"The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock"
@@ -648,13 +640,20 @@ "hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs"
@@ -732,11 +721,17 @@ In Horonobe communities farther from the tunnels, abundant Syntrophobacterales are predicted to be autotrophic sulfate reducers that may produce H2 supporting methanogenesis by abundant Methanospirillum, linking the shared hydrogen and sulfate functional core to Horonobe-biased methane metabolism.
+ PARTIAL - in Horonobe samples farther from tunnels, the authors propose that putative autotrophic sulfate-reducing Syntrophobacterales may produce hydrogen supporting Methanospirillum methanogenesis. Genomic capacities and community profiles motivate this model, without directly measuring partner-resolved hydrogen transfer, necessity or simultaneous sulfate reduction and hydrogen export. The canonical Horonobe community placeholder does not resolve those partners as individual grounded taxa.
+ "predicted to be autotrophic sulfate-reducers that may also produce H2, supporting methanogenesis by abundant Methanospirillum"
@@ -800,7 +795,7 @@ "near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL"
@@ -862,7 +862,7 @@ "the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period"
@@ -875,7 +875,7 @@ Desulfosporosinus sp. MAG003 and possibly other early enrichment members initiated sulfate reduction at roughly pH 3.0 with glycerol as the supplied carbon and electron source, producing acetate that could inhibit cells unless consumed by a downstream partner.
+ PARTIAL - the authors propose Desulfosporosinus sp. MAG003 as an initiator of glycerol-associated sulfate reduction and acetate production near pH 3. Bulk chemistry and taxon profiles support this model, but both dominant MAGs encode glycerol-to-acetate potential and do not establish exclusive MAG003 flux. The canonical participant remains MAG003 for this proposed initiating role; possible minor acidogens remain unresolved. Inoculum was added again on days 32 and 86, so the time course is not unassisted succession.
@@ -698,7 +698,7 @@ "Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product."
@@ -727,7 +727,7 @@ "While genes coding for glycerol, pyruvate, and acetyl-CoA oxidation (from glycerol to acetate) were found in both MAGs"
@@ -743,7 +743,7 @@ Once pH increased to about 4.0, Acididesulfobacillus sp. MAG013 was inferred to oxidize acetate fully to CO2 while continuing sulfate reduction, creating a carbon-flow network that removed acetate and limited organic-acid toxicity in the acidic enrichment.
+ PARTIAL - the authors propose that Acididesulfobacillus sp. MAG013 consumes acetate while reducing sulfate after pH rises toward 4. TCA-cycle annotations support a potential acetate-oxidation route, not measured MAG013-specific carbon dioxide flux, an exclusive substrate role or a selectively established pH threshold. Acetate removal could relieve organic-acid stress, but toxicity mediation and complete carbon mineralization were not demonstrated; residual acetate remained at day 160.
@@ -806,7 +806,7 @@ "Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source"
@@ -819,7 +819,7 @@ "genes for the TCA cycle (from acetate to CO2) were mainly found in Acididesulfobacillus-MAG"
@@ -871,7 +871,7 @@
-
The partner-specific proteomic shifts and reduced functional overlap were frequently associated with increased productivity across the gut-derived isolate, pairwise, and four-member community experiments.
+
Lower annotated functional overlap was associated with higher community productivity across the analyzed communities. Methods define productivity using total consortium qPCR abundance divided by mean monoculture abundance, not the sum or best monoculture. qPCR gene-copy abundance is not direct viable-cell biomass, and greater community yield does not demonstrate reciprocal benefit to every member. The pooled association was not a simple linear dose-response and does not establish that reduced overlap caused productivity.
+
+
Participating Taxa:
+
+ Eubacterium hallii,
+
+ Roseburia intestinalis,
+
+ Marvinbryantia formatexigens,
+
+ Faecalibacterium prausnitzii
+
+
@@ -843,6 +869,25 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Does altered proteome overlap cause higher community productivity?
+
+
The positive controlled proteomic responses and overlap metric are distinct from proposed niche partitioning and resource savings. Competition and coexistence were not directly measured. Protein coverage thresholds and abundance-matched mixed-isolate controls matter; all four canonical human taxa are not guaranteed detectable in every comparison. Preserve carbon effects, separate pooled human/rumen statistics from exact human conditions, and use the Methods mean-monoculture denominator. Pathway or regulatory perturbations, resource budgets and flux measurements would test the two retained PARTIAL arrows; no organism-level mutualism or specific butyrate/formate/acetate exchange is demonstrated. Non-graph strain, medium and capability metadata is preserved, not recertified.
+
+
Attaches to: ecological_interactions#Partner-Specific Proteome Remodelling, ecological_interactions#Reduced Annotated Proteomic Functional Overlap, ecological_interactions#Community qPCR Productivity Association
+
+
+
+
+
@@ -1216,7 +1261,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1240,11 +1285,28 @@
Evidence
+ var participantKeys = [
+
+ "Eubacterium hallii",
+
+ "Roseburia intestinalis",
+
+ "Marvinbryantia formatexigens",
+
+ "Faecalibacterium prausnitzii"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:1";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1261,7 +1323,7 @@
Evidence
nodes.push({
id: intId,
- label: "Reduced Functional Overlap and Metabolic Complementarity",
+ label: "Reduced Annotated Proteomic Functional Overlap",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1272,11 +1334,28 @@
Evidence
+ var participantKeys = [
+
+ "Eubacterium hallii",
+
+ "Roseburia intestinalis",
+
+ "Marvinbryantia formatexigens",
+
+ "Faecalibacterium prausnitzii"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1289,7 +1368,7 @@
Evidence
nodes.push({
id: intId,
- label: "Increased Community Productivity",
+ label: "Community qPCR Productivity Association",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1300,6 +1379,23 @@
Evidence
+ var participantKeys = [
+
+ "Eubacterium hallii",
+
+ "Roseburia intestinalis",
+
+ "Marvinbryantia formatexigens",
+
+ "Faecalibacterium prausnitzii"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/history/records/Horonobe_Mizunami_URL_Subsurface_Microbiome/2026-10-06T153824Z-codex-7a4424.yaml b/history/records/Horonobe_Mizunami_URL_Subsurface_Microbiome/2026-10-06T153824Z-codex-7a4424.yaml
new file mode 100644
index 000000000..d367736c3
--- /dev/null
+++ b/history/records/Horonobe_Mizunami_URL_Subsurface_Microbiome/2026-10-06T153824Z-codex-7a4424.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml
+ slug: Horonobe_Mizunami_URL_Subsurface_Microbiome
+session:
+ id: 2026-10-06T153824Z-codex-7a4424
+ timestamp: '2026-10-06T15:38:24Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1501
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Bound URL genomic functions and remove two contextual arrows.
+ details: Source-based self-adversarial existing-graph repair. reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
diff --git a/history/records/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium/2026-10-06T153824Z-codex-bb95e3.yaml b/history/records/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium/2026-10-06T153824Z-codex-bb95e3.yaml
new file mode 100644
index 000000000..1148286ad
--- /dev/null
+++ b/history/records/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium/2026-10-06T153824Z-codex-bb95e3.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml
+ slug: Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium
+session:
+ id: 2026-10-06T153824Z-codex-bb95e3
+ timestamp: '2026-10-06T15:38:24Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1502
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Qualify MAG-specific carbon flow; retain unresolved remediation outcome extension.
+ details: Source-based self-adversarial existing-graph repair. reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
diff --git a/history/records/Human_Gut_FourMember_Proteome_Complementarity_Consortium/2026-10-06T153825Z-codex-97b741.yaml b/history/records/Human_Gut_FourMember_Proteome_Complementarity_Consortium/2026-10-06T153825Z-codex-97b741.yaml
new file mode 100644
index 000000000..57e329826
--- /dev/null
+++ b/history/records/Human_Gut_FourMember_Proteome_Complementarity_Consortium/2026-10-06T153825Z-codex-97b741.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml
+ slug: Human_Gut_FourMember_Proteome_Complementarity_Consortium
+session:
+ id: 2026-10-06T153825Z-codex-97b741
+ timestamp: '2026-10-06T15:38:25Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1503
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Separate measured proteomic overlap and qPCR yield from proposed mediation.
+ details: Source-based self-adversarial existing-graph repair. reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
diff --git a/kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml b/kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml
index 1e7148d06..d0d51b541 100644
--- a/kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml
+++ b/kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml
@@ -65,11 +65,12 @@ taxonomy:
explanation: Supports the Mizunami granitic URL community and CPR selection
at high-flow zones.
ecological_interactions:
-- name: Lithology-Driven Community Divergence
- description: Sedimentary versus granitic host rock yields dissimilar URL
- microbiomes despite shared deep-subsurface chemistry, indicating lithology
- as a primary structuring factor.
- interaction_type: NICHE_PARTITIONING
+- name: Site-Associated URL Community Divergence
+ description: Groundwater metagenomes distinguish the sedimentary Horonobe and granitic Mizunami microbiomes. Host
+ rock, location, groundwater chemistry and tunnel/flow context covary, so the comparison supports a site-associated
+ pattern and a proposed lithological explanation, not an isolated lithology effect or demonstrated competitive
+ niche partitioning. The two canonical habitat-level participants share a broad cellular-organisms CURIE but
+ denote different sampled communities.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: methane
@@ -80,24 +81,28 @@ ecological_interactions:
term:
id: CHEBI:16526
label: carbon dioxide
- downstream:
- - target: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
- description: The sedimentary Horonobe URL is organic- and CO2-rich and
- methane-biased, providing the geochemical context for sulfate reducers
- predicted to produce H2 that supports methanogenesis.
evidence:
- reference: PMID:39696556
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: The Horonobe and Mizunami microbiomes are dissimilar, likely because
- the Mizunami URL is hosted in granitic rock and the Horonobe URL in
- sedimentary rock
- explanation: Supports lithology as the divergence driver.
-- name: Shared Deep-Subsurface Functional Core
- description: Despite community-level dissimilarity, both URLs share well-
- represented hydrogen metabolism, rubisco-based CO2 fixation, nitrogen
- reduction, and sulfate reduction functions.
- interaction_type: CROSS_FEEDING
+ evidence_source: COMPUTATIONAL
+ snippet: The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in
+ granitic rock and the Horonobe URL in sedimentary rock
+ explanation: Supports distinct microbiomes and the authors' likely lithological explanation, not a selectively
+ established driver.
+ participating_taxa:
+ - preferred_term: Horonobe sedimentary URL groundwater microbiome
+ term:
+ id: NCBITaxon:131567
+ label: cellular organisms
+ - preferred_term: Mizunami granitic URL groundwater microbiome
+ term:
+ id: NCBITaxon:131567
+ label: cellular organisms
+- name: Shared Deep-Subsurface Genomic Functional Potential
+ description: Genome marker annotations in both URLs support widespread coding potential for hydrogen metabolism,
+ Rubisco-based carbon fixation, nitrogen reduction and sulfate reduction. The positive genomic result is not
+ measurement of pathway expression, biogeochemical flux, or exchange between every organism carrying those genes.
+ A functional repertoire is not itself cross-feeding.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: dihydrogen
@@ -121,25 +126,28 @@ ecological_interactions:
term:
id: GO:0019420
label: dissimilatory sulfate reduction
- downstream:
- - target: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
- description: Hydrogen metabolism and sulfate reduction are represented in
- both URLs and include Horonobe Syntrophobacterales predicted to produce
- H2 while reducing sulfate, feeding abundant Methanospirillum.
evidence:
- reference: PMID:39696556
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: hydrogen metabolism, rubisco-based CO2 fixation, reduction of
- nitrogen compounds and sulfate reduction are well represented functions
- in microbiomes from both URLs
- explanation: Supports the shared deep-subsurface functional repertoire.
+ evidence_source: COMPUTATIONAL
+ snippet: hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction
+ are well represented functions in microbiomes from both URLs
+ explanation: Supports the genomic functional repertoire, not direct activity or interspecies transfer.
+ participating_taxa:
+ - preferred_term: Horonobe sedimentary URL groundwater microbiome
+ term:
+ id: NCBITaxon:131567
+ label: cellular organisms
+ - preferred_term: Mizunami granitic URL groundwater microbiome
+ term:
+ id: NCBITaxon:131567
+ label: cellular organisms
- name: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
- description: In Horonobe communities farther from the tunnels, abundant
- Syntrophobacterales are predicted to be autotrophic sulfate reducers that
- may produce H2 supporting methanogenesis by abundant Methanospirillum,
- linking the shared hydrogen and sulfate functional core to Horonobe-biased
- methane metabolism.
+ description: PARTIAL - in Horonobe samples farther from tunnels, the authors propose that putative autotrophic
+ sulfate-reducing Syntrophobacterales may produce hydrogen supporting Methanospirillum methanogenesis. Genomic
+ capacities and community profiles motivate this model, without directly measuring partner-resolved hydrogen
+ transfer, necessity or simultaneous sulfate reduction and hydrogen export. The canonical Horonobe community
+ placeholder does not resolve those partners as individual grounded taxa.
interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
metabolites:
@@ -166,24 +174,29 @@ ecological_interactions:
label: methanogenesis
evidence:
- reference: PMID:39696556
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: predicted to be autotrophic sulfate-reducers that may also produce H2,
- supporting methanogenesis by abundant Methanospirillum
- explanation: Supports predicted hydrogen transfer from Horonobe sulfate
- reducers to methanogens.
+ snippet: predicted to be autotrophic sulfate-reducers that may also produce H2, supporting methanogenesis by
+ abundant Methanospirillum
+ explanation: Supports the proposed Horonobe hydrogen-transfer model or its genomic context, not measured partner-resolved
+ exchange.
- reference: PMID:39696556
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL
- explanation: Supports the Horonobe-specific methane-metabolism context for
- the predicted sulfate-reducer to methanogen coupling.
+ explanation: Supports the proposed Horonobe hydrogen-transfer model or its genomic context, not measured partner-resolved
+ exchange.
+ participating_taxa:
+ - preferred_term: Horonobe sedimentary URL groundwater microbiome
+ term:
+ id: NCBITaxon:131567
+ label: cellular organisms
- name: Genotypic Homogeneity Across Depths in Horonobe
- description: Near-identical genotypes for approximately one third of detected
- organisms recur at multiple Horonobe depths with detectable but slow in
- situ growth, suggesting historical dispersal under different hydrological
- regimes.
- interaction_type: COLONIZATION_FACILITATION
+ description: Near-identical genotypes recur across Horonobe depths for approximately one third of genomically
+ defined organisms. Coverage-qualified iRep estimates for a subset support replication, not direct absolute growth
+ rates for all taxa. Historical groundwater mobility is a proposed explanation for present genotype similarity;
+ the data do not directly establish migration, colonization facilitation or mutation rates, and current low conductivity
+ and heterogeneous chemistry argue against assuming ongoing intersite dispersal.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: growth
@@ -193,22 +206,27 @@ ecological_interactions:
evidence:
- reference: PMID:39696556
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: near-identical genotypes for approximately one third of all
- genomically defined organisms at multiple depths within the Horonobe URL
- explanation: Supports cross-depth genotypic homogeneity.
+ evidence_source: COMPUTATIONAL
+ snippet: near-identical genotypes for approximately one third of all genomically defined organisms at multiple
+ depths within the Horonobe URL
+ explanation: Supports the sequence-based cross-depth similarity observation.
- reference: PMID:39696556
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: the Horonobe URL microbiome homogeneity may be explained by higher
- groundwater mobility during the last glacial period
- explanation: Supports paleo-hydrological dispersal as the proposed mechanism.
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the
+ last glacial period
+ explanation: Supports a proposed prior hydrological explanation, not observed historical transport.
- reference: PMID:39696556
supports: SUPPORT
- evidence_source: IN_VIVO
+ evidence_source: COMPUTATIONAL
snippet: in situ growth was detected for some bacteria, albeit at slow rates
- explanation: Supports slow ongoing growth by Horonobe genotypes despite
- their cross-depth genomic similarity.
+ explanation: Supports the authors' replication inference from a coverage-qualified iRep subset, not direct absolute
+ growth-rate measurements.
+ participating_taxa:
+ - preferred_term: Horonobe sedimentary URL groundwater microbiome
+ term:
+ id: NCBITaxon:131567
+ label: cellular organisms
environmental_factors:
- name: Depth interval
value: 140 to 400 m below surface
@@ -273,3 +291,28 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth element processing role is curated for this
deep-subsurface groundwater microbiome.
+discussions:
+- discussion_id: url_function_and_dispersal_limits
+ prompt: Which processes connect URL genomic potential to activity and dispersal?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Site-Associated URL Community Divergence
+ - ecological_interactions#Shared Deep-Subsurface Genomic Functional Potential
+ - ecological_interactions#Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
+ - ecological_interactions#Genotypic Homogeneity Across Depths in Horonobe
+ rationale: 'Remove both overview-to-hydrogen arrows: contrasting sites provides context, and membership of a shared
+ functional repertoire provides inclusion, neither an experimentally resolved upstream cause of the proposed
+ transfer. Expression, isotope/flux measurements and partner perturbations would test the retained hydrogen hypothesis.
+ Distinct rpS3 and genome-ANI species definitions yield different overlap counts and must not be conflated. Broad
+ habitat placeholders are not organism-resolved donor/recipient groundings. Methanoperedens iron-coupling, tunnel-associated
+ mobilization and historical dispersal are additional proposals, not newly demonstrated branches or an exhaustive
+ mechanism expansion. Non-graph metadata is preserved, not recertified.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T15:38:23Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Bound URL genomic functions and remove two contextual arrows. Issue #1501; reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml b/kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml
index 2ed418cbb..b2e776f31 100644
--- a/kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml
+++ b/kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml
@@ -172,11 +172,11 @@ taxonomy:
oxidizer in the AMD enrichment.
ecological_interactions:
- name: Glycerol-to-Acetate Sulfate Reduction
- description: >-
- Desulfosporosinus sp. MAG003 and possibly other early enrichment members
- initiated sulfate reduction at roughly pH 3.0 with glycerol as the supplied
- carbon and electron source, producing acetate that could inhibit cells
- unless consumed by a downstream partner.
+ description: PARTIAL - the authors propose Desulfosporosinus sp. MAG003 as an initiator of glycerol-associated
+ sulfate reduction and acetate production near pH 3. Bulk chemistry and taxon profiles support this model, but
+ both dominant MAGs encode glycerol-to-acetate potential and do not establish exclusive MAG003 flux. The canonical
+ participant remains MAG003 for this proposed initiating role; possible minor acidogens remain unresolved. Inoculum
+ was added again on days 32 and 86, so the time course is not unassisted succession.
interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
participating_taxa:
@@ -209,34 +209,31 @@ ecological_interactions:
label: dissimilatory sulfate reduction
downstream:
- target: Acetate-Fed Acididesulfobacillus Sulfate Reduction
- description: >-
- Acididesulfobacillus sp. MAG013 is inferred to consume acetate produced
- during glycerol oxidation after the consortium raises the pH.
+ description: PARTIAL - proposed glycerol oxidation can supply acetate to the later MAG013-associated sulfate-reducing
+ route as the medium becomes less acidic. Bulk chemistry and genomes support the model, but do not resolve
+ the exact donor-to-recipient flux, demonstrate acetate-toxicity rescue or isolate pH from reinoculation and
+ other time-varying conditions.
evidence:
- reference: PMID:42029028
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: >-
- Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol
- as the carbon source and acetate as the waste product.
- explanation: >-
- Supports the first inferred phase of sulfate reduction and acetate
- production from glycerol.
+ snippet: Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate
+ as the waste product.
+ explanation: Supports the authors' organism-level metabolic model from genomic potential and bulk observations,
+ not direct MAG-specific activity or a selectively established pH requirement.
- reference: PMID:42029028
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: >-
- While genes coding for glycerol, pyruvate, and acetyl-CoA oxidation (from
- glycerol to acetate) were found in both MAGs
- explanation: >-
- Supports genomic capacity for glycerol oxidation to acetate in the two
- dominant sulfate-reducing MAGs.
+ snippet: While genes coding for glycerol, pyruvate, and acetyl-CoA oxidation (from glycerol to acetate) were
+ found in both MAGs
+ explanation: Supports the authors' organism-level metabolic model from genomic potential and bulk observations,
+ not direct MAG-specific activity or a selectively established pH requirement.
- name: Acetate-Fed Acididesulfobacillus Sulfate Reduction
- description: >-
- Once pH increased to about 4.0, Acididesulfobacillus sp. MAG013 was
- inferred to oxidize acetate fully to CO2 while continuing sulfate reduction,
- creating a carbon-flow network that removed acetate and limited organic-acid
- toxicity in the acidic enrichment.
+ description: PARTIAL - the authors propose that Acididesulfobacillus sp. MAG013 consumes acetate while reducing
+ sulfate after pH rises toward 4. TCA-cycle annotations support a potential acetate-oxidation route, not measured
+ MAG013-specific carbon dioxide flux, an exclusive substrate role or a selectively established pH threshold.
+ Acetate removal could relieve organic-acid stress, but toxicity mediation and complete carbon mineralization
+ were not demonstrated; residual acetate remained at day 160.
interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
participating_taxa:
@@ -272,23 +269,18 @@ ecological_interactions:
label: dissimilatory sulfate reduction
evidence:
- reference: PMID:42029028
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: >-
- Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate
- reduction with acetate as a carbon source
- explanation: >-
- Supports the second inferred sulfate-reduction phase in which
- Acididesulfobacillus used acetate after pH rose.
+ snippet: Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon
+ source
+ explanation: Supports the authors' organism-level metabolic model from genomic potential and bulk observations,
+ not direct MAG-specific activity or a selectively established pH requirement.
- reference: PMID:42029028
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: >-
- genes for the TCA cycle (from acetate to CO2) were mainly found in
- Acididesulfobacillus-MAG
- explanation: >-
- Supports the genome-based inference that Acididesulfobacillus oxidized
- acetate to CO2.
+ snippet: genes for the TCA cycle (from acetate to CO2) were mainly found in Acididesulfobacillus-MAG
+ explanation: Supports the authors' organism-level metabolic model from genomic potential and bulk observations,
+ not direct MAG-specific activity or a selectively established pH requirement.
environmental_factors:
- name: Synthetic AMD acidity and sulfate
value: pH 2.9; 50.53 mM sulfate
@@ -612,17 +604,39 @@ external_resources:
explanation: Identifies the seed publication for the curated community.
discussions:
- discussion_id: HUALGAYOC_MINOR_ACIDOGENS
- prompt: >-
- Stage-1 Negativicutes and Clostridiaceae may have fermented glycerol to
- acetate before sulfate reduction became active, but they were not resolved
- as named MAG members in the source; this record therefore keeps the
- high-quality aSRB MAGs as members and treats the minor fermenters as an
- open compositional detail.
+ prompt: Stage-1 Negativicutes and Clostridiaceae may have fermented glycerol to acetate before sulfate reduction
+ became active, but they were not resolved as named MAG members in the source; this record therefore keeps the
+ high-quality aSRB MAGs as members and treats the minor fermenters as an open compositional detail.
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- taxonomy
- rationale: >-
- Resolving the acidogenic fermenters with MAGs would clarify how much of the
- early glycerol-to-acetate flux was performed by Desulfosporosinus versus
- non-aSRB community members.
+ rationale: Resolving the acidogenic fermenters with MAGs would clarify how much of the early glycerol-to-acetate
+ flux was performed by Desulfosporosinus versus non-aSRB community members.
+- discussion_id: hualgayoc_flux_and_outcome_structure
+ prompt: Which MAGs drive carbon flow, and how should the positive remediation outcome enter the graph?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Glycerol-to-Acetate Sulfate Reduction
+ - ecological_interactions#Acetate-Fed Acididesulfobacillus Sulfate Reduction
+ rationale: 'Biotic treatment versus abiotic controls supports positive sulfate-reducing chemistry, pH increase
+ and dissolved-metal removal, independently of inferred MAG assignments. Bulk 16S rRNA transcripts were measured;
+ this is not MAG-resolved metabolic expression. Relative amplicon and metagenome profiles are different measurements
+ and do not resolve flux. Both dominant MAGs have glycerol-to-acetate potential; other acidogens and organic
+ amendments prevent assuming a closed two-member carbon balance. Mineral saturation modeling and poorly crystalline
+ XRD do not prove exact precipitate identities; cell coating does not identify every coated cell as a sulfate
+ reducer or exclude sulfide/acetate toxicity. The missing positive metal-removal/neutralization outcome structure
+ remains unresolved under #1504. The original #815 rendering complaint was addressed by removal in merged PR814;
+ restoring source-backed outcome structure is a distinct task. One-community Edison dry run succeeded without
+ API calls or charges; the report and source-backed node/arrow extension remain pending specific provider authorization.
+ Preserve #816''s already-present MAG003-only initiating participant. Existing minor-acidogen discussion and
+ non-graph blocks remain unchanged, not recertified.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T15:38:24Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Qualify MAG-specific carbon flow; retain unresolved remediation outcome extension. Issue #1502; reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml b/kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml
index 94be078ac..e17db83f8 100644
--- a/kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml
+++ b/kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml
@@ -139,13 +139,11 @@ taxonomy:
explanation: Names the fourth member and its principal fermentation product.
ecological_interactions:
- name: Partner-Specific Proteome Remodelling
- description: >
- Members modulate protein abundance in response to which specific partners
- are present, producing reproducible partner-specific expression shifts. Because
- the response depends on partner identity rather than on the carbon source, the
- division of labour is regulatory: the members reshape their realised niche by
- what they express.
- interaction_type: NICHE_PARTITIONING
+ description: Co-cultured gut strains showed partner-associated protein-expression changes. Abundance-matched mixed-isolate
+ protein controls help separate expression changes from composition and detection effects. Both community context
+ and carbon source affected proteomes; partner effects were not absence of carbon effects. The four canonical
+ participants define the human consortium, not a claim that every strain met protein-detection thresholds in
+ every condition. Pooled human/rumen analyses must not be assigned wholesale to the human four-member condition.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: regulation of gene expression
@@ -153,85 +151,138 @@ ecological_interactions:
id: GO:0010468
label: regulation of gene expression
downstream:
- - target: Reduced Functional Overlap and Metabolic Complementarity
- description: Partner-specific protein-abundance shifts reduce functional overlap
- and promote metabolic complementarity between the co-cultured gut anaerobes.
+ - target: Reduced Annotated Proteomic Functional Overlap
+ description: PARTIAL - partner-dependent expression changes can change which annotated functions overlap among
+ detected community members. Co-culture and matched mixed-isolate comparisons support a proteomic response,
+ but do not selectively identify the regulatory pathway or establish competitive niche partitioning and metabolite
+ flux.
evidence:
- reference: PMID:42032280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: These interactions led to reproducible, partner-specific expression shifts that
- significantly reduced functional overlap and were frequently associated with increased
- community productivity
- explanation: States that biotic interactions cause reproducible, partner-specific
- protein-abundance shifts.
+ snippet: These interactions led to reproducible, partner-specific expression shifts that significantly reduced
+ functional overlap and were frequently associated with increased community productivity
+ explanation: Supports positive partner-associated proteomic responses, not a selectively identified regulatory
+ mechanism or measured substrate exchange.
- reference: PMID:42032280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: We found that biotic interactions, rather than abiotic conditions, were the dominant
- drivers of proteomic variation
- explanation: Recorded on this interaction rather than as a separate edge, because "partner
- identity outweighed carbon source" is a property of the same partner-specific remodelling
- rather than a second interaction between taxa. The design varied carbon source independently,
- which is what gives the comparison force.
-- name: Reduced Functional Overlap and Metabolic Complementarity
- description: >
- Partner-specific protein shifts significantly reduce overlap in the functions
- expressed by the four gut anaerobes, promoting butyrate-, formate-, and
- acetate-centered metabolic complementarity across the community.
- interaction_type: NICHE_PARTITIONING
+ snippet: We found that biotic interactions, rather than abiotic conditions, were the dominant drivers of proteomic
+ variation
+ explanation: Supports the study-level predominance of biotic effects, not absence of abiotic effects or identical
+ responses in every human community.
+ participating_taxa:
+ - preferred_term: Eubacterium hallii
+ term:
+ id: NCBITaxon:39488
+ label: Anaerobutyricum hallii
+ - preferred_term: Roseburia intestinalis
+ term:
+ id: NCBITaxon:166486
+ label: Roseburia intestinalis
+ - preferred_term: Marvinbryantia formatexigens
+ term:
+ id: NCBITaxon:168384
+ label: Marvinbryantia formatexigens
+ - preferred_term: Faecalibacterium prausnitzii
+ term:
+ id: NCBITaxon:853
+ label: Faecalibacterium prausnitzii
+- name: Reduced Annotated Proteomic Functional Overlap
+ description: Protein-to-KEGG annotation and presence/absence comparisons showed reduced expressed functional overlap
+ in many tested communities relative to corresponding monoculture expectations. This positive proteomic metric
+ does not directly measure competition, coexistence, substrate partitioning or metabolite transfer. Butyrate,
+ formate and acetate are contextual member capabilities, not quantified exchanged products in this analysis.
+ Study-wide frequencies pooled human and rumen communities and do not establish the same result for every human
+ strain combination or carbon condition.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: butyrate
term:
id: CHEBI:17968
label: butyrate
- notes: Terminal product of three of the four members, and part of the functional redundancy that
- partner-specific expression reduces.
+ notes: Contextual member metabolic capability, not a measured interspecies exchange or flux in this proteomic
+ analysis.
- preferred_term: formate
term:
id: CHEBI:15740
label: formate
- notes: Fermentation end product of Marvinbryantia formatexigens.
+ notes: Contextual member metabolic capability, not a measured interspecies exchange or flux in this proteomic
+ analysis.
- preferred_term: acetate
term:
id: CHEBI:30089
label: acetate
- notes: Fermentation end product of Marvinbryantia formatexigens.
+ notes: Contextual member metabolic capability, not a measured interspecies exchange or flux in this proteomic
+ analysis.
downstream:
- - target: Increased Community Productivity
- description: The reduction in functional redundancy was frequently associated
- with increased productivity of the assembled gut-derived communities.
+ - target: Community qPCR Productivity Association
+ description: PARTIAL - reduced redundant expression could spare resources and contribute to greater community
+ productivity. The observed association supports this proposed explanation, but regulatory or energetic-cost
+ perturbations did not selectively establish that reduced annotated overlap mediates the qPCR yield difference.
evidence:
- reference: PMID:42032280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: These interactions led to reproducible, partner-specific expression shifts that
- significantly reduced functional overlap and were frequently associated with increased
- community productivity
- explanation: States the central result — partner-specific, reproducible shifts that reduce
- functional overlap — which is what makes this niche partitioning rather than a generic
- co-culture effect.
-- name: Increased Community Productivity
- description: The partner-specific proteomic shifts and reduced functional overlap
- were frequently associated with increased productivity across the gut-derived
- isolate, pairwise, and four-member community experiments.
- interaction_type: MUTUALISM
+ snippet: These interactions led to reproducible, partner-specific expression shifts that significantly reduced
+ functional overlap and were frequently associated with increased community productivity
+ explanation: Supports the observed annotated-proteome overlap result and associated productivity, not demonstrated
+ competitive niche partitioning.
+ participating_taxa:
+ - preferred_term: Eubacterium hallii
+ term:
+ id: NCBITaxon:39488
+ label: Anaerobutyricum hallii
+ - preferred_term: Roseburia intestinalis
+ term:
+ id: NCBITaxon:166486
+ label: Roseburia intestinalis
+ - preferred_term: Marvinbryantia formatexigens
+ term:
+ id: NCBITaxon:168384
+ label: Marvinbryantia formatexigens
+ - preferred_term: Faecalibacterium prausnitzii
+ term:
+ id: NCBITaxon:853
+ label: Faecalibacterium prausnitzii
+- name: Community qPCR Productivity Association
+ description: Lower annotated functional overlap was associated with higher community productivity across the analyzed
+ communities. Methods define productivity using total consortium qPCR abundance divided by mean monoculture abundance,
+ not the sum or best monoculture. qPCR gene-copy abundance is not direct viable-cell biomass, and greater community
+ yield does not demonstrate reciprocal benefit to every member. The pooled association was not a simple linear
+ dose-response and does not establish that reduced overlap caused productivity.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: butyrate
term:
id: CHEBI:17968
label: butyrate
+ notes: Contextual metabolic product, not the measured productivity endpoint.
evidence:
- reference: PMID:42032280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: These interactions led to reproducible, partner-specific expression shifts that
- significantly reduced functional overlap and were frequently associated with increased
- community productivity
- explanation: Links partner-specific proteome remodeling to the downstream
- community-productivity phenotype.
+ snippet: These interactions led to reproducible, partner-specific expression shifts that significantly reduced
+ functional overlap and were frequently associated with increased community productivity
+ explanation: Supports a study-level overlap/productivity association, not selective mediation, every-condition
+ enhancement or mutual benefit.
+ participating_taxa:
+ - preferred_term: Eubacterium hallii
+ term:
+ id: NCBITaxon:39488
+ label: Anaerobutyricum hallii
+ - preferred_term: Roseburia intestinalis
+ term:
+ id: NCBITaxon:166486
+ label: Roseburia intestinalis
+ - preferred_term: Marvinbryantia formatexigens
+ term:
+ id: NCBITaxon:168384
+ label: Marvinbryantia formatexigens
+ - preferred_term: Faecalibacterium prausnitzii
+ term:
+ id: NCBITaxon:853
+ label: Faecalibacterium prausnitzii
growth_media:
- name: YCFA with wheat straw fibre, anaerobic Hungate tubes
composition:
@@ -351,3 +402,27 @@ environmental_factors:
evidence_source: IN_VITRO
snippet: Using synthetic gut-derived consortia exposed to distinct carbon sources
explanation: Records carbon source as the varied abiotic condition in the design.
+discussions:
+- discussion_id: gut_proteome_overlap_mediation
+ prompt: Does altered proteome overlap cause higher community productivity?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Partner-Specific Proteome Remodelling
+ - ecological_interactions#Reduced Annotated Proteomic Functional Overlap
+ - ecological_interactions#Community qPCR Productivity Association
+ rationale: The positive controlled proteomic responses and overlap metric are distinct from proposed niche partitioning
+ and resource savings. Competition and coexistence were not directly measured. Protein coverage thresholds and
+ abundance-matched mixed-isolate controls matter; all four canonical human taxa are not guaranteed detectable
+ in every comparison. Preserve carbon effects, separate pooled human/rumen statistics from exact human conditions,
+ and use the Methods mean-monoculture denominator. Pathway or regulatory perturbations, resource budgets and
+ flux measurements would test the two retained PARTIAL arrows; no organism-level mutualism or specific butyrate/formate/acetate
+ exchange is demonstrated. Non-graph strain, medium and capability metadata is preserved, not recertified.
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T15:38:24Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Separate measured proteomic overlap and qPCR yield from proposed mediation. Issue #1503; reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml'
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 508d760c6..55f6b06e0 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,22 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch52: URLs, Hualgayoc And Gut Proteomes
+
+[Decisions](decisions/20261006-urls-amd-proteome-batch52.yaml),
+[validation](validation-20261006-batch52.json) and
+[self-adversarial review](adversarial-review-20261006-batch52.yaml) retain
+nine nodes, remove two contextual URL arrows and qualify three proposed links.
+Genomic potential remains distinct from measured flux; MAG assignments remain
+distinct from bulk remediation chemistry. Controlled proteome responses and
+annotated overlap remain distinct from demonstrated niche partitioning or yield
+mediation. Both URL habitat labels remain explicit despite their shared CURIE.
+Hualgayoc remains `needs_research` under #1504 for its missing positive outcome
+structure: an Edison dry run succeeded, but no paid report has been obtained.
+Complete cached primary main texts, Methods and embedded captions were read,
+not original images, supplementary files, raw data or code. Non-graph metadata
+is preserved, not recertified.
+
## Batch51: Enrichments And Core-20
[Decisions](decisions/20261006-enrichments-core20-batch51.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch52.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch52.yaml
new file mode 100644
index 000000000..c0cc4db61
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch52.yaml
@@ -0,0 +1,170 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 51a58f926d4a7bcf07dfd19c036e498ef6d290d6
+scope:
+- kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml
+- kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml
+- kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch52.json
+findings:
+- issue: 1501
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound URL genomic functions and remove two contextual arrows.
+ disposition: Close only after protected main merge.
+- issue: 1502
+ severity: P2
+ status: addressed_in_this_change
+ finding: Qualify MAG-specific carbon flow; retain unresolved remediation outcome extension.
+ disposition: Close only after protected main merge.
+- issue: 1503
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate measured proteomic overlap and qPCR yield from proposed mediation.
+ disposition: Close only after protected main merge.
+- issue: 1504
+ severity: P2
+ status: unresolved_research
+ finding: Missing positive Hualgayoc remediation outcome structure.
+ disposition: Keep open; one-community paid research/report review and source-backed extension remain
+ pending.
+adversarial_checks:
+- Whole275-line URL,628-line Hualgayoc and353-line gut records reviewed, including every original node
+ and arrow. Complete cached primary main texts, Methods and embedded captions read, with Hualgayoc Table1.
+ No original figure images, supplementary files, raw data or code audited.
+- URL site/lithology association is not an isolated causal driver. Genome-based functional potential remains
+ positive SUPPORT/COMPUTATIONAL evidence, not measured pathway flux. The two overview-to-hydrogen arrows
+ were context/inclusion, not established causal direction, and are removed without deleting the distinct
+ findings.
+- Both canonical URL habitat labels sharing NCBITaxon131567 remain distinct. Horonobe-only transfer/genotype
+ claims use only its participant. Hydrogen transfer stays PARTIAL without implying simultaneous sulfate
+ reduction and hydrogen export. Genotypic similarity and coverage-qualified iRep do not establish transport,
+ absolute growth rates or mutation rates.
+- Hualgayoc retains the already-present MAG003-only first participant under816, and both participants
+ for proposed acetate coupling. Both genomes encode glycerol-to-acetate potential. Organism assignment,
+ pH threshold, acetate-toxicity relief and mineral phase are hypotheses distinct from the positive bulk
+ chemistry. Repeated inoculation is explicit; bulk16S rRNA transcripts were measured, not absent.
+- 'Hualgayoc remains needs_research under1504: the removed positive remediation outcome requires new structure.
+ A real one-community dry run succeeded; the14343-character query is hash-bound. No paid provider job,
+ report or new outcome node/arrow. Existing minor-acidogen discussion is semantically unchanged; no unsupported
+ enum is added to hide the rendering issue.'
+- Gut partner-associated protein changes remain positive controlled findings, with abundance-matched mixed-isolate
+ controls. Carbon effects are not denied. Detection thresholds and combined human/rumen scope prevent
+ assigning all pooled results to every human member or condition.
+- Annotated KO overlap is a proteomic metric, not measured competition, coexistence or metabolite flux.
+ The exact Methods productivity denominator is mean monoculture qPCR abundance, not a sum or best-monoculture
+ benchmark. Yield is not direct viable biomass or every-member mutualism. Both proposed directions stay
+ PARTIAL without selective mediation.
+- Full record diffs and focused tests inspected. Nine nodes retained, two contextual arrows removed, three
+ arrows PARTIAL. Only graph, discussion and curation-history fields changed.457 other records,920 caches
+ and non-graph raw blocks preserved, not certified. Two participant registry entries added; measured
+ connectivity census unchanged.
+- Actual schema, strict, terms, references, snippets, rank and history gates passed. Network equals baseline
+ with34 existing findings and no structural errors. Repeat renders deterministic; exact node/arrow descriptions
+ across456 pages parser-checked, not browser screenshots. Post-commit docs-current remains a separate
+ publication gate.
+- Dedup checked809 all-state titles/bodies and14 ignored/hidden local files; prior merged PR814 inspected,
+ not every historical comment/review.1501/1502/1503 are repaired findings open until protected-main merge.1504
+ remains unresolved; original815 rendering complaint was addressed by removal in PR814. Source-based
+ self-adversarial review is not independent approval.
+verification:
+ combined_regressions: 495 passed in 198.66s (0:03:18)
+ new_regression_tests: 6
+ schema_strict_terms_history: Passed with actual output digests
+ references: CLI Total checks counts reported issues, not executed checks. Exit0 is no reported issues,
+ not source verification. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache
+ provenance (#1362) remain limitations.
+ snippet_counts_by_record:
+ kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml:
+ MATCH: 13
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml:
+ MATCH: 31
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network:
+ existing_findings_preserved: 34
+ added_findings: {}
+ removed_findings: {}
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml: dca1ccadf55067fc169f67a18b738ba22b195153590515fa4563c183900d02e5
+ tests/test_causal_review_batch52.py: d095dafc310dab3c7a40c0dc5bcd4d03946675d6ff848902deec1641065fd217
+ tests/test_participating_taxa.py: 7dd4e44c118c9eec279e5d4f4d487a39fee7f007bc4494158335d623f8b21337
+ kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml: 16a754cbe3b613ccff8bc58d6977583343afb00734dd6552311b9ae8b3c34bbd
+ kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml: 123c3e9e5a107b28346350c70a739cda2a27079917779f2d91d4797157c5f5af
+ kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml: d69abd3a1b4d3c0f41c90130143c41f5d4d234f5aec7926f3526894bfaa3b2a2
+ reports/causal_graph_review/README.md: a1b04b35765d486163b550725397bd0e6f7f0d65de079dba10cddb69f4b166c4
+ post_commit_docs_current: Separate publication gate; not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 389
+ mixed: 127
+ community_level_only: 262
+ taxa: 1498
+ credited_solely_by_the_rule: 1222
+ current:
+ records: 460
+ with_community_level: 389
+ mixed: 127
+ community_level_only: 262
+ taxa: 1498
+ credited_solely_by_the_rule: 1222
+ interpretation: Nine community nodes retain their scopes. URL and gut participants made explicit, with
+ two registry entries added; measured census unchanged. No production matching or census-bound changes.
+corpus:
+ records: 460
+ nodes: 1465
+ edges: 672
+ review_status_counts:
+ needs_research: 15
+ pending: 264
+ reviewed: 181
+limitations:
+- Whole three records and all nine original nodes/five arrows reviewed against complete cached primary
+ main texts, Methods and embedded captions; Hualgayoc main Table1 read. No original figure images, supplementary
+ files, raw data or code audited.
+- Nine nodes retained, two URL contextual arrows removed and three proposed arrows qualified PARTIAL.
+ No new causal structure added. Broad canonical participant identities and labels preserved; two explicit
+ participant registry entries added.
+- URL coding potential is not activity; site/lithology association is not an isolated effect. Genotype
+ similarity and qualified iRep are not direct transport, absolute growth-rate or mutation measurements.
+ Canonical habitat placeholders share a CURIE but preserve distinct labels.
+- 'Hualgayoc remains needs_research under #1504 for positive remediation outcome structure. One-community
+ Edison dry run completed; 14343-character prompt SHA256 5c7c9be15df120f51deb6aa48ea797ec98d3b84ae104e0f6889cec82c6a05bd2.
+ No provider call, paid job or report; specific payload/spend authorization pending. Existing #816 participant
+ narrowing retained, not newly performed.'
+- Hualgayoc positive bulk chemistry remains distinct from genomic MAG assignments, repeated inoculation,
+ pH thresholds, toxin rescue and uncertain mineral phases. Existing minor-acidogen discussion preserved.
+ Existing-structure repair is not complete graph extension.
+- Gut proteome matched mixed-isolate controls support expression responses; KO overlap and qPCR productivity
+ are distinct from measured niche partitioning, metabolite flux, all-member benefit or selective mediation.
+ Carbon effects, detection thresholds, human/rumen scope and mean-monoculture denominator preserved.
+- 'All other record files, all920 caches and non-graph raw blocks preserved, not recertified. SupportingReference
+ #476, Linux DOI-cache lookup #1091, selected-cache provenance #1362 and writer artifact #1095 remain
+ outside scope. Reference CLI Total checks counts reported issues.'
+- 'Dedup checked809 all-state issue titles/bodies and14 ignored/hidden local files. Earlier merged PR814
+ body/comments/review inspected; not every issue comment or PR review read. #1504 remains unresolved;
+ original #815 rendering complaint was addressed in PR814; #816 requests narrowing already present. Issues1501/1502/1503
+ stay open until protected-main merge. This is self-adversarial review, not independent approval.'
+issue_scope_correction: 'Self-adversarial correction before publication: do not conflate the already-addressed
+ #815 rendering complaint with the distinct source-backed outcome restoration tracked under #1504. Earlier
+ actual verification receipts retained as superseded and every gate rerun against corrected output.'
diff --git a/reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml b/reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
new file mode 100644
index 000000000..c0a7f34d9
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
@@ -0,0 +1,266 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 51a58f926d4a7bcf07dfd19c036e498ef6d290d6
+baseline_commit: 51a58f926d4a7bcf07dfd19c036e498ef6d290d6
+base_tree: 2d03e85012428338d9f8734e7cea9463c99af02b
+pre_source_baseline_sha256: 21a65189700184aa7f3e8a0d311dc4a6ccfb101cf3cdc244303fd14b8eee21c2
+issues:
+- 1501
+- 1502
+- 1503
+unresolved_research_issues:
+- 1504
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 809
+ ignored_hidden_local_search: true
+ matching_issues:
+ - 815
+ - 816
+ matching_local_files: 14
+ disposition: 'Existing #816 participant narrowing retained. Original #815 rendering complaint was addressed by
+ removal in merged PR814; distinct source-backed restoration is newly tracked under1504. New repair findings
+ cover separate inference and causal-direction issues.'
+ limitations: PR814 inspected, not all historical comments/reviews.
+reference_cache_original_hashes:
+ references_cache/PMID_39696556.md: 2dcf2c95f9af4987753d2016d550a58b62e27fb3d56d697e1e3648dd54b194a5
+ references_cache/PMID_42029028.txt: 47cde42470db1b13f2cf75cf5f3131dda202cc1ce1dd9b736ee9789dc4fe6937
+ references_cache/PMID_42032280.txt: ccf31256def3e8249906ea575771f40608686ba4387154b3f658768c71108266
+limitations:
+- Whole three records and all nine original nodes/five arrows reviewed against complete cached primary main texts,
+ Methods and embedded captions; Hualgayoc main Table1 read. No original figure images, supplementary files, raw
+ data or code audited.
+- Nine nodes retained, two URL contextual arrows removed and three proposed arrows qualified PARTIAL. No new causal
+ structure added. Broad canonical participant identities and labels preserved; two explicit participant registry
+ entries added.
+- URL coding potential is not activity; site/lithology association is not an isolated effect. Genotype similarity
+ and qualified iRep are not direct transport, absolute growth-rate or mutation measurements. Canonical habitat
+ placeholders share a CURIE but preserve distinct labels.
+- 'Hualgayoc remains needs_research under #1504 for positive remediation outcome structure. One-community Edison
+ dry run completed; 14343-character prompt SHA256 5c7c9be15df120f51deb6aa48ea797ec98d3b84ae104e0f6889cec82c6a05bd2.
+ No provider call, paid job or report; specific payload/spend authorization pending. Existing #816 participant
+ narrowing retained, not newly performed.'
+- Hualgayoc positive bulk chemistry remains distinct from genomic MAG assignments, repeated inoculation, pH thresholds,
+ toxin rescue and uncertain mineral phases. Existing minor-acidogen discussion preserved. Existing-structure repair
+ is not complete graph extension.
+- Gut proteome matched mixed-isolate controls support expression responses; KO overlap and qPCR productivity are
+ distinct from measured niche partitioning, metabolite flux, all-member benefit or selective mediation. Carbon
+ effects, detection thresholds, human/rumen scope and mean-monoculture denominator preserved.
+- 'All other record files, all920 caches and non-graph raw blocks preserved, not recertified. SupportingReference
+ #476, Linux DOI-cache lookup #1091, selected-cache provenance #1362 and writer artifact #1095 remain outside scope.
+ Reference CLI Total checks counts reported issues.'
+- 'Dedup checked809 all-state issue titles/bodies and14 ignored/hidden local files. Earlier merged PR814 body/comments/review
+ inspected; not every issue comment or PR review read. #1504 remains unresolved; original #815 rendering complaint
+ was addressed in PR814; #816 requests narrowing already present. Issues1501/1502/1503 stay open until protected-main
+ merge. This is self-adversarial review, not independent approval.'
+records:
+- path: kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml
+ id: CommunityMech:000218
+ original_sha256: 5478558435b0618f8a5d333ae2281a2af611766be3cb9c2a3cc6875e9ec59feb
+ record_sha256: 16a754cbe3b613ccff8bc58d6977583343afb00734dd6552311b9ae8b3c34bbd
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
+ scope: Whole record and every original node/arrow; bounded existing structure, with Hualgayoc extension explicitly
+ pending.
+ summary: Bound URL genomic functions and remove two contextual arrows.
+ renamed_nodes:
+ Lithology-Driven Community Divergence: Site-Associated URL Community Divergence
+ Shared Deep-Subsurface Functional Core: Shared Deep-Subsurface Genomic Functional Potential
+ node_decisions:
+ - node: Site-Associated URL Community Divergence
+ rationale: Retain the positive site comparison without an isolated lithology driver or niche-partitioning claim.
+ - node: Shared Deep-Subsurface Genomic Functional Potential
+ rationale: Retain positive genomic coding potential without measured flux or unqualified cross-feeding.
+ - node: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
+ rationale: Retain the author-proposed hydrogen-transfer hypothesis as PARTIAL with the Horonobe-only participant.
+ - node: Genotypic Homogeneity Across Depths in Horonobe
+ rationale: Retain genotype similarity and qualified iRep interpretation, not demonstrated transport or facilitation.
+ removed_node_decisions: []
+ edges_before:
+ - source: Lithology-Driven Community Divergence
+ target: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
+ description: The sedimentary Horonobe URL is organic- and CO2-rich and methane-biased, providing the geochemical
+ context for sulfate reducers predicted to produce H2 that supports methanogenesis.
+ - source: Shared Deep-Subsurface Functional Core
+ target: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
+ description: Hydrogen metabolism and sulfate reduction are represented in both URLs and include Horonobe Syntrophobacterales
+ predicted to produce H2 while reducing sulfate, feeding abundant Methanospirillum.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Lithology-Driven Community Divergence
+ target: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
+ description: The sedimentary Horonobe URL is organic- and CO2-rich and methane-biased, providing the geochemical
+ context for sulfate reducers predicted to produce H2 that supports methanogenesis.
+ rationale: Context or membership of a functional overview is not demonstrated upstream causation of partner
+ hydrogen transfer.
+ - source: Shared Deep-Subsurface Functional Core
+ target: Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
+ description: Hydrogen metabolism and sulfate reduction are represented in both URLs and include Horonobe Syntrophobacterales
+ predicted to produce H2 while reducing sulfate, feeding abundant Methanospirillum.
+ rationale: Context or membership of a functional overview is not demonstrated upstream causation of partner
+ hydrogen transfer.
+ references:
+ - PMID:39696556
+ issues:
+ - 1501
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Horonobe_Mizunami_URL_Subsurface_Microbiome/2026-10-06T153824Z-codex-7a4424.yaml
+ source_review:
+ PMID:39696556:
+ cache: references_cache/PMID_39696556.md
+ url: https://pubmed.ncbi.nlm.nih.gov/39696556/
+ scope: Whole 275-line record; complete cached primary abstract and appended main text, Methods and Figures
+ 1-7 captions, despite abstract-only cache metadata. Publisher main text corroborated. No original images,
+ supplements, raw data or code audited.
+ sha256: 2dcf2c95f9af4987753d2016d550a58b62e27fb3d56d697e1e3648dd54b194a5
+- path: kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml
+ id: CommunityMech:000353
+ original_sha256: 7b1ed8410d6c23f032ae27b4041756125c8bf971aa58827fa87ea34164b1c9d4
+ record_sha256: 123c3e9e5a107b28346350c70a739cda2a27079917779f2d91d4797157c5f5af
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
+ scope: Whole record and every original node/arrow; bounded existing structure, with Hualgayoc extension explicitly
+ pending.
+ summary: Qualify MAG-specific carbon flow; retain unresolved remediation outcome extension.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Glycerol-to-Acetate Sulfate Reduction
+ rationale: Retain the existing MAG003-only initiating hypothesis while distinguishing shared genomic potential
+ and repeated inoculation from exclusive flux.
+ - node: Acetate-Fed Acididesulfobacillus Sulfate Reduction
+ rationale: Retain the proposed acetate-consuming partner model without measured complete mineralization, selective
+ pH threshold or toxicity rescue; outcome extension remains needs_research.
+ removed_node_decisions: []
+ edges_before:
+ - source: Glycerol-to-Acetate Sulfate Reduction
+ target: Acetate-Fed Acididesulfobacillus Sulfate Reduction
+ description: Acididesulfobacillus sp. MAG013 is inferred to consume acetate produced during glycerol oxidation
+ after the consortium raises the pH.
+ edges_after:
+ - source: Glycerol-to-Acetate Sulfate Reduction
+ target: Acetate-Fed Acididesulfobacillus Sulfate Reduction
+ description: PARTIAL - proposed glycerol oxidation can supply acetate to the later MAG013-associated sulfate-reducing
+ route as the medium becomes less acidic. Bulk chemistry and genomes support the model, but do not resolve
+ the exact donor-to-recipient flux, demonstrate acetate-toxicity rescue or isolate pH from reinoculation and
+ other time-varying conditions.
+ retained_edge_decisions:
+ - source: Glycerol-to-Acetate Sulfate Reduction
+ target: Acetate-Fed Acididesulfobacillus Sulfate Reduction
+ description: PARTIAL - proposed glycerol oxidation can supply acetate to the later MAG013-associated sulfate-reducing
+ route as the medium becomes less acidic. Bulk chemistry and genomes support the model, but do not resolve
+ the exact donor-to-recipient flux, demonstrate acetate-toxicity rescue or isolate pH from reinoculation and
+ other time-varying conditions.
+ rationale: Retain the author-proposed direction as PARTIAL, distinguishing measured endpoints from untested
+ selective mediation.
+ removed_edge_decisions: []
+ references:
+ - PMID:42029028
+ issues:
+ - 1502
+ - 1504
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium/2026-10-06T153824Z-codex-bb95e3.yaml
+ source_review:
+ PMID:42029028:
+ cache: references_cache/PMID_42029028.txt
+ url: https://pubmed.ncbi.nlm.nih.gov/42029028/
+ scope: Whole 628-line record; complete cached primary abstract, main text, Methods, Table 1 and Figures 1-6
+ captions. Publisher identity corroborated. No original images, supplements, raw data or code audited.
+ sha256: 47cde42470db1b13f2cf75cf5f3131dda202cc1ce1dd9b736ee9789dc4fe6937
+- path: kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml
+ id: CommunityMech:000317
+ original_sha256: 899e722c69660db1def097d713a22b6e95d7ed43c26a1aacd6386ad9312dac29
+ record_sha256: d69abd3a1b4d3c0f41c90130143c41f5d4d234f5aec7926f3526894bfaa3b2a2
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml
+ scope: Whole record and every original node/arrow; bounded existing structure, with Hualgayoc extension explicitly
+ pending.
+ summary: Separate measured proteomic overlap and qPCR yield from proposed mediation.
+ renamed_nodes:
+ Reduced Functional Overlap and Metabolic Complementarity: Reduced Annotated Proteomic Functional Overlap
+ Increased Community Productivity: Community qPCR Productivity Association
+ node_decisions:
+ - node: Partner-Specific Proteome Remodelling
+ rationale: Preserve controlled partner-associated proteomics without denying carbon effects or assigning all
+ pooled results to every human condition.
+ - node: Reduced Annotated Proteomic Functional Overlap
+ rationale: Preserve annotated overlap as a measured metric without demonstrated competitive niches or metabolite
+ transfer.
+ - node: Community qPCR Productivity Association
+ rationale: Preserve the qPCR productivity association and exact benchmark without mutualism, direct biomass
+ or selective causal mediation.
+ removed_node_decisions: []
+ edges_before:
+ - source: Partner-Specific Proteome Remodelling
+ target: Reduced Functional Overlap and Metabolic Complementarity
+ description: Partner-specific protein-abundance shifts reduce functional overlap and promote metabolic complementarity
+ between the co-cultured gut anaerobes.
+ - source: Reduced Functional Overlap and Metabolic Complementarity
+ target: Increased Community Productivity
+ description: The reduction in functional redundancy was frequently associated with increased productivity of
+ the assembled gut-derived communities.
+ edges_after:
+ - source: Partner-Specific Proteome Remodelling
+ target: Reduced Annotated Proteomic Functional Overlap
+ description: PARTIAL - partner-dependent expression changes can change which annotated functions overlap among
+ detected community members. Co-culture and matched mixed-isolate comparisons support a proteomic response,
+ but do not selectively identify the regulatory pathway or establish competitive niche partitioning and metabolite
+ flux.
+ - source: Reduced Annotated Proteomic Functional Overlap
+ target: Community qPCR Productivity Association
+ description: PARTIAL - reduced redundant expression could spare resources and contribute to greater community
+ productivity. The observed association supports this proposed explanation, but regulatory or energetic-cost
+ perturbations did not selectively establish that reduced annotated overlap mediates the qPCR yield difference.
+ retained_edge_decisions:
+ - source: Partner-Specific Proteome Remodelling
+ target: Reduced Annotated Proteomic Functional Overlap
+ description: PARTIAL - partner-dependent expression changes can change which annotated functions overlap among
+ detected community members. Co-culture and matched mixed-isolate comparisons support a proteomic response,
+ but do not selectively identify the regulatory pathway or establish competitive niche partitioning and metabolite
+ flux.
+ rationale: Retain the author-proposed direction as PARTIAL, distinguishing measured endpoints from untested
+ selective mediation.
+ - source: Reduced Annotated Proteomic Functional Overlap
+ target: Community qPCR Productivity Association
+ description: PARTIAL - reduced redundant expression could spare resources and contribute to greater community
+ productivity. The observed association supports this proposed explanation, but regulatory or energetic-cost
+ perturbations did not selectively establish that reduced annotated overlap mediates the qPCR yield difference.
+ rationale: Retain the author-proposed direction as PARTIAL, distinguishing measured endpoints from untested
+ selective mediation.
+ removed_edge_decisions: []
+ references:
+ - PMID:42032280
+ issues:
+ - 1503
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Human_Gut_FourMember_Proteome_Complementarity_Consortium/2026-10-06T153825Z-codex-97b741.yaml
+ source_review:
+ PMID:42032280:
+ cache: references_cache/PMID_42032280.txt
+ url: https://pubmed.ncbi.nlm.nih.gov/42032280/
+ scope: Whole 353-line record; complete cached primary abstract, main text, Methods and Figures 1-6 / Extended
+ Data 1-10 captions. Publisher identity corroborated. No original images, supplements, source data or code
+ audited.
+ sha256: ccf31256def3e8249906ea575771f40608686ba4387154b3f658768c71108266
+issue_scope_correction: 'Self-adversarial correction before publication: do not conflate the already-addressed #815
+ rendering complaint with the distinct source-backed outcome restoration tracked under #1504. Earlier actual verification
+ receipts retained as superseded and every gate rerun against corrected output.'
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 7b6d3c425..b7be8946c 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -194,9 +194,9 @@ kb/communities/Hexamine_Formaldehyde_Consortium_C6.yaml CommunityMech:000405 275
kb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml CommunityMech:000350 9c1ecf68184260fe68327386dea7b0ca0c056fb610975b21cb9cbd8352042f14 3 2 100.0 reports/causal_graph_review/decisions/20261006-enrichments-core20-batch51.yaml reviewed
kb/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.yaml CommunityMech:000194 89902153cb8c0086b9305528173ec5147c6dcc6c0fa0c9ba9980011a559b7aac 3 2 90.0 reports/causal_graph_review/decisions/20261006-enrichments-core20-batch51.yaml reviewed
kb/communities/Honeybee_Core20_Defined_Microbiota.yaml CommunityMech:000124 9f955b7498ec80ad343cc5afc8ee5121fd0f9370d456bb94009088d8fcd6efae 3 2 100.0 reports/causal_graph_review/decisions/20261006-enrichments-core20-batch51.yaml reviewed
-kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml CommunityMech:000218 5478558435b0618f8a5d333ae2281a2af611766be3cb9c2a3cc6875e9ec59feb 4 2 100.0 pending
-kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml CommunityMech:000353 7b1ed8410d6c23f032ae27b4041756125c8bf971aa58827fa87ea34164b1c9d4 2 1 85.0 pending
-kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml CommunityMech:000317 899e722c69660db1def097d713a22b6e95d7ed43c26a1aacd6386ad9312dac29 3 2 100.0 pending
+kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml CommunityMech:000218 16a754cbe3b613ccff8bc58d6977583343afb00734dd6552311b9ae8b3c34bbd 4 0 67.5 reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml reviewed
+kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml CommunityMech:000353 123c3e9e5a107b28346350c70a739cda2a27079917779f2d91d4797157c5f5af 2 1 85.0 reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml needs_research
+kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml CommunityMech:000317 d69abd3a1b4d3c0f41c90130143c41f5d4d234f5aec7926f3526894bfaa3b2a2 3 2 90.0 reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml reviewed
kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml CommunityMech:000034 bc5b3e371afc61a51b2d9c6795ac704e7bbe2a98b08854b36c871388fe071ec7 5 3 100.0 pending
kb/communities/Industrial_Bioreactor_Consortium.yaml CommunityMech:000035 442e1edeb00a23737e070386d509f4caf336248af81c199d2975b7cde6c88060 9 3 100.0 pending
kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml CommunityMech:000152 185edc0766d39779bce9b43edf1fac1d5872fea92620b678262b2c29f54e785a 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index b1800a4b1..e1230379c 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
"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": 1465,
- "edges": 674,
+ "edges": 672,
"records_without_nodes": 8,
- "records_without_edges": 151,
+ "records_without_edges": 152,
"review_status_counts": {
- "needs_research": 14,
- "pending": 267,
- "reviewed": 179
+ "needs_research": 15,
+ "pending": 264,
+ "reviewed": 181
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch52.json b/reports/causal_graph_review/validation-20261006-batch52.json
new file mode 100644
index 000000000..a798415da
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch52.json
@@ -0,0 +1,1435 @@
+{
+ "base_commit": "51a58f926d4a7bcf07dfd19c036e498ef6d290d6",
+ "scope": [
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-strict.tsv",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-strict.log",
+ "log_sha256": "dfb19c725ca7acff17618c76bef83910ab888c708ffa5ca75936319af15238fd",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch52/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-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-strict.tsv\n"
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-references.log",
+ "log_sha256": "9c30d0a27c1b92581383204d023fd5e023b0afeef7add91bdd123e4356c0794e",
+ "output_tail": "Validating kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.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/Horonobe_Mizunami_URL_Subsurface_Microbiome.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": "Horonobe_Mizunami_URL_Subsurface_Microbiome-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
+ "output_tail": "# 13 evidence snippets scanned across 1 files\n MATCH 13\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": "Horonobe_Mizunami_URL_Subsurface_Microbiome-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-rank.log",
+ "log_sha256": "1aba538fae8b2333f6cc9e197d59c97225f4f3ecac0bd1bdaffc4a08269e90c0",
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+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Horonobe_Mizunami_URL_Subsurface_Microbiome/2026-10-06T153824Z-codex-7a4424.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-strict.tsv",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-strict.log",
+ "log_sha256": "10bf17c93b71f725bd348930a3f41dc97fa4f3d0d9360256a8a0d524066459db",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch52/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-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-references.log",
+ "log_sha256": "6642e9e9fed0252a1a8901c151e60bc8ecc34081c1de54a62041d034a69cf5e8",
+ "output_tail": "Validating kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.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/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.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": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-snippets.log",
+ "log_sha256": "7cb30458f959a4a7649fd96c05ca0aecb145f69b34e2ebea471b4c38e6956f10",
+ "output_tail": "# 31 evidence snippets scanned across 1 files\n MATCH 31\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": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-rank.log",
+ "log_sha256": "ff77b921f90e7a75cabbfe2ec44d41dd1b71badf1ff033152571e0d315e622d8",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000353\",\n \"name\": \"Hualgayoc Acidic Sulfate-Reducing AMD Consortium\",\n \"score\": 85.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"additional_downstream\"\n ],\n \"path\": \"kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium/2026-10-06T153824Z-codex-bb95e3.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-strict.tsv",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-strict.log",
+ "log_sha256": "d84704598367c0f0ec0fd29e416d8602eb560081be83503a87c1938d3c306118",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch52/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-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-references.log",
+ "log_sha256": "0a3a4f0ff5ec84ba4200e60899e9bb3a156d407e35fcac78de351d45dcd99164",
+ "output_tail": "Validating kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.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/Human_Gut_FourMember_Proteome_Complementarity_Consortium.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": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-snippets.log",
+ "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+ "output_tail": "# 17 evidence snippets scanned across 1 files\n MATCH 17\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": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-rank.log",
+ "log_sha256": "315cf5d45f20cd03f611cfd8d688017b6f83a8e9d5ecf24f7faa0bbe78f4fa54",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000317\",\n \"name\": \"Human Gut Four-Member Proteome-Complementarity Consortium\",\n \"score\": 90.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Human_Gut_FourMember_Proteome_Complementarity_Consortium/2026-10-06T153825Z-codex-97b741.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/Human_Gut_FourMember_Proteome_Complementarity_Consortium-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-batch52/inventory.log",
+ "log_sha256": "743cb4c95ef32f92cab77c26091960f1c81b7656247dbbdf512e7754f4afa4bb",
+ "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\": 1465,\n \"edges\": 672,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 152,\n \"review_status_counts\": {\n \"needs_research\": 15,\n \"pending\": 264,\n \"reviewed\": 181\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-batch52/network.log",
+ "log_sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "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-batch52/rank-all.log",
+ "log_sha256": "b451b9a71f4e96533ed6ce324c7828bf2ae9c97de0ed5823c1b20e8d9baf20f4",
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Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite 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"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/render.log",
+ "log_sha256": "6e2de0fa4a27545c4bc32f12d8ed4a800d209221bf15788bbc1021a4c4d46bf5",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch52/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch52/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch52/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-batch52/render-repeat.log",
+ "log_sha256": "6e2de0fa4a27545c4bc32f12d8ed4a800d209221bf15788bbc1021a4c4d46bf5",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch52/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch52/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch52/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json, pathlib, runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline', pathlib.Path('/private/tmp/communitymech-causal-batch51')), ('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda: paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/connectivity-survey.log",
+ "log_sha256": "d1f8cb53fc02a66edb17ed342b6a42f93828fdfc7d58e11aaea1140c633be1e1",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 389, \"mixed\": 127, \"community_level_only\": 262, \"taxa\": 1498, \"credited_solely_by_the_rule\": 1222}, \"current\": {\"records\": 460, \"with_community_level\": 389, \"mixed\": 127, \"community_level_only\": 262, \"taxa\": 1498, \"credited_solely_by_the_rule\": 1222}}\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_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.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",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/regressions.log",
+ "log_sha256": "a44e41a686722732a03a6fee116967d9d7384b3c35157131becd920536a0dae4",
+ "output_tail": "........................................................................ [ 14%]\n........................................................................ [ 29%]\n........................................................................ [ 43%]\n........................................................................ [ 58%]\n........................................................................ [ 72%]\n........................................................................ [ 87%]\n............................................................... [100%]\n495 passed in 198.66s (0:03:18)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/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_batch52.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/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-batch52/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Whole three records and all nine original nodes/five arrows reviewed against complete cached primary main texts, Methods and embedded captions; Hualgayoc main Table1 read. No original figure images, supplementary files, raw data or code audited.",
+ "Nine nodes retained, two URL contextual arrows removed and three proposed arrows qualified PARTIAL. No new causal structure added. Broad canonical participant identities and labels preserved; two explicit participant registry entries added.",
+ "URL coding potential is not activity; site/lithology association is not an isolated effect. Genotype similarity and qualified iRep are not direct transport, absolute growth-rate or mutation measurements. Canonical habitat placeholders share a CURIE but preserve distinct labels.",
+ "Hualgayoc remains needs_research under #1504 for positive remediation outcome structure. One-community Edison dry run completed; 14343-character prompt SHA256 5c7c9be15df120f51deb6aa48ea797ec98d3b84ae104e0f6889cec82c6a05bd2. No provider call, paid job or report; specific payload/spend authorization pending. Existing #816 participant narrowing retained, not newly performed.",
+ "Hualgayoc positive bulk chemistry remains distinct from genomic MAG assignments, repeated inoculation, pH thresholds, toxin rescue and uncertain mineral phases. Existing minor-acidogen discussion preserved. Existing-structure repair is not complete graph extension.",
+ "Gut proteome matched mixed-isolate controls support expression responses; KO overlap and qPCR productivity are distinct from measured niche partitioning, metabolite flux, all-member benefit or selective mediation. Carbon effects, detection thresholds, human/rumen scope and mean-monoculture denominator preserved.",
+ "All other record files, all920 caches and non-graph raw blocks preserved, not recertified. SupportingReference #476, Linux DOI-cache lookup #1091, selected-cache provenance #1362 and writer artifact #1095 remain outside scope. Reference CLI Total checks counts reported issues.",
+ "Dedup checked809 all-state issue titles/bodies and14 ignored/hidden local files. Earlier merged PR814 body/comments/review inspected; not every issue comment or PR review read. #1504 remains unresolved; original #815 rendering complaint was addressed in PR814; #816 requests narrowing already present. Issues1501/1502/1503 stay open until protected-main merge. This is self-adversarial review, not independent approval.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+ "CLI Total checks counts reported issues, not executed checks. Exit0 is no reported issues, not source verification. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations."
+ ],
+ "superseded_checks": [
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Horonobe_Mizunami_URL_Subsurface_Microbiome-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-strict.tsv",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Horonobe_Mizunami_URL_Subsurface_Microbiome-strict.log",
+ "log_sha256": "dfb19c725ca7acff17618c76bef83910ab888c708ffa5ca75936319af15238fd",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch52/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-batch52/Horonobe_Mizunami_URL_Subsurface_Microbiome-strict.tsv\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Horonobe_Mizunami_URL_Subsurface_Microbiome-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Horonobe_Mizunami_URL_Subsurface_Microbiome-references.log",
+ "log_sha256": "9c30d0a27c1b92581383204d023fd5e023b0afeef7add91bdd123e4356c0794e",
+ "output_tail": "Validating kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.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/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Horonobe_Mizunami_URL_Subsurface_Microbiome-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
+ "output_tail": "# 13 evidence snippets scanned across 1 files\n MATCH 13\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",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Horonobe_Mizunami_URL_Subsurface_Microbiome-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Horonobe_Mizunami_URL_Subsurface_Microbiome-rank.log",
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+ "command": [
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+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
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+ {
+ "check": "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-snippets",
+ "command": [
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+ "command": [
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+ "command": [
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+ "command": [
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+ ],
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+ "command": [
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+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
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+ "command": [
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+ "validate-data",
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+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Human_Gut_FourMember_Proteome_Complementarity_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Human_Gut_FourMember_Proteome_Complementarity_Consortium-references.log",
+ "log_sha256": "0a3a4f0ff5ec84ba4200e60899e9bb3a156d407e35fcac78de351d45dcd99164",
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+ "explained_output_tail": "Validating kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "Human_Gut_FourMember_Proteome_Complementarity_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Human_Gut_FourMember_Proteome_Complementarity_Consortium-snippets.log",
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+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
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+ "command": [
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+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Human_Gut_FourMember_Proteome_Complementarity_Consortium-rank.log",
+ "log_sha256": "315cf5d45f20cd03f611cfd8d688017b6f83a8e9d5ecf24f7faa0bbe78f4fa54",
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+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Human_Gut_FourMember_Proteome_Complementarity_Consortium/2026-10-06T153825Z-codex-97b741.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/Human_Gut_FourMember_Proteome_Complementarity_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "expected_exit_codes": [
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+ ],
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+ "log_sha256": "743cb4c95ef32f92cab77c26091960f1c81b7656247dbbdf512e7754f4afa4bb",
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+ },
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+ "check": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/network.log",
+ "log_sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "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",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/rank-all.log",
+ "log_sha256": "b451b9a71f4e96533ed6ce324c7828bf2ae9c97de0ed5823c1b20e8d9baf20f4",
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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",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/render.log",
+ "log_sha256": "6e2de0fa4a27545c4bc32f12d8ed4a800d209221bf15788bbc1021a4c4d46bf5",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch52/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch52/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch52/docs/index.html\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "communitymech.render"
+ ],
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+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/render-repeat.log",
+ "log_sha256": "6e2de0fa4a27545c4bc32f12d8ed4a800d209221bf15788bbc1021a4c4d46bf5",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch52/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch52/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch52/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch52/docs/index.html\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json, pathlib, runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline', pathlib.Path('/private/tmp/communitymech-causal-batch51')), ('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda: paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/connectivity-survey.log",
+ "log_sha256": "d1f8cb53fc02a66edb17ed342b6a42f93828fdfc7d58e11aaea1140c633be1e1",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 389, \"mixed\": 127, \"community_level_only\": 262, \"taxa\": 1498, \"credited_solely_by_the_rule\": 1222}, \"current\": {\"records\": 460, \"with_community_level\": 389, \"mixed\": 127, \"community_level_only\": 262, \"taxa\": 1498, \"credited_solely_by_the_rule\": 1222}}\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "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_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.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",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/regressions.log",
+ "log_sha256": "0fc78601030f3c58038bfb5b50598bbf945da7af6738369a27338bb9a845c55c",
+ "output_tail": "........................................................................ [ 14%]\n........................................................................ [ 29%]\n........................................................................ [ 43%]\n........................................................................ [ 58%]\n........................................................................ [ 72%]\n........................................................................ [ 87%]\n............................................................... [100%]\n495 passed in 193.88s (0:03:13)\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/black.log",
+ "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch52/before-issue-scope-correction/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": "",
+ "superseded_reason": "Pre-publication correction of issue attribution; command actually executed against earlier reviewed text. Rerun all gates against corrected outputs."
+ }
+ ],
+ "resume_note": "Existing command receipts reused only after command identity, exit status, log hash, record hashes and unchanged source-cache checks. Any interrupted verification retains its original receipts; no unexecuted check is counted as passed.",
+ "snippet_counts_by_record": {
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml": {
+ "MATCH": 13,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml": {
+ "MATCH": 31,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml": {
+ "MATCH": 17,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 48,
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 920,
+ "network_delta": {
+ "existing_findings_preserved": 34,
+ "added_findings": {},
+ "removed_findings": {}
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1451,
+ "arrows": 664
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 389,
+ "mixed": 127,
+ "community_level_only": 262,
+ "taxa": 1498,
+ "credited_solely_by_the_rule": 1222
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 389,
+ "mixed": 127,
+ "community_level_only": 262,
+ "taxa": 1498,
+ "credited_solely_by_the_rule": 1222
+ }
+ },
+ "interpretation": "Nine community nodes retain their scopes. URL and gut participants made explicit, with two registry entries added; measured census unchanged. No production matching or census-bound changes."
+ },
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1465,
+ "edges": 672,
+ "records_without_nodes": 8,
+ "records_without_edges": 152,
+ "review_status_counts": {
+ "needs_research": 15,
+ "pending": 264,
+ "reviewed": 181
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml": "dca1ccadf55067fc169f67a18b738ba22b195153590515fa4563c183900d02e5",
+ "tests/test_causal_review_batch52.py": "d095dafc310dab3c7a40c0dc5bcd4d03946675d6ff848902deec1641065fd217",
+ "tests/test_participating_taxa.py": "7dd4e44c118c9eec279e5d4f4d487a39fee7f007bc4494158335d623f8b21337",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml": "16a754cbe3b613ccff8bc58d6977583343afb00734dd6552311b9ae8b3c34bbd",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml": "123c3e9e5a107b28346350c70a739cda2a27079917779f2d91d4797157c5f5af",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml": "d69abd3a1b4d3c0f41c90130143c41f5d4d234f5aec7926f3526894bfaa3b2a2",
+ "reports/causal_graph_review/README.md": "a1b04b35765d486163b550725397bd0e6f7f0d65de079dba10cddb69f4b166c4"
+ },
+ "status": "verified_urls_amd_proteome_graph_repair",
+ "issue_scope_correction": "Self-adversarial correction before publication: do not conflate the already-addressed #815 rendering complaint with the distinct source-backed outcome restoration tracked under #1504. Earlier actual verification receipts retained as superseded and every gate rerun against corrected output.",
+ "superseded_check_context": {
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml": "198ed3873cc0e9a73425af2f373c05b2d5647b4e3cb286740d6ab26fac0420d7",
+ "tests/test_causal_review_batch52.py": "7da033bbd1426fafbbca9eb8898790c6660396ca4ad85c6a896d52e791dd8c59",
+ "tests/test_participating_taxa.py": "7dd4e44c118c9eec279e5d4f4d487a39fee7f007bc4494158335d623f8b21337",
+ "kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml": "16a754cbe3b613ccff8bc58d6977583343afb00734dd6552311b9ae8b3c34bbd",
+ "kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml": "0a18efa3046ba438a4b1f88f2ba93d33613ea9d762a938a9e01a520de455d194",
+ "kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml": "d69abd3a1b4d3c0f41c90130143c41f5d4d234f5aec7926f3526894bfaa3b2a2",
+ "reports/causal_graph_review/README.md": "0c113082dcdeabda398b1cc7184d34d14c5bc8c797b00b5aeedeb0c855e738ca"
+ },
+ "validation_before_correction_sha256": "be275bf709bb569ecb73e445584a76175d5c950404ec528e6c2c22e5f944b6ec",
+ "reason": "Self-adversarial correction before publication: do not conflate the already-addressed #815 rendering complaint with the distinct source-backed outcome restoration tracked under #1504. Earlier actual verification receipts retained as superseded and every gate rerun against corrected output."
+ },
+ "reference_validator_caveat": "CLI Total checks counts reported issues, not executed checks. Exit0 is no reported issues, not source verification. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.",
+ "pre_research_baseline": {
+ "base_commit": "51a58f926d4a7bcf07dfd19c036e498ef6d290d6",
+ "base_tree": "2d03e85012428338d9f8734e7cea9463c99af02b",
+ "research_worktree": "/private/tmp/communitymech-causal-batch51",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch52/baseline-rank.log",
+ "sha256": "d5ca03319728761eb8aa3343de0e0b37718c14b8f5445694b39cbdbe9775d1a1",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite 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-batch52/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-batch52/baseline-network.log",
+ "sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": " \"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-batch52/baseline-downstream.log",
+ "sha256": "ba2d674b7619ec104e04ea95906c13ce3aaa582000383d8a58b29c3d1136e796",
+ "output_tail": "ichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml:135: downstream:\nkb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml:173: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:121: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:149: downstream:\nkb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml:147: downstream:\nkb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml:222: downstream:\nkb/communities/BioModels_MODEL2204300001_Kefir_Community_Model.yaml:203: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml:83: downstream:\nkb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml:121: downstream:\nkb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml:141: 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/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:191: downstream:\nkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml:196: downstream:\nkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml:242: downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:80: downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:117: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:268: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:315: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "21a65189700184aa7f3e8a0d311dc4a6ccfb101cf3cdc244303fd14b8eee21c2"
+ },
+ "edison_dry_run": {
+ "command": [
+ "just",
+ "research-community-causal",
+ "Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium",
+ "--dry-run",
+ "--out-dir",
+ "/private/tmp/communitymech-batch52/hualgayoc-dry-run"
+ ],
+ "exit_code": 0,
+ "status": "dry-run",
+ "job": "LITERATURE",
+ "query_chars": 14343,
+ "query_sha256": "5c7c9be15df120f51deb6aa48ea797ec98d3b84ae104e0f6889cec82c6a05bd2",
+ "metadata_path": "/private/tmp/communitymech-batch52/hualgayoc-dry-run/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium-edison-literature-causal-meta.yaml",
+ "metadata_sha256": "6347ec4006d57d286677388f20b3dfa4023ac070891a8bd3c125e1e5f2b9b786",
+ "provider_calls": 0,
+ "paid_report_obtained": false,
+ "scope": "Dry run only. Optional model-cost metadata fetch fell back locally; no Edison API call or credit spend."
+ }
+}
diff --git a/tests/test_causal_review_batch52.py b/tests/test_causal_review_batch52.py
new file mode 100644
index 000000000..b4e1b26d5
--- /dev/null
+++ b/tests/test_causal_review_batch52.py
@@ -0,0 +1,134 @@
+"""Keep genomic and proteomic observations separate from untested mediation."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ return ledger, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in ledger["records"]]
+
+
+def canonical(doc, indices):
+ return [
+ {
+ "preferred_term": doc["taxonomy"][i]["taxon_term"]["preferred_term"],
+ "term": doc["taxonomy"][i]["taxon_term"]["term"],
+ }
+ for i in indices
+ ]
+
+
+def test_urls_keep_distinct_habitat_participants_without_contextual_arrows():
+ _, (doc, _, _) = records()
+ nodes = doc["ecological_interactions"]
+ for node, indexes in zip(nodes, [[0, 1], [0, 1], [0], [0]], strict=True):
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert node["participating_taxa"] == canonical(doc, indexes)
+ assert not node.get("downstream")
+ assert not {"source_taxon", "target_taxon"} & node.keys()
+ participants = nodes[0]["participating_taxa"]
+ assert participants[0]["term"]["id"] == participants[1]["term"]["id"]
+ assert participants[0]["preferred_term"] != participants[1]["preferred_term"]
+ assert all("interaction_type" not in nodes[i] for i in [0, 1, 3])
+ assert nodes[2]["interaction_type"] == "CROSS_FEEDING"
+ assert nodes[2]["description"].startswith("PARTIAL -")
+ assert "simultaneous sulfate reduction and hydrogen export" in nodes[2]["description"]
+
+
+def test_urls_bound_genomic_functions_and_replication_estimates():
+ _, (doc, _, _) = records()
+ sites, functions, _, genotypes = doc["ecological_interactions"]
+ assert "not an isolated lithology effect" in sites["description"]
+ assert "coding potential" in functions["description"]
+ assert "not measurement of pathway expression" in functions["description"]
+ assert functions["evidence"][0]["supports"] == "SUPPORT"
+ assert functions["evidence"][0]["evidence_source"] == "COMPUTATIONAL"
+ assert "Coverage-qualified iRep" in genotypes["description"]
+ assert "not direct absolute growth rates" in genotypes["description"]
+ assert genotypes["evidence"][1]["supports"] == "PARTIAL"
+
+
+def test_hualgayoc_preserves_existing_participant_subsets_and_partial_flux():
+ _, (_, doc, _) = records()
+ glycerol, acetate = doc["ecological_interactions"]
+ assert glycerol["participating_taxa"] == canonical(doc, [0])
+ assert acetate["participating_taxa"] == canonical(doc, [0, 1])
+ for node in [glycerol, acetate]:
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert node["interaction_type"] == "CROSS_FEEDING"
+ assert node["description"].startswith("PARTIAL -")
+ assert all(ev["supports"] == "PARTIAL" for ev in node["evidence"])
+ assert "both dominant MAGs encode" in glycerol["description"]
+ assert "days 32 and 86" in glycerol["description"]
+ assert "residual acetate remained" in acetate["description"]
+ assert "selectively established pH threshold" in acetate["description"]
+ assert doc["discussions"][0]["discussion_id"] == "HUALGAYOC_MINOR_ACIDOGENS"
+
+
+def test_hualgayoc_extension_remains_unresolved_after_existing_graph_repairs():
+ ledger, (_, doc, _) = records()
+ assert ledger["records"][1]["status"] == "needs_research"
+ assert ledger["unresolved_research_issues"] == [1504]
+ assert [row["status"] for row in ledger["records"]] == [
+ "reviewed",
+ "needs_research",
+ "reviewed",
+ ]
+ rationale = doc["discussions"][-1]["rationale"]
+ assert "positive sulfate-reducing chemistry" in rationale
+ assert "Bulk 16S rRNA transcripts were measured" in rationale
+ assert "dry run succeeded without API calls or charges" in rationale
+ assert "#1504" in rationale and "#816" in rationale
+
+
+def test_proteome_positive_controls_and_exact_yield_benchmark_are_preserved():
+ _, (_, _, doc) = records()
+ expression, overlap, productivity = doc["ecological_interactions"]
+ for node in [expression, overlap, productivity]:
+ assert node["participating_taxa"] == canonical(doc, range(4))
+ assert not {"interaction_type", "source_taxon", "target_taxon"} & node.keys()
+ assert node["evidence"][0]["supports"] == "SUPPORT"
+ assert "Abundance-matched mixed-isolate" in expression["description"]
+ assert "Both community context and carbon source" in expression["description"]
+ assert "Pooled human/rumen" in expression["description"]
+ assert "does not directly measure competition" in overlap["description"]
+ assert all("not a measured interspecies exchange" in t["notes"] for t in overlap["metabolites"])
+ assert "divided by mean monoculture abundance" in productivity["description"]
+ assert "not the sum or best monoculture" in productivity["description"]
+ assert "does not demonstrate reciprocal benefit" in productivity["description"]
+
+
+def test_every_node_and_arrow_has_a_hash_bound_decision():
+ ledger, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1501, 1502, 1503]
+ assert ledger["issue_deduplication"]["ignored_hidden_local_search"] is True
+ for index, (row, doc) in enumerate(zip(ledger["records"], docs, strict=True)):
+ nodes = doc["ecological_interactions"]
+ names = {node["name"] for node in nodes}
+ assert len(nodes) == [4, 2, 3][index]
+ assert {decision["node"] for decision in row["node_decisions"]} == names
+ assert len(row["edges_before"]) == [2, 1, 2][index]
+ assert len(row["retained_edge_decisions"]) == [0, 1, 2][index]
+ assert len(row["removed_edge_decisions"]) == [2, 0, 0][index]
+ assert row["removed_node_decisions"] == []
+ for node in nodes:
+ for edge in node.get("downstream", []):
+ assert edge["target"] in names
+ assert edge["description"].startswith("PARTIAL -")
+ for gap in doc["discussions"]:
+ for anchor in gap["attaches_to"]:
+ if anchor.startswith("ecological_interactions#"):
+ assert anchor.split("#", 1)[1] in names
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).is_file()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ for path, digest in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 5884f4ce6..dc58dc52b 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -288,7 +288,9 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Hexamine_Formaldehyde_Consortium_C6.yaml",
"High_Solids_Switchgrass_Methanogenic_Microbiome.yaml",
"Honeybee_Core20_Defined_Microbiota.yaml",
+ "Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml",
"Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml",
+ "Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
"Iberian_Pit_Lake_Stratified_Community.yaml",
"Industrial_Bioreactor_Consortium.yaml",
"Infant_Gut_Strain_Persistence_Maternal_Community.yaml",