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Repair R2A model attribution and antagonism claims (batch58) - #1534
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Source-based self-adversarial review at exact head 277b725; not independent approval.
Repair #1532 addressed; existing #1533 remains unresolved.
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Separate R2A FBA predictions from MOPS CF313 attribution and agar antagonism.
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Whole R2A record, all3 original nodes and2 arrows reviewed against the full extracted primary main text, Methods2.1-2.6, Results3.1-3.5, Tables1-2 and main captions. No original image pixels, supplements/raw data or independent KBase execution/model replication.
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R2A uses YR343,GM17,AP49 in the three-member model; CF313 belongs to the four-member MOPS model. Remove the transplanted CF313 cross-feeding node and Pantoea-to-CF313 arrow rather than silently moving MOPS predictions into R2A. Partial canonical participants explicitly exclude missing AP49; no invented CURIE.
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Preserve positive R2A exchange predictions and model-dependent Pantoea growth improvement. Gapfilling, final-passage16S ratios and calibrated uptake bounds are assumptions. Metaproteomics detects relevant enzymes but does not measure transferred flux or establish mutualism; 16S and protein abundance estimates differ.
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Preserve experimentally measured GM17-to-CF313 R2A-agar inhibition at25C/48h. It is a distinct pairwise assay, not evidence of CF313 membership in the R2A model. No inhibitory molecule or selective metabolic rescue was demonstrated.
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Remove the antagonism-to-cross-feeding arrow. Shared-metabolite compensation is proposed, while liquid-versus-static-agar conditions are an explicit alternative. Antagonistic pressure does not itself establish a causal cross-feeding response.
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Both removed arrows and the removed node have individual decisions; retained nodes carry exact OPEN knowledge-gap anchors. Broad metabolite classes remain without fictitious concentrations. GO and CHEBI preferred labels align with the retained canonical labels.
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All raw non-graph blocks remain byte-identical, not certified.1533 stays OPEN for canonical membership/strain grounding, CF313 role and ten-isolate assembly versus selected-member model. All920 caches and459 other records unchanged; four graph snippets independently matched to fresh primary and cache.
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Complete biological diff, test assertions and decision ledger reviewed. Both-root participant census unchanged;36 baseline network warnings preserved with zero structural defects. No connectivity matching rule or canonical membership change.
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Initial regression run had535 passes and one failure: the exact participating_taxa USERS set lacked R2A. Added only that intentional new user after the unchanged census was measured; kept the exact-set guard and original failed output/digest, then reran the complete suite.
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Actual schema/strict/term/reference/snippet/history/rank/regression gates and output digests recorded. Deterministic repeat rendering and456-page exact description parser verification passed; no browser-screenshot claim. Post-commit docs-current is a separate publication gate.
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834 all-state issue titles/bodies searched and85 scoped ignored/hidden local matches; relevant issues read, not every historical comment/PR or matching file.1532 addressed but OPEN until protected-main merge;1533 unresolved. Exact-head GitHub review must be COMMENT, not independent approval.
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This is an R2A-only repair, without new structure or provider spend. Dairy/kefir source research is not credited as reviewed. Dairy one-community Edison dry run spent zero credits; the separate paid request/report remains pending.
536 passed in 179.05s (0:02:59); five new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 11 snippets match selected caches; all920 cache files unchanged. Four graph fragments independently primary-matched. MATCH does not certify all cached or non-graph content; existing1533 remains unresolved. CLI Total checks counts reported issues, not executed checks; coverage476, Linux DOI lookup1091 and writer artifact1095 remain limitations.
All3 original nodes and2 arrows reviewed; one MOPS-misattributed node and both arrows removed. Conditional R2A model predictions and observed agar inhibition preserved. Zero structural errors; all36 baseline network warnings remain without additions.459 other records/raw non-graph blocks unchanged. Measured census:{"community_level_only": 266, "credited_solely_by_the_rule": 1236, "mixed": 124, "records": 460, "taxa": 1505, "with_community_level": 390}.
Repeat renders deterministic and descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 193c9d4777ae8151066380a746715ea054b3b815cec977a99806f51f1a5f300f.
Every-node/every-arrow decisions, actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch58. Not independent approval. Corpus192 reviewed /250 pending /18 needs_research; corpus-wide work is not complete.
Protected-main merge remains 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 integration review at exact head ce5ba631a0006d1fe7c10d6e807e8d63220f93ce. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 277b7254fa7d78c16d801e45972e13469e4e5027, 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 9593fda22b9870dae379ee47397f14bc94646ee3241e44d38a04cb80a5b4d046). 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 678e2f7ee734f207b729cbdb390cf3580b1b1a22
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0d91f7aaebd29541c41e8629a13dc7aee76433bf.
The batch-owned binary patch is byte-identical
(SHA-256 9593fda22b9870dae379ee47397f14bc94646ee3241e44d38a04cb80a5b4d046); 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 178b042ecdebd34667f5fafa08f9dff5b1a8504c. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 678e2f7ee734f207b729cbdb390cf3580b1b1a22, 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 9593fda22b9870dae379ee47397f14bc94646ee3241e44d38a04cb80a5b4d046). 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 950408e5eff1df5343661c937865b9e42503464f.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 9593fda22b9870dae379ee47397f14bc94646ee3241e44d38a04cb80a5b4d046.
Tree 472bd39ead0d5815818c6ef417f1c8c3982912b0 matches the independently computed clean merge.
Compared with historical tree 206c9f26861c361c7add0cd44fb506217e814580, 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 #1532.
Related #1533 remains OPEN: R2A canonical membership, strain grounding and ten-isolate assembly metadata are unresolved.
Adversarial Review
Verification And Output Records
536 passed in 179.05s (0:02:59); five new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 11 snippets match selected caches; all920 cache files unchanged. Four graph fragments independently primary-matched. MATCH does not certify all cached or non-graph content; existing1533 remains unresolved. CLI Total checks counts reported issues, not executed checks; coverage476, Linux DOI lookup1091 and writer artifact1095 remain limitations.
All3 original nodes and2 arrows reviewed; one MOPS-misattributed node and both arrows removed. Conditional R2A model predictions and observed agar inhibition preserved. Zero structural errors; all36 baseline network warnings remain without additions.459 other records/raw non-graph blocks unchanged. Measured census:{"community_level_only": 266, "credited_solely_by_the_rule": 1236, "mixed": 124, "records": 460, "taxa": 1505, "with_community_level": 390}.
Repeat renders deterministic and descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 193c9d4777ae8151066380a746715ea054b3b815cec977a99806f51f1a5f300f.
Every-node/every-arrow decisions, actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch58. Not independent approval. Corpus192 reviewed /250 pending /18 needs_research; corpus-wide work is not complete.
Dependency
Draft depends on #1531. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after parent merges. Move dependent PRs before deleting parent branches. No Edison submission/spend or new graph structure.