Bioos — the complete, unedited output of the deterministic mcptrustchecker engine v1.9.0, scanned . Every finding, capability tag and score component below is exactly what the engine produced — no AI, no post-processing.
{
"tool": {
"name": "mcptrustchecker",
"version": "1.9.0",
"methodologyVersion": "mcptrustchecker-1.9"
},
"target": {
"id": "bioos-mcp-server",
"source": {
"kind": "package",
"origin": "bioos-mcp-server"
},
"server": {
"name": "bioos-mcp-server"
}
},
"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-1.9"
},
"capability": {
"level": "high",
"reasons": [
"ingests untrusted external content (a prompt-injection entry point)",
"can send data / act on an external service",
"can execute shell commands or code"
],
"tags": [
"untrusted-input",
"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 (16 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/bioos-mcp-server.js)",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "In the server's implementation (`bin/bioos-mcp-server.js:3`): 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/bioos-mcp-server.js"
},
"evidence": "st { spawn } = require('child_process'); const path = require('path'); const serverScript = path.resolve(__dirname, '..",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "bin/bioos-mcp-server.js",
"line": 3,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in server code (src/bioos_mcp/bioos_mcp_server.py)",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "In the server's implementation (`src/bioos_mcp/bioos_mcp_server.py:305`): 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/bioos_mcp/bioos_mcp_server.py"
},
"evidence": "_path] result = subprocess.run(validate_wdl_cmd, capture_output=True,",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "src/bioos_mcp/bioos_mcp_server.py",
"line": 305,
"nonRuntime": false
}
},
{
"ruleId": "MTC-SRC-003",
"title": "Hardcoded egress to an external endpoint (src/bioos_mcp/bioos_mcp_server.py)",
"category": "exfiltration",
"severity": "medium",
"confidence": "strong",
"description": "In the server's implementation (`src/bioos_mcp/bioos_mcp_server.py:833`): 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/bioos_mcp/bioos_mcp_server.py"
},
"evidence": "t 参数 response = requests.post(\"http://10.20.16.38:3001/build\", files=files,",
"owasp": "LLM02:2025 Sensitive Information Disclosure",
"data": {
"rule": "MTC-SRC-003",
"file": "src/bioos_mcp/bioos_mcp_server.py",
"line": 833,
"nonRuntime": false
}
}
],
"toxicFlows": [],
"capabilities": [
{
"tool": "generate_wdl_runtime",
"tags": [],
"reasons": {}
},
{
"tool": "validate_wdl",
"tags": [],
"reasons": {}
},
{
"tool": "import_workflow",
"tags": [],
"reasons": {}
},
{
"tool": "generate_inputs_json_template",
"tags": [],
"reasons": {}
},
{
"tool": "compose_input_json",
"tags": [],
"reasons": {}
},
{
"tool": "validate_workflow_input_json",
"tags": [],
"reasons": {}
},
{
"tool": "submit_workflow",
"tags": [],
"reasons": {}
},
{
"tool": "check_workflow_run_status",
"tags": [],
"reasons": {}
},
{
"tool": "check_workflow_import_status",
"tags": [],
"reasons": {}
},
{
"tool": "get_workflow_logs",
"tags": [],
"reasons": {}
},
{
"tool": "search_dockstore",
"tags": [],
"reasons": {}
},
{
"tool": "fetch_wdl_from_dockstore",
"tags": [
"untrusted-input"
],
"reasons": {
"untrusted-input": [
"keyword \"fetch\""
]
}
},
{
"tool": "generate_dockerfile",
"tags": [],
"reasons": {}
},
{
"tool": "get_docker_image_url",
"tags": [],
"reasons": {}
},
{
"tool": "build_docker_image",
"tags": [],
"reasons": {}
},
{
"tool": "check_build_status",
"tags": [],
"reasons": {}
}
],
"surfaceDigest": "ea775dcbd1d116ff2ad2786cfc390ca0fd88774f271e325a6c51044d5be5e142",
"stats": {
"tools": 16,
"prompts": 0,
"resources": 0,
"findingsBySeverity": {
"critical": 0,
"high": 2,
"medium": 1,
"low": 0,
"info": 0
}
}
}