The SynCom's community-level degradation emerges from combining fucose specialists, rare-sugar specialists, and generalists whose enzyme repertoires unlock distinct fractions of the sulfated F. vesiculosus fucoidan substrate.
+Across the seven-degrader panel, V4/V25 preferentially degrade fucose, F12/F40/F94 rare sugars, and V69/F56 act as generalists. Genomic predictions were compared with experimental LC-MS monomer depletion. Monomer degradation combines cleavage of fucoidan-bound sugars and uptake, not measured CO2 mineralization. Cell-free residual-fucoidan and purified-enzyme assays support complementary substrate accessibility without requiring contact or small-molecule cross-feeding. Six of nine tested soluble enzymes had detectable activity; this does not establish each enzyme as necessary in every community. Participants identify the panel, not seven obligatory partners in every assay. G88 and the algal substrate producer are not members.
+Participating Taxa: + + Algibacter sp. AS12, + + Algibacter lectus AS40, + + Mariniflexile sp. AS56, + + Zobellia laminariae AS94, + + Luteolibacter sp. AS25, + + Roseibacillus persicicus AS69, + + Lentimonas sp. CC4 + +
+ @@ -1066,7 +1084,7 @@The complete non-empty panel of seven fucoidan degraders produced a smooth community-function landscape in which synergism remained common even among combinations approaching nearly complete degradation.
+All 127 nonempty combinations of the seven listed degraders were assayed, not a single invariant seven-member community. The reported maximum 97.1% monomer degradation occurred in the five-member F40/F56/V69/F94/V4 subset. Functional synergism, reported for 80% of interactions relative to the resource-partitioning null, is distinct from reciprocal fitness benefit; pairwise outcomes include commensalism, amensalism and competition. The mutualistic V69/G88 pair lies outside this panel. Initial OD600 was 0.01 per strain, so total inoculum varied with richness. These endpoint assays do not isolate a richness-only effect or establish ocean carbon-sequestration rates. The model is fitted prediction, not independent enzyme-necessity evidence.
+ + + +Participating Taxa: + Algibacter sp. AS12, + Algibacter lectus AS40, + + Mariniflexile sp. AS56, + + Zobellia laminariae AS94, + + Luteolibacter sp. AS25, + + Roseibacillus persicicus AS69, + + Lentimonas sp. CC4 + +
@@ -1224,7 +1260,7 @@Supplementary Table 2 maps LCC_4 to Lentimonas sp. CC4, Verruco4, and V4, and the full-combinatorial Methods use V4. One article paragraph refers to the previously characterized CC4 degrader as strain V43, so this record follows the spreadsheet and Methods convention for the member code.
+Publisher HTML inspected on 2026-10-06 shows V4 immediately followed by a superscript link to reference 3, not strain V43. The selected-text cache flattened this citation into V43. Table 2 selected rows and combinatorial Methods consistently use V4 for Lentimonas sp. CC4. Preserve the historical question and original cache, but do not treat the rendering artifact as a biological alias. The decision ledger retains the source HTML hash and exact DOM fragment.
Attaches to: taxonomy#Lentimonas sp. CC4
Full public primary main body and Methods read. Cell-free residual substrate and six active purified enzymes support complementary accessibility; no universal contact requirement, small-molecule exchange or reciprocal benefit follows. Depletion combines cleavage and uptake, not CO2 mineralization. Preserve the five-member maximum, G88 exclusion, variable total inoculum and experimental/model distinction. The Results describe fitting one-, two- and three-member communities while Methods more generally reference the 127-community data; code and raw data were not audited, so no independent train/test verification is claimed. New structure is pending #1465 after the one-community Edison dry run; specific credit authorization requested, no job or spend. Two corrected existing nodes and zero arrows are not a completed causal expansion. Figure images and original supplements were not inspected.
+ +Attaches to: ecological_interactions#Complementary fucoidan monomer degradation, ecological_interactions#Seven-degrader synergistic function landscape
GENIA integrated pollutant-growth phenotypes and whole-genome annotations to assemble a community with complementary lignin, atrazine, and PFAS degradation potential across hub and specialist strains. -
+HYPOTHESIZED: Genome annotations and computational network models predict complementary degradation potential across nine selected members, including five predicted generalists and four specialists. Agreement between GENIA and iNAP is computational cross-validation, not measured interspecies metabolite transfer, active expression or catalytic necessity. Growth-screen fluorescence does not independently establish pollutant degradation. The assembly workflow is not itself a biological cause of the measured removal phenotype; no design-to-removal arrow is retained.
+ + + + +Participating Taxa: + + Atlantibacter hermannii, + + Bacillus cabrialesii, + Bacillus licheniformis, + Bacillus pseudomycoides, + Micrococcus luteus, + + Paenibacillus polymyxa, + + Pantoea dispersa, + + Pseudomonas fulva, + + Pseudomonas pergaminensis + +
@@ -928,35 +943,7 @@Biological Processes:
-The genome-informed community architecture yielded synergistic PFOS, atrazine, and lignin removal in minimal medium. -
-The assembled nine-member SynCom degraded lignin, atrazine, and PFOS in M9 minimal-medium assays at levels greater than the best individually assayed member. -
+The source reports consortium removal above the best assayed monoculture: PFOS 93.1%, atrazine 91.4% and lignin 91.6% in the separate treatment comparisons. A distinct seven-day mixed-pollutant experiment reports PFOS 87.1%, atrazine 84.7% and lignin 88.9%; do not substitute the higher figures for this mixture. LC-MS/MS loss and lignin UV-visible changes are community-level endpoints, not proof of reciprocal member benefit, assigned cross-feeding or complete carbon mineralization. The paper reports fluoride and intermediates, but its PFOS fluorine denominator and atrazine nitrogen/method descriptions conflict; removal is retained as source-reported, not independent certification of defluorination efficiency or complete mineralization. Supplements and raw data were not audited.
+ + + + +Participating Taxa: + Atlantibacter hermannii, + Bacillus cabrialesii, + Bacillus licheniformis, + + Bacillus pseudomycoides, + + Micrococcus luteus, + + Paenibacillus polymyxa, + + Pantoea dispersa, + + Pseudomonas fulva, + + Pseudomonas pergaminensis + +
@@ -1050,20 +1057,53 @@Full-length 16S rRNA tracking over the seven-day degradation assay showed that all nine inoculated strains persisted, with the predicted Paenibacillus polymyxa and Pseudomonas pergaminensis hub strains increasing in relative abundance while specialist strains remained detectable. -
+Full-length 16S rRNA gene profiles track relative DNA composition during removal; predicted hub taxa increased in relative abundance and other inoculated taxa remained detectable. These measurements do not establish absolute viable persistence, member-resolved flux or hub necessity. The source also compares self-organizing communities with daily dilution/remixing to equal ratios, reporting lower PFOS and atrazine removal in the remixed condition; the lignin comparison had p=0.092. PARTIAL: this treatment comparison supports a composition-management association with performance, but does not isolate a particular taxon, metabolite or persistence-mediated pathway from the handling intervention.
+ + + + +Participating Taxa: + + Atlantibacter hermannii, + + Bacillus cabrialesii, + + Bacillus licheniformis, + Bacillus pseudomycoides, + Micrococcus luteus, + Paenibacillus polymyxa, + + Pantoea dispersa, + + Pseudomonas fulva, + + Pseudomonas pergaminensis + +
@@ -1075,9 +1115,8 @@Persistence of the complete inoculated roster maintained the multispecies degradation network during the pollutant-removal time course. -
+ → Reported GENIA Liquid Pollutant Removal +PARTIAL: Allowing composition to reorganize was associated with greater PFOS and atrazine removal than daily equal-ratio dilution/remixing. This reported intervention supports a bounded community-management effect, not selective proof that persistence or a particular cross-feeding network causes removal. Dilution/remixing changes handling as well as ratios; the reported lignin difference was not significant at p<0.05.
Retain reported removal and relative DNA profiles, not mutualism, measured handoffs or necessary hubs. The daily equal-ratio intervention supports only PARTIAL management-level causality because handling and composition change together; lignin p=0.092. A PFOS-only inventory at the stated 37.1 micromolar gives approximately 12.0 mg/L fluorine, not the alternatively stated 64.08 mg/L. Methods also mention a PFOA/PFOS mixture, so the true denominator needs treatment-specific reconciliation rather than a blanket impossibility claim. Atrazine concentrations, nitrogen yield and Nessler versus indophenol methods also conflict. Source-reported fluoride/intermediates are not ignored, but no efficiency or complete-mineralization certification follows. Raw data and supplements were not inspected; follow-up #1468 remains open. Existing graph corrections address #1466 without new structure or provider spend.
+ +Attaches to: ecological_interactions#Predicted GENIA Metabolic Complementarity, ecological_interactions#Reported GENIA Liquid Pollutant Removal, ecological_interactions#GENIA DNA Composition and Ratio-Management Comparison
Community members interact chemically through small molecules, extracellular enzymes, and antibiotics in shared medium.
- - - - - - -Metabolites: - - N-acyl-L-homoserine lactone - (CHEBI:55474), - - antibacterial agent - (CHEBI:33282) - -
- - - -Biological Processes:
-Chromobacterium violaceum Cv017 produces acyl-homoserine lactones that diffuse through the Transwell reservoir and induce quorum sensing, vioC transcription, and violacein production in the physically separated Cv026 biosensor. -
+In the two-strain reporter demonstration, AHL-producing Cv017 induced violacein and vioC transcription in physically separated Cv026 through the shared reservoir. Replated Cv026 returned to a nonpigmented phenotype, supporting signal-dependent response rather than contamination or a stable pigmented mutant. This supports diffusible signaling in this assay, not a quantified signal dose, all extracellular enzyme classes or causation of the separate three-member metabolomics phenotype. The canonical record currently has only a Bacteria umbrella; exact strain participants remain unresolved rather than being assigned invented CURIEs.
@@ -652,8 +591,7 @@A stationary-phase Burkholderia thailandensis, Chromobacterium violaceum and Pseudomonas syringae Transwell community produced a reproducible nonpolar exometabolite profile in which mass features were depleted, produced de novo, or enriched at early and mid time points. -
+The separate B. thailandensis E264, source-labeled C. violaceum and P. syringae DC3000 stationary-phase assay showed time-varying nonpolar mass features over 15-35 hours. The 977 features are not 977 identified metabolites, and changes do not resolve producer-consumer flux. Bactobolin was identified separately by polar HILIC-MS/MS; its accumulation does not selectively establish the cause of lower P. syringae live-cell counts in B. thailandensis-containing cultures. No bactobolin-to-inhibition or AHL-to-metabolomics arrow is asserted. The source has a Chromobacterium strain-number discrepancy; taxonomy and a separately supported antagonism node remain pending under #1467.
@@ -699,6 +637,25 @@The platform-capability umbrella node is removed; prior workflow-arrow pruning remains intact. The AHL reporter pair and three-member stationary-phase series are distinct experiments. The full primary body supports lower P. syringae live-cell counts with B. thailandensis, but bactobolin accumulation is not selective mediator necessity. New antagonism structure and exact canonical members remain pending #1467; Bacteria/NCBITaxon:2 must not become invented species participants or a self-edge. The source uses SC11,368 in prose versus SC11,378/ATCC31532 in its strain table. One-community Edison dry run completed; specific credit authorization requested, no job or spend. Metadata still conflates test-tube versus Transwell cultivation and different assay media; those preserved fields are not certified. Main body, table text and captions read, not figure images, separate supplements or raw spectra.
+ +Attaches to: ecological_interactions#AHL Diffusion and Violacein Induction, ecological_interactions#Three-Member Exometabolite Time Series
From these enrichments, we established a strain collection that reflects the taxonomic + and functional diversity of the community (Fig. 1b). We isolated 5 exploiters, 16 + scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) + and four members of the Flavobacteriia (F12, F40, F56 and F94). We additionally included the previously + characterized degrader Lentimonas sp. CC4 as strain V43. Isolate + classification was experimentally validated by confirming that degraders grow on fucoidan, exploiters + grow on fucose (but not fucoidan), and scavengers are unable to utilize either substrate (Supplementary + Fig. 1). + Although several degraders were not previously described, we found that in particular V69 and V4 co-occur + across many macroalgae-associated coastal habitats (Supplementary Fig. 2 and Supplementary + Note 2), + highlighting the ecological relevance of this strain collection. Collectively, these 29 strains provide + a foundation for dissecting the mechanisms of fucoidan degradation in microbial communities.
+ unresolved_graph_structure: Existing-node corrections do not complete new causal structure. One-community Edison + dry run completed; specific credit authorization requested. Issue remains open. +- path: kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml + id: CommunityMech:000352 + original_sha256: 1daada660d8dad257e3a5b04d861665bb03bd631c598322ebdea22ff452fac3f + record_sha256: 72fcc1720a4bb6b3a0a464f98524ab2bbf999b2b73eaf71efa0fa98be433b9c3 + status: reviewed + outcome: changed + review_file: reports/causal_graph_review/decisions/20261006-three-records-batch42.yaml + scope: Whole record and all original nodes/arrows assessed; source-access limits explicit. Non-graph fields preserved, + not certified. + summary: Retain computational complementarity as a hypothesis and remove the workflow-to-removal arrow.; Retain + distinct reported removal endpoints without mutualism, assigned flux or certified mineralization.; Retain DNA + composition and the bounded daily-ratio intervention; qualify its existing removal arrow as PARTIAL. + renamed_nodes: + GENIA Multipollutant Assembly: Predicted GENIA Metabolic Complementarity + Liquid Multipollutant Degradation: Reported GENIA Liquid Pollutant Removal + Community Stability During Degradation: GENIA DNA Composition and Ratio-Management Comparison + node_decisions: + - node: Predicted GENIA Metabolic Complementarity + rationale: Retain computational complementarity as a hypothesis and remove the workflow-to-removal arrow. + - node: Reported GENIA Liquid Pollutant Removal + rationale: Retain distinct reported removal endpoints without mutualism, assigned flux or certified mineralization. + - node: GENIA DNA Composition and Ratio-Management Comparison + rationale: Retain DNA composition and the bounded daily-ratio intervention; qualify its existing removal arrow + as PARTIAL. + removed_node_decisions: [] + edges_before: + - source: GENIA Multipollutant Assembly + target: Liquid Multipollutant Degradation + description: 'The genome-informed community architecture yielded synergistic PFOS, atrazine, and lignin removal + in minimal medium. + + ' + - source: Community Stability During Degradation + target: Liquid Multipollutant Degradation + description: 'Persistence of the complete inoculated roster maintained the multispecies degradation network + during the pollutant-removal time course. + + ' + edges_after: + - source: GENIA DNA Composition and Ratio-Management Comparison + target: Reported GENIA Liquid Pollutant Removal + description: 'PARTIAL: Allowing composition to reorganize was associated with greater PFOS and atrazine removal + than daily equal-ratio dilution/remixing. This reported intervention supports a bounded community-management + effect, not selective proof that persistence or a particular cross-feeding network causes removal. Dilution/remixing + changes handling as well as ratios; the reported lignin difference was not significant at p<0.05.' + retained_edge_decisions: + - source: GENIA DNA Composition and Ratio-Management Comparison + target: Reported GENIA Liquid Pollutant Removal + rationale: 'PARTIAL: Allowing composition to reorganize was associated with greater PFOS and atrazine removal + than daily equal-ratio dilution/remixing. This reported intervention supports a bounded community-management + effect, not selective proof that persistence or a particular cross-feeding network causes removal. Dilution/remixing + changes handling as well as ratios; the reported lignin difference was not significant at p<0.05.' + removed_edge_decisions: + - source: GENIA Multipollutant Assembly + target: Liquid Multipollutant Degradation + rationale: Computational assembly is a workflow, not an experimentally isolated biological mediator of pollutant + removal. + references: + - PMID:42036878 + issues: + - 1466 + allowed_changed_fields: + - curation_history + - discussions + - ecological_interactions + curation_events_added: 1 + history_files: + - history/records/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom/2026-10-06T110349Z-codex-2abd02.yaml + source_review: + PMID:42036878: + cache: references_cache/PMID_42036878.txt + url: https://doi.org/10.1021/acs.est.6c01112 + scope: Complete cached primary main body, Methods, Results, Discussion and embedded captions read. Public + PMC browser path presented reCAPTCHA; no bypass. No figures, separate supplements or raw data independently + inspected. +- path: kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml + id: CommunityMech:000091 + original_sha256: f7791cb413836f0ac9e8b7624d661cad0a1e31ef5bee4d58b38b6b8506a62da9 + record_sha256: 8d1ef9c4d9c8b8b0f2c203a984747b02cfa32e10fe648d3fd5bf0a9548c8208f + status: needs_research + outcome: changed + review_file: reports/causal_graph_review/decisions/20261006-three-records-batch42.yaml + scope: Whole record and all original nodes/arrows assessed; source-access limits explicit. Non-graph fields preserved, + not certified. + summary: Retain the bounded Cv017/Cv026 diffusible reporter response without invented canonical strain endpoints.; + Retain nonpolar time-series observations, distinguishing polar bactobolin and live-cell counts from resolved + causal mediation. + renamed_nodes: {} + node_decisions: + - node: AHL Diffusion and Violacein Induction + rationale: Retain the bounded Cv017/Cv026 diffusible reporter response without invented canonical strain endpoints. + - node: Three-Member Exometabolite Time Series + rationale: Retain nonpolar time-series observations, distinguishing polar bactobolin and live-cell counts from + resolved causal mediation. + removed_node_decisions: + - node: Exometabolite-Mediated Interaction + rationale: Generic assay-platform capability, not a separate observed ecological interaction. + edges_before: [] + edges_after: [] + retained_edge_decisions: [] + removed_edge_decisions: [] + references: + - PMID:29152587 + issues: + - 1467 + allowed_changed_fields: + - curation_history + - discussions + - ecological_interactions + curation_events_added: 1 + history_files: + - history/records/GLBRC_Exometabolite_Transwell_SynCom/2026-10-06T110349Z-codex-80fddf.yaml + source_review: + PMID:29152587: + cache: references_cache/PMID_29152587.txt + url: https://journals.asm.org/doi/10.1128/msystems.00129-17 + scope: Complete cached primary main body and Methods, strain table text and embedded captions read using folded + text to avoid truncation. No figure images, separate supplements or raw spectra independently inspected. + unresolved_graph_structure: Existing-node corrections do not complete new causal structure. One-community Edison + dry run completed; specific credit authorization requested. Issue remains open. diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv index c6ccebe33..32caec1ee 100644 --- a/reports/causal_graph_review/inventory.tsv +++ b/reports/causal_graph_review/inventory.tsv @@ -173,9 +173,9 @@ kb/communities/FOS_Lactobacillus_MinimalCore_GutLiver_SynCom.yaml CommunityMech: kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml CommunityMech:000027 08e60d74c495dfee5ec77a2a8ed63da4da51b1ebe1adb527350591d0e5b6340b 4 1 82.5 reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml reviewed kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml CommunityMech:000457 e23f7534b2c596261fdb8f6a69225c64ee0fcc4b10b95eb27bfccc7a48e2b0fe 2 0 62.5 reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml reviewed kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml CommunityMech:000432 e6123414e5fb18492837dd471cc7a12496821032306fdb6a6fba9b938e7908fb 0 0 0.0 reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml needs_research -kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml CommunityMech:000449 c6b8a0d748ce7750e0435947e3a0b781a6d2387bca3dc85dcafbdee7c2059737 2 0 60.0 pending -kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml CommunityMech:000352 1daada660d8dad257e3a5b04d861665bb03bd631c598322ebdea22ff452fac3f 3 2 98.3 pending -kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml CommunityMech:000091 f7791cb413836f0ac9e8b7624d661cad0a1e31ef5bee4d58b38b6b8506a62da9 3 0 75.0 pending +kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml CommunityMech:000449 61c3e21e1a830b7d0b3e2d3ee2fc7bc17ecc1724aa79414c106e04312c63f468 2 0 60.0 reports/causal_graph_review/decisions/20261006-three-records-batch42.yaml needs_research +kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml CommunityMech:000352 72fcc1720a4bb6b3a0a464f98524ab2bbf999b2b73eaf71efa0fa98be433b9c3 3 1 78.3 reports/causal_graph_review/decisions/20261006-three-records-batch42.yaml reviewed +kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml CommunityMech:000091 8d1ef9c4d9c8b8b0f2c203a984747b02cfa32e10fe648d3fd5bf0a9548c8208f 2 0 70.0 reports/causal_graph_review/decisions/20261006-three-records-batch42.yaml needs_research kb/communities/GLBRC_Populus_Variovorax_SynCom28.yaml CommunityMech:000028 e6b9446f0f493eb1c8b2666dae051146e4375795c7d5bf51f485d09cb1e8170d 3 2 100.0 pending kb/communities/GLBRC_UFMP_Fermentation_Community.yaml CommunityMech:000029 da03a0180a9a75c6105755fe0f061f05964c258bf108a21ecd7ad11c4b14b755 3 2 100.0 pending kb/communities/GOM_Oil_Degrading_Consortium.yaml CommunityMech:000030 6b90550db3bc1cc1a75459278ec2541043eab31f177007facca1d41229489f2f 3 2 100.0 pending diff --git a/reports/causal_graph_review/reference-validator-correction-20261006-batch42.json b/reports/causal_graph_review/reference-validator-correction-20261006-batch42.json new file mode 100644 index 000000000..5f0c96ac4 --- /dev/null +++ b/reports/causal_graph_review/reference-validator-correction-20261006-batch42.json @@ -0,0 +1,657 @@ +{ + "baseline_head": "12c0771525564259d767ae1a98265d069a45d1e4", + "initial_failed_attempt": { + "base_commit": "12c0771525564259d767ae1a98265d069a45d1e4", + "scope": [ + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml" + ], + "reference_validator_version": "0.1.7", + "results": [ + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/initial-Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n", + "original_log_path": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema.log" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/initial-Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.log", + "log_sha256": "7acf7af78b98616f10115c9438ee198648374c715394e4f2471c8235c983701f", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch42/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv\n", + "original_log_path": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.log" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/initial-Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n", + "original_log_path": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms.log" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 1, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/initial-Fucoidan_Seven_Degrader_Combinatorial_SynCom-references.log", + "log_sha256": "7f1e7b50052a19851074e45c281a87b665d0c762147811e02ea2e28da5342a24", + "output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n", + "explained_output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n", + "original_log_path": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-references.log" + } + ], + "limitations": [ + "Three complete primary main bodies and Methods read, including text captions; no figure images, separate supplements or raw analytical data independently inspected. Fucoidan cached Table 2 selected rows are not original-spreadsheet verification.", + "Seven existing nodes retained, one generic platform node removed; one PARTIAL management-effect arrow retained and one workflow arrow removed. Three node renames. No new structure or provider spend.", + "Fucoidan and Transwell remain needs_research. Corrected existing graphs and gap discussions are not completed expansion; #1465/#1467 remain open.", + "Canonical taxonomy, prior history, original source caches and non-graph raw blocks preserved, not certified. GENIA evidence/non-graph follow-up #1468 remains open; Transwell assay/roster follow-up included in #1467.", + "V4 discussion resolved from publisher citation DOM; original cache rendering artifact preserved and explicitly disclosed, not recast as a biological alias.", + "Source-based self-adversarial review is not independent approval, protected merge or full-corpus completion. Reference-validator 0.1.7 performs zero effective checks for this schema; snippet matching is textual, not scientific validation.", + "Edison dry runs emitted a remote cost-map warning and used a local fallback; no API job or price estimate was supplied.", + "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate." + ] + }, + "baseline_reference_command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "baseline_reference_exit": 1, + "baseline_reference_output": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n", + "baseline_reference_log_sha256": "7f1e7b50052a19851074e45c281a87b665d0c762147811e02ea2e28da5342a24", + "original_taxonomy_unchanged": true, + "all_14_findings_match_supplement_sidecar": true, + "missing_snippets": [ + "isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1", + "Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader", + "isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1", + "Algibacter lectus AS40 | Flavo40 | F40 | degrader", + "isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1", + "Mariniflexile sp. AS56 | Flavo56 | F56 | degrader", + "isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1", + "Zobellia laminariae AS94 | Flavo94 | F94 | degrader", + "isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1", + "Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader", + "isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1", + "Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader", + "LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1", + "Lentimonas sp. CC4 | Verruco4 | V4 | degrader" + ], + "canary_command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "pytest", + "-q", + "tests/test_reference_validator_actually_validates.py" + ], + "canary_output": "..... [100%]\n5 passed in 14.74s\n", + "canary_exit": 0, + "cli": { + "path": "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/lib/python3.13/site-packages/linkml_reference_validator/cli/validate.py", + "sha256": "8435d1aed40c99e9dee763004776f90ddeee99439a6ec9b2dfc2e666ec783e63", + "counter_statement": "Total checks: {len(all_results)}", + "interpretation": "Number of validation issues, not number of executed checks." + }, + "fetcher": { + "path": "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/lib/python3.13/site-packages/linkml_reference_validator/etl/reference_fetcher.py", + "sha256": "4f3d6d590cb38886fb2849e59bfcf8fd019e05d0ef36387634cd8774c24b9728" + }, + "historical_candidate_files": { + "reports/causal_graph_review/adversarial-review-20261006-batch35.yaml": "2e8c17652af5c990e8600b5a935001b812414cde2f26fae7629c1e7601de7a49", + "reports/causal_graph_review/adversarial-review-20261006-batch32.yaml": "fb31af941ac34e88b7c749a987c6fef46ab8a95dc173b8ccbdd890e23ee1c279", + "reports/causal_graph_review/validation-20261006-batch34.json": "fb5c3b62db09d88c13fab9826a2b2de2a1b5115670bc6b73aaea458641e90d2f", + "reports/causal_graph_review/adversarial-review-20261006-batch36.yaml": "411a075ced01f0daaf59db828b6bfc2163a00d6d040ecae1328b5aee70b5452e", + "reports/causal_graph_review/adversarial-review-20261006-batch33.yaml": "bbc95a9fdbe89641db5ed5315e01160fea0aed3524a6252080b2aa806e81d4ae", + "reports/causal_graph_review/validation-20261006-batch32.json": "291e49842642eaf938ff287278ff0a357f89763d37bec60a86f237ffdf921d85", + "reports/causal_graph_review/validation-20261006-batch37.json": "1129fa733ce586e6dacbd7649137cd4b8ea9e70c62d8bb375c9a97daf150a307", + "reports/causal_graph_review/validation-20261006-batch33.json": "55f4a03646d10c6365106b420cd75a4a251cd132e870131ae22f3373c78cf451", + "reports/causal_graph_review/adversarial-review-20261006-batch31.yaml": "2c1e54bb636d8534313e280c6a19fdee4bedaa235c76d0e5ff5a17f71d573541", + "reports/causal_graph_review/adversarial-review-20261006-batch41.yaml": "44cef924e165c081ab6e25a0aff69791ff8ad15033822a94892da50942d92a37", + "reports/causal_graph_review/adversarial-review-20261006-batch40.yaml": "6753c3c652290b010a45e003d8baa2321127b6e338be8c49958a412b45fa96bf", + "reports/causal_graph_review/adversarial-review-20261006-batch37.yaml": "c1674f7ad8d33b6a7d903c022b21f51e026d6e9bd3d0a445d1520494e12c27ac", + "reports/causal_graph_review/validation-20261006-batch36.json": "74a51607a5d2de0fa98d7936dadcbee8753c112316fd5f3cf8bf77747f5e89fe", + "reports/causal_graph_review/validation-20261006-batch38.json": "5d5c892e1170e1d724f22ec71d239be6b950d88a9ae91a5600cb168f77d7397b", + "reports/causal_graph_review/validation-20261006-batch35.json": "dda3f91dfad6a28436e5fa4acd144e34f2e7064ab01c7f0742d2905a7fd58c24", + "reports/causal_graph_review/adversarial-review-20261006-batch39.yaml": "2a70cf9c4ecccac2139f0917993ee38f7bc17ee573b8d5314fc23f1559a17a92", + "reports/causal_graph_review/validation-20261006-batch39.json": "b0e176e0fff1e270ce36672da2f5f1292a34447d0250380885714516aa71ee2f", + "reports/causal_graph_review/validation-20261006-batch31.json": "0bc604d1282f6313908b213e41443a1a33044bfcc214fc67cac087aca74f0654", + "reports/causal_graph_review/validation-20261006-batch41.json": "3c1a052d101654b74167b7cd032fc501b8628bd1384fa60966e95e8b20f33cb9", + "reports/causal_graph_review/validation-20261006-batch40.json": "6861f3173971067c8a198c744e2ffa3eca5ffb5d78ff64fac8c28713ea293dc9", + "reports/causal_graph_review/adversarial-review-20261006-batch34.yaml": "3a44d2f69b8390801b62eb251ddd652ffd2f0804a1c02c193a159bec2b9eff20", + "reports/causal_graph_review/adversarial-review-20261006-batch38.yaml": "9b9be5ad62e42821f1503482f9a623174aaf62bc780c9bddb16e4b63dcb20323", + "reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml": "80329e3dcae2352d3b6937185835394e337f6405310643363b57b841588a62e0", + "reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml": "4f0a70fa0459dfeeb6c9871c54f2440b9067a4ee5037d80808c4c4be7a07dda6" + }, + "scan": "rg --no-ignore --hidden; candidate matches include quoted or correctly negated claims and require interpretation, not blanket error labeling.", + "limitations": "14 unchanged taxonomy failures are a real reference-CLI failure, not a pass. Supplement sidecar text matching is not independent inspection of original Table 2. Existing SupportingReference coverage gap #476 and selected-excerpt trust issue #1362 remain open.", + "issue": 1469, + "correction": "Historical claims that Total checks: 0 establishes zero executed checks or a no-op are withdrawn. The CLI counter counts reported issues. Passing canaries establish real EvidenceItem validation; SupportingReference coverage remains incomplete under #476. Historical raw outputs are preserved, not rerun or rewritten by this correction.", + "initial_attempt_json_sha256": "5ce2ef9341cb14872feb106d7e03609118c83ae381986df6067c9cccdee093a2", + "baseline_snippet_audit": { + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "output": "# 50 evidence snippets scanned across 1 files\n MATCH 35\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 15\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n\n# MISMATCH/WEAK detail\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter lectus AS40 | Flavo40 | F40 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Mariniflexile sp. AS56 | Flavo56 | F56 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Zobellia laminariae AS94 | Flavo94 | F94 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n", + "log_sha256": "153bd814f6e018df35b47ca7ebd961e235049fcc533a79749359635213824c0d", + "unchanged_counts": { + "MATCH": 35, + "MISMATCH": 15, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "NOCONTENT": 0 + }, + "explanation": "The same 14 taxonomy excerpts plus the identical V4 Table 2 discussion excerpt are absent from article-only source coverage. They are present in the separate supplemental cache; the original spreadsheet was not independently inspected. CLI exit 0 is not a zero-mismatch result." + }, + "second_failed_attempt": { + "base_commit": "12c0771525564259d767ae1a98265d069a45d1e4", + "scope": [ + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml" + ], + "reference_validator_version": "0.1.7", + "results": [ + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.log", + "log_sha256": "7acf7af78b98616f10115c9438ee198648374c715394e4f2471c8235c983701f", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch42/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 1, + "expected_exit_codes": [ + 1 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-references.log", + "log_sha256": "7f1e7b50052a19851074e45c281a87b665d0c762147811e02ea2e28da5342a24", + "output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n", + "explained_output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-snippets.log", + "log_sha256": "153bd814f6e018df35b47ca7ebd961e235049fcc533a79749359635213824c0d", + "output_tail": "# 50 evidence snippets scanned across 1 files\n MATCH 35\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 15\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n\n# MISMATCH/WEAK detail\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter lectus AS40 | Flavo40 | F40 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Mariniflexile sp. AS56 | Flavo56 | F56 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Zobellia laminariae AS94 | Flavo94 | F94 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n" + } + ], + "limitations": [ + "Three complete primary main bodies and Methods read, including text captions; no figure images, separate supplements or raw analytical data independently inspected. Fucoidan cached Table 2 selected rows are not original-spreadsheet verification.", + "Seven existing nodes retained, one generic platform node removed; one PARTIAL management-effect arrow retained and one workflow arrow removed. Three node renames. No new structure or provider spend.", + "Fucoidan and Transwell remain needs_research. Corrected existing graphs and gap discussions are not completed expansion; #1465/#1467 remain open.", + "Canonical taxonomy, prior history, original source caches and non-graph raw blocks preserved, not certified. GENIA evidence/non-graph follow-up #1468 remains open; Transwell assay/roster follow-up included in #1467.", + "V4 discussion resolved from publisher citation DOM; original cache rendering artifact preserved and explicitly disclosed, not recast as a biological alias.", + "Source-based self-adversarial review is not independent approval, protected merge or full-corpus completion. Reference-validator 0.1.7 reports issue counts as Total checks, not executed-check counts. Fucoidan has 14 unchanged supplementary-taxonomy findings; the other records must be evaluated separately. SupportingReference field discovery remains incomplete under issue 476. Snippet matching is textual, not scientific validation. Reporting correction is tracked by issue 1469.", + "Edison dry runs emitted a remote cost-map warning and used a local fallback; no API job or price estimate was supplied.", + "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate." + ], + "reference_cli_known_failure": "14 unchanged Fucoidan taxonomy snippets are present in the separate supplement sidecar, which the installed reference fetcher does not combine with article text. Baseline output exactly reproduced; this is not a clean pass." + }, + "second_failed_attempt_reason": "An overstrict batch-helper assertion required all snippets to MATCH. The 15 mismatches were then reproduced unchanged at the pre-edit baseline, not fixed by changing sources or weakening the repository auditor.", + "baseline_snippet_probe_preflight": "The first scratch probe lacked PYTHONPATH for the source checkout and exited before establishing a baseline. It was corrected to set the checkout src path; only the successful repeated output is used for comparison.", + "other_snippet_baselines": [ + { + "stem": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "baseline": { + "exit_code": 0, + "counts": { + "MATCH": 20, + "RENDERING": 9, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "output": "# 29 evidence snippets scanned across 1 files\n MATCH 20\n RENDERING 9\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 9 kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n", + "sha256": "812267826dad217d0d0603e1df7ff68f2079aa494aab10197e892a551e1d33b8" + }, + "current": { + "exit_code": 0, + "counts": { + "MATCH": 22, + "RENDERING": 9, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "output": "# 31 evidence snippets scanned across 1 files\n MATCH 22\n RENDERING 9\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 9 kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n", + "sha256": "e3d952810bc609e323eabfafd5da6310980f3555769db937925f5a8213bf9490" + } + }, + { + "stem": "GLBRC_Exometabolite_Transwell_SynCom", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "baseline": { + "exit_code": 0, + "counts": { + "MATCH": 10, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "output": "# 10 evidence snippets scanned across 1 files\n MATCH 10\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n", + "sha256": "1835af07ebf0373785ca2d25de18c6984a3cbcfdec0d2610f1d8437504408710" + }, + "current": { + "exit_code": 0, + "counts": { + "MATCH": 9, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "output": "# 9 evidence snippets scanned across 1 files\n MATCH 9\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n", + "sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358" + } + } + ], + "third_failed_attempt": { + "base_commit": "12c0771525564259d767ae1a98265d069a45d1e4", + "scope": [ + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml" + ], + "reference_validator_version": "0.1.7", + "results": [ + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.log", + "log_sha256": "7acf7af78b98616f10115c9438ee198648374c715394e4f2471c8235c983701f", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch42/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 1, + "expected_exit_codes": [ + 1 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-references.log", + "log_sha256": "7f1e7b50052a19851074e45c281a87b665d0c762147811e02ea2e28da5342a24", + "output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n", + "explained_output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-snippets.log", + "log_sha256": "153bd814f6e018df35b47ca7ebd961e235049fcc533a79749359635213824c0d", + "output_tail": "# 50 evidence snippets scanned across 1 files\n MATCH 35\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 15\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n\n# MISMATCH/WEAK detail\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter lectus AS40 | Flavo40 | F40 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Mariniflexile sp. AS56 | Flavo56 | F56 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Zobellia laminariae AS94 | Flavo94 | F94 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-rank.log", + "log_sha256": "2fa482c6cba4626844e5533485d6802c3edd4f0b39aae6334a666858c34b77ee", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000449\",\n \"name\": \"Fucoidan Seven-Degrader Combinatorial SynCom\",\n \"score\": 60.0,\n \"taxonomy\": 7,\n \"connected_taxa\": 7,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\"\n }\n]\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/Fucoidan_Seven_Degrader_Combinatorial_SynCom/2026-10-06T110348Z-codex-5b5854.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-history-0.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict.tsv", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict.log", + "log_sha256": "4c0b0535cc42134b6cc4a9f57b0cde08f392df803109fa79792bd6c87ba7dd9c", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch42/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict.tsv\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-references.log", + "log_sha256": "32ef19b2de79565be241fdf4c34b80bb1b1d688439d758113d6efdf53ba7fc84", + "output_tail": "Validating kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n", + "explained_output_tail": "Validating kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-snippets.log", + "log_sha256": "e3d952810bc609e323eabfafd5da6310980f3555769db937925f5a8213bf9490", + "output_tail": "# 31 evidence snippets scanned across 1 files\n MATCH 22\n RENDERING 9\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 9 kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n" + } + ], + "limitations": [ + "Three complete primary main bodies and Methods read, including text captions; no figure images, separate supplements or raw analytical data independently inspected. Fucoidan cached Table 2 selected rows are not original-spreadsheet verification.", + "Seven existing nodes retained, one generic platform node removed; one PARTIAL management-effect arrow retained and one workflow arrow removed. Three node renames. No new structure or provider spend.", + "Fucoidan and Transwell remain needs_research. Corrected existing graphs and gap discussions are not completed expansion; #1465/#1467 remain open.", + "Canonical taxonomy, prior history, original source caches and non-graph raw blocks preserved, not certified. GENIA evidence/non-graph follow-up #1468 remains open; Transwell assay/roster follow-up included in #1467.", + "V4 discussion resolved from publisher citation DOM; original cache rendering artifact preserved and explicitly disclosed, not recast as a biological alias.", + "Source-based self-adversarial review is not independent approval, protected merge or full-corpus completion. Reference-validator 0.1.7 reports issue counts as Total checks, not executed-check counts. Fucoidan has 14 unchanged supplementary-taxonomy findings; the other records must be evaluated separately. SupportingReference field discovery remains incomplete under issue 476. Snippet matching is textual, not scientific validation. Reporting correction is tracked by issue 1469.", + "Edison dry runs emitted a remote cost-map warning and used a local fallback; no API job or price estimate was supplied.", + "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate." + ], + "resume_note": "Existing command receipts reused only after command identity, exit status, log hash, record hashes and unchanged source-cache checks. Two earlier batch-helper failures are preserved in the correction receipt; baseline mismatches are explicitly retained.", + "reference_cli_known_failure": "14 unchanged Fucoidan taxonomy snippets are present in the separate supplement sidecar, which the installed reference fetcher does not combine with article text. Baseline output exactly reproduced; this is not a clean pass.", + "snippet_counts_by_record": { + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml": { + "MATCH": 35, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 15, + "NOCONTENT": 0 + } + }, + "snippet_audit_known_findings": "35 Fucoidan MATCH and 15 unchanged supplement-sidecar MISMATCH. Exact baseline output preserved; this is not an all-MATCH result." + }, + "third_failed_attempt_reason": "Batch helper incorrectly demanded all-MATCH for GENIA; baseline retained RENDERING classes are faithful punctuation/spacing variants, not new mismatches. Source quotes and repository auditor unchanged." +} diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json index fc4271c67..39a3a502b 100644 --- a/reports/causal_graph_review/summary.json +++ b/reports/causal_graph_review/summary.json @@ -2,14 +2,14 @@ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.", "semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.", "records": 460, - "nodes": 1469, - "edges": 687, + "nodes": 1468, + "edges": 686, "records_without_nodes": 8, "records_without_edges": 146, "review_status_counts": { - "needs_research": 10, - "pending": 288, - "reviewed": 162 + "needs_research": 12, + "pending": 285, + "reviewed": 163 }, "structural_defects": [], "network_audit": [ diff --git a/reports/causal_graph_review/validation-20261006-batch42.json b/reports/causal_graph_review/validation-20261006-batch42.json new file mode 100644 index 000000000..7232afe88 --- /dev/null +++ b/reports/causal_graph_review/validation-20261006-batch42.json @@ -0,0 +1,845 @@ +{ + "base_commit": "12c0771525564259d767ae1a98265d069a45d1e4", + "scope": [ + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml" + ], + "reference_validator_version": "0.1.7", + "results": [ + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.log", + "log_sha256": "7acf7af78b98616f10115c9438ee198648374c715394e4f2471c8235c983701f", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch42/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-strict.tsv\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 1, + "expected_exit_codes": [ + 1 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-references.log", + "log_sha256": "7f1e7b50052a19851074e45c281a87b665d0c762147811e02ea2e28da5342a24", + "output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n", + "explained_output_tail": "Validating kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (14):\n [ERROR] Text part not found as substring: 'isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1'\n Location: taxonomy[0].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader'\n Location: taxonomy[0].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1'\n Location: taxonomy[1].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Algibacter lectus AS40 | Flavo40 | F40 | degrader'\n Location: taxonomy[1].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1'\n Location: taxonomy[2].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Mariniflexile sp. AS56 | Flavo56 | F56 | degrader'\n Location: taxonomy[2].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1'\n Location: taxonomy[3].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Zobellia laminariae AS94 | Flavo94 | F94 | degrader'\n Location: taxonomy[3].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1'\n Location: taxonomy[4].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader'\n Location: taxonomy[4].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1'\n Location: taxonomy[5].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader'\n Location: taxonomy[5].evidence[2].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1'\n Location: taxonomy[6].evidence[1].snippet\n Reference: PMID:42649294\n [ERROR] Text part not found as substring: 'Lentimonas sp. CC4 | Verruco4 | V4 | degrader'\n Location: taxonomy[6].evidence[2].snippet\n Reference: PMID:42649294\n\nValidation Summary:\n Total checks: 14\n Issues found: 14\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-snippets.log", + "log_sha256": "153bd814f6e018df35b47ca7ebd961e235049fcc533a79749359635213824c0d", + "output_tail": "# 50 evidence snippets scanned across 1 files\n MATCH 35\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 15\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n\n# MISMATCH/WEAK detail\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Algibacter lectus AS40 | Flavo40 | F40 | degrader...\n [MISMATCH cov=0.07] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Mariniflexile sp. AS56 | Flavo56 | F56 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Zobellia laminariae AS94 | Flavo94 | F94 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1...\n [MISMATCH cov=0.04] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader...\n [MISMATCH cov=0.05] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n [MISMATCH cov=0.03] kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml PMID:42649294\n Lentimonas sp. CC4 | Verruco4 | V4 | degrader...\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-rank.log", + "log_sha256": "2fa482c6cba4626844e5533485d6802c3edd4f0b39aae6334a666858c34b77ee", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000449\",\n \"name\": \"Fucoidan Seven-Degrader Combinatorial SynCom\",\n \"score\": 60.0,\n \"taxonomy\": 7,\n \"connected_taxa\": 7,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\"\n }\n]\n" + }, + { + "check": "Fucoidan_Seven_Degrader_Combinatorial_SynCom-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/Fucoidan_Seven_Degrader_Combinatorial_SynCom/2026-10-06T110348Z-codex-5b5854.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/Fucoidan_Seven_Degrader_Combinatorial_SynCom-history-0.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict.tsv", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict.log", + "log_sha256": "4c0b0535cc42134b6cc4a9f57b0cde08f392df803109fa79792bd6c87ba7dd9c", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch42/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-strict.tsv\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-references.log", + "log_sha256": "32ef19b2de79565be241fdf4c34b80bb1b1d688439d758113d6efdf53ba7fc84", + "output_tail": "Validating kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n", + "explained_output_tail": "Validating kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-snippets.log", + "log_sha256": "e3d952810bc609e323eabfafd5da6310980f3555769db937925f5a8213bf9490", + "output_tail": "# 31 evidence snippets scanned across 1 files\n MATCH 22\n RENDERING 9\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 9 kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-rank.log", + "log_sha256": "b5ad6ab5704c03224351691e638479e11eeae25765b64a962124f9d92b527382", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000352\",\n \"name\": \"GENIA Nine-Member Multi-Pollutant Bioremediation SynCom\",\n \"score\": 78.3,\n \"taxonomy\": 9,\n \"connected_taxa\": 9,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml\"\n }\n]\n" + }, + { + "check": "GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom/2026-10-06T110349Z-codex-2abd02.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom-history-0.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "GLBRC_Exometabolite_Transwell_SynCom-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "GLBRC_Exometabolite_Transwell_SynCom-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-strict.tsv", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-strict.log", + "log_sha256": "3b749daea2c24e2d921c61513c47c54ec8d1bed1b6f40a3016e58f1c120eb8f6", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch42/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-strict.tsv\n" + }, + { + "check": "GLBRC_Exometabolite_Transwell_SynCom-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "GLBRC_Exometabolite_Transwell_SynCom-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-references.log", + "log_sha256": "2ca9ba7de08639725a2fb14eb8115562bbf1fd500329a675ba24affaf7654eb2", + "output_tail": "Validating kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n", + "explained_output_tail": "Validating kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n" + }, + { + "check": "GLBRC_Exometabolite_Transwell_SynCom-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-snippets.log", + "log_sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358", + "output_tail": "# 9 evidence snippets scanned across 1 files\n MATCH 9\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n" + }, + { + "check": "GLBRC_Exometabolite_Transwell_SynCom-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-rank.log", + "log_sha256": "ad533e188d176fcdcd427d7bb2281916f5e92129a455cef7b2c1c238008dc50e", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000091\",\n \"name\": \"GLBRC Exometabolite Transwell SynCom System\",\n \"score\": 70.0,\n \"taxonomy\": 1,\n \"connected_taxa\": 1,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 2,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\"\n ],\n \"path\": \"kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml\"\n }\n]\n" + }, + { + "check": "GLBRC_Exometabolite_Transwell_SynCom-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/GLBRC_Exometabolite_Transwell_SynCom/2026-10-06T110349Z-codex-80fddf.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/GLBRC_Exometabolite_Transwell_SynCom-history-0.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "inventory", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "reports/causal_graph_review/build_inventory.py" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/inventory.log", + "log_sha256": "31ad1d5132319d0c575d841dd32a7c382b90bb7d631bb1cbe9a964ba80d9c257", + "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1468,\n \"edges\": 686,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 146,\n \"review_status_counts\": {\n \"needs_research\": 12,\n \"pending\": 285,\n \"reviewed\": 163\n },\n \"structural_defects\": []\n}\n" + }, + { + "check": "network", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "communitymech.cli", + "audit-network", + "--json" + ], + "exit_code": 1, + "expected_exit_codes": [ + 1 + ], + "log": "/private/tmp/communitymech-batch42/network.log", + "log_sha256": "c035fe6ed0bbf90371ab58d6557716c51eea79ac628e204173d70075f9efaa26", + "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n" + }, + { + "check": "rank-all", + "command": [ + "just", + "rank-causal-graphs" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/rank-all.log", + "log_sha256": 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Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch42/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch42/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch42/docs/index.html\n" + }, + { + "check": "render-repeat", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "communitymech.render" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/render-repeat.log", + "log_sha256": "e4697b3ddb98ab1736e3dc4ba9351323deffeca876fde19f61f485008d7e6611", + "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch42/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch42/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch42/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch42/docs/index.html\n" + }, + { + "check": "connectivity-survey", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-c", + "import json,runpy; print(json.dumps(runpy.run_path(\"tests/test_community_level_connectivity_credit.py\")[\"_survey\"](),sort_keys=True))" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/connectivity-survey.log", + "log_sha256": "fb47676e0ec6945737e5aeeba11192e7b8ff073a9e93ce8809972a4316c7c565", + "output_tail": "{\"community_level_only\": 263, \"credited_solely_by_the_rule\": 1219, \"mixed\": 124, \"records\": 460, \"taxa\": 1494, \"with_community_level\": 387}\n" + }, + { + "check": "regressions", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "pytest", + "-q", + "tests/test_causal_review_batch10.py", + "tests/test_causal_review_batch11.py", + "tests/test_causal_review_batch12.py", + "tests/test_causal_review_batch13.py", + "tests/test_causal_review_batch14.py", + "tests/test_causal_review_batch15.py", + "tests/test_causal_review_batch16.py", + "tests/test_causal_review_batch17.py", + "tests/test_causal_review_batch18.py", + "tests/test_causal_review_batch19.py", + "tests/test_causal_review_batch20.py", + "tests/test_causal_review_batch21.py", + "tests/test_causal_review_batch22.py", + "tests/test_causal_review_batch23.py", + "tests/test_causal_review_batch24.py", + "tests/test_causal_review_batch25.py", + "tests/test_causal_review_batch27.py", + "tests/test_causal_review_batch28.py", + "tests/test_causal_review_batch29.py", + "tests/test_causal_review_batch30.py", + "tests/test_causal_review_batch31.py", + "tests/test_causal_review_batch32.py", + "tests/test_causal_review_batch33.py", + "tests/test_causal_review_batch34.py", + "tests/test_causal_review_batch35.py", + "tests/test_causal_review_batch36.py", + "tests/test_causal_review_batch37.py", + "tests/test_causal_review_batch38.py", + "tests/test_causal_review_batch39.py", + "tests/test_causal_review_batch40.py", + "tests/test_causal_review_batch41.py", + "tests/test_causal_review_batch42.py", + "tests/test_causal_review_batch5.py", + "tests/test_causal_review_batch6.py", + "tests/test_causal_review_batch7.py", + "tests/test_causal_review_batch8.py", + "tests/test_causal_review_batch9.py", + "tests/test_site_audit_fixes.py", + "tests/test_causal_review_inventory.py", + "tests/test_rank_causal_graph_readiness.py", + "tests/test_network_auditor.py", + "tests/test_participating_taxa.py", + "tests/test_causal_descriptions_are_published.py", + "tests/test_published_pages_name_real_records.py", + "tests/test_reference_validator_actually_validates.py", + "tests/test_snippet_audit_artefact_classes.py", + "tests/test_reference_error_annotation.py", + "tests/test_community_level_connectivity_credit.py", + 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[ 16%]\n........................................................................ [ 32%]\n........................................................................ [ 49%]\n........................................................................ [ 65%]\n........................................................................ [ 81%]\n........................................................................ [ 98%]\n........ [100%]\n440 passed in 203.92s (0:03:23)\n" + }, + { + "check": "black", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black", + "--check", + "tests/test_causal_review_batch42.py", + "tests/test_participating_taxa.py" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/black.log", + "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c", + "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n" + }, + { + "check": "ruff", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff", + "check", + "tests/test_causal_review_batch42.py", + "tests/test_participating_taxa.py" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/ruff.log", + "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18", + "output_tail": "All checks passed!\n" + }, + { + "check": "diff-check", + "command": [ + "git", + "diff", + "--check" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch42/diff-check.log", + "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", + "output_tail": "" + } + ], + "limitations": [ + "Three complete primary main bodies and Methods read, including text captions; no figure images, separate supplements or raw analytical data independently inspected. Fucoidan cached Table 2 selected rows are not original-spreadsheet verification.", + "Seven existing nodes retained, one generic platform node removed; one PARTIAL management-effect arrow retained and one workflow arrow removed. Three node renames. No new structure or provider spend.", + "Fucoidan and Transwell remain needs_research. Corrected existing graphs and gap discussions are not completed expansion; #1465/#1467 remain open.", + "Canonical taxonomy, prior history, original source caches and non-graph raw blocks preserved, not certified. GENIA evidence/non-graph follow-up #1468 remains open; Transwell assay/roster follow-up included in #1467.", + "V4 discussion resolved from publisher citation DOM; original cache rendering artifact preserved and explicitly disclosed, not recast as a biological alias.", + "Source-based self-adversarial review is not independent approval, protected merge or full-corpus completion. Reference-validator 0.1.7 reports issue counts as Total checks, not executed-check counts. Fucoidan has 14 unchanged supplementary-taxonomy findings; the other records must be evaluated separately. SupportingReference field discovery remains incomplete under issue 476. Snippet matching is textual, not scientific validation. Reporting correction is tracked by issue 1469.", + "Edison dry runs emitted a remote cost-map warning and used a local fallback; no API job or price estimate was supplied.", + "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.", + "The CLI Total checks counter counts reported issues, not executed checks. Fucoidan has 14 unchanged taxonomy failures against article-only text; all match its separate supplement sidecar. GENIA and Transwell report zero issues and exit 0. SupportingReference coverage remains incomplete under #476. See the committed correction receipt and #1469; no clean Fucoidan reference-CLI pass is claimed." + ], + "resume_note": "Existing command receipts reused after command identity, exit status, log hash, record hashes and unchanged source-cache checks. Three earlier batch-helper failures are preserved in the correction receipt, plus a scratch-probe PYTHONPATH correction. Baseline mismatches and rendering classes remain explicit; no repository auditor was weakened.", + "reference_cli_known_failure": "14 unchanged Fucoidan taxonomy snippets are present in the separate supplement sidecar, which the installed reference fetcher does not combine with article text. Baseline output exactly reproduced; this is not a clean pass.", + "snippet_counts_by_record": { + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml": { + "MATCH": 35, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 15, + "NOCONTENT": 0 + }, + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml": { + "MATCH": 22, + "RENDERING": 9, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml": { + "MATCH": 9, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + } + }, + "snippet_audit_known_findings": "35 Fucoidan MATCH and 15 unchanged supplement-sidecar MISMATCH. Exact baseline output preserved; this is not an all-MATCH result.", + "unchanged_raw_blocks": 45, + "unchanged_record_files": 457, + "unchanged_cache_files": 920, + "network_delta": { + "existing_findings_preserved": 33, + "new_disconnected": 0, + "added_findings": {}, + "rationale": "All baseline warnings exactly preserved; no invented graph links to suppress warnings." + }, + "render_determinism": true, + "published_description_coverage": { + "pages": 456, + "nodes": 1454, + "arrows": 678 + }, + "participant_census": { + "connectivity_before": { + "community_level_only": 263, + "credited_solely_by_the_rule": 1219, + "mixed": 124, + "records": 460, + "taxa": 1494, + "with_community_level": 387 + }, + "connectivity_after": { + "community_level_only": 263, + "credited_solely_by_the_rule": 1219, + "mixed": 124, + "records": 460, + "taxa": 1494, + "with_community_level": 387 + }, + "exact_change": "Two canonical panel rosters added: 187 to 189 registered records. Transwell retains unresolved Bacteria umbrella and needs_research. Connectivity census and numeric bounds unchanged; taxonomy preserved.", + "numeric_bounds_changed": false + }, + "corpus": { + "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.", + "records": 460, + "nodes": 1468, + "edges": 686, + "records_without_nodes": 8, + "records_without_edges": 146, + "review_status_counts": { + "needs_research": 12, + "pending": 285, + "reviewed": 163 + }, + "structural_defects": [] + }, + "tested_file_sha256": { + "reports/causal_graph_review/decisions/20261006-three-records-batch42.yaml": "c0b2c349054635e9d6993082265669faede9e45656a6ae48549c87df053df645", + "tests/test_causal_review_batch42.py": "fb13bd5f9bb330039a84669fcede705b037515ce4897fbcb562616e6eed1a6a3", + "tests/test_participating_taxa.py": "77a1f6e458a1ea58c2f00fc04d0d7f412944c75d9ef21920566e9873d89e475a", + "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml": "61c3e21e1a830b7d0b3e2d3ee2fc7bc17ecc1724aa79414c106e04312c63f468", + "kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml": "72fcc1720a4bb6b3a0a464f98524ab2bbf999b2b73eaf71efa0fa98be433b9c3", + "kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml": "8d1ef9c4d9c8b8b0f2c203a984747b02cfa32e10fe648d3fd5bf0a9548c8208f", + "reports/causal_graph_review/README.md": "6db1c56cc36836b694fa92b3929ba296e8a7173169246c1c25e65255e6da90ed", + "reports/causal_graph_review/reference-validator-correction-20261006-batch42.json": "9718d69ee2c5f87c174b3bc8e8bf170f483ffd1b32c9ccd789ff96e9c041f2ab" + }, + "status": "verified_one_completed_review_and_two_research_pending_graphs", + "reference_validator_caveat": "The CLI Total checks counter counts reported issues, not executed checks. Fucoidan has 14 unchanged taxonomy failures against article-only text; all match its separate supplement sidecar. GENIA and Transwell report zero issues and exit 0. SupportingReference coverage remains incomplete under #476. See the committed correction receipt and #1469; no clean Fucoidan reference-CLI pass is claimed.", + "pre_research_baseline": { + "base_commit": "12c0771525564259d767ae1a98265d069a45d1e4", + "base_tree": "d6664ec28961715038f08b1565bcbffc98383a50", + "research_worktree": "/private/tmp/communitymech-causal-batch41", + "checks": [ + { + "name": "rank", + "command": [ + "just", + "rank-causal-graphs" + ], + "exit_code": 0, + "expected_exit_code": 0, + "log": "/private/tmp/communitymech-batch42/baseline-rank.log", + "sha256": "ba634290f8566afd0cb1a1cc38bd0f1d35e125f96dd1a96eb84fb5d1ba5edf22", + "output_tail": "nol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate 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Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n" + }, + { + "name": "just-network", + "command": [ + "just", + "audit-network-json" + ], + "exit_code": 2, + "expected_exit_code": 2, + "log": "/private/tmp/communitymech-batch42/baseline-just-network.log", + "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff", + "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n" + }, + { + "name": "network", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "communitymech.cli", + "audit-network", + "--json" + ], + "exit_code": 1, + "expected_exit_code": 1, + "log": "/private/tmp/communitymech-batch42/baseline-network.log", + "sha256": "c035fe6ed0bbf90371ab58d6557716c51eea79ac628e204173d70075f9efaa26", + "output_tail": " DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n" + }, + { + "name": "downstream", + "command": [ + "rg", + "--no-ignore", + "--hidden", + "-n", + "downstream:", + "kb/communities", + "data/isolates", + "--glob", + "*.yaml" + ], + "exit_code": 0, + "expected_exit_code": 0, + "log": "/private/tmp/communitymech-batch42/baseline-downstream.log", + "sha256": "eb0e9f249a60e320342c1661391c850fb784051618df1580a1f0185d2b9c3649", + "output_tail": "unar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:285: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:324: downstream:\nkb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml:143: downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:311: downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:365: downstream:\nkb/communities/GOM_Oil_Degrading_Consortium.yaml:119: downstream:\nkb/communities/GOM_Oil_Degrading_Consortium.yaml:160: downstream:\nkb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:125: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:104: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:127: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:157: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:203: downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:247: downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:344: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:342: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:381: downstream:\nkb/communities/PMI_Variovorax_Thermotolerance_Collection.yaml:330: downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:120: downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:152: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:138: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:182: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:232: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:65: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:98: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:131: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:155: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:295: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\nkb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:336: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:281: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:401: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:199: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:267: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\n" + } + ] + }, + "edison_dryruns": [ + { + "community": "Fucoidan_Seven_Degrader_Combinatorial_SynCom", + "dryrun_meta_sha256": "d9430a62ac20a1a78c662337e4db37e9d1b0e10da5a3dda08c935506101ab37d", + "dryrun_meta": { + "slug": "Fucoidan_Seven_Degrader_Combinatorial_SynCom", + "community_path": "kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "community_id": "CommunityMech:000449", + "job": "LITERATURE", + "job_id": "job-futurehouse-paperqa3", + "label": "causal", + "template_path": "templates/community_causal_graph_research.md", + "template_vars": { + "community_name": "Fucoidan Seven-Degrader Combinatorial SynCom", + "community_id": "CommunityMech:000449", + "community_file": "Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml", + "community_slug": "Fucoidan_Seven_Degrader_Combinatorial_SynCom", + "community_category": "BIOTECHNOLOGY", + "ecological_state": "ENGINEERED", + "community_origin": "SYNTHETIC", + "description": "A defined seven-member marine bacterial SynCom assembled from the fucoidan degraders F12, F40, F56, F94, V25, V69, and V4 to quantify complementary fucose- and rare-sugar-monomer degradation of Fucus vesiculosus fucoidan. Sichert et al. constructed all 127 possible non-empty combinations of these degraders at equal OD600 in MBL medium with 0.2% fucoidan, measured total and monomer-specific degradation by liquid chromatography mass spectrometry, and resolved a functionally synergistic community landscape in which specialized degrader combinations reached up to 97.1% total degradation.", + "source_summary": "", + "environment_summary": "laboratory environment | ENVO:01001405 | The curated entity is a defined laboratory SynCom grown on purified brown-algal fucoidan in MBL medium.", + "taxonomy_summary": "Algibacter sp. AS12 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F12; rare-sugar specialist. | Algibacter lectus AS40 (Algibacter lectus) - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F40; rare-sugar specialist and member of the highest-degradation five-strain community. | Mariniflexile sp. AS56 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F56; generalist and member of the highest-degradation five-strain community. | Zobellia laminariae AS94 (Zobellia laminariae) - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F94; rare-sugar specialist and member of the highest-degradation five-strain community. | Luteolibacter sp. AS25 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member V25; fucose specialist. | Roseibacillus persicicus AS69 (Roseibacillus persicicus) - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member V69; generalist and member of the highest-degradation five-strain community. | Lentimonas sp. CC4 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member V4; fucose specialist and member of the highest-degradation five-strain community.", + "interaction_summary": "Complementary fucoidan monomer degradation - The SynCom's community-level degradation emerges from combining fucose specialists, rare-sugar specialists, and generalists whose enzyme repertoires unlock distinct fractions of the sulfated F. vesiculosus fucoidan substrate. | Seven-degrader synergistic function landscape - The complete non-empty panel of seven fucoidan degraders produced a smooth community-function landscape in which synergism remained common even among combinations approaching nearly complete degradation.", + "environmental_factor_summary": "", + "growth_media_summary": "MBL medium with 0.2% Fucus vesiculosus fucoidan - Seven-degrader combinations were inoculated at equal OD600 into MBL medium with 0.2% w/v Fucus vesiculosus fucoidan as the sole carbon source before five-day endpoint degradation analysis.", + "dataset_summary": "PRJNA996876 - https://www.ncbi.nlm.nih.gov/bioproject/PRJNA996876 | doi:10.6069/r2z3-7b10 - https://doi.org/10.6069/r2z3-7b10 | zenodo.19591477 - https://zenodo.org/records/19591477 | Nature article DOI - doi:10.1038/s41586-026-10980-z - https://doi.org/10.1038/s41586-026-10980-z | Sichert2025_Fucoidan GitHub workflow - EnvSysMicroLAB/Sichert2025_Fucoidan - https://github.com/EnvSysMicroLAB/Sichert2025_Fucoidan | Global ocean fucoidan-degrader GitHub analysis - tpriest0/Global_ocean_microbial_fucoidan_degrader_analysis - https://github.com/tpriest0/Global_ocean_microbial_fucoidan_degrader_analysis", + "evidence_summary": "PMID:42649294: To systematically evaluate synergistic interactions in fucoidan degradation, we constructed all 127 possible combinations of the seven degraders F12, F40, F56, F94, V25, V69 and V4, along with a no-cell negative control. (Names the seven strains and the complete non-empty combinatorial panel.) | PMID:42649294: Each community was assembled by mixing strains at equal optical density (OD600) at 0.01 each and inoculating into 1.8 ml of MBL medium supplemented with 0.2% (w/v) fucoidan from F. vesiculosus as the sole carbon source. (Supports the equal-OD inoculation strategy and the MBL plus F. vesiculosus fucoidan medium.) | PMID:42649294: Total degradation increased with community richness, ranging from 4% to a maximum of 97.1% in the 5-member community F40, F56, V69, F94 and V4 (Supports the measured upper end of the community-function landscape.) | PMID:42649294: The only exception was G88, which increased degradation when paired with V69, but acted as an exploiter when paired with V4 and V25. (Supports G88 as a context-dependent degrader that was not carried into the seven-degrader full-combinatorial design.) | PMID:42649294: To systematically evaluate synergistic interactions in fucoidan degradation, we constructed all 127 possible combinations of the seven degraders F12, F40, F56, F94, V25, V69 and V4 (Names the exact full-combinatorial panel, excluding G88 from the seven strains retained for the 127-community experiment.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F12 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1 (Supports the assembly accession for isolate_12.) | PMID:42649294: Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader (Maps isolate_12 to the F12 strain code and degrader role.) | PMID:42649294: F12, F40 and F94 are rare-sugar specialists. (Supports the rare-sugar specialist role of F12, F40, and F94.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F40 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1 (Supports the assembly accession for isolate_40.) | PMID:42649294: Algibacter lectus AS40 | Flavo40 | F40 | degrader (Maps isolate_40 to the F40 strain code and degrader role.) | PMID:42649294: F12, F40 and F94 are rare-sugar specialists. (Supports the rare-sugar specialist role of F12, F40, and F94.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F56 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1 (Supports the assembly accession for isolate_56.) | PMID:42649294: Mariniflexile sp. AS56 | Flavo56 | F56 | degrader (Maps isolate_56 to the F56 strain code and degrader role.) | PMID:42649294: V69 and F56 function as generalists (Supports the generalist role of F56 and V69.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F94 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1 (Supports the assembly accession for isolate_94.) | PMID:42649294: Zobellia laminariae AS94 | Flavo94 | F94 | degrader (Maps isolate_94 to the F94 strain code and degrader role.) | PMID:42649294: F12, F40 and F94 are rare-sugar specialists. (Supports the rare-sugar specialist role of F12, F40, and F94.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports V25 as the Luteolibacter fucoidan degrader.) | PMID:42649294: isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1 (Supports the assembly accession for isolate_25.) | PMID:42649294: Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader (Maps isolate_25 to the V25 strain code and degrader role.) | PMID:42649294: V4, V25 and G88 are fucose-specialists (Supports the fucose-specialist role of V4 and V25.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports V69 as the Roseibacillus fucoidan degrader.) | PMID:42649294: isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1 (Supports the assembly accession for isolate_69.) | PMID:42649294: Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader (Maps isolate_69 to the V69 strain code and degrader role.) | PMID:42649294: V69 and F56 function as generalists (Supports the generalist role of F56 and V69.) | PMID:42649294: To systematically evaluate synergistic interactions in fucoidan degradation, we constructed all 127 possible combinations of the seven degraders F12, F40, F56, F94, V25, V69 and V4 (Supports V4 as one of the seven full-combinatorial degrader members.) | PMID:42649294: LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1 (Supports the assembly accession for LCC_4.) | PMID:42649294: Lentimonas sp. CC4 | Verruco4 | V4 | degrader (Maps LCC_4 to the V4 strain code and degrader role.) | PMID:42649294: V4, V25 and G88 are fucose-specialists (Supports the fucose-specialist role of V4 and V25.) | PMID:42649294: V69 and F56 function as generalists, whereas V4, V25 and G88 are fucose-specialists and F12, F40 and F94 are rare-sugar specialists. (Supports division of the isolated degraders into fucose specialists, rare-sugar specialists, and generalists.) | PMID:42649294: access to complementary substrate fractions--rather than enzyme count--limits fucoidan degradation, such that complete breakdown emerges from interactions among metabolically complementary degraders. (Supports the source article's mechanism for community-level fucoidan breakdown.) | PMID:42649294: Total degradation increased with community richness, ranging from 4% to a maximum of 97.1% in the 5-member community F40, F56, V69, F94 and V4 (Supports the observed degradation range across the seven-member composition landscape.) | PMID:42649294: even when approaching near-complete degradation, 80% of interactions were still synergistic beyond what would be expected from simple resource partitioning (Supports persistence of synergism across high-degradation communities.) | PMID:42649294: Each community was assembled by mixing strains at equal optical density (OD600) at 0.01 each and inoculating into 1.8 ml of MBL medium supplemented with 0.2% (w/v) fucoidan from F. vesiculosus as the sole carbon source. (Supports medium identity, fucoidan concentration, inoculation OD, and working volume.) | PMID:42649294: Cultures were incubated for 5 days (n = 3 biological replicates), after which supernatants were collected for degradation analysis. (Supports the five-day triplicate endpoint for the combinatorial panel.) | PMID:42649294: Each community was assembled by mixing strains at equal optical density (OD600) at 0.01 each and inoculating into 1.8 ml of MBL medium (Supports batch assembly into 1.8 mL culture volumes.)" + }, + "query_chars": 15343, + "query": "# Microbial Community Causal-Graph Research Template\n\n## Target Community\n- **Community name:** Fucoidan Seven-Degrader Combinatorial SynCom\n- **Community id:** CommunityMech:000449\n- **Community file:** Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n- **Community category:** BIOTECHNOLOGY\n- **Ecological state:** ENGINEERED\n- **Community origin:** SYNTHETIC\n- **Environment:** laboratory environment | ENVO:01001405 | The curated entity is a defined laboratory SynCom grown on purified brown-algal fucoidan in MBL medium.\n- **Description:** A defined seven-member marine bacterial SynCom assembled from the fucoidan degraders F12, F40, F56, F94, V25, V69, and V4 to quantify complementary fucose- and rare-sugar-monomer degradation of Fucus vesiculosus fucoidan. Sichert et al. constructed all 127 possible non-empty combinations of these degraders at equal OD600 in MBL medium with 0.2% fucoidan, measured total and monomer-specific degradation by liquid chromatography mass spectrometry, and resolved a functionally synergistic community landscape in which specialized degrader combinations reached up to 97.1% total degradation.\n\n## Existing Record Context\n- **Taxa:** Algibacter sp. AS12 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F12; rare-sugar specialist. | Algibacter lectus AS40 (Algibacter lectus) - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F40; rare-sugar specialist and member of the highest-degradation five-strain community. | Mariniflexile sp. AS56 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F56; generalist and member of the highest-degradation five-strain community. | Zobellia laminariae AS94 (Zobellia laminariae) - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member F94; rare-sugar specialist and member of the highest-degradation five-strain community. | Luteolibacter sp. AS25 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member V25; fucose specialist. | Roseibacillus persicicus AS69 (Roseibacillus persicicus) - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member V69; generalist and member of the highest-degradation five-strain community. | Lentimonas sp. CC4 - PRIMARY_DEGRADER - Equal-OD seven-degrader SynCom member V4; fucose specialist and member of the highest-degradation five-strain community.\n- **Known ecological interactions:** Complementary fucoidan monomer degradation - The SynCom's community-level degradation emerges from combining fucose specialists, rare-sugar specialists, and generalists whose enzyme repertoires unlock distinct fractions of the sulfated F. vesiculosus fucoidan substrate. | Seven-degrader synergistic function landscape - The complete non-empty panel of seven fucoidan degraders produced a smooth community-function landscape in which synergism remained common even among combinations approaching nearly complete degradation.\n- **Environmental factors:** \n- **Growth media / culture conditions:** MBL medium with 0.2% Fucus vesiculosus fucoidan - Seven-degrader combinations were inoculated at equal OD600 into MBL medium with 0.2% w/v Fucus vesiculosus fucoidan as the sole carbon source before five-day endpoint degradation analysis.\n- **Associated datasets / resources:** PRJNA996876 - https://www.ncbi.nlm.nih.gov/bioproject/PRJNA996876 | doi:10.6069/r2z3-7b10 - https://doi.org/10.6069/r2z3-7b10 | zenodo.19591477 - https://zenodo.org/records/19591477 | Nature article DOI - doi:10.1038/s41586-026-10980-z - https://doi.org/10.1038/s41586-026-10980-z | Sichert2025_Fucoidan GitHub workflow - EnvSysMicroLAB/Sichert2025_Fucoidan - https://github.com/EnvSysMicroLAB/Sichert2025_Fucoidan | Global ocean fucoidan-degrader GitHub analysis - tpriest0/Global_ocean_microbial_fucoidan_degrader_analysis - https://github.com/tpriest0/Global_ocean_microbial_fucoidan_degrader_analysis\n- **Existing evidence:** PMID:42649294: To systematically evaluate synergistic interactions in fucoidan degradation, we constructed all 127 possible combinations of the seven degraders F12, F40, F56, F94, V25, V69 and V4, along with a no-cell negative control. (Names the seven strains and the complete non-empty combinatorial panel.) | PMID:42649294: Each community was assembled by mixing strains at equal optical density (OD600) at 0.01 each and inoculating into 1.8 ml of MBL medium supplemented with 0.2% (w/v) fucoidan from F. vesiculosus as the sole carbon source. (Supports the equal-OD inoculation strategy and the MBL plus F. vesiculosus fucoidan medium.) | PMID:42649294: Total degradation increased with community richness, ranging from 4% to a maximum of 97.1% in the 5-member community F40, F56, V69, F94 and V4 (Supports the measured upper end of the community-function landscape.) | PMID:42649294: The only exception was G88, which increased degradation when paired with V69, but acted as an exploiter when paired with V4 and V25. (Supports G88 as a context-dependent degrader that was not carried into the seven-degrader full-combinatorial design.) | PMID:42649294: To systematically evaluate synergistic interactions in fucoidan degradation, we constructed all 127 possible combinations of the seven degraders F12, F40, F56, F94, V25, V69 and V4 (Names the exact full-combinatorial panel, excluding G88 from the seven strains retained for the 127-community experiment.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F12 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_12 | 99.34 | 0.38 | high-quality draft | GCA_046736315.1 (Supports the assembly accession for isolate_12.) | PMID:42649294: Algibacter_B amylolyticus AS12 | Flavo12 | F12 | degrader (Maps isolate_12 to the F12 strain code and degrader role.) | PMID:42649294: F12, F40 and F94 are rare-sugar specialists. (Supports the rare-sugar specialist role of F12, F40, and F94.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F40 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_40 | 99.67 | 0.71 | high-quality draft | GCA_046736305.1 (Supports the assembly accession for isolate_40.) | PMID:42649294: Algibacter lectus AS40 | Flavo40 | F40 | degrader (Maps isolate_40 to the F40 strain code and degrader role.) | PMID:42649294: F12, F40 and F94 are rare-sugar specialists. (Supports the rare-sugar specialist role of F12, F40, and F94.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F56 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_56 | 99.67 | 1.96 | high-quality draft | GCA_046736295.1 (Supports the assembly accession for isolate_56.) | PMID:42649294: Mariniflexile sp. AS56 | Flavo56 | F56 | degrader (Maps isolate_56 to the F56 strain code and degrader role.) | PMID:42649294: V69 and F56 function as generalists (Supports the generalist role of F56 and V69.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports F94 as one of the Flavobacteriia fucoidan degraders.) | PMID:42649294: isolate_94 | 94.9 | 1.2 | high-quality draft | GCA_030553095.1 (Supports the assembly accession for isolate_94.) | PMID:42649294: Zobellia laminariae AS94 | Flavo94 | F94 | degrader (Maps isolate_94 to the F94 strain code and degrader role.) | PMID:42649294: F12, F40 and F94 are rare-sugar specialists. (Supports the rare-sugar specialist role of F12, F40, and F94.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports V25 as the Luteolibacter fucoidan degrader.) | PMID:42649294: isolate_25 | 99.86 | 1.7 | high-quality draft | GCA_046736275.1 (Supports the assembly accession for isolate_25.) | PMID:42649294: Luteolibacter UBA1315 sp. AS25 | Verruco25 | V25 | degrader (Maps isolate_25 to the V25 strain code and degrader role.) | PMID:42649294: V4, V25 and G88 are fucose-specialists (Supports the fucose-specialist role of V4 and V25.) | PMID:42649294: We isolated 5 exploiters, 16 scavengers and 7 degraders, namely V25 (Luteolibacter), V69 (Roseibacillus), G88 (Pseudocolwellia) and four members of the Flavobacteriia (F12, F40, F56 and F94). (Supports V69 as the Roseibacillus fucoidan degrader.) | PMID:42649294: isolate_69 | 100 | 0.57 | high-quality draft | GCA_046736285.1 (Supports the assembly accession for isolate_69.) | PMID:42649294: Roseibacillus_A persicicus AS69 | Verruco69 | V69 | degrader (Maps isolate_69 to the V69 strain code and degrader role.) | PMID:42649294: V69 and F56 function as generalists (Supports the generalist role of F56 and V69.) | PMID:42649294: To systematically evaluate synergistic interactions in fucoidan degradation, we constructed all 127 possible combinations of the seven degraders F12, F40, F56, F94, V25, V69 and V4 (Supports V4 as one of the seven full-combinatorial degrader members.) | PMID:42649294: LCC_4 | 99.32 | 2.03 | high-quality draft | GCA_902728235.1 (Supports the assembly accession for LCC_4.) | PMID:42649294: Lentimonas sp. CC4 | Verruco4 | V4 | degrader (Maps LCC_4 to the V4 strain code and degrader role.) | PMID:42649294: V4, V25 and G88 are fucose-specialists (Supports the fucose-specialist role of V4 and V25.) | PMID:42649294: V69 and F56 function as generalists, whereas V4, V25 and G88 are fucose-specialists and F12, F40 and F94 are rare-sugar specialists. (Supports division of the isolated degraders into fucose specialists, rare-sugar specialists, and generalists.) | PMID:42649294: access to complementary substrate fractions--rather than enzyme count--limits fucoidan degradation, such that complete breakdown emerges from interactions among metabolically complementary degraders. (Supports the source article's mechanism for community-level fucoidan breakdown.) | PMID:42649294: Total degradation increased with community richness, ranging from 4% to a maximum of 97.1% in the 5-member community F40, F56, V69, F94 and V4 (Supports the observed degradation range across the seven-member composition landscape.) | PMID:42649294: even when approaching near-complete degradation, 80% of interactions were still synergistic beyond what would be expected from simple resource partitioning (Supports persistence of synergism across high-degradation communities.) | PMID:42649294: Each community was assembled by mixing strains at equal optical density (OD600) at 0.01 each and inoculating into 1.8 ml of MBL medium supplemented with 0.2% (w/v) fucoidan from F. vesiculosus as the sole carbon source. (Supports medium identity, fucoidan concentration, inoculation OD, and working volume.) | PMID:42649294: Cultures were incubated for 5 days (n = 3 biological replicates), after which supernatants were collected for degradation analysis. (Supports the five-day triplicate endpoint for the combinatorial panel.) | PMID:42649294: Each community was assembled by mixing strains at equal optical density (OD600) at 0.01 each and inoculating into 1.8 ml of MBL medium (Supports batch assembly into 1.8 mL culture volumes.)\n\n## Research Objective\n\nBuild a source-backed **causal interaction graph** for the microbial community\n**Fucoidan Seven-Degrader Combinatorial SynCom**, suitable for the `ecological_interactions` block of\n`kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml`. The graph's **nodes are mechanistic\ninteractions** and its **directed edges are causal links** (\"interaction A\nenables / drives / suppresses interaction B\"). Extract only relationships the\nprimary literature supports; do not infer edges that are not stated or directly\nimplied by an experiment.\n\n## Required Findings\n\n### 1. Interaction nodes (the vertices)\n\nFor each mechanistic interaction, report as a table row:\n\n- **name** \u2014 a short, unique interaction name (used as the node id and as the\n `target` of any causal edge that points to it).\n- **interaction_type** \u2014 one of: MUTUALISM, COMMENSALISM, CROSS_FEEDING,\n COMPETITION, PREDATION, SYNTROPHY, NICHE_PARTITIONING, STRAIN_COMPETITION,\n COLONIZATION_FACILITATION (or state \"OTHER: