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musharna

data-aggregator-mcp

fetch

Download files from research data repositories (Zenodo, SRA, GEO, Figshare, Dataverse, OSF) and open-access literature to local disk, with checksum verification and a sidecar metadata file.

Instructions

Download a resource's files to local disk and return the PATHS (never the file contents). Fetchable: Zenodo, SRA (ENA FASTQ), GEO supplementary files, and DataCite-discovered Figshare/Dataverse/OSF deposits (md5-verified), and open-access literature full text (EuropePMC XML / Unpaywall PDF, unverified); a DataCite Dryad id is manifest-only (resolve lists its files but fetch fails loud), and other DataCite repos plus paywalled/non-OA literature ids fail loud. Fails loud if selected files exceed max_bytes unless force=true. Verifies checksums; writes a .dataresource.json sidecar.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesSource-prefixed id or bare Zenodo id
destNoDestination dir (default managed cache)
filesNoGlob over file names (default all)
max_bytesNoByte ceiling before failing loud
forceNoOverride max_bytes
extractNoUnpack downloaded zip/tar archives into the destination (default false). Path-traversal-guarded; counts against max_bytes.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathsNo
bytesNo
skippedNo
Behavior5/5

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

With no annotations, the description fully discloses key behaviors: returns paths never contents, checksum verification, sidecar file writing, per-source fetchability, extraction options with path-traversal guarding, and failure conditions. This is comprehensive.

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?

The description is dense and front-loaded with the main purpose, then details sources and behavior. Every sentence adds value, though it is lengthy due to the tool's complexity. It could be slightly more structured, but is effective.

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?

Given the complexity, lack of annotations, and presence of output schema, the description covers all critical aspects: sources, failure modes, parameter interactions, side effects (sidecar), and behaviors (checksum, extraction). An agent has enough to decide and invoke correctly.

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%, but the description adds significant context beyond the schema: defaults (dest, max_bytes, force, extract), path-traversal guarding for extract, and counting extract size against max_bytes. This provides important nuance for correct invocation.

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?

The description clearly states the tool downloads files and returns paths (not contents), enumerates specific fetchable sources (Zenodo, SRA, GEO, etc.), and distinguishes from sibling tools by specifying its core function.

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

Usage Guidelines4/5

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

The description provides explicit details on when to use the tool (fetchable sources), conditions like max_bytes and force, and failure modes (e.g., Dryad manifest-only, paywalled literature). However, it does not explicitly mention alternative tools for cases where fetch fails, though it implies them.

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

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