@ websearch_to_tsquery('english'::regconfig,?))")
else:
where.append('p.id IN (SELECT rowid FROM papers_fts WHERE papers_fts MATCH ?)')
params.append(args.query)
if args.tag:
namespace,value = args.tag.split('=',1)
where.append('EXISTS(SELECT 1 FROM paper_tags pt JOIN tags t ON t.id=pt.tag_id WHERE pt.paper_id=p.id AND t.namespace=? AND t.value=?)'); params.extend([namespace,value])
@@ -63,9 +77,9 @@ def main(argv=None, *, prog=None):
clause = ['1=1']
if args.venue:
if conn.execute("SELECT 1 FROM sqlite_master WHERE type='table' AND name='venue_aliases'").fetchone():
clause.append('(v.acronym=? COLLATE NOCASE OR EXISTS(SELECT 1 FROM venue_aliases va WHERE va.venue_id=v.id AND va.alias=? COLLATE NOCASE))'); params.extend([args.venue,args.venue])
clause.append('(lower(v.acronym)=lower(?) OR EXISTS(SELECT 1 FROM venue_aliases va WHERE va.venue_id=v.id AND lower(va.alias)=lower(?)))'); params.extend([args.venue,args.venue])
else:
clause.append('v.acronym=? COLLATE NOCASE');params.append(args.venue)
clause.append('lower(v.acronym)=lower(?)');params.append(args.venue)
if args.track:
clause.append('e.track=?');params.append(args.track)
if args.year:
+34 -1
View File
@@ -12,7 +12,9 @@
"ijcai": "https://www.ijcai.org/all_proceedings/",
"dblp": "https://dblp.org/db/conf/",
"colm": "https://proceedings.colm.cc/",
"iclr_program": "https://iclr.cc/virtual/2026/papers.html"
"iclr_program": "https://iclr.cc/virtual/2026/papers.html",
"mlsys": "https://proceedings.mlsys.org/",
"acmmm": "https://www.acmmm.org/"
},
"venues": [
{
@@ -643,6 +645,37 @@
"main"
],
"coverage": "pending"
},
{
"acronym": "MLSys",
"field": "ml_systems",
"venue_type": "conference",
"discovery_sources": [
"mlsys",
"dblp"
],
"scope": "user_confirmed_related",
"years": "all_publicly_available",
"tracks": [
"main"
],
"coverage": "pending"
},
{
"acronym": "MM",
"field": "multimodal",
"venue_type": "conference",
"discovery_sources": [
"dblp",
"acmmm",
"openreview"
],
"scope": "user_confirmed_related",
"years": "all_publicly_available",
"tracks": [
"main"
],
"coverage": "pending"
}
],
"additional_tracks": [
+3
View File
@@ -10,6 +10,9 @@ readme = "README.md"
requires-python = ">=3.12"
dependencies = ["PyYAML==6.0.3"]
[project.optional-dependencies]
postgres = ["psycopg[binary]==3.3.8"]
[project.scripts]
paper-atlas = "paper_atlas.cli:main"
+138
View File
@@ -0,0 +1,138 @@
import fcntl
import json
from pathlib import Path
import tempfile
import unittest
import sqlite3
from unittest.mock import patch
from paper_atlas.audits.arxiv_tags import audit, main
from paper_atlas.db.store import Store
from paper_atlas.ingestion.arxiv import refresh_categories
class ArxivTagAuditTests(unittest.TestCase):
def setUp(self):
self.temp = tempfile.TemporaryDirectory()
self.addCleanup(self.temp.cleanup)
self.root = Path(self.temp.name)
self.db = self.root / 'papers.sqlite'
self.out = self.root / 'audit.json'
self.store = Store(self.db)
self.addCleanup(self.store.conn.close)
self.records = []
for external in ('one', 'two'):
paper, record = self.store.record('arxiv', external, 'https://arxiv.org/abs/' + external,
'Same research work', 'Abstract', [], {'doi': '10.1234/same'},
{'categories': 'cs.AI cs.LG cs.AI'})
refresh_categories(self.store, paper, record, 'cs.AI cs.LG cs.AI')
self.records.append(record)
self.paper = paper
tag = self.store.conn.execute("INSERT INTO tags(namespace,value) VALUES('custom:topic','cs.AI')").lastrowid
self.store.conn.execute("INSERT INTO paper_tags VALUES(?,?,NULL,'manual:1')", (paper, tag))
self.store.conn.commit()
def test_all_merged_records_keep_their_own_categories_and_custom_tags_are_untouched(self):
before = self.store.conn.execute('SELECT * FROM paper_tags ORDER BY evidence_key,tag_id').fetchall()
result = audit(self.db, self.out, batch_size=1)
self.assertEqual(result['status'], 'passed')
self.assertEqual(result['records_checked'], 2)
self.assertEqual(result['expected_evidence'], 4)
self.assertEqual(result['actual_evidence'], 4)
self.assertEqual(result['evidence_without_arxiv_record'], 0)
self.assertEqual(self.store.conn.execute('SELECT * FROM paper_tags ORDER BY evidence_key,tag_id').fetchall(), before)
def test_zero_legacy_keys_does_not_hide_missing_categories_and_cli_fails(self):
self.store.conn.execute("DELETE FROM paper_tags WHERE source_record_id IS NOT NULL")
self.store.conn.commit()
with self.assertRaises(SystemExit):
main(['--db', str(self.db), '--out', str(self.out)])
result = json.loads(self.out.read_text())
self.assertEqual(result['status'], 'failed')
self.assertEqual(result['legacy_evidence'], 0)
self.assertEqual(result['missing_evidence'], 4)
self.assertEqual(result['records_with_mismatches'], 2)
def test_wrong_canonical_paper_or_stale_key_is_detected(self):
other, _ = self.store.record('example', 'other', 'https://example.org', 'Different work', 'AB', [])
self.store.conn.execute("UPDATE paper_tags SET paper_id=?,evidence_key='arxiv:categories' WHERE source_record_id=?", (other, self.records[0]))
self.store.conn.commit()
result = audit(self.db, self.out)
self.assertEqual(result['status'], 'failed')
self.assertEqual(result['records_with_mismatches'], 1)
self.assertEqual(result['legacy_evidence'], 2)
self.assertEqual(result['missing_evidence'], 2)
self.assertEqual(result['unexpected_evidence'], 2)
def test_wrong_source_and_unowned_category_rows_cannot_escape_the_full_audit(self):
paper, record = self.store.record('example', 'other', 'https://example.org', 'Other work', 'AB', [])
tag = self.store.conn.execute("SELECT id FROM tags WHERE namespace='arxiv:category' AND value='cs.AI'").fetchone()[0]
self.store.conn.execute('INSERT INTO paper_tags VALUES(?,?,?,?)', (paper, tag, record, 'wrong-source'))
self.store.conn.execute('INSERT INTO paper_tags VALUES(?,?,NULL,?)', (paper, tag, 'unowned'))
self.store.conn.commit()
result = audit(self.db, self.out)
self.assertEqual(result['status'], 'failed')
self.assertEqual(result['records_with_mismatches'], 0)
self.assertEqual(result['evidence_without_arxiv_record'], 2)
self.assertEqual(len(result['unscoped_examples']), 2)
def test_active_writer_and_incomplete_repair_are_rejected_before_publishing(self):
with Path(str(self.db) + '.maintenance.lock').open('a') as lock:
fcntl.flock(lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
with self.assertRaises(BlockingIOError):
audit(self.db, self.out)
self.assertFalse(self.out.exists())
repair = self.root / 'repair.json'
repair.write_text(json.dumps({'status': 'running'}))
with self.assertRaisesRegex(ValueError, 'not completed'):
audit(self.db, self.out, repair)
self.assertFalse(self.out.exists())
def test_repair_report_scope_and_completed_audit_are_not_silently_reused(self):
repair = self.root / 'repair.json'
repair.write_text(json.dumps({'status': 'complete', 'records_refreshed': 2, 'db': str(self.db),
'source_id': 1, 'source_record_count': 2, 'maximum_source_record_id': 999}))
with self.assertRaisesRegex(ValueError, 'different source inventory'):
audit(self.db, self.out, repair)
result = audit(self.db, self.out)
before = self.out.read_bytes()
with self.assertRaisesRegex(ValueError, 'report exists'):
audit(self.db, self.out)
self.assertEqual(self.out.read_bytes(), before)
self.assertEqual(result['status'], 'passed')
def test_invalid_source_metadata_is_an_error_not_a_partial_pass(self):
self.store.conn.execute('UPDATE source_records SET metadata_json=? WHERE id=?',
(json.dumps({'categories': ['invalid']}), self.records[0]))
self.store.conn.commit()
with self.assertRaisesRegex(ValueError, 'categories must be text'):
audit(self.db, self.out)
self.assertEqual(json.loads(self.out.read_text())['status'], 'error')
def test_interleaved_sources_use_bounded_primary_key_batches_without_sorting(self):
self.store.record('example', 'interleaved', 'https://example.org', 'Other source', 'AB', [])
paper, record = self.store.record('arxiv', 'three', 'https://arxiv.org/abs/three',
'A third record', 'AB', [], metadata={'categories': 'cs.AI'})
refresh_categories(self.store, paper, record, 'cs.AI')
self.store.conn.commit()
queries = []
connect = sqlite3.connect
def traced(*args, **kwargs):
connection = connect(*args, **kwargs)
connection.set_trace_callback(queries.append)
return connection
with patch('paper_atlas.audits.arxiv_tags.sqlite3.connect', side_effect=traced):
result = audit(self.db, self.out, batch_size=1)
self.assertEqual(result['status'], 'passed')
self.assertEqual(result['records_checked'], 3)
self.assertEqual(result['last_record_id'], record)
batches = [sql for sql in queries if sql.startswith('SELECT id,external_id,paper_id,metadata_json')]
self.assertEqual(len(batches), 4) # Includes the bounded final empty read.
for sql in batches:
plan = ' '.join(row[3] for row in self.store.conn.execute('EXPLAIN QUERY PLAN ' + sql))
self.assertIn('INTEGER PRIMARY KEY', plan)
self.assertNotIn('TEMP B-TREE', plan)
if __name__ == '__main__':
unittest.main()
+4 -1
View File
@@ -18,7 +18,10 @@ class CliTests(unittest.TestCase):
def test_unified_import_and_query_use_shipped_schema_and_registry(self):
from paper_atlas.config import DEFAULT_REGISTRY
self.assertEqual(len(json.loads(DEFAULT_REGISTRY.read_text())['venues']),41)
venues = json.loads(DEFAULT_REGISTRY.read_text())['venues']
names = [venue['acronym'] for venue in venues]
self.assertTrue({'COLM', 'MM', 'MLSys'} <= set(names))
self.assertEqual(len(names), len(set(names)))
with tempfile.TemporaryDirectory() as tmp:
root=Path(tmp);db=root/'db.sqlite';source=root/'records.jsonl'
source.write_text(json.dumps({'source':'example','external_id':'one','url':'https://example.org','title':'CLI paper','abstract':'Abstract','authors':['Jane Doe'],'venue':'Example','year':2026,'track':'main','status':'accepted'})+'\n')
+1
View File
@@ -64,6 +64,7 @@ class ICLRTests(unittest.TestCase):
rows,_=self.parse([dict(row,paper_pdf_url=None)],year=2020)
self.assertEqual(rows[0]['metadata']['identity_state'],'program_only')
self.assertEqual(rows[0]['identifiers'],{})
self.assertEqual(rows[0]['url'],'https://iclr.cc/virtual/2020/papers.html')
def test_only_referenced_official_assets_and_real_navigation_years(self):
html='<a href="/archive/2013/">2013</a><a href="/Conferences/2026">2026</a><a href="https://other.example/2025">2025</a>'
+143
View File
@@ -0,0 +1,143 @@
import copy
import hashlib
import json
from pathlib import Path
import tempfile
import unittest
from unittest.mock import patch
from paper_atlas.audits import iclr_legacy
from paper_atlas.ingestion.backfill import backfill, queue_files
from paper_atlas.ingestion.records import ingest_file
from paper_atlas.db.store import Store
class ICLRLegacyTests(unittest.TestCase):
def program(self):
return {'source': 'iclr_program', 'external_id': '2020/program-42', 'venue': 'ICLR',
'year': 2020, 'track': 'main', 'status': 'accepted',
'url': 'https://iclr.cc/virtual/2020/papers.html', 'title': 'Historical paper title',
'abstract': 'Historical abstract', 'authors': ['Jane Doe', 'John Smith'],
'identifiers': {}, 'raw_decision': 'listed in official program',
'evidence_url': 'https://iclr.cc/virtual/2020/papers.html',
'metadata': {'program_identity_type': 'submission', 'program_source_id': 42}}
def snapshot(self):
return {'source': 'openreview_snapshot', 'external_id': '2020/realForum', 'venue': 'ICLR',
'year': 2020, 'track': 'main', 'status': 'accepted',
'url': 'https://openreview.net/forum?id=realForum', 'title': 'Historical paper title',
'abstract': 'Historical abstract', 'authors': ['Jane Doe', 'John Smith'],
'identifiers': {'openreview': 'realForum'},
'submission_identifiers': [{'scheme': 'openreview', 'value': 'realForum'},
{'scheme': 'iclr_number', 'value': '42'}],
'decision_events': [{'status': 'accepted', 'raw_value': 'Accept',
'source_decision_id': 'decision1', 'evidence_url': 'https://openreview.net/forum?id=realForum&noteId=decision1',
'authority': {'public_readers_verified': True}}],
'metadata': {'source_submission_number': 42, 'public_readers_verified': True}}
def legacy(self):
return {'id': 'realForum', 'forum': 'realForum', 'content': {
'iclr_id': 'realForum', 'title': 'Historical paper title', 'authors': ['Jane Doe', 'John Smith']}}
def test_independent_legacy_identity_preserves_existing_source_id_and_text(self):
program, submission = self.program(), self.snapshot()
submission.update(title='A later title', abstract='A later abstract', authors=['Jane Doe'])
rows, checks = iclr_legacy.reconcile([program], {'realForum': submission}, [self.legacy()])
self.assertEqual(rows[0]['external_id'], '2020/program-42')
self.assertEqual(rows[0]['url'], 'https://iclr.cc/virtual_2020/poster_realForum.html')
for field in ('title', 'abstract', 'authors'):
self.assertEqual(rows[0][field], program[field])
self.assertEqual(rows[0]['identifiers']['openreview'], 'realForum')
self.assertTrue(rows[0]['metadata']['program_submission_number_verified'])
self.assertEqual(checks['independent_legacy'], 1)
self.assertEqual(program['identifiers'], {})
def test_program_number_and_shared_authors_alone_do_not_assign_a_forum(self):
program = self.program()
program.update(title='A different paper', abstract='An unrelated abstract')
with self.assertRaisesRegex(ValueError, 'number alone'):
iclr_legacy.reconcile([program], {'realForum': self.snapshot()}, [self.legacy()])
def test_independent_snapshot_title_and_abstract_handle_legacy_name_variants(self):
legacy = self.legacy()
legacy['content']['authors'] = ['J. Doe', 'J. Smith']
rows, checks = iclr_legacy.reconcile([self.program()], {'realForum': self.snapshot()}, [legacy])
self.assertEqual(checks['independent_snapshot'], 1)
self.assertEqual(rows[0]['identifiers']['openreview'], 'realForum')
def test_reviewed_title_variant_is_exact_and_requires_public_author_corroboration(self):
variant = iclr_legacy.REVIEWED_TITLE_VARIANT
program, submission, legacy = self.program(), self.snapshot(), self.legacy()
program['title'] = variant['program']
submission.update(title=variant['snapshot'], abstract='A different revision')
submission['identifiers']['openreview'] = variant['forum']
legacy.update(id=variant['forum'], forum=variant['forum'])
legacy['content'].update(iclr_id=variant['forum'], title=variant['legacy'])
rows, checks = iclr_legacy.reconcile([program], {variant['forum']: submission}, [legacy])
self.assertEqual(checks['reviewed_title_variant'], 1)
self.assertTrue(rows[0]['metadata']['program_identity_verification']['reviewed_title_variant'])
program['authors'] = ['Jane Doe']
with self.assertRaisesRegex(ValueError, 'number alone'):
iclr_legacy.reconcile([program], {variant['forum']: submission}, [legacy])
def test_conflicting_forum_ambiguous_number_and_repeated_legacy_identity_fail(self):
p = self.program()
p['identifiers']['openreview'] = 'anotherForum'
with self.assertRaisesRegex(ValueError, 'conflicts'):
iclr_legacy.reconcile([p], {'realForum': self.snapshot()}, [self.legacy()])
duplicate = copy.deepcopy(self.snapshot())
duplicate['identifiers']['openreview'] = 'otherForum'
with self.assertRaisesRegex(ValueError, 'ambiguous'):
iclr_legacy.reconcile([self.program()], {'realForum': self.snapshot(), 'otherForum': duplicate}, [self.legacy()])
with self.assertRaisesRegex(ValueError, 'repeated'):
iclr_legacy.reconcile([self.program()], {'realForum': self.snapshot()}, [self.legacy(), self.legacy()])
def write_file(self, path, rows, source):
path.write_text(''.join(json.dumps(row) + '\n' for row in rows))
manifest = {'source': source, 'venue': 'ICLR', 'year': 2020, 'track': 'main',
'parser_version': 2, 'count': len(rows), 'missing_abstract_count': 0,
'list_url': 'https://iclr.cc/virtual/2020/papers.html', 'status': 'collected',
'submission_status_counts': {status: sum(r['status'] == status for r in rows)
for status in {r['status'] for r in rows}}}
path.with_suffix('.manifest.json').write_text(json.dumps(manifest))
def test_audited_bridge_then_snapshot_import_keeps_one_accepted_attempt(self):
with tempfile.TemporaryDirectory() as tmp:
root = Path(tmp)
program_path, snapshot_path, legacy_path = (root / name for name in ('program.jsonl', 'snapshot.jsonl', 'legacy.json'))
self.write_file(program_path, [self.program()], 'iclr_program')
self.write_file(snapshot_path, [self.snapshot()], 'openreview_snapshot')
raw = json.dumps([self.legacy()]).encode()
legacy_path.write_bytes(raw)
with patch.multiple(iclr_legacy, LEGACY_BYTES=len(raw), LEGACY_SHA256=hashlib.sha256(raw).hexdigest(), EXPECTED=1):
report = iclr_legacy.audit(program_path, snapshot_path, legacy_path, root / 'out')
db = root / 'papers.sqlite'
ingest_file(db, program_path)
queue = root / 'out/iclr-2020-backfill-queue.json'
result = backfill(db, queue_files(queue))
self.assertEqual(result['submissions_before'], result['submissions_after'])
ingest_file(db, report['backfill_queue']['files'][0])
ingest_file(db, snapshot_path)
store = Store(db)
try:
self.assertEqual(store.conn.execute('SELECT count(*) FROM papers').fetchone()[0], 1)
self.assertEqual(store.conn.execute('SELECT count(*) FROM submissions').fetchone()[0], 1)
self.assertEqual(store.conn.execute('SELECT count(*) FROM submission_sources').fetchone()[0], 2)
self.assertEqual(store.conn.execute('SELECT url FROM source_records WHERE external_id=?', ('2020/program-42',)).fetchone()[0],
'https://iclr.cc/virtual_2020/poster_realForum.html')
self.assertEqual(store.conn.execute('PRAGMA foreign_key_check').fetchall(), [])
finally:
store.conn.close()
def test_unverified_legacy_bytes_publish_no_output(self):
with tempfile.TemporaryDirectory() as tmp:
root = Path(tmp)
legacy = root / 'legacy.json'
legacy.write_text('[]')
with self.assertRaisesRegex(ValueError, 'checksum'):
iclr_legacy.audit(root / 'program', root / 'snapshot', legacy, root / 'out')
self.assertFalse((root / 'out').exists())
if __name__ == '__main__':
unittest.main()
+3 -3
View File
@@ -55,7 +55,7 @@ class StoreTests(unittest.TestCase):
def test_manifest_count_mismatch_rolls_back_records(self):
path=Path(self.tmp.name)/'source.jsonl'
path.write_text(json.dumps({'source':'pmlr','external_id':'v1/paper','url':'https://example.org/paper','title':'Paper','abstract':'Abstract','authors':[],'venue':'ICML','year':2025,'track':'main','status':'accepted'})+'\n')
path.write_text(json.dumps({'source':'pmlr','external_id':'v1/paper','url':'https://example.org/paper','title':'Paper','abstract':'Abstract','authors':[],'venue':'ICML','year':2023,'track':'main','status':'accepted'})+'\n')
path.with_suffix('.manifest.json').write_text(json.dumps({'source':'pmlr','list_url':'https://example.org/list','count':2}))
with self.assertRaisesRegex(ValueError,'differs'):
ingest_file(self.db,path)
@@ -100,7 +100,7 @@ class StoreTests(unittest.TestCase):
def test_missing_abstract_is_checked_even_when_manifest_claims_complete(self):
path=Path(self.tmp.name)/'incomplete.jsonl'
row={'source':'pmlr','external_id':'v1/paper','url':'https://example.org/paper','title':'Paper','abstract':None,'authors':[],'venue':'ICML','year':2025,'track':'main','status':'accepted'}
row={'source':'pmlr','external_id':'v1/paper','url':'https://example.org/paper','title':'Paper','abstract':None,'authors':[],'venue':'ICML','year':2023,'track':'main','status':'accepted'}
path.write_text(json.dumps(row)+'\n')
path.with_suffix('.manifest.json').write_text(json.dumps({'source':'pmlr','list_url':'https://example.org/list','count':1,'status':'collected','missing_abstract_count':0}))
ingest_file(self.db,path)
@@ -108,7 +108,7 @@ class StoreTests(unittest.TestCase):
def test_manifest_edition_mismatch_rolls_back_instead_of_marking_coverage(self):
path=Path(self.tmp.name)/'wrong-edition.jsonl'
row={'source':'pmlr','external_id':'v1/paper','url':'https://example.org/paper','title':'Paper','abstract':'Abstract','authors':[],'venue':'ICML','year':2025,'track':'main','status':'accepted'}
row={'source':'pmlr','external_id':'v1/paper','url':'https://example.org/paper','title':'Paper','abstract':'Abstract','authors':[],'venue':'ICML','year':2023,'track':'main','status':'accepted'}
path.write_text(json.dumps(row)+'\n')
path.with_suffix('.manifest.json').write_text(json.dumps({'source':'pmlr','list_url':'https://example.org/list','count':1,'year':2024}))
with self.assertRaisesRegex(ValueError,'edition differs'):
+166
View File
@@ -0,0 +1,166 @@
import hashlib
import json
from contextlib import closing
from pathlib import Path
import sqlite3
import tempfile
import unittest
from unittest.mock import patch
from paper_atlas.collectors.proceedings import discover, parse_paper
from paper_atlas.collectors.dblp import XML_SHA
from paper_atlas.collectors.dblp_records import identifiers, normalize_row, collect
from paper_atlas.collectors.dblp_scope import scope
from paper_atlas.collectors.public_openreview import normalize
from paper_atlas.db.submissions import identities_for_row
from paper_atlas.ingestion.records import ingest_file
from paper_atlas.io.publication_ids import mlsys_id
HASH = '0123456789abcdef' * 2
ROOT = 'https://proceedings.mlsys.org/'
def page(year=2026, modern=True):
return ROOT + ('paper_files/paper/' if modern else 'paper/') + str(year) + '/hash/' + HASH + ('-Abstract-Conference.html' if modern else '-Abstract.html')
def raw_row(family='mm', book='ACM Multimedia', year=2024):
return {'record_type': 'inproceedings', 'key': f'conf/{family}/Paper24', 'publtype': None,
'fields': {'title': ['A published paper'], 'author': ['Jane Doe', 'John Smith'],
'booktitle': [book], 'year': [str(year)], 'crossref': [f'conf/{family}/{year}']}}
def volume(family='mm', year=2024, title=None):
return {'record_type': 'proceedings', 'key': f'conf/{family}/{year}',
'fields': {'title': [title or f'ACM Multimedia {year}'], 'year': [str(year)]}}
class MlsysMultimediaTests(unittest.TestCase):
def test_mlsys_discovery_retains_all_official_years_and_ignores_pdf_or_other_host(self):
html = ''.join(f'<a href="/paper_files/paper/{year}">MLSys {year}</a>' for year in range(2019, 2027))
html += '<a href="https://example.org/paper_files/paper/2018">Other</a><a href="/paper/2026/file/paper.pdf">PDF</a>'
with patch('paper_atlas.collectors.proceedings.fetch', return_value=html.encode()):
self.assertEqual([year for _, year in discover('mlsys', '/unused')], list(range(2019, 2027)))
def test_mlsys_metadata_has_stable_publisher_identity_and_explicit_track(self):
html = '<meta name="citation_title" content="A title"><meta name="citation_author" content="Doe, Jane"><span class="paper-track">Conference</span><h2>Abstract</h2><p>Real abstract.</p><h4>Name Change Policy</h4><p>Footer.</p>'
row = parse_paper(html, page(), 'mlsys', 2026, ROOT + 'paper_files/paper/2026')
self.assertEqual((row['venue'], row['track'], row['abstract'], row['authors']), ('MLSys', 'main', 'Real abstract.', ['Jane Doe']))
self.assertEqual(row['identifiers']['publication_mlsys'], '2026/' + HASH)
with self.assertRaisesRegex(ValueError, 'Unclassified'):
parse_paper(html.replace('Conference', 'New Unknown Track'), page(), 'mlsys', 2026, ROOT)
with self.assertRaisesRegex(ValueError, 'publication year'):
parse_paper(html, page(), 'mlsys', 2025, ROOT)
with self.assertRaisesRegex(ValueError, 'non-archival'):
parse_paper(html, page(2018), 'mlsys', 2018, ROOT)
def test_year_label_and_retained_bibliography_links_bridge_the_2023_format(self):
url = page(2023).replace('-Conference.html', '-mlsys2023.html')
self.assertEqual(mlsys_id(url), '2023/' + HASH)
self.assertIsNone(mlsys_id(url.replace('mlsys2023.html', 'mlsys2022.html')))
official = parse_paper('<h1>Updated title</h1><span class="paper-track">mlsys2023</span><p class="paper-abstract">Official abstract</p>', url, 'mlsys', 2023, ROOT)
self.assertEqual(official['track'], 'main')
legacy = {'source': 'dblp', 'external_id': 'conf/mlsys/paper23', 'url': 'https://dblp.org/rec/conf/mlsys/paper23',
'venue': 'MLSys', 'year': 2023, 'track': 'main', 'status': 'accepted', 'title': 'Bibliographic title',
'abstract': None, 'authors': [], 'identifiers': {}, 'metadata': {'bibliography': {'ee': [url]}}}
self.assertEqual(identities_for_row(legacy), [('publication_mlsys', '2023/' + HASH)])
self.assertEqual(identities_for_row({**legacy, 'status': 'unknown'}), [])
with tempfile.TemporaryDirectory() as tmp:
root = Path(tmp); db = root / 'papers.sqlite'
for row in [legacy, official]:
path = root / (row['source'] + '.jsonl'); path.write_text(json.dumps(row) + '\n')
path.with_suffix('.manifest.json').write_text(json.dumps({'source': row['source'], 'parser_version': 2, 'list_url': ROOT, 'count': 1}))
ingest_file(db, path)
with closing(sqlite3.connect(db)) as c:
self.assertEqual(c.execute('SELECT count(*) FROM papers').fetchone()[0], 1)
self.assertEqual(c.execute('SELECT count(*) FROM submissions').fetchone()[0], 1)
self.assertEqual(c.execute('SELECT count(*) FROM submission_sources').fetchone()[0], 2)
def test_legacy_mlsys_and_sysml_alias_preserve_same_publication_identity(self):
self.assertEqual(mlsys_id(page(2019, False)), mlsys_id(page(2019)))
self.assertIsNone(mlsys_id(page().replace('proceedings.mlsys.org', 'example.org')))
own, ambiguous = identifiers({'ee': [page(2019, False), page(2019)], 'cite': [page(2025)]})
self.assertEqual(own, {'publication_mlsys': '2019/' + HASH}); self.assertFalse(ambiguous)
_, ambiguous = identifiers({'ee': [page(2019), page(2019).replace(HASH, 'a' * 32)]})
self.assertEqual(len(ambiguous['publication_mlsys']), 2)
row = parse_paper('<h1>Legacy</h1><p class="paper-abstract">Abstract</p>', page(2019, False), 'mlsys', 2019, ROOT)
self.assertEqual(row['venue_aliases'], ['SysML'])
self.assertEqual(row['track'], 'main')
def test_mm_main_numbered_parts_and_workshops_remain_separate(self):
for book in ['ACM Multimedia', 'ACM Multimedia (1)', 'ACM Multimedia (2)']:
result, reason = scope(raw_row(book=book), volume())
self.assertIsNone(reason); self.assertEqual(result['venue'], 'MM'); self.assertEqual(result['track'], 'proceedings_unspecified')
self.assertIn('per-paper section', result['track_scope_note'])
self.assertIn('ACMMM', result['venue_aliases'])
self.assertEqual(scope(raw_row(book='ACM Multimedia Workshops'), volume())[0]['track'], 'workshop')
self.assertEqual(scope(raw_row(book='ACM Multimedia (Thematic Workshops)'), volume())[0]['track'], 'workshop')
self.assertIsNone(scope(raw_row(book='MMSports@MM'), volume())[0])
self.assertEqual(normalize_row(raw_row(book='ACM Multimedia Workshops'), {'conf/mm/2024': volume()}, {'MM'})[1], 'separate_workshop')
def test_sysml_alias_requires_machine_learning_proceedings(self):
row = raw_row('mlsys', 'SysML', 2019)
result, reason = scope(row, volume('mlsys', 2019, 'Conference on Machine Learning and Systems, SysML 2019'))
self.assertIsNone(reason); self.assertEqual(result['venue'], 'MLSys'); self.assertEqual(result['venue_aliases'], ['SysML'])
self.assertIsNone(scope(row, volume('mlsys', 2019, 'Systems Modeling Language 2019'))[0])
def test_bibliography_and_official_abstract_import_as_one_paper_and_submission(self):
raw = raw_row('mlsys', 'SysML', 2019); raw['fields']['ee'] = [page(2019, False)]
bib, reason = normalize_row(raw, {'conf/mlsys/2019': volume('mlsys', 2019, 'Machine Learning and Systems 2019')}, {'MLSys'})
self.assertIsNone(reason)
official = parse_paper('<meta name="citation_title" content="An updated title"><p class="paper-abstract">The official abstract.</p>', page(2019), 'mlsys', 2019, ROOT)
# Different title and absent official authors deliberately prevent a title-based bridge.
with tempfile.TemporaryDirectory() as tmp:
root = Path(tmp); db = root / 'papers.sqlite'
for row in [bib, official]:
path = root / (row['source'] + '.jsonl'); path.write_text(json.dumps(row) + '\n')
path.with_suffix('.manifest.json').write_text(json.dumps({'source': row['source'], 'parser_version': 2,
'list_url': ROOT, 'count': 1, 'venue': 'MLSys', 'year': 2019, 'track': 'main'}))
ingest_file(db, path)
with closing(sqlite3.connect(db)) as c:
self.assertEqual(c.execute('SELECT count(*) FROM papers').fetchone()[0], 1)
self.assertEqual(c.execute('SELECT count(*) FROM submissions').fetchone()[0], 1)
self.assertEqual(c.execute('SELECT count(*) FROM submission_sources').fetchone()[0], 2)
self.assertEqual(c.execute('SELECT abstract FROM papers').fetchone()[0], 'The official abstract.')
self.assertEqual(c.execute('PRAGMA foreign_key_check').fetchall(), [])
def test_publisher_identity_cannot_bridge_rejection_other_year_or_venue(self):
row = {'source': 'mlsys', 'venue': 'MLSys', 'year': 2026, 'status': 'accepted',
'identifiers': {'publication_mlsys': '2026/' + HASH}}
self.assertEqual(identities_for_row(row), [('publication_mlsys', '2026/' + HASH)])
self.assertEqual(identities_for_row({**row, 'status': 'rejected'}), [])
with self.assertRaisesRegex(ValueError, 'Invalid authoritative'):
identities_for_row({**row, 'identifiers': {}})
for changed in [dict(year=2025), dict(venue='MM'), dict(source='curated')]:
bad = {**row, **changed, 'submission_identifiers': [{'scheme': 'publication_mlsys', 'value': '2026/' + HASH}]}
with self.assertRaisesRegex(ValueError, 'Invalid authoritative'):
identities_for_row(bad)
def test_explicit_mm_negative_assertion_maps_to_mm_without_inventing_labels(self):
provenance = {'source_file': 'https://example.org/pinned', 'source_line': 1}
row = {'id': 'realForum1', 'title': 'A title', 'abstract': 'An abstract', 'track': 'main', 'status': 'Reject'}
normalized, reason = normalize(row, 'acmmm', 2025, provenance)
self.assertIsNone(reason); self.assertEqual(normalized['venue'], 'MM')
self.assertEqual(normalized['status'], 'rejected')
self.assertIsNone(normalize({**row, 'status': 'Submitted'}, 'acmmm', 2025, provenance)[0])
def test_old_candidate_subset_cannot_silently_omit_new_requested_venues(self):
with tempfile.TemporaryDirectory() as tmp:
root = Path(tmp); catalogue = root / 'dblp-catalogue.sqlite'
with closing(sqlite3.connect(catalogue)) as c, c:
c.execute('CREATE TABLE proceedings(key TEXT PRIMARY KEY,metadata_json TEXT)')
c.execute('INSERT INTO proceedings VALUES(?,?)', ('conf/mm/2024', json.dumps(volume())))
candidates = root / 'candidates.jsonl'; candidates.write_text(json.dumps(raw_row()) + '\n')
original = candidates.read_bytes()
catalogue.with_name('dblp-ai-candidates.manifest.json').write_text(json.dumps({
'snapshot_sha256': XML_SHA, 'candidate_sha256': hashlib.sha256(original).hexdigest(),
'candidate_family_counts': {'aaai': 1}, 'record_types': {'proceedings': 1}}))
with self.assertRaisesRegex(ValueError, 'original --archive'):
collect(catalogue, root / 'out', ['MM'], candidates=candidates)
self.assertEqual(candidates.read_bytes(), original)
self.assertFalse((root / 'out').exists())
if __name__ == '__main__':
unittest.main()
+1 -1
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@@ -25,7 +25,7 @@ class MetadataTests(unittest.TestCase):
self.assertEqual(venue_key('ECML-PKDD'),'ECML-PKDD')
def test_missing_abstract_is_reported_as_partial_collection(self):
config=b'shortname: ICML\nyear: 2025\nbooktitle: ICML\n'
config=b'shortname: ICML\nyear: 2023\nbooktitle: ICML\n'
paper='---\nid: paper1\nlayout: inproceedings\ntitle: Paper\nabstract:\n---\n'
with tempfile.TemporaryDirectory() as tmp,patch('paper_atlas.collectors.pmlr.fetch',return_value=config),patch('paper_atlas.collectors.pmlr.metadata_texts',return_value=iter([('paper.md',paper)])):
result=collect_volume(999,tmp,tmp)
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@@ -0,0 +1,156 @@
import copy
import fcntl
import hashlib
import json
from pathlib import Path
import sqlite3
import tempfile
import unittest
from unittest.mock import patch
from paper_atlas.collectors.pmlr_tracks import program_tracks, record_track
from paper_atlas.db.store import Store
from paper_atlas.db.submissions import identities_for_row
from paper_atlas.ingestion.pmlr_tracks import reclassify, plan
from paper_atlas.ingestion.records import ingest_file
from tests.test_pmlr_tracks import event, program, record
class PmlrMigrationTests(unittest.TestCase):
def setUp(self):
self.tmp = tempfile.TemporaryDirectory(); self.addCleanup(self.tmp.cleanup)
self.root = Path(self.tmp.name); self.db = self.root / 'papers.sqlite'
self.inventory = self.root / 'inventory.json'
self.rows = [record(title='A main research paper'),
record('position1', 'v267/paper2', title='A position paper')]
self.proof = {'url': 'https://icml.cc/static/virtual/data/icml-2025-orals-posters.json', 'sha256': 'a' * 64}
mapping, _ = program_tracks(program(event(), event('position1', 'Position_Paper_Track', 2)), 2025)
store = Store(self.db); c = store.conn
for row in self.rows:
row.update(url='https://proceedings.mlr.press/' + row['external_id'] + '.html',
list_url='https://proceedings.mlr.press/v267/', status='accepted')
paper, source = store.record('pmlr', row['external_id'], row['url'], row['title'], row['abstract'],
row['authors'], row['identifiers'], {'openreview': row['identifiers']['openreview']})
store.decision(paper, source, 'ICML', 2025, 'main', row['external_id'], row['url'],
'accepted', 'listed in official proceedings', identities=identities_for_row(row))
record_track(row, mapping, self.proof)
c.execute("INSERT INTO tags(namespace,value) VALUES('custom:topic','keep me')")
c.execute("INSERT INTO paper_tags VALUES(1,1,NULL,'custom:manual')")
c.commit(); c.close()
self.write_inventory()
def write_inventory(self):
files = []
for row in self.rows:
path = self.root / (row['track'] + '.jsonl')
data = (json.dumps(row) + '\n').encode(); path.write_bytes(data)
m = {'source': 'pmlr', 'venue': 'ICML', 'year': 2025, 'volume': 267,
'parser_version': 3, 'track': row['track'], 'track_program': self.proof,
'count': 1, 'file': str(path), 'file_sha256': hashlib.sha256(data).hexdigest(),
'missing_abstract_count': 0, 'list_url': row['list_url'], 'status': 'collected'}
path.with_suffix('.manifest.json').write_text(json.dumps(m)); files.append(m)
self.inventory.write_text(json.dumps({'source': 'pmlr', 'venue': 'ICML', 'year': 2025,
'volume': 267, 'parser_version': 3, 'track_program': self.proof,
'count': 2, 'files': files}))
def tracks(self):
with sqlite3.connect(self.db) as c:
return c.execute('SELECT s.id,e.track FROM submissions s JOIN editions e ON e.id=s.edition_id ORDER BY s.id').fetchall()
def test_plan_is_read_only_and_reports_exact_original_event(self):
result = reclassify(self.db, [self.inventory], self.root / 'plan.json')
self.assertEqual((result['status'], result['records_verified'], result['events_to_move']), ('planned', 2, 1))
self.assertEqual(result['changes'][0]['submission_id'], 2)
self.assertEqual(self.tracks(), [(1, 'main'), (2, 'main')])
def test_apply_preserves_ids_decisions_text_tags_and_is_idempotent(self):
with sqlite3.connect(self.db) as c:
before = {table: c.execute('SELECT * FROM ' + table).fetchall() for table in ('papers', 'decisions', 'decision_sources', 'submission_sources', 'paper_tags')}
result = reclassify(self.db, [self.inventory], self.root / 'apply.json', True)
self.assertEqual((result['status'], result['events_moved']), ('complete', 1))
self.assertEqual(self.tracks(), [(1, 'main'), (2, 'position')])
with sqlite3.connect(self.db) as c:
for table, rows in before.items():
self.assertEqual(c.execute('SELECT * FROM ' + table).fetchall(), rows, table)
self.assertEqual(c.execute('SELECT count(*) FROM submission_identifiers i JOIN submissions s ON s.id=i.submission_id WHERE i.edition_id<>s.edition_id').fetchone()[0], 0)
self.assertEqual(c.execute('SELECT e.track,es.imported_count FROM edition_sources es JOIN editions e ON e.id=es.edition_id ORDER BY e.track').fetchall(), [('main', 1), ('position', 1)])
self.assertEqual(c.execute('PRAGMA foreign_key_check').fetchall(), [])
again = reclassify(self.db, [self.inventory], self.root / 'again.json', True)
self.assertEqual(again['events_moved'], 0)
for m in json.loads(self.inventory.read_text())['files']:
ingest_file(self.db, m['file'])
self.assertEqual(self.tracks(), [(1, 'main'), (2, 'position')])
with sqlite3.connect(self.db) as c:
self.assertEqual(c.execute('SELECT * FROM decisions').fetchall(), before['decisions'])
def test_conflicting_target_event_stops_without_merging_history(self):
store = Store(self.db)
_, source = store.record('other', 'position1', 'https://example.org', 'Other evidence', None, [], {'openreview': 'position1'})
store.decision(2, source, 'ICML', 2025, 'position', 'position1', 'https://example.org', 'rejected', 'Reject', identities=[('openreview', 'position1')])
store.conn.commit(); store.conn.close()
before = self.tracks()
with self.assertRaisesRegex(ValueError, 'another event'):
reclassify(self.db, [self.inventory], self.root / 'blocked.json', True)
self.assertEqual(self.tracks(), before)
def test_shared_event_requires_reconciliation_and_keeps_all_sources(self):
store = Store(self.db)
_, source = store.record('mirror', 'position1', 'https://example.org', 'Mirror title', None, [], {'openreview': 'position1'})
store.conn.execute('INSERT INTO submission_sources VALUES(?,?,?)', (2, source, 'position1'))
store.conn.commit(); store.conn.close()
with self.assertRaisesRegex(ValueError, 'multiple sources'):
reclassify(self.db, [self.inventory], self.root / 'shared.json', True)
self.assertEqual(self.tracks(), [(1, 'main'), (2, 'main')])
def test_text_mismatch_in_last_record_prevents_any_changes(self):
with sqlite3.connect(self.db) as c:
c.execute("UPDATE source_records SET abstract='Changed elsewhere' WHERE id=2")
with self.assertRaisesRegex(ValueError, 'preserve existing publisher text'):
reclassify(self.db, [self.inventory], self.root / 'text.json', True)
self.assertEqual(self.tracks(), [(1, 'main'), (2, 'main')])
def test_mutation_failure_rolls_back_editions_metadata_and_identifiers(self):
calls = 0
def fail_after_updates(c, scopes):
nonlocal calls
calls += 1
if calls == 2:
raise ValueError('Injected post-migration failure')
return plan(c, scopes)
with sqlite3.connect(self.db) as c:
before = c.execute('SELECT * FROM source_records').fetchall()
with patch('paper_atlas.ingestion.pmlr_tracks.plan', side_effect=fail_after_updates):
with self.assertRaisesRegex(ValueError, 'Injected'):
reclassify(self.db, [self.inventory], self.root / 'rollback.json', True)
self.assertEqual(self.tracks(), [(1, 'main'), (2, 'main')])
with sqlite3.connect(self.db) as c:
self.assertEqual(c.execute('SELECT * FROM source_records').fetchall(), before)
self.assertEqual(c.execute("SELECT count(*) FROM editions WHERE track='position'").fetchone()[0], 0)
self.assertEqual(json.loads((self.root / 'rollback.json').read_text())['status'], 'error')
def test_changed_evidence_and_active_writer_are_refused(self):
out = self.root / 'blocked.json'
with Path(str(self.db) + '.maintenance.lock').open('a') as lock:
fcntl.flock(lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
with self.assertRaises(BlockingIOError):
reclassify(self.db, [self.inventory], out, True)
self.assertFalse(out.exists())
path = self.root / 'position.jsonl'; path.write_text(path.read_text() + ' ')
with self.assertRaisesRegex(ValueError, 'differs from its verified inventory'):
reclassify(self.db, [self.inventory], out, True)
self.assertEqual(self.tracks(), [(1, 'main'), (2, 'main')])
def test_input_report_and_duplicate_forums_are_refused(self):
original = self.inventory.read_bytes()
with self.assertRaisesRegex(ValueError, 'preserve evidence'):
reclassify(self.db, [self.inventory], self.inventory, True)
self.assertEqual(self.inventory.read_bytes(), original)
self.rows[1]['identifiers']['openreview'] = self.rows[0]['identifiers']['openreview']
self.rows[1]['metadata']['track_evidence']['identity_value'] = self.rows[0]['identifiers']['openreview']
self.write_inventory()
with self.assertRaisesRegex(ValueError, 'repeated forum'):
reclassify(self.db, [self.inventory], self.root / 'duplicate.json', True)
if __name__ == '__main__':
unittest.main()
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@@ -0,0 +1,148 @@
import copy
import json
from pathlib import Path
import tempfile
import unittest
from unittest.mock import patch
from paper_atlas.collectors.pmlr import collect_volume
from paper_atlas.collectors.pmlr_tracks import program_tracks, record_track, position_list_policy
from paper_atlas.ingestion.records import ingest_file
from paper_atlas.ingestion.backfill import backfill
def event(forum='realForum1', track='Conference', event_id=1, year=2025, **values):
return {'id': event_id, 'sourceid': event_id, 'name': 'A published paper',
'sourceurl': f'https://openreview.net/group?id=ICML.cc/{year}/' + track,
'paper_url': 'https://openreview.net/forum?id=' + forum,
'decision': 'Accept (Poster)', **values}
def program(*events, **changes):
return json.dumps({'count': len(events), 'results': list(events), **changes}).encode()
def record(forum='realForum1', external='v267/paper1', year=2025, title='A published paper'):
return {'source': 'pmlr', 'external_id': external, 'venue': 'ICML', 'year': year,
'title': title, 'abstract': 'Original abstract', 'authors': ['Jane Doe', 'John Smith'],
'identifiers': {'openreview': forum}, 'metadata': {}, 'track': 'main'}
class PmlrTrackTests(unittest.TestCase):
def provenance(self):
return {'url': 'https://icml.cc/static/virtual/data/icml-2025-orals-posters.json', 'sha256': 'a' * 64}
def test_real_groups_not_title_prefixes_determine_modern_tracks(self):
mapping, inventory = program_tracks(program(
event(name='Position: still a main-track paper'),
event('position1', 'Position_Paper_Track', 2, name='No prefix needed'),
event('2025-Oral-fake', event_id=3, sourceid=-1),
event('workshop1', 'Workshop', 4)), 2025)
main = record(title='Position: still a main-track paper')
position = record('position1', 'v267/paper2', title='No prefix needed')
record_track(main, mapping, self.provenance()); record_track(position, mapping, self.provenance())
self.assertEqual((main['track'], position['track']), ('main', 'position'))
self.assertEqual(inventory['paper_identity_count'], 2)
self.assertEqual(inventory['excluded_events'], {'synthetic_oral_event': 1, 'other_source': 1})
def test_conflicting_forums_pagination_and_missing_real_ids_fail(self):
for data in [program(event(), event(track='Position_Paper_Track', event_id=2)),
program(event(), next='page2'), program(event(), count=2),
program(event(paper_url='')), program(event(decision='Reject')),
program(event(), event())]:
with self.subTest(data=data), self.assertRaises(ValueError):
program_tracks(data, 2025)
def test_missing_publication_identity_has_no_main_track_fallback(self):
mapping, _ = program_tracks(program(event()), 2025)
with self.assertRaisesRegex(ValueError, 'absent'):
record_track(record('unknownForum'), mapping, self.provenance())
def test_2024_requires_organizer_endorsed_list_and_publisher_self_links(self):
html = b'<a href="/virtual/2024/papers.html?filter=titles&amp;search=position%3A">position papers</a>'
policy = position_list_policy(html)
with self.assertRaises(ValueError):
position_list_policy(html.replace(b'2024', b'2023'))
e = event(year=2024, name='Position: An explicit position', paper_url='',
paper_pdf_url='https://proceedings.mlr.press/v235/paper1.html')
with self.assertRaisesRegex(ValueError, 'policy'):
program_tracks(program(e), 2024)
mapping, _ = program_tracks(program(e), 2024, policy)
row = record(external='v235/paper1', year=2024)
record_track(row, mapping, {**self.provenance(), 'position_list_policy': policy})
self.assertEqual(row['track'], 'position')
self.assertEqual(row['metadata']['track_evidence']['identity_scheme'], 'pmlr')
def test_reviewed_2024_link_alias_still_needs_title_and_two_authors(self):
e = event(year=2024, paper_url='', paper_pdf_url='https://proceedings.mlr.press/v235/theo24a.html',
authors=[{'fullname': 'Jane Doe'}, {'fullname': 'John Smith'}])
mapping, _ = program_tracks(program(e), 2024, {'verified': True})
row = record(external='v235/guyard24a', year=2024)
record_track(row, mapping, self.provenance())
self.assertEqual(row['metadata']['track_evidence']['corroborating_author_count'], 2)
self.assertNotIn('_authors', row['metadata']['track_evidence'])
for changed in [dict(title='Different title'), dict(authors=['Someone Else'])]:
bad = record(external='v235/guyard24a', year=2024); bad.update(changed)
with self.assertRaisesRegex(ValueError, 'corroboration'):
record_track(bad, mapping, self.provenance())
def test_collector_splits_tracks_preserves_ids_and_imports_one_event_each(self):
config = b'shortname: ICML\nyear: 2025\nbooktitle: ICML\n'
template = '---\nid: {id}\nlayout: inproceedings\ntitle: {title}\nabstract: Original abstract\nopenreview: {forum}\n---\n'
posts = [('a.md', template.format(id='paper1', title='Main paper', forum='realForum1')),
('b.md', template.format(id='paper2', title='Position paper', forum='position1'))]
mapping, inventory = program_tracks(program(event(), event('position1', 'Position_Paper_Track', 2)), 2025)
with tempfile.TemporaryDirectory() as tmp, patch('paper_atlas.collectors.pmlr.fetch', return_value=config), \
patch('paper_atlas.collectors.pmlr.metadata_texts', return_value=iter(posts)), \
patch('paper_atlas.collectors.pmlr.collect_track_evidence', return_value=(mapping, self.provenance())):
result = collect_volume(267, tmp, tmp)
self.assertNotIn('file', result)
self.assertEqual(result['track'], 'mixed')
self.assertEqual({m['track']: m['count'] for m in result['files']}, {'main': 1, 'position': 1})
self.assertEqual(result['count'], 2)
db = Path(tmp) / 'papers.sqlite'
for manifest in result['files']:
ingest_file(db, manifest['file'])
import sqlite3
with sqlite3.connect(db) as c:
self.assertEqual(c.execute('SELECT count(*) FROM submissions').fetchone()[0], 2)
self.assertEqual(c.execute('SELECT track,count(*) FROM submissions s JOIN editions e ON s.edition_id=e.id GROUP BY track').fetchall(), [('main', 1), ('position', 1)])
self.assertEqual(c.execute('PRAGMA foreign_key_check').fetchall(), [])
def test_unknown_track_does_not_replace_existing_volume_output(self):
config = b'shortname: ICML\nyear: 2025\nbooktitle: ICML\n'
post = '---\nid: paper1\nlayout: inproceedings\ntitle: Paper\nopenreview: missing123\n---\n'
with tempfile.TemporaryDirectory() as tmp, patch('paper_atlas.collectors.pmlr.fetch', return_value=config), \
patch('paper_atlas.collectors.pmlr.metadata_texts', return_value=iter([('a.md', post)])), \
patch('paper_atlas.collectors.pmlr.collect_track_evidence', return_value=({}, self.provenance())):
old = Path(tmp) / 'pmlr-v267.jsonl'; old.write_text('previous collection')
with self.assertRaisesRegex(ValueError, 'absent'):
collect_volume(267, tmp, tmp)
self.assertEqual(old.read_text(), 'previous collection')
self.assertFalse((Path(tmp) / 'pmlr-v267.inventory.json').exists())
def test_old_mixed_manifest_is_rejected_before_opening_database(self):
with tempfile.TemporaryDirectory() as tmp:
path = Path(tmp) / 'pmlr-v267.jsonl'; path.write_text('')
path.with_suffix('.manifest.json').write_text(json.dumps({'source': 'pmlr', 'venue': 'ICML', 'year': 2025, 'parser_version': 2}))
db = Path(tmp) / 'absent.sqlite'
for action in [lambda: ingest_file(db, path), lambda: backfill(db, [path])]:
with self.assertRaisesRegex(ValueError, 'Recollect mixed'):
action()
self.assertFalse(db.exists())
def test_changed_track_or_own_identity_rolls_back_import(self):
from paper_atlas.collectors.pmlr_tracks import require_track_record
row = record(); mapping, _ = program_tracks(program(event()), 2025)
record_track(row, mapping, self.provenance())
manifest = {'source': 'pmlr', 'venue': 'ICML', 'year': 2025, 'parser_version': 3,
'track_program': self.provenance()}
require_track_record(row, manifest)
for change in [dict(track='position'), dict(identifiers={'openreview': 'otherForum'})]:
bad = copy.deepcopy(row); bad.update(change)
with self.assertRaises(ValueError):
require_track_record(bad, manifest)
if __name__ == '__main__':
unittest.main()
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import contextlib
from contextlib import closing
import io
import json
import os
from pathlib import Path
import sqlite3
import tempfile
import unittest
from unittest.mock import patch
import uuid
from paper_atlas.db.store import Store
from paper_atlas.postgres import schema
from paper_atlas.postgres.client import ReadConnection, Row, connect
from paper_atlas.postgres.migration import migrate
from paper_atlas import querying
class SchemaTests(unittest.TestCase):
def setUp(self):
self.temporary = tempfile.TemporaryDirectory()
self.addCleanup(self.temporary.cleanup)
self.path = Path(self.temporary.name) / 'source.sqlite'
self.store = Store(self.path)
self.addCleanup(self.store.conn.close)
def test_every_business_table_is_included_and_engine_tables_are_excluded(self):
plan = schema.inspect(self.store.conn)
self.assertEqual(set(plan), set(schema.TABLES))
self.assertEqual(len(plan), 21)
self.assertNotIn('papers_fts', plan)
self.assertEqual(plan['paper_tags']['pk'], ['paper_id', 'tag_id', 'evidence_key'])
self.assertEqual(len(plan['source_records']['foreign_keys']), 2)
sql = schema.table_sql('stage', 'papers', plan['papers'])
self.assertIn('GENERATED BY DEFAULT AS IDENTITY', sql)
self.assertIn('TEXT COLLATE "C"', sql)
def test_unknown_tables_and_check_constraints_fail_before_copy(self):
self.store.conn.execute('CREATE TABLE extra(id INTEGER PRIMARY KEY)')
with self.assertRaisesRegex(ValueError, 'Unexpected business'):
schema.inspect(self.store.conn)
self.store.conn.execute('DROP TABLE extra')
self.store.conn.execute('ALTER TABLE papers ADD COLUMN extra TEXT CHECK(extra IS NULL)')
with self.assertRaisesRegex(ValueError, 'CHECK'):
schema.inspect(self.store.conn)
def test_cutover_stops_legacy_writers_but_keeps_read_access(self):
self.store.conn.commit(); self.store.conn.close()
Path(str(self.path) + '.postgresql-cutover.json').write_text('{"status":"active"}')
with self.assertRaisesRegex(RuntimeError, 'cut over'):
Store(self.path)
with sqlite3.connect(self.path.as_uri() + '?mode=ro', uri=True) as c:
self.assertEqual(c.execute('SELECT count(*) FROM papers').fetchone()[0], 0)
def test_rows_support_mapping_and_positional_query_access(self):
row = Row(['id', 'title'], (7, 'A'))
self.assertEqual(row[0], row['id'])
self.assertEqual(dict(row), {'id': 7, 'title': 'A'})
def test_connection_services_cannot_be_password_urls(self):
with self.assertRaisesRegex(ValueError, 'service name'):
connect('postgresql://user:secret@host/db')
def test_checks_compare_literal_values_not_only_constraint_counts(self):
clauses = schema.checks_in("CREATE TABLE t(x TEXT CHECK(x IN ('a','b)')),y TEXT CHECK(y IS NULL))")
self.assertEqual(clauses, ["x IN ('a','b)')", 'y IS NULL'])
self.assertEqual(schema.normalize_check("x IN ( 'a' )"), schema.normalize_check("x in('a')"))
self.assertNotEqual(schema.normalize_check("x IN ('A')"), schema.normalize_check("x IN ('a')"))
@unittest.skipUnless(os.environ.get('PAPER_ATLAS_TEST_PG_SERVICE'), 'Requires an explicitly configured remote PostgreSQL test service')
class PostgreSQLIntegrationTests(unittest.TestCase):
def setUp(self):
self.service = os.environ['PAPER_ATLAS_TEST_PG_SERVICE']
self.target = 'pa_test_' + uuid.uuid4().hex[:14]
self.temporary = tempfile.TemporaryDirectory()
self.addCleanup(self.temporary.cleanup)
self.db = Path(self.temporary.name) / 'source.sqlite'
self.out = Path(self.temporary.name) / 'report.json'
store = Store(self.db)
paper, record = store.record('arxiv', '2401.00001', 'https://arxiv.org/abs/2401.00001',
'Quiet graph models — 研究', 'Graph models learn reinforcement policies.\nQuoted "text", tabs\tand Unicode α.',
['Jane Doe', 'John Smith'], {'arxiv': '2401.00001'}, {'nested': {'a': ['α', None, 1]}, 'raw': '\\n'})
store.record_tags(paper, record, 'arxiv', [{'namespace': 'arxiv:category', 'value': 'cs.AI'}])
store.decision(paper, record, 'ICLR', 2024, 'main', 'forum-reject', 'https://example.org/reject',
'rejected', 'Reject', identities=[{'scheme': 'openreview', 'value': 'forum-reject'}], observed_at='2024-01-01T00:00:00Z')
same, second = store.record('official', '2025/paper', 'https://example.org/accepted',
'Quiet graph models — 研究', 'Graph models learn reinforcement policies.', ['Jane Doe', 'John Smith'], {'arxiv': '2401.00001'})
self.assertEqual(same, paper)
store.decision(paper, second, 'COLM', 2025, 'main', 'forum-accept', 'https://example.org/accept',
'accepted', 'Accept', ['Conference on Language Modeling'], observed_at='2025-01-01T00:00:00Z')
store.record('arxiv', '2401.00002', 'https://arxiv.org/abs/2401.00002', 'Empty abstract', None, [])
tag = store.conn.execute("INSERT INTO tags(namespace,value) VALUES('custom:topic','manual')").lastrowid
store.conn.execute('INSERT INTO paper_tags VALUES(?,?,NULL,?)', (paper, tag, 'manual:one'))
store.conn.execute("INSERT INTO paper_merges(former_paper_id,surviving_paper_id,reason) VALUES(900,?,'fixture')", (paper,))
store.conn.execute("INSERT INTO submission_merges VALUES(5000,1,'fixture',CURRENT_TIMESTAMP)")
store.conn.execute("INSERT INTO decision_merges VALUES(6000,1,'fixture',CURRENT_TIMESTAMP)")
store.conn.execute("UPDATE sqlite_sequence SET seq=1000 WHERE name='papers'")
store.conn.commit(); store.conn.close()
self.addCleanup(self.cleanup_schemas)
def cleanup_schemas(self):
with connect(self.service) as pg:
names = pg.execute('SELECT nspname FROM pg_namespace WHERE starts_with(nspname,%s)', (self.target,)).fetchall()
for name, in names:
pg.execute('DROP SCHEMA ' + schema.quote(name) + ' CASCADE')
def migrate(self):
with contextlib.redirect_stdout(io.StringIO()):
return migrate(self.db, self.service, self.out, schema=self.target, min_free_gib=0)
def published(self):
with connect(self.service) as pg:
return bool(pg.execute('SELECT 1 FROM pg_namespace WHERE nspname=%s', (self.target,)).fetchone())
def test_full_content_history_tags_sequences_and_readonly_queries(self):
report = self.migrate()
self.assertEqual(report['status'], 'complete')
self.assertEqual(len(report['tables']), 21)
for entry in report['tables'].values():
self.assertEqual(entry['source_rows'], entry['target_rows'])
self.assertEqual(entry['source_sha256'], entry['target_sha256'])
with connect(self.service) as pg, pg.transaction(force_rollback=True):
prefix = schema.quote(self.target) + '.'
value = pg.execute('INSERT INTO ' + prefix + 'papers(title,title_key) VALUES(%s,%s) RETURNING id', ('new', 'new')).fetchone()[0]
self.assertGreater(value, 1000)
record = pg.execute('INSERT INTO ' + prefix + "source_records(source_id,external_id,paper_id,url,title,abstract,authors_json,metadata_json) SELECT source_id,'new',%s,url,title,abstract,authors_json,metadata_json FROM " + prefix + 'source_records LIMIT 1 RETURNING id', (value,)).fetchone()[0]
edition = pg.execute('SELECT id FROM ' + prefix + 'editions LIMIT 1').fetchone()[0]
submission = pg.execute('INSERT INTO ' + prefix + 'submissions(paper_id,edition_id,source_record_id,source_submission_id) VALUES(%s,%s,%s,%s) RETURNING id', (value, edition, record, 'new')).fetchone()[0]
decision = pg.execute('INSERT INTO ' + prefix + "decisions(submission_id,status,raw_value,evidence_url,observed_at) VALUES(%s,'unknown','fixture','https://example.org/new','2026-01-01T00:00:00Z') RETURNING id", (submission,)).fetchone()[0]
self.assertGreater(submission, 5000)
self.assertGreater(decision, 6000)
real = ReadConnection
with patch('paper_atlas.postgres.client.ReadConnection', lambda service: real(service, self.target)):
output = io.StringIO()
with contextlib.redirect_stdout(output):
querying.main(['--pg-service', self.service, '--query', 'graph models', '--status', 'rejected', '--outcome', 'accepted'])
results = json.loads(output.getvalue())
self.assertEqual(len(results), 1)
self.assertEqual(results[0]['known_acceptances'][0]['venue'], 'COLM')
output = io.StringIO()
with contextlib.redirect_stdout(output):
querying.main(['--pg-service', self.service, '--venue', 'conference on language modeling', '--tag', 'custom:topic=manual', '--paper', '1'])
detail = json.loads(output.getvalue())[0]
self.assertEqual(len(detail['submissions']), 2)
self.assertEqual({t['namespace'] for t in detail['tags']}, {'arxiv:category', 'custom:topic'})
output = io.StringIO()
with contextlib.redirect_stdout(output):
querying.main(['--pg-service', self.service, '--stats'])
stats = json.loads(output.getvalue())
self.assertEqual(stats['papers'], 2)
self.assertEqual(stats['papers_with_known_acceptance'], 1)
reader = real(self.service, self.target)
try:
import psycopg
with self.assertRaises(psycopg.errors.ReadOnlySqlTransaction):
reader.execute('DELETE FROM papers')
finally:
reader.close()
def interrupt_after_first_table(self):
calls = 0
def interrupt(*args):
nonlocal calls
calls += 1
if calls == 3:
raise RuntimeError('controlled interruption')
with patch('paper_atlas.postgres.migration.free_space', side_effect=interrupt):
with self.assertRaisesRegex(RuntimeError, 'controlled interruption'):
self.migrate()
self.assertFalse(self.published())
def test_interrupted_copy_resumes_without_duplicate_rows(self):
self.interrupt_after_first_table()
self.assertEqual(self.migrate()['status'], 'complete')
def test_resume_rejects_a_changed_source_snapshot(self):
self.interrupt_after_first_table()
with closing(sqlite3.connect(self.db)) as source, source:
source.execute("UPDATE papers SET abstract='changed' WHERE id=1")
with self.assertRaisesRegex(ValueError, 'exact same'):
self.migrate()
self.assertFalse(self.published())
def test_full_hash_detects_tampering_in_a_completed_staging_table(self):
self.interrupt_after_first_table()
with connect(self.service) as pg:
stage = pg.execute('SELECT stage FROM ' + schema.quote(self.target + '_migration') + '.run WHERE id=1').fetchone()[0]
pg.execute('UPDATE ' + schema.quote(stage) + ".sources SET homepage='tampered'")
with self.assertRaisesRegex(ValueError, 'content verification'):
self.migrate()
self.assertFalse(self.published())
def test_foreign_key_violation_never_publishes_target(self):
with closing(sqlite3.connect(self.db)) as source, source:
source.execute('PRAGMA foreign_keys=OFF')
source.execute("INSERT INTO identifiers VALUES('orphan','bad',999999)")
import psycopg
with self.assertRaises(psycopg.errors.ForeignKeyViolation):
self.migrate()
self.assertFalse(self.published())
def test_published_target_cannot_be_overwritten(self):
self.migrate()
self.out.unlink()
with self.assertRaisesRegex(ValueError, 'never be overwritten'):
self.migrate()
if __name__ == '__main__':
unittest.main()