From cdcbdecdb63092a0a9d46ef2f317e8645c5052b3 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Thu, 8 Oct 2026 09:21:50 -0700
Subject: [PATCH] Bound wheat treatment outcomes and inferred mechanisms
(batch122)
---
...Wheat_CrownRot_TB_CrossKingdom_SynCom.html | 105 +-
.../Wheat_DT_Rhizosphere_SynCom.html | 73 +-
...heat_Straw_Biogas_Pretreatment_SynCom.html | 76 +-
...Wheat_SynCom_SASW01_Drought_Inoculant.html | 106 +-
.../2026-10-08T160003Z-codex-e66225.yaml | 26 +
.../2026-10-08T160004Z-codex-72b999.yaml | 26 +
.../2026-10-08T160004Z-codex-49a7c7.yaml | 27 +
.../2026-10-08T160004Z-codex-53385b.yaml | 26 +
...Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml | 80 +-
.../Wheat_DT_Rhizosphere_SynCom.yaml | 125 +-
...heat_Straw_Biogas_Pretreatment_SynCom.yaml | 96 +-
...Wheat_SynCom_SASW01_Drought_Inoculant.yaml | 92 +-
reports/causal_graph_review/README.md | 27 +
.../adversarial-review-20261008-batch122.yaml | 420 +++++++
.../cache-provenance-20261008-batch122.json | 268 ++++
.../20261008-four-records-batch122.yaml | 671 ++++++++++
reports/causal_graph_review/inventory.tsv | 8 +-
reports/causal_graph_review/summary.json | 4 +-
.../validation-20261008-batch122.json | 1094 +++++++++++++++++
tests/test_causal_review_batch122.py | 179 +++
20 files changed, 3317 insertions(+), 212 deletions(-)
create mode 100644 history/records/Wheat_CrownRot_TB_CrossKingdom_SynCom/2026-10-08T160003Z-codex-e66225.yaml
create mode 100644 history/records/Wheat_DT_Rhizosphere_SynCom/2026-10-08T160004Z-codex-72b999.yaml
create mode 100644 history/records/Wheat_Straw_Biogas_Pretreatment_SynCom/2026-10-08T160004Z-codex-49a7c7.yaml
create mode 100644 history/records/Wheat_SynCom_SASW01_Drought_Inoculant/2026-10-08T160004Z-codex-53385b.yaml
create mode 100644 reports/causal_graph_review/adversarial-review-20261008-batch122.yaml
create mode 100644 reports/causal_graph_review/cache-provenance-20261008-batch122.json
create mode 100644 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
create mode 100644 reports/causal_graph_review/validation-20261008-batch122.json
create mode 100644 tests/test_causal_review_batch122.py
diff --git a/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html b/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html
index 9343fa28a..4a9c89637 100644
--- a/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html
+++ b/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html
@@ -595,7 +595,7 @@ Ecological Interactions
Ecological interaction network for Wheat Crown-Rot TB Cross-Kingdom SynCom
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for competition, colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -603,13 +603,8 @@
Ecological Interactions
-
-
@@ -618,9 +613,8 @@ Ecological Interactions
-
Soil drenching with the T. harzianum T19 / B. rugosus PM16 TB SynCom suppressed Fusarium-pseudograminearum-driven wheat crown rot in the controlled pot experiment, alongside improved wheat biomass, chlorophyll content, and yield-related traits.
+
The two-member T19/PM16 TB inoculum suppressed Fusarium pseudograminearum crown rot in controlled wheat pots, with reported biocontrol efficacy of 70.97% and improved biomass, chlorophyll and yield-related traits. The listed fungus is the challenge organism, not a TB member. These positive whole-inoculum outcomes do not establish bilateral competition, reciprocal microbial benefit or a unique immune mechanism. The plant experiment has no single-member treatment that isolates each member contribution.
@@ -670,6 +664,19 @@
Evidence
+
+
+
+ "with a biocontrol efficacy of 70.97%"
+
+
+
Evidence
-
TB SynCom inoculation remodeled the resident wheat rhizosphere community, including enrichment of beneficial taxa and reduction of pathogen-associated fungi, during the 45-day Fusarium challenge assay.
+
TB treatment changed rhizosphere DNA-based community profiles, including relative enrichment of Mortierella and reduced pathogen-associated fungi. Relative sequence abundance does not establish absolute viable abundance or strain-resolved persistence of T19/PM16. Genus annotations and correlation networks do not establish beneficial function, nutrient exchange or microbial necessity. Network robustness was assessed by simulated node removal, not biological removal experiments. Remodeling is not isolated as the cause of the positive disease-control outcome.
@@ -688,17 +694,6 @@
TB-associated rhizosphere remodeling
-
Biological Processes:
-
-
-
- regulation of defense response
- (GO:0031347 )
-
-
-
-
@@ -719,6 +714,19 @@
Evidence
+
+
+
+ "Hub-targeted simulations showed a similar trend"
+
+
+
Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which TB-dependent mechanisms explain protection beyond correlated community and soil-metabolite changes?
+
+
T19 plate inhibition and PM16 growth-promoting screens support separate traits; compatibility is not reciprocal fitness or proof of synergy in the host. Soil metabolites were measured, not directly collected root exudates. The paper explicitly limits daidzein origin and recruitment claims; quorum sensing and volatile effects remain working hypotheses. Structural-equation paths and simulated network attacks are not selective biological perturbations. Do not transfer exogenous-metabolite validation from the distinct six-strain SMC study.
+
+
Attaches to: ecological_interactions#Fusarium pseudograminearum WCR suppression by TB, ecological_interactions#TB-associated rhizosphere remodeling
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
these QS- and volatile-mediated effects are proposed as working hypotheses and were not directly tested in the present study.
+
+
+
+
+
@@ -1068,7 +1115,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1077,7 +1124,7 @@ Evidence
processes.push("defense response to fungus");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1111,16 +1158,12 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("regulation of defense response");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/docs/communities/Wheat_DT_Rhizosphere_SynCom.html b/docs/communities/Wheat_DT_Rhizosphere_SynCom.html
index 90d044318..e9be2ba3f 100644
--- a/docs/communities/Wheat_DT_Rhizosphere_SynCom.html
+++ b/docs/communities/Wheat_DT_Rhizosphere_SynCom.html
@@ -1085,8 +1085,7 @@ Ecological Interactions
- Barley seedlings root-inoculated with the wheat-origin DT-SynCom showed lower Blumeria graminis f. sp. hordei DAF fluorescence intensity than mock-treated controls after pathogen challenge, consistent with SynCom-induced systemic resistance under the assay conditions.
-
+ The wheat-origin, 16-member DT-SynCom reduced barley leaf powdery-mildew DAF fluorescence by 43.3% relative to mock treatment after Blumeria graminis f. sp. hordei challenge. All three inoculants protected plants; their pairwise differences were not significant. This supports ISR-like protection but does not assign necessity to JA, ethylene or SA signaling. PEG-tolerant isolate selection is not a test of whole-plant drought protection.
@@ -1138,8 +1137,7 @@ Evidence
- The wheat-origin DT-SynCom produced selective metatranscriptomic changes in the barley rhizosphere, including downregulation of PF02868, PF01614, and the KEGG stress-induced DnaJ-like molecular chaperone term K05516, rather than a broad shift in rhizosphere functional profiles.
-
+ Before pathogen challenge, the wheat DT-SynCom treatment produced selective changes in measured barley-rhizosphere RNA features, including downregulation of PF02868, PF01614 and K05516. Overall functional profiles and bacterial community structure showed no significant treatment shift. These are metatranscriptomic observations, not PICRUSt predictions. Similarity-based contig annotations do not attribute transcripts to individual inoculant strains, and no perturbation establishes these changes as necessary mediators of the later disease-protection outcome.
@@ -1183,6 +1181,19 @@ Evidence
+
+
+
+ "The metatranscriptomic contigs were assigned based on sequence similarity (not reference SynCom genomes)"
+
+
+
@@ -1229,7 +1240,7 @@ Associated Datasets
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -1245,6 +1256,56 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which pre-infection responses mediate wheat DT-SynCom disease protection in barley?
+
+
Molecular samples preceded the pathogen assay, so these profiles cannot be described as post-infection responses. No significant pairwise difference establishes a superior inoculant. The authors could not assign ISR to specific hormone pathways. OTU matches at 99% identity suggest persistence of related taxa, not unique viable-strain identification. Preserve the prior selective-versus-broad correction and the dated BioProject-visibility discussion.
+
+
Attaches to: ecological_interactions#Wheat DT-SynCom powdery mildew resistance, ecological_interactions#Wheat DT-SynCom selective rhizosphere functional shifts
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
Although our data did not allow direct assignment of ISR to specific JA-, ET-, or SA-dependent pathways
+
+
+
+
Although strain-level identity cannot be confirmed by 16S rRNA gene-based identification alone
+
+
+
+
@@ -1732,7 +1793,7 @@ Evidence
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
diff --git a/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html b/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html
index 5458ba341..e71a8ddc2 100644
--- a/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html
+++ b/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html
@@ -657,7 +657,7 @@ Ecological Interactions
Ecological interaction network for Wheat Straw Biogas Pretreatment SynCom
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -665,8 +665,8 @@
Ecological Interactions
@@ -675,9 +675,8 @@ Ecological Interactions
-
The four Bacillus, Acinetobacter, Trichoderma, and Aspergillus degraders are assembled as synthetic microbial communities for fermentation-enzyme production, yielding the crude enzyme solution used for wheat-straw pretreatment.
+
The four reported bacterial/fungal degraders form an enzyme-producing inoculum that yields the crude enzyme solution used for wheat-straw pretreatment. This positive process output does not measure reciprocal fitness, member-specific enzyme contributions or metabolite cross-feeding. The accessible abstract does not resolve strain identities or establish that the four isolates constitute the downstream anaerobic-digestion community.
@@ -724,7 +723,7 @@
Synthetic Community Fermentation-Enzyme Production
→ Lignocellulose Enzyme Pretreatment
-
Crude enzyme from the fermentation-production community was applied to wheat straw for the enzyme pretreatment that depolymerizes cellulose, hemicellulose, and lignin.
+
Fermentation supplies the crude enzyme solution applied to wheat straw, enabling the measured polymer-degradation pretreatment. This is an enzyme-mediated material-transfer step, not proof that the living four-member inoculum colonizes every subsequent process stage.
Evidence
-
Bacterial and fungal enzyme producers jointly degrade wheat straw polymers before anaerobic digestion.
+
Crude enzyme solution from the synthetic community was applied to wheat straw before anaerobic digestion. Reported cellulose, hemicellulose and lignin degradation rates were 39.85%, 36.99% and 19.21%, respectively. The treatment acts through the enzyme preparation; these values do not establish reciprocal microbial benefit or living producer growth on the pretreated substrate.
@@ -811,7 +809,7 @@
Lignocellulose Enzyme Pretreatment
→ Enhanced Biogas Production after Anaerobic Digestion
-
Improved wheat-straw enzymatic digestion feeds downstream anaerobic digestion and increases the cumulative biogas yield.
+
The enzyme-pretreated straw supplies substrate to subsequent anaerobic digestion, where cumulative biogas was higher than with untreated straw or either commercial-enzyme pretreatment. Retain this process-level treatment effect without assigning gas production to the four enzyme producers or to one uniquely necessary polymer-degradation route.
Evidence
-
Wheat straw pretreated with the synthetic-community crude enzyme solution produced the highest cumulative biogas in the subsequent anaerobic digestion stage, outperforming untreated straw and both commercial enzyme pretreatments.
+
Subsequent anaerobic digestion of synthetic-community enzyme-pretreated straw yielded 801.16 mL/g TS cumulative biogas, higher than untreated straw and both commercial-enzyme pretreatments. Biogas volume is not a methane-only yield. The abstract does not identify the digestion community or demonstrate methanogenesis by the four enzyme-producing isolates.
-
Metabolites:
-
- methane
- (CHEBI:16183 )
-
-
-
@@ -902,6 +891,45 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How do enzyme producers and the downstream digestion community contribute to the biogas benefit?
+
+
The accessible abstract supports the existing enzyme-production to pretreatment to digestion sequence and positive polymer and total-biogas outcomes. It does not resolve individual-strain contributions, reciprocal benefit, digestor membership, methane fraction or a uniquely necessary enzyme. Primary full methods and supplementary information were not inspected; publisher access attempts failed. This is a bounded access limitation, not a claim that full text or supplements do not exist.
+
+
Attaches to: ecological_interactions#Synthetic Community Fermentation-Enzyme Production, ecological_interactions#Lignocellulose Enzyme Pretreatment, ecological_interactions#Enhanced Biogas Production after Anaerobic Digestion
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS
+
+
+
+
+
@@ -1054,7 +1082,7 @@
Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1090,7 +1118,7 @@
Environmental Factors
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1130,13 +1158,9 @@
Environmental Factors
(function() {
var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("methane");
-
-
var processes = [];
var evidenceCount = 1;
diff --git a/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html b/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html
index 41a329dd4..6b078e253 100644
--- a/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html
+++ b/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html
@@ -669,7 +669,7 @@
Ecological Interactions
Ecological interaction network for Wheat SynCom-SASW01 Drought-Resistance Inoculant
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -677,8 +677,8 @@
Ecological Interactions
Ecological Interactions
-
SynCom-SASW01 treatment ameliorated drought-induced water deficits and was interpreted to stabilize the rhizosphere in part through exopolysaccharide secretion by core community members.
+
In drought-stressed wheat pots, the combined SynCom-SASW01 plus coating-matrix treatment (BCC) increased rhizosphere relative water content versus untreated NC. EPS-mediated water retention is HYPOTHESIZED, not selectively demonstrated: the matrix includes biochar and other additives. The design also includes coating-only CC and SynCom-only BC, but a BCC-versus-NC contrast does not isolate the microbial or EPS contribution. This water outcome is not itself evidence of colonization facilitation.
@@ -711,13 +710,26 @@
Evidence
PMID:42513902
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"SynCom-SASW01 treatment significantly ameliorated drought-induced water deficits, which may be partly attributable to the EPS secretion capacity of the consortium’s core members."
+
+
+
+ "rhizosphere soil RWC in the BCC (biochar-consortium coating) treatment was significantly higher than that in the uninoculated control (NC) group"
+
+
+
@@ -725,9 +737,8 @@ Evidence
-
The SynCom-SASW01 biological coating reorganized wheat root-associated bacterial communities under drought stress and especially shifted the root endosphere.
+
The BCC biological coating shifted wheat root-associated bacterial DNA profiles under drought, particularly in the endosphere, with relative enrichment of Pseudomonas and other taxa. The microbiome comparison was BCC versus NC, not SynCom alone versus coating alone. Matching 16S ASVs do not uniquely identify viable inoculant strains or establish priority-effect causality. Correlation/RDA and PICRUSt2 functional predictions do not prove BCAA transfer, taxon necessity or a community-to-antioxidant causal cascade.
@@ -749,13 +760,26 @@
Evidence
PMID:42513902
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"the exogenous synthetic community efficiently colonized the endosphere and promoted the enrichment of keystone genera such as Pseudomonas."
+
+
+
+ "in the endosphere, En_BCC samples exhibited a clear separation from En_NC samples"
+
+
+
@@ -766,7 +790,7 @@ Evidence
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -781,6 +805,56 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which microbial effects are separable from the coating matrix in SASW01-associated drought benefits?
+
+
Positive BCC field yields and pot water, nutrient and physiological outcomes remain real treatment observations. Field comparisons contain only NC and BCC; the two-site yield benefit is not a SynCom-only or EPS-specific effect. Amplicon matching, inferred functions and correlations cannot establish a priority-effect or BCAA-transfer mechanism. Prior removal of assembly and PICRUSt-derived mechanism nodes remains intact. Source yield percentages differ between Results and Conclusions; non-graph reconciliation is separate.
+
+
Attaches to: ecological_interactions#SynCom-SASW01 biocoating-associated water retention, ecological_interactions#SynCom-SASW01 root endosphere reshaping
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
Two treatments were established: NC (control) and BCC (SynCom-SASW01 biological coating).
+
+
+
+
Functional potential prediction was conducted using PICRUSt2 (2.6.0) based on MetaCyc Level 3 pathways
+
+
+
+
@@ -1140,16 +1214,16 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "EPS-associated rhizosphere water retention",
+ label: "SynCom-SASW01 biocoating-associated water retention",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1164,12 +1238,12 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/history/records/Wheat_CrownRot_TB_CrossKingdom_SynCom/2026-10-08T160003Z-codex-e66225.yaml b/history/records/Wheat_CrownRot_TB_CrossKingdom_SynCom/2026-10-08T160003Z-codex-e66225.yaml
new file mode 100644
index 000000000..d6561f286
--- /dev/null
+++ b/history/records/Wheat_CrownRot_TB_CrossKingdom_SynCom/2026-10-08T160003Z-codex-e66225.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml
+ slug: Wheat_CrownRot_TB_CrossKingdom_SynCom
+session:
+ id: 2026-10-08T160003Z-codex-e66225
+ timestamp: '2026-10-08T16:00:03Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1947
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve positive TB pot disease control without bilateral competition or individual-member
+ necessity.; Keep relative community profiles and simulated robustness distinct from colonization
+ facilitation and demonstrated immune mediation.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
diff --git a/history/records/Wheat_DT_Rhizosphere_SynCom/2026-10-08T160004Z-codex-72b999.yaml b/history/records/Wheat_DT_Rhizosphere_SynCom/2026-10-08T160004Z-codex-72b999.yaml
new file mode 100644
index 000000000..f52070f3c
--- /dev/null
+++ b/history/records/Wheat_DT_Rhizosphere_SynCom/2026-10-08T160004Z-codex-72b999.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml
+ slug: Wheat_DT_Rhizosphere_SynCom
+session:
+ id: 2026-10-08T160004Z-codex-72b999
+ timestamp: '2026-10-08T16:00:04Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1948
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain positive barley protection without inferring inoculant superiority, hormone-pathway
+ necessity or plant drought protection.; Preserve selective measured RNA changes and broad-profile
+ nulls, with pre-challenge timing and no strain-level or causal-pathway assignment.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
diff --git a/history/records/Wheat_Straw_Biogas_Pretreatment_SynCom/2026-10-08T160004Z-codex-49a7c7.yaml b/history/records/Wheat_Straw_Biogas_Pretreatment_SynCom/2026-10-08T160004Z-codex-49a7c7.yaml
new file mode 100644
index 000000000..c5183e688
--- /dev/null
+++ b/history/records/Wheat_Straw_Biogas_Pretreatment_SynCom/2026-10-08T160004Z-codex-49a7c7.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml
+ slug: Wheat_Straw_Biogas_Pretreatment_SynCom
+session:
+ id: 2026-10-08T160004Z-codex-49a7c7
+ timestamp: '2026-10-08T16:00:04Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1949
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain enzyme-production output without reciprocal mutualism or attribution of
+ downstream digestion to the inoculum.; Preserve polymer-degradation values and enzyme
+ transfer rather than living-cell mutualism.; Keep positive downstream biogas yield distinct
+ from methane-only yield or four-isolate methanogenesis.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
diff --git a/history/records/Wheat_SynCom_SASW01_Drought_Inoculant/2026-10-08T160004Z-codex-53385b.yaml b/history/records/Wheat_SynCom_SASW01_Drought_Inoculant/2026-10-08T160004Z-codex-53385b.yaml
new file mode 100644
index 000000000..829f149b2
--- /dev/null
+++ b/history/records/Wheat_SynCom_SASW01_Drought_Inoculant/2026-10-08T160004Z-codex-53385b.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml
+ slug: Wheat_SynCom_SASW01_Drought_Inoculant
+session:
+ id: 2026-10-08T160004Z-codex-53385b
+ timestamp: '2026-10-08T16:00:04Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1950
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain measured combined-treatment water retention while marking EPS mediation
+ as hypothesized and coating-confounded.; Keep relative DNA-profile shifts distinct from
+ unique-strain colonization, priority effects and predicted metabolic causality.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
diff --git a/kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml b/kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml
index 3ae9784ce..a3206d5e0 100644
--- a/kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml
+++ b/kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml
@@ -109,10 +109,11 @@ taxonomy:
explanation: Identifies PM16 as Bacillus rugosus.
ecological_interactions:
- name: Fusarium pseudograminearum WCR suppression by TB
- description: Soil drenching with the T. harzianum T19 / B. rugosus PM16 TB SynCom suppressed Fusarium-pseudograminearum-driven
- wheat crown rot in the controlled pot experiment, alongside improved wheat biomass, chlorophyll content, and yield-related
- traits.
- interaction_type: COMPETITION
+ description: The two-member T19/PM16 TB inoculum suppressed Fusarium pseudograminearum crown rot in controlled
+ wheat pots, with reported biocontrol efficacy of 70.97% and improved biomass, chlorophyll and yield-related
+ traits. The listed fungus is the challenge organism, not a TB member. These positive whole-inoculum outcomes
+ do not establish bilateral competition, reciprocal microbial benefit or a unique immune mechanism. The plant
+ experiment has no single-member treatment that isolates each member contribution.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Trichoderma harzianum T19
@@ -136,27 +137,36 @@ ecological_interactions:
- reference: PMID:41821943
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: The SynCom significantly suppressed WCR and promoted wheat growth under pathogen pressure, improving biomass,
- chlorophyll content, and yield-related traits.
- explanation: Reports the WCR suppression and growth promotion measured in the TB SynCom treatment under Fusarium pathogen
- pressure.
+ snippet: The SynCom significantly suppressed WCR and promoted wheat growth under pathogen pressure, improving
+ biomass, chlorophyll content, and yield-related traits.
+ explanation: Reports the WCR suppression and growth promotion measured in the TB SynCom treatment under Fusarium
+ pathogen pressure.
+ - reference: PMID:41821943
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: with a biocontrol efficacy of 70.97%
+ explanation: Direct positive disease-control estimate for the TB treatment.
- name: TB-associated rhizosphere remodeling
- description: TB SynCom inoculation remodeled the resident wheat rhizosphere community, including enrichment of beneficial
- taxa and reduction of pathogen-associated fungi, during the 45-day Fusarium challenge assay.
- interaction_type: COLONIZATION_FACILITATION
+ description: TB treatment changed rhizosphere DNA-based community profiles, including relative enrichment of Mortierella
+ and reduced pathogen-associated fungi. Relative sequence abundance does not establish absolute viable abundance
+ or strain-resolved persistence of T19/PM16. Genus annotations and correlation networks do not establish beneficial
+ function, nutrient exchange or microbial necessity. Network robustness was assessed by simulated node removal,
+ not biological removal experiments. Remodeling is not isolated as the cause of the positive disease-control
+ outcome.
scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: regulation of defense response
- term:
- id: GO:0031347
- label: regulation of defense response
evidence:
- reference: PMID:41821943
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom inoculation remodeled the rhizosphere microbiome by enriching beneficial taxa (e.g., Mortierella) and
- reducing pathogen-associated fungi
- explanation: Supports TB-driven restructuring of the wheat rhizosphere microbiome.
+ snippet: SynCom inoculation remodeled the rhizosphere microbiome by enriching beneficial taxa (e.g., Mortierella)
+ and reducing pathogen-associated fungi
+ explanation: Supports community-profile shifts; beneficial labels are author interpretations, not taxon-specific
+ functional assays.
+ - reference: PMID:41821943
+ supports: SUPPORT
+ evidence_source: OTHER
+ snippet: Hub-targeted simulations showed a similar trend
+ explanation: The network robustness result comes from simulated removal.
growth_media:
- name: wheat non-sterile topsoil pot assay
temperature: 25
@@ -275,7 +285,33 @@ curation_history:
- timestamp: '2026-09-20T08:58:45Z'
curator: codex
action: CREATE_RECORD
- changes: Created CommunityMech:000391 for the Trichoderma harzianum T19 / Bacillus rugosus PM16 TB cross-kingdom wheat crown-rot
- SynCom from PMID:41821943, including exact strain membership, pot-assay cultivation, Fusarium challenge design, biocontrol
- and rhizosphere-remodeling outcomes, and linked BioProject/MetaboLights datasets.
+ changes: Created CommunityMech:000391 for the Trichoderma harzianum T19 / Bacillus rugosus PM16 TB cross-kingdom
+ wheat crown-rot SynCom from PMID:41821943, including exact strain membership, pot-assay cultivation, Fusarium
+ challenge design, biocontrol and rhizosphere-remodeling outcomes, and linked BioProject/MetaboLights datasets.
+ llm_assisted: true
+- timestamp: '2026-10-08T16:00:02Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Preserve positive TB pot disease control without bilateral competition or individual-member necessity.;
+ Keep relative community profiles and simulated robustness distinct from colonization facilitation and demonstrated
+ immune mediation. Issue#1947; reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
llm_assisted: true
+discussions:
+- discussion_id: tb_causal_scope_batch122
+ prompt: Which TB-dependent mechanisms explain protection beyond correlated community and soil-metabolite changes?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Fusarium pseudograminearum WCR suppression by TB
+ - ecological_interactions#TB-associated rhizosphere remodeling
+ rationale: T19 plate inhibition and PM16 growth-promoting screens support separate traits; compatibility is not
+ reciprocal fitness or proof of synergy in the host. Soil metabolites were measured, not directly collected root
+ exudates. The paper explicitly limits daidzein origin and recruitment claims; quorum sensing and volatile effects
+ remain working hypotheses. Structural-equation paths and simulated network attacks are not selective biological
+ perturbations. Do not transfer exogenous-metabolite validation from the distinct six-strain SMC study.
+ evidence:
+ - reference: PMID:41821943
+ snippet: these QS- and volatile-mediated effects are proposed as working hypotheses and were not directly tested
+ in the present study.
+ posed_by: codex
+ posed_date: '2026-10-08'
diff --git a/kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml b/kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml
index 7b5f8ec22..84a7a44cc 100644
--- a/kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml
+++ b/kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml
@@ -379,55 +379,63 @@ taxonomy:
explanation: Identifies Ensifer sp. W16 as a Wheat DT-SynCom member.
ecological_interactions:
- name: Wheat DT-SynCom powdery mildew resistance
- description: >
- Barley seedlings root-inoculated with the wheat-origin DT-SynCom showed
- lower Blumeria graminis f. sp. hordei DAF fluorescence intensity than
- mock-treated controls after pathogen challenge, consistent with
- SynCom-induced systemic resistance under the assay conditions.
+ description: The wheat-origin, 16-member DT-SynCom reduced barley leaf powdery-mildew DAF fluorescence by 43.3%
+ relative to mock treatment after Blumeria graminis f. sp. hordei challenge. All three inoculants protected plants;
+ their pairwise differences were not significant. This supports ISR-like protection but does not assign necessity
+ to JA, ethylene or SA signaling. PEG-tolerant isolate selection is not a test of whole-plant drought protection.
scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42453107
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Mean fluorescence was reduced by 50.4% in the barley SynCom treatment,
- 43.3% in the wheat SynCom treatment, and 34.9% in the WCS417r treatment,
- relative to the mock treatment.
+ snippet: 'Mean fluorescence was reduced by 50.4% in the barley SynCom treatment, 43.3% in the wheat SynCom treatment,
+ and 34.9% in the WCS417r treatment, relative to the mock treatment.
+
+ '
explanation: Quantifies the barley and wheat SynCom disease-protection phenotypes.
- reference: PMID:42453107
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- These results demonstrate that both the barley and wheat SynComs induce
- ISR in a manner similar to that of the ISR-eliciting bacterium WCS417r.
- explanation: Supports the systemic-resistance interpretation for both SynComs.
+ snippet: 'These results demonstrate that both the barley and wheat SynComs induce ISR in a manner similar to
+ that of the ISR-eliciting bacterium WCS417r.
+
+ '
+ explanation: The authors interpret the positive host phenotype as ISR; specific hormone-pathway dependence was
+ not assigned.
- name: Wheat DT-SynCom selective rhizosphere functional shifts
- description: >
- The wheat-origin DT-SynCom produced selective metatranscriptomic changes in
- the barley rhizosphere, including downregulation of PF02868, PF01614, and
- the KEGG stress-induced DnaJ-like molecular chaperone term K05516, rather
- than a broad shift in rhizosphere functional profiles.
+ description: Before pathogen challenge, the wheat DT-SynCom treatment produced selective changes in measured barley-rhizosphere
+ RNA features, including downregulation of PF02868, PF01614 and K05516. Overall functional profiles and bacterial
+ community structure showed no significant treatment shift. These are metatranscriptomic observations, not PICRUSt
+ predictions. Similarity-based contig annotations do not attribute transcripts to individual inoculant strains,
+ and no perturbation establishes these changes as necessary mediators of the later disease-protection outcome.
scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42453107
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Inoculation with wheat SynCom resulted in downregulation of PF02868,
- PF01614 (PFAM; IclR-family transcriptional regulator, C-terminal domain),
- and K05516 (KEGG; stress-induced DnaJ-like molecular chaperone)
- explanation: >
- Supports selective rhizosphere metatranscriptomic feature shifts after
- Wheat DT-SynCom inoculation.
+ snippet: 'Inoculation with wheat SynCom resulted in downregulation of PF02868, PF01614 (PFAM; IclR-family transcriptional
+ regulator, C-terminal domain), and K05516 (KEGG; stress-induced DnaJ-like molecular chaperone)
+
+ '
+ explanation: 'Supports selective rhizosphere metatranscriptomic feature shifts after Wheat DT-SynCom inoculation.
+
+ '
- reference: PMID:42453107
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Overall, bioinoculants induced selective, function-specific shifts in
- rhizosphere microbial gene expression, not broad community changes.
- explanation: >
- Supports the distinction between the observed differential functional
- features and broad community-level shifts.
+ snippet: 'Overall, bioinoculants induced selective, function-specific shifts in rhizosphere microbial gene expression,
+ not broad community changes.
+
+ '
+ explanation: 'Supports the distinction between the observed differential functional features and broad community-level
+ shifts.
+
+ '
+ - reference: PMID:42453107
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: The metatranscriptomic contigs were assigned based on sequence similarity (not reference SynCom genomes)
+ explanation: Explains why functional RNA changes are not assigned to individual inoculant strains.
environmental_factors:
- name: GCEF wheat isolate source
value: Wheat cultivar RGT Reform rhizosphere
@@ -558,12 +566,31 @@ discussions:
status: OPEN
attaches_to:
- associated_datasets#PRJNA1405459
- rationale: >
- The paper reports PRJNA1405459 for the generated sequencing data, but NCBI
- BioProject returned a "not public" placeholder for accession 1405459 during
- curation on 2026-09-24.
+ rationale: 'The paper reports PRJNA1405459 for the generated sequencing data, but NCBI BioProject returned a "not
+ public" placeholder for accession 1405459 during curation on 2026-09-24.
+
+ '
posed_by: codex
posed_date: '2026-09-24'
+- discussion_id: dt_causal_scope_batch122
+ prompt: Which pre-infection responses mediate wheat DT-SynCom disease protection in barley?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Wheat DT-SynCom powdery mildew resistance
+ - ecological_interactions#Wheat DT-SynCom selective rhizosphere functional shifts
+ rationale: Molecular samples preceded the pathogen assay, so these profiles cannot be described as post-infection
+ responses. No significant pairwise difference establishes a superior inoculant. The authors could not assign
+ ISR to specific hormone pathways. OTU matches at 99% identity suggest persistence of related taxa, not unique
+ viable-strain identification. Preserve the prior selective-versus-broad correction and the dated BioProject-visibility
+ discussion.
+ evidence:
+ - reference: PMID:42453107
+ snippet: Although our data did not allow direct assignment of ISR to specific JA-, ET-, or SA-dependent pathways
+ - reference: PMID:42453107
+ snippet: Although strain-level identity cannot be confirmed by 16S rRNA gene-based identification alone
+ posed_by: codex
+ posed_date: '2026-10-08'
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -575,19 +602,25 @@ curation_history:
- timestamp: '2026-09-24T07:33:22Z'
curator: codex
action: ADD_COMMUNITY_RECORD
- changes: >
- Added CommunityMech:000429 for the sixteen-strain wheat-origin DT-SynCom
- from PMID:42453107 / doi:10.3389/fmicb.2026.1818676, including exact Table
- 1 member rows at genus plus strain-code resolution, equal-proportion
- YME-grown inoculum assembly, barley powdery mildew assay evidence,
- PRJNA1405459 dataset metadata, and an open discussion for the non-public
- BioProject.
+ changes: 'Added CommunityMech:000429 for the sixteen-strain wheat-origin DT-SynCom from PMID:42453107 / doi:10.3389/fmicb.2026.1818676,
+ including exact Table 1 member rows at genus plus strain-code resolution, equal-proportion YME-grown inoculum
+ assembly, barley powdery mildew assay evidence, PRJNA1405459 dataset metadata, and an open discussion for the
+ non-public BioProject.
+
+ '
llm_assisted: true
- timestamp: '2026-09-24T07:44:58Z'
curator: codex
action: FIX_ADVERSARIAL_REVIEW_FINDINGS
- changes: >
- Addressed issue #1070 from local adversarial review by adding source
- evidence for the Wheat DT-SynCom metatranscriptome interaction's selective,
- not broad, rhizosphere functional-shift clause.
+ changes: 'Addressed issue #1070 from local adversarial review by adding source evidence for the Wheat DT-SynCom
+ metatranscriptome interaction''s selective, not broad, rhizosphere functional-shift clause.
+
+ '
+ llm_assisted: true
+- timestamp: '2026-10-08T16:00:02Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain positive barley protection without inferring inoculant superiority, hormone-pathway necessity
+ or plant drought protection.; Preserve selective measured RNA changes and broad-profile nulls, with pre-challenge
+ timing and no strain-level or causal-pathway assignment. Issue#1948; reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
llm_assisted: true
diff --git a/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml b/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml
index e01e9316f..d806a44b0 100644
--- a/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml
+++ b/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml
@@ -99,11 +99,11 @@ taxonomy:
- *id001
ecological_interactions:
- name: Synthetic Community Fermentation-Enzyme Production
- description: The four Bacillus, Acinetobacter, Trichoderma, and Aspergillus
- degraders are assembled as synthetic microbial communities for
- fermentation-enzyme production, yielding the crude enzyme solution used for
- wheat-straw pretreatment.
- interaction_type: MUTUALISM
+ description: The four reported bacterial/fungal degraders form an enzyme-producing inoculum that yields the crude
+ enzyme solution used for wheat-straw pretreatment. This positive process output does not measure reciprocal
+ fitness, member-specific enzyme contributions or metabolite cross-feeding. The accessible abstract does not
+ resolve strain identities or establish that the four isolates constitute the downstream anaerobic-digestion
+ community.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: lignocellulose
@@ -125,21 +125,20 @@ ecological_interactions:
label: lignin catabolic process
downstream:
- target: Lignocellulose Enzyme Pretreatment
- description: Crude enzyme from the fermentation-production community was
- applied to wheat straw for the enzyme pretreatment that depolymerizes
- cellulose, hemicellulose, and lignin.
+ description: Fermentation supplies the crude enzyme solution applied to wheat straw, enabling the measured polymer-degradation
+ pretreatment. This is an enzyme-mediated material-transfer step, not proof that the living four-member inoculum
+ colonizes every subsequent process stage.
evidence:
- reference: PMID:38748977
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: synthetic microbial communities were constructed for fermentation-enzyme
- production
- explanation: Supports the fermentation-enzyme production step driven by
- the constructed degrader community.
+ snippet: synthetic microbial communities were constructed for fermentation-enzyme production
+ explanation: Supports the fermentation-enzyme production step driven by the constructed degrader community.
- name: Lignocellulose Enzyme Pretreatment
- description: Bacterial and fungal enzyme producers jointly degrade wheat straw polymers before anaerobic
- digestion.
- interaction_type: MUTUALISM
+ description: Crude enzyme solution from the synthetic community was applied to wheat straw before anaerobic digestion.
+ Reported cellulose, hemicellulose and lignin degradation rates were 39.85%, 36.99% and 19.21%, respectively.
+ The treatment acts through the enzyme preparation; these values do not establish reciprocal microbial benefit
+ or living producer growth on the pretreated substrate.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: cellulose
@@ -169,36 +168,37 @@ ecological_interactions:
label: lignin catabolic process
downstream:
- target: Enhanced Biogas Production after Anaerobic Digestion
- description: Improved wheat-straw enzymatic digestion feeds downstream
- anaerobic digestion and increases the cumulative biogas yield.
+ description: The enzyme-pretreated straw supplies substrate to subsequent anaerobic digestion, where cumulative
+ biogas was higher than with untreated straw or either commercial-enzyme pretreatment. Retain this process-level
+ treatment effect without assigning gas production to the four enzyme producers or to one uniquely necessary
+ polymer-degradation route.
evidence:
- - *id001
- reference: PMID:38748977
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99,
- and 19.21%, respectively.
- explanation: Quantifies degradation of the three major wheat-straw
- polymers by the synthetic microbial community enzyme pretreatment.
+ snippet: 'Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, Acinetobacter
+ johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading abilities among
+ samples from three environments: pile retting wheat straw (WS), WS returned to soil, and forest soil.'
+ explanation: Supports the defined synthetic community design and represented community context.
+ - reference: PMID:38748977
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, and 19.21%, respectively.
+ explanation: Quantifies degradation of the three major wheat-straw polymers by the synthetic microbial community
+ enzyme pretreatment.
- name: Enhanced Biogas Production after Anaerobic Digestion
- description: Wheat straw pretreated with the synthetic-community crude enzyme
- solution produced the highest cumulative biogas in the subsequent anaerobic
- digestion stage, outperforming untreated straw and both commercial enzyme
- pretreatments.
- interaction_type: MUTUALISM
+ description: Subsequent anaerobic digestion of synthetic-community enzyme-pretreated straw yielded 801.16 mL/g
+ TS cumulative biogas, higher than untreated straw and both commercial-enzyme pretreatments. Biogas volume is
+ not a methane-only yield. The abstract does not identify the digestion community or demonstrate methanogenesis
+ by the four enzyme-producing isolates.
scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: methane
- term:
- id: CHEBI:16183
- label: methane
evidence:
- reference: PMID:38748977
supports: SUPPORT
evidence_source: IN_VITRO
snippet: SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS
- explanation: Supports the anaerobic-digestion endpoint after synthetic
- microbial community enzyme-producing pretreatment.
+ explanation: Supports the anaerobic-digestion endpoint after synthetic microbial community enzyme-producing
+ pretreatment.
environmental_factors:
- name: defined synthetic community design
value: Core microorganisms with lignocellulose-degrading abilities were screened from straw and forest
@@ -246,3 +246,31 @@ related_ingredients:
snippet: yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99,
explanation: Reports a measured hemicellulose degradation rate, anchoring hemicellulose as a central
substrate of the pretreatment.
+discussions:
+- discussion_id: straw_causal_scope_batch122
+ prompt: How do enzyme producers and the downstream digestion community contribute to the biogas benefit?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Synthetic Community Fermentation-Enzyme Production
+ - ecological_interactions#Lignocellulose Enzyme Pretreatment
+ - ecological_interactions#Enhanced Biogas Production after Anaerobic Digestion
+ rationale: The accessible abstract supports the existing enzyme-production to pretreatment to digestion sequence
+ and positive polymer and total-biogas outcomes. It does not resolve individual-strain contributions, reciprocal
+ benefit, digestor membership, methane fraction or a uniquely necessary enzyme. Primary full methods and supplementary
+ information were not inspected; publisher access attempts failed. This is a bounded access limitation, not a
+ claim that full text or supplements do not exist.
+ evidence:
+ - reference: PMID:38748977
+ snippet: SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T16:00:03Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain enzyme-production output without reciprocal mutualism or attribution of downstream digestion to
+ the inoculum.; Preserve polymer-degradation values and enzyme transfer rather than living-cell mutualism.; Keep
+ positive downstream biogas yield distinct from methane-only yield or four-isolate methanogenesis. Issue#1949;
+ reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
+ llm_assisted: true
diff --git a/kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml b/kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml
index eb09f40cb..ffdac2c30 100644
--- a/kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml
+++ b/kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml
@@ -194,32 +194,47 @@ taxonomy:
snippet: E. ludwigii FWP1205, P. putida FWP0405, and S. maltophilia HLPD6
explanation: Identifies Stenotrophomonas maltophilia HLPD6 as a SynCom-SASW01 member.
ecological_interactions:
-- name: EPS-associated rhizosphere water retention
- description: SynCom-SASW01 treatment ameliorated drought-induced water deficits and was interpreted to stabilize the rhizosphere
- in part through exopolysaccharide secretion by core community members.
- interaction_type: COLONIZATION_FACILITATION
+- name: SynCom-SASW01 biocoating-associated water retention
+ description: 'In drought-stressed wheat pots, the combined SynCom-SASW01 plus coating-matrix treatment (BCC) increased
+ rhizosphere relative water content versus untreated NC. EPS-mediated water retention is HYPOTHESIZED, not selectively
+ demonstrated: the matrix includes biochar and other additives. The design also includes coating-only CC and
+ SynCom-only BC, but a BCC-versus-NC contrast does not isolate the microbial or EPS contribution. This water
+ outcome is not itself evidence of colonization facilitation.'
scope: COMMUNITY_LEVEL
evidence:
+ - reference: PMID:42513902
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: SynCom-SASW01 treatment significantly ameliorated drought-induced water deficits, which may be partly
+ attributable to the EPS secretion capacity of the consortium’s core members.
+ explanation: The authors explicitly qualify EPS attribution; it is not a selective EPS perturbation or a matrix-controlled
+ causal estimate.
- reference: PMID:42513902
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom-SASW01 treatment significantly ameliorated drought-induced water deficits, which may be partly attributable
- to the EPS secretion capacity of the consortium’s core members.
- explanation: Supports the paper's community-level interpretation that EPS-producing SynCom-SASW01 members helped improve
- rhizosphere water retention.
+ snippet: rhizosphere soil RWC in the BCC (biochar-consortium coating) treatment was significantly higher than
+ that in the uninoculated control (NC) group
+ explanation: Directly supports the measured combined-treatment water outcome.
- name: SynCom-SASW01 root endosphere reshaping
- description: The SynCom-SASW01 biological coating reorganized wheat root-associated bacterial communities under drought
- stress and especially shifted the root endosphere.
- interaction_type: COLONIZATION_FACILITATION
+ description: The BCC biological coating shifted wheat root-associated bacterial DNA profiles under drought, particularly
+ in the endosphere, with relative enrichment of Pseudomonas and other taxa. The microbiome comparison was BCC
+ versus NC, not SynCom alone versus coating alone. Matching 16S ASVs do not uniquely identify viable inoculant
+ strains or establish priority-effect causality. Correlation/RDA and PICRUSt2 functional predictions do not prove
+ BCAA transfer, taxon necessity or a community-to-antioxidant causal cascade.
scope: COMMUNITY_LEVEL
evidence:
+ - reference: PMID:42513902
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: the exogenous synthetic community efficiently colonized the endosphere and promoted the enrichment
+ of keystone genera such as Pseudomonas.
+ explanation: An author-level interpretation of relative community profiles; it does not independently establish
+ unique-strain viability or keystone necessity.
- reference: PMID:42513902
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: the exogenous synthetic community efficiently colonized the endosphere and promoted the enrichment of keystone
- genera such as Pseudomonas.
- explanation: Supports SynCom-SASW01 endosphere colonization and enrichment of Pseudomonas-associated beneficial taxa after
- inoculation.
+ snippet: in the endosphere, En_BCC samples exhibited a clear separation from En_NC samples
+ explanation: Supports the observed community-profile contrast without assigning its mediator.
environmental_factors:
- name: Host crop
value: Triticum aestivum
@@ -291,26 +306,53 @@ external_resources:
explanation: Identifies the primary publication for the curated SynCom-SASW01 record.
discussions:
- discussion_id: wheat_sasw01_isolation_and_individual_pgp_traits
- prompt: Which original isolation sites and individual plant-growth-promoting traits belong to each SynCom-SASW01 strain?
+ prompt: Which original isolation sites and individual plant-growth-promoting traits belong to each SynCom-SASW01
+ strain?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- taxonomy
- rationale: The article body names Supplementary Table S1 for strain isolation sites and Supplementary Table S2 for individual
- plant-growth-promoting traits, but the curated record has not inspected those tables. The current taxonomy asserts only
- the strain names and species supported by the article Methods section.
+ rationale: The article body names Supplementary Table S1 for strain isolation sites and Supplementary Table S2
+ for individual plant-growth-promoting traits, but the curated record has not inspected those tables. The current
+ taxonomy asserts only the strain names and species supported by the article Methods section.
+- discussion_id: sasw_causal_scope_batch122
+ prompt: Which microbial effects are separable from the coating matrix in SASW01-associated drought benefits?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#SynCom-SASW01 biocoating-associated water retention
+ - ecological_interactions#SynCom-SASW01 root endosphere reshaping
+ rationale: Positive BCC field yields and pot water, nutrient and physiological outcomes remain real treatment
+ observations. Field comparisons contain only NC and BCC; the two-site yield benefit is not a SynCom-only or
+ EPS-specific effect. Amplicon matching, inferred functions and correlations cannot establish a priority-effect
+ or BCAA-transfer mechanism. Prior removal of assembly and PICRUSt-derived mechanism nodes remains intact. Source
+ yield percentages differ between Results and Conclusions; non-graph reconciliation is separate.
+ evidence:
+ - reference: PMID:42513902
+ snippet: 'Two treatments were established: NC (control) and BCC (SynCom-SASW01 biological coating).'
+ - reference: PMID:42513902
+ snippet: Functional potential prediction was conducted using PICRUSt2 (2.6.0) based on MetaCyc Level 3 pathways
+ posed_by: codex
+ posed_date: '2026-10-08'
curation_history:
- timestamp: '2026-09-21T16:09:11Z'
curator: codex
action: CREATE_RECORD
- changes: Created CommunityMech:000409 for the five-strain SynCom-SASW01 wheat drought-resistance inoculant from PMID:42513902,
- including exact strain membership, equal-ratio assembly, seed-coating deployment, moderate-drought pot setup, dual-site
- field design, and rhizosphere/endosphere response evidence.
+ changes: Created CommunityMech:000409 for the five-strain SynCom-SASW01 wheat drought-resistance inoculant from
+ PMID:42513902, including exact strain membership, equal-ratio assembly, seed-coating deployment, moderate-drought
+ pot setup, dual-site field design, and rhizosphere/endosphere response evidence.
llm_assisted: true
- timestamp: '2026-09-21T16:12:15Z'
curator: codex
action: UPDATE_EVIDENCE
- changes: 'Addressed adversarial review issues #1016 and #1017 by removing equal-ratio inoculum assembly and the PICRUSt2
- BCAA/antioxidant association from ecological_interactions, while retaining OD600 normalization and 1:1:1:1:1 assembly
- as engineering_design evidence.'
+ changes: 'Addressed adversarial review issues #1016 and #1017 by removing equal-ratio inoculum assembly and the
+ PICRUSt2 BCAA/antioxidant association from ecological_interactions, while retaining OD600 normalization and
+ 1:1:1:1:1 assembly as engineering_design evidence.'
+ llm_assisted: true
+- timestamp: '2026-10-08T16:00:03Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain measured combined-treatment water retention while marking EPS mediation as hypothesized and coating-confounded.;
+ Keep relative DNA-profile shifts distinct from unique-strain colonization, priority effects and predicted metabolic
+ causality. Issue#1950; reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 483518cae..b7a97d4cc 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,33 @@ 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`.
+## Batch122: Treatment Outcomes And Mechanism Limits
+
+[Decisions](decisions/20261008-four-records-batch122.yaml),
+[provenance](cache-provenance-20261008-batch122.json),
+[validation](validation-20261008-batch122.json), and
+[self-adversarial review](adversarial-review-20261008-batch122.yaml) cover
+wheat crown-rot TB, wheat-origin DT-SynCom, straw enzyme pretreatment and SASW01.
+All nine nodes and both arrows remain, with one rename and no new topology.
+
+TB keeps positive pot efficacy while distinguishing relative DNA profiles and
+simulated network robustness from biological causality. DT keeps barley disease
+protection and selective pre-challenge RNA changes, not inoculant superiority or
+proven hormone-pathway dependence. Straw keeps enzyme-mediated pretreatment and
+improved downstream biogas, not reciprocal mutualism or methane-only yield.
+SASW01 retains combined biocoating outcomes with EPS mediation hypothesized and
+coating effects distinct from SynCom-only contributions.
+
+Three open main bodies and all four abstracts were read; straw is abstract-bounded.
+Original figure pixels, separate supplements, raw data and code were not audited.
+All 23 graph/discussion quotes match fresh primary sources and existing caches.
+All 923 caches and 456 other records remain unchanged. Four append-only histories
+record the repairs. No Edison submission or spend was needed.
+
+Repairs #1947-#1950 await protected-main merge. Source timing/figure and yield
+follow-ups #1951-#1952 remain open. This is source-based self-review, not
+independent approval or completion of the overall review and protected merge.
+
## Batch121: Plant Outcomes And Mixture Contrasts
[Decisions](decisions/20261008-four-records-batch121.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch122.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch122.yaml
new file mode 100644
index 000000000..9a3a7137b
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch122.yaml
@@ -0,0 +1,420 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: ec8ee08b153173a5ad77ae95aad9f38d34468d85
+scope:
+- kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml
+- kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml
+- kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml
+- kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch122.json
+findings:
+- issue: 1947
+ severity: P2
+ finding: Bound TB wheat crown-rot protection and rhizosphere mechanism claims
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1948
+ severity: P2
+ finding: Bound wheat DT-SynCom pre-challenge RNA findings and disease-protection interpretation
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1949
+ severity: P2
+ finding: Separate wheat-straw enzyme pretreatment and biogas endpoint from mutualism and methane claims
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1950
+ severity: P2
+ finding: Separate SASW01 biocoating outcomes from EPS, colonization and predicted mechanism claims
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1951
+ severity: P2
+ finding: Reconcile TB wheat crown-rot sampling clocks and figure references
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1952
+ severity: P2
+ finding: Reconcile SASW01 field-yield discrepancy and treatment scope outside the graph
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- All nine nodes and both process directions retained,one rename,no new topology. No empty downstream lists,dangling
+ targets or anchors. All four canonical diffs read after mutation; prior history entries and unrelated fields preserved.
+- TB retains positive70.97%pot efficacy,growth and grain-related outcomes without bilateral competition or unique
+ immune mediation. Challenge fungus is not a TB member. No single-member plant arms demonstrate individual necessity.
+ Simulated network attacks are not biological removal; genus assignments do not prove functions. Soil metabolites
+ are not root-exudate collections; no compound-intervention evidence transferred from the different six-member
+ study.
+- DT retains43.3%barley disease fluorescence reduction and no significant differences between inoculants. Specific
+ JA/ET/SA dependence is not assigned. PEG-tolerant isolates are not whole-plant drought validation. Pre-challenge
+ measured RNA changes retain the prior selective/not-broad evidence; contig similarity does not identify inoculant
+ strain transcription.99%OTU matches do not establish unique viable strains.
+- Straw retains crude enzyme production,enzyme transfer and subsequent substrate digestion,both arrows and39.85/36.99/19.21%polymer
+ degradation.801.16mL/gTS is positive total biogas,not methane-only yield. Removing the methane annotation does
+ not claim methane absence. Four enzyme producers are not assumed to be the downstream methanogenic community;
+ no reciprocal fitness inferred.
+- SASW retains combined BCC water and profile outcomes. EPS mediation remains HYPOTHESIZED with PARTIAL support;
+ separate positive water evidence stays SUPPORT. BCC-versus-NC cannot isolate SynCom from coating. Relative profiles
+ and ASV matching do not prove unique viable strains or priority effects; PICRUSt2 and correlations do not establish
+ BCAA transfer or keystone necessity. Prior assembly/PICRUSt-node removals and uninspected-S1/S2 discussion preserved.
+- All17graph and6discussion quotes match fresh sources and unchanged caches. Three open main bodies read; straw
+ abstract-bounded. Original figure pixels,external supplements,raw data and code not audited. No new cache content
+ or protocol optimization. Source timing/figure and yield inconsistencies remain separate1951/1952.
+- Fifteen focused tests and12actual control/mutation/restored-control probes pass. Mutations reject restored competition/mutualism,erased
+ TB efficacy,simulation-to-biological promotion,DT superiority and erased nulls,dropped straw arrow/degradation,methane
+ annotation,erased coating confounding,EPS promotion and profile-to-colonization promotion. Canonical files unchanged
+ by probes.
+- Four records pass schema,strict,terms,full-record references,snippets,rank and history.1161selected tests pass,not
+ full Linux CI certification.57unchanged network warnings and zero structural defects. Exact descriptions on456pages,1359nodes,522arrows
+ and deterministic rendering verified,not screenshot QA.
+- All456otherrecords,923caches and prior history/decision files unchanged. Participant lists and scopes unchanged:299list
+ users,414community-level,136mixed,278community-only,1568taxa,1281solely credited. Scope credit is not actual-participant
+ certification. No connectivity logic,threshold or schema changes.
+- Repairs1947-1950 addressed pending protected-main merge;1951/1952 remain non-graph follow-ups. Self-review is
+ not independent approval. No Edison invocation or spend; Ruegeria1883 authentication blocker not retried unchanged.
+ Root1836 and actual protected exact-head checks remain required.
+- Corpus396reviewed,10pending,54needs_research across460records. Overall objective,protected merge and branch deletion
+ incomplete. Postcommit docs-current and exact-head publication are separate checks,not preasserted here.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Restore TB competition
+ test: test_tb_retains_positive_disease_control_without_competition
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 21
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/interaction_type
+ before: null
+ after: COMPETITION
+ - mutation: Erase TB positive efficacy
+ test: test_tb_retains_positive_disease_control_without_competition
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 23
+ assertion: assert "70.97%" in node["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/evidence/1/snippet
+ before: with a biocontrol efficacy of 70.97%
+ after: No efficacy occurred.
+ - mutation: Promote simulation to biological removal
+ test: test_tb_network_robustness_is_simulated_not_biological_removal
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 32
+ assertion: assert "not biological removal experiments" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/description
+ before: TB treatment changed rhizosphere DNA-based community profiles, including relative enrichment of
+ Mortierella and reduced pathogen-associated fungi. Relative sequence abundance does not establish absolute
+ viable abundance or strain-resolved persistence of T19/PM16. Genus annotations and correlation networks
+ do not establish beneficial function, nutrient exchange or microbial necessity. Network robustness was
+ assessed by simulated node removal, not biological removal experiments. Remodeling is not isolated as
+ the cause of the positive disease-control outcome.
+ after: Biological removal proved robustness.
+ - mutation: Assert DT superiority
+ test: test_dt_protection_is_not_inoculant_superiority_or_drought_validation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 50
+ assertion: assert "pairwise differences were not significant" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/0/description
+ before: The wheat-origin, 16-member DT-SynCom reduced barley leaf powdery-mildew DAF fluorescence by 43.3%
+ relative to mock treatment after Blumeria graminis f. sp. hordei challenge. All three inoculants protected
+ plants; their pairwise differences were not significant. This supports ISR-like protection but does not
+ assign necessity to JA, ethylene or SA signaling. PEG-tolerant isolate selection is not a test of whole-plant
+ drought protection.
+ after: 43.3% reduction establishes superior drought protection.
+ - mutation: Erase DT broad-profile null
+ test: test_dt_rna_changes_precede_challenge_and_keep_broad_null
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 61
+ assertion: assert "not broad community changes" in node["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/evidence/1/snippet
+ before: 'Overall, bioinoculants induced selective, function-specific shifts in rhizosphere microbial gene
+ expression, not broad community changes.
+
+ '
+ after: Broad community changes were significant.
+ - mutation: Restore straw mutualism
+ test: test_straw_process_outputs_are_not_reciprocal_mutualism
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 77
+ assertion: assert len(nodes) == 3 and all("interaction_type" not in n for n in nodes)
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/interaction_type
+ before: null
+ after: MUTUALISM
+ - mutation: Erase enzyme-transfer arrow
+ test: test_straw_retains_both_material_transfer_directions
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 85
+ assertion: assert len(a["downstream"]) == len(b["downstream"]) == 1
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/downstream
+ before:
+ - target: Lignocellulose Enzyme Pretreatment
+ description: Fermentation supplies the crude enzyme solution applied to wheat straw, enabling the measured
+ polymer-degradation pretreatment. This is an enzyme-mediated material-transfer step, not proof that
+ the living four-member inoculum colonizes every subsequent process stage.
+ after: []
+ - mutation: Erase positive polymer degradation
+ test: test_straw_preserves_positive_polymer_degradation_values
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 95
+ assertion: assert all(v in node["description"] for v in ["39.85%", "36.99%", "19.21%"])
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/description
+ before: Crude enzyme solution from the synthetic community was applied to wheat straw before anaerobic digestion.
+ Reported cellulose, hemicellulose and lignin degradation rates were 39.85%, 36.99% and 19.21%, respectively.
+ The treatment acts through the enzyme preparation; these values do not establish reciprocal microbial
+ benefit or living producer growth on the pretreated substrate.
+ after: No degradation occurred.
+ - mutation: Reannotate total biogas as methane
+ test: test_straw_total_biogas_is_not_methane_only_or_isolate_methanogenesis
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 105
+ assertion: assert "metabolites" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/2/metabolites
+ before: null
+ after:
+ - preferred_term: methane
+ - mutation: Erase SASW coating confounding
+ test: test_sasw_water_outcome_is_combined_biocoating_not_syncom_alone
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 113
+ assertion: assert "coating-only CC and SynCom-only BC" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/0/description
+ before: 'In drought-stressed wheat pots, the combined SynCom-SASW01 plus coating-matrix treatment (BCC)
+ increased rhizosphere relative water content versus untreated NC. EPS-mediated water retention is HYPOTHESIZED,
+ not selectively demonstrated: the matrix includes biochar and other additives. The design also includes
+ coating-only CC and SynCom-only BC, but a BCC-versus-NC contrast does not isolate the microbial or EPS
+ contribution. This water outcome is not itself evidence of colonization facilitation.'
+ after: SynCom alone caused the water benefit.
+ - mutation: Promote EPS hypothesis to support
+ test: test_sasw_eps_mediation_remains_hypothesized
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 123
+ assertion: assert node["evidence"][0]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/0/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Promote SASW profiles to colonization facilitation
+ test: test_sasw_profiles_do_not_establish_viable_strains_or_causal_cascade
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 130
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/1/interaction_type
+ before: null
+ after: COLONIZATION_FACILITATION
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml: d355a605023b423a1b2d61dc1f49177d9f90f4c0a0510abef0f074b085216002
+ kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml: ee5b482655aeb0d187e29cfe8b18016b247b355f3d63dbba2db3b591c84f05ef
+ kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml: f7eb74b6868f91109757655407c0934a7e1971e9692283f52c51ecbf329c9df4
+ kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml: 613f8b97efa732c213fae320935a4f8cafa8cb899718e6c18a7c1f47f9ba0420
+ tests/test_causal_review_batch122.py: 00bfbda6721badbc73893b0dbdaea5ec146f84d33e581b86f75df8cfa8ab189e
+ probe_script_sha256: 611a8d0a56a617ee06ec9540ba151757ecddea057e4c688c2d7d43fec33a52e1
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch122/adversarial-regression-proof.json
+ sha256: 6463b5db5ebe7657a6f25dd3789714bff35431566a81de7d8b6335c15cd011bb
+verification:
+ combined_regressions: 1161 passed in 600.56s (0:10:00)
+ new_regression_tests: 15
+ total_recorded_gate_outputs: 41
+ primary_graph_snippet_proof:
+ graph_quotations: 17
+ discussion_quotations: 6
+ fresh_primary_literal_matches: 23
+ all_cached_literal_matches: 23
+ retained_nodes: 9
+ removed_nodes: 0
+ renamed_nodes: 1
+ retained_arrows: 2
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml:
+ MATCH: 20
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml:
+ MATCH: 33
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml:
+ MATCH: 14
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml:
+ MATCH: 22
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9084
+ categories:
+ MATCH: 8936
+ RENDERING: 31
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 57
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml: c77c5eb2fb20969b2f3b50aa34646df937cfb86c2f96c308ea2350f016cf080e
+ tests/test_causal_review_batch122.py: 00bfbda6721badbc73893b0dbdaea5ec146f84d33e581b86f75df8cfa8ab189e
+ tests/test_participating_taxa.py: f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1
+ tests/test_community_level_connectivity_credit.py: 996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a
+ tests/test_causal_review_batch109.py: ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73
+ tests/test_datamodel.py: f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25
+ reports/causal_graph_review/cache-provenance-20261008-batch122.json: 10c911cdfc0852678c5ea2e3a5ffab604750c835a6455f723ca69a6d85a4e03b
+ kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml: d355a605023b423a1b2d61dc1f49177d9f90f4c0a0510abef0f074b085216002
+ kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml: ee5b482655aeb0d187e29cfe8b18016b247b355f3d63dbba2db3b591c84f05ef
+ kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml: f7eb74b6868f91109757655407c0934a7e1971e9692283f52c51ecbf329c9df4
+ kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml: 613f8b97efa732c213fae320935a4f8cafa8cb899718e6c18a7c1f47f9ba0420
+ history_sha256:
+ history/records/Wheat_CrownRot_TB_CrossKingdom_SynCom/2026-10-08T160003Z-codex-e66225.yaml: ee4848501ada32eae957eb80150b29b9306836a8293ae32e0a4b0e338684d2f9
+ history/records/Wheat_DT_Rhizosphere_SynCom/2026-10-08T160004Z-codex-72b999.yaml: e8e555d4fcba8287a1fb0b7b87be34ddeecced4d404d287b7b73dd165573322b
+ history/records/Wheat_Straw_Biogas_Pretreatment_SynCom/2026-10-08T160004Z-codex-49a7c7.yaml: 0da445e681c09a225c84ad433230c504a57056a06eefad0493a5fa1b9c260b57
+ history/records/Wheat_SynCom_SASW01_Drought_Inoculant/2026-10-08T160004Z-codex-53385b.yaml: 1d58e45ffb16360ac90bed8e48c2f6a00b42ab0f2f6ace1fb23eaeba7a39fbc8
+ unchanged_records: 456
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 899
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation;
+ no unchanged-state retry.'
+ post_commit_docs_current: Separate publication gate,not preasserted.
+participant_census:
+ current:
+ records: 460
+ with_community_level: 414
+ mixed: 136
+ community_level_only: 278
+ taxa: 1568
+ credited_solely_by_the_rule: 1281
+ delta_from_batch121:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ explanation: All participant lists and scopes are unchanged;299participant-list users. Scope credit is not certification
+ of actual participant coverage. Connectivity logic and thresholds are unchanged.
+corpus:
+ records: 460
+ nodes: 1373
+ edges: 530
+ review_status_counts:
+ needs_research: 54
+ pending: 10
+ reviewed: 396
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Both-root pre-source baseline covers460records and923caches,57existing warnings and zero structural defects. Four
+ whole target records and nine nodes/two arrows reviewed; all retained,one rename,no new topology.
+- Four fresh EuropePMC metadata/abstract and Crossref identities checked. Complete open TB,DT and SASW main-body
+ text,methods,results,discussion and available table/caption text read. SASW Figure4 caption additionally checked
+ via PubMed. No original figure pixels,separate supplementary files,raw data or analysis code audit.
+- Straw repairs are abstract-bounded. EuropePMC lists no PMCID; ACS primary search result gives abstract and supporting-information
+ listing,but publisher article access returned403 and the attempted SI endpoint was inaccessible. No full text
+ or supplement inspected,no access bypass or exhaustive absence claim.
+- TB retains positive pot disease control,70.97%biocontrol efficacy and growth traits. No in-vivo single-member
+ arms identify necessity or synergy. Relative DNA profiles are not viable-strain persistence; network robustness
+ used simulated removal. Soil metabolites are not directly sampled root exudates,QS/volatiles remain hypotheses,and
+ metabolite validation from the separate six-strain paper is not transferred.
+- DT retains43.3%barley disease-assay fluorescence reduction,selective pre-challenge measured RNA changes and broad-profile
+ nulls. No significant inoculant pairwise differences or assigned JA/ET/SA pathway dependence. Similarity-based
+ annotations do not identify inoculant transcripts;99%OTU matching does not establish unique viable strains. Prior1070and
+ dated BioProject discussion preserved; access status not rechecked.
+- Straw retains both process directions and39.85/36.99/19.21%polymer degradation and801.16mL/gTS total biogas. Crude
+ enzymes rather than living producers mediate pretreatment; no reciprocal-fitness evidence or four-isolate methanogenesis
+ inferred. Removed methane annotation does not assert that methane was absent.
+- SASW retains positive combined BCC outcomes with coating matrix distinct from SynCom-only effects. EPS mediation
+ remains HYPOTHESIZED/PARTIAL; relative16S profiles,100%ASV matching,PICRUSt2 and Mantel/RDA do not establish viable-strain
+ identity,priority-effect causality,BCAA transfer or keystone necessity. Prior1016/1017 removals and S1/S2 knowledge
+ gap preserved.
+- All17graph and6discussion quotations independently matched to fresh primary and existing local caches. Relevant
+ cache excerpts and complete short straw cache read; no claim of manual whole-cache reading for long flattened
+ bodies. Literal matches are not entailment proof. No cache changes or full-body imports. Three retrieved open
+ papers carry CC BY4.0; ACS does not.
+- Fresh1182all-state issue titles/bodies searched with expanded DOIs and aliases;five matching bodies and two prior
+ YAML review reports read.150matching local paths found with hidden/ignored inclusion,excluding.git,docs,site,references_cache
+ and credentials. Closed1072label drift,1070selective RNA evidence,1069Barley typo,1016assembly and1017PICRUSt
+ removals are distinct and preserved. Not a historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML fields and all prior history/decision
+ artifacts. Four append-only histories and curation events. Taxa,participant lists and scopes unchanged; evidence
+ aliases detached. TB external challenge participant remains explicitly distinguished from inoculum membership.
+- No Edison submission or credits,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication
+ blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent
+ approval. Overall goal,protected merge and branch deletion remain incomplete.
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new file mode 100644
index 000000000..7ee55bb95
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+ "doi": "10.3389/fmicb.2026.1818676",
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+ "title": "Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community.",
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+ "doi": "10.3390/microorganisms14071396",
+ "pmcid": "PMC13414153",
+ "title": "Regulatory Mechanisms of Microbial Consortium Inoculant SynCom-SASW01 in Modulating Rhizosphere-Endophytic Interactions and Enhancing Drought Resistance in Wheat.",
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+ "status": "retrieved"
+ },
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+ "primary_text_sha256": "18608ebec9cc725821985d1f7a8c2b9d1f07e47f094745ce0ecaf4346a74aa1c",
+ "license": [
+ "https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license."
+ ],
+ "crossref": "/private/tmp/communitymech-batch122/sasw-crossref.json",
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+ },
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+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ }
+ ]
+ }
+ },
+ "actual_read_scope": [
+ "Four fresh EuropePMC metadata/abstract and Crossref identities checked. Complete open TB,DT and SASW main-body text,methods,results,discussion and available table/caption text read. SASW Figure4 caption additionally checked via PubMed. No original figure pixels,separate supplementary files,raw data or analysis code audit.",
+ "Straw repairs are abstract-bounded. EuropePMC lists no PMCID; ACS primary search result gives abstract and supporting-information listing,but publisher article access returned403 and the attempted SI endpoint was inaccessible. No full text or supplement inspected,no access bypass or exhaustive absence claim.",
+ "TB retains positive pot disease control,70.97%biocontrol efficacy and growth traits. No in-vivo single-member arms identify necessity or synergy. Relative DNA profiles are not viable-strain persistence; network robustness used simulated removal. Soil metabolites are not directly sampled root exudates,QS/volatiles remain hypotheses,and metabolite validation from the separate six-strain paper is not transferred.",
+ "DT retains43.3%barley disease-assay fluorescence reduction,selective pre-challenge measured RNA changes and broad-profile nulls. No significant inoculant pairwise differences or assigned JA/ET/SA pathway dependence. Similarity-based annotations do not identify inoculant transcripts;99%OTU matching does not establish unique viable strains. Prior1070and dated BioProject discussion preserved; access status not rechecked.",
+ "Straw retains both process directions and39.85/36.99/19.21%polymer degradation and801.16mL/gTS total biogas. Crude enzymes rather than living producers mediate pretreatment; no reciprocal-fitness evidence or four-isolate methanogenesis inferred. Removed methane annotation does not assert that methane was absent.",
+ "SASW retains positive combined BCC outcomes with coating matrix distinct from SynCom-only effects. EPS mediation remains HYPOTHESIZED/PARTIAL; relative16S profiles,100%ASV matching,PICRUSt2 and Mantel/RDA do not establish viable-strain identity,priority-effect causality,BCAA transfer or keystone necessity. Prior1016/1017 removals and S1/S2 knowledge gap preserved."
+ ]
+ },
+ "limitations": [
+ "Both-root pre-source baseline covers460records and923caches,57existing warnings and zero structural defects. Four whole target records and nine nodes/two arrows reviewed; all retained,one rename,no new topology.",
+ "Four fresh EuropePMC metadata/abstract and Crossref identities checked. Complete open TB,DT and SASW main-body text,methods,results,discussion and available table/caption text read. SASW Figure4 caption additionally checked via PubMed. No original figure pixels,separate supplementary files,raw data or analysis code audit.",
+ "Straw repairs are abstract-bounded. EuropePMC lists no PMCID; ACS primary search result gives abstract and supporting-information listing,but publisher article access returned403 and the attempted SI endpoint was inaccessible. No full text or supplement inspected,no access bypass or exhaustive absence claim.",
+ "TB retains positive pot disease control,70.97%biocontrol efficacy and growth traits. No in-vivo single-member arms identify necessity or synergy. Relative DNA profiles are not viable-strain persistence; network robustness used simulated removal. Soil metabolites are not directly sampled root exudates,QS/volatiles remain hypotheses,and metabolite validation from the separate six-strain paper is not transferred.",
+ "DT retains43.3%barley disease-assay fluorescence reduction,selective pre-challenge measured RNA changes and broad-profile nulls. No significant inoculant pairwise differences or assigned JA/ET/SA pathway dependence. Similarity-based annotations do not identify inoculant transcripts;99%OTU matching does not establish unique viable strains. Prior1070and dated BioProject discussion preserved; access status not rechecked.",
+ "Straw retains both process directions and39.85/36.99/19.21%polymer degradation and801.16mL/gTS total biogas. Crude enzymes rather than living producers mediate pretreatment; no reciprocal-fitness evidence or four-isolate methanogenesis inferred. Removed methane annotation does not assert that methane was absent.",
+ "SASW retains positive combined BCC outcomes with coating matrix distinct from SynCom-only effects. EPS mediation remains HYPOTHESIZED/PARTIAL; relative16S profiles,100%ASV matching,PICRUSt2 and Mantel/RDA do not establish viable-strain identity,priority-effect causality,BCAA transfer or keystone necessity. Prior1016/1017 removals and S1/S2 knowledge gap preserved.",
+ "All17graph and6discussion quotations independently matched to fresh primary and existing local caches. Relevant cache excerpts and complete short straw cache read; no claim of manual whole-cache reading for long flattened bodies. Literal matches are not entailment proof. No cache changes or full-body imports. Three retrieved open papers carry CC BY4.0; ACS does not.",
+ "Fresh1182all-state issue titles/bodies searched with expanded DOIs and aliases;five matching bodies and two prior YAML review reports read.150matching local paths found with hidden/ignored inclusion,excluding.git,docs,site,references_cache and credentials. Closed1072label drift,1070selective RNA evidence,1069Barley typo,1016assembly and1017PICRUSt removals are distinct and preserved. Not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML fields and all prior history/decision artifacts. Four append-only histories and curation events. Taxa,participant lists and scopes unchanged; evidence aliases detached. TB external challenge participant remains explicitly distinguished from inoculum membership.",
+ "No Edison submission or credits,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent approval. Overall goal,protected merge and branch deletion remain incomplete."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
new file mode 100644
index 000000000..06f0d0cae
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
@@ -0,0 +1,671 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: ec8ee08b153173a5ad77ae95aad9f38d34468d85
+baseline_commit: ec8ee08b153173a5ad77ae95aad9f38d34468d85
+base_tree: a0eac0886a3e4e3df6f557ccbe02037155931356
+pre_source_baseline_sha256: e61ca7f5b24b54529160712e89f47b943a167f4cc0dd99feeac9fcc4a9124e9d
+issues:
+- 1947
+- 1948
+- 1949
+- 1950
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1951
+- 1952
+source_access:
+ retrieval_manifest:
+ tb:
+ pmid: '41821943'
+ doi: 10.3389/fpls.2026.1758273
+ pmcid: PMC12977338
+ title: A minimal cross-kingdom SynCom promotes plant growth and suppresses wheat crown rot via coordinated
+ rhizosphere microbiome remodeling.
+ metadata: /private/tmp/communitymech-batch122/tb-metadata.json
+ metadata_sha256: d681da4e6d63c986375fa2b53374f0962f2770d4b636f1aa4f46d667006fcb33
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41821943+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12977338/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch122/tb-abstract.txt
+ abstract_sha256: 8f4779c5f2a36f118344c012621acd7849692e09df86f10103a86612fc4fd412
+ xml: /private/tmp/communitymech-batch122/tb-primary.xml
+ xml_sha256: 85195b3a1511f99ee26151460185983fd486cbe9c62139765ba80b75d973a68f
+ primary_text: /private/tmp/communitymech-batch122/tb-primary.txt
+ primary_text_sha256: 49c7fc4983cc371b6f69d3048acc80030d1393ff5ffacd9b1e3dad233d4992c4
+ license:
+ - https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of
+ the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums
+ is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original
+ publication in this journal is cited, in accordance with accepted academic practice. No use, distribution
+ or reproduction is permitted which does not comply with these terms.
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+ pmcid: PMC13365038
+ title: Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without
+ major shifts in the native bacterial community.
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+ BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s)
+ and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance
+ with accepted academic practice. No use, distribution or reproduction is permitted which does not comply
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+ title: Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of Wheat Straw for Biogas
+ Production via Anaerobic Digestion.
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+ doi: 10.3390/microorganisms14071396
+ pmcid: PMC13414153
+ title: Regulatory Mechanisms of Microbial Consortium Inoculant SynCom-SASW01 in Modulating Rhizosphere-Endophytic
+ Interactions and Enhancing Drought Resistance in Wheat.
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+ article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
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+ actual_read_scope:
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+ text,methods,results,discussion and available table/caption text read. SASW Figure4 caption additionally checked
+ via PubMed. No original figure pixels,separate supplementary files,raw data or analysis code audit.
+ - Straw repairs are abstract-bounded. EuropePMC lists no PMCID; ACS primary search result gives abstract and supporting-information
+ listing,but publisher article access returned403 and the attempted SI endpoint was inaccessible. No full text
+ or supplement inspected,no access bypass or exhaustive absence claim.
+ - TB retains positive pot disease control,70.97%biocontrol efficacy and growth traits. No in-vivo single-member
+ arms identify necessity or synergy. Relative DNA profiles are not viable-strain persistence; network robustness
+ used simulated removal. Soil metabolites are not directly sampled root exudates,QS/volatiles remain hypotheses,and
+ metabolite validation from the separate six-strain paper is not transferred.
+ - DT retains43.3%barley disease-assay fluorescence reduction,selective pre-challenge measured RNA changes and
+ broad-profile nulls. No significant inoculant pairwise differences or assigned JA/ET/SA pathway dependence.
+ Similarity-based annotations do not identify inoculant transcripts;99%OTU matching does not establish unique
+ viable strains. Prior1070and dated BioProject discussion preserved; access status not rechecked.
+ - Straw retains both process directions and39.85/36.99/19.21%polymer degradation and801.16mL/gTS total biogas.
+ Crude enzymes rather than living producers mediate pretreatment; no reciprocal-fitness evidence or four-isolate
+ methanogenesis inferred. Removed methane annotation does not assert that methane was absent.
+ - SASW retains positive combined BCC outcomes with coating matrix distinct from SynCom-only effects. EPS mediation
+ remains HYPOTHESIZED/PARTIAL; relative16S profiles,100%ASV matching,PICRUSt2 and Mantel/RDA do not establish
+ viable-strain identity,priority-effect causality,BCAA transfer or keystone necessity. Prior1016/1017 removals
+ and S1/S2 knowledge gap preserved.
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+ scope: Normalized contiguous literal match, not entailment proof.
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+ cache_artifact: references_cache/PMID_38748977.txt
+ scope: Normalized contiguous literal match, not entailment proof.
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+ reference: PMID:38748977
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+ matched_artifact: /private/tmp/communitymech-batch122/straw-abstract.txt
+ cache_artifact: references_cache/PMID_38748977.txt
+ scope: Normalized contiguous literal match, not entailment proof.
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+ matched_artifact: /private/tmp/communitymech-batch122/straw-abstract.txt
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+ cache_artifact: references_cache/PMID_42513902.txt
+ scope: Normalized contiguous literal match, not entailment proof.
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+ node: SynCom-SASW01 biocoating-associated water retention
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+ reference: PMID:42513902
+ cache_matched: true
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+ matched_artifact: /private/tmp/communitymech-batch122/sasw-primary.txt
+ cache_artifact: references_cache/PMID_42513902.txt
+ scope: Normalized contiguous literal match, not entailment proof.
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+ node: SynCom-SASW01 root endosphere reshaping
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+ reference: PMID:42513902
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+ matched_artifact: /private/tmp/communitymech-batch122/sasw-primary.txt
+ cache_artifact: references_cache/PMID_42513902.txt
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+ evidence_index: 1
+ reference: PMID:42513902
+ cache_matched: true
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+ matched_artifact: /private/tmp/communitymech-batch122/sasw-primary.txt
+ cache_artifact: references_cache/PMID_42513902.txt
+ scope: Normalized contiguous literal match, not entailment proof.
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+ node: tb_causal_scope_batch122
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+ reference: PMID:41821943
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch122/tb-primary.txt
+ cache_artifact: references_cache/PMID_41821943.txt
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+ cache_matched: true
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+cache_changes: []
+edison:
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+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation; no
+ unchanged-state retry.'
+limitations:
+- Both-root pre-source baseline covers460records and923caches,57existing warnings and zero structural defects. Four
+ whole target records and nine nodes/two arrows reviewed; all retained,one rename,no new topology.
+- Four fresh EuropePMC metadata/abstract and Crossref identities checked. Complete open TB,DT and SASW main-body
+ text,methods,results,discussion and available table/caption text read. SASW Figure4 caption additionally checked
+ via PubMed. No original figure pixels,separate supplementary files,raw data or analysis code audit.
+- Straw repairs are abstract-bounded. EuropePMC lists no PMCID; ACS primary search result gives abstract and supporting-information
+ listing,but publisher article access returned403 and the attempted SI endpoint was inaccessible. No full text
+ or supplement inspected,no access bypass or exhaustive absence claim.
+- TB retains positive pot disease control,70.97%biocontrol efficacy and growth traits. No in-vivo single-member
+ arms identify necessity or synergy. Relative DNA profiles are not viable-strain persistence; network robustness
+ used simulated removal. Soil metabolites are not directly sampled root exudates,QS/volatiles remain hypotheses,and
+ metabolite validation from the separate six-strain paper is not transferred.
+- DT retains43.3%barley disease-assay fluorescence reduction,selective pre-challenge measured RNA changes and broad-profile
+ nulls. No significant inoculant pairwise differences or assigned JA/ET/SA pathway dependence. Similarity-based
+ annotations do not identify inoculant transcripts;99%OTU matching does not establish unique viable strains. Prior1070and
+ dated BioProject discussion preserved; access status not rechecked.
+- Straw retains both process directions and39.85/36.99/19.21%polymer degradation and801.16mL/gTS total biogas. Crude
+ enzymes rather than living producers mediate pretreatment; no reciprocal-fitness evidence or four-isolate methanogenesis
+ inferred. Removed methane annotation does not assert that methane was absent.
+- SASW retains positive combined BCC outcomes with coating matrix distinct from SynCom-only effects. EPS mediation
+ remains HYPOTHESIZED/PARTIAL; relative16S profiles,100%ASV matching,PICRUSt2 and Mantel/RDA do not establish viable-strain
+ identity,priority-effect causality,BCAA transfer or keystone necessity. Prior1016/1017 removals and S1/S2 knowledge
+ gap preserved.
+- All17graph and6discussion quotations independently matched to fresh primary and existing local caches. Relevant
+ cache excerpts and complete short straw cache read; no claim of manual whole-cache reading for long flattened
+ bodies. Literal matches are not entailment proof. No cache changes or full-body imports. Three retrieved open
+ papers carry CC BY4.0; ACS does not.
+- Fresh1182all-state issue titles/bodies searched with expanded DOIs and aliases;five matching bodies and two prior
+ YAML review reports read.150matching local paths found with hidden/ignored inclusion,excluding.git,docs,site,references_cache
+ and credentials. Closed1072label drift,1070selective RNA evidence,1069Barley typo,1016assembly and1017PICRUSt
+ removals are distinct and preserved. Not a historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML fields and all prior history/decision
+ artifacts. Four append-only histories and curation events. Taxa,participant lists and scopes unchanged; evidence
+ aliases detached. TB external challenge participant remains explicitly distinguished from inoculum membership.
+- No Edison submission or credits,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication
+ blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent
+ approval. Overall goal,protected merge and branch deletion remain incomplete.
+records:
+- path: kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml
+ id: CommunityMech:000391
+ original_sha256: 9683a30be6276fa5ee8b726a80349b69e211633394d73127a6cde7c9b7131a37
+ record_sha256: d355a605023b423a1b2d61dc1f49177d9f90f4c0a0510abef0f074b085216002
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Preserve positive TB pot disease control without bilateral competition or individual-member necessity.;
+ Keep relative community profiles and simulated robustness distinct from colonization facilitation and demonstrated
+ immune mediation.
+ node_decisions:
+ - node: Fusarium pseudograminearum WCR suppression by TB
+ rationale: Preserve positive TB pot disease control without bilateral competition or individual-member necessity.
+ - node: TB-associated rhizosphere remodeling
+ rationale: Keep relative community profiles and simulated robustness distinct from colonization facilitation
+ and demonstrated immune mediation.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:41821943
+ issues:
+ - 1947
+ - 1951
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wheat_CrownRot_TB_CrossKingdom_SynCom/2026-10-08T160003Z-codex-e66225.yaml
+- path: kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml
+ id: CommunityMech:000429
+ original_sha256: b68dea3c5b4af59f9ebf86a64ac55ab18c7a3ab42dbb60cd110ddf63b9238172
+ record_sha256: ee5b482655aeb0d187e29cfe8b18016b247b355f3d63dbba2db3b591c84f05ef
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain positive barley protection without inferring inoculant superiority, hormone-pathway necessity
+ or plant drought protection.; Preserve selective measured RNA changes and broad-profile nulls, with pre-challenge
+ timing and no strain-level or causal-pathway assignment.
+ node_decisions:
+ - node: Wheat DT-SynCom powdery mildew resistance
+ rationale: Retain positive barley protection without inferring inoculant superiority, hormone-pathway necessity
+ or plant drought protection.
+ - node: Wheat DT-SynCom selective rhizosphere functional shifts
+ rationale: Preserve selective measured RNA changes and broad-profile nulls, with pre-challenge timing and no
+ strain-level or causal-pathway assignment.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42453107
+ issues:
+ - 1948
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wheat_DT_Rhizosphere_SynCom/2026-10-08T160004Z-codex-72b999.yaml
+- path: kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml
+ id: CommunityMech:000118
+ original_sha256: f2bb440b5a0d802fb677fb80f49caf5dc915f7fb34a7cad164bd5d91db2ccccb
+ record_sha256: f7eb74b6868f91109757655407c0934a7e1971e9692283f52c51ecbf329c9df4
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain enzyme-production output without reciprocal mutualism or attribution of downstream digestion to
+ the inoculum.; Preserve polymer-degradation values and enzyme transfer rather than living-cell mutualism.; Keep
+ positive downstream biogas yield distinct from methane-only yield or four-isolate methanogenesis.
+ node_decisions:
+ - node: Synthetic Community Fermentation-Enzyme Production
+ rationale: Retain enzyme-production output without reciprocal mutualism or attribution of downstream digestion
+ to the inoculum.
+ - node: Lignocellulose Enzyme Pretreatment
+ rationale: Preserve polymer-degradation values and enzyme transfer rather than living-cell mutualism.
+ - node: Enhanced Biogas Production after Anaerobic Digestion
+ rationale: Keep positive downstream biogas yield distinct from methane-only yield or four-isolate methanogenesis.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id001
+ source: Synthetic Community Fermentation-Enzyme Production
+ target: Lignocellulose Enzyme Pretreatment
+ description: Crude enzyme from the fermentation-production community was applied to wheat straw for the enzyme
+ pretreatment that depolymerizes cellulose, hemicellulose, and lignin.
+ - &id003
+ source: Lignocellulose Enzyme Pretreatment
+ target: Enhanced Biogas Production after Anaerobic Digestion
+ description: Improved wheat-straw enzymatic digestion feeds downstream anaerobic digestion and increases the
+ cumulative biogas yield.
+ edges_after:
+ - &id002
+ source: Synthetic Community Fermentation-Enzyme Production
+ target: Lignocellulose Enzyme Pretreatment
+ description: Fermentation supplies the crude enzyme solution applied to wheat straw, enabling the measured polymer-degradation
+ pretreatment. This is an enzyme-mediated material-transfer step, not proof that the living four-member inoculum
+ colonizes every subsequent process stage.
+ - &id004
+ source: Lignocellulose Enzyme Pretreatment
+ target: Enhanced Biogas Production after Anaerobic Digestion
+ description: The enzyme-pretreated straw supplies substrate to subsequent anaerobic digestion, where cumulative
+ biogas was higher than with untreated straw or either commercial-enzyme pretreatment. Retain this process-level
+ treatment effect without assigning gas production to the four enzyme producers or to one uniquely necessary
+ polymer-degradation route.
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: Fermentation supplies the crude enzyme solution applied to wheat straw, enabling the measured polymer-degradation
+ pretreatment. This is an enzyme-mediated material-transfer step, not proof that the living four-member inoculum
+ colonizes every subsequent process stage.
+ - before: *id003
+ after: *id004
+ rationale: The enzyme-pretreated straw supplies substrate to subsequent anaerobic digestion, where cumulative
+ biogas was higher than with untreated straw or either commercial-enzyme pretreatment. Retain this process-level
+ treatment effect without assigning gas production to the four enzyme producers or to one uniquely necessary
+ polymer-degradation route.
+ removed_edge_decisions: []
+ references:
+ - PMID:38748977
+ issues:
+ - 1949
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wheat_Straw_Biogas_Pretreatment_SynCom/2026-10-08T160004Z-codex-49a7c7.yaml
+- path: kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml
+ id: CommunityMech:000409
+ original_sha256: 1ac7ad0c4f4dc417e86c4a4b969caf0fe84d18f1666e6d1fb7701e191f0fbc1a
+ record_sha256: 613f8b97efa732c213fae320935a4f8cafa8cb899718e6c18a7c1f47f9ba0420
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain measured combined-treatment water retention while marking EPS mediation as hypothesized and coating-confounded.;
+ Keep relative DNA-profile shifts distinct from unique-strain colonization, priority effects and predicted metabolic
+ causality.
+ node_decisions:
+ - node: SynCom-SASW01 biocoating-associated water retention
+ rationale: Retain measured combined-treatment water retention while marking EPS mediation as hypothesized and
+ coating-confounded.
+ - node: SynCom-SASW01 root endosphere reshaping
+ rationale: Keep relative DNA-profile shifts distinct from unique-strain colonization, priority effects and predicted
+ metabolic causality.
+ removed_node_decisions: []
+ renamed_nodes:
+ EPS-associated rhizosphere water retention: SynCom-SASW01 biocoating-associated water retention
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42513902
+ issues:
+ - 1950
+ - 1952
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wheat_SynCom_SASW01_Drought_Inoculant/2026-10-08T160004Z-codex-53385b.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 6bc340f0c..a6b35e8ab 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -446,10 +446,10 @@ kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml CommunityMech
kb/communities/Wheat_Consortium_C1.yaml CommunityMech:000076 96fe252612fed33b257aed133760e929462f7021eef085750dfbb4469b1e6f26 2 0 60.0 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml reviewed
kb/communities/Wheat_Consortium_C6.yaml CommunityMech:000077 e0fca5ba8eedf1676949159803aa46771fa28af92dab641d102f531d3adc2c87 5 0 65.0 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml reviewed
kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml CommunityMech:000414 cf2ae08aab3fed7a94f5a0068db6d108baf734b22152547241ebe258f52d15ce 2 0 57.5 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml reviewed
-kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml CommunityMech:000391 9683a30be6276fa5ee8b726a80349b69e211633394d73127a6cde7c9b7131a37 2 0 70.0 pending
-kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml CommunityMech:000429 b68dea3c5b4af59f9ebf86a64ac55ab18c7a3ab42dbb60cd110ddf63b9238172 2 0 55.0 pending
-kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml CommunityMech:000118 f2bb440b5a0d802fb677fb80f49caf5dc915f7fb34a7cad164bd5d91db2ccccb 3 2 100.0 pending
-kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml CommunityMech:000409 1ac7ad0c4f4dc417e86c4a4b969caf0fe84d18f1666e6d1fb7701e191f0fbc1a 2 0 65.0 pending
+kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml CommunityMech:000391 d355a605023b423a1b2d61dc1f49177d9f90f4c0a0510abef0f074b085216002 2 0 57.5 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml reviewed
+kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml CommunityMech:000429 ee5b482655aeb0d187e29cfe8b18016b247b355f3d63dbba2db3b591c84f05ef 2 0 55.0 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml reviewed
+kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml CommunityMech:000118 f7eb74b6868f91109757655407c0934a7e1971e9692283f52c51ecbf329c9df4 3 2 88.3 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml reviewed
+kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml CommunityMech:000409 613f8b97efa732c213fae320935a4f8cafa8cb899718e6c18a7c1f47f9ba0420 2 0 55.0 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml reviewed
kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml CommunityMech:000465 29c5ffbc44052dbaf61fdeffa2ba7c0495f4c37cd1f9a246834d1bee9ed07e16 3 0 68.3 pending
kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml CommunityMech:000438 ff36b0a04edec258678a5f4d0ba1e640469d034fdc190621f02a7a311b9ecfcc 3 0 63.3 pending
kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml CommunityMech:000360 9f793b34cca134cc17f6d4919f37e56336b155b1a9423f22973f4cd701cd4be9 2 0 67.5 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index c49f2002f..9c6e6586e 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -8,8 +8,8 @@
"records_without_edges": 189,
"review_status_counts": {
"needs_research": 54,
- "pending": 14,
- "reviewed": 392
+ "pending": 10,
+ "reviewed": 396
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch122.json b/reports/causal_graph_review/validation-20261008-batch122.json
new file mode 100644
index 000000000..e2ed36ad6
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch122.json
@@ -0,0 +1,1094 @@
+{
+ "base_commit": "ec8ee08b153173a5ad77ae95aad9f38d34468d85",
+ "scope": [
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml",
+ "kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml",
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml",
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch122.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/focused.log",
+ "log_sha256": "2840e28a5a0a0b2fd700b91caf80bed6a38e762e4aec4de78a53d987894e77df",
+ "output_tail": "............... [100%]\n15 passed in 3.86s\n"
+ },
+ {
+ "check": "Wheat_CrownRot_TB_CrossKingdom_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_CrownRot_TB_CrossKingdom_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_CrownRot_TB_CrossKingdom_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch122/Wheat_CrownRot_TB_CrossKingdom_SynCom-strict.tsv",
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_CrownRot_TB_CrossKingdom_SynCom-strict.log",
+ "log_sha256": "d297b93cee6cc99968c1d4a986fdd5932b3d0fc9761af393d72055f9bd4df3c1",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch122/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-batch122/Wheat_CrownRot_TB_CrossKingdom_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Wheat_CrownRot_TB_CrossKingdom_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_CrownRot_TB_CrossKingdom_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wheat_CrownRot_TB_CrossKingdom_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_CrownRot_TB_CrossKingdom_SynCom-references.log",
+ "log_sha256": "b8e7f730313e1fe3459fec05c07bf0f0b84b8948d7dbffb811b1427d416b70ba",
+ "output_tail": "Validating kb/communities/Wheat_CrownRot_TB_CrossKingdom_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/Wheat_CrownRot_TB_CrossKingdom_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": "Wheat_CrownRot_TB_CrossKingdom_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_CrownRot_TB_CrossKingdom_SynCom-snippets.log",
+ "log_sha256": "32d5c17677a000100a0b22db07734e7af95b7e2b40f82a74ed21b581b1a6d4f5",
+ "output_tail": "# 20 evidence snippets scanned across 1 files\n MATCH 20\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": "Wheat_CrownRot_TB_CrossKingdom_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_CrownRot_TB_CrossKingdom_SynCom-rank.log",
+ "log_sha256": "07bddd9240850ce9b7fe45035d2fc26a23c7a8f23992b05ffb0472ef87d60f68",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000391\",\n \"name\": \"Wheat Crown-Rot TB Cross-Kingdom SynCom\",\n \"score\": 57.5,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Wheat_CrownRot_TB_CrossKingdom_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/Wheat_CrownRot_TB_CrossKingdom_SynCom/2026-10-08T160003Z-codex-e66225.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_CrownRot_TB_CrossKingdom_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_DT_Rhizosphere_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
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+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_DT_Rhizosphere_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_DT_Rhizosphere_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
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+ "/private/tmp/communitymech-batch122/Wheat_DT_Rhizosphere_SynCom-strict.tsv",
+ "kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_DT_Rhizosphere_SynCom-strict.log",
+ "log_sha256": "b0566212ee415ee77c49298bdbae653adb51f976e5e168ff10ae788a60812daf",
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+ },
+ {
+ "check": "Wheat_DT_Rhizosphere_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_DT_Rhizosphere_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wheat_DT_Rhizosphere_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_DT_Rhizosphere_SynCom-references.log",
+ "log_sha256": "3f13944025e5eadbec1935f10d7a5ca40e2601244e7ea414e83d6215a4e4e366",
+ "output_tail": "Validating kb/communities/Wheat_DT_Rhizosphere_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/Wheat_DT_Rhizosphere_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": "Wheat_DT_Rhizosphere_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "command": [
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+ "scripts/rank_causal_graph_readiness.py",
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+ "--format",
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+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_DT_Rhizosphere_SynCom-rank.log",
+ "log_sha256": "cff484cefd41edf993beb66d57bf2f9437fbd0c13f10829ffa69e448c1ac5ce8",
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wheat_DT_Rhizosphere_SynCom/2026-10-08T160004Z-codex-72b999.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_DT_Rhizosphere_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "src/communitymech/schema/communitymech.yaml",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_Straw_Biogas_Pretreatment_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_Straw_Biogas_Pretreatment_SynCom-strict",
+ "command": [
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+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch122/Wheat_Straw_Biogas_Pretreatment_SynCom-strict.tsv",
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_Straw_Biogas_Pretreatment_SynCom-strict.log",
+ "log_sha256": "e30e59452a4049e435866f1540b9269c7a7fe55bfe4235dd5050dd08a27b90f3",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch122/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-batch122/Wheat_Straw_Biogas_Pretreatment_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Wheat_Straw_Biogas_Pretreatment_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_Straw_Biogas_Pretreatment_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wheat_Straw_Biogas_Pretreatment_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_Straw_Biogas_Pretreatment_SynCom-references.log",
+ "log_sha256": "1d7c6b5eb0a7add0a2632be1f2a7cf2c8c0513d6f1281921fdc547b8a38a000c",
+ "output_tail": "Validating kb/communities/Wheat_Straw_Biogas_Pretreatment_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/Wheat_Straw_Biogas_Pretreatment_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": "Wheat_Straw_Biogas_Pretreatment_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_Straw_Biogas_Pretreatment_SynCom-snippets.log",
+ "log_sha256": "872637a69e95b3997368edea80eba5db2a2155e0ac9344b758394dcf97491410",
+ "output_tail": "# 14 evidence snippets scanned across 1 files\n MATCH 14\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"
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+ {
+ "check": "Wheat_Straw_Biogas_Pretreatment_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_Straw_Biogas_Pretreatment_SynCom-rank.log",
+ "log_sha256": "b5c1c52b3681e6b58fe3789b67b71953b0bfa53935e82e2959c5a710771d793d",
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wheat_Straw_Biogas_Pretreatment_SynCom/2026-10-08T160004Z-codex-49a7c7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_Straw_Biogas_Pretreatment_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
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+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_SynCom_SASW01_Drought_Inoculant-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_SynCom_SASW01_Drought_Inoculant-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch122/Wheat_SynCom_SASW01_Drought_Inoculant-strict.tsv",
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_SynCom_SASW01_Drought_Inoculant-strict.log",
+ "log_sha256": "071796a545d7e0f9fd23edd646b79490d6547c20f17e62aa9b5e9e7259a66a85",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch122/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-batch122/Wheat_SynCom_SASW01_Drought_Inoculant-strict.tsv\n"
+ },
+ {
+ "check": "Wheat_SynCom_SASW01_Drought_Inoculant-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_SynCom_SASW01_Drought_Inoculant-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wheat_SynCom_SASW01_Drought_Inoculant-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_SynCom_SASW01_Drought_Inoculant-references.log",
+ "log_sha256": "31b950dd9c0c7c5719735a83557ee32cc222721758a6dd68c38188fbf688a3a0",
+ "output_tail": "Validating kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.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/Wheat_SynCom_SASW01_Drought_Inoculant.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": "Wheat_SynCom_SASW01_Drought_Inoculant-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_SynCom_SASW01_Drought_Inoculant-snippets.log",
+ "log_sha256": "96a23c88588d68e990af5d62f9c27df12879566b4125e7703a275c3bfa7adcd7",
+ "output_tail": "# 22 evidence snippets scanned across 1 files\n MATCH 22\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": "Wheat_SynCom_SASW01_Drought_Inoculant-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_SynCom_SASW01_Drought_Inoculant-rank.log",
+ "log_sha256": "e58f3e899215686bb71d485c0e21a5ee7d4d0c56c080ac4c1e2aa011a8fb6302",
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+ },
+ {
+ "check": "Wheat_SynCom_SASW01_Drought_Inoculant-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wheat_SynCom_SASW01_Drought_Inoculant/2026-10-08T160004Z-codex-53385b.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/Wheat_SynCom_SASW01_Drought_Inoculant-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-batch122/verification/inventory.log",
+ "log_sha256": "3f20a9c6a1da01a3c3f4553b7350404f826832bae8ab55e85c29275d91607356",
+ "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\": 1373,\n \"edges\": 530,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 189,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 10,\n \"reviewed\": 396\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-batch122/verification/network.log",
+ "log_sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9",
+ "output_tail": "\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 \"Tinto_River_Iron_Cycling_Community\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Basidiomycota\",\n \"taxon_id\": \"NCBITaxon:5204\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Basidiomycota\",\n \"term\": {\n \"id\": \"NCBITaxon:5204\",\n \"label\": \"Basidiomycota\"\n },\n \"gtdb_grounding_status\": \"NO_GTDB_EQUIVALENT\",\n \"notes\": \"Acidophilic fungi including Hortaea werneckii (black yeast) detected in Rio Tinto sediments and water. Fungi contribute to organic matter degradation, biofilm formation, and nutrient cycling through extracellular enzyme secretion.\\n\"\n },\n \"functional_role\": [\n \"PRIMARY_DEGRADER\"\n ],\n \"abundance_level\": \"RARE\",\n \"evidence\": [\n {\n \"reference\": \"PMID:25369810\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons\",\n \"explanation\": \"Documents fungal presence\"\n }\n ]\n },\n \"message\": \"Taxon 'Basidiomycota' 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-batch122/verification/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-batch122/verification/rank-all.log",
+ "log_sha256": "b2bca44c33343718910a23b42b9fa2df49ed350b20be9f5287877e8bac366024",
+ "output_tail": "e\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n405\t96.7\tkb/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.yaml\tCommunityMech:000174\tClostridium cellulovorans-Methanosarcina barkeri Cellulose Methane Coculture\t2\t2\t0\t3\t2\t8\tinteraction_type\t0\t0\n406\t96.7\tkb/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.yaml\tCommunityMech:000206\tClostridium-Saccharomyces Cellulose Ethanol Coculture\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n407\t96.7\tkb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml\tCommunityMech:000297\tDIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n408\t96.7\tkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml\tCommunityMech:000023\tDesulfovibrio-Methanococcus Syntrophic 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Mutualism\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n413\t96.7\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n414\t96.7\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n415\t96.7\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t9\tinteraction_type\t0\t0\n416\t96.7\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t9\tinteraction_type\t0\t0\n417\t96.7\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic 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Ramichloridium-Talaromyces Fungal Consortium\t2\t2\t0\t3\t2\t5\tmetabolites_or_biological_processes\t0\t0\n428\t98.8\tdata/isolates/Chromobacterium_Gold_Biocyanidation.yaml\tCommunityMech:000273\tChromobacterium Gold Biocyanidation Platform\t1\t1\t0\t4\t2\t7\tmetabolites_or_biological_processes\t0\t0\n429\t100.0\tdata/isolates/Aspergillus_Indium_LED_Recovery.yaml\tCommunityMech:000320\tAspergillus Indium LCD Recovery Platform\t1\t1\t0\t5\t4\t6\t\t0\t0\n430\t100.0\tdata/isolates/Methylobacterium_REE_Ewaste_Platform.yaml\tCommunityMech:000322\tMethylobacterium REE E-waste Platform\t1\t1\t0\t4\t2\t6\t\t0\t0\n431\t100.0\tkb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml\tCommunityMech:000276\tANME/SRB Anaerobic Methanotrophic Syntrophic Consortia\t6\t6\t0\t3\t2\t7\t\t0\t0\n432\t100.0\tkb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml\tCommunityMech:000307\tAnabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium\t1\t1\t0\t5\t2\t7\t\t0\t0\n433\t100.0\tkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml\tCommunityMech:000245\tAvena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds\t1\t1\t0\t5\t2\t7\t\t0\t0\n434\t100.0\tkb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml\tCommunityMech:000142\tBacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism\t2\t2\t0\t3\t2\t3\t\t0\t0\n435\t100.0\tkb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml\tCommunityMech:000012\tBioModels MODEL2405300001 Infant Gut HMO SynCom\t13\t13\t0\t3\t2\t6\t\t0\t0\n436\t100.0\tkb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml\tCommunityMech:000215\tCalifornia Grassland Precipitation Legacy Soil Community\t1\t1\t0\t3\t2\t6\t\t0\t0\n437\t100.0\tkb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml\tCommunityMech:000089\tCellulose-to-Methane Quad-Culture SynCom\t4\t4\t0\t6\t5\t9\t\t0\t0\n438\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n439\t100.0\tkb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml\tCommunityMech:000301\tDehalococcoides mccartyi CWV2 Dechlorinating Consortium\t1\t1\t0\t5\t2\t6\t\t0\t0\n440\t100.0\tkb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml\tCommunityMech:000296\tEscherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture\t2\t2\t0\t3\t2\t6\t\t0\t0\n441\t100.0\tkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml\tCommunityMech:000350\tHigh-Ammonia Biogas 0B Butyrate-Oxidizing Enrichment\t4\t4\t0\t3\t2\t6\t\t0\t0\n442\t100.0\tkb/communities/Honeybee_Core20_Defined_Microbiota.yaml\tCommunityMech:000124\tHoneybee Core-20 Defined Microbiota\t1\t1\t0\t3\t2\t3\t\t0\t0\n443\t100.0\tkb/communities/Microbacterium_Terrabacter_Sulfadiazine_CrossFeeding_Coculture.yaml\tCommunityMech:000462\tMicrobacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n444\t100.0\tkb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml\tCommunityMech:000157\tMicrocoleus-Massilia Cyanosphere Urea Mutualism\t2\t2\t0\t3\t2\t5\t\t0\t0\n445\t100.0\tkb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml\tCommunityMech:000119\tMultiomics Corn Straw Degradation SynCom\t1\t1\t0\t4\t3\t9\t\t0\t0\n446\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n447\t100.0\tkb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml\tCommunityMech:000190\tPelotomaculum-Methanocella Propionate RNA-Seq Coculture\t2\t2\t0\t4\t2\t9\t\t0\t0\n448\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n449\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n450\t100.0\tkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml\tCommunityMech:000290\tPhosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture\t2\t2\t0\t3\t2\t4\t\t0\t0\n451\t100.0\tkb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\tCommunityMech:000289\tPseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n453\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n454\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\n455\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\n456\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\n457\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\n458\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\n459\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\n460\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/render.log",
+ "log_sha256": "ceb6fcd2a1f486e5d426911037718e82ff1c481ef1403a0ed0f697f610ee029b",
+ "output_tail": "unitymech-causal-batch122/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch122/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch122/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch122/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-batch122/verification/render-repeat.log",
+ "log_sha256": "ceb6fcd2a1f486e5d426911037718e82ff1c481ef1403a0ed0f697f610ee029b",
+ "output_tail": "unitymech-causal-batch122/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch122/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch122/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch122/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch122/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']()))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/connectivity-survey.log",
+ "log_sha256": "6dba3d2251cf8431c1fc7f04f3c0806d8a8c166c0901fd6be1fcbc268a1730a4",
+ "output_tail": "{\"records\": 460, \"with_community_level\": 414, \"mixed\": 136, \"community_level_only\": 278, \"taxa\": 1568, \"credited_solely_by_the_rule\": 1281}\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_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch110.py",
+ "tests/test_causal_review_batch111.py",
+ "tests/test_causal_review_batch112.py",
+ "tests/test_causal_review_batch113.py",
+ "tests/test_causal_review_batch114.py",
+ "tests/test_causal_review_batch115.py",
+ "tests/test_causal_review_batch116.py",
+ "tests/test_causal_review_batch117.py",
+ "tests/test_causal_review_batch118.py",
+ "tests/test_causal_review_batch119.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch120.py",
+ "tests/test_causal_review_batch121.py",
+ "tests/test_causal_review_batch122.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_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_network_palette.py",
+ "tests/test_datamodel.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-batch122/verification/regressions.log",
+ "log_sha256": "0e4aaa8e3db884a945770e477ff7df958df484deb95ce5eba42092244b24d949",
+ "output_tail": "........................................................................ [ 6%]\n........................................................................ [ 12%]\n........................................................................ [ 18%]\n........................................................................ [ 24%]\n........................................................................ [ 31%]\n........................................................................ [ 37%]\n........................................................................ [ 43%]\n........................................................................ [ 49%]\n........................................................................ [ 55%]\n........................................................................ [ 62%]\n........................................................................ [ 68%]\n........................................................................ [ 74%]\n........................................................................ [ 80%]\n........................................................................ [ 86%]\n........................................................................ [ 93%]\n........................................................................ [ 99%]\n......... [100%]\n1161 passed in 600.56s (0:10:00)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/just-lint.log",
+ "log_sha256": "fa45ed859a09d8b3d818bc45cf7456c93df4ccfffe750caba4dae4ce5debacf5",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n375 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/audit-snippets-all.log",
+ "log_sha256": "38a4d0b5ca41b69cc399ca2ec3939cf3d5951065c93c3748c5f1654777b8a4e7",
+ "output_tail": "# 9084 evidence snippets scanned across 460 files\n MATCH 8936\n RENDERING 31\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\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\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch122/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Both-root pre-source baseline covers460records and923caches,57existing warnings and zero structural defects. Four whole target records and nine nodes/two arrows reviewed; all retained,one rename,no new topology.",
+ "Four fresh EuropePMC metadata/abstract and Crossref identities checked. Complete open TB,DT and SASW main-body text,methods,results,discussion and available table/caption text read. SASW Figure4 caption additionally checked via PubMed. No original figure pixels,separate supplementary files,raw data or analysis code audit.",
+ "Straw repairs are abstract-bounded. EuropePMC lists no PMCID; ACS primary search result gives abstract and supporting-information listing,but publisher article access returned403 and the attempted SI endpoint was inaccessible. No full text or supplement inspected,no access bypass or exhaustive absence claim.",
+ "TB retains positive pot disease control,70.97%biocontrol efficacy and growth traits. No in-vivo single-member arms identify necessity or synergy. Relative DNA profiles are not viable-strain persistence; network robustness used simulated removal. Soil metabolites are not directly sampled root exudates,QS/volatiles remain hypotheses,and metabolite validation from the separate six-strain paper is not transferred.",
+ "DT retains43.3%barley disease-assay fluorescence reduction,selective pre-challenge measured RNA changes and broad-profile nulls. No significant inoculant pairwise differences or assigned JA/ET/SA pathway dependence. Similarity-based annotations do not identify inoculant transcripts;99%OTU matching does not establish unique viable strains. Prior1070and dated BioProject discussion preserved; access status not rechecked.",
+ "Straw retains both process directions and39.85/36.99/19.21%polymer degradation and801.16mL/gTS total biogas. Crude enzymes rather than living producers mediate pretreatment; no reciprocal-fitness evidence or four-isolate methanogenesis inferred. Removed methane annotation does not assert that methane was absent.",
+ "SASW retains positive combined BCC outcomes with coating matrix distinct from SynCom-only effects. EPS mediation remains HYPOTHESIZED/PARTIAL; relative16S profiles,100%ASV matching,PICRUSt2 and Mantel/RDA do not establish viable-strain identity,priority-effect causality,BCAA transfer or keystone necessity. Prior1016/1017 removals and S1/S2 knowledge gap preserved.",
+ "All17graph and6discussion quotations independently matched to fresh primary and existing local caches. Relevant cache excerpts and complete short straw cache read; no claim of manual whole-cache reading for long flattened bodies. Literal matches are not entailment proof. No cache changes or full-body imports. Three retrieved open papers carry CC BY4.0; ACS does not.",
+ "Fresh1182all-state issue titles/bodies searched with expanded DOIs and aliases;five matching bodies and two prior YAML review reports read.150matching local paths found with hidden/ignored inclusion,excluding.git,docs,site,references_cache and credentials. Closed1072label drift,1070selective RNA evidence,1069Barley typo,1016assembly and1017PICRUSt removals are distinct and preserved. Not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML fields and all prior history/decision artifacts. Four append-only histories and curation events. Taxa,participant lists and scopes unchanged; evidence aliases detached. TB external challenge participant remains explicitly distinguished from inoculum membership.",
+ "No Edison submission or credits,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent approval. Overall goal,protected merge and branch deletion remain incomplete."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml": {
+ "MATCH": 20,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml": {
+ "MATCH": 33,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml": {
+ "MATCH": 14,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml": {
+ "MATCH": 22,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 57,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "new_nodes_or_directions": 0,
+ "prior_extension_blocker": "Ruegeria1883: configured authentication unavailable in prior approved invocation; no unchanged-state retry."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch122/baseline.json": "e61ca7f5b24b54529160712e89f47b943a167f4cc0dd99feeac9fcc4a9124e9d",
+ "/private/tmp/communitymech-batch122/dt-abstract.txt": "07bfdc2486fb23566b6637d7dba6b082beb0dc117bccf292212a8bbbd764b63a",
+ "/private/tmp/communitymech-batch122/dt-crossref.json": "37a8286063241be43a9d85313b47eafc4f14f98cd33ef72bdfba058aeeee2d01",
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+ "/private/tmp/communitymech-batch122/dt-primary.txt": "c8fec230a0470d85b4959186e74d6c1559c371daabec2977960631baf6414fcd",
+ "/private/tmp/communitymech-batch122/dt-primary.xml": "c8066e122aba23d26289edd0274a598b033506f553649e3c00aa457ae8d5a800",
+ "/private/tmp/communitymech-batch122/issue-dedup-current.json": "aee05151279e74a8318df75cec6c66776f23878b3e97bc3cc6666422eeac1c0f",
+ "/private/tmp/communitymech-batch122/local-matches-expanded.txt": "bf0d1ae00bdd7cd71c419883f6c75a60b9bfd44e217687e907210e6a86829575",
+ "/private/tmp/communitymech-batch122/local-matches.txt": "7f3e874bec989b71ef5da3d52f57149cdc6382844bccb4a76f498a2c9e5aec53",
+ "/private/tmp/communitymech-batch122/primary-manifest.json": "61b1f347f54927c19d9a212111eac18f057bd4d21dc3e247719375492686ed92",
+ "/private/tmp/communitymech-batch122/sasw-abstract.txt": "4d0fe80ce1faab79afe415ac7338c544406f3f09b9c16edd43c8cae9cb14c27a",
+ "/private/tmp/communitymech-batch122/sasw-crossref.json": "5a459e51b725c72ecc4c78e0f305c9d17cec91c32d4fdd201860680c471888dd",
+ "/private/tmp/communitymech-batch122/sasw-metadata.json": "c95cebb60f9e362879a9a758314aa55fa2d0f0d7b093c906c0f1317bdb3d4121",
+ "/private/tmp/communitymech-batch122/sasw-primary.txt": "18608ebec9cc725821985d1f7a8c2b9d1f07e47f094745ce0ecaf4346a74aa1c",
+ "/private/tmp/communitymech-batch122/sasw-primary.xml": "db1a208ae84d935db3052b5d1ff8e1880123353761ab117ed981917372c1fbec",
+ "/private/tmp/communitymech-batch122/straw-abstract.txt": "b2e0b49c1e71c016e9f951028f7be67cba289b978f751fa672f83559a6d99e4f",
+ "/private/tmp/communitymech-batch122/straw-crossref.json": "11c6cf15c1747a1e170d2c1dcf51d60163c032abde912aa6a23becf6014df257",
+ "/private/tmp/communitymech-batch122/straw-metadata.json": "341861133ea2b84656b8d773fc676ec4afa235c279925085446a5cc84f9b0a80",
+ "/private/tmp/communitymech-batch122/target-baseline.json": "ba0e4169a24aa2f27d10d556f6eeefa7aec276b42a954b87759f8212c7f88537",
+ "/private/tmp/communitymech-batch122/tb-abstract.txt": "8f4779c5f2a36f118344c012621acd7849692e09df86f10103a86612fc4fd412",
+ "/private/tmp/communitymech-batch122/tb-crossref.json": "d54182ea01491431e02000e4f91ed4a110aa0837d1b3c4a92e0b50d3d63c1b54",
+ "/private/tmp/communitymech-batch122/tb-metadata.json": "d681da4e6d63c986375fa2b53374f0962f2770d4b636f1aa4f46d667006fcb33",
+ "/private/tmp/communitymech-batch122/tb-primary.txt": "49c7fc4983cc371b6f69d3048acc80030d1393ff5ffacd9b1e3dad233d4992c4",
+ "/private/tmp/communitymech-batch122/tb-primary.xml": "85195b3a1511f99ee26151460185983fd486cbe9c62139765ba80b75d973a68f",
+ "references_cache/PMID_38748977.txt": "52573e7edacce7f974f357984bfe31e0252248a700fa4d61d1bdb9aa5efe3d3b",
+ "references_cache/PMID_41821943.txt": "cdd00a96ee98263dfad6e5c662d160110551f6f1d11a224106abb72530044903",
+ "references_cache/PMID_42453107.txt": "5682e995818c11a0c5f44063731dd42ac3734c6d28f30354c818592133674417",
+ "references_cache/PMID_42513902.txt": "f36426f264438e022eeed4077aba924504d3192b25fac5b7d7a34ca5d8fd655e"
+ },
+ "immutable_prior_history_and_decision_files": 899,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 17,
+ "discussion_quotations": 6,
+ "fresh_primary_literal_matches": 23,
+ "all_cached_literal_matches": 23,
+ "retained_nodes": 9,
+ "removed_nodes": 0,
+ "renamed_nodes": 1,
+ "retained_arrows": 2,
+ "removed_arrows": 0,
+ "new_nodes_or_directions": 0
+ },
+ "network_delta": {
+ "existing_findings_preserved": 57,
+ "added_findings": {},
+ "removed_findings": {},
+ "structural_defects": 0
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1359,
+ "arrows": 522
+ },
+ "render_scope": "Deterministic rendering and exact HTML description parsing, not screenshots; postcommit docs-current still required.",
+ "participant_census": {
+ "current": {
+ "records": 460,
+ "with_community_level": 414,
+ "mixed": 136,
+ "community_level_only": 278,
+ "taxa": 1568,
+ "credited_solely_by_the_rule": 1281
+ },
+ "delta_from_batch121": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "explanation": "All participant lists and scopes are unchanged;299participant-list users. Scope credit is not certification of actual participant coverage. Connectivity logic and thresholds are unchanged."
+ },
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary established Python3.13 lint environment; project dependencies unchanged."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 9084,
+ "categories": {
+ "MATCH": 8936,
+ "RENDERING": 31,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Informational audit exit0 is not clean-corpus or entailment certification.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1373,
+ "edges": 530,
+ "records_without_nodes": 10,
+ "records_without_edges": 189,
+ "review_status_counts": {
+ "needs_research": 54,
+ "pending": 10,
+ "reviewed": 396
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml": "c77c5eb2fb20969b2f3b50aa34646df937cfb86c2f96c308ea2350f016cf080e",
+ "tests/test_causal_review_batch122.py": "00bfbda6721badbc73893b0dbdaea5ec146f84d33e581b86f75df8cfa8ab189e",
+ "tests/test_participating_taxa.py": "f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1",
+ "tests/test_community_level_connectivity_credit.py": "996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a",
+ "tests/test_causal_review_batch109.py": "ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73",
+ "tests/test_datamodel.py": "f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25",
+ "reports/causal_graph_review/cache-provenance-20261008-batch122.json": "10c911cdfc0852678c5ea2e3a5ffab604750c835a6455f723ca69a6d85a4e03b",
+ "kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml": "d355a605023b423a1b2d61dc1f49177d9f90f4c0a0510abef0f074b085216002",
+ "kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml": "ee5b482655aeb0d187e29cfe8b18016b247b355f3d63dbba2db3b591c84f05ef",
+ "kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml": "f7eb74b6868f91109757655407c0934a7e1971e9692283f52c51ecbf329c9df4",
+ "kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml": "613f8b97efa732c213fae320935a4f8cafa8cb899718e6c18a7c1f47f9ba0420"
+ },
+ "pre_research_baseline": {
+ "base_commit": "ec8ee08b153173a5ad77ae95aad9f38d34468d85",
+ "base_tree": "a0eac0886a3e4e3df6f557ccbe02037155931356",
+ "research_worktree": "/private/tmp/communitymech-causal-batch122",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch122/baseline-rank.log",
+ "sha256": "8084657da95074bb9bb07e0ae16e9cd243302301d6f23768983197735c3efe76"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch122/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "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-batch122/baseline-network.log",
+ "sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9"
+ },
+ {
+ "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-batch122/baseline-downstream.log",
+ "sha256": "74395ccb7dd16e83fe2fd729959c060a093b7be46f88c46249f95a5546b7fd6e"
+ }
+ ],
+ "baseline_sha256": "e61ca7f5b24b54529160712e89f47b943a167f4cc0dd99feeac9fcc4a9124e9d"
+ },
+ "reference_validator_caveat": "Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment. Total checks in the reference CLI counts issues, not examined snippets.",
+ "status": "verified_existing_graph_repairs",
+ "total_recorded_gate_outputs": 41
+}
diff --git a/tests/test_causal_review_batch122.py b/tests/test_causal_review_batch122.py
new file mode 100644
index 000000000..460b0fa82
--- /dev/null
+++ b/tests/test_causal_review_batch122.py
@@ -0,0 +1,179 @@
+"""Preserve treatment benefits without inventing the mediating mechanism."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch122.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_tb_retains_positive_disease_control_without_competition():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][0]
+ assert "interaction_type" not in node
+ assert "70.97%" in node["description"]
+ assert "70.97%" in node["evidence"][1]["snippet"]
+ assert "not a TB member" in node["description"]
+ assert len(node["participating_taxa"]) == 3
+
+
+def test_tb_network_robustness_is_simulated_not_biological_removal():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][1]
+ assert "interaction_type" not in node and "biological_processes" not in node
+ assert "not biological removal experiments" in node["description"]
+ assert "Hub-targeted simulations" in node["evidence"][1]["snippet"]
+ assert "absolute viable abundance" in node["description"]
+
+
+def test_tb_hypotheses_do_not_borrow_other_study_perturbations():
+ _, _, docs = records()
+ discussion = docs[0]["discussions"][-1]
+ assert "working hypotheses" in discussion["evidence"][0]["snippet"]
+ assert "not directly collected root exudates" in discussion["rationale"]
+ assert "distinct six-strain SMC study" in discussion["rationale"]
+ assert not any(n.get("downstream") for n in docs[0]["ecological_interactions"])
+
+
+def test_dt_protection_is_not_inoculant_superiority_or_drought_validation():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][0]
+ assert "43.3%" in node["description"]
+ assert "pairwise differences were not significant" in node["description"]
+ assert "not a test of whole-plant drought protection" in node["description"]
+ assert "50.4%" in node["evidence"][0]["snippet"]
+
+
+def test_dt_rna_changes_precede_challenge_and_keep_broad_null():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][1]
+ assert "Before pathogen challenge" in node["description"]
+ assert "no significant treatment shift" in node["description"]
+ assert "not PICRUSt predictions" in node["description"]
+ assert "not broad community changes" in node["evidence"][1]["snippet"]
+ assert "not reference SynCom genomes" in node["evidence"][2]["snippet"]
+ assert not node.get("downstream")
+
+
+def test_dt_pathway_and_strain_identity_limits_remain_explicit():
+ _, _, docs = records()
+ discussion = docs[1]["discussions"][-1]
+ assert "did not allow direct assignment" in discussion["evidence"][0]["snippet"]
+ assert "strain-level identity cannot be confirmed" in discussion["evidence"][1]["snippet"]
+ assert docs[1]["discussions"][0]["discussion_id"] == "prjna1405459_visibility"
+
+
+def test_straw_process_outputs_are_not_reciprocal_mutualism():
+ _, _, docs = records()
+ nodes = docs[2]["ecological_interactions"]
+ assert len(nodes) == 3 and all("interaction_type" not in n for n in nodes)
+ assert "does not measure reciprocal fitness" in nodes[0]["description"]
+ assert "downstream anaerobic-digestion community" in nodes[0]["description"]
+
+
+def test_straw_retains_both_material_transfer_directions():
+ _, _, docs = records()
+ a, b, c = docs[2]["ecological_interactions"]
+ assert len(a["downstream"]) == len(b["downstream"]) == 1
+ assert a["downstream"][0]["target"] == b["name"]
+ assert b["downstream"][0]["target"] == c["name"]
+ assert "enzyme-mediated material-transfer" in a["downstream"][0]["description"]
+ assert "supplies substrate" in b["downstream"][0]["description"]
+
+
+def test_straw_preserves_positive_polymer_degradation_values():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][1]
+ assert all(v in node["description"] for v in ["39.85%", "36.99%", "19.21%"])
+ assert "acts through the enzyme preparation" in node["description"]
+ assert "39.85" in node["evidence"][1]["snippet"]
+
+
+def test_straw_total_biogas_is_not_methane_only_or_isolate_methanogenesis():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][2]
+ assert "801.16 mL/g TS" in node["description"]
+ assert "not a methane-only yield" in node["description"]
+ assert "metabolites" not in node
+ assert "cumulative biogas" in node["evidence"][0]["snippet"]
+
+
+def test_sasw_water_outcome_is_combined_biocoating_not_syncom_alone():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][0]
+ assert "biocoating-associated" in node["name"]
+ assert "coating-only CC and SynCom-only BC" in node["description"]
+ assert "does not isolate the microbial or EPS contribution" in node["description"]
+ assert "BCC (biochar-consortium coating)" in node["evidence"][1]["snippet"]
+
+
+def test_sasw_eps_mediation_remains_hypothesized():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][0]
+ assert "interaction_type" not in node
+ assert "HYPOTHESIZED" in node["description"]
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+ assert node["evidence"][1]["supports"] == "SUPPORT"
+
+
+def test_sasw_profiles_do_not_establish_viable_strains_or_causal_cascade():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][1]
+ assert "interaction_type" not in node
+ assert "do not uniquely identify viable inoculant strains" in node["description"]
+ assert "do not prove BCAA transfer" in node["description"]
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+ assert "En_BCC samples" in node["evidence"][1]["snippet"]
+
+
+def test_sasw_prior_removals_and_positive_field_context_survive():
+ _, _, docs = records()
+ assert len(docs[3]["ecological_interactions"]) == 2
+ assert not any(n.get("downstream") for n in docs[3]["ecological_interactions"])
+ discussion = docs[3]["discussions"][-1]
+ assert "Positive BCC field yields" in discussion["rationale"]
+ assert "Two treatments were established" in discussion["evidence"][0]["snippet"]
+ assert "PICRUSt2" in discussion["evidence"][1]["snippet"]
+ assert docs[3]["discussions"][0]["attaches_to"] == ["taxonomy"]
+
+
+def test_ledger_accounts_for_topology_history_and_unchanged_caches():
+ ledger, rows, docs = records()
+ counts = ledger["reviewed_counts"]
+ assert (counts["original_nodes"], counts["retained_nodes"], counts["removed_nodes"]) == (
+ 9,
+ 9,
+ 0,
+ )
+ assert (counts["original_arrows"], counts["retained_arrows"], counts["removed_arrows"]) == (
+ 2,
+ 2,
+ 0,
+ )
+ assert counts["renamed_nodes"] == 1
+ assert (counts["graph_quotations"], counts["discussion_quotations"]) == (17, 6)
+ assert not ledger["cache_changes"] and not ledger["independent_approval"]
+ assert ledger["edison"]["provider_submissions"] == 0
+ assert ledger["unresolved_non_graph_issues"] == [1951, 1952]
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["history_files"]) == 1 and doc["curation_history"][-1]["llm_assisted"]
+ names = [n["name"] for n in doc["ecological_interactions"]]
+ assert [n["node"] for n in row["node_decisions"]] == names
+ assert all(
+ a.removeprefix("ecological_interactions#") in names
+ for a in doc["discussions"][-1]["attaches_to"]
+ )
+ assert all(
+ e["target"] in names
+ for n in doc["ecological_interactions"]
+ for e in n.get("downstream", [])
+ )