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musharna

data-aggregator-mcp

fetch

Download and verify files from diverse research data repositories, returning local file paths while enforcing size limits and checksum integrity.

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)
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
resumedNo
Behavior5/5

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

The description extensively discloses behavioral traits: reads from remote sources, writes to local disk, verifies checksums (md5/SHA-256), writes a sidecar file, and fails loudly on certain conditions. These details go far beyond the minimal annotations (which are all false), providing rich context for the agent.

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 core action. It lists many backends in an organized manner, which is valuable for capability awareness. While long, each sentence earns its place by providing necessary detail for selection and execution.

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 (multiple backends, verification, sidecar, size limits, extraction), the description covers all essential aspects. It explains failure modes, verification status per backend, and the sidecar file. It is sufficiently complete for an agent to use the tool correctly.

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?

The input schema has 100% description coverage, so the baseline is 3. The description adds minimal parameter-specific context beyond what the schema already provides; it mentions force and max_bytes interaction but does not significantly enhance understanding of each parameter.

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's core purpose: downloading a resource's files to local disk and returning paths, not contents. It enumerates many supported backends and their behaviors, leaving no ambiguity about what the tool does. It distinguishes itself from siblings by specifying it returns paths, not contents.

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 conditions for use, such as failing loud when max_bytes is exceeded unless force=true, and notes which backends are unsupported (e.g., Dryad manifest-only, certain DataCite repos fail loud). However, it does not explicitly contrast with sibling tools, though siblings are not file-download focused, so this is acceptable.

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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