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rewire-bio

genomics-mcp

Official
by rewire-bio

list_samples

Read-only

Retrieve the list of samples for a genomic study or dataset by providing its source and accession.

Instructions

List samples of a study/dataset as supplied by the source. Not implemented in this build: returns error code 'unsupported' (E6, E7).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cursorNo
sourceYes
accessionYes
max_recordsNoLower the record limit.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dataNo
errorNoSet when status is error.
errorsNoPer-source failures in partial results.
limitsNo
statusYes
warningsNo
operationYes
provenanceNo
truncationNo
source_statusNo
schema_versionNo1

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A3.6/5.0
Behavior5/5

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

The description explicitly discloses that the tool is not implemented and will return error code 'unsupported' (E6, E7). This is a critical behavioral trait that the annotations (readOnlyHint, openWorldHint) do not convey. The agent is clearly informed that invoking this tool will fail, which is excellent transparency.

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

Conciseness5/5

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

The description is two short sentences. The purpose is stated first, and the crucial 'not implemented' caveat is front-loaded in the second sentence. Every word earns its place; there is no redundant or extraneous detail.

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

Completeness4/5

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

An output schema exists and annotations already cover the safety profileVERT. The description adds the decisive fact that the tool always errors, so an agent can make an informed decision not to call it. The missing parameter meanings are a gap, but because the tool is universally unsupported, they are less critical than they would be for a working tool.

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

Parameters2/5

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

Schema description coverage is only 25%, with only max_records having a description in the schema. The tool description does not explain source, accession, or cursor semantics, and only vaguely hints that a 'study/dataset' is involved. The description fails to compensate for the schema's lack of parameter documentation, leaving most parameters underspecified.

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

Purpose4/5

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

The description states a clear verb and resource: 'List samples of a study/dataset'. This distinguishes it from siblings like list_sources and list_files by naming the specific entity (samples). The phrase 'as supplied by the source' adds slight ambiguity about the nature of the list, and the intent is somewhat undercut by the 'Not implemented' caveat, but the core purpose is still evident.

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

Usage Guidelines2/5

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

The description gives no explicit when-to-use or alternative tool guidance. The statement 'Not implemented in this build' is an implicit warning not to use the tool, but it does not point to an alternative for listing samples. Unlike strong definitions that name sibling alternatives, this one leaves the agent to infer whether another tool can serve the same function.

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