biomcp_configure
Inspect BioMCP feature status, update configuration, or reset parameters in one atomic batch. Validate changes with dry-run, then apply them by restarting the client.
Instructions
Inspect and configure biomcp — unified observability and restricted controllability for every parameter.
What it covers: three optional feature groups (database, analysis_r, analysis_biowasm) whose knobs live in the .biomcp.json project config file (written by this tool, loaded at server startup — a restart applies changes), plus every environment-only parameter (API keys, proxy, security boundaries), which is query-only.
Actions:
status (default; call with {}): per-feature running state (with each feature's settable_keys), config file health, conflicts (e.g. an env var vetoing the file), pending-restart flags, dependency prerequisites, and parameter counts. The full parameter catalog is NOT inlined — use filter for detailed rows: 'file', 'env', a feature id ('analysis_r'), or a dotted-id prefix ('features.database').
set: create/modify file parameters in one atomic batch. Enable/disable is just features..enabled. null removes a key (restores default). Sensitive keys (connection targets, mirrors) require confirm_sensitive=true. Nothing is written when any key is invalid (dry_run=true validates and diffs without writing).
reset: remove a feature section (target: feature id) or specific keys (target: [dotted ids]).
Hard rules: environment parameters are never settable here (the response tells you how to set them in your client's env block); env var values are never displayed (masked: presence + fingerprint only); the file write is refused when the server's working directory is not a project root — the response then carries a paste-ready env block instead.
Examples: {"action":"status"} · {"action":"status","filter":"features.analysis_r"} · {"action":"set","values":{"features.analysis_biowasm.enabled":true}} · {"action":"set","values":{"features.database.enabled":true,"features.database.type":"sqlite","features.database.sqlite_path":["data/geo.db"]}} · {"action":"set","values":{"features.analysis_r.mirror_url":null}} · {"action":"reset","target":"analysis_r"}
Changes apply at server startup: finish dependency prerequisites first (see prerequisites in the response), then restart the client/session once, then re-call this tool with {} to verify running_now.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| action | No | status = inspect (default, works with no other arguments); set = create/modify file parameters; reset = remove. | status |
| filter | No | For status: "file" | "env" | feature id | dotted-id prefix — returns detailed rows (effects, how-to-set). | |
| target | No | For reset: a feature id ("database" | "analysis_r" | "analysis_biowasm") removes the whole section, or a list of dotted file-param ids removes those keys. | |
| values | No | For set: {"<dotted file-param id>": <value|null>} — e.g. {"features.analysis_r.enabled": true}. null removes the key. Valid ids are listed by status. | |
| dry_run | No | Validate and diff without writing (set/reset). | |
| confirm_sensitive | No | Required true when set/reset touches sensitive keys (connection targets, mirrors, credentials). |