BioMCP

biomcp_configure

DestructiveIdempotent

Inspect, set, or reset project config file parameters for database and analysis features, validate changes with dry runs, and detect conflicts or pending restarts before applying them.

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).

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedv1.6.0-alpha.10Oct 25, 2026
- removedInput schema / additionalProperties
```
Removed value: -false
```
- addedInput schema / properties / values / propertyNames
```
Added value: +{
+  "maxLength": 256,
+  "type": "string"
+}
```
Addedv1.0.0Sep 1, 2026

TDQS

A4.6/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already flag destructive and non-read-only, and the description adds real beyond-schema behavior: writes are atomic, nothing is written if any key is invalid, null restores defaults, sensitive keys demand confirm_sensitive, env values are masked to presence+fingerprint, and the write is refused outside a project root. It doesn't state whether a reset of a feature section is recoverable, which is the one gap for a destructive tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with what it covers, then actions, hard rules and examples — a well-organized layout for a complex tool. The opening clause ('unified observability and restricted controllability') is jargon that carries no operational information, and the examples block is long relative to the rest.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

No output schema exists, and the description compensates by describing the status response contents (settable_keys, config file health, conflicts, pending-restart flags, prerequisites). Combined with the restart workflow and error-path behavior, an agent has enough to call it correctly and interpret the result.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so per-parameter meaning is already documented; the description still adds value through worked examples, the null-removes-key convention, and the cross-parameter rule that confirm_sensitive is required when values touch connection targets or mirrors. The interaction with dry_run on both set and reset is clarified beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb pair (inspect/configure) and the exact resource (biomcp: three file-backed feature groups plus env-only parameters). The scope enumeration lets an agent distinguish it immediately from every sibling, which are all bio-data retrieval tools.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly names each action and its trigger (status default with {}, set for atomic batch writes, reset for removals), states when to use filter instead of status, and excludes env parameters from set/reset. It also gives the operational sequence: finish prerequisites, restart once, re-call with {} to verify.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

biomcp_configure

Instructions

Input Schema

Schema Changelog

TDQS

Other Tools