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Resolve Cycle 9 Stage 4 review findings on CommunityMech:000331, 000455, and 000461 (#2713) - #2714
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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. |
realmarcin
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Nov 7, 2026
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Summary
reviews/workflow/latest.yamlwith the verified Cycle 9 Stage 4 closure entry (#2712, merge commitfc0c501b9dea3fc24eb9eb60fa4bacd6f1521446) fromverified-evidence-index.json.reviews/workflow/mech-goal-sequence-20261019/cycle-000009/stage-04/revision-0001/evidence.yaml) into 8 root-cause issue groups (cm-c09-s05-g001throughcm-c09-s05-g008) deduplicated against real GitHub issues (#2713for the 3 actionable open findings across 3 community records, and#765,#1467,#1657,#1681,#1699,#1841,#1847for the 7 source-limited deferred findings).abundance_levelrepairs viarecord_curation_event(..., llm_assisted=True)+write_validated_community:kb/communities/Pseudomonas_Paracoccus_Bifenthrin_Degradation_Consortium.yaml(CommunityMech:000331): addsabundance_level: DOMINANTand verbatim two-strain synthetic consortium evidence (PMID:42269294,doi:10.1016/j.jhazmat.2026.142626) onPseudomonas aeruginosa PA(NCBITaxon:287,taxonomy[0]) andParacoccus pantotrophus PP(NCBITaxon:82367,taxonomy[1]), with provenance sidecarhistory/records/Pseudomonas_Paracoccus_Bifenthrin_Degradation_Consortium/2026-11-07T051500Z-antigravity-2713a1.yaml.kb/communities/Ecoli_K12_MG1655_Arg_Met_CrossFeeding_Coculture.yaml(CommunityMech:000455): addsabundance_level: DOMINANTand verbatim two-strain obligate mutualistic coculture evidence (PMID:42592155,PMC13463769,doi:10.1093/nsr/nwag357) onEscherichia coli K-12 MG1655 ΔargA-ΔmetJ(NCBITaxon:511145,taxonomy[0]) andEscherichia coli K-12 MG1655 ΔmetA-ΔargR(NCBITaxon:511145,taxonomy[1]), with provenance sidecarhistory/records/Ecoli_K12_MG1655_Arg_Met_CrossFeeding_Coculture/2026-11-07T051500Z-antigravity-2713a2.yaml.kb/communities/Pseudomonas_Acidovorax_Aniline_Degradation_SynCom.yaml(CommunityMech:000461): addsabundance_level: DOMINANTonPseudomonas sp. RF(NCBITaxon:286,taxonomy[0]) andabundance_level: ABUNDANTonAcidovorax sp. PH(NCBITaxon:12916,taxonomy[1]) with verbatim 3:1 inoculation-ratio evidence (PMID:41900437,PMC13029111,doi:10.3390/microorganisms14030678), with provenance sidecarhistory/records/Pseudomonas_Acidovorax_Aniline_Degradation_SynCom/2026-11-07T051500Z-antigravity-2713a3.yaml.reports/causal_graph_review/decisions/20261107-c9s5-review-remediation.yaml, updatesreports/causal_graph_review/inventory.tsvand batch regression tests (test_causal_review_batch37.py,test_causal_review_batch88.py,test_causal_review_batch89.py), regenerates community HTML pages indocs/communities/, saves post-remediation structured review verification (reviews/structured/20261107T052000Z-c9s5-remediation-verification/), and records Cycle 9 Stage 5 workflow evidence (reviews/workflow/mech-goal-sequence-20261019/cycle-000009/stage-05/revision-0001/).Closes #2713