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Bound UFMP, GOM oil and garlic SynCom causal graphs (batch44) - #1477
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Source-based self-adversarial review at exact head 7bdc938; not independent approval.
Issues #1474/#1475/#1476 addressed after primary-text, graph diff and validation-output review.
Three existing graphs bounded after complete primary main-body review:
- UFMP: genome-based roles and both model arrows remain HYPOTHESIZED/PARTIAL. Distinguish CLOS1 lactate/butyrate, LCO1 direct lactose and inconclusive ACID1 ethanol. Exact canonical guild participants; no traced flux, obligatory syntrophy, complete conversion or stereospecific lactate claim. SPH2 remains outside these existing nodes rather than receiving an invented interaction.
- GOM: retain positive n-alkane/PAH measurements and higher gross oil removal. The ~62% gross endpoint includes abiotic loss; per-strain 1e8 CFU/mL inocula give different total starting CFUs. Do not infer synergy or niche partitioning. Two unsupported class-to-comparative-endpoint arrows removed; panel heterogeneity and methylated versus generic phenanthrene distinguished.
- Garlic: remove selection/assembly workflow nodes; preserve the two-day radish length response and earlier arrow-removal history. IN_VIVO host evidence, not garlic field yield, proven six-member synergy or a resolved strain roster.
Nine original nodes to seven; four arrows to two. No new graph structure or Edison/provider spend.
451 passed in 209.31s (0:03:29); six new focused tests. Schema, strict, terms, reference and history checks pass for all three records. Snippet matching: UFMP27, GOM10, Garlic5; no other snippet classes. CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference #476 coverage remains incomplete and textual matching is not scientific support or independent provenance.
Both-root pre-paper baseline retained. Zero structural errors; 33 existing network warnings preserved exactly plus one explicitly documented DISCONNECTED SPH2 warning. No links invented to suppress it. 457 other records, all920 source caches, canonical taxonomy, non-graph raw blocks and prior history artifacts preserved. Participant registry190 to193; corrected connectivity survey and bounds unchanged. Repeat renders deterministic; exact descriptions checked across all456 published pages. No browser screenshot claim.
A verification-helper assertion initially treated the network JSON object as a list. Corrected only that comparison; retained the failed-run receipt, hash-checked completed command logs, and completed remaining validation without changing curated bytes. Actual outputs and limitations are committed under reports/causal_graph_review, batch44.
Actual post-commit just check-docs-current exited0 with a clean tree, log SHA256 b0869e042a209a8e6feb4de12097714bc793db5a40cb1e58700e721ee372fa4f.
Whole records and complete primary main bodies/Methods/tables/captions read. No figure images, separate supplements, raw data or analysis code independently inspected. GOM cache is only abstract plus one Methods sentence despite its FULL TEXT marker; separately read publisher text is hash-identified, not silently appended to the cache. Non-graph metadata is preserved, not certified.
Source-based self-adversarial review, not independent approval.
Protected main merge and full-corpus completion remain pending.
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
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Self-adversarial review refreshed at exact head 4442732e781a8c35541015ab861cab6a589ab083
after protected main merge of #1328. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree ae873b509fa12c69970cbafa96265ab9d55b8eb5.
The batch-owned binary patch is byte-identical
(SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial review refreshed at exact head 0bdaea52208f6b932658971464da8f490f576204
after protected main merge of #1334. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree ae873b509fa12c69970cbafa96265ab9d55b8eb5.
The batch-owned binary patch is byte-identical
(SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial review refreshed at exact head d3d0e95a8bfe254b07382d6add55fd36f3627fb9
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree ae873b509fa12c69970cbafa96265ab9d55b8eb5.
The batch-owned binary patch is byte-identical
(SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial review refreshed at exact head 823a6bfb21b374169724ff7fe3f2066e7ddeeeff
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree ae873b509fa12c69970cbafa96265ab9d55b8eb5.
The batch-owned binary patch is byte-identical
(SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial review refreshed at exact head ef8e4395fa98e076672d39fdb4a5959843fd9486
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree ae873b509fa12c69970cbafa96265ab9d55b8eb5.
The batch-owned binary patch is byte-identical
(SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial review refreshed at exact head 32d4d922b61f4b2b42df646f6c81d10200327a86
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree ae873b509fa12c69970cbafa96265ab9d55b8eb5.
The batch-owned binary patch is byte-identical
(SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial integration review at exact head 7e7794fd4180117a82c53e7a1144eabccb088ecd. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 32d4d922b61f4b2b42df646f6c81d10200327a86, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.
Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.
An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.
Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.
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Self-adversarial review refreshed at exact head c0e3acc502e6d45430a1a74c3a8819a431ffae4b
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 466837ecbee2cf40f1acbb917d0ac01a40a6af8e.
The batch-owned binary patch is byte-identical
(SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial governance integration review at exact head e16d0729f10d6871ba8e22bf50e7441dd82096f3. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head c0e3acc502e6d45430a1a74c3a8819a431ffae4b, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.
Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.
Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.
Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.
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Exact-head self-adversarial restack review at 192a17c3a6aeedb36bb9b1dacc36c7945cf23651.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 b44387c4cbb8eb4d2bca0de7aff2e2f8ec48de522920ef63591996a34f649c62.
Tree 62f87767dab2440fc66ef501660d08f806e423e7 matches the independently computed clean merge.
Compared with historical tree 229c506f500c105c58107fab91bf05bccfb1e011, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.
This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.
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Superseded by the protected cumulative merge #1975 at Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files. |
1 participant
Scope
Closes #1474. Closes #1475. Closes #1476.
Three existing graphs bounded after complete primary main-body review:
Nine original nodes to seven; four arrows to two. No new graph structure or Edison/provider spend.
Verification And Output Records
451 passed in 209.31s (0:03:29); six new focused tests. Schema, strict, terms, reference and history checks pass for all three records. Snippet matching: UFMP27, GOM10, Garlic5; no other snippet classes. CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference #476 coverage remains incomplete and textual matching is not scientific support or independent provenance.
Both-root pre-paper baseline retained. Zero structural errors; 33 existing network warnings preserved exactly plus one explicitly documented DISCONNECTED SPH2 warning. No links invented to suppress it. 457 other records, all920 source caches, canonical taxonomy, non-graph raw blocks and prior history artifacts preserved. Participant registry190 to193; corrected connectivity survey and bounds unchanged. Repeat renders deterministic; exact descriptions checked across all456 published pages. No browser screenshot claim.
A verification-helper assertion initially treated the network JSON object as a list. Corrected only that comparison; retained the failed-run receipt, hash-checked completed command logs, and completed remaining validation without changing curated bytes. Actual outputs and limitations are committed under reports/causal_graph_review, batch44.
Actual post-commit just check-docs-current exited0 with a clean tree, log SHA256 b0869e042a209a8e6feb4de12097714bc793db5a40cb1e58700e721ee372fa4f.
Whole records and complete primary main bodies/Methods/tables/captions read. No figure images, separate supplements, raw data or analysis code independently inspected. GOM cache is only abstract plus one Methods sentence despite its FULL TEXT marker; separately read publisher text is hash-identified, not silently appended to the cache. Non-graph metadata is preserved, not certified.
Source-based self-adversarial review, not independent approval.
Corpus:167 reviewed /281 pending /12 needs_research across460 records. Full-corpus completion is not claimed.
Dependency
Draft depends on #1473. Do not merge into the topic parent. Require eligible exact-head checks and the protected main queue after parents merge; move dependents before deleting merged branches.