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musharna

data-aggregator-mcp

by musharna

fetch

Download files from research repositories (Zenodo, GEO, SRA, etc.) to local disk, verifying checksums and returning file paths.

Instructions

Download a resource's files to local disk and return the PATHS (never the file contents). Fetchable backends: Zenodo (md5-verified); SRA via ENA FASTQ (md5-verified); GEO supplementary files (unverified); DataCite sub-repos — Figshare/Dataverse/OSF (md5-verified), OpenNeuro (snapshot manifest, unverified), Dryad is manifest-only (resolve lists files, fetch fails loud), Mendeley + other DataCite repos fail loud; PubMed/OpenAIRE open-access full text (EuropePMC XML / Unpaywall PDF, unverified); HuggingFace Hub (unverified); DataONE Member-Node objects (md5/SHA-256-verified); OmicsDI — PRIDE + MetaboLights only (unverified), MassIVE/GNPS/PeptideAtlas/Metabolomics Workbench fail loud; DANDI dandisets (302→S3, unverified); CZ CELLxGENE H5AD/RDS assets (unverified); OpenML ARFF (md5-verified); RCSB PDB .cif/.pdb structure files (unverified). 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)
forceNoOverride max_bytes
extractNoUnpack downloaded zip/tar archives into the destination (default false). Path-traversal-guarded; counts against max_bytes.
max_bytesNoByte ceiling before failing loud

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
bytesNo
pathsNo
resumedNo
skippedNo
unverifiedNo
Behavior5/5

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

The description adds substantial behavioral context beyond annotations: it describes checksum verification, sidecar writing, failure behavior on size/backends, and unverified sources. There is no contradiction with annotations.

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 long but well-organized: it front-loads the core purpose, then lists backends with verification status, then general behavior. Every sentence adds information, though it could be slightly more concise.

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 tool's complexity (many backends, multiple parameters, output schema exists), the description is comprehensive. It covers backend-specific behavior, failure modes, sidecar file, and checksum verification, with no obvious gaps.

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

Parameters3/5

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

Schema description coverage is 100%, so the schema already documents all parameters. The description adds global context about 'max_bytes' and 'force' but does not significantly enhance individual parameter semantics beyond what the schema provides.

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 it downloads a resource's files to local disk and returns paths, not contents. It lists specific backends, distinguishing this tool from siblings like search or resolve.

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 context about when to use this tool (e.g., downloading from various backends) and mentions failure conditions (e.g., Dryad, Mendeley). However, it does not explicitly state when not to use it or suggest alternatives beyond naming sibling tools.

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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