Agr Mcp Server Enhanced — the complete, unedited output of the deterministic mcptrustchecker engine v1.13.0, scanned . Every finding, capability tag and score component below is exactly what the engine produced — no AI, no post-processing.
{
"tool": {
"name": "mcptrustchecker",
"version": "1.13.0",
"methodologyVersion": "mcptrustchecker-1.13"
},
"target": {
"id": "agr-mcp-server-enhanced",
"source": {
"kind": "package",
"origin": "agr-mcp-server-enhanced"
},
"server": {
"name": "agr-mcp-server-enhanced"
}
},
"grade": "A",
"score": {
"score": 93,
"threatScore": 100,
"grade": "A",
"band": "A",
"categorySubtotals": {
"injection": 0,
"exfiltration": 0,
"permissions": 0,
"supply-chain": 0,
"network": 0,
"hygiene": 0
},
"vector": [
{
"kind": "client",
"term": "capability-exposure",
"level": "high",
"label": "capability blast radius (high) — client exposure if the model is manipulated",
"appliedPenalty": 6
},
{
"kind": "client",
"term": "verification-discount",
"level": "repo",
"label": "publisher verification (public source) — no provenance, but the source is public and inspectable",
"appliedPenalty": 1
},
{
"kind": "client",
"term": "coverage-honesty",
"level": "source",
"label": "inspection depth (source) — how much of the target the scan could see",
"appliedPenalty": 0
}
],
"gatesFired": [],
"methodologyVersion": "mcptrustchecker-1.13"
},
"capability": {
"level": "high",
"reasons": [
"can send data / act on an external service",
"can execute shell commands or code"
],
"tags": [
"code-exec",
"external-sink"
]
},
"coverage": {
"level": "source",
"inputs": {
"toolSurface": true,
"implementationSource": true,
"packageMetadata": true,
"liveTransport": false
},
"caveats": [
"Tools were statically extracted from the published source (28 recovered), not enumerated from a running server. Tool-poisoning, Unicode-smuggling, capability and toxic-flow analysis ran on this inferred surface, but a mis-parsed registration could be missed or mis-attributed, so tool-derived findings are capped below “confirmed”. To grade the real runtime surface, scan the running server: --command \"npx -y <package>\"."
]
},
"findings": [
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in server code (bin/agr-chat.js)",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "In the server's implementation (`bin/agr-chat.js:13`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "bin/agr-chat.js"
},
"evidence": "import { spawn } from 'child_process'; import path from 'path'; import { fileURLToPath } from 'url'; const __filename",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "bin/agr-chat.js",
"line": 13,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in server code (bin/alliance.js)",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "In the server's implementation (`bin/alliance.js:11`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "bin/alliance.js"
},
"evidence": "import { spawn } from 'child_process'; import { join, dirname } from 'path'; import { fileURLToPath } from 'url'; cons",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "bin/alliance.js",
"line": 11,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in server code (src/agr-server-simple-natural-wrapper.cjs)",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "In the server's implementation (`src/agr-server-simple-natural-wrapper.cjs:20`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "src/agr-server-simple-natural-wrapper.cjs"
},
"evidence": "st { spawn } = require('child_process'); const path = require('path'); // The actual ESM server is in the same dire",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "src/agr-server-simple-natural-wrapper.cjs",
"line": 20,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in server code (src/agr-server-simple-wrapper.cjs)",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "In the server's implementation (`src/agr-server-simple-wrapper.cjs:20`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "src/agr-server-simple-wrapper.cjs"
},
"evidence": "st { spawn } = require('child_process'); const path = require('path'); // The actual ESM server is in the same dire",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "src/agr-server-simple-wrapper.cjs",
"line": 20,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-003",
"title": "Hardcoded egress to an external endpoint (src/scientific/gene-expression.js)",
"category": "exfiltration",
"severity": "medium",
"confidence": "strong",
"description": "In the server's implementation (`src/scientific/gene-expression.js:157`): A hardcoded outbound call to a fixed external host inside server code is a classic exfiltration/telemetry channel — especially paired with reads of local data. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "src/scientific/gene-expression.js"
},
"evidence": "const response = await axios.get( 'https://gtexportal.org/rest/v1/expression/medianGeneExpression',",
"owasp": "LLM02:2025 Sensitive Information Disclosure",
"data": {
"rule": "MTC-SRC-003",
"file": "src/scientific/gene-expression.js",
"line": 157,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-003",
"title": "Hardcoded egress to an external endpoint (src/scientific/protein-structure.js)",
"category": "exfiltration",
"severity": "medium",
"confidence": "strong",
"description": "In the server's implementation (`src/scientific/protein-structure.js:163`): A hardcoded outbound call to a fixed external host inside server code is a classic exfiltration/telemetry channel — especially paired with reads of local data. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "src/scientific/protein-structure.js"
},
"evidence": "const response = await axios.get( `https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/${uniprotId}`, { tim",
"owasp": "LLM02:2025 Sensitive Information Disclosure",
"data": {
"rule": "MTC-SRC-003",
"file": "src/scientific/protein-structure.js",
"line": 163,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-003",
"title": "Hardcoded egress to an external endpoint (src/scientific/variant-analysis.js)",
"category": "exfiltration",
"severity": "medium",
"confidence": "strong",
"description": "In the server's implementation (`src/scientific/variant-analysis.js:317`): A hardcoded outbound call to a fixed external host inside server code is a classic exfiltration/telemetry channel — especially paired with reads of local data. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "src/scientific/variant-analysis.js"
},
"evidence": "const response = await axios.post( 'https://rest.ensembl.org/vep/human/hgvs', { hgvs_notations: [varian",
"owasp": "LLM02:2025 Sensitive Information Disclosure",
"data": {
"rule": "MTC-SRC-003",
"file": "src/scientific/variant-analysis.js",
"line": 317,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-003",
"title": "Hardcoded egress to an external endpoint in packaging/dev tooling (scripts/benchmark.js)",
"category": "exfiltration",
"severity": "low",
"confidence": "heuristic",
"description": "In a packaging/dev/install script (shipped, but not the server runtime) (`scripts/benchmark.js:231`): A hardcoded outbound call to a fixed external host inside server code is a classic exfiltration/telemetry channel — especially paired with reads of local data. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "scripts/benchmark.js"
},
"evidence": "try { await axios.get('https://www.alliancegenome.org/api/search', { params: { q: `test_${i}`, lim",
"owasp": "LLM02:2025 Sensitive Information Disclosure",
"data": {
"rule": "MTC-SRC-003",
"file": "scripts/benchmark.js",
"line": 231,
"nonRuntime": true
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in packaging/dev tooling (scripts/easy-query.js)",
"category": "permissions",
"severity": "low",
"confidence": "heuristic",
"description": "In a packaging/dev/install script (shipped, but not the server runtime) (`scripts/easy-query.js:8`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "scripts/easy-query.js"
},
"evidence": "import { spawn } from 'child_process'; // Simple query functions const queries = { genes: (query, limit = 5) => ({",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "scripts/easy-query.js",
"line": 8,
"nonRuntime": true
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in packaging/dev tooling (scripts/query-helper.js)",
"category": "permissions",
"severity": "low",
"confidence": "heuristic",
"description": "In a packaging/dev/install script (shipped, but not the server runtime) (`scripts/query-helper.js:8`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "scripts/query-helper.js"
},
"evidence": "import { spawn } from 'child_process'; import { createInterface } from 'readline'; class AGRQueryHelper { constructo",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "scripts/query-helper.js",
"line": 8,
"nonRuntime": true
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in packaging/dev tooling (scripts/test-mcp-setup.js)",
"category": "permissions",
"severity": "low",
"confidence": "heuristic",
"description": "In a packaging/dev/install script (shipped, but not the server runtime) (`scripts/test-mcp-setup.js:8`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
"remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
"location": {
"kind": "server",
"name": "scripts/test-mcp-setup.js"
},
"evidence": "import { spawn } from 'child_process'; import { fileURLToPath } from 'url'; import { dirname, join } from 'path'; impor",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "scripts/test-mcp-setup.js",
"line": 8,
"nonRuntime": true
}
}
],
"toxicFlows": [],
"capabilities": [
{
"tool": "search_genes",
"tags": [],
"reasons": {}
},
{
"tool": "get_gene_info",
"tags": [],
"reasons": {}
},
{
"tool": "get_gene_diseases",
"tags": [],
"reasons": {}
},
{
"tool": "search_diseases",
"tags": [],
"reasons": {}
},
{
"tool": "get_gene_expression",
"tags": [],
"reasons": {}
},
{
"tool": "find_orthologs",
"tags": [],
"reasons": {}
},
{
"tool": "blast_sequence",
"tags": [],
"reasons": {}
},
{
"tool": "complex_search",
"tags": [],
"reasons": {}
},
{
"tool": "faceted_search",
"tags": [],
"reasons": {}
},
{
"tool": "get_species_list",
"tags": [],
"reasons": {}
},
{
"tool": "get_cache_stats",
"tags": [],
"reasons": {}
},
{
"tool": "clear_cache",
"tags": [],
"reasons": {}
},
{
"tool": "search_literature",
"tags": [],
"reasons": {}
},
{
"tool": "find_gene_relationships",
"tags": [],
"reasons": {}
},
{
"tool": "analyze_research_trends",
"tags": [],
"reasons": {}
},
{
"tool": "build_phylogenetic_tree",
"tags": [],
"reasons": {}
},
{
"tool": "get_conservation_score",
"tags": [],
"reasons": {}
},
{
"tool": "get_gene_pathways",
"tags": [],
"reasons": {}
},
{
"tool": "pathway_enrichment",
"tags": [],
"reasons": {}
},
{
"tool": "analyze_variant",
"tags": [],
"reasons": {}
},
{
"tool": "get_drug_interactions",
"tags": [],
"reasons": {}
},
{
"tool": "get_protein_structure",
"tags": [],
"reasons": {}
},
{
"tool": "get_expression_heatmap",
"tags": [],
"reasons": {}
},
{
"tool": "functional_enrichment_analysis",
"tags": [],
"reasons": {}
},
{
"tool": "process_natural_query",
"tags": [],
"reasons": {}
},
{
"tool": "continue_conversation",
"tags": [],
"reasons": {}
},
{
"tool": "explain_understanding",
"tags": [],
"reasons": {}
},
{
"tool": "ask",
"tags": [],
"reasons": {}
}
],
"surfaceDigest": "fcf47829c7514139a9fbf2129c87f3824600609e80bf43d74334a7dc3d295761",
"stats": {
"tools": 28,
"prompts": 0,
"resources": 0,
"findingsBySeverity": {
"critical": 0,
"high": 4,
"medium": 3,
"low": 4,
"info": 0
}
}
}