Clio Kit MCP Server
clio-kit
PyPI
v2.10.6
Published by iowarp — no publish provenance, so origin is unverified, but the source is public: the repository link below is self-declared yet readable, so you can inspect the code before adopting it.
CLIO Kit - MCP Servers, Clients, and Tools for AI Agents
The grade answers one question — how safe is this server for you to adopt — so it is computed in two auditable stages. Nothing below is an opinion or an LLM's guess; every line is a real term the deterministic engine applied, and the same input always yields the same number.
1. Threat score — 100 − 0 = 100. What the published surface and source actually contain:
The deterministic scan raised no scored threat in the surface it inspected — the threat score stayed at 100. Capability observations and advisory notes are recorded but never lower it.
2. Client adoption risk — 100 − 7 = 93. Three small, subtract-only factors that reflect your risk in adopting it — a clean scan proves less on a powerful, unverified or barely-inspectable package, so the grade says so plainly:
| Points | Adoption-risk factor |
|---|---|
| −6 | capability blast radius (high) — client exposure if the model is manipulated |
| −1 | publisher verification (public source) — no provenance, but the source is public and inspectable |
Capability observations and info notes are shown under Findings but never scored.
Open any row's finding below for the file, line and evidence behind a deduction.
Findings 12
high Dynamic code execution in server code (clio-kit-mcp-servers/hdf5/src/hdf5_mcp/server.py)MTC-SRC-001
In the server's implementation (`clio-kit-mcp-servers/hdf5/src/hdf5_mcp/server.py:943`): Evaluating strings as code is the most direct RCE primitive; if any tool input reaches it, the server executes attacker-chosen code. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.
Evidence: slice_obj = eval(f"np.s_[{slice_spec}]") except Exception: return f"Error: Invalid slice
Fix: 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: server clio-kit-mcp-servers/hdf5/src/hdf5_mcp/server.py
high Shell/command execution in server code (clio-agentic-search/src/clio_agentic_search/tasks.py)MTC-SRC-002
In the server's implementation (`clio-agentic-search/src/clio_agentic_search/tasks.py:9`): 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.
Evidence: -> int: completed = subprocess.run(command, check=False) return completed.returncode def lint() -> None: r
Fix: 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: server clio-agentic-search/src/clio_agentic_search/tasks.py
high Shell/command execution in server code (clio-kit-mcp-servers/chronolog/src/chronomcp/utils/helpers.py)MTC-SRC-002
In the server's implementation (`clio-kit-mcp-servers/chronolog/src/chronomcp/utils/helpers.py:34`): 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.
Evidence: r(cmd_args): proc = subprocess.run( cmd_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True
Fix: 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: server clio-kit-mcp-servers/chronolog/src/chronomcp/utils/helpers.py
high Shell/command execution in server code (clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py)MTC-SRC-002
In the server's implementation (`clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py:2322`): 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.
Evidence: : process = subprocess.Popen( argv, stdin=stdin_file, stdout
Fix: 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: server clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py
high Shell/command execution in server code (clio-kit-mcp-servers/jarvis/src/jarvis_mcp/windows_job.py)MTC-SRC-002
In the server's implementation (`clio-kit-mcp-servers/jarvis/src/jarvis_mcp/windows_job.py:99`): 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.
Evidence: SystemExit(125) child = subprocess.Popen(command, shell=message["shell"], stdin=descriptor) raise SystemExit(child.wait(
Fix: 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: server clio-kit-mcp-servers/jarvis/src/jarvis_mcp/windows_job.py
high Shell/command execution in server code (clio-kit-mcp-servers/ndp/src/ndp_mcp/server.py)MTC-SRC-002
In the server's implementation (`clio-kit-mcp-servers/ndp/src/ndp_mcp/server.py:168`): 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.
Evidence: ry: completed = subprocess.run( command, check=False, capture_output=True,
Fix: 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: server clio-kit-mcp-servers/ndp/src/ndp_mcp/server.py
high Shell/command execution in server code (clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/remote_node_info.py)MTC-SRC-002
In the server's implementation (`clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/remote_node_info.py:216`): 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.
Evidence: ommand result = subprocess.run( ssh_cmd, capture_output=True, text=True,
Fix: 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: server clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/remote_node_info.py
high Shell/command execution in server code (clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/utils.py)MTC-SRC-002
In the server's implementation (`clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/utils.py:35`): 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.
Evidence: try: result = subprocess.run( command, capture_output=True, text=True, timeout=timeout )
Fix: 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: server clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/utils.py
medium Untrusted input can drive an external actionMTC-FLOW-005
Untrusted-input tools ([download_paper_pdf, download_multiple_pdfs]) co-exist with external-action tools ([export_to_bibtex, export_to_json, export_to_csv, export_to_text]). A prompt injection could cause unwanted external actions, though no direct sensitive-data leak path was found.
Evidence: untrusted [download_paper_pdf, download_multiple_pdfs] → sinks [export_to_bibtex, export_to_json, export_to_csv, export_to_text]
Fix: Require confirmation for state-changing/egress actions triggered after processing untrusted content.
Location: flow download_paper_pdf → export_to_bibtex
low Shell/command execution in packaging/dev tooling (clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py)MTC-SRC-002
In a packaging/dev/install script (shipped, but not the server runtime) (`clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py:36`): 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.
Evidence: self.process = subprocess.Popen( command, stdin=subprocess.PIPE, stdout=sub
Fix: 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: server clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py
low Shell/command execution in packaging/dev tooling (clio-kit-mcp-servers/paraview/scripts/automate_setup.py)MTC-SRC-002
In a packaging/dev/install script (shipped, but not the server runtime) (`clio-kit-mcp-servers/paraview/scripts/automate_setup.py:52`): 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.
Evidence: process = subprocess.Popen( cmd, cwd=cwd or self.project_root,
Fix: 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: server clio-kit-mcp-servers/paraview/scripts/automate_setup.py
low Shell/command execution in packaging/dev tooling (clio-kit-mcp-servers/paraview/scripts/build_paraview.py)MTC-SRC-002
In a packaging/dev/install script (shipped, but not the server runtime) (`clio-kit-mcp-servers/paraview/scripts/build_paraview.py:23`): 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.
Evidence: d.split() result = subprocess.run(cmd, cwd=cwd, capture_output=False, text=True) if check and result.returncode
Fix: 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: server clio-kit-mcp-servers/paraview/scripts/build_paraview.py
Tools 154
Each tool and what it can reach — statically extracted from the published source.
download_multiple_pdfsingests untrusted inputdownload_paper_pdfingests untrusted inputexport_to_bibtexnetwork egressexport_to_csvnetwork egressexport_to_jsonnetwork egressexport_to_textnetwork egressallocate_slurm_nodesno sensitive capabilityanalyze_file_access_patternsno sensitive capabilityanalyze_log_statisticsno sensitive capabilityanalyze_mpiio_operationsno sensitive capability
Show 144 more tools ↓
analyze_posix_operationsno sensitive capabilityappend_pkgno sensitive capabilityapply_field_coloringno sensitive capabilityapply_filter_presetno sensitive capabilitybuild_pipeline_envno sensitive capabilitycancel_slurm_jobno sensitive capabilitycheck_job_statusno sensitive capabilityclean_datano sensitive capabilitycompare_darshan_logsno sensitive capabilitycompress_file_toolno sensitive capabilitycompute_surface_areano sensitive capabilityconfigure_pkgno sensitive capabilityconfigure_volume_displayno sensitive capabilitycreate_data_sliceno sensitive capabilitycreate_geometric_shapeno sensitive capabilitycreate_pipelineno sensitive capabilitydata_infono sensitive capabilitydeallocate_slurm_nodesno sensitive capabilitydecompress_file_toolno sensitive capabilitydestroy_pipelineno sensitive capabilitydetect_log_patternsno sensitive capabilityedit_volume_opacityno sensitive capabilityexport_pipelineno sensitive capabilityfilter_by_keywordno sensitive capabilityfilter_by_time_rangeno sensitive capabilityfilter_datano sensitive capabilityfilter_logsno sensitive capabilityfind_similar_papersno sensitive capabilitygenerate_flow_streamlinesno sensitive capabilitygenerate_io_summary_reportno sensitive capabilitygenerate_isosurfaceno sensitive capabilitygenerate_summary_reportno sensitive capabilityget_active_source_names_by_typeno sensitive capabilityget_allocation_statusno sensitive capabilityget_available_arraysno sensitive capabilityget_column_preview_toolno sensitive capabilityget_cpu_infono sensitive capabilityget_dataset_detailsno sensitive capabilityget_disk_infono sensitive capabilityget_gpu_infono sensitive capabilityget_histogramno sensitive capabilityget_io_performance_metricsno sensitive capabilityget_job_detailsno sensitive capabilityget_job_outputno sensitive capabilityget_job_summaryno sensitive capabilityget_memory_infono sensitive capabilityget_network_infono sensitive capabilityget_node_infono sensitive capabilityget_paper_detailsno sensitive capabilityget_pdf_urlno sensitive capabilityget_performance_infono sensitive capabilityget_pipelineno sensitive capabilityget_pkg_configno sensitive capabilityget_process_infono sensitive capabilityget_queue_infono sensitive capabilityget_recent_papersno sensitive capabilityget_remote_node_infono sensitive capabilityget_sensor_infono sensitive capabilityget_slurm_infono sensitive capabilityget_system_infono sensitive capabilityget_timeline_analysisno sensitive capabilityhandle_missing_datano sensitive capabilityhealth_checkno sensitive capabilityidentify_io_bottlenecksno sensitive capabilityinspect_attributesno sensitive capabilityinspect_variablesno sensitive capabilityinspect_variables_at_stepno sensitive capabilityjm_add_repono sensitive capabilityjm_bootstrap_fromno sensitive capabilityjm_bootstrap_listno sensitive capabilityjm_cdno sensitive capabilityjm_construct_pkgno sensitive capabilityjm_create_configno sensitive capabilityjm_get_repono sensitive capabilityjm_graph_buildno sensitive capabilityjm_graph_modifyno sensitive capabilityjm_graph_showno sensitive capabilityjm_list_pipelinesno sensitive capabilityjm_list_reposno sensitive capabilityjm_load_configno sensitive capabilityjm_promote_repono sensitive capabilityjm_remove_repono sensitive capabilityjm_save_configno sensitive capabilityjm_set_hostfileno sensitive capabilitylist_available_hdf5_filesno sensitive capabilitylist_bp5no sensitive capabilitylist_commandsno sensitive capabilitylist_organizationsno sensitive capabilitylist_slurm_jobsno sensitive capabilityload_darshan_logno sensitive capabilityload_datano sensitive capabilityload_pipelineno sensitive capabilitymerge_datasetsno sensitive capabilitymodule_availno sensitive capabilitymodule_listno sensitive capabilitymodule_loadno sensitive capabilitymodule_restoreno sensitive capabilitymodule_saveno sensitive capabilitymodule_savelistno sensitive capabilitymodule_showno sensitive capabilitymodule_spiderno sensitive capabilitymodule_swapno sensitive capabilitymodule_unloadno sensitive capabilityoptimize_memoryno sensitive capabilityparallel_sort_large_fileno sensitive capabilitypivot_tableno sensitive capabilityplot_over_lineno sensitive capabilityprofile_csvno sensitive capabilityprofile_datano sensitive capabilityread_slice_toolno sensitive capabilityread_variable_at_stepno sensitive capabilityrecord_interactionno sensitive capabilityrefresh_hdf5_resourcesno sensitive capabilityreset_camerano sensitive capabilityretrieve_interactionno sensitive capabilityrotate_camerano sensitive capabilityrun_pipelineno sensitive capabilitysave_contour_as_stlno sensitive capabilitysave_datano sensitive capabilitysearch_arxivno sensitive capabilitysearch_by_abstractno sensitive capabilitysearch_by_subjectno sensitive capabilitysearch_by_titleno sensitive capabilitysearch_datasetsno sensitive capabilitysearch_date_rangeno sensitive capabilitysearch_papers_by_authorno sensitive capabilityset_active_sourceno sensitive capabilityset_color_mapno sensitive capabilityset_color_map_presetno sensitive capabilityset_representation_typeno sensitive capabilityshow_screenshot_previewno sensitive capabilitysort_log_by_timestampno sensitive capabilitystart_chronologno sensitive capabilitystatistical_summaryno sensitive capabilitystop_chronologno sensitive capabilitysubmit_array_jobno sensitive capabilitysubmit_slurm_jobno sensitive capabilitysummarize_toolno sensitive capabilitytake_viewport_screenshotno sensitive capabilitytime_series_operationsno sensitive capabilitytoggle_visibilityno sensitive capabilityupdate_pipelineno sensitive capabilityvalidate_datano sensitive capabilitywarp_by_vectorno sensitive capability
Toxic flows 1
Cross-tool combinations that form a data-exfiltration primitive (untrusted input → sensitive source → external sink).
What this scan could not see
- Tools were statically extracted from the published source (154 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>".
Versions 10
Scan history per published version. The engine is deterministic — the same version always yields the same score, so a changed score means the package itself changed.
| Version | Score | Findings | Engine | Scanned |
|---|---|---|---|---|
v2.10.6 latest |
A 93/100 | 12 | 1.13.0 | 2026-08-29 |
v2.10.5 |
A 93/100 | 12 | 1.13.0 | 2026-08-25 |
v2.10.3 |
A 93/100 | 12 | 1.12.1 | 2026-08-21 |
v2.10.1 |
A 93/100 | 12 | 1.12.1 | 2026-08-19 |
v2.9.0 |
A 93/100 | 12 | 1.12.1 | 2026-08-14 |
Show 5 more versions ↓
v2.7.2 |
A 93/100 | 12 | 1.12.1 | 2026-08-09 |
v2.7.0 |
A 93/100 | 11 | 1.12.1 | 2026-08-07 |
v2.6.5 |
A 93/100 | 12 | 1.12.1 | 2026-07-27 |
v2.6.3 |
A 93/100 | 12 | 1.9.0 | 2026-07-24 |
v2.6.2 |
A 93/100 | 12 | 1.9.0 | 2026-07-23 |
Embed this score
Show this server's live Trust Score in your README, docs or website. The badge is served straight from the registry and updates automatically after every rescan — no API key needed. It links back to this page, so anyone who sees the grade can also read the findings behind it instead of taking a number on faith.
Verify this score yourself
The score above is reproducible: the same package version always yields the same result. Run it locally or over the free API — no account, no LLM, fully deterministic.
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