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Qualify Arg-Met and electrostimulated community causal mechanisms (batch 37) - #1437
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Source-based self-adversarial review at exact head a22f0f8; not independent approval.
Addressed existing-graph defects #1431/#1432/#1433 after primary-source and complete diff review at the recorded access scope.
Eleven existing nodes retained; three unsupported VFA arrows removed and two qualified. No added connectivity or provider job/charge.
Arg/Met retains genotype-specific reciprocal exchange under nutrient limitation and a fluorescence-CV endpoint, not universal obligation or intrinsic transcriptional noise. Remove the interspecies GO annotation for the same-species pair. Its source-backed mechanism expansion remains needs_research under #1436; one-community Edison dry run completed but no actual job submitted.
VFA distinguishes sequential operational context, endpoint compartment profiles, computed potential and bulk outputs. Remove composition-to-prediction, prediction-to-acetate and IC-removal-to-acetate arrows; retain operational selection as PARTIAL and architecture-to-removal as HYPOTHESIZED. Three canonical participants are representative, not the complete roster or required contributors. Remove categorical cross-feeding/syntrophy and unsupported process annotations.
Toluene retains three abstract-supported candidate mechanisms and zero arrows. Preserve alternate methanogens and transfer routes, MAG-specific evidence, distinct MAG116/MAG60 identities, and prior #1120/#1121 fixes. All mechanisms are HYPOTHESIZED/PARTIAL; no measured transfer flux or unaccessed full-text evidence is claimed.
399 passed in 179.40s (0:02:59); seven new regression tests. Focused schema, strict, term, independent snippet and history checks passed. Three reference-validator commands exit 0 but perform zero checks: a no-op, not evidence validation. Textual matches are not scientific support.
Zero structural errors; all 33 baseline warnings preserved exactly, none added. VFA joins the participant registry (183 to 184 users). Connectivity census and numeric bounds remain unchanged.
Three guarded writes and append-only histories; non-graph raw blocks, 457 other records and 920 caches unchanged. Repeat renders deterministic, with exact descriptions checked across 456 pages. Actual post-commit docs-current passed with clean tree.
Committed decisions, actual validation output including baseline, and self-adversarial review are under reports/causal_graph_review, dated 20261006, batch37. Primary main-body access for Arg/Met and the publicly mirrored VFA preprint; toluene abstract only. No visual figures, separate supplements or raw-data review claimed. This is source-based self-adversarial review, not independent approval.
#373/#1434/#1435/#1436 remain OPEN. Protected main merge and full-corpus completion are not asserted.
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 fbc597c1ac5130a6bd65cb69bcb1d895fef03a6d
after protected main merge of #1315. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 bd4a2a44e66eba5a9078222affa65565e8a606b0
after protected main merge of #1318. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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.
|
Reference-counter correction (#1469) The earlier statement that linkml-reference-validator 0.1.7's The source-backed correction and historical candidate inventory are committed in #1470 at The new Fucoidan batch separately retains 14 baseline reference-CLI failures and 15 baseline snippet-audit mismatches for supplement-sidecar excerpts. Those are not failures attributed to this older PR. This correction is self-review, not independent approval or merge authorization beyond the existing protected workflow. |
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Self-adversarial review refreshed at exact head bf2ca2b8bb0e58d7a0a9bbe1a646b9c1e8056883
after protected main merge of #1323. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 13582f87df1a2426bfb927f565e0f980c3f80e20
after protected main merge of #1328. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 97009d410068b6419926c2935b9b61989e213773
after protected main merge of #1334. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 36a42df112d82b010d9f2faad8d402d029091e9f
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 d7953dd91eeef7cb9d6a74ecb1e0f596926bda48
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 789571df9921dd0ea4094c7bbdeb5959a0a13d7f
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 feba184d1d35f95e854f90feed6c018c793310d3
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 53fbd8501df23432e22ae64785408cff1c614027.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 b13de274b6f95b5a58305a9e74d271ad5711a530. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head feba184d1d35f95e854f90feed6c018c793310d3, 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 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8). 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 aa3597539f93314f90ec156535d6a3404e1ed0da
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0c2d1805a55c46b7d6498116ba11a1f9bd122105.
The batch-owned binary patch is byte-identical
(SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8); 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 17620c40a0e34749517792dcda18860fc09f527c. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head aa3597539f93314f90ec156535d6a3404e1ed0da, 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 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8). 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 cc9a34941aa417cc119faef2b6717f55711e3398.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 aba1c0e0d3188c645a28f8708ead1e3708757bbe76529a8337a198a41c1074f8.
Tree 5ce5344d50cb44f3756e6f482d201ea7e665081a matches the independently computed clean merge.
Compared with historical tree 1fbd9f6e5ce034f6062753264c62b6fd3c2a4db6, 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. |
Scope
Existing-graph repairs for Arg/Met and two electrostimulated communities. Two reviews complete; Arg/Met expansion remains pending. Corpus: 152 reviewed / 300 pending / 8 needs_research across 460 records in both roots.
Closes #1431. Closes #1432. Closes #1433. Non-graph #373/#1434/#1435 and graph expansion #1436 remain open. Existing #373 was reopened for its live recurrence, not duplicated.
Changes
Eleven existing nodes retained; three unsupported VFA arrows removed and two qualified. No added connectivity or provider job/charge.
Arg/Met retains genotype-specific reciprocal exchange under nutrient limitation and a fluorescence-CV endpoint, not universal obligation or intrinsic transcriptional noise. Remove the interspecies GO annotation for the same-species pair. Its source-backed mechanism expansion remains needs_research under #1436; one-community Edison dry run completed but no actual job submitted.
VFA distinguishes sequential operational context, endpoint compartment profiles, computed potential and bulk outputs. Remove composition-to-prediction, prediction-to-acetate and IC-removal-to-acetate arrows; retain operational selection as PARTIAL and architecture-to-removal as HYPOTHESIZED. Three canonical participants are representative, not the complete roster or required contributors. Remove categorical cross-feeding/syntrophy and unsupported process annotations.
Toluene retains three abstract-supported candidate mechanisms and zero arrows. Preserve alternate methanogens and transfer routes, MAG-specific evidence, distinct MAG116/MAG60 identities, and prior #1120/#1121 fixes. All mechanisms are HYPOTHESIZED/PARTIAL; no measured transfer flux or unaccessed full-text evidence is claimed.
Verification And Output Records
399 passed in 179.40s (0:02:59); seven new regression tests. Focused schema, strict, term, independent snippet and history checks passed. Three reference-validator commands exit 0 but perform zero checks: a no-op, not evidence validation. Textual matches are not scientific support.
Zero structural errors; all 33 baseline warnings preserved exactly, none added. VFA joins the participant registry (183 to 184 users). Connectivity census and numeric bounds remain unchanged.
Three guarded writes and append-only histories; non-graph raw blocks, 457 other records and 920 caches unchanged. Repeat renders deterministic, with exact descriptions checked across 456 pages. Actual post-commit docs-current passed with clean tree.
Committed decisions, actual validation output including baseline, and self-adversarial review are under reports/causal_graph_review, dated 20261006, batch37. Primary main-body access for Arg/Met and the publicly mirrored VFA preprint; toluene abstract only. No visual figures, separate supplements or raw-data review claimed. This is source-based self-adversarial review, not independent approval.
Dependency
Draft depends on #1430; do not merge into the topic parent. Require eligible exact-head checks and the protected main merge queue after parents merge. Move dependents before branch deletion. Full-corpus completion is not claimed.