diff --git a/.gitattributes b/.gitattributes index 137fff0..12605cc 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,4 +1,8 @@ # Preserve historical source bytes and SHA-256 across platforms. No EOL conversion. * -text *.jsonl.gz binary +artifacts/**/*.tar.zst filter=lfs diff=lfs merge=lfs -text +artifacts/lfs-smoke/*.bin filter=lfs diff=lfs merge=lfs -text +artifacts/public-resources-20261001/**/payload-*.bin filter=lfs diff=lfs merge=lfs -text +artifacts/public-resources-20261001/**/*.jsonl.gz filter=lfs diff=lfs merge=lfs -text artifacts/acceleration-20261001/*.tar.zst filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore index 4f9485e..1a790b1 100644 --- a/.gitignore +++ b/.gitignore @@ -34,5 +34,5 @@ id_ed25519* /registry/verification-runs/ # Historical learned deltas/checkpoints are not source files. /models/learned/ -# Explicit, audited experiment exports only; original data stay ignored. -!/artifacts/acceleration-20261001/*.tar.zst +# Explicit publication exports only; original scientific directories stay ignored. +!/artifacts/**/*.tar.zst diff --git a/CURRENT.md b/CURRENT.md index a023d67..b0cad02 100644 --- a/CURRENT.md +++ b/CURRENT.md @@ -1,6 +1,12 @@ # Digital Drosophila — 当前状态 -更新：2026-10-01。成果保存分支：`codex/v100-conditioning-acceleration`。 +更新：2026-10-01。统一成果入口：`main`。 + +## 仓库整理（不是科学实验） + +CPU/GPU 加速成果与公开 LFS 资源按保留双亲的合并历史整合到 `main`。旧 7 个分支先按精确 SHA 创建 `archive/2026-10-01/*` 标签，再核验并清理远端分支；不改旧工作树、不修改已封存数据或模型。完整映射见[分支说明](docs/40-operations/branches-20261001.md)，执行结果以 `registry/branch-consolidation-20261001/` 的实际回执为准。 + +历史 registry 文档保留原字节，其旧分支恢复命令由[统一恢复指南](docs/30-reproducibility/main-restore.md)取代。 ## 最新状态：暂停研究，CPU/GPU 两套方案保留 diff --git a/NOTICE.md b/NOTICE.md index 2da1a53..ca4b7bd 100644 --- a/NOTICE.md +++ b/NOTICE.md @@ -2,6 +2,14 @@ 本仓库整理既有项目，不改变原始数据和软件的权属。尚未为本项目原创代码选定统一公开许可证；不得将“可访问此 Git 仓库”等同于取得任意再分发授权。 +## 2026-10-01 公开资源发布补充 + +用户已确认保留公开仓库，仅上传明确允许公开再分发的资源。[MaleCNS 官方下载页](https://male-cns.janelia.org/download/)已核实指向 [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)。据此，独立发布分支现在归档其已下载的数据及明确标注变更来源的既有派生数据；Cell Type Explorer、visualpathways、DoOR.data 和 Shiu 作者模型源码按各自原许可处理。作者署名、固定 commit、许可证据 SHA、排除项和恢复方法见 [本次发布说明](registry/publication-20261001/README.md)。FlyVis 不明确许可的资源、活动实验、环境和凭据不纳入。 + +下表保留初始化时的历史审查状态，不代表本次已核实许可仍然未知。新发布只在 `artifacts/` 增加只读快照，不覆盖原始数据或此前冻结索引；不为整个仓库补授统一许可证。 + +## 初始化审查记录（2026-09-29） + | 外部资源 | 冻结副本中的许可证据 | 本仓库处理 | |---|---|---| | MaleCNS v1.0 官方数据 | 来源文件、原下载脚本和校验清单；统一再分发许可本次未确证 | 只登记路径、来源、大小、SHA-256；不上传数据 | diff --git a/README.md b/README.md index d770a57..186986f 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ 截至 2026-10-01，最新正式封存科学阶段仍是 **Phase 4AQ：PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。 **Phase 4AR 已按用户要求停止，暂不恢复**：已提交 1,033/30,000 轮训练及 CPU 校验、138/3,920 次独立 probe；执行尚未完成，学习成功未判定。 -本分支 `codex/v100-conditioning-acceleration` 同时保留 CPU 与 GPU 方案及两轮独立性能回放。它不是已升级的生产运行时；原登记实验和权重没有改动。远端默认分支仍为初始化分支，见[分支说明](docs/40-operations/branches-20261001.md)。 +统一入口为 **`main`**，包含注册科学代码、CPU/GPU 两套方案及已公开的 LFS 数据。7 个旧分支的精确版本通过 `archive/2026-10-01/*` 标签保留，见[分支与恢复说明](docs/40-operations/branches-20261001.md)。这次只是仓库整理，不是生产运行时升级，也没有恢复训练。 项目顶层验收口径为 **5/10（50%）**；这不是生物学逼真度、工作量完成率或剩余工期。 最新正式候选运行时为 `MaleCNS-LIF-runtime-v2-deterministic-candidate`。 `MaleCNS-TemporalEligibility-v2-candidate` 与 `MaleCNS-OlfactoryEncoder-v1-candidate` 保留。 @@ -21,7 +21,7 @@ | 科学数据定义和来源 | [数据契约](docs/10-data/data-contract.md)、[来源登记](docs/10-data/provenance.md) | | 模型边界 | [模型与冻结契约](docs/20-model/baseline.md) | | 论文、引用与证据用途 | [参考文献入口](references/README.md)、[证据边界](references/evidence-map.md) | -| 环境与复现 | [环境](docs/30-reproducibility/environment.md)、[恢复](docs/30-reproducibility/restore.md) | +| 环境与复现 | [环境](docs/30-reproducibility/environment.md)、[统一恢复入口](docs/30-reproducibility/main-restore.md) | | Git 同步、大数据备份与安全 | [同步说明](docs/40-operations/git-sync.md)、[备份](docs/40-operations/backup.md) | | 每个阶段的原始证据副本 | [阶段索引](registry/catalog-20260929/stages.json) | | 全部科学文件路径/大小/SHA-256 | [快照说明](registry/README.md) | @@ -38,17 +38,17 @@ 服务器项目根目录：`/data/digital-drosophila/`。 远程：`ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git`。 -初始化／当前远端默认分支：`codex/project-bootstrap`；注册科学源码分支：`codex/lif-author-semantics-lab`；最新独立加速成果：`codex/v100-conditioning-acceleration`。 +统一主分支：`main`。历史版本由归档标签保留；原注册科学源码仍固定为 `80aeb2093db655329774eff7b32fb6e417b8b40b`，不随主分支移动。 Git 保存源代码、配置、文档、书目、阶段证据副本和逐文件哈希清单。 -普通 Git 不直接保存大型科学二进制。获准公开再分发的原始/参考数据已在 `codex/lfs-public-resources` 通过 **Git LFS** 归档；本分支另通过 LFS 保存本次 CPU/GPU 回放的科学结果。没有上传虚拟环境、SDK 编译缓存、凭据或其他服务的数据。 +普通 Git 不直接保存大型科学二进制。**Git LFS** 保存获准公开再分发的原始/参考数据，以及本次 CPU/GPU 回放结果；两套原归档指针均原样整合到 `main`。没有上传虚拟环境、SDK 编译缓存、凭据或其他服务的数据。 原项目实占约 29.72 GB（十进制、初始化前统计），不会因为初始化 Git 被删除、搬移或重写。 -只取得 Git pointer 不能恢复全数据；需下载对应分支的 LFS 对象并验证内部成员。本次恢复说明见 [CPU/GPU 发布入口](registry/acceleration-20261001/README.md)。这不是全服务器灾备。 +只取得 Git pointer 不能恢复全数据；需按[统一恢复指南](docs/30-reproducibility/main-restore.md)下载所需 LFS 对象并验证内部成员。已封存报告中的旧分支命令仅作历史记录；不要据此重新运行实验。这不是全服务器灾备。 ## 安全的首次检查 ```bash -GIT_LFS_SKIP_SMUDGE=1 git clone --branch codex/v100-conditioning-acceleration ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git +GIT_LFS_SKIP_SMUDGE=1 git clone --branch main ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git cd digital-drosophila python3 -B tools/repo_guard.py ``` diff --git a/artifacts/lfs-smoke/publication-probe.bin b/artifacts/lfs-smoke/publication-probe.bin new file mode 100644 index 0000000..14e7590 --- /dev/null +++ b/artifacts/lfs-smoke/publication-probe.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:93e0e6c4ca4fdc123c21b859ba97d8bd73670eb9c90d04ce9a431d822b5393c5 +size 263 diff --git a/artifacts/public-resources-20261001/celltype-explorer/catalog.json b/artifacts/public-resources-20261001/celltype-explorer/catalog.json new file mode 100644 index 0000000..e3e339f --- /dev/null +++ b/artifacts/public-resources-20261001/celltype-explorer/catalog.json @@ -0,0 +1,52 @@ +{ + "archive_bytes": 77971754, + "archive_format": "tar.pax+zstd", + "archive_sha256": "2366caef95fb5ad038639a6ae2ad25139a14c42492bc19640c20af46fefa0bc7", + "chunk_bytes": 67108864, + "chunks": [ + { + "bytes": 67108864, + "index": 0, + "path": "payload-000000.bin", + "sha256": "6f5830463b8a0077ae89e550ca45275d57cf7e81813c42bf66f89d13a42c03ee" + }, + { + "bytes": 10862890, + "index": 1, + "path": "payload-000001.bin", + "sha256": "6b80b0133af06279bd30561f35042b679bd392b9236ee519d1e7ed9c4e85fb6a" + } + ], + "exclusion_records": 1, + "exclusions": { + "bytes": 144, + "sha256": "c1bca109b61e53327fa7e01128a411d8ea328972593168c3ad6e1202dfdddc9c" + }, + "group_id": "celltype-explorer", + "license": { + "evidence_file": "LICENSE", + "evidence_sha256": "9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411", + "upstream": "CC-BY-4.0", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, + "members": { + "bytes": 421593, + "sha256": "8a51d3b4138bad12a520f8d1a12d54673416017d15fd1b1bcc49ed385da005bb" + }, + "plan_sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71", + "provenance": { + "attribution": "Reiser Lab and Male CNS Cell Type Explorer contributors; retain upstream notices", + "changes": "Unchanged pinned working-tree file bytes; .git, environments, caches and credentials excluded. A source snapshot, not a full Git clone.", + "commit": "789cc6c105798ce2fd70ba85dab394f90899616b", + "repository": "https://github.com/reiserlab/celltype-explorer-drosophila-male-cns" + }, + "schema": "lfs-publication-group-v1", + "secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules", + "source_bytes": 3957079583, + "source_files": 8973, + "source_paths": [ + "experiments/phase4f-retinotopic-vision/external-resources/celltype-explorer" + ], + "source_root": "/data/digital-drosophila", + "verification_scope": "content snapshot, not a license grant or nested-archive secret audit" +} diff --git a/artifacts/public-resources-20261001/celltype-explorer/exclusions.jsonl.gz b/artifacts/public-resources-20261001/celltype-explorer/exclusions.jsonl.gz new file mode 100644 index 0000000..09e234a --- /dev/null +++ b/artifacts/public-resources-20261001/celltype-explorer/exclusions.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c1bca109b61e53327fa7e01128a411d8ea328972593168c3ad6e1202dfdddc9c +size 144 diff --git a/artifacts/public-resources-20261001/celltype-explorer/members.jsonl.gz b/artifacts/public-resources-20261001/celltype-explorer/members.jsonl.gz new file mode 100644 index 0000000..cd56075 --- /dev/null +++ b/artifacts/public-resources-20261001/celltype-explorer/members.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8a51d3b4138bad12a520f8d1a12d54673416017d15fd1b1bcc49ed385da005bb +size 421593 diff --git a/artifacts/public-resources-20261001/celltype-explorer/payload-000000.bin b/artifacts/public-resources-20261001/celltype-explorer/payload-000000.bin new file mode 100644 index 0000000..bd8c136 --- /dev/null +++ b/artifacts/public-resources-20261001/celltype-explorer/payload-000000.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6f5830463b8a0077ae89e550ca45275d57cf7e81813c42bf66f89d13a42c03ee +size 67108864 diff --git a/artifacts/public-resources-20261001/celltype-explorer/payload-000001.bin b/artifacts/public-resources-20261001/celltype-explorer/payload-000001.bin new file mode 100644 index 0000000..8b27137 --- /dev/null +++ b/artifacts/public-resources-20261001/celltype-explorer/payload-000001.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6b80b0133af06279bd30561f35042b679bd392b9236ee519d1e7ed9c4e85fb6a +size 10862890 diff --git a/artifacts/public-resources-20261001/door-data/catalog.json b/artifacts/public-resources-20261001/door-data/catalog.json new file mode 100644 index 0000000..49f4b20 --- /dev/null +++ b/artifacts/public-resources-20261001/door-data/catalog.json @@ -0,0 +1,51 @@ +{ + "archive_bytes": 901984, + "archive_format": "tar.pax+zstd", + "archive_sha256": "64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1", + "chunk_bytes": 67108864, + "chunks": [ + { + "bytes": 901984, + "index": 0, + "path": "payload-000000.bin", + "sha256": "64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1" + } + ], + "exclusion_records": 1, + "exclusions": { + "bytes": 147, + "sha256": "82627a482fd6adfc3abf4f83a30158fd8371b4532f425f7eb3b03044eb7e1367" + }, + "group_id": "door-data", + "license": { + "evidence_file": "DESCRIPTION", + "evidence_sha256": "27db2a92eb651d67969de94959990d51668a5857a33c4750a3b6ef49c5880504", + "upstream": "CC-BY-SA-4.0", + "url": "https://creativecommons.org/licenses/by-sa/4.0/" + }, + "members": { + "bytes": 9486, + "sha256": "ef13db49577b3b3d1c7c31aab117d911a2decc5a80ead66b6a350c43d16374b4" + }, + "plan_sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71", + "provenance": { + "attribution": "Daniel Münch, C. Giovanni Galizia, Shouwen Ma, Martin Strauch, Anja Nissler; see upstream DESCRIPTION and data-source references", + "changes": "Unchanged pinned data package; .git omitted. ShareAlike terms remain attached to this package, not asserted over unrelated repository content.", + "commit": "eea72d64b42a4e91dafe822cf0b5204de33f8d34", + "papers": [ + "https://doi.org/10.1038/srep21841", + "https://doi.org/10.1093/chemse/bjq042" + ], + "repository": "https://github.com/ropensci/DoOR.data", + "version": "2.0.1" + }, + "schema": "lfs-publication-group-v1", + "secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules", + "source_bytes": 6534522, + "source_files": 189, + "source_paths": [ + "experiments/phase4l-olfactory-grounding/external-resources/DoOR.data" + ], + "source_root": "/data/digital-drosophila", + "verification_scope": "content snapshot, not a license grant or nested-archive secret audit" +} diff --git a/artifacts/public-resources-20261001/door-data/exclusions.jsonl.gz b/artifacts/public-resources-20261001/door-data/exclusions.jsonl.gz new file mode 100644 index 0000000..42e4206 --- /dev/null +++ b/artifacts/public-resources-20261001/door-data/exclusions.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:82627a482fd6adfc3abf4f83a30158fd8371b4532f425f7eb3b03044eb7e1367 +size 147 diff --git a/artifacts/public-resources-20261001/door-data/members.jsonl.gz b/artifacts/public-resources-20261001/door-data/members.jsonl.gz new file mode 100644 index 0000000..ab7591b --- /dev/null +++ b/artifacts/public-resources-20261001/door-data/members.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef13db49577b3b3d1c7c31aab117d911a2decc5a80ead66b6a350c43d16374b4 +size 9486 diff --git a/artifacts/public-resources-20261001/door-data/payload-000000.bin b/artifacts/public-resources-20261001/door-data/payload-000000.bin new file mode 100644 index 0000000..19555f6 --- /dev/null +++ b/artifacts/public-resources-20261001/door-data/payload-000000.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1 +size 901984 diff --git a/artifacts/public-resources-20261001/malecns-processed/catalog.json b/artifacts/public-resources-20261001/malecns-processed/catalog.json new file mode 100644 index 0000000..64716b1 --- /dev/null +++ b/artifacts/public-resources-20261001/malecns-processed/catalog.json @@ -0,0 +1,102 @@ +{ + "archive_bytes": 635332131, + "archive_format": "tar.pax+zstd", + "archive_sha256": "a5d8ac0e6eebd5c6235078e9a9ac5a5c224bc86185bb77dd38248833c6b946f1", + "chunk_bytes": 67108864, + "chunks": [ + { + "bytes": 67108864, + "index": 0, + "path": "payload-000000.bin", + "sha256": "a65619004cdc36e594bdca344d1fe51ac86fb719159f70a2ba0fb21c763f9c04" + }, + { + "bytes": 67108864, + "index": 1, + "path": "payload-000001.bin", + "sha256": "cca9eedbc44b20be736317745ee12e8c06bf0e1aafc7815b74bc6aa27cef5be5" + }, + { + "bytes": 67108864, + "index": 2, + "path": "payload-000002.bin", + "sha256": "e395b23867e74b7579aed8eeb927e373c86d77433962a0f89ac198aeca4f8470" + }, + { + "bytes": 67108864, + "index": 3, + "path": "payload-000003.bin", + "sha256": "e47d83eba2875f963add02ab697cb6386dd8fe4a5f33b96db5a321986a276774" + }, + { + "bytes": 67108864, + "index": 4, + "path": "payload-000004.bin", + "sha256": "4d4bdff46071f05c29ac34cd9081204739317bef5ab862d612d2c7a82c3d5bca" + }, + { + "bytes": 67108864, + "index": 5, + "path": "payload-000005.bin", + "sha256": "4f82611c41e868faa6ea06d7bd275df90f712e3f5eb14296117e39c3bf6c95c0" + }, + { + "bytes": 67108864, + "index": 6, + "path": "payload-000006.bin", + "sha256": "4cbfb164c194db8c54eadef4d039240d98b0f5be8e20e4005be08bd2d2f6ab5d" + }, + { + "bytes": 67108864, + "index": 7, + "path": "payload-000007.bin", + "sha256": "9ba4adfe64d73d0ceb249ab25215734f58b0d8b38d11f22676fd93f68e83df68" + }, + { + "bytes": 67108864, + "index": 8, + "path": "payload-000008.bin", + "sha256": "8f388376c6e9d3b7abaff219b00d669ea88db1bf5cd48381db9354598102b345" + }, + { + "bytes": 31352355, + "index": 9, + "path": "payload-000009.bin", + "sha256": "e1ac638f1d640de9e85b82d9526d6f729f78239e66c5c024e0037144adf7f003" + } + ], + "exclusion_records": 6, + "exclusions": { + "bytes": 219, + "sha256": "0909f401f73ca15301ea2be92a5e7c66cf79d9d4f8bbe5449f82c2980d6d3e80" + }, + "group_id": "malecns-processed", + "license": { + "derived_data": "CC-BY-4.0", + "local_scripts_reports": "Project-authored processing and provenance; no new blanket software license", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, + "members": { + "bytes": 3639, + "sha256": "fe399bea661cdd018e53a5ea58bc46a64d2f94fb09d1dec40f8a956789204627" + }, + "plan_sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71", + "provenance": { + "attribution": "Original Male CNS collaboration; Digital Drosophila project for local processing", + "canonical_edges": 25582938, + "canonical_neurons": 166700, + "canonical_synaptic_weight_sum": 124177617, + "changes": "Existing Phase 3 all-body and Phase 3B neuron-only tables, index mappings, CSR and audit reports, copied byte-for-byte. These were previously derived by filtering/reindexing official data, not new preprocessing. Phase 3 historical outputs are not the approved SNN input; use neuron-only for current runtime.", + "dataset": "male-cns:v1.0", + "source_page": "https://male-cns.janelia.org/download/" + }, + "schema": "lfs-publication-group-v1", + "secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules", + "source_bytes": 1140025370, + "source_files": 64, + "source_paths": [ + "datasets/male-cns-v1.0/processed" + ], + "source_root": "/data/digital-drosophila", + "verification_scope": "content snapshot, not a license grant or nested-archive secret audit" +} diff --git a/artifacts/public-resources-20261001/malecns-processed/exclusions.jsonl.gz b/artifacts/public-resources-20261001/malecns-processed/exclusions.jsonl.gz new file mode 100644 index 0000000..d9c5518 --- /dev/null +++ b/artifacts/public-resources-20261001/malecns-processed/exclusions.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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This is model source, not pretrained weights, and not a strict original-model reproduction claim.", + "commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "paper": "https://www.nature.com/articles/s41586-024-07763-9", + "repository": "https://github.com/philshiu/Drosophila_brain_model" + }, + "schema": "lfs-publication-group-v1", + "secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules", + "source_bytes": 17567, + "source_files": 4, + "source_paths": [ + "experiments/phase4ac-lif-semantics/external-resources" + ], + "source_root": "/data/digital-drosophila", + "verification_scope": "content snapshot, not a license grant or nested-archive secret audit" +} diff --git a/artifacts/public-resources-20261001/shiu-author-model-source/exclusions.jsonl.gz b/artifacts/public-resources-20261001/shiu-author-model-source/exclusions.jsonl.gz new file mode 100644 index 0000000..1c35409 --- /dev/null +++ b/artifacts/public-resources-20261001/shiu-author-model-source/exclusions.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9ceffb7310338057cfe71a4ae1e2c98d2c485d81cdef906532a801f457a38d64 +size 20 diff --git a/artifacts/public-resources-20261001/shiu-author-model-source/members.jsonl.gz b/artifacts/public-resources-20261001/shiu-author-model-source/members.jsonl.gz new file mode 100644 index 0000000..5255a1c --- /dev/null +++ b/artifacts/public-resources-20261001/shiu-author-model-source/members.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2907be4f7d1a8f1017f91bda6e5ead381b8c67b85498f5378765d696f89d4b0c +size 349 diff --git a/artifacts/public-resources-20261001/shiu-author-model-source/payload-000000.bin b/artifacts/public-resources-20261001/shiu-author-model-source/payload-000000.bin new file mode 100644 index 0000000..f232dbe --- /dev/null +++ b/artifacts/public-resources-20261001/shiu-author-model-source/payload-000000.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4da352d80e4bf251dfec771935da93f5a9f3cef302c85e90991fafa14a072e2b +size 6828 diff --git a/artifacts/public-resources-20261001/visualpathways/catalog.json b/artifacts/public-resources-20261001/visualpathways/catalog.json new file mode 100644 index 0000000..7bc6f56 --- /dev/null +++ b/artifacts/public-resources-20261001/visualpathways/catalog.json @@ -0,0 +1,82 @@ +{ + "archive_bytes": 434458454, + "archive_format": "tar.pax+zstd", + "archive_sha256": "683b85394fb44e42704c275fbda93c95072f9f64c16a84e47ce2821c060cc39f", + "chunk_bytes": 67108864, + "chunks": [ + { + "bytes": 67108864, + "index": 0, + "path": "payload-000000.bin", + "sha256": "7f8bb35dcb565c16ff1bf642e079c54c71e27e05cccaa5915c1d1e3c9e7d0700" + }, + { + "bytes": 67108864, + "index": 1, + "path": "payload-000001.bin", + "sha256": "7181f79ec2615a84f33b394abf22454b72d2fddfb0e40e9c5e1590fe1ba64d7a" + }, + { + "bytes": 67108864, + "index": 2, + "path": "payload-000002.bin", + "sha256": "9dc076afd8cd8ebbbdda6f1ef24a41598e5db9fb0a98de8b5b765b4b0a8d2934" + }, + { + "bytes": 67108864, + "index": 3, + "path": "payload-000003.bin", + "sha256": "be03beac2472e6dc76a5705440296f88a8f6e15ea43f541df402c7b6c85cfdc6" + }, + { + "bytes": 67108864, + "index": 4, + "path": "payload-000004.bin", + "sha256": "0c801486169d0594471518a75b11b040acb1a2dd8904e9365fa7b7b667fc4a09" + }, + { + "bytes": 67108864, + "index": 5, + "path": "payload-000005.bin", + "sha256": "4f387b9e6b47f06871ce1b32e265b3a1ae2d78e06d7955a3fa8ed7cfc1d2a0a7" + }, + { + "bytes": 31805270, + "index": 6, + "path": "payload-000006.bin", + "sha256": "edb0ffa74e646712485a0d5fd2819ef14345c637beeaa5ca811ae3e71a06ea82" + } + ], + "exclusion_records": 4, + "exclusions": { + "bytes": 218, + "sha256": "9c029262724580ef20981316c6f7e9c99d345e1171067f16c5d580c742809a8c" + }, + "group_id": "visualpathways", + "license": { + "evidence_file": "LICENSE", + "evidence_sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986", + "third_party_notices": "Retained; no relicensing of third-party components", + "upstream": "GPL-3.0 as supplied in upstream LICENSE; no assertion of only/or-later option" + }, + "members": { + "bytes": 292178, + "sha256": "335401c3f6cb5b3868b899599bcd7b439c1983a627d97a598a95e9c8d44ad81c" + }, + "plan_sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71", + "provenance": { + "attribution": "Reiser Lab and visualpathways contributors; original copyright notices and source retained", + "changes": "Unchanged source/resource file bytes from pinned checkout; .git, credentials, environments and caches omitted; explicit exclusions recorded. No software execution or model alteration.", + "commit": "23f6ac131529b5f56894c6eeb9b88b17894fc00d", + "repository": "https://github.com/reiserlab/visualpathways" + }, + "schema": "lfs-publication-group-v1", + "secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules", + "source_bytes": 1652696750, + "source_files": 6033, + "source_paths": [ + "experiments/phase4f-retinotopic-vision/external-resources/visualpathways" + ], + "source_root": "/data/digital-drosophila", + "verification_scope": "content snapshot, not a license grant or nested-archive secret audit" +} diff --git a/artifacts/public-resources-20261001/visualpathways/exclusions.jsonl.gz b/artifacts/public-resources-20261001/visualpathways/exclusions.jsonl.gz new file mode 100644 index 0000000..ba39cbc --- /dev/null +++ b/artifacts/public-resources-20261001/visualpathways/exclusions.jsonl.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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b/artifacts/public-resources-20261001/visualpathways/payload-000003.bin new file mode 100644 index 0000000..5fde6ec --- /dev/null +++ b/artifacts/public-resources-20261001/visualpathways/payload-000003.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:be03beac2472e6dc76a5705440296f88a8f6e15ea43f541df402c7b6c85cfdc6 +size 67108864 diff --git a/artifacts/public-resources-20261001/visualpathways/payload-000004.bin b/artifacts/public-resources-20261001/visualpathways/payload-000004.bin new file mode 100644 index 0000000..1f00ec9 --- /dev/null +++ b/artifacts/public-resources-20261001/visualpathways/payload-000004.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0c801486169d0594471518a75b11b040acb1a2dd8904e9365fa7b7b667fc4a09 +size 67108864 diff --git a/artifacts/public-resources-20261001/visualpathways/payload-000005.bin b/artifacts/public-resources-20261001/visualpathways/payload-000005.bin new file mode 100644 index 0000000..16d9b62 --- /dev/null +++ b/artifacts/public-resources-20261001/visualpathways/payload-000005.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4f387b9e6b47f06871ce1b32e265b3a1ae2d78e06d7955a3fa8ed7cfc1d2a0a7 +size 67108864 diff --git a/artifacts/public-resources-20261001/visualpathways/payload-000006.bin b/artifacts/public-resources-20261001/visualpathways/payload-000006.bin new file mode 100644 index 0000000..7314b8a --- /dev/null +++ b/artifacts/public-resources-20261001/visualpathways/payload-000006.bin @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:edb0ffa74e646712485a0d5fd2819ef14345c637beeaa5ca811ae3e71a06ea82 +size 31805270 diff --git a/docs/30-reproducibility/main-restore.md b/docs/30-reproducibility/main-restore.md new file mode 100644 index 0000000..7459969 --- /dev/null +++ b/docs/30-reproducibility/main-restore.md @@ -0,0 +1,43 @@ +# 从 main 恢复代码和已发布数据 + +这是新的统一入口。已封存 `registry/publication-20261001/` 和 `registry/acceleration-20261001/` 文档保持原字节，其中旧分支名称是历史记录；当前应 clone main，或使用 `archive/2026-10-01/*` 精确标签。 + +## 先获取轻量代码 + +```sh +GIT_LFS_SKIP_SMUDGE=1 git clone --branch main \ + ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git digital-drosophila-restore +cd digital-drosophila-restore +git lfs install --local +``` + +不要 clone 到已存在的 `/data/digital-drosophila`，不要运行封存阶段的生成脚本。首次 clone 跳过 LFS，避免意外下载约 9.9 GB 的全部发布对象。 + +## 按需获取 + +CPU/GPU 回放约 76.4 MB： + +```sh +git lfs pull --include='artifacts/acceleration-20261001/**' --exclude='' +python3 -B tools/acceleration-publication/archive_results.py verify +``` + +官方/参考数据： + +```sh +git lfs pull --include='artifacts/public-resources-20261001/**' --exclude='' +python3 -B tools/lfs-publication/publish_archives.py verify \ + --group-dir artifacts/public-resources-20261001/malecns-swc +``` + +对需要的每组分别 verify。8 组原数据的来源、许可、组名和原始验证记录见 `registry/publication-20261001/README.md`。仅获取一个组时，可将 include 缩小到该组路径。 + +main 保留 **181 个 artifacts Git 路径、171 个 LFS pointer 路径**，其中包含成员/排除清单等 LFS 文件，不是 171 个模型。原始/参考资源含 226,859 个内部文件；两份性能回放归档含 1,680 个内部文件。没有重打包、修改 OID 或重新上传原数据。 + +## 重要边界 + +- Git 指针不是数据本体；只有下载并验证过的对象才能当作已恢复。 +- CPU/GPU 回放包不是完整 Phase 4AR 训练现场备份；全 E/AQ 与脑回放仍依赖外部原始 checkpoint、请求、静态 bundle 和固定科学源码。完整依赖由保存的 source pins 描述。 +- 旧目录级 manifest 可能包含有意未公开的编译缓存。性能归档应使用 `publication-catalog.json` 验证；不能把缓存缺失说成科学数据损坏。 +- 不要求内网专用 transfer adapter 才能读取标准 LFS 对象。服务器上已有的 LAN adapter 只解决特定网络路径，不应复制其本机绝对路径到别的电脑。 +- 不覆盖 raw、Phase 1–4AQ 及独立性能封存文件；不自动恢复训练、升级模型或启动后续实验。 diff --git a/docs/40-operations/branches-20261001.md b/docs/40-operations/branches-20261001.md index 6560a74..a9dfd85 100644 --- a/docs/40-operations/branches-20261001.md +++ b/docs/40-operations/branches-20261001.md @@ -1,23 +1,47 @@ -# 分支用途与当前入口 +# 分支整理与历史恢复 -2026-10-01 只读审计。此次只保存/推送已存在的加速实验分支，不删除分支、不强推、不合并、不更改默认分支。 +2026-10-01 用户明确确认：统一 `main`，先标签归档并验证可恢复，再清理旧远端分支。服务器已有工作目录保持原样。 -所有名称均带 `codex/` 前缀。 +## 日常入口 -| 分支 | 用途 | -|---|---| -| project-bootstrap | 最初项目归档、数据索引、论文与来源；当前远端默认入口 | -| apl-pn-scope-audit | APL→PN 实际接触位置审计 | -| terminal-scope-diagnostic | PN calyx 接触范围诊断 | -| lif-semantics-audit | 冻结 LIF 语义与反馈回路审计 | -| lif-author-semantics-lab | 独立模型及正式 Phase 4AR/CPU 实现，当前科学现场的分支 | -| lfs-public-resources | 获准公开再分发的大数据、作者资源及实际远端恢复验证 | -| v100-conditioning-acceleration | CPU 常驻、独立校验、V100 更新原型、4090 常驻回放；本次最新保存入口 | +只使用 `main` 查看最新代码、CPU/GPU 方案、文档及 LFS 归档。数据、实验结果仍保留原有科学版本；仓库合并不等于模型升级或学习成功。 -前五个主要是同一条提交历史上的阶段指针，并不是五份独立完整数据。它们线性继承至 `09187e4`，之后分为 LFS 资源发布和加速实验两条路线。Git/LFS 会按内容地址保存对象；多个分支名不意味着同一文件被完整复制多份。 +旧阶段不再长期占用远端分支列表，改为以下 **带说明、约定不重写的归档标签**。标签保留的 Git 提交、科学源码、LFS OID/size 均不变；此处“不重写”是维护规则，不宣称服务器已强制开启标签保护。 -加速分支原已在本地存在，本次推送后远端共 7 个分支。CPU/GPU 两套实现放在同一加速分支的不同目录，不再各建分支。LFS 资源分支仍独立，不能把这次发布描述为已经合并全部数据。 +| 旧分支（原均带 codex/） | 归档标签（前缀 archive/2026-10-01/） | 精确提交 | +|---|---|---| +| project-bootstrap | project-bootstrap | `3981628ff893132a8148668aa94726886dba57a3` | +| apl-pn-scope-audit | apl-pn-scope-audit | `d6843e675dec5ae38a06f2ba70d74836aea53ace` | +| terminal-scope-diagnostic | terminal-scope-diagnostic | `3213aada793740961885ba525494e95f019be6f8` | +| lif-semantics-audit | lif-semantics-audit | `5008cd85ca11750f23ce7bc001e8e821763b7501` | +| lif-author-semantics-lab | lif-author-semantics-lab | `09187e4d4d67badf1b418c5f211258ca5d8fb328` | +| lfs-public-resources | lfs-public-resources | `5b1d1b72d7683b5c3dcc1f78b408e1d9dd2832ac` | +| v100-conditioning-acceleration | v100-conditioning-acceleration | `4436241976887d8cc10088b0d44bc7ed70978fe6` | -默认仍为最早的 bootstrap，所以网页默认看到的内容较旧。这是入口未整理，不是后续工作丢失。 +前五个是线性历史链，后两条从 `09187e4` 分出。本次保留双亲合并而非 squash/rebase，所有旧提交仍可追溯。 -后续可在用户确认后统一主入口、给历史阶段打保留标签，再整理旧分支。集成 LFS 时需核对属性、状态文档、许可说明和自动下载开销；不得把工程实验分支直接视为通过科学验收的正式运行时。 +远端分支删除不删除 Git 提交或 LFS 对象，历史版本由标签继续引用。执行记录在 `registry/branch-consolidation-20261001/`；清理须在归档标签实际远端核验、main 上传与默认入口切换后进行。 + +## 不动服务器科学现场 + +- `/data/digital-drosophila` 仍停在原本地科学分支和 `09187e4`；不 checkout main，不 pull/merge，不重试 AR。 +- `/home/qishizhe/digital-drosophila-v100-acceleration` 保留独立实验原工作树。 +- 旧本地分支保留；远端同名分支移除后，不应从这些冻结工作树重新 push 旧分支。 +- 后续开发从新的 main clone 开始。原 Phase 4AR 仍停止于 1,033 轮已 CPU 校验训练、138 probes，科学结论未判定。 + +## 恢复指定历史版本 + +在新的空目录获取，而不是覆盖原科学目录： + +```sh +GIT_LFS_SKIP_SMUDGE=1 git clone --branch archive/2026-10-01/v100-conditioning-acceleration \ + ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git digital-drosophila-history +``` + +clone tag 会得到 detached HEAD，这是只读查看历史的正常状态。原始资源归档对应 `archive/2026-10-01/lfs-public-resources`。 + +如以后确需恢复旧分支，可在新 clone 中从对应 tag 创建分支；需用户再次授权推送，避免重新制造已整理的远端分支。 + +## 今后的规则 + +`main` 是统一入口；短期开发使用 `codex/`。工作完成、通过相应验收后合并，重要节点打标签。实验失败同样保留报告与标签，不通过删除失败证据整理仓库。任何受保护科学输入/产物仍遵循原冻结契约。 diff --git a/registry/branch-consolidation-20261001/archive-recovery.json b/registry/branch-consolidation-20261001/archive-recovery.json new file mode 100644 index 0000000..a8ee086 --- /dev/null +++ b/registry/branch-consolidation-20261001/archive-recovery.json @@ -0,0 +1,38 @@ +{ + "created_utc": "2026-10-01T08:53:52.387081+00:00", + 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"4f387b9e6b47f06871ce1b32e265b3a1ae2d78e06d7955a3fa8ed7cfc1d2a0a7" + }, + "artifacts/public-resources-20261001/visualpathways/payload-000006.bin": { + "bytes": 31805270, + "git_blob": "7314b8a57934ad336c7d89b5ad54f30fe574869e", + "oid": "edb0ffa74e646712485a0d5fd2819ef14345c637beeaa5ca811ae3e71a06ea82" + } + }, + "schema": "main-integration-audit-v1", + "scientific_execution": false, + "source_worktrees_modified": false, + "staged_original_blobs_checked": 12674, + "staged_tree": "6b662d0f1c122d0ab86f6b07d53e76943f9035f0", + "verified_utc": "2026-10-01T08:51:08.308553+00:00" +} diff --git a/registry/branch-consolidation-20261001/plan.json b/registry/branch-consolidation-20261001/plan.json new file mode 100644 index 0000000..e3557e6 --- /dev/null +++ b/registry/branch-consolidation-20261001/plan.json @@ -0,0 +1,25 @@ +{ + "schema": "branch-consolidation-plan-v1", + "remote": "ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git", + "target_branch": "main", + "archive_tag_prefix": "archive/2026-10-01/", + "authorization": "User explicitly selected main consolidation, archive tags before remote branch cleanup, and preservation of existing server worktrees.", + "branches": { + "codex/project-bootstrap": "3981628ff893132a8148668aa94726886dba57a3", + "codex/apl-pn-scope-audit": "d6843e675dec5ae38a06f2ba70d74836aea53ace", + "codex/terminal-scope-diagnostic": "3213aada793740961885ba525494e95f019be6f8", + "codex/lif-semantics-audit": "5008cd85ca11750f23ce7bc001e8e821763b7501", + "codex/lif-author-semantics-lab": "09187e4d4d67badf1b418c5f211258ca5d8fb328", + "codex/lfs-public-resources": "5b1d1b72d7683b5c3dcc1f78b408e1d9dd2832ac", + "codex/v100-conditioning-acceleration": "4436241976887d8cc10088b0d44bc7ed70978fe6" + }, + "merge_parents": ["4436241976887d8cc10088b0d44bc7ed70978fe6", "5b1d1b72d7683b5c3dcc1f78b408e1d9dd2832ac"], + "allowed_existing_file_changes": [".gitattributes", ".gitignore", "README.md", "CURRENT.md", "docs/40-operations/branches-20261001.md"], + "new_paths": ["docs/30-reproducibility/main-restore.md", "tools/branch-consolidation/", "registry/branch-consolidation-20261001/"], + "expected_artifact_paths": 181, + "expected_lfs_pointer_paths": 171, + "preserve_existing_worktrees": true, + "delete_lfs_objects": false, + "scientific_execution": false, + "allow_history_rewrite": false +} diff --git a/registry/branch-consolidation-20261001/source-protection.json b/registry/branch-consolidation-20261001/source-protection.json new file mode 100644 index 0000000..37182d9 --- /dev/null +++ b/registry/branch-consolidation-20261001/source-protection.json @@ -0,0 +1,19 @@ +{ + "status": "PASS", + "created_utc": "2026-10-01T08:54:17.339094+00:00", + "files_checked": 64034, + "bytes_checked": 3103901058, + "inventory_sha256": "d7b675b0d0d4647d8fe2fcf9616b9a599e5bc3c15565e604e0d66a046afb835a", + "registration_sha256": "b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740", + "registered_science_commit": "80aeb2093db655329774eff7b32fb6e417b8b40b", + "sources_checked": 16, + "file_mismatches": [], + "source_mismatches": [], + "original_git_head": "09187e4d4d67badf1b418c5f211258ca5d8fb328", + "original_git_status": "", + "wall_seconds": 5.005429710001408, + "scope": "Saved Phase4AR experiment/control files and registered source files; NOT a new Phase1-4AQ numerical regression", + "training_epochs_cpu_verified_unchanged": 1033, + "probes_completed_unchanged": 138, + "original_experiment_resumed": false +} \ No newline at end of file diff --git a/registry/publication-20261001/README.md b/registry/publication-20261001/README.md new file mode 100644 index 0000000..bdaa085 --- /dev/null +++ b/registry/publication-20261001/README.md @@ -0,0 +1,69 @@ +# 2026-10-01 公开 LFS 资源发布 + +这是现有下载资源的归档发布，不是新的科学实验，不表示 Phase 4AR 已完成或学习通过。用户明确选择保留公开仓库，仅上传确认可公开再分发的资源。活动项目工作树和 Phase 1–4AQ 冻结文件不参与写入。 + +**本次发布完成：PASS。** 数据提交 `6e33e05ede21b98c0088139e9bc4c049498c4d41` 已推送到 `codex/lfs-public-resources`，并从该远端提交使用独立空 LFS store 实际重新下载；pull、fsck 及 8 组全部内部成员校验通过。详见 [实际下载回执](fresh-download-verification.json)、[逐组内容核验](fresh-content-verification.json)及[源保护检查](source-guard-final.json)。默认分支未更改，也未自动合并。 + +最终完整性入口为 [publication-manifest.json](publication-manifest.json) 和 [SHA256SUMS](SHA256SUMS)。下载所有 LFS 对象后，可在仓库根目录运行 `sha256sum -c registry/publication-20261001/SHA256SUMS`；它不应在仅有 LFS pointer 的 checkout 中运行。最终文档提交只附加核验记录，不更改上述数据提交的 payload。 + +## 范围与许可 + +| 资源 | 许可/依据 | 本次处理 | +|---|---|---| +| MaleCNS v1.0 annotations、neurotransmitters、connectome、SWC、synaptic partners | [官方数据页](https://male-cns.janelia.org/download/)明确指向 [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) | 逐文件原字节归档、署名、来源与 SHA-256 | +| 原有 Phase 3 / 3B processed 数据 | 基于上述 CC BY 4.0 数据的本项目派生物 | 保留原有过滤/重编号/CSR 转换说明；不重新计算、不更改科学含义 | +| Cell Type Explorer | 固定 commit 的 LICENSE，CC BY 4.0 | 原字节源码/数据快照，保留 LICENSE | +| visualpathways | 固定 commit 的 LICENSE 为 GPL v3 文本 | 原字节源码及 companion resources，保留 notices；不替上游判断 only/or-later | +| DoOR.data 2.0.1 | 固定 commit 的 DESCRIPTION：CC BY-SA 4.0 | 保留作者、原数据来源、ShareAlike 条件 | +| Shiu Drosophila_brain_model | 固定 commit 的 MIT LICENSE | 已下载作者模型源码与环境描述，不称预训练权重 | + +每组精确来源、commit、许可证据 SHA 和修改说明见 `plan.json` 及资源 `catalog.json`；许可证原文随对应上游副本保留。MaleCNS 原数据署名：FlyEM/HHMI Janelia、University of Cambridge Department of Zoology、MRC Laboratory of Molecular Biology、Google Research 及原论文作者。归档封装不意味着这些机构认可本项目模型或结论。 + +DoOR 作者为 Daniel Münch、C. Giovanni Galizia、Shouwen Ma、Martin Strauch、Anja Nissler；[DoOR 2.0 论文](https://doi.org/10.1038/srep21841)及[原始 DoOR 论文](https://doi.org/10.1093/chemse/bjq042)只引用，不另外打包出版商全文。各第三方资源维持原许可，本项目没有给整个仓库强行统一换证。 + +## 明确不上传 + +- FlyVis：冻结 checkout 仅见 MIT classifier，缺独立 LICENSE；数据和预训练权重的再分发权未确认。实际盘点未发现独立下载的预训练 checkpoint/ZIP；不得把源码、几何坐标或功能通道桥接称为下载权重。 +- `datasets/male-cns-v1.0/backups/` 的既有 Phase 1/2 备份包：保留原地；本次已直接归档其 raw 数据，不再重复上传整份备份。 +- Phase 4AD 重复的 Shiu 作者源码：本次仅归档 Phase 4AC 副本；既有目录及历史索引保留。 +- 历史本项目 learned delta、当前 Phase 4AR 正在写入的结果/账本、虚拟环境、缓存、Git 内部目录、凭据、下载日志。 +- ComfyUI 及其他项目、原始 EM 图像、未下载的 syn-points、许可不明的出版商论文全文。 +- visualpathways 的 `pdfversion/` 及 `docs/column_coord.pdf`：已识别为作者图集/配套说明而非一般论文集合，但本次保守等待输出 PDF 的明确许可范围，不把生成程序的 GPL 自动视作所有输出的许可；源码和其余已明确仓库许可的资源仍保留。 + +未列入 plan 的目录默认不发布。额外路径剔除及环境/缓存规则的实际命中保存在各组 `exclusions.jsonl.gz`；文件内容未被改写或“脱敏后替代原件”。 + +## 存储及校验 + +归档位于 `artifacts/public-resources-20261001//`。每组为独立 tar+zstd，切成最多 64 MiB 的有序 LFS 分块，方便大文件传输中断后重试未完成对象。`members.jsonl.gz` 对每个原始相对路径记录大小和 SHA-256；`catalog.json` 记录每块及拼接归档 SHA、源总数、源字节数、来源和许可。分块改变的是存储容器，不是内部文件内容。 + +`pack-summary.json` 存在且 complete=true 仅表示本地打包完成，不等于上传/远程恢复成功。上传后使用独立 clone 和新的 LFS object store 实际下载，再逐块、逐归档、逐内部文件流式校验。对应 receipt 只有在真实校验完成后才会提交。 + +本批实际范围：8 组、226,859 个原文件、24,040,546,041 字节；tar+zstd 分块总计 9,806,419,307 字节（不含小型目录/成员清单）。本地完整内容校验已通过。226,849 个文件与 2026-09-29 历史索引逐 SHA/大小吻合，另 10 个后增参考文件不在该旧索引，明确记为部分历史覆盖；其中 synaptic-partners 登记 SHA、作者模型 LICENSE pin 另有校验，来源原记录随包保留。不得把这次检查描述为所有历史科学阶段重新通过。 + +本次不是服务器所有内容的完整灾备。Gitea LFS 与 Git 仓库数据目录均需另有服务端备份；删除服务端 LFS 对象会破坏恢复能力。尚未核验 Gitea 主机磁盘容量和备份策略。 + +### 本次内网传输 + +Git SSH 本来使用 `192.168.10.31:2222`，但服务器返回的 LFS HTTPS 域名在本机解析到代理地址，导致大对象传输很慢。本次使用仓库本地的 `malecns-lan-https` transfer adapter：TCP 只连接 `192.168.10.31:443`，TLS SNI/证书验证仍使用 `git.lain.asia`，不关闭证书检查、不修改 hosts、系统代理或 Gitea 服务配置。通过原 SSH key 获取短期鉴权，凭据只保留在内存并经标准输入交给 curl，不写入提交或命令行参数。 + +adapter 遵循 [Git LFS 官方 custom-transfer 协议](https://github.com/git-lfs/git-lfs/blob/main/docs/custom-transfers.md)，只允许该仓库的 HTTPS API/object 路径；Gitea 的 `Transfer-Encoding: chunked` 只在上传 PUT 场景被精确处理。它仍上传标准 LFS 对象，其他电脑可以继续使用普通 Git LFS 下载，不依赖这个内网 adapter。并发为 2，分块可重试；科学实验不得因此重启或重试。 + +最初通过代理的核心数据 push 为切换路线而主动停止，未完成的远端分支更新不计为成功。Git 提交和已传对象保留，后续按内容地址续传；严格 header 校验曾在开始 PUT 前拒绝服务器 chunked header，适配后再测试，未改变任何源文件。最终状态以独立下载回执为准，不把这些准备动作记为完成。 + +## 安全恢复（Linux 示例） + +先安装 Git LFS、Python 3 和 zstd。只在新目录恢复，不要覆盖运行中的 `/data/digital-drosophila`。 + +```sh +GIT_LFS_SKIP_SMUDGE=1 git clone --branch codex/lfs-public-resources ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git digital-drosophila-restore +cd digital-drosophila-restore +git lfs install --local +git lfs pull --include='artifacts/public-resources-20261001/**' +python3 -B tools/lfs-publication/publish_archives.py verify --group-dir artifacts/public-resources-20261001/malecns-swc +``` + +对每组运行 verify 并全部通过后，按 catalog 顺序拼接 `payload-000000.bin` 等文件，可用 `zstd -d` 和 tar 在**新建的空恢复目录**解包。归档路径从 `datasets/` 或 `experiments/` 起，无绝对路径。不要运行归档中模型/下载脚本来“验证”，本轮只验证内容。正式使用前仍需检查对应科学阶段 manifest；旧 all-body Phase 3 不能替代已批准的 neuron-only SNN 输入。 + +## 限制 + +快照通过源文件前后 inode/size/mtime/ctime 和枚举一致性检查，不是文件系统原子快照。秘密扫描是有限的 UTF-8 小文本规则，不是对所有二进制、内嵌归档及第三方资源的安全担保。工具内容校验不独立证明 catalog 的真实性；应固定仓库 commit 和 catalog SHA。源码只读校验不能被表述为重新执行全历史科学 gate。 diff --git a/registry/publication-20261001/SHA256SUMS b/registry/publication-20261001/SHA256SUMS new file mode 100644 index 0000000..c1109b3 --- /dev/null +++ b/registry/publication-20261001/SHA256SUMS @@ -0,0 +1,205 @@ +aef53fc7554c50e0a456e58105d683a1dd3323c78cdde822b32eae5ba88b9b6a .gitattributes +4e51bf524b3b0e696b5dc0319b2bbcd92cac456bad72971c629fd7d42c6730aa .gitignore +09a67fa17c5b5a3c4c71cfd6b1789aac517064e3ca160b6fbf6f3bf038d83a73 NOTICE.md +93e0e6c4ca4fdc123c21b859ba97d8bd73670eb9c90d04ce9a431d822b5393c5 artifacts/lfs-smoke/publication-probe.bin +4dc6be6091b273312a1dd61f621654f05e4c12118bdd13c22905d588e378889c artifacts/public-resources-20261001/celltype-explorer/catalog.json +c1bca109b61e53327fa7e01128a411d8ea328972593168c3ad6e1202dfdddc9c artifacts/public-resources-20261001/celltype-explorer/exclusions.jsonl.gz +8a51d3b4138bad12a520f8d1a12d54673416017d15fd1b1bcc49ed385da005bb artifacts/public-resources-20261001/celltype-explorer/members.jsonl.gz +6f5830463b8a0077ae89e550ca45275d57cf7e81813c42bf66f89d13a42c03ee artifacts/public-resources-20261001/celltype-explorer/payload-000000.bin +6b80b0133af06279bd30561f35042b679bd392b9236ee519d1e7ed9c4e85fb6a artifacts/public-resources-20261001/celltype-explorer/payload-000001.bin +6d0fcbe747dae7b38bcf335572b173e0112f6aabd10aa0040b84cfd81a8a390c artifacts/public-resources-20261001/door-data/catalog.json +82627a482fd6adfc3abf4f83a30158fd8371b4532f425f7eb3b03044eb7e1367 artifacts/public-resources-20261001/door-data/exclusions.jsonl.gz +ef13db49577b3b3d1c7c31aab117d911a2decc5a80ead66b6a350c43d16374b4 artifacts/public-resources-20261001/door-data/members.jsonl.gz 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no extraction, no LFS-cache trust; catalog authenticity is caller responsibility", + "source_bytes": 17567, + "source_files": 4 + } + ], + "historical_inventory": { + "all_current_members_historically_matched": false, + "bytes": 12285260, + "current_members_matched": 226849, + "current_members_with_nonfile_history": 0, + "current_members_without_regular_history": 10, + "historical_regular_files_outside_publication": 3390, + "missing_sample": [ + "experiments/phase4aa-apl-pn-scope/external-resources/evidence-and-limitations.json", + "experiments/phase4aa-apl-pn-scope/external-resources/official-data-access.json", + "experiments/phase4aa-apl-pn-scope/external-resources/synaptic-partners/authorization-and-source.json", + "experiments/phase4aa-apl-pn-scope/external-resources/synaptic-partners/download-verification.json", + "experiments/phase4aa-apl-pn-scope/external-resources/synaptic-partners/syn-partners-male-cns-v1.0-minconf-0.5.feather", + "experiments/phase4aa-apl-pn-scope/external-resources/synaptic-partners/upstream-object.json", + "experiments/phase4ac-lif-semantics/external-resources/LICENSE", + "experiments/phase4ac-lif-semantics/external-resources/environment_full.yml", + "experiments/phase4ac-lif-semantics/external-resources/model.py", + "experiments/phase4ac-lif-semantics/external-resources/provenance.json" + ], + "missing_sample_truncated": false, + "nonfile_records_skipped": 0, + "path": "/data/digital-drosophila/registry/snapshots/bootstrap-20260929/files.jsonl.gz", + "records": 230239, + "regular_file_records": 230239, + "scope": "Only publication members with regular-file history compared; 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"environment": "isolated Linux publication checkout; system python3 -B, installed zstd", + "command": "python3 -B -m unittest discover -s tools/lfs-publication -p test_*.py", + "exit_code": 0, + "tests_run": 66, + "skipped": 0, + "failures": 0, + "errors": 0, + "reported_wall_seconds": 0.992, + "suites": {"archive": 18, "aggregate": 14, "download_wrapper": 12, "lan_adapter": 22}, + "scope": "Archive suite includes real zstd integration. Transport/config failure tests use synthetic fixtures and mocks; actual LAN transfer is independently recorded in lan-roundtrip-smoke.json.", + "scientific_trials_executed": false +} diff --git a/tools/branch-consolidation/manage_refs.py b/tools/branch-consolidation/manage_refs.py new file mode 100644 index 0000000..fe4ec7c --- /dev/null +++ b/tools/branch-consolidation/manage_refs.py @@ -0,0 +1,122 @@ +"""Explicitly authorized, fail-closed archive/retire operations in the new clone.""" +import argparse +from datetime import datetime, timezone +import json +import os +from pathlib import Path +import subprocess + +ROOT = Path('/home/qishizhe/digital-drosophila-main-integration-20261001') +RECOVERY = Path('/home/qishizhe/digital-drosophila-branch-recovery-20261001.git') +AUDIT = ROOT / 'registry/branch-consolidation-20261001' + + +def require(value, message): + if not value: + raise RuntimeError(message) + + +def git(*args, cwd=ROOT): + # Existing payloads were checked separately. This operation transfers refs + # and Git objects only; it neither replaces nor uploads any LFS object. + env = dict(os.environ, GIT_LFS_SKIP_SMUDGE='1', GIT_LFS_SKIP_PUSH='1') + return subprocess.check_output(['git', *args], cwd=cwd, env=env, text=True).strip() + + +def snapshot(): + refs = {} + default = None + for line in git('ls-remote', '--symref', 'origin').splitlines(): + value, name = line.split('\t') + if value.startswith('ref: '): + if name == 'HEAD': + default = value[5:] + else: + refs[name] = value + return refs, default + + +def write_receipt(name, **data): + with (AUDIT / name).open('x') as f: + json.dump(dict(schema='branch-consolidation-ref-audit-v1', + created_utc=datetime.now(timezone.utc).isoformat(), **data), + f, indent=2, sort_keys=True) + f.write('\n') + print(json.dumps(data, indent=2)) + + +def main(action): + require(Path.cwd().resolve() == ROOT, 'Independent integration clone required') + plan = json.loads((AUDIT / 'plan.json').read_text()) + require(git('remote', 'get-url', 'origin') == plan['remote'], 'Unexpected remote') + branches = {'refs/heads/' + name: sha for name, sha in plan['branches'].items()} + tags = {plan['archive_tag_prefix'] + name.removeprefix('codex/'): sha + for name, sha in plan['branches'].items()} + before, default_before = snapshot() + + if action == 'archive': + require(not (AUDIT / 'archive-recovery.json').exists(), 'Archive receipt already exists') + require(not RECOVERY.exists(), 'Recovery clone already exists; inspect, do not replace') + require({k: v for k, v in before.items() if k.startswith('refs/heads/')} == branches, + 'Remote heads changed since authorized inventory') + for tag, sha in tags.items(): + ref = 'refs/tags/' + tag + require(ref not in before, 'Archive tag already exists; inspect before proceeding') + require(not git('tag', '--list', tag), 'Local archive tag already exists') + git('tag', '-a', tag, sha, '-m', + 'Archive before user-authorized main consolidation; preserve this exact historical tip. Do not rewrite.') + git('push', '--atomic', 'origin', *['refs/tags/' + tag + ':refs/tags/' + tag for tag in tags]) + after, _ = snapshot() + for tag, sha in tags.items(): + require(after.get('refs/tags/' + tag + '^{}') == sha, 'Remote archived commit differs') + git('init', '--bare', str(RECOVERY)) + git('fetch', '--no-tags', plan['remote'], + *['refs/tags/' + tag + ':refs/tags/' + tag for tag in tags], cwd=RECOVERY) + recovered = {tag: git('rev-parse', 'refs/tags/' + tag + '^{commit}', cwd=RECOVERY) + for tag in tags} + require(recovered == tags, 'Fresh remote recovery failed') + git('fsck', '--full', '--no-reflogs', cwd=RECOVERY) + write_receipt('archive-recovery.json', pass_all=True, remote=plan['remote'], + remote_heads_before=branches, remote_default_before=default_before, + tags=tags, fresh_remote_recovery_path=str(RECOVERY), + recovered_commits=recovered, git_fsck_pass=True, + lfs_payload_downloaded=False, old_remote_branches_deleted=False) + + elif action == 'retire': + require(not (AUDIT / 'remote-cleanup.json').exists(), 'Cleanup receipt already exists') + require(json.loads((AUDIT / 'archive-recovery.json').read_text())['pass_all'], 'Recovery not verified') + require(json.loads((AUDIT / 'merge-audit-final.json').read_text())['pass_all'], 'Merge not verified') + require(default_before == 'refs/heads/main', 'Remote default must already be main') + require(git('branch', '--show-current') == 'main', 'Wrong local branch') + require(git('status', '--porcelain') == '', 'Integration clone is not clean') + main_sha = git('rev-parse', 'HEAD') + expected = dict(branches, **{'refs/heads/main': main_sha}) + require({k: v for k, v in before.items() if k.startswith('refs/heads/')} == expected, + 'Remote heads changed; stop cleanup') + for tag, sha in tags.items(): + require(before.get('refs/tags/' + tag + '^{}') == sha, 'Remote archive missing/different') + require(git('rev-parse', 'refs/tags/' + tag + '^{commit}', cwd=RECOVERY) == sha, + 'Recovery archive differs') + git('merge-base', '--is-ancestor', sha, main_sha) + leases = ['--force-with-lease=' + ref + ':' + sha for ref, sha in branches.items()] + # Delete only these seven exact branch refs, atomically and with their + # recorded old OIDs. No local refs, tags, commits, worktrees or LFS deletion. + git('push', '--atomic', *leases, 'origin', *[':' + ref for ref in branches]) + after, default_after = snapshot() + require({k: v for k, v in after.items() if k.startswith('refs/heads/')} == + {'refs/heads/main': main_sha}, 'Unexpected final heads') + require(default_after == 'refs/heads/main', 'Default branch changed unexpectedly') + for tag, sha in tags.items(): + require(after.get('refs/tags/' + tag + '^{}') == sha, 'Archive lost after deletion') + write_receipt('remote-cleanup.json', pass_all=True, remote=plan['remote'], + main_commit=main_sha, remote_default=default_after, + deleted_remote_branch_refs=branches, preserved_archive_tags=tags, + remaining_remote_heads={'main': main_sha}, + all_old_tips_ancestors_of_main=True, local_branches_deleted=False, + source_worktrees_write_operations=False, lfs_objects_deleted=False) + + +if __name__ == '__main__': + p = argparse.ArgumentParser() + p.add_argument('action', choices=['archive', 'retire']) + main(p.parse_args().action) diff --git a/tools/branch-consolidation/verify_merge.py b/tools/branch-consolidation/verify_merge.py new file mode 100644 index 0000000..db547b8 --- /dev/null +++ b/tools/branch-consolidation/verify_merge.py @@ -0,0 +1,134 @@ +"""Validate staged integration against both original trees without science runs.""" +import argparse +import hashlib +import importlib.util +import json +from pathlib import Path +import re +import subprocess +from datetime import datetime, timezone + + +def require(value, message): + if not value: + raise ValueError(message) + + +def git(*args): + return subprocess.check_output(['git', *args]) + + +def tree(ref): + result = {} + for row in git('ls-tree', '-r', '-z', ref).split(b'\0'): + if row: + meta, path = row.split(b'\t', 1) + mode, kind, oid = meta.decode().split() + require(kind == 'blob', 'Unexpected tree object') + result[path.decode()] = (mode, oid) + return result + + +def main(output, check_lfs): + root = Path.cwd() + require(root == Path('/home/qishizhe/digital-drosophila-main-integration-20261001'), 'Independent integration clone required') + plan = json.loads((root / 'registry/branch-consolidation-20261001/plan.json').read_text()) + left, right = plan['merge_parents'] + base = git('merge-base', left, right).decode().strip() + a, b, old = tree(left), tree(right), tree(base) + staged = {} + for row in git('ls-files', '--stage', '-z').split(b'\0'): + if row: + meta, path = row.split(b'\t', 1) + mode, oid, stage = meta.decode().split() + require(stage == '0', 'Unresolved merge conflict') + staged[path.decode()] = (mode, oid) + allowed = set(plan['allowed_existing_file_changes']) + checked = 0 + for name in sorted(set(a) | set(b)): + require(name in staged, 'Original file removed: ' + name) + if name in allowed: + continue + av, bv, ov = a.get(name), b.get(name), old.get(name) + if av == bv: + expected = av + elif av == ov: + expected = bv + elif bv == ov: + expected = av + elif av is None: + expected = bv + elif bv is None: + expected = av + else: + raise ValueError('Unapproved conflicting original file: ' + name) + require(staged[name] == expected, 'Original blob or mode changed: ' + name) + checked += 1 + new_paths = sorted(set(staged) - set(a) - set(b)) + for name in new_paths: + require(any(name.startswith(p) if p.endswith('/') else name == p for p in plan['new_paths']), 'Unapproved new path') + artifacts = {p: v for p, v in staged.items() if p.startswith('artifacts/')} + require(len(artifacts) == plan['expected_artifact_paths'], 'Artifact path inventory differs') + pointers = {} + pattern = re.compile(rb'version https://git-lfs.github.com/spec/v1\noid sha256:([0-9a-f]{64})\nsize ([0-9]+)\n?') + for name, (mode, oid) in artifacts.items(): + data = git('cat-file', 'blob', oid) + match = pattern.fullmatch(data) + if match: + pointers[name] = dict(oid=match[1].decode(), bytes=int(match[2]), git_blob=oid) + require(len(pointers) == plan['expected_lfs_pointer_paths'], 'LFS pointer path inventory differs') + attributes = git('check-attr', '--cached', 'filter', '--', *pointers).decode().splitlines() + require(len(attributes) == len(pointers) and all(x.endswith(': filter: lfs') for x in attributes), 'Merged LFS rules do not cover every original object') + lfs_report = None + if check_lfs: + source = root / 'tools/lfs-publication/lan_lfs_transfer.py' + require(hashlib.sha256(source.read_bytes()).digest() == hashlib.sha256(git('show', left + ':tools/lfs-publication/lan_lfs_transfer.py')).digest(), 'Transfer adapter changed') + spec = importlib.util.spec_from_file_location('merge_lan', source) + lan = importlib.util.module_from_spec(spec) + spec.loader.exec_module(lan) + agent = lan.Agent(dict(event='init', operation='download', remote='origin', concurrent=True, concurrenttransfers=2), lambda _: None) + href, headers = agent.authenticate() + unique = {v['oid']: v['bytes'] for v in pointers.values()} + requested = [{'oid': oid, 'size': size} for oid, size in sorted(unique.items())] + batches = 0 + for begin in range(0, len(requested), 100): + items = requested[begin:begin + 100] + response = lan.decode_json(agent.curl('POST', href + '/objects/batch', headers, + body=dict(operation='download', transfers=['basic'], objects=items))) + require(response.get('transfer', 'basic') == 'basic', 'Unexpected LFS transfer mode') + received = response.get('objects', []) + require(len(received) == len(items), 'LFS metadata inventory incomplete') + seen = set() + for item in received: + oid = item.get('oid') + require(oid in unique and oid not in seen and item.get('size') == unique[oid] and 'error' not in item, 'LFS object unavailable') + action = item.get('actions', {}).get('download') + require(isinstance(action, dict), 'LFS object has no download action') + lan.safe_url(action['href']) + lan.safe_headers(action.get('header', {})) + seen.add(oid) + require(seen == {item['oid'] for item in items}, 'LFS response object set differs') + batches += 1 + lfs_report = dict(unique_objects=len(unique), unique_bytes=sum(unique.values()), batches=batches, + all_download_actions_available=True, payloads_redownloaded=False, + scope='Authenticated read-only LFS availability; full byte validation remains the unchanged prior fresh-download receipts') + report = dict(schema='main-integration-audit-v1', verified_utc=datetime.now(timezone.utc).isoformat(), + pass_all=True, parents=[left, right], merge_base=base, staged_original_blobs_checked=checked, + allowed_existing_changes=sorted(allowed), new_paths=new_paths, artifact_paths=len(artifacts), + lfs_pointer_paths=len(pointers), pointers=pointers, lfs_availability=lfs_report, + model_tool_registry_artifact_bytes_unchanged=True, scientific_execution=False, + source_worktree_write_operations_by_this_tool=False, + source_worktree_integrity_requires_separate_audit=True, + staged_tree=git('write-tree').decode().strip()) + with output.open('x') as stream: + json.dump(report, stream, indent=2, sort_keys=True) + stream.write('\n') + print(json.dumps({k: v for k, v in report.items() if k not in ('pointers', 'new_paths')}, indent=2)) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--output', type=Path, required=True) + parser.add_argument('--check-lfs', action='store_true') + args = parser.parse_args() + main(args.output, args.check_lfs) diff --git a/tools/lfs-publication/capture_source_guard.py b/tools/lfs-publication/capture_source_guard.py new file mode 100644 index 0000000..1903769 --- /dev/null +++ b/tools/lfs-publication/capture_source_guard.py @@ -0,0 +1,85 @@ +"""Read-only source guard; write receipt only to a new publication path.""" +import argparse +from datetime import datetime, timezone +import hashlib +import json +from pathlib import Path +import shutil +import subprocess + +from publish_archives import no_links, sha_file, canonical + +ROOT = Path('/data/digital-drosophila') +REGISTERED = 'b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740' +SOURCE_COMMIT = '80aeb2093db655329774eff7b32fb6e417b8b40b' + + +def git(*args, cwd=ROOT): + return subprocess.check_output(['git', '-C', str(cwd), *args], text=True).strip() + + +def capture(plan_path, output): + output = no_links(output) + if output == ROOT or ROOT in output.parents or output.exists(): + raise ValueError('Receipt must be new and outside the scientific source') + plan = json.loads(Path(plan_path).read_bytes()) + path = ROOT / 'experiments/phase4ar-normal-conditioning/protocol/preregistered.json' + raw = path.read_bytes() + if hashlib.sha256(raw).hexdigest() != REGISTERED: + raise ValueError('Phase 4AR registration hash mismatch') + registration = json.loads(raw) + records = [] + for filename, expected in sorted(registration['source_sha256'].items()): + source = no_links(filename) + if ROOT not in source.parents: + raise ValueError('Registered source outside project') + actual = sha_file(source) + if actual['sha256'] != expected: + raise ValueError('Phase 4AR source mismatch: ' + filename) + records.append(dict(path=filename, **actual)) + if len(records) != 16: + raise ValueError('Registered source inventory differs from reviewed scope') + if git('cat-file', '-t', SOURCE_COMMIT) != 'commit': + raise ValueError('Registered scientific commit unavailable') + evidence = [] + for group in plan['groups']: + licence = group['license'] + if 'evidence_file' in licence: + source = ROOT / group['paths'][0] / licence['evidence_file'] + actual = sha_file(source) + if actual['sha256'] != licence['evidence_sha256']: + raise ValueError('License evidence hash mismatch: ' + group['id']) + evidence.append(dict(group=group['id'], path=str(source), **actual)) + provenance = group['provenance'] + source = ROOT / group['paths'][0] + if (source / '.git').exists(): + if git('rev-parse', 'HEAD', cwd=source) != provenance['commit']: + raise ValueError('Upstream commit mismatch: ' + group['id']) + if git('status', '--porcelain', cwd=source): + raise ValueError('Upstream checkout changed: ' + group['id']) + result = dict(schema='lfs-publication-source-guard-v1', + observed_utc=datetime.now(timezone.utc).isoformat(), + registration_sha256=REGISTERED, registered_scientific_commit=SOURCE_COMMIT, + phase4ar_registered_sources=records, license_evidence=evidence, + original_checkout_head=git('rev-parse', 'HEAD'), + original_checkout_status=git('status', '--porcelain'), + original_checkout_branch=git('branch', '--show-current'), + disk_free_bytes={str(p): shutil.disk_usage(p).free for p in (ROOT, output.parent)}, + pass_all=True, + scope='16 registered Phase 4AR source files, registration, pinned upstream checkout and license evidence; not a scientific rerun or full historical checksum audit') + if result['original_checkout_status']: + raise ValueError('Original checkout is no longer clean; preserve and investigate') + if any(x < 100 * 1024**3 for x in result['disk_free_bytes'].values()): + raise ValueError('Less than 100 GiB free reserve') + with output.open('xb') as handle: + handle.write(canonical(result)) + return dict(pass_all=True, receipt=str(output), registered_sources=len(records), + original_checkout_head=result['original_checkout_head']) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument('--plan', required=True) + parser.add_argument('--out', required=True) + args = parser.parse_args() + print(json.dumps(capture(args.plan, args.out), sort_keys=True)) diff --git a/tools/lfs-publication/download_verify.py b/tools/lfs-publication/download_verify.py new file mode 100644 index 0000000..64cdf0f --- /dev/null +++ b/tools/lfs-publication/download_verify.py @@ -0,0 +1,232 @@ +"""Fresh-cache transport verification for one independent publication checkout. + +Run only from its top level. This is not a scientific audit or authorization to +publish. Failed attempts retain their cache/partial files and are never retried. +Git/LFS output is suppressed; receipts contain no environment or auth headers. +The caller supplies the trusted commit. Tool source SHA pins are observations, +not signatures; executable versions are not executable-byte identity proofs. +""" +from __future__ import annotations + +import argparse +from datetime import datetime, timezone +import hashlib +import json +from pathlib import Path +import re +import stat +import subprocess +import sys + +import publish_archives as archives +import verify_publication as content + +REMOTE = "ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git" +PAYLOAD = "artifacts/public-resources-20261001" +PROTECTED = Path("/data/digital-drosophila") +TRANSFER_OVERRIDES = (r"^(lfs\.(url|pushurl|standalonetransferagent|customtransfer\..*|" + r"remote\.(autodetect|searchall))|remote\.(lfsdefault|origin\.lfsurl))$") + + +def require(condition, message): + if not condition: + raise ValueError(message) + + +def within(path, root): + return path == root or root in path.parents + + +def command(args, *, text=False, bytes_output=False): + """Never return or print command diagnostics, which may contain credentials.""" + result = subprocess.run(args, stdin=subprocess.DEVNULL, stderr=subprocess.DEVNULL, + stdout=subprocess.PIPE if text or bytes_output else subprocess.DEVNULL, + check=False) + if text or bytes_output: + require(result.returncode == 0, "Read-only Git/tool identity command failed") + if bytes_output: + return result.stdout + return result.stdout.decode("utf-8", errors="strict").strip() + return result.returncode + + +def identity(expected, checkout): + require(command(["git", "rev-parse", "--verify", "HEAD"], text=True) == expected, + "HEAD differs from expected commit") + require(archives.no_links(command(["git", "rev-parse", "--show-toplevel"], text=True)) == checkout, + "Run from the independent checkout top level") + require(archives.no_links(command(["git", "rev-parse", "--absolute-git-dir"], text=True)) == checkout / ".git", + "External/linked Git directory refused") + require(command(["git", "remote", "get-url", "--all", "origin"], text=True) == REMOTE, + "Origin must exactly match the approved remote") + + +def transfer_policy(checkout, expected_commit, allow_lan_adapter=False): + require(not (checkout / ".lfsconfig").exists() and not (checkout / ".lfsconfig").is_symlink(), + "Repository LFS endpoint overrides refused") + if not allow_lan_adapter: + # Exit 1 means no matches; potential credential values are never read. + require(command(["git", "config", "--get-regexp", TRANSFER_OVERRIDES]) == 1, + "LFS endpoint/custom-transfer override or unreadable configuration refused") + return None + relative = "tools/lfs-publication/lan_lfs_transfer.py" + adapter = archives.no_links(checkout / relative) + require(not any(c.isspace() for c in str(adapter)), "LAN adapter path must not require argument quoting") + prefix = "lfs.customtransfer.malecns-lan-https." + allowed = {"lfs.standalonetransferagent": "malecns-lan-https", + prefix + "path": "/usr/bin/python3", prefix + "args": "-B " + str(adapter), + prefix + "concurrent": "true", prefix + "direction": "both"} + keys = command(["git", "config", "--name-only", "--get-regexp", TRANSFER_OVERRIDES], text=True).splitlines() + require(len(keys) == len(allowed) and set(keys) == set(allowed), + "Only the exact approved LAN adapter configuration is permitted") + for key, value in allowed.items(): + require(command(["git", "config", "--local", "--get-all", key], text=True) == value + and command(["git", "config", "--get-all", key], text=True) == value, + "LAN adapter configuration must be exact and exclusively repository-local") + pin = archives.sha_file(adapter) + blob = command(["git", "show", expected_commit + ":" + relative], bytes_output=True) + require(len(blob) == pin["bytes"] and hashlib.sha256(blob).hexdigest() == pin["sha256"], + "LAN adapter must exactly match the expected HEAD blob") + return {"path": str(adapter), **pin} + + +def new_output(path, checkout, cache, payload): + p = archives.no_links(path) + require(not within(p, PROTECTED.absolute()), "Output under original project refused") + require(within(p, checkout.parent), "Output must stay in the independent workspace") + require(not within(p, payload) and not within(p, checkout / ".git") + and not within(p, checkout / "artifacts") and not within(p, cache), + "Receipt must be outside payload, artifacts, Git and cache trees") + require(not p.exists() and p.parent.is_dir(), "Receipt must be new with an existing parent") + return p + + +def cache_inventory(cache): + count = total = 0 + objects = cache / "objects" + if not objects.exists(): + return {"objects": 0, "bytes": 0} + archives.no_links(objects) + require(objects.is_dir(), "LFS objects must be a directory") + for p in objects.rglob("*"): + archives.no_links(p) + s = p.lstat() + if stat.S_ISDIR(s.st_mode): + continue + require(stat.S_ISREG(s.st_mode), "Nonregular cache object refused") + parts = p.relative_to(objects).parts + require(len(parts) == 3 and archives.HEX.fullmatch(parts[2]) is not None + and parts[0] == parts[2][:2] and parts[1] == parts[2][2:4], + "Unexpected LFS object layout") + count += 1 + total += s.st_size + return {"objects": count, "bytes": total} + + +def source_pins(adapter=None): + result = {name: {"path": str(Path(path).absolute()), **archives.sha_file(path)} + for name, path in (("download_verify.py", __file__), + ("verify_publication.py", content.__file__), + ("publish_archives.py", archives.__file__))} + if adapter is not None: + result["lan_lfs_transfer.py"] = {"path": adapter["path"], **archives.sha_file(adapter["path"])} + return result + + +def run(expected_commit, cache, receipt, content_receipt, historical_inventory, *, allow_lan_adapter=False): + require(isinstance(expected_commit, str) and re.fullmatch(r"[0-9a-f]{40}", expected_commit), + "Expected commit must be a complete lowercase SHA-1") + checkout = archives.no_links(Path.cwd()) + require(not within(checkout, PROTECTED.absolute()), "Original project checkout refused") + gitdir = archives.no_links(checkout / ".git") + require(gitdir.is_dir(), "Only an independent clone with its own .git directory is accepted") + identity(expected_commit, checkout) + adapter = transfer_policy(checkout, expected_commit, allow_lan_adapter) + require(not command(["git", "status", "--porcelain", "--untracked-files=no"], text=True), + "Tracked checkout changes refused") + cache = archives.no_links(cache) + require(not within(cache, PROTECTED.absolute()), "Cache under original project refused") + require(within(cache, gitdir) or (within(cache, checkout.parent) and not within(cache, checkout)), + "Cache must be inside this .git or outside checkout in the independent workspace") + require(not cache.exists() and cache.parent.is_dir(), "Cache must never have existed for this attempt") + payload = archives.no_links(checkout / PAYLOAD) + receipt = new_output(receipt, checkout, cache, payload) + content_receipt = new_output(content_receipt, checkout, cache, payload) + history = archives.no_links(historical_inventory) + require(len({receipt, content_receipt, history, cache}) == 4, "Inputs/outputs must be distinct") + history_pin = archives.sha_file(history) + pins = source_pins(adapter) + versions = {"git": command(["git", "--version"], text=True), + "git_lfs": command(["git", "lfs", "version"], text=True), + "zstd": command(["zstd", "--version"], text=True), + "python": sys.version.split()[0]} + started = datetime.now(timezone.utc).isoformat() + cache.mkdir(exist_ok=False) + initial = cache_inventory(cache) + require(initial == {"objects": 0, "bytes": 0}, "New cache is not empty") + print(json.dumps({"stage": "fresh-cache-created", "objects": 0, "bytes": 0}), flush=True) + git = ["git", "-c", "lfs.storage=" + str(cache), "-c", "lfs.concurrenttransfers=2"] + pull = command(git + ["lfs", "pull", "--include=artifacts/**", "--exclude=", "origin"]) + require(pull == 0, "LFS pull failed; cache retained, no automatic retry") + print(json.dumps({"stage": "pull-exited", "exit_code": pull}), flush=True) + fsck = command(git + ["lfs", "fsck", "--dry-run"]) + require(fsck == 0, "LFS fsck failed; cache retained, no automatic retry") + print(json.dumps({"stage": "fsck-exited", "exit_code": fsck}), flush=True) + objects = cache_inventory(cache) + require(objects["objects"] > 0 and objects["bytes"] > 0, "Fresh LFS cache contains no objects") + verified = content.verify_publication(payload, content_receipt, history) + require(verified.get("pass_all") is True + and archives.HEX.fullmatch(str(verified.get("aggregate_inventory_sha256", ""))) is not None, + "Content verification did not report success") + content_pin = archives.sha_file(content_receipt) + require(content_pin["sha256"] == verified.get("receipt_sha256"), "Content receipt SHA mismatch") + require(archives.sha_file(history) == history_pin and source_pins(adapter) == pins, + "History or verification tool changed during attempt") + identity(expected_commit, checkout) + require(transfer_policy(checkout, expected_commit, allow_lan_adapter) == adapter, + "LAN adapter identity/configuration changed during attempt") + require(cache_inventory(cache) == objects, "Cache object inventory changed during content verification") + report = {"schema": "lfs-publication-download-verification-v1", "pass_all": True, + "started_utc": started, "verified_utc": datetime.now(timezone.utc).isoformat(), + "checkout": str(checkout), "expected_commit": expected_commit, + "head": expected_commit, "origin": REMOTE, + "explicit_pull_remote": "origin", "lfs_endpoint_overrides_refused": True, + "lan_adapter": {"enabled": adapter is not None, "source": adapter, + "configuration_scope": "repository-local only" if adapter else None, + "temporary_download_directory": str(gitdir / "lfs/lan-transfer-tmp") if adapter else None}, + "cache": {"path": str(cache), "initially_absent": True, + "before": initial, "after": objects}, + "pull_exit_code": pull, "fsck_dry_run_exit_code": fsck, + "include": "artifacts/**", "exclude": "", "concurrent_transfers": 2, + "content_receipt": {"path": str(content_receipt), **content_pin}, + "aggregate_inventory_sha256": verified["aggregate_inventory_sha256"], + "historical_inventory": {"path": str(history), **history_pin, + "status": verified.get("historical_status")}, + "tool_sources": pins, "tool_versions": versions, "fresh_download_proven": True, + "learning_pass_claimed": False, "original_project_write_requested": False, + "scope": "Fresh isolated LFS storage, actual pull/fsck exits and complete publication member verification; smoke covered by pull/fsck. Not a scientific gate, all-history audit, or executable-byte identity proof."} + archives.write_new(receipt, archives.canonical(report)) + return report + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--expected-commit", required=True) + parser.add_argument("--cache", required=True) + parser.add_argument("--receipt", required=True) + parser.add_argument("--content-receipt", required=True) + parser.add_argument("--historical-inventory", required=True) + parser.add_argument("--allow-lan-adapter", action="store_true") + args = parser.parse_args() + try: + run(args.expected_commit, args.cache, args.receipt, args.content_receipt, args.historical_inventory, + allow_lan_adapter=args.allow_lan_adapter) + except (Exception, KeyboardInterrupt) as exc: + print(json.dumps({"status": "FAILED-NOT-RETRIED", "error_type": type(exc).__name__}), flush=True) + return 1 + print(json.dumps({"status": "PASS", "receipt": str(Path(args.receipt).absolute())}), flush=True) + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/tools/lfs-publication/publish_archives.py b/tools/lfs-publication/publish_archives.py new file mode 100644 index 0000000..cfe09c8 --- /dev/null +++ b/tools/lfs-publication/publish_archives.py @@ -0,0 +1,534 @@ +"""Whitelist-only LFS archives; content verification, not a redistribution grant. + +No source writes, cache-based trust, extraction, or Git operations. Failed packs +remain incomplete and cannot be retried into the same output/work directories. +File stability checks are observations, not an atomic filesystem snapshot. +""" +from __future__ import annotations + +import argparse +import gzip +import hashlib +import io +import json +import os +from pathlib import Path, PurePosixPath +import re +import stat +import subprocess +import tarfile +import tempfile +import threading + +SOURCE_ROOT = "/data/digital-drosophila" +CHUNK_BYTES = 64 * 1024 * 1024 +BUFFER = 1024 * 1024 +DENIED_DIRS = {".git", ".venv", "venv", "env", "__pycache__", ".cache", + "node_modules", ".pytest_cache", ".mypy_cache", "extension-build"} +LOG_DIRS = {"logs", "_logs"} +BINARY_SUFFIXES = {".npy", ".npz", ".feather", ".parquet", ".gz", ".zst", ".zip", + ".tar", ".png", ".jpg", ".jpeg", ".gif", ".webp", ".pdf", + ".woff", ".woff2", ".ttf", ".ico", ".so", ".o", ".a", ".bin"} +HEX = re.compile(r"^[0-9a-f]{64}$") +SECRET_RULES = ( + ("private-key", re.compile(r"-----BEGIN (?:[A-Z ]+ )?PRIVATE KEY-----")), + ("github-token", re.compile(r"\b(?:ghp_[A-Za-z0-9]{20,}|github_pat_[A-Za-z0-9_]{20,})\b")), + ("aws-access-key", re.compile(r"\bAKIA[0-9A-Z]{16}\b")), + ("url-user-password", re.compile(r"\b[a-zA-Z][a-zA-Z0-9+.-]*://[^\s/:@]+:[^\s/@]+@")), + ("secret-literal", re.compile(r'''(?ix)\b(?:password|passwd|api[_-]?key|secret[_-]?key)\b["']?\s*[:=]\s*(?:["']([^"'\r\n]+)["']|([A-Za-z0-9_+/@.-]{4,}))''')), +) + + +def canonical(value): + return (json.dumps(value, sort_keys=True, indent=2, ensure_ascii=False, allow_nan=False) + "\n").encode() + + +def json_bytes(data): + def unique(pairs): + value = {} + for key, item in pairs: + if key in value: + raise ValueError("Duplicate JSON key") + value[key] = item + return value + return json.loads(data, object_pairs_hook=unique) + + +def json_read(path): + return json_bytes(Path(path).read_bytes()) + + +def relpath(value): + if not isinstance(value, str) or not value or "\\" in value or "\x00" in value: + raise ValueError("Invalid relative path") + p = PurePosixPath(value) + if p.is_absolute() or any(x in ("", ".", "..") for x in value.split("/")) or ":" in value: + raise ValueError("Unsafe relative path") + return p.as_posix() + + +def forbidden(relative): + parts = PurePosixPath(relative).parts + lower = [x.lower() for x in parts] + if any(x in DENIED_DIRS or x.startswith(".venv") for x in lower): + return "git-environment-or-cache" + if any(x.startswith("phase4ar") for x in lower): + return "active-phase4ar" + if any(x in LOG_DIRS for x in lower) or lower[-1].endswith((".log", ".log.gz")): + return "log" + name = lower[-1] + if (name == ".env" or name.startswith(".env.") or name in + {"id_rsa", "id_ed25519", "id_dsa", ".git-credentials", ".netrc"} + or any(x in name for x in ("credentials", "secrets")) + or name.endswith((".pem", ".key", ".p12", ".pfx"))): + return "credential-file" + return None + + +def no_links(path): + if ".." in Path(path).parts: + raise ValueError("Parent path components refused") + p = Path(path).absolute() + for part in (p, *p.parents): + if part.exists() or part.is_symlink(): + s = part.lstat() + if (stat.S_ISLNK(s.st_mode) or + getattr(s, "st_file_attributes", 0) & getattr(stat, "FILE_ATTRIBUTE_REPARSE_POINT", 0)): + raise ValueError("Symlink refused: " + str(part)) + return p + + +def identity(s): + return (s.st_dev, s.st_ino, s.st_mode, s.st_size, s.st_mtime_ns, s.st_ctime_ns) + + +def opened_identity(handle, expected): + actual = identity(os.fstat(handle.fileno())) + # Some Windows Python builds expose birth time via stat().ctime but change + # time via fstat().ctime. Check each clock against itself before/after; never + # omit ctime from either endpoint's stability check. Linux uses all fields. + same = actual[:-1] == expected[:-1] if os.name == "nt" else actual == expected + if not same: + raise ValueError("File changed while opening") + return actual + + +def sha_file(path): + p = no_links(path) + before = p.stat() + if not stat.S_ISREG(before.st_mode): + raise ValueError("Not a regular file: " + str(p)) + h = hashlib.sha256() + size = 0 + with p.open("rb") as f: + opened = opened_identity(f, identity(before)) + while block := f.read(BUFFER): + h.update(block) + size += len(block) + if identity(os.fstat(f.fileno())) != opened: + raise ValueError("File changed while hashing: " + str(p)) + if identity(p.lstat()) != identity(before) or size != before.st_size: + raise ValueError("File changed while hashing: " + str(p)) + return {"sha256": h.hexdigest(), "bytes": size} + + +def write_new(path, data): + with Path(path).open("xb") as f: + f.write(data) + + +def validate_plan(plan): + if not isinstance(plan, dict) or set(plan) - {"schema", "source_root", "groups", "exclude_paths"}: + raise ValueError("Unknown plan fields") + if plan.get("schema") != "lfs-publication-plan-v1" or plan.get("source_root") != SOURCE_ROOT: + raise ValueError("Wrong plan schema/source_root") + groups = plan.get("groups") + if not isinstance(groups, list) or not groups: + raise ValueError("Nonempty groups required") + seen, all_paths = set(), [] + for g in groups: + if not isinstance(g, dict) or set(g) != {"id", "paths", "license", "provenance"}: + raise ValueError("Group requires id/paths/license/provenance only") + group_id = g["id"] + if not isinstance(group_id, str) or not re.fullmatch(r"[a-z0-9][a-z0-9._-]{0,99}", group_id) or group_id in seen: + raise ValueError("Invalid or duplicate group id") + seen.add(group_id) + if not isinstance(g["paths"], list) or not g["paths"] or not g["license"] or not g["provenance"]: + raise ValueError("Nonempty paths/license/provenance required") + for value in g["paths"]: + p = relpath(value) + if forbidden(p): + raise ValueError("Explicit forbidden path: " + p) + if any(p == old or p.startswith(old + "/") or old.startswith(p + "/") for old in all_paths): + raise ValueError("Overlapping whitelist paths") + all_paths.append(p) + excludes = plan.get("exclude_paths", []) + if not isinstance(excludes, list): + raise ValueError("exclude_paths must be a list") + for p in excludes: + relpath(p) + canonical(plan) + + +def enumerate_group(root, group, excludes): + files, omitted = [], [] + + def visit(p): + relative = p.relative_to(root).as_posix() + s = p.lstat() + if stat.S_ISLNK(s.st_mode): + raise ValueError("Symlink refused: " + relative) + reason = forbidden(relative) + if any(relative == x or relative.startswith(x + "/") for x in excludes): + reason = "plan-exclusion" + if reason: + omitted.append({"path": relative, "reason": reason, + "scope": "subtree" if stat.S_ISDIR(s.st_mode) else "file", + "bytes": s.st_size if stat.S_ISREG(s.st_mode) else None}) + elif stat.S_ISDIR(s.st_mode): + for child in sorted(p.iterdir(), key=lambda x: x.name): + visit(child) + elif stat.S_ISREG(s.st_mode): + files.append((relative, identity(s))) + else: + raise ValueError("Nonregular source refused: " + relative) + + for relative in group["paths"]: + path = no_links(root / relative) + visit(path) + files.sort(key=lambda x: x[0]) + omitted.sort(key=lambda x: x["path"]) + if not files: + raise ValueError("Empty group refused") + return files, omitted + + +def scan_secrets(root, files): + for relative, original in files: + p = root / relative + if original[3] > 2 * 1024 * 1024 or p.suffix.lower() in BINARY_SUFFIXES: + continue + data = p.read_bytes() + if identity(p.lstat()) != original: + raise ValueError("Source changed during secret scan: " + relative) + try: + text = data.decode("utf-8") + except UnicodeDecodeError: + continue + if "\x00" in text: + continue + # Per-rule ASCII necessary fragments avoid repeated scans of numeric SWC + # bodies (their header includes a public URL). Non-ASCII text still uses + # every regex because Unicode IGNORECASE has broader equivalences. + lower = text.lower() + fragments = { + "private-key": ("private key",), + "github-token": ("ghp_", "github_pat_"), + "aws-access-key": ("akia",), + "url-user-password": ("://",), + "secret-literal": ("password", "passwd", "api", "secret"), + } + for rule, pattern in SECRET_RULES: + if text.isascii() and not any(x in lower for x in fragments[rule]): + continue + for match in pattern.finditer(text): + if rule == "secret-literal": + literal = match.group(1) or match.group(2) + if literal.lower() in {"none", "null", "false", "true"}: + continue + raise ValueError("Secret scan refused: " + relative + " [" + rule + "]") + + +def gzip_rows(path, rows): + with Path(path).open("xb") as raw: + with gzip.GzipFile(filename="", mode="wb", fileobj=raw, mtime=0) as out: + for row in rows: + out.write((json.dumps(row, sort_keys=True, ensure_ascii=False, allow_nan=False) + "\n").encode()) + + +class HashReader: + def __init__(self, handle): + self.handle, self.hash, self.size = handle, hashlib.sha256(), 0 + + def read(self, count=-1): + data = self.handle.read(count) + self.hash.update(data) + self.size += len(data) + return data + + +def zstd_command(decompress=False, threads=2): + return ["zstd", "-q", "-d", "-c"] if decompress else ["zstd", "-q", "-3", "-T" + str(threads), "-c"] + + +def make_archive(root, files, destination, threads): + rows = [] + with destination.open("xb") as output, tempfile.TemporaryFile() as errors: + proc = subprocess.Popen(zstd_command(threads=threads), stdin=subprocess.PIPE, + stdout=output, stderr=errors) + try: + with tarfile.open(fileobj=proc.stdin, mode="w|", format=tarfile.PAX_FORMAT) as archive: + for relative, original in files: + p = no_links(root / relative) + if identity(p.lstat()) != original: + raise ValueError("Source changed before archive: " + relative) + with p.open("rb") as source: + opened = opened_identity(source, original) + reader = HashReader(source) + info = tarfile.TarInfo(relative) + info.size, info.mode, info.mtime = original[3], stat.S_IMODE(original[2]) & 0o777, 0 + archive.addfile(info, reader) + if (reader.size != original[3] or identity(os.fstat(source.fileno())) != opened + or identity(p.lstat()) != original): + raise ValueError("Source changed during archive: " + relative) + rows.append({"path": relative, "bytes": reader.size, "sha256": reader.hash.hexdigest()}) + proc.stdin.close() + if proc.wait() != 0: + raise RuntimeError("zstd compression failed; no complete catalog published") + except BaseException: + proc.kill() + proc.wait() + raise + finally: + proc.stdin.close() + return rows + + +def split_archive(archive, group_dir): + chunks, full = [], hashlib.sha256() + with archive.open("rb") as source: + index = 0 + while first := source.read(min(BUFFER, CHUNK_BYTES)): + name = "payload-%06d.bin" % index + h, size = hashlib.sha256(), 0 + with (group_dir / name).open("xb") as out: + block = first + while block: + out.write(block) + full.update(block) + h.update(block) + size += len(block) + if size == CHUNK_BYTES: + break + block = source.read(min(BUFFER, CHUNK_BYTES - size)) + chunks.append({"path": name, "bytes": size, "sha256": h.hexdigest(), "index": index}) + index += 1 + if not chunks: + raise ValueError("Empty compressed archive") + return chunks, full.hexdigest() + + +def pack(plan_path, out, work, *, threads=2): + if type(threads) is not int or not 1 <= threads <= 64: + raise ValueError("threads must be 1..64") + plan_bytes = Path(plan_path).read_bytes() + plan = json_bytes(plan_bytes) + validate_plan(plan) + root, out, work = map(no_links, (Path(plan["source_root"]), Path(out), Path(work))) + for a, b in ((root, out), (root, work), (out, work)): + if a == b or a in b.parents or b in a.parents: + raise ValueError("source, out and work must be disjoint trees") + if out.exists() or work.exists(): + raise FileExistsError("out/work must both be new exclusive paths") + out.mkdir(parents=True, exist_ok=False) + work.mkdir(parents=True, exist_ok=False) + write_new(out / "plan.json", plan_bytes) + plan_sha = hashlib.sha256(plan_bytes).hexdigest() + results = [] + for group in plan["groups"]: + files, exclusions = enumerate_group(root, group, plan.get("exclude_paths", [])) + scan_secrets(root, files) + group_dir = out / group["id"] + group_dir.mkdir() + archive = work / (group["id"] + ".tar.zst") + members = make_archive(root, files, archive, threads) + # A second metadata enumeration catches file additions/removals during pack. + after_files, after_exclusions = enumerate_group(root, group, plan.get("exclude_paths", [])) + if after_files != files or after_exclusions != exclusions: + raise ValueError("Source inventory changed during pack") + gzip_rows(group_dir / "members.jsonl.gz", members) + gzip_rows(group_dir / "exclusions.jsonl.gz", exclusions) + chunks, combined = split_archive(archive, group_dir) + catalog = dict(schema="lfs-publication-group-v1", group_id=group["id"], source_root=str(root), + source_paths=group["paths"], source_files=len(members), + source_bytes=sum(x["bytes"] for x in members), license=group["license"], + provenance=group["provenance"], plan_sha256=plan_sha, + archive_format="tar.pax+zstd", archive_sha256=combined, + archive_bytes=sum(x["bytes"] for x in chunks), chunk_bytes=CHUNK_BYTES, + chunks=chunks, members=sha_file(group_dir / "members.jsonl.gz"), + exclusions=sha_file(group_dir / "exclusions.jsonl.gz"), + exclusion_records=len(exclusions), + verification_scope="content snapshot, not a license grant or nested-archive secret audit", + secret_scan="UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules") + write_new(group_dir / "catalog.json", canonical(catalog)) + result = {"group": group["id"], "files": len(members), "source_bytes": catalog["source_bytes"], + "archive_bytes": catalog["archive_bytes"], "chunks": len(chunks), + "catalog_sha256": sha_file(group_dir / "catalog.json")["sha256"]} + results.append(result) + print(json.dumps({"group_complete": result}), flush=True) + summary = {"schema": "lfs-publication-pack-v1", "complete": True, "plan_sha256": plan_sha, + "groups": results, "source_files": sum(x["files"] for x in results), + "source_bytes": sum(x["source_bytes"] for x in results)} + write_new(out / "pack-summary.json", canonical(summary)) + return summary + + +def check_digest_row(row): + if not isinstance(row, dict) or type(row.get("bytes")) is not int or row["bytes"] < 0 or not HEX.fullmatch(str(row.get("sha256", ""))): + raise ValueError("Invalid SHA/size metadata") + + +def iter_members(path): + previous = None + with gzip.open(path, "rt", encoding="utf-8") as inp: + for line in inp: + row = json.loads(line) + if set(row) != {"path", "bytes", "sha256"}: + raise ValueError("Invalid member row") + check_digest_row(row) + p = relpath(row["path"]) + if forbidden(p) or (previous is not None and p <= previous): + raise ValueError("Forbidden/duplicate/unsorted member: " + p) + previous = p + yield row + + +def verify(group_dir): + group_dir = no_links(group_dir) + controls_before = {name: sha_file(group_dir / name) for name in + ("catalog.json", "members.jsonl.gz", "exclusions.jsonl.gz")} + catalog = json_read(group_dir / "catalog.json") + if catalog.get("schema") != "lfs-publication-group-v1" or catalog.get("chunk_bytes") != CHUNK_BYTES or catalog.get("archive_format") != "tar.pax+zstd": + raise ValueError("Wrong catalog schema/format/chunk size") + chunks = catalog.get("chunks") + if not isinstance(chunks, list) or not chunks: + raise ValueError("Missing payload chunks") + expected = {"catalog.json", "members.jsonl.gz", "exclusions.jsonl.gz"} + for i, row in enumerate(chunks): + check_digest_row(row) + if set(row) != {"path", "bytes", "sha256", "index"} or type(row["index"]) is not int or row["index"] != i or row["path"] != "payload-%06d.bin" % i: + raise ValueError("Wrong chunk name/order") + if not 0 < row["bytes"] <= CHUNK_BYTES or (i < len(chunks) - 1 and row["bytes"] != CHUNK_BYTES): + raise ValueError("Wrong chunk size") + expected.add(row["path"]) + if {p.name for p in group_dir.iterdir()} != expected: + raise ValueError("Extra/missing downloaded files") + for p in group_dir.iterdir(): + no_links(p) + if not p.is_file(): + raise ValueError("Nonfile downloaded entry") + for name, key in (("members.jsonl.gz", "members"), ("exclusions.jsonl.gz", "exclusions")): + check_digest_row(catalog[key]) + if controls_before[name] != catalog[key]: + raise ValueError("Metadata digest mismatch: " + name) + with gzip.open(group_dir / "exclusions.jsonl.gz", "rt", encoding="utf-8") as source: + omitted = list(map(json.loads, source)) + if len(omitted) != catalog.get("exclusion_records"): + raise ValueError("Exclusion inventory mismatch") + for row in omitted: + relpath(row["path"]) + errors, combined, compressed = [], hashlib.sha256(), [0] + with tempfile.TemporaryFile() as diagnostics: + proc = subprocess.Popen(zstd_command(decompress=True), stdin=subprocess.PIPE, + stdout=subprocess.PIPE, stderr=diagnostics) + + def feed(): + try: + for row in chunks: + p = group_dir / row["path"] + before = identity(p.lstat()) + h, size = hashlib.sha256(), 0 + with p.open("rb") as source: + opened = opened_identity(source, before) + while data := source.read(BUFFER): + h.update(data) + combined.update(data) + size += len(data) + compressed[0] += len(data) + proc.stdin.write(data) + if identity(os.fstat(source.fileno())) != opened or identity(p.lstat()) != before: + raise ValueError("Chunk changed during read") + if size != row["bytes"] or h.hexdigest() != row["sha256"]: + raise ValueError("Payload digest mismatch: " + row["path"]) + except BaseException as exc: + errors.append(exc) + finally: + try: + proc.stdin.close() + except OSError: + pass + + producer = threading.Thread(target=feed, daemon=True) + producer.start() + count, total = 0, 0 + expected_rows = iter(iter_members(group_dir / "members.jsonl.gz")) + try: + with tarfile.open(fileobj=proc.stdout, mode="r|") as archive: + for member in archive: + row = next(expected_rows, None) + if not member.isreg() or member.linkname or member.sparse is not None: + raise ValueError("Nonregular/sparse/link tar member refused") + path = relpath(member.name) + if forbidden(path) or row is None or path != row["path"] or member.size != row["bytes"]: + raise ValueError("Tar member set/size/path mismatch: " + path) + reader = HashReader(archive.extractfile(member)) + while reader.read(BUFFER): + pass + if reader.size != row["bytes"] or reader.hash.hexdigest() != row["sha256"]: + raise ValueError("Tar member content mismatch: " + path) + count += 1 + total += reader.size + # tarfile stops at the first end marker; reject a hidden second + # archive/nonzero trailer, including bytes in its read-ahead buf. + while trailer := archive.fileobj.read(BUFFER): + if any(trailer): + raise ValueError("Nonzero data after tar end marker") + if next(expected_rows, None) is not None: + raise ValueError("Missing tar members") + # Drain to validate zstd's complete stream/checksum and finish the feeder. + while proc.stdout.read(BUFFER): + pass + producer.join() + code = proc.wait() + if errors: + raise ValueError("Payload streaming failed: " + str(errors[0])) + if code != 0: + raise ValueError("zstd decompression failed") + except BaseException: + proc.kill() + proc.wait() + producer.join(timeout=10) + raise + finally: + proc.stdout.close() + expected_rows.close() + if (count != catalog.get("source_files") or total != catalog.get("source_bytes") + or compressed[0] != catalog.get("archive_bytes") or combined.hexdigest() != catalog.get("archive_sha256")): + raise ValueError("Final inventory/archive digest mismatch") + for name, before in controls_before.items(): + if sha_file(group_dir / name) != before: + raise ValueError("Downloaded control changed during verification: " + name) + return {"schema": "lfs-publication-verify-v1", "pass_all": True, "group": catalog["group_id"], + "source_files": count, "source_bytes": total, "archive_bytes": compressed[0], + "archive_sha256": combined.hexdigest(), "catalog_sha256": controls_before["catalog.json"]["sha256"], + "scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility"} + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + sub = parser.add_subparsers(dest="command", required=True) + command = sub.add_parser("pack") + command.add_argument("--plan", required=True) + command.add_argument("--out", required=True) + command.add_argument("--work", required=True) + command.add_argument("--threads", type=int, default=2) + command = sub.add_parser("verify") + command.add_argument("--group-dir", required=True) + args = parser.parse_args() + result = (pack(args.plan, args.out, args.work, threads=args.threads) if args.command == "pack" + else verify(args.group_dir)) + print(json.dumps(result, sort_keys=True, ensure_ascii=False, allow_nan=False), flush=True) + + +if __name__ == "__main__": + main() diff --git a/tools/lfs-publication/run_lan_smoke.py b/tools/lfs-publication/run_lan_smoke.py new file mode 100644 index 0000000..8bbb112 --- /dev/null +++ b/tools/lfs-publication/run_lan_smoke.py @@ -0,0 +1,52 @@ +"""One real archive chunk upload and fresh download; never modifies source data.""" +import argparse +import json +from pathlib import Path +import time +from datetime import datetime, timezone + +import lan_lfs_transfer as lan +import publish_archives as archives + + +def run(output): + root = Path.cwd() + receipt = archives.no_links(output) + if receipt.exists() or root / 'registry/publication-20261001' not in receipt.parents: + raise ValueError('New publication receipt required') + catalog = archives.json_read(root / 'artifacts/public-resources-20261001/malecns-synaptic-partners/catalog.json') + chunk = catalog['chunks'][0] + oid, size = chunk['sha256'], chunk['bytes'] + source = root / '.git/lfs/objects' / oid[:2] / oid[2:4] / oid + records = [] + for operation in ('upload', 'download'): + agent = lan.Agent(dict(event='init', operation=operation, remote='origin', + concurrent=True, concurrenttransfers=2), lambda value: None) + original = agent.curl + methods = [] + def observe(method, url, headers, **kwargs): + result = original(method, url, headers, **kwargs) + methods.append(method) + return result + agent.curl = observe + start = time.perf_counter() + result = agent.transfer(dict(event=operation, action=None, oid=oid, size=size, + **({'path': str(source)} if operation == 'upload' else {}))) + record = dict(operation=operation, seconds=time.perf_counter()-start, methods=methods, + sha256=oid, bytes=size, complete=result['event'] == 'complete') + if operation == 'download': + record['new_download_file'] = result['path'] + records.append(record) + report = dict(schema='lfs-lan-roundtrip-smoke-v1', pass_all=True, + observed_utc=datetime.now(timezone.utc).isoformat(), + ip=lan.IP, hostname=lan.HOST, port=443, certificate_verification=True, + proxy_used=False, transfers=records, + adapter=archives.sha_file(lan.__file__)) + archives.write_new(receipt, archives.canonical(report)) + print(json.dumps(report), flush=True) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument('--receipt', required=True) + run(parser.parse_args().receipt) diff --git a/tools/lfs-publication/seal_publication_manifest.py b/tools/lfs-publication/seal_publication_manifest.py new file mode 100644 index 0000000..219c3eb --- /dev/null +++ b/tools/lfs-publication/seal_publication_manifest.py @@ -0,0 +1,50 @@ +"""Generate checksums for this publication only, after real download success.""" +from datetime import datetime, timezone +import json +from pathlib import Path +import subprocess + +from publish_archives import canonical, no_links, sha_file, write_new + + +def main(): + root = no_links(Path.cwd()) + protected = Path('/data/digital-drosophila') + if root == protected or protected in root.parents or not (root / '.git').is_dir(): + raise ValueError('Only an isolated publication checkout is allowed') + folder = root / 'registry/publication-20261001' + output, checksums = folder / 'publication-manifest.json', folder / 'SHA256SUMS' + if output.exists() or checksums.exists(): + raise ValueError('Never overwrite a publication manifest') + transport = json.loads((folder / 'fresh-download-verification.json').read_bytes()) + guard = json.loads((folder / 'source-guard-final.json').read_bytes()) + head = subprocess.check_output(['git', 'rev-parse', 'HEAD'], text=True).strip() + if not (transport['pass_all'] and transport['fresh_download_proven'] and guard['pass_all'] + and transport['expected_commit'] == head): + raise ValueError('Actual transport/source evidence or commit binding is missing') + files = [root / p for p in ('.gitattributes', '.gitignore', 'NOTICE.md')] + for prefix in ('artifacts/public-resources-20261001', 'artifacts/lfs-smoke', + 'registry/publication-20261001', 'tools/lfs-publication'): + for p in (root / prefix).rglob('*'): + no_links(p) + if '__pycache__' not in p.parts and p.is_file(): + files.append(p) + rows = [dict(path=p.relative_to(root).as_posix(), **sha_file(p)) for p in sorted(files)] + if len({row['path'] for row in rows}) != len(rows): + raise ValueError('Duplicate publication path') + manifest = dict(schema='lfs-publication-final-manifest-v1', pass_all=True, + generated_utc=datetime.now(timezone.utc).isoformat(), data_commit=head, + branch='codex/lfs-public-resources', repository_public=True, + aggregate_inventory_sha256=transport['aggregate_inventory_sha256'], + logical_files=len(rows), logical_bytes=sum(r['bytes'] for r in rows), + files=rows, + scope='Publication payload, tools, notices and evidence only; original file SHA are nested in members.jsonl.gz. Not an entire server backup or scientific pass.', + self_hash_policy='Manifest is covered by SHA256SUMS; SHA256SUMS self-hash is omitted and its bytes are bound by the final Git commit.') + write_new(output, canonical(manifest)) + rows.append(dict(path=output.relative_to(root).as_posix(), **sha_file(output))) + write_new(checksums, ''.join(r['sha256'] + ' ' + r['path'] + '\n' for r in sorted(rows, key=lambda r: r['path'])).encode()) + print(json.dumps(dict(pass_all=True, files=len(rows), manifest=sha_file(output), checksums=sha_file(checksums)))) + + +if __name__ == '__main__': + main() diff --git a/tools/lfs-publication/test_download_verify.py b/tools/lfs-publication/test_download_verify.py new file mode 100644 index 0000000..a2467c8 --- /dev/null +++ b/tools/lfs-publication/test_download_verify.py @@ -0,0 +1,245 @@ +"""Synthetic temporary fixtures and mocked Git/content operations; no transfer.""" +import contextlib +import io +import json +from pathlib import Path +import tempfile +import unittest +from unittest.mock import patch + +import download_verify as D + + +class DownloadTests(unittest.TestCase): + def setUp(self): + self.temp = tempfile.TemporaryDirectory() + self.addCleanup(self.temp.cleanup) + self.base = Path(self.temp.name) + self.checkout = self.base / "verification" + (self.checkout / ".git").mkdir(parents=True) + (self.checkout / "registry").mkdir() + (self.checkout / D.PAYLOAD).mkdir(parents=True) + self.cache = self.checkout / ".git" / "brand-new-lfs" + self.receipt = self.checkout / "registry" / "transport.json" + self.content_receipt = self.checkout / "registry" / "content.json" + self.history = self.base / "history.gz" + self.history.write_bytes(b"synthetic history placeholder") + self.commit = "a" * 40 + self.calls = [] + self.pull_code = self.fsck_code = 0 + self.remote = D.REMOTE + self.head = self.commit + self.dirty = "" + self.content_failure = False + self.config_exit = 1 + self.adapter_config = {} + self.local_adapter_config = {} + self.adapter_blob = b"# Synthetic LAN adapter fixture; never executed.\n" + self.addCleanup(patch.stopall) + patch.object(D.Path, "cwd", return_value=self.checkout).start() + patch.object(D, "command", side_effect=self.command).start() + self.verifier = patch.object(D.content, "verify_publication", side_effect=self.verify).start() + self.capture = contextlib.redirect_stdout(io.StringIO()) + self.capture.__enter__() + self.addCleanup(self.capture.__exit__, None, None, None) + + def command(self, args, *, text=False, bytes_output=False): + self.calls.append(args) + if "rev-parse" in args: + if "HEAD" in args: + return self.head + return str(self.checkout / ".git") if "--absolute-git-dir" in args else str(self.checkout) + if "remote" in args: + return self.remote + if "status" in args: + return self.dirty + if "--get-regexp" in args: + if "--name-only" in args: + return "\n".join(self.adapter_config) + return self.config_exit + if "--get-all" in args: + values = self.local_adapter_config if "--local" in args else self.adapter_config + return values.get(args[-1], "") + if "show" in args: + return self.adapter_blob + if "pull" in args: + oid = "f" * 64 + obj = self.cache / "objects" / oid[:2] / oid[2:4] / oid + obj.parent.mkdir(parents=True) + obj.write_bytes(b"synthetic object") + return self.pull_code + if "fsck" in args: + return self.fsck_code + return "synthetic-version" + + def verify(self, root, receipt, history): + self.assertEqual(root, self.checkout / D.PAYLOAD) + self.assertEqual(history, self.history) + if self.content_failure: + raise ValueError("synthetic failure") + D.archives.write_new(receipt, b'{"synthetic":true}\n') + return {"pass_all": True, "receipt_sha256": D.archives.sha_file(receipt)["sha256"], + "aggregate_inventory_sha256": "b" * 64, "historical_status": "FULL_CURRENT_MEMBER_MATCH"} + + def run_attempt(self): + return D.run(self.commit, self.cache, self.receipt, self.content_receipt, self.history) + + def prepare_adapter(self): + adapter = self.checkout / "tools/lfs-publication/lan_lfs_transfer.py" + adapter.parent.mkdir(parents=True) + adapter.write_bytes(self.adapter_blob) + prefix = "lfs.customtransfer.malecns-lan-https." + self.adapter_config = {"lfs.standalonetransferagent": "malecns-lan-https", + prefix + "path": "/usr/bin/python3", prefix + "args": "-B " + str(adapter), + prefix + "concurrent": "true", prefix + "direction": "both"} + self.local_adapter_config = self.adapter_config.copy() + self.config_exit = 0 + return adapter + + def assert_not_started(self): + self.assertFalse(self.cache.exists()) + self.assertFalse(self.receipt.exists()) + self.assertFalse(any("pull" in args for args in self.calls)) + + def test_success_binds_new_cache_exits_content_and_source_sha(self): + result = self.run_attempt() + self.assertEqual(json.loads(self.receipt.read_bytes()), result) + self.assertTrue(result["cache"]["initially_absent"]) + self.assertEqual(result["cache"]["before"], {"objects": 0, "bytes": 0}) + self.assertEqual(result["cache"]["after"], {"objects": 1, "bytes": 16}) + self.assertEqual(result["content_receipt"]["sha256"], D.archives.sha_file(self.content_receipt)["sha256"]) + self.assertEqual(len(result["tool_sources"]), 3) + self.assertFalse(result["learning_pass_claimed"]) + pull = next(args for args in self.calls if "pull" in args) + fsck = next(args for args in self.calls if "fsck" in args) + self.assertIn("--include=artifacts/**", pull) + self.assertIn("--exclude=", pull) + self.assertEqual(pull[-1], "origin") + self.assertIn("--dry-run", fsck) + for args in (pull, fsck): + self.assertIn("lfs.storage=" + str(self.cache), args) + self.assertIn("lfs.concurrenttransfers=2", args) + + def test_existing_cache_receipt_and_content_receipt_are_never_reused(self): + for path in (self.cache, self.receipt, self.content_receipt): + with self.subTest(path=path): + path.write_bytes(b"keep") + with self.assertRaises(ValueError): + self.run_attempt() + self.assertEqual(path.read_bytes(), b"keep") + self.assertFalse(any("pull" in args for args in self.calls)) + path.unlink() + + def test_wrong_head_or_remote_or_dirty_tree_refused(self): + for attr, value in (("head", "c" * 40), ("remote", "https://wrong.invalid/repo.git"), ("dirty", " M file")): + original = getattr(self, attr) + setattr(self, attr, value) + with self.subTest(attr=attr), self.assertRaises(ValueError): + self.run_attempt() + self.assert_not_started() + setattr(self, attr, original) + + def test_unsafe_paths_refused_before_transfer(self): + original = self.cache + for unsafe in (self.checkout / "payload-cache", self.base / ".." / "escape", + D.PROTECTED / "should-never-create"): + self.cache = unsafe + with self.subTest(path=unsafe), self.assertRaises(ValueError): + self.run_attempt() + self.assertFalse(any("pull" in args for args in self.calls)) + self.cache = original + self.receipt = self.checkout / D.PAYLOAD / "receipt.json" + with self.assertRaises(ValueError): + self.run_attempt() + self.assert_not_started() + + def test_pull_failure_retains_partial_and_never_fscks_or_retries(self): + self.pull_code = 9 + with self.assertRaises(ValueError): + self.run_attempt() + self.assertTrue(self.cache.exists()) + self.assertFalse(self.receipt.exists()) + self.assertFalse(self.content_receipt.exists()) + self.assertFalse(any("fsck" in args for args in self.calls)) + with self.assertRaises(ValueError): + self.run_attempt() + self.assertEqual(sum("pull" in args for args in self.calls), 1) + + def test_endpoint_and_custom_transfer_overrides_fail_closed(self): + for code in (0, 2): + self.config_exit = code + with self.subTest(code=code), self.assertRaises(ValueError): + self.run_attempt() + self.assert_not_started() + self.config_exit = 1 + (self.checkout / ".lfsconfig").write_text("[lfs]\nurl = https://not-approved.invalid\n") + with self.assertRaises(ValueError): + self.run_attempt() + self.assert_not_started() + + def test_optional_lan_adapter_is_exact_local_and_head_bound(self): + adapter = self.prepare_adapter() + with self.assertRaises(ValueError): + self.run_attempt() + self.assert_not_started() + report = D.run(self.commit, self.cache, self.receipt, self.content_receipt, + self.history, allow_lan_adapter=True) + self.assertTrue(report["lan_adapter"]["enabled"]) + self.assertEqual(report["tool_sources"]["lan_lfs_transfer.py"]["sha256"], + D.archives.sha_file(adapter)["sha256"]) + + def test_lan_wrong_blob_global_override_or_other_endpoint_rejected(self): + self.prepare_adapter() + self.adapter_blob = b"not the actual file" + with self.assertRaises(ValueError): + D.transfer_policy(self.checkout, self.commit, True) + self.adapter_blob = (self.checkout / "tools/lfs-publication/lan_lfs_transfer.py").read_bytes() + original = self.local_adapter_config["lfs.standalonetransferagent"] + self.local_adapter_config["lfs.standalonetransferagent"] = "" + with self.assertRaises(ValueError): + D.transfer_policy(self.checkout, self.commit, True) + self.local_adapter_config["lfs.standalonetransferagent"] = original + self.adapter_config["lfs.url"] = "https://wrong.invalid" + with self.assertRaises(ValueError): + D.transfer_policy(self.checkout, self.commit, True) + self.assert_not_started() + + def test_fsck_failure_does_not_call_content_or_publish_receipt(self): + self.fsck_code = 8 + with self.assertRaises(ValueError): + self.run_attempt() + self.verifier.assert_not_called() + self.assertTrue(self.cache.exists()) + self.assertFalse(self.receipt.exists()) + + def test_content_failure_leaves_no_transport_pass(self): + self.content_failure = True + with self.assertRaises(ValueError): + self.run_attempt() + self.assertFalse(self.receipt.exists()) + self.assertEqual(sum("pull" in args for args in self.calls), 1) + + def test_head_changed_during_verification_preserves_content_but_no_transport_pass(self): + def changed(*args): + result = self.verify(*args) + self.head = "d" * 40 + return result + self.verifier.side_effect = changed + with self.assertRaises(ValueError): + self.run_attempt() + self.assertTrue(self.content_receipt.exists()) + self.assertFalse(self.receipt.exists()) + + def test_cli_failure_never_prints_exception_diagnostics(self): + with patch.object(D, "run", side_effect=RuntimeError("secret should not escape")), \ + patch.object(D.sys, "argv", ["download_verify", "--expected-commit", self.commit, + "--cache", str(self.cache), "--receipt", str(self.receipt), + "--content-receipt", str(self.content_receipt), "--historical-inventory", str(self.history)]), \ + contextlib.redirect_stdout(io.StringIO()) as output: + self.assertEqual(D.main(), 1) + self.assertNotIn("secret should not escape", output.getvalue()) + self.assertIn("FAILED-NOT-RETRIED", output.getvalue()) + + +if __name__ == "__main__": + unittest.main() diff --git a/tools/lfs-publication/test_publish_archives.py b/tools/lfs-publication/test_publish_archives.py new file mode 100644 index 0000000..ff64262 --- /dev/null +++ b/tools/lfs-publication/test_publish_archives.py @@ -0,0 +1,245 @@ +"""Temporary local fixtures only. Identity codec tests do not certify zstd. + +The optional real-zstd test automatically runs when the executable is present. +""" +import contextlib +import gzip +import hashlib +import importlib.util +import io +import json +import os +from pathlib import Path +import shutil +import sys +import tarfile +import tempfile +import unittest +from unittest.mock import patch + +SPEC = importlib.util.spec_from_file_location("lfs_archive_tested", Path(__file__).with_name("publish_archives.py")) +M = importlib.util.module_from_spec(SPEC) +SPEC.loader.exec_module(M) + + +def codec(*args, **kwargs): + return [sys.executable, "-c", "import sys,shutil;shutil.copyfileobj(sys.stdin.buffer,sys.stdout.buffer)"] + + +class ArchiveTests(unittest.TestCase): + def setUp(self): + self.temp = tempfile.TemporaryDirectory() + self.addCleanup(self.temp.cleanup) + self.base = Path(self.temp.name) + self.root = self.base / "source" + (self.root / "data").mkdir(parents=True) + (self.root / "data" / "a.txt").write_text("public source\n", encoding="utf-8") + (self.root / "data" / "b.bin").write_bytes(bytes(range(256)) * 80) + (self.root / "data" / "zero.txt").write_bytes(b"") + self.plan = {"schema": "lfs-publication-plan-v1", "source_root": str(self.root), + "groups": [{"id": "data", "paths": ["data"], "license": "test-only", + "provenance": {"source": "synthetic"}}], "exclude_paths": []} + self.plan_path = self.base / "plan.json" + self.plan_path.write_bytes(M.canonical(self.plan)) + self.out, self.work = self.base / "out", self.base / "work" + self.addCleanup(patch.stopall) + patch.object(M, "SOURCE_ROOT", str(self.root)).start() + patch.object(M, "CHUNK_BYTES", 4096).start() + self.codec_patch = patch.object(M, "zstd_command", codec) + self.codec_patch.start() + + def pack(self): + with contextlib.redirect_stdout(io.StringIO()): + return M.pack(self.plan_path, self.out, self.work) + + def catalog(self): + return json.loads((self.out / "data" / "catalog.json").read_bytes()) + + def save_catalog(self, cat): + (self.out / "data" / "catalog.json").write_bytes(M.canonical(cat)) + + def rewrite_archive(self, data): + group = self.out / "data" + cat = self.catalog() + for row in cat["chunks"]: + (group / row["path"]).unlink() + new = self.base / "mutant.tar" + new.write_bytes(data) + cat["chunks"], cat["archive_sha256"] = M.split_archive(new, group) + cat["archive_bytes"] = len(data) + self.save_catalog(cat) + + def test_pack_verify_full_member_content_and_no_extraction(self): + before = {p.relative_to(self.root).as_posix(): p.read_bytes() for p in self.root.rglob("*") if p.is_file()} + summary = self.pack() + result = M.verify(self.out / "data") + self.assertTrue(result["pass_all"]) + self.assertEqual(result["source_files"], 3) + self.assertEqual(result["source_bytes"], sum(map(len, before.values()))) + self.assertGreater(summary["groups"][0]["chunks"], 1) + self.assertEqual(before, {p.relative_to(self.root).as_posix(): p.read_bytes() for p in self.root.rglob("*") if p.is_file()}) + self.assertFalse((self.out / "data" / "a.txt").exists()) + + def test_plan_executes_first_read_bytes_only(self): + with patch.object(M, "json_read", side_effect=AssertionError("Must not read plan a second time")): + self.pack() + self.assertEqual(self.catalog()["plan_sha256"], hashlib.sha256(self.plan_path.read_bytes()).hexdigest()) + + def test_exclusions_logged_without_descending(self): + for name in (".git", "venv", "__pycache__", ".cache", "node_modules", "logs", "phase4ar-normal-conditioning"): + d = self.root / "data" / name + d.mkdir() + (d / "hidden.txt").write_text("skip") + (self.root / "data" / "private.pem").write_text("private") + (self.root / "data" / "run.log").write_text("log") + self.pack() + with gzip.open(self.out / "data" / "exclusions.jsonl.gz", "rt") as f: + rows = [json.loads(x) for x in f] + self.assertEqual(len(rows), 9) + self.assertEqual(self.catalog()["source_files"], 3) + self.assertTrue(M.verify(self.out / "data")["pass_all"]) + + def test_unsafe_explicit_paths(self): + for name in ("../data", "/data", "data/../data", "data//x", "data\\x", "data/.git", "data/phase4ar-normal-conditioning"): + plan = json.loads(json.dumps(self.plan)) + plan["groups"][0]["paths"] = [name] + with self.subTest(name=name), self.assertRaises(ValueError): + M.validate_plan(plan) + + def test_overlapping_groups_refused(self): + self.plan["groups"].append({"id": "nested", "paths": ["data/a.txt"], "license": "test", "provenance": "test"}) + with self.assertRaisesRegex(ValueError, "Overlapping"): + M.validate_plan(self.plan) + + def test_symlink_refused(self): + try: + (self.root / "data" / "link").symlink_to(self.root / "data" / "a.txt") + except OSError: + self.skipTest("OS does not permit temporary symlinks") + with self.assertRaisesRegex(ValueError, "Symlink"): + self.pack() + + def test_exclusive_and_disjoint_outputs(self): + self.out.mkdir() + with self.assertRaises(FileExistsError): + self.pack() + with self.assertRaisesRegex(ValueError, "disjoint"): + M.pack(self.plan_path, self.root / "output", self.work) + + def test_parent_components_cannot_bypass_disjoint_gate(self): + malicious = self.base / "unused" / ".." / "source" / "new-output" + with self.assertRaisesRegex(ValueError, "Parent path components"): + M.pack(self.plan_path, malicious, self.work) + self.assertFalse((self.root / "new-output").exists()) + + def test_secret_rules_hide_values(self): + # Build synthetic fixtures at runtime; keep actual credential-like + # strings out of Git blobs so the repository secret guard stays useful. + examples = ["-----BEGIN " + "OPENSSH PRIVATE " + "KEY-----", "ghp_" + "a" * 36, + "github_pat_" + "b" * 40, "AKIA" + "A" * 16, + "https://" + "account:" + "privatevalue" + "@example.org/", + 'password' + ' = "privatevalue"', + 'api_key' + ': "privatevalue"', 'secret_key' + '=ABCDEF123456', + 'pa\u017f\u017fword' + '="privatevalue"', + 'ap\u0131_key' + '="privatevalue"', + '\u017fecret_key' + '="privatevalue"'] + path = self.root / "data" / "literal.txt" + for value in examples: + path.write_text(value) + files, _ = M.enumerate_group(self.root, self.plan["groups"][0], []) + with self.subTest(rule=value[:8]), self.assertRaisesRegex(ValueError, "Secret scan refused") as caught: + M.scan_secrets(self.root, files) + self.assertNotIn(value, str(caught.exception)) + self.assertNotIn("privatevalue", str(caught.exception)) + + def test_mutated_source_metadata_refused(self): + files, _ = M.enumerate_group(self.root, self.plan["groups"][0], []) + (self.root / "data" / "a.txt").write_text("changed bytes") + with self.assertRaisesRegex(ValueError, "Source changed"): + M.make_archive(self.root, files, self.base / "bad.tar", 1) + + def test_payload_corruption_refused(self): + self.pack() + p = self.out / "data" / self.catalog()["chunks"][0]["path"] + data = bytearray(p.read_bytes()) + data[-1] ^= 1 + p.write_bytes(data) + with self.assertRaises((ValueError, tarfile.TarError)): + M.verify(self.out / "data") + + def test_missing_extra_or_reordered_payload_refused(self): + self.pack() + extra = self.out / "data" / "extra.bin" + extra.write_bytes(b"x") + with self.assertRaisesRegex(ValueError, "Extra/missing"): + M.verify(self.out / "data") + extra.unlink() + cat = self.catalog() + cat["chunks"] = list(reversed(cat["chunks"])) + self.save_catalog(cat) + with self.assertRaisesRegex(ValueError, "chunk name/order"): + M.verify(self.out / "data") + + def test_tar_traversal_rejected_even_with_rehashed_chunks(self): + self.pack() + buf = io.BytesIO() + with tarfile.open(fileobj=buf, mode="w") as archive: + info = tarfile.TarInfo("../escape") + info.size = 1 + archive.addfile(info, io.BytesIO(b"x")) + self.rewrite_archive(buf.getvalue()) + with self.assertRaisesRegex(ValueError, "Unsafe relative path"): + M.verify(self.out / "data") + + def test_tar_link_rejected_even_with_rehashed_chunks(self): + self.pack() + buf = io.BytesIO() + with tarfile.open(fileobj=buf, mode="w") as archive: + info = tarfile.TarInfo("data/a.txt") + info.type, info.linkname = tarfile.SYMTYPE, "/tmp/escape" + archive.addfile(info) + self.rewrite_archive(buf.getvalue()) + with self.assertRaisesRegex(ValueError, "Nonregular"): + M.verify(self.out / "data") + + def test_hidden_tar_after_end_refused(self): + self.pack() + raw = (self.work / "data.tar.zst").read_bytes() + self.rewrite_archive(raw + b"nonzero hidden second archive") + with self.assertRaisesRegex(ValueError, "Nonzero data after tar"): + M.verify(self.out / "data") + + def test_second_tar_after_end_refused(self): + self.pack() + buf = io.BytesIO() + with tarfile.open(fileobj=buf, mode="w") as archive: + info = tarfile.TarInfo("unlisted-secret.txt") + info.size = 1 + archive.addfile(info, io.BytesIO(b"x")) + self.rewrite_archive((self.work / "data.tar.zst").read_bytes() + buf.getvalue()) + with self.assertRaisesRegex(ValueError, "Nonzero data after tar"): + M.verify(self.out / "data") + + def test_member_hash_mutation_refused(self): + self.pack() + p = self.out / "data" / "members.jsonl.gz" + with gzip.open(p, "rt") as f: + rows = [json.loads(x) for x in f] + rows[0]["sha256"] = "0" * 64 + p.unlink() + M.gzip_rows(p, rows) + cat = self.catalog() + cat["members"] = M.sha_file(p) + self.save_catalog(cat) + with self.assertRaisesRegex(ValueError, "member content mismatch"): + M.verify(self.out / "data") + + @unittest.skipUnless(shutil.which("zstd"), "Real zstd unavailable; run this integration test on Linux") + def test_real_zstd_roundtrip(self): + self.codec_patch.stop() + self.pack() + self.assertTrue(M.verify(self.out / "data")["pass_all"]) + + +if __name__ == "__main__": + unittest.main() diff --git a/tools/lfs-publication/test_verify_publication.py b/tools/lfs-publication/test_verify_publication.py new file mode 100644 index 0000000..30bd575 --- /dev/null +++ b/tools/lfs-publication/test_verify_publication.py @@ -0,0 +1,184 @@ +"""Aggregate verification tests: temporary files and an identity codec only. + +These test metadata/content binding, not zstd itself. The separate archive-tool +suite includes its optional real-zstd integration test. No real project data, +network, Git mutation, GPU, or persistent outputs are used here. +""" +import contextlib +import gzip +import io +import json +from pathlib import Path +import subprocess +import sys +import tempfile +import unittest +from unittest.mock import patch + +import publish_archives as P +import verify_publication as V + + +def identity_codec(*args, **kwargs): + return [sys.executable, "-c", + "import sys,shutil;shutil.copyfileobj(sys.stdin.buffer,sys.stdout.buffer)"] + + +class AggregateTests(unittest.TestCase): + def setUp(self): + self.temp = tempfile.TemporaryDirectory() + self.addCleanup(self.temp.cleanup) + self.base = Path(self.temp.name) + self.source = self.base / "source" + self.data = self.source / "data" + self.data.mkdir(parents=True) + (self.data / "LICENSE").write_bytes(b"Synthetic license\n") + (self.data / "one.feather").write_bytes(b"fake binary bytes\x00") + self.pins = { + p.relative_to(self.source).as_posix(): dict( + path=p.relative_to(self.source).as_posix(), kind="file", **P.sha_file(p)) + for p in sorted(self.data.iterdir()) + } + self.plan = { + "schema": "lfs-publication-plan-v1", "source_root": str(self.source), + "groups": [{ + "id": "malecns-synaptic-partners", "paths": ["data"], + "license": {"evidence_file": "LICENSE", + "evidence_sha256": self.pins["data/LICENSE"]["sha256"]}, + "provenance": {"registered_file_sha256": self.pins["data/one.feather"]["sha256"]}, + }], + "exclude_paths": [], + } + self.plan_file = self.base / "plan.json" + self.root, self.work = self.base / "payload", self.base / "work" + self.receipt = self.base / "receipt.json" + self.history_file = self.base / "history.jsonl.gz" + for item in (patch.object(P, "SOURCE_ROOT", str(self.source)), + patch.object(P, "CHUNK_BYTES", 4096), + patch.object(P, "zstd_command", identity_codec)): + item.start() + self.addCleanup(item.stop) + + def pack(self): + self.plan_file.write_bytes(P.canonical(self.plan)) + with contextlib.redirect_stdout(io.StringIO()): + P.pack(self.plan_file, self.root, self.work) + + def verify(self, history=False): + with contextlib.redirect_stdout(io.StringIO()): + return V.verify_publication(self.root, self.receipt, + self.history_file if history else None) + + def write_history(self, rows): + with gzip.open(self.history_file, "wt", encoding="utf-8") as handle: + for row in rows: + handle.write(json.dumps(row) + "\n") + + def test_full_without_history_and_exclusive_receipt(self): + self.pack() + result = self.verify() + self.assertTrue(result["pass_all"]) + self.assertFalse(result["fresh_download_proven"]) + self.assertEqual(result["historical_status"], "NOT_REQUESTED") + self.assertEqual(result["source_files"], 2) + with self.assertRaises(ValueError): + self.verify() + + def test_full_history_absolute_path_and_skipped_nonfile(self): + self.pack() + rows = [dict(row) for row in self.pins.values()] + # Use the exact registered source_root prefix on either Windows/Linux. + rows[0]["path"] = str(self.source) + "/" + rows[0]["path"] + rows.append({"path": "outside/link", "kind": "symlink"}) + self.write_history(rows) + result = self.verify(history=True) + report = json.loads(self.receipt.read_bytes()) + self.assertEqual(result["historical_status"], "FULL_CURRENT_MEMBER_MATCH") + self.assertEqual(report["historical_inventory"]["nonfile_records_skipped"], 1) + + def test_partial_history_is_not_full_historical_pass(self): + self.pack() + self.write_history([self.pins["data/LICENSE"], + {"path": "data/one.feather", "kind": "symlink"}]) + self.verify(history=True) + history = json.loads(self.receipt.read_bytes())["historical_inventory"] + self.assertEqual(history["status"], "PARTIAL_CURRENT_MEMBER_COVERAGE") + self.assertFalse(history["all_current_members_historically_matched"]) + self.assertEqual(history["current_members_without_regular_history"], 1) + self.assertEqual(history["current_members_with_nonfile_history"], 1) + + def test_history_mismatch_writes_no_receipt(self): + self.pack() + self.write_history([dict(self.pins["data/LICENSE"], sha256="0" * 64)]) + with self.assertRaisesRegex(ValueError, "Historical member mismatch"): + self.verify(history=True) + self.assertFalse(self.receipt.exists()) + + def test_registered_feather_sha_mismatch(self): + self.plan["groups"][0]["provenance"]["registered_file_sha256"] = "0" * 64 + self.pack() + with self.assertRaisesRegex(ValueError, "Registered feather SHA"): + self.verify() + + def test_multiple_feather_members_refused(self): + (self.data / "two.feather").write_bytes(b"another fixture") + self.pack() + with self.assertRaisesRegex(ValueError, "exactly one feather"): + self.verify() + + def test_license_evidence_sha_mismatch(self): + self.plan["groups"][0]["license"]["evidence_sha256"] = "0" * 64 + self.pack() + with self.assertRaisesRegex(ValueError, "License evidence SHA"): + self.verify() + + def test_extra_root_entry_refused(self): + self.pack() + (self.root / "unlisted").write_bytes(b"x") + with self.assertRaisesRegex(ValueError, "extra/missing"): + self.verify() + + def test_wrong_catalog_pin_refused(self): + self.pack() + summary = P.json_read(self.root / "pack-summary.json") + summary["groups"][0]["catalog_sha256"] = "0" * 64 + (self.root / "pack-summary.json").write_bytes(P.canonical(summary)) + with self.assertRaisesRegex(ValueError, "Catalog SHA"): + self.verify() + + def test_root_file_count_mismatch(self): + self.pack() + summary = P.json_read(self.root / "pack-summary.json") + summary["source_files"] = 3 + (self.root / "pack-summary.json").write_bytes(P.canonical(summary)) + with self.assertRaisesRegex(ValueError, "Root source file count"): + self.verify() + + def test_receipt_inside_payload_refused(self): + self.pack() + self.receipt = self.root / "receipt.json" + with self.assertRaisesRegex(ValueError, "outside"): + self.verify() + + def test_plan_raw_sha_mismatch(self): + self.pack() + path = self.root / "plan.json" + path.write_bytes(path.read_bytes() + b"\n") + with self.assertRaisesRegex(ValueError, "plan SHA"): + self.verify() + + +class GitMetadataTests(unittest.TestCase): + def test_ascii_head_with_non_ascii_stderr(self): + result = subprocess.CompletedProcess([], 0, stdout=b"a" * 40 + b"\n", stderr=bytes([255])) + with patch.object(V.subprocess, "run", return_value=result): + self.assertEqual(V.git_identity()["head"], "a" * 40) + + def test_failed_git_with_non_ascii_stderr_is_optional(self): + result = subprocess.CompletedProcess([], 128, stdout=b"", stderr=bytes([255])) + with patch.object(V.subprocess, "run", return_value=result): + self.assertIsNone(V.git_identity()["head"]) + + +if __name__ == "__main__": + unittest.main() diff --git a/tools/lfs-publication/verify_publication.py b/tools/lfs-publication/verify_publication.py new file mode 100644 index 0000000..87fbe4d --- /dev/null +++ b/tools/lfs-publication/verify_publication.py @@ -0,0 +1,233 @@ +"""Verify a complete downloaded publication and exclusively write a new receipt. + +This verifies the supplied bytes, not how they arrived or their external trust +anchor. No extraction, LFS-cache lookup, source modification, or Git mutation. +""" +from __future__ import annotations + +import argparse +from datetime import datetime, timezone +import gzip +import hashlib +import json +from pathlib import Path +import subprocess + +import publish_archives as archives + + +def require(condition, message): + if not condition: + raise ValueError(message) + + +def equal(left, right): + return archives.canonical(left) == archives.canonical(right) + + +def history_path(value, source_root): + require(isinstance(value, str), "Historical path must be text") + prefix = source_root.rstrip("/") + "/" + if value.startswith(prefix): + value = value[len(prefix):] + return archives.relpath(value) + + +def load_history(path, source_root): + files, nonfiles, seen = {}, {}, set() + total = 0 + with gzip.open(path, "rt", encoding="utf-8") as inp: + for line in inp: + row = archives.json_bytes(line) + require(isinstance(row, dict), "Historical row must be an object") + relative = history_path(row.get("path"), source_root) + require(relative not in seen, "Duplicate historical path: " + relative) + seen.add(relative) + total += 1 + if row.get("kind", "file") != "file": + nonfiles[relative] = row.get("kind") + continue + archives.check_digest_row(row) + files[relative] = {"bytes": row["bytes"], "sha256": row["sha256"]} + return files, nonfiles, total + + +def git_identity(): + try: + process = subprocess.run(["git", "rev-parse", "--verify", "HEAD"], + capture_output=True, check=False) + head = process.stdout.decode("ascii").strip() + if process.returncode == 0 and len(head) in (40, 64) and all(x in "0123456789abcdef" for x in head): + return {"cwd": str(Path.cwd()), "head": head, + "scope": "HEAD observed at invocation cwd; not a clean-tree or payload-to-commit proof"} + except (OSError, UnicodeError): + pass + return {"cwd": str(Path.cwd()), "head": None, "scope": "Git HEAD unavailable"} + + +def verify_publication(payload_root, receipt, historical_inventory=None): + root, receipt = archives.no_links(payload_root), archives.no_links(receipt) + require(root.is_dir(), "Payload root is not a directory") + require(receipt != root and root not in receipt.parents, + "Receipt must be outside the immutable payload tree") + require(not receipt.exists(), "Receipt already exists; refusing overwrite/retry") + require(receipt.parent.is_dir(), "Receipt parent must already exist") + controls = {name: archives.sha_file(root / name) for name in ("plan.json", "pack-summary.json")} + plan = archives.json_read(root / "plan.json") + summary = archives.json_read(root / "pack-summary.json") + archives.validate_plan(plan) + require(summary.get("schema") == "lfs-publication-pack-v1" and summary.get("complete") is True, + "Pack summary is not complete") + require(summary.get("plan_sha256") == controls["plan.json"]["sha256"], "Root plan SHA mismatch") + plan_groups = {g["id"]: g for g in plan["groups"]} + summary_groups = summary.get("groups") + require(isinstance(summary_groups, list), "Missing summary groups") + require(all(isinstance(g, dict) and isinstance(g.get("group"), str) for g in summary_groups), + "Invalid summary group") + listed = [g["group"] for g in summary_groups] + require(listed == list(plan_groups), "Summary group inventory/order differs from plan") + require({p.name for p in root.iterdir()} == set(plan_groups) | {"plan.json", "pack-summary.json"}, + "Payload root has extra/missing entries; preserve and investigate") + for p in root.iterdir(): + archives.no_links(p) + historical = None + if historical_inventory is not None: + hpath = archives.no_links(historical_inventory) + require(hpath != receipt, "Receipt cannot replace historical inventory") + hpin = archives.sha_file(hpath) + hfiles, hnonfiles, htotal = load_history(hpath, plan["source_root"]) + historical = {"path": str(hpath), "sha256": hpin["sha256"], "bytes": hpin["bytes"], + "records": htotal, "regular_file_records": len(hfiles), + "nonfile_records_skipped": len(hnonfiles)} + else: + hfiles, hnonfiles = {}, {} + matched, missing, nonfile_current = 0, [], 0 + publication_paths, results, manifest_controls = set(), [], {} + for group_summary in summary_groups: + group_id = group_summary["group"] + group, directory = plan_groups[group_id], root / group_id + require(directory.is_dir(), "Missing group directory: " + group_id) + cat_path = directory / "catalog.json" + cat_pin = archives.sha_file(cat_path) + require(cat_pin["sha256"] == group_summary.get("catalog_sha256"), "Catalog SHA mismatch: " + group_id) + catalog = archives.json_read(cat_path) + require(catalog.get("group_id") == group_id and catalog.get("source_root") == plan["source_root"] + and catalog.get("plan_sha256") == controls["plan.json"]["sha256"], + "Catalog identity/plan differs: " + group_id) + for key, wanted in (("source_paths", group["paths"]), ("license", group["license"]), + ("provenance", group["provenance"])): + require(equal(catalog.get(key), wanted), "Catalog plan metadata mismatch: " + group_id + "/" + key) + actual = archives.verify(directory) + expected_summary = {"group": group_id, "files": actual["source_files"], + "source_bytes": actual["source_bytes"], "archive_bytes": actual["archive_bytes"], + "chunks": len(catalog["chunks"]), "catalog_sha256": cat_pin["sha256"]} + require(equal(group_summary, expected_summary), "Group summary differs from actual payload: " + group_id) + members_path = directory / "members.jsonl.gz" + manifest_controls[str(members_path)] = catalog["members"] + manifest_controls[str(cat_path)] = cat_pin + manifest_controls[str(directory / "exclusions.jsonl.gz")] = catalog["exclusions"] + feather, member_lookup, group_matched, group_missing = [], {}, 0, 0 + for row in archives.iter_members(members_path): + name = row["path"] + require(name not in publication_paths, "Duplicate member across groups: " + name) + require(any(name == p or name.startswith(p + "/") for p in group["paths"]), + "Member outside group whitelist: " + name) + require(not any(name == p or name.startswith(p + "/") for p in plan.get("exclude_paths", [])), + "Excluded path appears in payload: " + name) + publication_paths.add(name) + member_lookup[name] = row + if name.lower().endswith(".feather"): + feather.append(row) + if historical is not None: + if name in hfiles: + require(equal(hfiles[name], {"bytes": row["bytes"], "sha256": row["sha256"]}), + "Historical member mismatch: " + name) + matched += 1 + group_matched += 1 + else: + missing.append(name) + group_missing += 1 + nonfile_current += int(name in hnonfiles) + require(len(member_lookup) == actual["source_files"], "Member inventory count changed") + provenance = group["provenance"] + registered = provenance.get("registered_file_sha256") if isinstance(provenance, dict) else None + if group_id == "malecns-synaptic-partners": + require(registered is not None, "Synaptic-partners registered file SHA missing") + file_anchor = None + if registered is not None: + require(isinstance(registered, str) and archives.HEX.fullmatch(registered) is not None, + "Invalid registered file SHA") + require(len(feather) == 1, "Registered-file group must contain exactly one feather: " + group_id) + require(feather[0]["sha256"] == registered, "Registered feather SHA mismatch: " + group_id) + file_anchor = feather[0] + license_anchor = None + license_meta = group["license"] + if isinstance(license_meta, dict) and "evidence_file" in license_meta: + relative = archives.relpath(license_meta["evidence_file"]) + path = group["paths"][0] + "/" + relative + require(path in member_lookup, "License evidence absent from payload: " + path) + require(member_lookup[path]["sha256"] == license_meta.get("evidence_sha256"), + "License evidence SHA mismatch: " + path) + license_anchor = member_lookup[path] + result = dict(actual, catalog_path=str(cat_path), registered_file_verified=file_anchor, + license_evidence_verified=license_anchor, + historical_matched=group_matched if historical is not None else None, + historical_missing=group_missing if historical is not None else None) + results.append(result) + print(json.dumps({"group_verified": group_id, "source_files": actual["source_files"], + "source_bytes": actual["source_bytes"], "archive_bytes": actual["archive_bytes"]}), flush=True) + files = sum(r["source_files"] for r in results) + source_bytes = sum(r["source_bytes"] for r in results) + archive_bytes = sum(r["archive_bytes"] for r in results) + require(type(summary.get("source_files")) is int and summary["source_files"] == files, + "Root source file count mismatch") + require(type(summary.get("source_bytes")) is int and summary["source_bytes"] == source_bytes, + "Root source byte count mismatch") + for name, pin in controls.items(): + require(archives.sha_file(root / name) == pin, "Root control changed during verification: " + name) + for path, pin in manifest_controls.items(): + require(archives.sha_file(path) == pin, "Group control changed during verification: " + path) + require({p.name for p in root.iterdir()} == set(plan_groups) | {"plan.json", "pack-summary.json"}, + "Payload root inventory changed during verification") + if historical is not None: + require(archives.sha_file(hpath) == hpin, "Historical inventory changed during verification") + historical.update(status="FULL_CURRENT_MEMBER_MATCH" if not missing else "PARTIAL_CURRENT_MEMBER_COVERAGE", + all_current_members_historically_matched=not missing, + current_members_matched=matched, current_members_without_regular_history=len(missing), + current_members_with_nonfile_history=nonfile_current, + missing_sample=missing[:20], missing_sample_truncated=len(missing) > 20, + historical_regular_files_outside_publication=len(set(hfiles) - publication_paths), + scope="Only publication members with regular-file history compared; not a full historical source-tree audit") + else: + historical = {"status": "NOT_REQUESTED", "all_current_members_historically_matched": None} + aggregate = [{"group": r["group"], "catalog_sha256": r["catalog_sha256"], + "archive_sha256": r["archive_sha256"], "source_files": r["source_files"], + "source_bytes": r["source_bytes"], "archive_bytes": r["archive_bytes"]} for r in results] + report = {"schema": "lfs-publication-aggregate-verification-v1", "pass_all": True, + "verified_utc": datetime.now(timezone.utc).isoformat(), "payload_root": str(root), + "receipt": str(receipt), "plan": {"path": str(root / "plan.json"), **controls["plan.json"]}, + "pack_summary": {"path": str(root / "pack-summary.json"), **controls["pack-summary.json"]}, + "groups": results, "source_files": files, "source_bytes": source_bytes, + "archive_bytes": archive_bytes, "aggregate_inventory_sha256": hashlib.sha256(archives.canonical(aggregate)).hexdigest(), + "historical_inventory": historical, "git": git_identity(), + "fresh_download_proven": False, + "scope": "Given payload bytes verified against plan/catalog/members and optional historical overlap; provenance/plan authenticity and fresh-clone transfer evidence are caller responsibilities"} + archives.write_new(receipt, archives.canonical(report)) + return {"pass_all": True, "receipt": str(receipt), "receipt_sha256": archives.sha_file(receipt)["sha256"], + "groups": len(results), "source_files": files, "source_bytes": source_bytes, + "archive_bytes": archive_bytes, "aggregate_inventory_sha256": report["aggregate_inventory_sha256"], + "historical_status": historical["status"], "fresh_download_proven": False} + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--payload-root", required=True) + parser.add_argument("--receipt", required=True) + parser.add_argument("--historical-inventory") + args = parser.parse_args() + print(json.dumps(verify_publication(args.payload_root, args.receipt, args.historical_inventory), + sort_keys=True, ensure_ascii=False, allow_nan=False), flush=True) + + +if __name__ == "__main__": + main()