Publish licensed data snapshots with LAN LFS transfer and content audits
This commit is contained in:
Digital Drosophila Archive
@@ -34,8 +34,18 @@ DoOR 作者为 Daniel Münch、C. Giovanni Galizia、Shouwen Ma、Martin Strauch
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`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。
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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。
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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。
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### 本次内网传输
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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。
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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。
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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。
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## 安全恢复（Linux 示例）
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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`。
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@@ -0,0 +1,40 @@
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{
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"adapter": {
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"bytes": 16661,
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"sha256": "21241d6a75d84108e720b4a051504fff00158b327f15c0ee06e5c57c6ad1c263"
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},
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"certificate_verification": true,
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"hostname": "git.lain.asia",
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"ip": "192.168.10.31",
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"observed_utc": "2026-09-30T19:40:34.704953+00:00",
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"pass_all": true,
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"port": 443,
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"proxy_used": false,
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"schema": "lfs-lan-roundtrip-smoke-v1",
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"transfers": [
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{
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"bytes": 67108864,
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"complete": true,
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"methods": [
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"POST",
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"PUT",
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"POST"
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],
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"operation": "upload",
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"seconds": 0.9692029840080068,
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"sha256": "a507fb9917a63f6221d97780727831735bcf419bb6d36b17546f2be04e8f6b6b"
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},
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{
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"bytes": 67108864,
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"complete": true,
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"methods": [
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"POST",
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"GET"
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],
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"new_download_file": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/.git/lfs/lan-transfer-tmp/a507fb9917a63f6221d97780727831735bcf419bb6d36b17546f2be04e8f6b6b.0vvk_cw4.partial",
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"operation": "download",
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"seconds": 0.6818166430020938,
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"sha256": "a507fb9917a63f6221d97780727831735bcf419bb6d36b17546f2be04e8f6b6b"
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}
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]
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}
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@@ -0,0 +1,206 @@
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{
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"aggregate_inventory_sha256": "88814458c772fc0e5b1708bc05e6c478097fc10b55271a83d538855ccfa81c84",
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"archive_bytes": 9806419307,
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"fresh_download_proven": false,
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"git": {
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"cwd": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo",
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"head": "13cd0e0be7a24ca9d7c036876bc48f9b22652968",
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"scope": "HEAD observed at invocation cwd; not a clean-tree or payload-to-commit proof"
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},
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"groups": [
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{
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"archive_bytes": 834266158,
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"archive_sha256": "feebf3fe3f3c2c9fea3db96fab8267330de49af7ab37008b84caeeea8dc272ed",
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"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/malecns-raw-core/catalog.json",
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"catalog_sha256": "8a7ea9abe5f75ce31318d207a1dbb491d5e151af27bd607dc1b59fb29d4aacf8",
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"group": "malecns-raw-core",
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"historical_matched": 17,
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"historical_missing": 0,
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"license_evidence_verified": null,
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"pass_all": true,
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"registered_file_verified": null,
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"schema": "lfs-publication-verify-v1",
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"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 1207032031,
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"source_files": 17
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},
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{
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"archive_bytes": 2760276945,
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"archive_sha256": "537644b322747b821580818aaa4154ab15714f0ddbcebc3183b587682760f57e",
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"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/malecns-swc/catalog.json",
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"catalog_sha256": "efc330317e2f74272e233634e5652982232ef9d3b6762f8e3cbd9eeaf05487cf",
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"group": "malecns-swc",
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"historical_matched": 211573,
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"historical_missing": 0,
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"license_evidence_verified": null,
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"pass_all": true,
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"registered_file_verified": null,
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"schema": "lfs-publication-verify-v1",
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"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 9299975999,
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"source_files": 211573
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},
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{
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"archive_bytes": 635332131,
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"archive_sha256": "a5d8ac0e6eebd5c6235078e9a9ac5a5c224bc86185bb77dd38248833c6b946f1",
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"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/malecns-processed/catalog.json",
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"catalog_sha256": "e1e42f654cb005d2f073d4e84c808af50f50c3feeb9cbcb0b0c1c51746bfdb47",
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"group": "malecns-processed",
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"historical_matched": 64,
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"historical_missing": 0,
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"license_evidence_verified": null,
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"pass_all": true,
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"registered_file_verified": null,
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"schema": "lfs-publication-verify-v1",
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"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 1140025370,
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"source_files": 64
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},
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{
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"archive_bytes": 5063205053,
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"archive_sha256": "cf2927389ecf3d20cbccaa269941265e8c709544c60068f28a40a0643c6be13d",
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"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/malecns-synaptic-partners/catalog.json",
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"catalog_sha256": "bdbc0354abdad63a9c256a2841fdf9df4c32258647b8de03d066afc89fa61053",
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"group": "malecns-synaptic-partners",
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"license_evidence_verified": null,
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"pass_all": true,
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"registered_file_verified": {
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"bytes": 6777179098,
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"path": "experiments/phase4aa-apl-pn-scope/external-resources/synaptic-partners/syn-partners-male-cns-v1.0-minconf-0.5.feather",
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"sha256": "959d8ef4173b35382a3e6acfaf5167c795b6d10b877572d146af04e1b487bc07"
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},
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"schema": "lfs-publication-verify-v1",
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"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 6777184219,
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"source_files": 6
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},
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{
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"archive_bytes": 77971754,
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"archive_sha256": "2366caef95fb5ad038639a6ae2ad25139a14c42492bc19640c20af46fefa0bc7",
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"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/celltype-explorer/catalog.json",
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"catalog_sha256": "4dc6be6091b273312a1dd61f621654f05e4c12118bdd13c22905d588e378889c",
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"group": "celltype-explorer",
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"historical_matched": 8973,
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"historical_missing": 0,
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"license_evidence_verified": {
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"bytes": 18657,
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"path": "experiments/phase4f-retinotopic-vision/external-resources/celltype-explorer/LICENSE",
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"sha256": "9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411"
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},
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"pass_all": true,
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"registered_file_verified": null,
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"schema": "lfs-publication-verify-v1",
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"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 3957079583,
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"source_files": 8973
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},
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{
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"archive_bytes": 434458454,
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"archive_sha256": "683b85394fb44e42704c275fbda93c95072f9f64c16a84e47ce2821c060cc39f",
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"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/visualpathways/catalog.json",
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"catalog_sha256": "bd824a656235ba08a35a67ad6d865467a946145cf985677226412280380939fc",
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"group": "visualpathways",
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"license_evidence_verified": {
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"bytes": 35149,
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"path": "experiments/phase4f-retinotopic-vision/external-resources/visualpathways/LICENSE",
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"sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986"
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},
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"pass_all": true,
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"registered_file_verified": null,
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"schema": "lfs-publication-verify-v1",
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"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 1652696750,
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"source_files": 6033
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},
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{
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"archive_bytes": 901984,
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"archive_sha256": "64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1",
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"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/door-data/catalog.json",
|
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"catalog_sha256": "6d0fcbe747dae7b38bcf335572b173e0112f6aabd10aa0040b84cfd81a8a390c",
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"group": "door-data",
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"license_evidence_verified": {
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"bytes": 1042,
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"path": "experiments/phase4l-olfactory-grounding/external-resources/DoOR.data/DESCRIPTION",
|
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"sha256": "27db2a92eb651d67969de94959990d51668a5857a33c4750a3b6ef49c5880504"
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|
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"pass_all": true,
|
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"registered_file_verified": null,
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"schema": "lfs-publication-verify-v1",
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"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 6534522,
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"source_files": 189
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},
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{
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"archive_bytes": 6828,
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"archive_sha256": "4da352d80e4bf251dfec771935da93f5a9f3cef302c85e90991fafa14a072e2b",
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||||
"catalog_path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/shiu-author-model-source/catalog.json",
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"catalog_sha256": "95c69e6e9e07625a1f9b273db67aa9ab480c66bb3bbb273c39c430aeedb9b910",
|
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"group": "shiu-author-model-source",
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"historical_matched": 0,
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||||
"historical_missing": 4,
|
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"license_evidence_verified": {
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"bytes": 1085,
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"path": "experiments/phase4ac-lif-semantics/external-resources/LICENSE",
|
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"sha256": "3621f6d6476189190e2960fa43f11b275ba4eca848fdac50a1ba2925de6223e8"
|
||||
},
|
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"pass_all": true,
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"registered_file_verified": null,
|
||||
"schema": "lfs-publication-verify-v1",
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||||
"scope": "downloaded payload bytes and streamed members; no extraction, no LFS-cache trust; catalog authenticity is caller responsibility",
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"source_bytes": 17567,
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"source_files": 4
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}
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],
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"historical_inventory": {
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"all_current_members_historically_matched": false,
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"bytes": 12285260,
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"current_members_matched": 226849,
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||||
"current_members_with_nonfile_history": 0,
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"current_members_without_regular_history": 10,
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"historical_regular_files_outside_publication": 3390,
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"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; not a full historical source-tree audit",
|
||||
"sha256": "6f186112e6102f2f7969de7442fa7ee4432200a3678586cfc4e10c490b31bca4",
|
||||
"status": "PARTIAL_CURRENT_MEMBER_COVERAGE"
|
||||
},
|
||||
"pack_summary": {
|
||||
"bytes": 2183,
|
||||
"path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/pack-summary.json",
|
||||
"sha256": "a097651a8f61009ec99a8bf6d1c3fcfaebd65fae16d6b0a14ebc2db841ae53cb"
|
||||
},
|
||||
"pass_all": true,
|
||||
"payload_root": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001",
|
||||
"plan": {
|
||||
"bytes": 7181,
|
||||
"path": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/artifacts/public-resources-20261001/plan.json",
|
||||
"sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71"
|
||||
},
|
||||
"receipt": "/tmp/malecns-lfs-publication-20261001-bI1u07/repo/registry/publication-20261001/local-content-verification.json",
|
||||
"schema": "lfs-publication-aggregate-verification-v1",
|
||||
"scope": "Given payload bytes verified against plan/catalog/members and optional historical overlap; provenance/plan authenticity and fresh-clone transfer evidence are caller responsibilities",
|
||||
"source_bytes": 24040546041,
|
||||
"source_files": 226859,
|
||||
"verified_utc": "2026-09-30T19:36:33.592474+00:00"
|
||||
}
|
||||
@@ -0,0 +1,123 @@
|
||||
{
|
||||
"disk_free_bytes": {
|
||||
"/data/digital-drosophila": 645520629760,
|
||||
"/tmp/malecns-lfs-publication-20261001-bI1u07/repo/registry/publication-20261001": 876361818112
|
||||
},
|
||||
"license_evidence": [
|
||||
{
|
||||
"bytes": 18657,
|
||||
"group": "celltype-explorer",
|
||||
"path": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision/external-resources/celltype-explorer/LICENSE",
|
||||
"sha256": "9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411"
|
||||
},
|
||||
{
|
||||
"bytes": 35149,
|
||||
"group": "visualpathways",
|
||||
"path": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision/external-resources/visualpathways/LICENSE",
|
||||
"sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986"
|
||||
},
|
||||
{
|
||||
"bytes": 1042,
|
||||
"group": "door-data",
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Reference in New Issue
Block a user