The removed CR/DR assembly and 200-generation nodes described workflow, retained in engineering_design. Endpoint-to-dominance and endpoint-to-stability-decomposition arrows did not establish those causal directions. All three positive biological findings remain. Exact-system main text was unavailable; the open companion all-Shewanella experiment is not interchangeable with this CR/DR design. Missing biological directions remain #1706 pending a scoped Edison report; no new reversed arrow. Non-graph medium equivalence, taxon-design evidence and greenhouse-gas wording remain #1709.
+ 2 evidence item(s)
+
+
+
IN_VITRO
+
SUPPORT
+
PMID:37207729
-
Evidence
-
-
-
-
+ high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities
+
+ Supports the experimentally observed function/stability advantage, not a particular interspecies transfer mechanism.
+
-
"higher stability through overyielding and asynchrony of species fluctuations
-"
+
+
+
IN_VITRO
+
SUPPORT
-
-
-
+ higher stability through overyielding and asynchrony of species fluctuations
+
+ Supports the reported ecological pattern and interpretation, without identifying compound-resolved niche partitioning or an experimentally isolated mediator.
+
-
"showed more complementarity than the CR group during the experimental evolution"
+
-
-
-
-
-
-
-
@@ -1141,63 +1046,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("denitrification");
-
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "CR and DR Denitrifying SynCom Design",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "NICHE_PARTITIONING";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("denitrification");
-
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "Two-Hundred-Generation SDC Evolution",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1224,8 +1073,8 @@
Evidence
})();
(function() {
- var intId = "interaction:3";
- var intType = "COMPETITION";
+ var intId = "interaction:1";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1252,8 +1101,8 @@
Evidence
})();
(function() {
- var intId = "interaction:4";
- var intType = "NICHE_PARTITIONING";
+ var intId = "interaction:2";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1298,7 +1147,7 @@
Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 7;
+ var nodeCount = 5;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.html b/docs/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.html
index b03c800aa..bd1e8641b 100644
--- a/docs/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.html
+++ b/docs/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.html
@@ -571,7 +571,7 @@
Ecological Interactions
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -586,6 +586,56 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which source-supported fermentation and host-response nodes belong in this currently absent graph?
+
+
Preserve the observed 24 h viable counts (9.32 and 7.05 log CFU/mL), carbohydrate utilization, acidification, increased bioactive compounds and simulated-digestion bioaccessibility. The fermented whole beverage promoted microbial recovery in vancomycin-treated BALB/c mice. These positives do not establish partner-resolved cross-feeding, reciprocal fitness, intestinal colonization, mediation by a specific compound, or benefit in humans. Primary access is abstract-only. New graph structure remains #1707; a one-community Edison dry run is not a reviewed paid report. No node or arrow is added in this discussion-only review.
+
+
Attaches to: engineering_design, growth_media#Oat-almond-sunflower plant-based beverage
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
The process facilitated carbohydrate utilization, acidification, and the generation of bioactive metabolites.
+
Supports fermentation-associated substrate use, acidification, and metabolite production by the defined co-culture.
+
+
+
Administration of the fermented beverage promoted microbial recovery
+
Supports testing the fermented co-culture beverage in a host dysbiosis recovery assay.
+
+
+
diff --git a/docs/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.html b/docs/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.html
index 2582046ab..7074d6c22 100644
--- a/docs/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.html
+++ b/docs/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.html
@@ -585,6 +585,60 @@
Ecological Interactions
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which treatment-specific removal and biomass phenotypes can be represented without inventing exchange mechanisms?
+
+
Pico-Bac achieved 72% COD and 96.4% polyphenol removal in 10% SWW and 80.4% hydrocarbon removal in 25% SWW. Preserve these positives, while Pico monoculture had the greatest oil-and-grease removal (62.2%) in 25% SWW. The abstract does not resolve the Pico/Pico-Bac arm for the 55 mg/g lipid endpoint or treated-water seed response; the existing phytotoxicity qualification remains correct. Pollutant removal does not establish complete mineralization, an O2/CO2 exchange route, or species-resolved bacterial function. Bacteria remains a broad canonical domain grounding. Primary access is abstract-only. New graph structure remains #1708 pending a scoped Edison report; no node or arrow is added by this discussion-only review.
+
+
Attaches to: engineering_design, environmental_factors#COD and polyphenol removal, environmental_factors#Hydrocarbon removal
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
Pico-Bac achieved maximum COD and polyphenol reductions of 72% and 96.4%
+
Quantifies the maximum COD and polyphenol removal attributed to the Pico-Bac consortium.
+
+
+
hydrocarbon removal was highest (80.4%) at 25% SWW
+
Quantifies the maximum hydrocarbon removal measured for the consortium.
+
+
+
+
diff --git a/docs/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.html b/docs/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.html
index 2aeb3bc51..20ef2d116 100644
--- a/docs/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.html
+++ b/docs/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.html
@@ -654,7 +654,7 @@
Ecological Interactions
Ecological interaction network for Pinus armandii Endophytic Biocontrol SynCom
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (mutualism, competition, niche partitioning).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -662,18 +662,8 @@
Ecological Interactions
-
-
-
-
Ecological Interactions
-
The community was assembled from endophytic isolates selected for complementary plant growth-promoting and antagonistic functions and for pairwise compatibility, yielding a functionally complementary and stable synthetic community rather than any single-strain effect.
-
-
+
The five constituent strains were selected using pairwise compatibility tests. Public Supplement Figure S3 shows an agar/filter-disc assay with no inhibition zones among the tested strains. Preserve assay-specific compatibility, not demonstrated long-term stable coexistence, resource partitioning or a causal contribution of complementarity to seedling growth. Screened nitrogen-fixing/IAA traits do not establish ammonia or IAA exchange within this SynCom.
-
Metabolites:
+
Participating Taxa:
- indole-3-acetic acid
- (CHEBI:16411 ),
+ Pseudomonas koreensis RC1,
- ammonia
- (CHEBI:16134 )
-
-
+ Paenibacillus terrae RE7,
+ Bacillus velezensis OB3,
+ Bacillus velezensis NA3,
-
Biological Processes:
-
+ Bacillus subtilis NA11
-
- nitrogen fixation
- (GO:0009399 )
-
+
-
-
-
Downstream Effects:
-
-
→ Pinus Seedling Growth Promotion
-
Pairwise-compatible strains with complementary plant growth-promoting traits form the optimized SynCom that increases Pinus armandii seedling height and biomass.
-
-
@@ -742,7 +712,7 @@
Evidence
- SUPPORT (IN_VITRO)
"this study screened endophytic bacteria with superior plant growth-promoting (PGP) and antagonistic functions to construct a functionally complementary and stable synthetic microbial community (SynCom)."
+ "Based on pairwise compatibility tests, a SynCom was constructed"
@@ -752,40 +722,28 @@ Evidence
-
Constituent strains were selected for antagonistic potential against the blister rust pathogen, assessed by dual-culture assays and inhibition of urediniospore germination; the assembled SynCom enhanced blister rust-associated host defense responses.
+
Selected isolates showed antagonistic activity in vitro. Public Supplement Table S2 and Figure S1 identify Phomopsis sp. as the plate-inhibition target, distinct from the separate urediniospore-germination assay with cell-free fermentation supernatants (Figure S2). NA11, NA3 and RE7 occur among the tested inhibitory isolates and in the final SynCom; RC1 and OB3 are not among the nine spore-assay treatments. Preserve isolate inhibition without assigning every result to the complete five-strain community or asserting that direct pathogen inhibition caused host defense-enzyme induction.
+
Participating Taxa:
+ Paenibacillus terrae RE7,
+ Bacillus velezensis NA3,
+ Bacillus subtilis NA11
-
Biological Processes:
-
-
-
Downstream Effects:
-
-
→ Blister Rust-Associated Defense Enzyme Induction
-
Antagonistic endophytic strains assembled into the optimized SynCom enhance polyphenol oxidase and peroxidase defense responses associated with Pinus armandii blister rust resistance.
-
-
@@ -801,7 +759,7 @@
Evidence
- SUPPORT (IN_VITRO)
"antagonistic potential using dual-culture assays and inhibition of urediniospore germination."
+ "nine strains with significant antagonistic activity"
@@ -812,35 +770,29 @@ Evidence
-
The optimized five-strain SynCom significantly increases Pinus armandii seedling height and biomass accumulation in pot experiments.
+
The optimized five-strain SynCom significantly increased Pinus armandii seedling height and biomass accumulation in pot experiments. Preserve this positive host-growth response. The accessible evidence does not isolate IAA production or nitrogen fixation as its mediator, demonstrate individual-strain necessity, or show reciprocal microbial fitness benefits.
+
Participating Taxa:
+ Pseudomonas koreensis RC1,
-
Metabolites:
+ Paenibacillus terrae RE7,
- indole-3-acetic acid
- (CHEBI:16411 )
+ Bacillus velezensis OB3,
-
+ Bacillus velezensis NA3,
+ Bacillus subtilis NA11
+
+
-
Biological Processes:
-
@@ -855,7 +807,7 @@
Evidence
PMID:42322490
- - SUPPORT (IN_VITRO)
+ - SUPPORT (IN_VIVO)
"significantly increased seedling height and biomass accumulation."
@@ -869,12 +821,25 @@ Evidence
-
SynCom treatment raises defense-related polyphenol oxidase and peroxidase activities relative to uninoculated Pinus armandii controls, consistent with priming blister rust-associated defense responses.
+
SynCom treatment increased host polyphenol oxidase (PPO) and peroxidase (POD) activities by 19.1% and 157.3% relative to controls in the pot experiment. Preserve these positive defense-associated enzyme endpoints. They do not alone demonstrate priming, resistance to infection or disease control; the abstract explicitly calls for subsequent in planta biocontrol evaluation.
+
+
Participating Taxa:
+
+ Pseudomonas koreensis RC1,
+
+ Paenibacillus terrae RE7,
+
+ Bacillus velezensis OB3,
+
+ Bacillus velezensis NA3,
+
+ Bacillus subtilis NA11
+
+
@@ -904,7 +869,7 @@
Evidence
PMID:42322490
- - SUPPORT (IN_VITRO)
+ - SUPPORT (IN_VIVO)
"SynCom treatment enhanced defense-related enzyme activities, increasing polyphenol oxidase (PPO) and peroxidase (POD) activities by 19.1% and 157.3% relative to the control"
@@ -920,6 +885,60 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which strain functions mediate the observed seedling responses and actual blister-rust protection?
+
+
Preserve compatibility, isolate antagonism, growth and enzyme responses as separate positive findings. Public Supplement Figures S1-S3 and Table S2 separate Phomopsis inhibition, cell-free urediniospore inhibition and compatibility; these assays do not demonstrate stable community coexistence or direct inhibition by the complete SynCom. Both removed arrows conflated isolate selection/screening with causal mediation of host outcomes. No untested IAA/nitrogen exchange or reciprocal mutualism is assigned. Disease-challenge, strain-removal and mediator perturbations would resolve mechanisms. Main text remains inaccessible, while both public supplements were read and all six PDF pages visually inspected. Non-graph priming/stability and assay-scope claims remain #1709.
+
+
Attaches to: ecological_interactions#Compatibility of Selected Endophytic Isolates, ecological_interactions#Antagonistic Activity of Selected Endophytic Isolates, ecological_interactions#Pinus Seedling Growth Promotion, ecological_interactions#Blister Rust-Associated Defense Enzyme Induction
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
nine strains with significant antagonistic activity
+
Supports the positive isolate-screen result. Public supplements distinguish Phomopsis plates from the cell-free urediniospore assay and delimit which isolates overlap the final SynCom; not a whole-SynCom inhibition experiment.
+
+
+
SynCom treatment enhanced defense-related enzyme activities, increasing polyphenol oxidase (PPO) and peroxidase (POD) activities by 19.1% and 157.3% relative to the control
+
Supports the measured host enzyme increases, not demonstrated infection resistance or a specific isolate-mediated mechanism.
+
+
+
+
@@ -1037,26 +1056,16 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("indole-3-acetic acid");
-
- metabolites.push("ammonia");
-
-
var processes = [];
-
- processes.push("nitrogen fixation");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Functionally complementary biocontrol SynCom assembly",
+ label: "Compatibility of Selected Endophytic Isolates",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1067,24 +1076,39 @@ Evidence
+ var participantKeys = [
+
+ "Pseudomonas koreensis RC1",
+
+ "Paenibacillus terrae RE7",
+
+ "Bacillus velezensis OB3",
+
+ "Bacillus velezensis NA3",
+
+ "Bacillus subtilis NA11"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("defense response");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Community antagonism of the blister rust pathogen",
+ label: "Antagonistic Activity of Selected Endophytic Isolates",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1095,22 +1119,29 @@ Evidence
- })();
-
- (function() {
- var intId = "interaction:2";
- var intType = "MUTUALISM";
- var metabolites = [];
+ var participantKeys = [
+ "Paenibacillus terrae RE7",
- metabolites.push("indole-3-acetic acid");
+ "Bacillus velezensis NA3",
+ "Bacillus subtilis NA11"
- var processes = [];
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+ })();
- processes.push("nitrogen fixation");
+ (function() {
+ var intId = "interaction:2";
+ var intType = "UNKNOWN";
+ var metabolites = [];
+ var processes = [];
var evidenceCount = 1;
@@ -1127,11 +1158,30 @@ Evidence
+ var participantKeys = [
+
+ "Pseudomonas koreensis RC1",
+
+ "Paenibacillus terrae RE7",
+
+ "Bacillus velezensis OB3",
+
+ "Bacillus velezensis NA3",
+
+ "Bacillus subtilis NA11"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:3";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1155,6 +1205,25 @@ Evidence
+ var participantKeys = [
+
+ "Pseudomonas koreensis RC1",
+
+ "Paenibacillus terrae RE7",
+
+ "Bacillus velezensis OB3",
+
+ "Bacillus velezensis NA3",
+
+ "Bacillus subtilis NA11"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/history/records/Phylogenetically_Diverse_Denitrifying_SynCom/2026-10-07T095834Z-codex-e0b6a8.yaml b/history/records/Phylogenetically_Diverse_Denitrifying_SynCom/2026-10-07T095834Z-codex-e0b6a8.yaml
new file mode 100644
index 000000000..9e452d8a8
--- /dev/null
+++ b/history/records/Phylogenetically_Diverse_Denitrifying_SynCom/2026-10-07T095834Z-codex-e0b6a8.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
+ slug: Phylogenetically_Diverse_Denitrifying_SynCom
+session:
+ id: 2026-10-07T095834Z-codex-e0b6a8
+ timestamp: '2026-10-07T09:58:34Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1704
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve positive DR function and stability without workflow causality.; Preserve
+ Paracoccus dominance/function association without competition or mediation claims.; Preserve
+ overyielding, asynchrony and complementarity without unmeasured resource mechanisms.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
diff --git a/history/records/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture/2026-10-07T095835Z-codex-663d7b.yaml b/history/records/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture/2026-10-07T095835Z-codex-663d7b.yaml
new file mode 100644
index 000000000..a49cf4841
--- /dev/null
+++ b/history/records/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture/2026-10-07T095835Z-codex-663d7b.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml
+ slug: Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture
+session:
+ id: 2026-10-07T095835Z-codex-663d7b
+ timestamp: '2026-10-07T09:58:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1707
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Document positive findings and assay limits for an empty graph pending scoped Edison
+ research; no topology added.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
diff --git a/history/records/Picocystis_Activated_Sludge_Refinery_SWW_Consortium/2026-10-07T095835Z-codex-a3e7a7.yaml b/history/records/Picocystis_Activated_Sludge_Refinery_SWW_Consortium/2026-10-07T095835Z-codex-a3e7a7.yaml
new file mode 100644
index 000000000..28d5d394a
--- /dev/null
+++ b/history/records/Picocystis_Activated_Sludge_Refinery_SWW_Consortium/2026-10-07T095835Z-codex-a3e7a7.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml
+ slug: Picocystis_Activated_Sludge_Refinery_SWW_Consortium
+session:
+ id: 2026-10-07T095835Z-codex-a3e7a7
+ timestamp: '2026-10-07T09:58:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1708
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Document positive findings and assay limits for an empty graph pending scoped Edison
+ research; no topology added.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
diff --git a/history/records/Pinus_armandii_Endophytic_Biocontrol_SynCom/2026-10-07T095835Z-codex-75dfd6.yaml b/history/records/Pinus_armandii_Endophytic_Biocontrol_SynCom/2026-10-07T095835Z-codex-75dfd6.yaml
new file mode 100644
index 000000000..3b14ce626
--- /dev/null
+++ b/history/records/Pinus_armandii_Endophytic_Biocontrol_SynCom/2026-10-07T095835Z-codex-75dfd6.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml
+ slug: Pinus_armandii_Endophytic_Biocontrol_SynCom
+session:
+ id: 2026-10-07T095835Z-codex-75dfd6
+ timestamp: '2026-10-07T09:58:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1705
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve measured pairwise compatibility without stability or niche claims.; Preserve
+ selected-isolate inhibition with correct assay targets and participants.; Preserve positive
+ pot-growth endpoint without untested trait mediation.; Preserve positive host enzyme induction
+ without asserting disease control.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
diff --git a/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
index 8bd7f8fff..06c5764c4 100644
--- a/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
+++ b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
@@ -61,91 +61,33 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: CR and DR Denitrifying SynCom Design
- description: >
- Synthetic denitrifying communities were assembled by phylogenetic distance
- into a closely related group made only from Shewanella strains and a
- distantly related group whose members came from different genera.
- scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- biological_processes:
- - preferred_term: denitrification
- term:
- id: GO:0019333
- label: denitrification pathway
- downstream:
- - target: Two-Hundred-Generation SDC Evolution
- description: >
- The phylogenetic-distance-based CR and DR SynComs seeded a
- 200-generation laboratory evolution experiment.
- evidence:
- - *id001
-- name: Two-Hundred-Generation SDC Evolution
- description: >
- All synthetic denitrifying communities were subjected to experimental
- evolution for 200 generations before evolved community function and
- stability were compared across the phylogenetic-diversity designs.
- scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- biological_processes:
- - preferred_term: denitrification
- term:
- id: GO:0019333
- label: denitrification pathway
- downstream:
- - target: High-Phylogenetic-Diversity Function and Stability
- description: >
- Experimental evolution exposed the functional and temporal-stability
- advantage of the high-phylogenetic-diversity DR communities.
- evidence:
- - reference: PMID:37207729
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- All synthetic denitrifying communities (SDCs) were experimentally evolved
- for 200 generations
- explanation: >
- Supports the 200-generation experimental-evolution treatment applied to
- all CR and DR synthetic denitrifying communities.
- name: High-Phylogenetic-Diversity Function and Stability
- description: >
- High phylogenetic diversity followed by experimental evolution improved
- synthetic denitrifying community productivity, denitrification rate, and
- temporal stability.
+ description: In the 200-generation experiment, the high-phylogenetic-diversity DR design showed greater productivity,
+ denitrification rate and temporal stability than the closely related Shewanella-only CR design. Preserve the
+ positive community comparison without treating the two designs as one coexisting Shewanella-Paracoccus pair
+ or asserting a measured compound-resolved niche mechanism.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
biological_processes:
- preferred_term: denitrification
term:
id: GO:0019333
label: denitrification pathway
- downstream:
- - target: Paracoccus-Dominated DR Denitrification
- description: >
- Evolved, distantly related communities had higher productivity and
- denitrification rates when Paracoccus denitrificans dominated them.
- - target: DR Overyielding and Asynchronous Stability
- description: >
- Evolved DR stability was decomposed into overyielding, asynchronous
- species fluctuations, and higher complementarity than the CR group.
evidence:
- reference: PMID:37207729
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- high phylogenetic diversity followed by experimental evolution promoted
- the function and stability of synthetic denitrifying communities
- explanation: >
- Supports improved function and stability in evolved
- phylogenetically diverse denitrifying SynComs.
+ snippet: 'high phylogenetic diversity followed by experimental evolution promoted the function and stability
+ of synthetic denitrifying communities
+
+ '
+ explanation: Supports the experimentally observed function/stability advantage, not a particular interspecies
+ transfer mechanism.
- name: Paracoccus-Dominated DR Denitrification
- description: >
- In the evolved distantly related communities, Paracoccus denitrificans
- dominance from the 50th generation onward coincided with significantly
- higher productivity and denitrification rates than in the closely related
- Shewanella-only communities.
+ description: Paracoccus denitrificans dominated the DR community from generation 50 onward, where productivity
+ and denitrification rates were significantly higher than in the CR communities. Preserve this positive abundance/function
+ observation. Dominance is not a demonstrated reciprocal competition assay, nor does this comparison isolate
+ Paracoccus abundance as the causal driver of higher function.
scope: COMMUNITY_LEVEL
- interaction_type: COMPETITION
biological_processes:
- preferred_term: denitrification
term:
@@ -155,17 +97,18 @@ ecological_interactions:
- reference: PMID:37207729
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: productivity and denitrification rates were significantly
- explanation: Supports denitrification as the process whose rate improved in
- the experimentally evolved, phylogenetically diverse synthetic community.
+ snippet: higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community
+ than those in the CR community
+ explanation: The abstract spells the genus Paracocus; retain canonical Paracoccus identity while preserving
+ the literal source. Supports dominance associated with higher productivity/denitrification, not a dominance
+ intervention.
- name: DR Overyielding and Asynchronous Stability
- description: >
- The evolved distantly related communities were more stable than the closely
- related Shewanella communities through overyielding and asynchronous
- fluctuations, and showed stronger complementarity across experimental
- evolution.
+ description: DR communities had significantly higher temporal stability, with overyielding and asynchronous species
+ fluctuations, and more complementarity than CR communities during evolution. Preserve the reported stability
+ result and statistical ecological interpretation. Aggregate complementarity/asynchrony does not identify exchanged
+ resources or demonstrate a species-resolved causal chain; higher stability is not an upstream cause of its own
+ decomposition.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
biological_processes:
- preferred_term: denitrification
term:
@@ -175,19 +118,17 @@ ecological_interactions:
- reference: PMID:37207729
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- higher stability through overyielding and asynchrony of species
- fluctuations
- explanation: >
- Supports overyielding and asynchronous species fluctuations as the
- stability basis in the distantly related community.
+ snippet: 'higher stability through overyielding and asynchrony of species fluctuations
+
+ '
+ explanation: Supports the reported ecological pattern and interpretation, without identifying compound-resolved
+ niche partitioning or an experimentally isolated mediator.
- reference: PMID:37207729
supports: SUPPORT
evidence_source: IN_VITRO
snippet: showed more complementarity than the CR group during the experimental evolution
- explanation: >
- Supports higher complementarity in DR than CR communities during the
- evolution experiment.
+ explanation: Supports the reported ecological pattern and interpretation, without identifying compound-resolved
+ niche partitioning or an experimentally isolated mediator.
environmental_factors:
- name: defined synthetic community design
value: Closely related communities used Shewanella strains; distantly related communities used constituents
@@ -267,3 +208,45 @@ growth_media:
snippet: as the electron acceptor
explanation: Supports 20 mM nitrate (NaNO3) supplied as the terminal electron acceptor for
anaerobic denitrification in the medium.
+discussions:
+- discussion_id: denitrifying-design-versus-biological-direction
+ prompt: Which biological mechanisms link phylogenetic diversity to denitrification and stability?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#High-Phylogenetic-Diversity Function and Stability
+ - ecological_interactions#Paracoccus-Dominated DR Denitrification
+ - ecological_interactions#DR Overyielding and Asynchronous Stability
+ rationale: 'The removed CR/DR assembly and 200-generation nodes described workflow, retained in engineering_design.
+ Endpoint-to-dominance and endpoint-to-stability-decomposition arrows did not establish those causal directions.
+ All three positive biological findings remain. Exact-system main text was unavailable; the open companion all-Shewanella
+ experiment is not interchangeable with this CR/DR design. Missing biological directions remain #1706 pending
+ a scoped Edison report; no new reversed arrow. Non-graph medium equivalence, taxon-design evidence and greenhouse-gas
+ wording remain #1709.'
+ evidence:
+ - reference: PMID:37207729
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'high phylogenetic diversity followed by experimental evolution promoted the function and stability
+ of synthetic denitrifying communities
+
+ '
+ explanation: Supports the experimentally observed function/stability advantage, not a particular interspecies
+ transfer mechanism.
+ - reference: PMID:37207729
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'higher stability through overyielding and asynchrony of species fluctuations
+
+ '
+ explanation: Supports the reported ecological pattern and interpretation, without identifying compound-resolved
+ niche partitioning or an experimentally isolated mediator.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T09:58:33Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve positive DR function and stability without workflow causality.; Preserve Paracoccus dominance/function
+ association without competition or mediation claims.; Preserve overyielding, asynchrony and complementarity
+ without unmeasured resource mechanisms. Issue #1704; reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml b/kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml
index ae11adcdc..dd483d32b 100644
--- a/kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml
+++ b/kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml
@@ -187,21 +187,43 @@ external_resources:
explanation: Lists the primary publication for the CCMA co-culture.
discussions:
- discussion_id: ccma_beverage_coculture_conditions
- prompt: >-
- Which inoculation ratio, beverage ingredient proportions, fermentation
- temperature, and aeration conditions were used for the CCMA 0743/CCMA 0615
- plant-based beverage co-culture?
+ prompt: Which inoculation ratio, beverage ingredient proportions, fermentation temperature, and aeration conditions
+ were used for the CCMA 0743/CCMA 0615 plant-based beverage co-culture?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- growth_media#Oat-almond-sunflower plant-based beverage
- rationale: >-
- The PubMed abstract identifies the two strains, the oat/almond/sunflower
- substrate, the 24 h fermentation endpoint, and measured metabolite and host
- endpoints, but it does not expose the recipe or inoculation parameters
+ rationale: The PubMed abstract identifies the two strains, the oat/almond/sunflower substrate, the 24 h fermentation
+ endpoint, and measured metabolite and host endpoints, but it does not expose the recipe or inoculation parameters
needed to fully reproduce the fermentation.
posed_by: codex
posed_date: '2026-09-11'
+- discussion_id: ccma-beverage-missing-biological-graph
+ prompt: Which source-supported fermentation and host-response nodes belong in this currently absent graph?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - engineering_design
+ - growth_media#Oat-almond-sunflower plant-based beverage
+ rationale: 'Preserve the observed 24 h viable counts (9.32 and 7.05 log CFU/mL), carbohydrate utilization, acidification,
+ increased bioactive compounds and simulated-digestion bioaccessibility. The fermented whole beverage promoted
+ microbial recovery in vancomycin-treated BALB/c mice. These positives do not establish partner-resolved cross-feeding,
+ reciprocal fitness, intestinal colonization, mediation by a specific compound, or benefit in humans. Primary
+ access is abstract-only. New graph structure remains #1707; a one-community Edison dry run is not a reviewed
+ paid report. No node or arrow is added in this discussion-only review.'
+ evidence:
+ - reference: PMID:42637394
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The process facilitated carbohydrate utilization, acidification, and the generation of bioactive metabolites.
+ explanation: Supports fermentation-associated substrate use, acidification, and metabolite production by the
+ defined co-culture.
+ - reference: PMID:42637394
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Administration of the fermented beverage promoted microbial recovery
+ explanation: Supports testing the fermented co-culture beverage in a host dysbiosis recovery assay.
+ posed_by: codex
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -209,3 +231,10 @@ metal_notes: >-
The cited abstract reports plant-based beverage fermentation and gut
microbiota recovery endpoints, not metal stress, metal transformation, or
metal cycling.
+curation_history:
+- timestamp: '2026-10-07T09:58:34Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Document positive findings and assay limits for an empty graph pending scoped Edison research; no topology
+ added. Issue #1707; reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml b/kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml
index f4554b4db..31518bde2 100644
--- a/kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml
+++ b/kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml
@@ -202,19 +202,54 @@ curation_history:
curator: codex
action: CREATE_PICOCYSTIS_REFINERY_SWW_CONSORTIUM
changes: Created CommunityMech:000439 from PMID:42397522 with Picocystis plus an activated-sludge bacterial consortium,
- refinery stripped wastewater photobioreactor conditions, pollutant-removal endpoints, and primary PubMed/DOI external
- resources.
+ refinery stripped wastewater photobioreactor conditions, pollutant-removal endpoints, and primary PubMed/DOI
+ external resources.
llm_assisted: true
- timestamp: '2026-09-26T17:03:56Z'
curator: codex
action: FIX_PICOCYSTIS_REVIEW_ISSUES
- changes: 'Addressed adversarial review issues #1116 and #1117 by adding activated-sludge and municipal-WWTP modeled environments,
- and by narrowing the phytotoxicity wording so treated 25% SWW detoxification is not assigned to a Pico or Pico-Bac treatment
- absent from the accessible abstract.'
+ changes: 'Addressed adversarial review issues #1116 and #1117 by adding activated-sludge and municipal-WWTP modeled
+ environments, and by narrowing the phytotoxicity wording so treated 25% SWW detoxification is not assigned to
+ a Pico or Pico-Bac treatment absent from the accessible abstract.'
llm_assisted: true
- timestamp: '2026-09-26T17:10:52Z'
curator: codex
action: FIX_PICOCYSTIS_ENVO_LABEL
- changes: Changed the ENVO:00002001 modeled_environment label from wastewater to the canonical waste water label reported
- by the OAK-backed label-correspondence CI gate.
+ changes: Changed the ENVO:00002001 modeled_environment label from wastewater to the canonical waste water label
+ reported by the OAK-backed label-correspondence CI gate.
llm_assisted: true
+- timestamp: '2026-10-07T09:58:34Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Document positive findings and assay limits for an empty graph pending scoped Edison research; no topology
+ added. Issue #1708; reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml'
+ llm_assisted: true
+discussions:
+- discussion_id: picocystis-treatment-specific-missing-graph
+ prompt: Which treatment-specific removal and biomass phenotypes can be represented without inventing exchange
+ mechanisms?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - engineering_design
+ - environmental_factors#COD and polyphenol removal
+ - environmental_factors#Hydrocarbon removal
+ rationale: 'Pico-Bac achieved 72% COD and 96.4% polyphenol removal in 10% SWW and 80.4% hydrocarbon removal in
+ 25% SWW. Preserve these positives, while Pico monoculture had the greatest oil-and-grease removal (62.2%) in
+ 25% SWW. The abstract does not resolve the Pico/Pico-Bac arm for the 55 mg/g lipid endpoint or treated-water
+ seed response; the existing phytotoxicity qualification remains correct. Pollutant removal does not establish
+ complete mineralization, an O2/CO2 exchange route, or species-resolved bacterial function. Bacteria remains
+ a broad canonical domain grounding. Primary access is abstract-only. New graph structure remains #1708 pending
+ a scoped Edison report; no node or arrow is added by this discussion-only review.'
+ evidence:
+ - reference: PMID:42397522
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Pico-Bac achieved maximum COD and polyphenol reductions of 72% and 96.4%
+ explanation: Quantifies the maximum COD and polyphenol removal attributed to the Pico-Bac consortium.
+ - reference: PMID:42397522
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: hydrocarbon removal was highest (80.4%) at 25% SWW
+ explanation: Quantifies the maximum hydrocarbon removal measured for the consortium.
+ posed_by: codex
diff --git a/kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml b/kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml
index e9a6203f1..cc727fcc8 100644
--- a/kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml
+++ b/kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml
@@ -139,91 +139,109 @@ taxonomy:
biomass accumulation.
explanation: Identifies Bacillus subtilis NA11 as a constituent strain of the optimized SynCom.
ecological_interactions:
-- name: Functionally complementary biocontrol SynCom assembly
- description: The community was assembled from endophytic isolates selected for complementary plant
- growth-promoting and antagonistic functions and for pairwise compatibility, yielding a
- functionally complementary and stable synthetic community rather than any single-strain effect.
- interaction_type: NICHE_PARTITIONING
+- name: Compatibility of Selected Endophytic Isolates
+ description: The five constituent strains were selected using pairwise compatibility tests. Public Supplement
+ Figure S3 shows an agar/filter-disc assay with no inhibition zones among the tested strains. Preserve assay-specific
+ compatibility, not demonstrated long-term stable coexistence, resource partitioning or a causal contribution
+ of complementarity to seedling growth. Screened nitrogen-fixing/IAA traits do not establish ammonia or IAA exchange
+ within this SynCom.
scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: indole-3-acetic acid
- term:
- id: CHEBI:16411
- label: indole-3-acetic acid
- notes: IAA was among the plant growth-promoting traits screened in the endophytic isolates.
- - preferred_term: ammonia
- term:
- id: CHEBI:16134
- label: ammonia
- notes: Nitrogen-fixing potential was among the screened plant growth-promoting traits.
- biological_processes:
- - preferred_term: nitrogen fixation
- term:
- id: GO:0009399
- label: nitrogen fixation
- downstream:
- - target: Pinus Seedling Growth Promotion
- description: Pairwise-compatible strains with complementary plant growth-promoting
- traits form the optimized SynCom that increases Pinus armandii seedling
- height and biomass.
evidence:
- reference: PMID:42322490
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: this study screened endophytic bacteria with superior plant growth-promoting (PGP) and
- antagonistic functions to construct a functionally complementary and stable synthetic microbial
- community (SynCom).
- explanation: Members were chosen for complementary PGP and antagonistic functions, a community-level
- niche/functional partitioning.
-- name: Community antagonism of the blister rust pathogen
- description: Constituent strains were selected for antagonistic potential against the blister rust
- pathogen, assessed by dual-culture assays and inhibition of urediniospore germination; the
- assembled SynCom enhanced blister rust-associated host defense responses.
- interaction_type: COMPETITION
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: defense response
+ snippet: Based on pairwise compatibility tests, a SynCom was constructed
+ explanation: The abstract supports compatibility-based selection; public Supplement Figure S3 specifies the
+ no-inhibition-zone assay, not long-term stability or growth mediation.
+ participating_taxa:
+ - preferred_term: Pseudomonas koreensis RC1
term:
- id: GO:0006952
- label: defense response
- downstream:
- - target: Blister Rust-Associated Defense Enzyme Induction
- description: Antagonistic endophytic strains assembled into the optimized SynCom
- enhance polyphenol oxidase and peroxidase defense responses associated with
- Pinus armandii blister rust resistance.
+ id: NCBITaxon:198620
+ label: Pseudomonas koreensis
+ - preferred_term: Paenibacillus terrae RE7
+ term:
+ id: NCBITaxon:159743
+ label: Paenibacillus terrae
+ - preferred_term: Bacillus velezensis OB3
+ term:
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
+ - preferred_term: Bacillus velezensis NA3
+ term:
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
+ - preferred_term: Bacillus subtilis NA11
+ term:
+ id: NCBITaxon:1423
+ label: Bacillus subtilis
+- name: Antagonistic Activity of Selected Endophytic Isolates
+ description: Selected isolates showed antagonistic activity in vitro. Public Supplement Table S2 and Figure S1
+ identify Phomopsis sp. as the plate-inhibition target, distinct from the separate urediniospore-germination
+ assay with cell-free fermentation supernatants (Figure S2). NA11, NA3 and RE7 occur among the tested inhibitory
+ isolates and in the final SynCom; RC1 and OB3 are not among the nine spore-assay treatments. Preserve isolate
+ inhibition without assigning every result to the complete five-strain community or asserting that direct pathogen
+ inhibition caused host defense-enzyme induction.
+ scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42322490
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: antagonistic potential using dual-culture assays and inhibition of urediniospore germination.
- explanation: Members were screened for antagonism (dual-culture inhibition, urediniospore germination
- suppression) against the rust pathogen.
-- name: Pinus Seedling Growth Promotion
- description: The optimized five-strain SynCom significantly increases Pinus
- armandii seedling height and biomass accumulation in pot experiments.
- interaction_type: MUTUALISM
- scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: indole-3-acetic acid
+ snippet: nine strains with significant antagonistic activity
+ explanation: Supports the positive isolate-screen result. Public supplements distinguish Phomopsis plates from
+ the cell-free urediniospore assay and delimit which isolates overlap the final SynCom; not a whole-SynCom
+ inhibition experiment.
+ participating_taxa:
+ - preferred_term: Paenibacillus terrae RE7
term:
- id: CHEBI:16411
- label: indole-3-acetic acid
- biological_processes:
- - preferred_term: nitrogen fixation
+ id: NCBITaxon:159743
+ label: Paenibacillus terrae
+ - preferred_term: Bacillus velezensis NA3
term:
- id: GO:0009399
- label: nitrogen fixation
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
+ - preferred_term: Bacillus subtilis NA11
+ term:
+ id: NCBITaxon:1423
+ label: Bacillus subtilis
+- name: Pinus Seedling Growth Promotion
+ description: The optimized five-strain SynCom significantly increased Pinus armandii seedling height and biomass
+ accumulation in pot experiments. Preserve this positive host-growth response. The accessible evidence does not
+ isolate IAA production or nitrogen fixation as its mediator, demonstrate individual-strain necessity, or show
+ reciprocal microbial fitness benefits.
+ scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42322490
supports: SUPPORT
- evidence_source: IN_VITRO
+ evidence_source: IN_VIVO
snippet: significantly increased seedling height and biomass accumulation.
- explanation: Supports the seedling-growth effect of the optimized five-strain SynCom.
+ explanation: Supports the significant host-growth endpoint in pot experiments, not demonstrated IAA/nitrogen
+ mediation or reciprocal mutualism.
+ participating_taxa:
+ - preferred_term: Pseudomonas koreensis RC1
+ term:
+ id: NCBITaxon:198620
+ label: Pseudomonas koreensis
+ - preferred_term: Paenibacillus terrae RE7
+ term:
+ id: NCBITaxon:159743
+ label: Paenibacillus terrae
+ - preferred_term: Bacillus velezensis OB3
+ term:
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
+ - preferred_term: Bacillus velezensis NA3
+ term:
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
+ - preferred_term: Bacillus subtilis NA11
+ term:
+ id: NCBITaxon:1423
+ label: Bacillus subtilis
- name: Blister Rust-Associated Defense Enzyme Induction
- description: SynCom treatment raises defense-related polyphenol oxidase and
- peroxidase activities relative to uninoculated Pinus armandii controls,
- consistent with priming blister rust-associated defense responses.
- interaction_type: MUTUALISM
+ description: SynCom treatment increased host polyphenol oxidase (PPO) and peroxidase (POD) activities by 19.1%
+ and 157.3% relative to controls in the pot experiment. Preserve these positive defense-associated enzyme endpoints.
+ They do not alone demonstrate priming, resistance to infection or disease control; the abstract explicitly calls
+ for subsequent in planta biocontrol evaluation.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: defense response
@@ -231,10 +249,73 @@ ecological_interactions:
id: GO:0006952
label: defense response
evidence:
+ - reference: PMID:42322490
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: SynCom treatment enhanced defense-related enzyme activities, increasing polyphenol oxidase (PPO) and
+ peroxidase (POD) activities by 19.1% and 157.3% relative to the control
+ explanation: Supports the measured host enzyme increases, not demonstrated infection resistance or a specific
+ isolate-mediated mechanism.
+ participating_taxa:
+ - preferred_term: Pseudomonas koreensis RC1
+ term:
+ id: NCBITaxon:198620
+ label: Pseudomonas koreensis
+ - preferred_term: Paenibacillus terrae RE7
+ term:
+ id: NCBITaxon:159743
+ label: Paenibacillus terrae
+ - preferred_term: Bacillus velezensis OB3
+ term:
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
+ - preferred_term: Bacillus velezensis NA3
+ term:
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
+ - preferred_term: Bacillus subtilis NA11
+ term:
+ id: NCBITaxon:1423
+ label: Bacillus subtilis
+discussions:
+- discussion_id: pine-assay-compatibility-and-host-causality
+ prompt: Which strain functions mediate the observed seedling responses and actual blister-rust protection?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Compatibility of Selected Endophytic Isolates
+ - ecological_interactions#Antagonistic Activity of Selected Endophytic Isolates
+ - ecological_interactions#Pinus Seedling Growth Promotion
+ - ecological_interactions#Blister Rust-Associated Defense Enzyme Induction
+ rationale: 'Preserve compatibility, isolate antagonism, growth and enzyme responses as separate positive findings.
+ Public Supplement Figures S1-S3 and Table S2 separate Phomopsis inhibition, cell-free urediniospore inhibition
+ and compatibility; these assays do not demonstrate stable community coexistence or direct inhibition by the
+ complete SynCom. Both removed arrows conflated isolate selection/screening with causal mediation of host outcomes.
+ No untested IAA/nitrogen exchange or reciprocal mutualism is assigned. Disease-challenge, strain-removal and
+ mediator perturbations would resolve mechanisms. Main text remains inaccessible, while both public supplements
+ were read and all six PDF pages visually inspected. Non-graph priming/stability and assay-scope claims remain
+ #1709.'
+ evidence:
- reference: PMID:42322490
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: SynCom treatment enhanced defense-related enzyme activities, increasing polyphenol
- oxidase (PPO) and peroxidase (POD) activities by 19.1% and 157.3% relative to the
- control
- explanation: Supports the enhanced defense-enzyme endpoint of the optimized SynCom.
+ snippet: nine strains with significant antagonistic activity
+ explanation: Supports the positive isolate-screen result. Public supplements distinguish Phomopsis plates from
+ the cell-free urediniospore assay and delimit which isolates overlap the final SynCom; not a whole-SynCom
+ inhibition experiment.
+ - reference: PMID:42322490
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: SynCom treatment enhanced defense-related enzyme activities, increasing polyphenol oxidase (PPO) and
+ peroxidase (POD) activities by 19.1% and 157.3% relative to the control
+ explanation: Supports the measured host enzyme increases, not demonstrated infection resistance or a specific
+ isolate-mediated mechanism.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T09:58:34Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve measured pairwise compatibility without stability or niche claims.; Preserve selected-isolate
+ inhibition with correct assay targets and participants.; Preserve positive pot-growth endpoint without untested
+ trait mediation.; Preserve positive host enzyme induction without asserting disease control. Issue #1705; reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml'
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 400d7fba3..31ec933b8 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,24 @@ 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`.
+## Batch85: Denitrification, Beverage, Refinery And Pine
+
+[Decisions](decisions/20261007-four-records-batch85.yaml),
+[validation](validation-20261007-batch85.json) and
+[self-adversarial review](adversarial-review-20261007-batch85.yaml) cover nine
+existing nodes, six arrows and two empty graphs. Seven biological nodes remain;
+two workflow nodes and six unsupported causal directions are removed. Positive
+denitrification, stability, isolate compatibility/inhibition, pot growth and
+defense-enzyme findings remain. Pine supplements separate Phomopsis plate assays
+from cell-free urediniospore inhibition; neither proves SynCom disease control.
+The beverage and refinery records receive discussion-only updates that preserve
+positive endpoints and treatment-specific limits without inventing exchange.
+Missing structures remain `needs_research` under #1706-#1708; non-graph claims
+remain #1709. Three one-community Edison dry runs are not completed paid reports.
+All existing caches and non-graph blocks are preserved, not recertified.
+Repair issues #1704/#1705 close only after protected-main merge. Self-review is
+not independent approval or whole-corpus completion.
+
## Batch84: Diatom, Phenol, Phormidium And Phosphite
[Decisions](decisions/20261007-four-records-batch84.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch85.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch85.yaml
new file mode 100644
index 000000000..8f961a1e7
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch85.yaml
@@ -0,0 +1,395 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 345eedc71e173c75dff8d5692ef946aeb3c908de
+scope:
+- kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
+- kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml
+- kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml
+- kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch85.json
+findings:
+- issue: 1704
+ severity: P2
+ status: addressed_in_this_change
+ finding: Repair workflow and causal-direction claims in denitrifying diversity graph
+ disposition: Close only after protected-main merge.
+- issue: 1705
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate pine isolate screening from SynCom growth and defense endpoints
+ disposition: Close only after protected-main merge.
+- issue: 1706
+ severity: P2
+ status: unresolved_research
+ finding: Review missing biological directions in denitrifying diversity graph
+ disposition: Keep OPEN after graph-repair merge.
+- issue: 1707
+ severity: P2
+ status: unresolved_research
+ finding: Add source-bounded CCMA beverage coculture graph coverage
+ disposition: Keep OPEN after graph-repair merge.
+- issue: 1708
+ severity: P2
+ status: unresolved_research
+ finding: Add treatment-specific Picocystis refinery consortium graph coverage
+ disposition: Keep OPEN after graph-repair merge.
+- issue: 1709
+ severity: P2
+ status: unresolved_non_graph
+ finding: Reconcile batch85 non-graph assay and medium identity claims
+ disposition: Keep OPEN after graph-repair merge.
+adversarial_checks:
+- Fresh post-schema two-root baseline preceded papers:460records921caches,1435nodes598arrows,48warnings0structural.
+ Whole four records and all nine original nodes/six arrows reviewed, including two empty graphs. Seven biological
+ nodes survive; no new topology.
+- Denitrifying CR/DR assembly and 200-generation evolution are workflow, already preserved in engineering_design.
+ Remove only these two nodes and their sequencing arrows. Preserve measured DR productivity/denitrification/stability
+ and Paracoccus dominance; no blanket downgrade of positive experiment.
+- Endpoint-to-dominance and endpoint-to-statistical-decomposition arrows do not establish those directions. Dominance
+ is not a competition intervention, and complementarity/asynchrony does not resolve exchanged compounds. No reversed
+ direction invented;1706requires scoped Edison report. Companion open main text is a different experiment, not
+ primary methods.
+- Beverage absent graph and refinery empty list remain sparse and needs_research. Discussion-only changes preserve
+ viable counts, fermentation/metabolite changes, simulated bioaccessibility and mouse whole-beverage response without
+ partner-resolved exchange, colonization, compound mediation or human extrapolation.
+- Refinery retains treatment-specific Pico-Bac removal positives and Pico-monoculture oil/grease counterexample.
+ Abstract does not resolve lipid/seed arms. Removal is not complete mineralization or measured O2/CO2 exchange.
+ Domain-level bacteria grounding unchanged. Research1707/1708remain unfinished.
+- Pine pairwise compatibility is a no-inhibition-zone assay, not longitudinal coexistence or resource partitioning.
+ Public S1/TableS2 identify Phomopsis plates; S2 uses cell-free supernatants against urediniospores. Explicit final-community
+ screened participants are NA11/NA3/RE7, not RC1/OB3 or every screened isolate. OB3/NA3 retain distinct labels
+ despite species-level shared id.
+- Pine positive pot growth and19.1%PPO/157.3%POD increases remain SUPPORT with IN_VIVO evidence. IAA/nitrogen mediation
+ and reciprocal mutualism are not demonstrated. Two selection/antagonism-to-host arrows removed. Defense-associated
+ enzymes alone are not priming or infection resistance; abstract calls for subsequent inplanta biocontrol evaluation.
+- 'Four primary abstracts and target caches read; main texts unavailable. Both pine supplements read: six rendered
+ PDF pages visually inspected and both XLSX sheets fully cell-parsed. Downloaded small main-figure previews not
+ used for numerical inference. Public source URLs, access scope and hashes retained. No paywall bypass or full-text
+ claim.'
+- All921caches,456otherrecords and raw non-graph blocks preserved byte-for-byte; four appended curation events and
+ histories. Alias-linked non-graph denitrifying evidence unchanged. Schema/strict/terms/references/snippets/history
+ gates pass; broad regressions and deterministic exact-description HTML checks recorded. Parser checks are not
+ browser screenshots;48warnings unchanged, zero structural defects.
+- Dedup978all-state issue titles/bodies and ignored/hidden local search with declared exclusions; closed1116/1117/1118read.
+ Comments/PRs not exhaustive. Three one-community Edison dry runs, zero jobs/credits; scoped paid request unanswered
+ and earlier denials unchanged. Repair1704/1705close only after actual protected-main merge;1706-1709stayOPEN.
+ Self-adversarial COMMENT is not independent approval or corpus completion.
+verification:
+ combined_regressions: 766 passed in 407.08s (0:06:47)
+ new_regression_tests: 10
+ schema_strict_terms_history: Passed with actual outputs/digests
+ references: Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.
+ Eight graph and eight new discussion quotations match independently fetched primary abstracts and existing caches.
+ Literal matching is not entailment or whole-record certification. Public pine supplements provide additional
+ assay context, not inaccessible primary main text.
+ snippet_counts_by_record:
+ kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:
+ MATCH: 15
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml:
+ MATCH: 12
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml:
+ MATCH: 16
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml:
+ MATCH: 11
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ caveat: Both-root recipe actually executed. Exit0 is informational, not a clean-corpus certificate; focused
+ edited-record gates separately pass.
+ output: "# 8908 evidence snippets scanned across 460 files\n MATCH 8773\n RENDERING 20\n ASSEMBLED\
+ \ 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but\
+ \ snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n\
+ \ 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n\
+ \ 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py\
+ \ \n"
+ primary_graph_snippet_proof:
+ primary_matched_graph_quotations: 8
+ primary_matched_new_discussion_quotations: 8
+ independent_abstracts: 4
+ original_pine_pdf_pages_visually_inspected:
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ pine_spreadsheet_tables_read:
+ - S1
+ - S2
+ primary_full_texts_for_target_records_read: 0
+ companion_main_texts_read: 1
+ retained_nodes: 7
+ removed_workflow_nodes: 2
+ retained_arrows: 0
+ removed_arrows: 6
+ new_nodes_or_arrows: 0
+ sparse_graphs_pending: 2
+ network:
+ existing_findings_preserved: 48
+ added_findings: {}
+ removed_findings: {}
+ interpretation: All48existingwarnings unchanged; zero structural defects. No taxonomy or auditor-rule changes.
+ Explicit pine participants retain distinct strain labels.
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml: 69d8051fe60a9a97abb76811bb274dca012274d3d3c44a124f663885b2631316
+ tests/test_causal_review_batch85.py: 51bec64bf36d4c4a3a4adae6946cef4332f41dc3f431f28d36ad882d07d3a73c
+ tests/test_participating_taxa.py: ee9f528f3bfe58149c99f2bf3761b82c0bf17a1d82a7fd96b28dfddc5183db55
+ kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml: 6c83e98d24d68c5be779516c7d8a827629f79a37d7b91597db85ca7e727a8bd6
+ kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml: 1dff5927ac9481854b9b13e67efb7fa7be2353674710553de2490207e9996dd9
+ kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml: a2ac824aec0e51a196e0fccaca9f7346f74b0fc331704c53e69b6b04ff731c12
+ kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml: 609a40bb20f1ec5b5bb35f3a8805707bd7478c87b345d517c3c32b3d8af41625
+ reports/causal_graph_review/README.md: 771752437833af154c2224f19cae844224fdf5a8148d82170d9795c5460dd4a5
+ unchanged_caches: 921
+ cache_changes: []
+ unchanged_records: 456
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000113
+ job: LITERATURE
+ query_chars: 11340
+ query_sha256: e629f63819e9d190cd7959db15899012fd0935475242c0e452d552a202de0447
+ meta_path: /private/tmp/communitymech-batch85/edison-denitrifying/Phylogenetically_Diverse_Denitrifying_SynCom-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes
+ unchanged.
+ - community_id: CommunityMech:000345
+ job: LITERATURE
+ query_chars: 7735
+ query_sha256: d716659ba349d168bf97f0e232e8cef2cc0cd5d6cb006f0f929b1762ec47458d
+ meta_path: /private/tmp/communitymech-batch85/edison-beverage/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes
+ unchanged.
+ - community_id: CommunityMech:000439
+ job: LITERATURE
+ query_chars: 8529
+ query_sha256: 6b302426070d69df43bfa4edb1a1a2fb899fb008f7c8b6586aba439e7ce5c234
+ meta_path: /private/tmp/communitymech-batch85/edison-refinery/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes
+ unchanged.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+ regression_correction: 'Preserved initial failure: explicit pine participating_taxa adds one intentional allowlist
+ user. Actual connectivity census unchanged. Added only that filename to the exact-use allowlist; no auditor
+ rule, census bound or production record changed to hide the failure.'
+ initial_failed_regression_output:
+ 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_batch53.py
+ - tests/test_causal_review_batch54.py
+ - tests/test_causal_review_batch55.py
+ - tests/test_causal_review_batch56.py
+ - tests/test_causal_review_batch57.py
+ - tests/test_causal_review_batch58.py
+ - tests/test_causal_review_batch59.py
+ - tests/test_causal_review_batch6.py
+ - tests/test_causal_review_batch60.py
+ - tests/test_causal_review_batch61.py
+ - tests/test_causal_review_batch62.py
+ - tests/test_causal_review_batch63.py
+ - tests/test_causal_review_batch64.py
+ - tests/test_causal_review_batch65.py
+ - tests/test_causal_review_batch66.py
+ - tests/test_causal_review_batch67.py
+ - tests/test_causal_review_batch68.py
+ - tests/test_causal_review_batch69.py
+ - tests/test_causal_review_batch7.py
+ - tests/test_causal_review_batch70.py
+ - tests/test_causal_review_batch71.py
+ - tests/test_causal_review_batch72.py
+ - tests/test_causal_review_batch73.py
+ - tests/test_causal_review_batch74.py
+ - tests/test_causal_review_batch75.py
+ - tests/test_causal_review_batch76.py
+ - tests/test_causal_review_batch77.py
+ - tests/test_causal_review_batch78.py
+ - tests/test_causal_review_batch79.py
+ - tests/test_causal_review_batch8.py
+ - tests/test_causal_review_batch80.py
+ - tests/test_causal_review_batch81.py
+ - tests/test_causal_review_batch82.py
+ - tests/test_causal_review_batch83.py
+ - tests/test_causal_review_batch84.py
+ - tests/test_causal_review_batch85.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: 1
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch85/regressions-initial.log
+ log_sha256: 4c79ba80daf30bf5192b578c7802740e601376e20b51f70aad0798431e0456ba
+ output_tail: "........................................................................ [ 9%]\n........................................................................\
+ \ [ 18%]\n........................................................................ [ 28%]\n........................................................................\
+ \ [ 37%]\n........................................................................ [ 46%]\n........................................................................\
+ \ [ 56%]\n........................................................................ [ 65%]\n........................................................................\
+ \ [ 75%]\n........................................................................ [ 84%]\n.....................................F..................................\
+ \ [ 93%]\n.............................................. [100%]\n===================================\
+ \ FAILURES ===================================\n_________________ test_the_corpus_is_unchanged_by_this_feature\
+ \ _________________\n\n def test_the_corpus_is_unchanged_by_this_feature():\n \"\"\"Only the records\
+ \ that mean to use the slot do.\n \n Asserted on the corpus rather than trusted from the schema:\
+ \ an\n `ifabsent` or a default that quietly populated the slot would change 312\n records' connectivity\
+ \ without anyone editing a record. That is still the\n failure this catches \u2014 a silent default\
+ \ would put every record in `users`,\n not just the three named below.\n \"\"\"\n users\
+ \ = {\n path.name\n for path in record_files()\n for interaction in (yaml.safe_load(path.read_text())\
+ \ or {}).get(\"ecological_interactions\")\n or []\n if isinstance(interaction, dict)\
+ \ and interaction.get(\"participating_taxa\")\n }\n> assert users == USERS, (\n f\"\
+ {len(users)} records use participating_taxa, expected {len(USERS)}. \"\n f\"Adding a user is fine\
+ \ \u2014 but the connectivity numbers in \"\n f\"tests/test_community_level_connectivity_credit.py\
+ \ were measured \"\n f\"before the slot was used, so re-check them and then update USERS. \"\n\
+ \ f\"Added: {sorted(users - USERS)}. Removed: {sorted(USERS - users)}\"\n )\nE AssertionError:\
+ \ 244 records use participating_taxa, expected 243. Adding a user is fine \u2014 but the connectivity numbers\
+ \ in tests/test_community_level_connectivity_credit.py were measured before the slot was used, so re-check\
+ \ them and then update USERS. Added: ['Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml']. Removed: []\nE\
+ \ assert {'AMD_Acidoph...re.yaml', ...} == {'AMD_Acidoph...re.yaml', ...}\nE \nE Extra\
+ \ items in the left set:\nE 'Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml'\nE Use -v to\
+ \ get more diff\n\ntests/test_participating_taxa.py:428: AssertionError\n=========================== short\
+ \ test summary info ============================\nFAILED tests/test_participating_taxa.py::test_the_corpus_is_unchanged_by_this_feature\n\
+ 1 failed, 765 passed in 277.98s (0:04:37)\n"
+ disposition: 'Preserved initial failure: explicit pine participating_taxa adds one intentional allowlist user.
+ Actual connectivity census unchanged. Added only that filename to the exact-use allowlist; no auditor rule,
+ census bound or production record changed to hide the failure.'
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 394
+ mixed: 126
+ community_level_only: 268
+ taxa: 1517
+ credited_solely_by_the_rule: 1243
+ current:
+ records: 460
+ with_community_level: 394
+ mixed: 126
+ community_level_only: 268
+ taxa: 1517
+ credited_solely_by_the_rule: 1243
+ delta:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ interpretation: Legacy community-level census unchanged. It counts members without pairwise representation, not
+ actual explicit participant coverage; no canonical taxon or auditor-rule change.
+corpus:
+ records: 460
+ nodes: 1433
+ edges: 592
+ review_status_counts:
+ needs_research: 47
+ pending: 152
+ reviewed: 261
+limitations:
+- Fresh post-schema before-paper two-root baseline:460records,921caches,1435nodes598arrows,48warnings and zero structural
+ defects. Nine original nodes/six arrows reviewed; seven biological nodes remain and no arrows. Two empty graphs
+ remain explicitly needs_research, not certified complete.
+- Four independent primary abstracts and all four existing target caches read. Primary main texts remain inaccessible;
+ publisher previews are not full texts. Open companion PMID37154752 main text read, but its all-Shewanella 60transfer/180day
+ experiment cannot establish exact CR/DR primary methods. No paywall bypass.
+- 'Both openly linked pine supplements read: all six PDF pages visually inspected after local rendering, XLSX tables
+ S1/S2 parsed as cells. Phomopsis plates, cell-free urediniospore inhibition and pairwise compatibility are distinct
+ assays. Small publisher main-figure previews were downloaded but not used for numerical claims; main figures/full
+ methods not audited.'
+- Preserve denitrification/productivity/stability positives and ecological decomposition, without dominance intervention
+ or compound-resolved niche claims. Remove workflow nodes and noncausal directions; biological direction research1706remains
+ open.
+- Preserve pine compatibility, selected-isolate inhibition, pot growth and PPO/POD increases. Remove reciprocal
+ mutualism, unsupported trait mediation and two isolate-to-host arrows. Explicit participants distinguish three
+ screened final-community isolates from all five pot/compatibility members; species-sharing OB3/NA3 remain distinct
+ labels. No disease-control or priming proof.
+- Beverage/refinery discussion-only edits preserve positive endpoints without adding structure. Whole-beverage mouse
+ response is not human benefit or specific-metabolite mediation. Pico monoculture wins oil/grease removal; ambiguous
+ lipid/seed treatment arms remain unassigned. New structure1707/1708requires reviewed scoped Edison report.
+- All921caches,456otherrecords and raw non-graph blocks unchanged. Four append-only histories and concrete curation
+ events. Existing non-graph claims preserved, not certified; metadata1709remains open. Denitrifying YAML alias
+ is preserved outside graph without mutation leakage.
+- Dedup current all-state issue titles/bodies and ignored/hidden local searches with explicit .git/docs/site/references_cache
+ exclusions; target caches separately read. Closed1116/1117/1118bodies read. Comments/PRs not exhaustive.
+- Three single-community Edison causal dry runs:11340/7735/8529characters, zero provider jobs or credits. Scoped
+ request unanswered; initial generic authorization and prior denied scopes do not authorize these jobs. Repair1704/1705close
+ only after protected-main merge;1706-1709remainOPEN.
+- Validation/rendering outputs are recorded separately, not preasserted. Self-adversarial review is not independent
+ approval, whole-record certification or corpus completion. Protected merge and dependent-safe branch cleanup remain
+ separate gates.
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
new file mode 100644
index 000000000..83ebd87e1
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
@@ -0,0 +1,493 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+source_access:
+- reference: PMID:37207729
+ url: https://doi.org/10.1016/j.envres.2023.116184
+ accessed_scope: Primary abstract; publisher full text inaccessible.
+- reference: PMID:42637394
+ url: https://doi.org/10.1016/j.foodres.2026.120292
+ accessed_scope: Primary abstract; publisher full text inaccessible.
+- reference: PMID:42397522
+ url: https://doi.org/10.1007/s12010-026-05746-2
+ accessed_scope: Primary abstract and public publisher preview, not main text.
+- reference: PMID:42322490
+ url: https://doi.org/10.1007/s11274-026-05099-2
+ accessed_scope: Primary abstract, public publisher preview and both public supplements, not main text.
+ supplements:
+ - url: https://media.springernature.com/original/springer-static/esm/art%3A10.1007%2Fs11274-026-05099-2/MediaObjects/11274_2026_5099_MOESM1_ESM.pdf
+ sha256: efaa04f5850577edce0842654602e8cee2aa22f20bf2a38f3399f3ed2e768790
+ inspected: All six pages rendered and visually read. S1 is Phomopsis plate inhibition;
+ S2 is cell-free supernatant urediniospore germination at 8/24/48 h;
+ S3 is no-inhibition-zone compatibility, not longitudinal stability.
+ - url: https://media.springernature.com/original/springer-static/esm/art%3A10.1007%2Fs11274-026-05099-2/MediaObjects/11274_2026_5099_MOESM2_ESM.xlsx
+ sha256: ba39d5946d0744d407969f7cd593b5af22e9ea5bae69d0cea4609db4ea7bf37b
+ inspected: All cells in Table S1 and Table S2 parsed and read. Table S2 identifies
+ Phomopsis sp. as the inhibition target, with NA11/NA3/RE7 in rows 4/5/12;
+ the other screened isolates are not automatically canonical SynCom members.
+- reference: PMID:37154752
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC10269844/
+ accessed_scope: Open primary main text and captions read. Separate all-Shewanella
+ experiment; not proof of identical CR/DR medium or methods.
+base_commit: 345eedc71e173c75dff8d5692ef946aeb3c908de
+baseline_commit: 345eedc71e173c75dff8d5692ef946aeb3c908de
+base_tree: 0c0a274b883e5ead55f62ef8f9a578564d934423
+pre_source_baseline_sha256: 21fa3bbb7162c1c290ae8ab4b3f4e419c121433f90bab34067fcd107a422c829
+issues:
+- 1704
+- 1705
+unresolved_non_graph_issues:
+- 1709
+unresolved_research_issues:
+- 1706
+- 1707
+- 1708
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 978
+ ignored_hidden_local_search: true
+ matching_issues:
+ - 1116
+ - 1117
+ - 1118
+primary_artifacts:
+ /private/tmp/communitymech-batch85/baseline-post-schema.json: 21fa3bbb7162c1c290ae8ab4b3f4e419c121433f90bab34067fcd107a422c829
+ /private/tmp/communitymech-batch85/beverage-primary.txt: 9462e28062aecdb2298147aa4dd96d13d947f58bc21b161b0824acd7bcb9cd29
+ /private/tmp/communitymech-batch85/denitrifying-companion-primary.txt: aab14ff5f927abf85448b28a1d41b4d310d20a7c06fc6e570183ed63fb9dde0c
+ /private/tmp/communitymech-batch85/denitrifying-companion-primary.xml: 04251a3d770a72369500f502eb002bf87fc3997975e2fd1d22b06cc458a2a1ce
+ /private/tmp/communitymech-batch85/denitrifying-primary.txt: 0034c270a4a3e08302057a43841faa47077a0564b817538526fc8dff75cc8b28
+ ? /private/tmp/communitymech-batch85/edison-beverage/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-edison-literature-causal-meta.yaml
+ : 7115175082671e89a41c65577009794910a55d3d5c5f8da7b14241b224e76c93
+ ? /private/tmp/communitymech-batch85/edison-denitrifying/Phylogenetically_Diverse_Denitrifying_SynCom-edison-literature-causal-meta.yaml
+ : 5a8e22061f3318cafa5b17f55388ea56663cd5d69820587dd7c03e90dcfece9d
+ ? /private/tmp/communitymech-batch85/edison-refinery/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-edison-literature-causal-meta.yaml
+ : 3f47b042593340e4db04fda874af133a64e8574c1f4773b44178adb2461377fe
+ /private/tmp/communitymech-batch85/issue-matches-current.json: 44d38b49d65e665a774d7b8fa6068f1449f524885cb502ff1c7736fd8640b6c9
+ /private/tmp/communitymech-batch85/issues-current.json: 92ccb1eeccd4e3c40c48c5340a733013528f9835c25a777d91143d9f39da1b0d
+ /private/tmp/communitymech-batch85/local-matches-current.txt: 04f774ac16be00150ce6b24f7db100295024f20af6442b1c792e303ec294e47c
+ /private/tmp/communitymech-batch85/pine-primary.txt: 1c35598339d51721e06073186086218d702b5671157b41dc878bc434ab94f407
+ /private/tmp/communitymech-batch85/pine-public-materials.json: f8595afe97bcc1533082e35c6576142e484fe280e35957c8e2fdb86697cf8dc5
+ /private/tmp/communitymech-batch85/pine-supplement-cells.json: 2d0f5615be64986428ba4cf9c5ab0b905b342bf4fc666795dcbff10a5739d797
+ /private/tmp/communitymech-batch85/pine-supplement-page-1.png: fa6b43c2a624e9ec0e1191a6de4baf0c7d924d097655013ec2f7509c374944b0
+ /private/tmp/communitymech-batch85/pine-supplement-page-2.png: 094502dc678704e367611338a6cab6c64c41362017e2709ef9230f28d5929afe
+ /private/tmp/communitymech-batch85/pine-supplement-page-3.png: 4f3508af00faee64e436d1d3c72fcfee9119b2a17bf46fc8d9f958633d65589e
+ /private/tmp/communitymech-batch85/pine-supplement-page-4.png: 87786140b55c09d6b7cfb392f9ac503905ae16c82e6e86a9ee8a1b0b33efd803
+ /private/tmp/communitymech-batch85/pine-supplement-page-5.png: fad7c1a7bee89c5f1e78712b07e5caeb7f811f3d6dfa6680e68322c0b49c2201
+ /private/tmp/communitymech-batch85/pine-supplement-page-6.png: 95d18cef9c7051ad6824ba582391da9dd385443fd24bc8867a8ca9b5c4b1f6ac
+ /private/tmp/communitymech-batch85/pine-supplement-text.txt: 16d6c3e6d277acc9422e7a3f681340e9d26afd653ba933a581e05f2d2703749f
+ /private/tmp/communitymech-batch85/pine-supplement.pdf: efaa04f5850577edce0842654602e8cee2aa22f20bf2a38f3399f3ed2e768790
+ /private/tmp/communitymech-batch85/pine-supplement.xlsx: ba39d5946d0744d407969f7cd593b5af22e9ea5bae69d0cea4609db4ea7bf37b
+ /private/tmp/communitymech-batch85/primary-manifest.json: ba334d0a9f473db0cdf5c0d6c6591699cf941d165368accddf4f1a2d490a60e7
+ /private/tmp/communitymech-batch85/refinery-primary.txt: 688e29004759b04ff3666fed2bf14ad13d7fcb78db50dd38c2f9732128e61434
+ references_cache/PMID_37207729.txt: 2225530d0227f4db6d687d6947445e42832558a0de1a08f8a6d460e7af021c1b
+ references_cache/PMID_42322490.md: d3d1b16bc84a9fcbe70aef2614f51e9945a14d5239de7a37cf0c558ce1068572
+ references_cache/PMID_42397522.txt: 3993a5e3f7cec682e5210c20c70918851c76701571d85c23ac2253d353415d60
+ references_cache/PMID_42637394.txt: 6536061250106cbf04fe8141d68ea9f733fbc8784cfd86dc3174939b4880607c
+primary_graph_snippet_count: 8
+independent_fresh_primary_graph_snippet_count: 8
+cache_matched_graph_snippet_count: 8
+snippet_checks:
+- record: Phylogenetically_Diverse_Denitrifying_SynCom
+ node: High-Phylogenetic-Diversity Function and Stability
+ reference: PMID:37207729
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/denitrifying-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Phylogenetically_Diverse_Denitrifying_SynCom
+ node: Paracoccus-Dominated DR Denitrification
+ reference: PMID:37207729
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/denitrifying-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Phylogenetically_Diverse_Denitrifying_SynCom
+ node: DR Overyielding and Asynchronous Stability
+ reference: PMID:37207729
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/denitrifying-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Phylogenetically_Diverse_Denitrifying_SynCom
+ node: DR Overyielding and Asynchronous Stability
+ reference: PMID:37207729
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/denitrifying-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pinus_armandii_Endophytic_Biocontrol_SynCom
+ node: Compatibility of Selected Endophytic Isolates
+ reference: PMID:42322490
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/pine-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pinus_armandii_Endophytic_Biocontrol_SynCom
+ node: Antagonistic Activity of Selected Endophytic Isolates
+ reference: PMID:42322490
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/pine-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pinus_armandii_Endophytic_Biocontrol_SynCom
+ node: Pinus Seedling Growth Promotion
+ reference: PMID:42322490
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/pine-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pinus_armandii_Endophytic_Biocontrol_SynCom
+ node: Blister Rust-Associated Defense Enzyme Induction
+ reference: PMID:42322490
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/pine-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+discussion_snippet_checks:
+- record: Phylogenetically_Diverse_Denitrifying_SynCom
+ node: denitrifying-design-versus-biological-direction
+ reference: PMID:37207729
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/denitrifying-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Phylogenetically_Diverse_Denitrifying_SynCom
+ node: denitrifying-design-versus-biological-direction
+ reference: PMID:37207729
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/denitrifying-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture
+ node: ccma-beverage-missing-biological-graph
+ reference: PMID:42637394
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/beverage-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture
+ node: ccma-beverage-missing-biological-graph
+ reference: PMID:42637394
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/beverage-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Picocystis_Activated_Sludge_Refinery_SWW_Consortium
+ node: picocystis-treatment-specific-missing-graph
+ reference: PMID:42397522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/refinery-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Picocystis_Activated_Sludge_Refinery_SWW_Consortium
+ node: picocystis-treatment-specific-missing-graph
+ reference: PMID:42397522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/refinery-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pinus_armandii_Endophytic_Biocontrol_SynCom
+ node: pine-assay-compatibility-and-host-causality
+ reference: PMID:42322490
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/pine-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+- record: Pinus_armandii_Endophytic_Biocontrol_SynCom
+ node: pine-assay-compatibility-and-host-causality
+ reference: PMID:42322490
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch85/pine-primary.txt
+ method: NFKD/case/whitespace/punctuation-normalized contiguous match to independently fetched primary abstract;
+ matching is not entailment.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000113
+ job: LITERATURE
+ query_chars: 11340
+ query_sha256: e629f63819e9d190cd7959db15899012fd0935475242c0e452d552a202de0447
+ meta_path: /private/tmp/communitymech-batch85/edison-denitrifying/Phylogenetically_Diverse_Denitrifying_SynCom-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes unchanged.
+ - community_id: CommunityMech:000345
+ job: LITERATURE
+ query_chars: 7735
+ query_sha256: d716659ba349d168bf97f0e232e8cef2cc0cd5d6cb006f0f929b1762ec47458d
+ meta_path: /private/tmp/communitymech-batch85/edison-beverage/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes unchanged.
+ - community_id: CommunityMech:000439
+ job: LITERATURE
+ query_chars: 8529
+ query_sha256: 6b302426070d69df43bfa4edb1a1a2fb899fb008f7c8b6586aba439e7ce5c234
+ meta_path: /private/tmp/communitymech-batch85/edison-refinery/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes unchanged.
+limitations:
+- Fresh post-schema before-paper two-root baseline:460records,921caches,1435nodes598arrows,48warnings and zero structural
+ defects. Nine original nodes/six arrows reviewed; seven biological nodes remain and no arrows. Two empty graphs
+ remain explicitly needs_research, not certified complete.
+- Four independent primary abstracts and all four existing target caches read. Primary main texts remain inaccessible;
+ publisher previews are not full texts. Open companion PMID37154752 main text read, but its all-Shewanella 60transfer/180day
+ experiment cannot establish exact CR/DR primary methods. No paywall bypass.
+- 'Both openly linked pine supplements read: all six PDF pages visually inspected after local rendering, XLSX tables
+ S1/S2 parsed as cells. Phomopsis plates, cell-free urediniospore inhibition and pairwise compatibility are distinct
+ assays. Small publisher main-figure previews were downloaded but not used for numerical claims; main figures/full
+ methods not audited.'
+- Preserve denitrification/productivity/stability positives and ecological decomposition, without dominance intervention
+ or compound-resolved niche claims. Remove workflow nodes and noncausal directions; biological direction research1706remains
+ open.
+- Preserve pine compatibility, selected-isolate inhibition, pot growth and PPO/POD increases. Remove reciprocal
+ mutualism, unsupported trait mediation and two isolate-to-host arrows. Explicit participants distinguish three
+ screened final-community isolates from all five pot/compatibility members; species-sharing OB3/NA3 remain distinct
+ labels. No disease-control or priming proof.
+- Beverage/refinery discussion-only edits preserve positive endpoints without adding structure. Whole-beverage mouse
+ response is not human benefit or specific-metabolite mediation. Pico monoculture wins oil/grease removal; ambiguous
+ lipid/seed treatment arms remain unassigned. New structure1707/1708requires reviewed scoped Edison report.
+- All921caches,456otherrecords and raw non-graph blocks unchanged. Four append-only histories and concrete curation
+ events. Existing non-graph claims preserved, not certified; metadata1709remains open. Denitrifying YAML alias
+ is preserved outside graph without mutation leakage.
+- Dedup current all-state issue titles/bodies and ignored/hidden local searches with explicit .git/docs/site/references_cache
+ exclusions; target caches separately read. Closed1116/1117/1118bodies read. Comments/PRs not exhaustive.
+- Three single-community Edison causal dry runs:11340/7735/8529characters, zero provider jobs or credits. Scoped
+ request unanswered; initial generic authorization and prior denied scopes do not authorize these jobs. Repair1704/1705close
+ only after protected-main merge;1706-1709remainOPEN.
+- Validation/rendering outputs are recorded separately, not preasserted. Self-adversarial review is not independent
+ approval, whole-record certification or corpus completion. Protected merge and dependent-safe branch cleanup remain
+ separate gates.
+records:
+- path: kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
+ id: CommunityMech:000113
+ original_sha256: bd336eec9803f039fb90ad644a4e2329856b624ab6f35fc0b1ec725550ccb4ef
+ record_sha256: 6c83e98d24d68c5be779516c7d8a827629f79a37d7b91597db85ca7e727a8bd6
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
+ scope: Whole record, all existing nodes/arrows and empty/missing structures; not whole-record certification.
+ summary: Preserve positive DR function and stability without workflow causality.; Preserve Paracoccus dominance/function
+ association without competition or mediation claims.; Preserve overyielding, asynchrony and complementarity
+ without unmeasured resource mechanisms.
+ renamed_nodes: {}
+ node_decisions:
+ - node: High-Phylogenetic-Diversity Function and Stability
+ original_node: High-Phylogenetic-Diversity Function and Stability
+ rationale: Preserve positive DR function and stability without workflow causality.
+ - node: Paracoccus-Dominated DR Denitrification
+ original_node: Paracoccus-Dominated DR Denitrification
+ rationale: Preserve Paracoccus dominance/function association without competition or mediation claims.
+ - node: DR Overyielding and Asynchronous Stability
+ original_node: DR Overyielding and Asynchronous Stability
+ rationale: Preserve overyielding, asynchrony and complementarity without unmeasured resource mechanisms.
+ removed_node_decisions:
+ - node: CR and DR Denitrifying SynCom Design
+ rationale: Experimental assembly/evolution workflow is already represented in engineering_design, not a biological
+ interaction.
+ - node: Two-Hundred-Generation SDC Evolution
+ rationale: Experimental assembly/evolution workflow is already represented in engineering_design, not a biological
+ interaction.
+ edges_before:
+ - source: CR and DR Denitrifying SynCom Design
+ target: Two-Hundred-Generation SDC Evolution
+ description: 'The phylogenetic-distance-based CR and DR SynComs seeded a 200-generation laboratory evolution
+ experiment.
+
+ '
+ - source: Two-Hundred-Generation SDC Evolution
+ target: High-Phylogenetic-Diversity Function and Stability
+ description: 'Experimental evolution exposed the functional and temporal-stability advantage of the high-phylogenetic-diversity
+ DR communities.
+
+ '
+ - source: High-Phylogenetic-Diversity Function and Stability
+ target: Paracoccus-Dominated DR Denitrification
+ description: 'Evolved, distantly related communities had higher productivity and denitrification rates when
+ Paracoccus denitrificans dominated them.
+
+ '
+ - source: High-Phylogenetic-Diversity Function and Stability
+ target: DR Overyielding and Asynchronous Stability
+ description: 'Evolved DR stability was decomposed into overyielding, asynchronous species fluctuations, and
+ higher complementarity than the CR group.
+
+ '
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: CR and DR Denitrifying SynCom Design
+ target: Two-Hundred-Generation SDC Evolution
+ description: 'The phylogenetic-distance-based CR and DR SynComs seeded a 200-generation laboratory evolution
+ experiment.
+
+ '
+ rationale: Workflow sequence or endpoint-to-component/statistical-decomposition wording does not support this
+ causal direction.
+ - source: Two-Hundred-Generation SDC Evolution
+ target: High-Phylogenetic-Diversity Function and Stability
+ description: 'Experimental evolution exposed the functional and temporal-stability advantage of the high-phylogenetic-diversity
+ DR communities.
+
+ '
+ rationale: Workflow sequence or endpoint-to-component/statistical-decomposition wording does not support this
+ causal direction.
+ - source: High-Phylogenetic-Diversity Function and Stability
+ target: Paracoccus-Dominated DR Denitrification
+ description: 'Evolved, distantly related communities had higher productivity and denitrification rates when
+ Paracoccus denitrificans dominated them.
+
+ '
+ rationale: Workflow sequence or endpoint-to-component/statistical-decomposition wording does not support this
+ causal direction.
+ - source: High-Phylogenetic-Diversity Function and Stability
+ target: DR Overyielding and Asynchronous Stability
+ description: 'Evolved DR stability was decomposed into overyielding, asynchronous species fluctuations, and
+ higher complementarity than the CR group.
+
+ '
+ rationale: Workflow sequence or endpoint-to-component/statistical-decomposition wording does not support this
+ causal direction.
+ references:
+ - PMID:37207729
+ issues:
+ - 1704
+ - 1706
+ - 1709
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Phylogenetically_Diverse_Denitrifying_SynCom/2026-10-07T095834Z-codex-e0b6a8.yaml
+- path: kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml
+ id: CommunityMech:000345
+ original_sha256: 5938d9747c5e6390c25c63b785274d3777ee3d001ee2ad0ae395df127924dc38
+ record_sha256: 1dff5927ac9481854b9b13e67efb7fa7be2353674710553de2490207e9996dd9
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
+ scope: Whole record, all existing nodes/arrows and empty/missing structures; not whole-record certification.
+ summary: Document positive findings and assay limits for an empty graph pending scoped Edison research; no topology
+ added.
+ renamed_nodes: {}
+ node_decisions: []
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42637394
+ issues:
+ - 1707
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture/2026-10-07T095835Z-codex-663d7b.yaml
+- path: kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml
+ id: CommunityMech:000439
+ original_sha256: 3b4e98ee0068741c69599d341f74912b58256dcdc28eacceed083f771439fde9
+ record_sha256: a2ac824aec0e51a196e0fccaca9f7346f74b0fc331704c53e69b6b04ff731c12
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
+ scope: Whole record, all existing nodes/arrows and empty/missing structures; not whole-record certification.
+ summary: Document positive findings and assay limits for an empty graph pending scoped Edison research; no topology
+ added.
+ renamed_nodes: {}
+ node_decisions: []
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42397522
+ issues:
+ - 1708
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ curation_events_added: 1
+ history_files:
+ - history/records/Picocystis_Activated_Sludge_Refinery_SWW_Consortium/2026-10-07T095835Z-codex-a3e7a7.yaml
+- path: kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml
+ id: CommunityMech:000280
+ original_sha256: 6e5198d8a50c9531122f64dcbbdbe1c4f7ecbcf86755b74c1f3057f6f6476149
+ record_sha256: 609a40bb20f1ec5b5bb35f3a8805707bd7478c87b345d517c3c32b3d8af41625
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml
+ scope: Whole record, all existing nodes/arrows and empty/missing structures; not whole-record certification.
+ summary: Preserve measured pairwise compatibility without stability or niche claims.; Preserve selected-isolate
+ inhibition with correct assay targets and participants.; Preserve positive pot-growth endpoint without untested
+ trait mediation.; Preserve positive host enzyme induction without asserting disease control.
+ renamed_nodes:
+ Functionally complementary biocontrol SynCom assembly: Compatibility of Selected Endophytic Isolates
+ Community antagonism of the blister rust pathogen: Antagonistic Activity of Selected Endophytic Isolates
+ node_decisions:
+ - node: Compatibility of Selected Endophytic Isolates
+ original_node: Functionally complementary biocontrol SynCom assembly
+ rationale: Preserve measured pairwise compatibility without stability or niche claims.
+ - node: Antagonistic Activity of Selected Endophytic Isolates
+ original_node: Community antagonism of the blister rust pathogen
+ rationale: Preserve selected-isolate inhibition with correct assay targets and participants.
+ - node: Pinus Seedling Growth Promotion
+ original_node: Pinus Seedling Growth Promotion
+ rationale: Preserve positive pot-growth endpoint without untested trait mediation.
+ - node: Blister Rust-Associated Defense Enzyme Induction
+ original_node: Blister Rust-Associated Defense Enzyme Induction
+ rationale: Preserve positive host enzyme induction without asserting disease control.
+ removed_node_decisions: []
+ edges_before:
+ - source: Functionally complementary biocontrol SynCom assembly
+ target: Pinus Seedling Growth Promotion
+ description: Pairwise-compatible strains with complementary plant growth-promoting traits form the optimized
+ SynCom that increases Pinus armandii seedling height and biomass.
+ - source: Community antagonism of the blister rust pathogen
+ target: Blister Rust-Associated Defense Enzyme Induction
+ description: Antagonistic endophytic strains assembled into the optimized SynCom enhance polyphenol oxidase
+ and peroxidase defense responses associated with Pinus armandii blister rust resistance.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Functionally complementary biocontrol SynCom assembly
+ target: Pinus Seedling Growth Promotion
+ description: Pairwise-compatible strains with complementary plant growth-promoting traits form the optimized
+ SynCom that increases Pinus armandii seedling height and biomass.
+ rationale: Isolate selection/antagonism does not establish mediation of host growth or enzyme induction.
+ - source: Community antagonism of the blister rust pathogen
+ target: Blister Rust-Associated Defense Enzyme Induction
+ description: Antagonistic endophytic strains assembled into the optimized SynCom enhance polyphenol oxidase
+ and peroxidase defense responses associated with Pinus armandii blister rust resistance.
+ rationale: Isolate selection/antagonism does not establish mediation of host growth or enzyme induction.
+ references:
+ - PMID:42322490
+ issues:
+ - 1705
+ - 1709
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pinus_armandii_Endophytic_Biocontrol_SynCom/2026-10-07T095835Z-codex-75dfd6.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index a88accacd..26cfb9598 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -304,10 +304,10 @@ kb/communities/Phaeodactylum_Aliivibrio_Diel_Coculture.yaml CommunityMech:000446
kb/communities/Phenol_Carboxylation_Consortium.yaml CommunityMech:000053 a778ef6c883f5d6b7c80dc22be5611de4027d08d4f9d3b23e9a0d330f3f768b1 3 3 100.0 reports/causal_graph_review/decisions/20261007-four-records-batch84.yaml reviewed
kb/communities/Phormidium_Alkaline_Consortium.yaml CommunityMech:000054 5bd6ec7333293e123e4b68212ddd64a6db8a8efd69f446912d154b260d79f2f5 4 1 81.7 reports/causal_graph_review/decisions/20261007-four-records-batch84.yaml needs_research
kb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml CommunityMech:000290 e2eda8deadaaa36ce6ee96ed15871e1cc8c674fea990cd76c77bc74d3e13695a 3 2 100.0 reports/causal_graph_review/decisions/20261007-four-records-batch84.yaml needs_research
-kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml CommunityMech:000113 bd336eec9803f039fb90ad644a4e2329856b624ab6f35fc0b1ec725550ccb4ef 5 4 100.0 pending
-kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml CommunityMech:000345 5938d9747c5e6390c25c63b785274d3777ee3d001ee2ad0ae395df127924dc38 0 0 0.0 pending
-kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml CommunityMech:000439 3b4e98ee0068741c69599d341f74912b58256dcdc28eacceed083f771439fde9 0 0 0.0 pending
-kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml CommunityMech:000280 6e5198d8a50c9531122f64dcbbdbe1c4f7ecbcf86755b74c1f3057f6f6476149 4 2 100.0 pending
+kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml CommunityMech:000113 6c83e98d24d68c5be779516c7d8a827629f79a37d7b91597db85ca7e727a8bd6 3 0 65.0 reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml needs_research
+kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml CommunityMech:000345 1dff5927ac9481854b9b13e67efb7fa7be2353674710553de2490207e9996dd9 0 0 0.0 reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml needs_research
+kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml CommunityMech:000439 a2ac824aec0e51a196e0fccaca9f7346f74b0fc331704c53e69b6b04ff731c12 0 0 0.0 reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml needs_research
+kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml CommunityMech:000280 609a40bb20f1ec5b5bb35f3a8805707bd7478c87b345d517c3c32b3d8af41625 4 0 61.2 reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml reviewed
kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml CommunityMech:000300 066483547309020752f7da23b7ecd4fd23e4b7091b9a534fcf5bb66f542766ff 6 2 100.0 pending
kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml CommunityMech:000055 bf7b035cea66dbda1dc465ab7388031bbcc401fa7a92d3f7c369e665062fa7b6 4 2 100.0 pending
kb/communities/Populus_Salt_Tolerant_SynComs.yaml CommunityMech:000090 d1b4f264cd166b2f2095edc86fb98867f19d9d4e39d37ea1ed03046f2ba79354 5 5 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 250c1e81f..01de4e3bc 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -2,14 +2,14 @@
"scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
- "nodes": 1435,
- "edges": 598,
+ "nodes": 1433,
+ "edges": 592,
"records_without_nodes": 8,
- "records_without_edges": 170,
+ "records_without_edges": 172,
"review_status_counts": {
- "needs_research": 44,
- "pending": 156,
- "reviewed": 260
+ "needs_research": 47,
+ "pending": 152,
+ "reviewed": 261
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261007-batch85.json b/reports/causal_graph_review/validation-20261007-batch85.json
new file mode 100644
index 000000000..92df786e8
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch85.json
@@ -0,0 +1,1201 @@
+{
+ "base_commit": "345eedc71e173c75dff8d5692ef946aeb3c908de",
+ "scope": [
+ "kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml",
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml",
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml",
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Phylogenetically_Diverse_Denitrifying_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Phylogenetically_Diverse_Denitrifying_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-strict.tsv",
+ "kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-strict.log",
+ "log_sha256": "b216d8c283363d4a9dee40d55c17dba5b1f4007fe10509eba5e9c1daec80347d",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch85/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-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Phylogenetically_Diverse_Denitrifying_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Phylogenetically_Diverse_Denitrifying_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-references.log",
+ "log_sha256": "2b17cf152bebcf34c3c4760abf5f160713a44e161783ab3937778176c1fec634",
+ "output_tail": "Validating kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Phylogenetically_Diverse_Denitrifying_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-snippets.log",
+ "log_sha256": "826e9c1ef5038bfe5995c8f56b27f9f6d8418cb9a40f124b1547f2d75876c305",
+ "output_tail": "# 15 evidence snippets scanned across 1 files\n MATCH 15\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": "Phylogenetically_Diverse_Denitrifying_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-rank.log",
+ "log_sha256": "f17a4a9e00bd9bf20250bc9ed2b8051bbdbee976297198e7aff46917ead16911",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000113\",\n \"name\": \"Phylogenetically Diverse Denitrifying SynCom\",\n \"score\": 65.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Phylogenetically_Diverse_Denitrifying_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Phylogenetically_Diverse_Denitrifying_SynCom/2026-10-07T095834Z-codex-e0b6a8.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Phylogenetically_Diverse_Denitrifying_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-strict.tsv",
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-strict.log",
+ "log_sha256": "364af962022ed314c557bc1ca98f94e048f5df1de52ef036675809c458704a3d",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch85/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-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-references.log",
+ "log_sha256": "d8712bddb7ed4c7e4a68f05eb2e6f1b4237af0152e58a5386e18d691ba3a791e",
+ "output_tail": "Validating kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.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/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.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": "Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-snippets.log",
+ "log_sha256": "389f1d2b093a1648cf407d53853e429a283f80eed2628a1a14cf1f38649ca780",
+ "output_tail": "# 12 evidence snippets scanned across 1 files\n MATCH 12\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": "Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-rank.log",
+ "log_sha256": "27854fcdb8c26ba6a32d2e6dfabec2ddf0f0b6bc56f0f1327809101e77cfddc3",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000345\",\n \"name\": \"Pichia-Lactiplantibacillus CCMA Plant Beverage Coculture\",\n \"score\": 0.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 0,\n \"disconnected_taxa\": 2,\n \"ecological_interactions\": 0,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 0,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"ecological_interactions\"\n ],\n \"path\": \"kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture/2026-10-07T095835Z-codex-663d7b.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Picocystis_Activated_Sludge_Refinery_SWW_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Picocystis_Activated_Sludge_Refinery_SWW_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-strict.tsv",
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-strict.log",
+ "log_sha256": "b1ff398a3419fba03d98449af33491caa4233e55c6927483e6e3e565f1bd73f7",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch85/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-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Picocystis_Activated_Sludge_Refinery_SWW_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Picocystis_Activated_Sludge_Refinery_SWW_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-references.log",
+ "log_sha256": "c0994039537e3e5416bb4a783553193800feba7a750c5abc24bbaff672db8e74",
+ "output_tail": "Validating kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_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/Picocystis_Activated_Sludge_Refinery_SWW_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": "Picocystis_Activated_Sludge_Refinery_SWW_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-snippets.log",
+ "log_sha256": "f77044cea09a90a006f3fc48666f62a208521829981c6819a3a36631506c4ec1",
+ "output_tail": "# 16 evidence snippets scanned across 1 files\n MATCH 16\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": "Picocystis_Activated_Sludge_Refinery_SWW_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-rank.log",
+ "log_sha256": "9398030ab34aa34931691873e7170db4729ee6bec2beaebb78d89a5857c4054c",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000439\",\n \"name\": \"Picocystis Activated-Sludge Refinery SWW Consortium\",\n \"score\": 0.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 0,\n \"disconnected_taxa\": 2,\n \"ecological_interactions\": 0,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 0,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"ecological_interactions\"\n ],\n \"path\": \"kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Picocystis_Activated_Sludge_Refinery_SWW_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/Picocystis_Activated_Sludge_Refinery_SWW_Consortium/2026-10-07T095835Z-codex-a3e7a7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pinus_armandii_Endophytic_Biocontrol_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pinus_armandii_Endophytic_Biocontrol_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-strict.tsv",
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-strict.log",
+ "log_sha256": "2eaca20ec90b28a80af0a3bfd2e887bd64cfec7454e25bd7c2d03cacf40dcfdc",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch85/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-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Pinus_armandii_Endophytic_Biocontrol_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pinus_armandii_Endophytic_Biocontrol_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-references.log",
+ "log_sha256": "f2ce2c2ed79bea99d47ec8a22d2d8f9e06a98fb1aae9524e6f93e3fdbbaa72e0",
+ "output_tail": "Validating kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Pinus_armandii_Endophytic_Biocontrol_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-snippets.log",
+ "log_sha256": "aec1f2712a64b5cd549f668dd69d5e1ab54d6d5693d8f53bbce26317b755b383",
+ "output_tail": "# 11 evidence snippets scanned across 1 files\n MATCH 11\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": "Pinus_armandii_Endophytic_Biocontrol_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-rank.log",
+ "log_sha256": "439a99f79f7ec73bd8f8b349f1a26af301e1dd5702f3bc50a70ff3e7c57afb92",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000280\",\n \"name\": \"Pinus armandii Endophytic Biocontrol SynCom\",\n \"score\": 61.2,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pinus_armandii_Endophytic_Biocontrol_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pinus_armandii_Endophytic_Biocontrol_SynCom/2026-10-07T095835Z-codex-75dfd6.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/Pinus_armandii_Endophytic_Biocontrol_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/inventory.log",
+ "log_sha256": "d515d62ae3e1a49e7e7d8892a7eb5f7d3b35e8e41872c809ce28fea13e757c74",
+ "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\": 1433,\n \"edges\": 592,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 172,\n \"review_status_counts\": {\n \"needs_research\": 47,\n \"pending\": 152,\n \"reviewed\": 261\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-batch85/network.log",
+ "log_sha256": "b29c775d4f7bfde5d562cffc9e3d2405cd9e015df8f886eba46d9752c17c623a",
+ "output_tail": "ganisms contribute to organic matter degradation, polysaccharide utilization, and nutrient cycling. They occupy ecological niches related to fermentation product utilization and compatible solute metabolism.\\n\"\n },\n \"functional_role\": [\n \"PRIMARY_DEGRADER\",\n \"SECONDARY_FERMENTER\"\n ],\n \"abundance_level\": \"COMMON\",\n \"evidence\": [\n {\n \"reference\": \"doi:10.3389/fmicb.2022.780346\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea\",\n \"explanation\": \"Documents presence of diverse Bacteroidota in the heterotrophic community\"\n }\n ]\n },\n \"message\": \"Taxon 'Bacteroidota members' 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": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch85/just-network-json.log",
+ "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"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/rank-all.log",
+ "log_sha256": "a14aee75e17d2ecdf8bb56796910744f14f2ddbaf35fdb343841ccaa6fbbd924",
+ "output_tail": "ities/Soybean_N_Fixation_sfSynCom.yaml\tCommunityMech:000064\tSoybean N-Fixation Simplified SynCom\t4\t4\t0\t3\t2\t3\t\t0\t0\n402\t100.0\tkb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml\tCommunityMech:000267\tSphingobium-Rhodococcus Lignin-Dimer Valorization Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n403\t100.0\tkb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\tCommunityMech:000326\tStaphylococcus-Candida Context-Dependent Biofilm Coculture\t2\t2\t0\t6\t2\t13\t\t0\t0\n404\t100.0\tkb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\tCommunityMech:000254\tStordalen Mire Methylotrophic Methanogenesis Community\t3\t3\t0\t4\t4\t9\t\t0\t0\n405\t100.0\tkb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\tCommunityMech:000335\tStreptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n436\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol 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": [
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+ ],
+ "log": "/private/tmp/communitymech-batch85/render.log",
+ "log_sha256": "071e14ec383dde684c5902d63c6807ecfc94bb3a1a5e2ef13c988dd214be2677",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch85/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch85/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch85/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": [
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+ ],
+ "log": "/private/tmp/communitymech-batch85/render-repeat.log",
+ "log_sha256": "071e14ec383dde684c5902d63c6807ecfc94bb3a1a5e2ef13c988dd214be2677",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch85/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch85/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch85/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch85/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-batch84')),('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-batch85/connectivity-survey.log",
+ "log_sha256": "5d18d2c8bdab44e7aacb33c8180a6a9707afcf88d4ce344c13dfd784eea77057",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 394, \"mixed\": 126, \"community_level_only\": 268, \"taxa\": 1517, \"credited_solely_by_the_rule\": 1243}, \"current\": {\"records\": 460, \"with_community_level\": 394, \"mixed\": 126, \"community_level_only\": 268, \"taxa\": 1517, \"credited_solely_by_the_rule\": 1243}}\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_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.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-batch85/regressions.log",
+ "log_sha256": "94ec237253085b3d572b6ea9f0c1d27fc1158d62fd7419cea8e67b744f2ca717",
+ "output_tail": "........................................................................ [ 9%]\n........................................................................ [ 18%]\n........................................................................ [ 28%]\n........................................................................ [ 37%]\n........................................................................ [ 46%]\n........................................................................ [ 56%]\n........................................................................ [ 65%]\n........................................................................ [ 75%]\n........................................................................ [ 84%]\n........................................................................ [ 93%]\n.............................................. [100%]\n766 passed in 407.08s (0:06:47)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/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_batch85.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/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-batch85/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "primary-graph-proof",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import hashlib,json,pathlib,re,unicodedata,yaml\nP=pathlib.Path\nl=yaml.safe_load(P('reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml').read_text())\ndef norm(s):return re.sub(r'[^a-z0-9]','',unicodedata.normalize('NFKD',s).casefold())\nfor p,h in l['primary_artifacts'].items():assert hashlib.sha256(P(p).read_bytes()).hexdigest()==h\nfor c in l['snippet_checks']+l['discussion_snippet_checks']:\n d=yaml.safe_load(P('kb/communities/'+c['record']+'.yaml').read_text())\n entries=[n for n in d.get('ecological_interactions',[]) if n['name']==c['node']]+[n for n in d['discussions'] if n['discussion_id']==c['node']]\n assert len(entries)==1\n for e in entries[0]['evidence']:\n assert norm(e['snippet']) in norm(P(c['matched_artifact']).read_text())\nassert len(l['snippet_checks'])==len(l['discussion_snippet_checks'])==8\nassert len(l['source_access'])==5\nprint(json.dumps(dict(primary_matched_graph_quotations=8,primary_matched_new_discussion_quotations=8,independent_abstracts=4,original_pine_pdf_pages_visually_inspected=[1,2,3,4,5,6],pine_spreadsheet_tables_read=['S1','S2'],primary_full_texts_for_target_records_read=0,companion_main_texts_read=1,retained_nodes=7,removed_workflow_nodes=2,retained_arrows=0,removed_arrows=6,new_nodes_or_arrows=0,sparse_graphs_pending=2)))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/primary-graph-proof.log",
+ "log_sha256": "ed26f8bac66ee2b9d688357fe8faa670a21084a19bd4694e3fd80f717a52a340",
+ "output_tail": "{\"primary_matched_graph_quotations\": 8, \"primary_matched_new_discussion_quotations\": 8, \"independent_abstracts\": 4, \"original_pine_pdf_pages_visually_inspected\": [1, 2, 3, 4, 5, 6], \"pine_spreadsheet_tables_read\": [\"S1\", \"S2\"], \"primary_full_texts_for_target_records_read\": 0, \"companion_main_texts_read\": 1, \"retained_nodes\": 7, \"removed_workflow_nodes\": 2, \"retained_arrows\": 0, \"removed_arrows\": 6, \"new_nodes_or_arrows\": 0, \"sparse_graphs_pending\": 2}\n"
+ },
+ {
+ "check": "focused-final",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch85.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/focused-final.log",
+ "log_sha256": "82a2a5dc31a76cb2a38c8e7714dd341f63455ca2041f3cfd6da3392c4a1f556b",
+ "output_tail": ".......... [100%]\n10 passed in 1.26s\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/audit-snippets-all.log",
+ "log_sha256": "4f0ec314a0496108e80342f2b84131b9684ace17c4bf32577397f4be810923fe",
+ "output_tail": "# 8908 evidence snippets scanned across 460 files\n MATCH 8773\n RENDERING 20\n ASSEMBLED 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ }
+ ],
+ "limitations": [
+ "Fresh post-schema before-paper two-root baseline:460records,921caches,1435nodes598arrows,48warnings and zero structural defects. Nine original nodes/six arrows reviewed; seven biological nodes remain and no arrows. Two empty graphs remain explicitly needs_research, not certified complete.",
+ "Four independent primary abstracts and all four existing target caches read. Primary main texts remain inaccessible; publisher previews are not full texts. Open companion PMID37154752 main text read, but its all-Shewanella 60transfer/180day experiment cannot establish exact CR/DR primary methods. No paywall bypass.",
+ "Both openly linked pine supplements read: all six PDF pages visually inspected after local rendering, XLSX tables S1/S2 parsed as cells. Phomopsis plates, cell-free urediniospore inhibition and pairwise compatibility are distinct assays. Small publisher main-figure previews were downloaded but not used for numerical claims; main figures/full methods not audited.",
+ "Preserve denitrification/productivity/stability positives and ecological decomposition, without dominance intervention or compound-resolved niche claims. Remove workflow nodes and noncausal directions; biological direction research1706remains open.",
+ "Preserve pine compatibility, selected-isolate inhibition, pot growth and PPO/POD increases. Remove reciprocal mutualism, unsupported trait mediation and two isolate-to-host arrows. Explicit participants distinguish three screened final-community isolates from all five pot/compatibility members; species-sharing OB3/NA3 remain distinct labels. No disease-control or priming proof.",
+ "Beverage/refinery discussion-only edits preserve positive endpoints without adding structure. Whole-beverage mouse response is not human benefit or specific-metabolite mediation. Pico monoculture wins oil/grease removal; ambiguous lipid/seed treatment arms remain unassigned. New structure1707/1708requires reviewed scoped Edison report.",
+ "All921caches,456otherrecords and raw non-graph blocks unchanged. Four append-only histories and concrete curation events. Existing non-graph claims preserved, not certified; metadata1709remains open. Denitrifying YAML alias is preserved outside graph without mutation leakage.",
+ "Dedup current all-state issue titles/bodies and ignored/hidden local searches with explicit .git/docs/site/references_cache exclusions; target caches separately read. Closed1116/1117/1118bodies read. Comments/PRs not exhaustive.",
+ "Three single-community Edison causal dry runs:11340/7735/8529characters, zero provider jobs or credits. Scoped request unanswered; initial generic authorization and prior denied scopes do not authorize these jobs. Repair1704/1705close only after protected-main merge;1706-1709remainOPEN.",
+ "Validation/rendering outputs are recorded separately, not preasserted. Self-adversarial review is not independent approval, whole-record certification or corpus completion. Protected merge and dependent-safe branch cleanup remain separate gates.",
+ "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+ ],
+ "superseded_checks": [
+ {
+ "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",
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+ "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": 1,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch85/regressions-initial.log",
+ "log_sha256": "4c79ba80daf30bf5192b578c7802740e601376e20b51f70aad0798431e0456ba",
+ "output_tail": "........................................................................ [ 9%]\n........................................................................ [ 18%]\n........................................................................ [ 28%]\n........................................................................ [ 37%]\n........................................................................ [ 46%]\n........................................................................ [ 56%]\n........................................................................ [ 65%]\n........................................................................ [ 75%]\n........................................................................ [ 84%]\n.....................................F.................................. [ 93%]\n.............................................. [100%]\n=================================== FAILURES ===================================\n_________________ test_the_corpus_is_unchanged_by_this_feature _________________\n\n def test_the_corpus_is_unchanged_by_this_feature():\n \"\"\"Only the records that mean to use the slot do.\n \n Asserted on the corpus rather than trusted from the schema: an\n `ifabsent` or a default that quietly populated the slot would change 312\n records' connectivity without anyone editing a record. That is still the\n failure this catches \u2014 a silent default would put every record in `users`,\n not just the three named below.\n \"\"\"\n users = {\n path.name\n for path in record_files()\n for interaction in (yaml.safe_load(path.read_text()) or {}).get(\"ecological_interactions\")\n or []\n if isinstance(interaction, dict) and interaction.get(\"participating_taxa\")\n }\n> assert users == USERS, (\n f\"{len(users)} records use participating_taxa, expected {len(USERS)}. \"\n f\"Adding a user is fine \u2014 but the connectivity numbers in \"\n f\"tests/test_community_level_connectivity_credit.py were measured \"\n f\"before the slot was used, so re-check them and then update USERS. \"\n f\"Added: {sorted(users - USERS)}. Removed: {sorted(USERS - users)}\"\n )\nE AssertionError: 244 records use participating_taxa, expected 243. Adding a user is fine \u2014 but the connectivity numbers in tests/test_community_level_connectivity_credit.py were measured before the slot was used, so re-check them and then update USERS. Added: ['Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml']. Removed: []\nE assert {'AMD_Acidoph...re.yaml', ...} == {'AMD_Acidoph...re.yaml', ...}\nE \nE Extra items in the left set:\nE 'Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml'\nE Use -v to get more diff\n\ntests/test_participating_taxa.py:428: AssertionError\n=========================== short test summary info ============================\nFAILED tests/test_participating_taxa.py::test_the_corpus_is_unchanged_by_this_feature\n1 failed, 765 passed in 277.98s (0:04:37)\n",
+ "disposition": "Preserved initial failure: explicit pine participating_taxa adds one intentional allowlist user. Actual connectivity census unchanged. Added only that filename to the exact-use allowlist; no auditor rule, census bound or production record changed to hide the failure."
+ }
+ ],
+ "snippet_counts_by_record": {
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+ },
+ "kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml": {
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+ "MISMATCH": 0,
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+ },
+ "kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml": {
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+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml": {
+ "MATCH": 11,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
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+ "MISMATCH": 0,
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+ }
+ },
+ "unchanged_raw_blocks": 52,
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 921,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": true,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [
+ {
+ "community_id": "CommunityMech:000113",
+ "job": "LITERATURE",
+ "query_chars": 11340,
+ "query_sha256": "e629f63819e9d190cd7959db15899012fd0935475242c0e452d552a202de0447",
+ "meta_path": "/private/tmp/communitymech-batch85/edison-denitrifying/Phylogenetically_Diverse_Denitrifying_SynCom-edison-literature-causal-meta.yaml",
+ "authorization": "Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes unchanged."
+ },
+ {
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+ "job": "LITERATURE",
+ "query_chars": 7735,
+ "query_sha256": "d716659ba349d168bf97f0e232e8cef2cc0cd5d6cb006f0f929b1762ec47458d",
+ "meta_path": "/private/tmp/communitymech-batch85/edison-beverage/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture-edison-literature-causal-meta.yaml",
+ "authorization": "Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes unchanged."
+ },
+ {
+ "community_id": "CommunityMech:000439",
+ "job": "LITERATURE",
+ "query_chars": 8529,
+ "query_sha256": "6b302426070d69df43bfa4edb1a1a2fb899fb008f7c8b6586aba439e7ce5c234",
+ "meta_path": "/private/tmp/communitymech-batch85/edison-refinery/Picocystis_Activated_Sludge_Refinery_SWW_Consortium-edison-literature-causal-meta.yaml",
+ "authorization": "Scoped asynchronous paid question unanswered; no submission. Earlier pending/denied scopes unchanged."
+ }
+ ]
+ },
+ "primary_artifacts": {
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+ "/private/tmp/communitymech-batch85/refinery-primary.txt": "688e29004759b04ff3666fed2bf14ad13d7fcb78db50dd38c2f9732128e61434",
+ "references_cache/PMID_37207729.txt": "2225530d0227f4db6d687d6947445e42832558a0de1a08f8a6d460e7af021c1b",
+ "references_cache/PMID_42322490.md": "d3d1b16bc84a9fcbe70aef2614f51e9945a14d5239de7a37cf0c558ce1068572",
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+ },
+ "network_delta": {
+ "existing_findings_preserved": 48,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "All48existingwarnings unchanged; zero structural defects. No taxonomy or auditor-rule changes. Explicit pine participants retain distinct strain labels."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1419,
+ "arrows": 584
+ },
+ "participant_census": {
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+ "with_community_level": 394,
+ "mixed": 126,
+ "community_level_only": 268,
+ "taxa": 1517,
+ "credited_solely_by_the_rule": 1243
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+ "with_community_level": 394,
+ "mixed": 126,
+ "community_level_only": 268,
+ "taxa": 1517,
+ "credited_solely_by_the_rule": 1243
+ }
+ },
+ "delta": {
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+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "Legacy community-level census unchanged. It counts members without pairwise representation, not actual explicit participant coverage; no canonical taxon or auditor-rule change."
+ },
+ "network_warning_count": 48,
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1433,
+ "edges": 592,
+ "records_without_nodes": 8,
+ "records_without_edges": 172,
+ "review_status_counts": {
+ "needs_research": 47,
+ "pending": 152,
+ "reviewed": 261
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
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+ },
+ "status": "verified_assay_boundary_graph_review",
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+ "total": 8908,
+ "categories": {
+ "MATCH": 8773,
+ "RENDERING": 20,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 38,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root recipe actually executed. Exit0 is informational, not a clean-corpus certificate; focused edited-record gates separately pass.",
+ "pre_research_baseline": {
+ "base_commit": "345eedc71e173c75dff8d5692ef946aeb3c908de",
+ "base_tree": "0c0a274b883e5ead55f62ef8f9a578564d934423",
+ "research_worktree": "/private/tmp/communitymech-causal-batch84",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch85/baseline-post-schema-rank.log",
+ "sha256": "8cadfd8bed269919a42b3a9c6d4c7ad54084b1924ca152e49fb1f5ff642939fc",
+ "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-batch85/baseline-post-schema-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-batch85/baseline-post-schema-network.log",
+ "sha256": "b29c775d4f7bfde5d562cffc9e3d2405cd9e015df8f886eba46d9752c17c623a",
+ "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-batch85/baseline-post-schema-downstream.log",
+ "sha256": "de6d98231acb6e35c104c308ffda7ad9cd27b84b770ea4c7f3e40246c366f3e6",
+ "output_tail": "izosphere_Detritusphere_Niche_Succession.yaml:104: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:127: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:167: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:198: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:251: downstream:\nkb/communities/Honeybee_Core20_Defined_Microbiota.yaml:71: downstream:\nkb/communities/Honeybee_Core20_Defined_Microbiota.yaml:101: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.yaml:157: downstream:\nkb/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.yaml:221: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:281: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:401: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:98: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:155: 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/Synechococcus_Saccharomyces_SPC.yaml:126: downstream:\nkb/communities/Synechococcus_Saccharomyces_SPC.yaml:161: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:342: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:381: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "21fa3bbb7162c1c290ae8ab4b3f4e419c121433f90bab34067fcd107a422c829"
+ },
+ "reference_validator_caveat": "Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. Eight graph and eight new discussion quotations match independently fetched primary abstracts and existing caches. Literal matching is not entailment or whole-record certification. Public pine supplements provide additional assay context, not inaccessible primary main text."
+}
diff --git a/tests/test_causal_review_batch85.py b/tests/test_causal_review_batch85.py
new file mode 100644
index 000000000..2b0040b18
--- /dev/null
+++ b/tests/test_causal_review_batch85.py
@@ -0,0 +1,143 @@
+"""Keep positive endpoints separate from workflow and untested mediation."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_denitrification_positives_survive_workflow_removal():
+ _, rows, docs = records()
+ nodes = docs[0]["ecological_interactions"]
+ assert len(nodes) == 3
+ assert (
+ "greater productivity, denitrification rate and temporal stability"
+ in nodes[0]["description"]
+ )
+ assert "generation 50" in nodes[1]["description"]
+ assert "overyielding and asynchronous" in nodes[2]["description"]
+ assert all(n.get("interaction_type") is None for n in nodes)
+ assert all("downstream" not in n for n in nodes)
+ assert len(rows[0]["removed_node_decisions"]) == 2
+ assert len(rows[0]["removed_edge_decisions"]) == 4
+ assert "200 generations" in docs[0]["engineering_design"]["perturbation_design"]
+
+
+def test_denitrification_direction_and_exact_system_limits_remain_open():
+ _, rows, docs = records()
+ assert rows[0]["status"] == "needs_research" and 1706 in rows[0]["issues"]
+ text = docs[0]["discussions"][-1]["rationale"]
+ assert "not interchangeable" in text and "no new reversed arrow" in text
+ assert (
+ "isolate Paracoccus abundance as the causal driver"
+ in docs[0]["ecological_interactions"][1]["description"]
+ )
+
+
+def test_beverage_empty_graph_is_not_misreported_as_complete():
+ _, rows, docs = records()
+ assert "ecological_interactions" not in docs[1]
+ assert rows[1]["status"] == "needs_research" and rows[1]["issues"] == [1707]
+ assert set(rows[1]["allowed_changed_fields"]) == {"discussions", "curation_history"}
+ text = docs[1]["discussions"][-1]["rationale"]
+ assert "9.32 and 7.05" in text and "BALB/c mice" in text
+ assert "specific compound, or benefit in humans" in text
+ assert docs[1]["discussions"][0]["discussion_id"] == "ccma_beverage_coculture_conditions"
+
+
+def test_refinery_removal_keeps_monoculture_counterexample_and_arm_uncertainty():
+ _, rows, docs = records()
+ assert docs[2]["ecological_interactions"] == []
+ assert rows[2]["status"] == "needs_research" and rows[2]["issues"] == [1708]
+ text = docs[2]["discussions"][-1]["rationale"]
+ assert "72% COD and 96.4%" in text and "80.4%" in text
+ assert "Pico monoculture" in text and "62.2%" in text
+ assert "does not resolve the Pico/Pico-Bac arm" in text
+ assert "does not establish complete mineralization" in text
+
+
+def test_pine_compatibility_is_not_stability_or_resource_partitioning():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][0]
+ assert node["name"] == "Compatibility of Selected Endophytic Isolates"
+ assert "no inhibition zones" in node["description"]
+ assert "not demonstrated long-term stable coexistence" in node["description"]
+ assert "metabolites" not in node and "biological_processes" not in node
+ assert len(node["participating_taxa"]) == 5
+
+
+def test_pine_inhibition_has_correct_assays_and_strain_participants():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][1]
+ assert "Phomopsis sp." in node["description"]
+ assert "cell-free fermentation supernatants" in node["description"]
+ assert {t["preferred_term"] for t in node["participating_taxa"]} == {
+ "Paenibacillus terrae RE7",
+ "Bacillus velezensis NA3",
+ "Bacillus subtilis NA11",
+ }
+ assert "RC1 and OB3 are not among" in node["description"]
+ assert "biological_processes" not in node
+
+
+def test_pine_positive_host_endpoints_are_in_vivo_without_mutualism():
+ _, rows, docs = records()
+ nodes = docs[3]["ecological_interactions"]
+ assert "significantly increased" in nodes[2]["description"]
+ assert "19.1% and 157.3%" in nodes[3]["description"]
+ assert all(e["evidence_source"] == "IN_VIVO" for n in nodes[2:] for e in n["evidence"])
+ assert "metabolites" not in nodes[2] and "biological_processes" not in nodes[2]
+ assert all("interaction_type" not in n and "downstream" not in n for n in nodes)
+ assert len(rows[3]["removed_edge_decisions"]) == 2
+
+
+def test_pine_disease_control_not_implied_by_enzymes():
+ _, rows, docs = records()
+ text = docs[3]["ecological_interactions"][3]["description"]
+ assert "do not alone demonstrate priming" in text
+ assert "subsequent in planta biocontrol evaluation" in text
+ assert rows[3]["status"] == "reviewed" and 1709 in rows[3]["issues"]
+
+
+def test_every_original_node_arrow_and_anchor_has_disposition():
+ ledger, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 7
+ assert sum(len(r["removed_node_decisions"]) for r in rows) == 2
+ assert sum(len(r["edges_before"]) for r in rows) == 6
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 6
+ assert all(r["edges_after"] == [] for r in rows)
+ assert ledger["primary_graph_snippet_count"] == 8
+ assert len(ledger["discussion_snippet_checks"]) == 8
+ for row, doc in zip(rows, docs, strict=True):
+ names = {n["name"] for n in doc.get("ecological_interactions", [])}
+ assert names == {n["node"] for n in row["node_decisions"]}
+ assert all(
+ a.split("#", 1)[1] in names
+ for d in doc["discussions"]
+ for a in d["attaches_to"]
+ if a.startswith("ecological_interactions#")
+ )
+
+
+def test_sources_history_and_pending_lifecycle_are_explicit():
+ ledger, rows, docs = records()
+ assert not ledger["independent_approval"]
+ assert ledger["issues"] == [1704, 1705]
+ assert ledger["unresolved_research_issues"] == [1706, 1707, 1708]
+ assert ledger["unresolved_non_graph_issues"] == [1709]
+ assert ledger["cache_changes"] == []
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert [d["query_chars"] for d in ledger["edison"]["dry_runs"]] == [11340, 7735, 8529]
+ for row, doc in zip(rows, docs, strict=True):
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert doc["curation_history"][-1]["llm_assisted"]
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 024dc80b0..561e0e753 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -363,6 +363,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Phaeodactylum_Aliivibrio_Diel_Coculture.yaml",
"Phormidium_Alkaline_Consortium.yaml",
"Phenol_Carboxylation_Consortium.yaml",
+ "Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml",
"Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml",
"Prymnesium_Parvum_B12_Limited_SynCom.yaml",
"Pseudomonas_Acidovorax_Aniline_Degradation_SynCom.yaml",