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Upload Genome

upload_genome
Idempotent

Parse raw DNA data from 23andMe or Genera files to enable pharmacogenomic analysis. Accepts local file paths or direct download URLs.

Instructions

Parse raw DNA data. Supports: 23andMe (.txt), Genera (.csv). CRITICAL: Genome files are 15-25MB (600k+ lines). NEVER read, inline, or chunk genome file contents — this WILL exceed your context window and crash the session. For REMOTE server (mcp.openpgx.ai): use get_upload_command to get a curl/python command, execute it in your code execution sandbox (or tell the user to run it in their terminal), then call load_profile with the returned code. For LOCAL server (stdio/npx): use file_path only. The url parameter is for direct download links (Google Drive, Dropbox, S3).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
file_pathNoLocal file path (stdio mode ONLY — remote server cannot access local files)
urlNoDirect download URL to the raw data file
Behavior5/5

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

Annotations indicate idempotentHint=true, but description adds critical behavioral details: genome files are 15-25MB (600k+ lines) and must not be read inline. No contradiction with annotations. Warns about context window overflow, which is essential for safe execution.

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 somewhat long but front-loaded with purpose and critical warnings. Every sentence earns its place, covering purpose, supported formats, size warning, mode-specific instructions, and parameter clarification. Could be slightly tighter but overall efficient.

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?

Given the complexity (two modes, large files, multi-step upload), the description covers key use cases, constraints, and required follow-up actions (load_profile). No output schema, but the tool's return is not critical for the agent to proceed. Provides sufficient context for safe and correct invocation.

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 description adds value by distinguishing file_path (local only) and url (direct download links like Google Drive, Dropbox, S3). Explains the context for each parameter beyond schema descriptions.

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 states 'Parse raw DNA data' and lists supported formats (23andMe .txt, Genera .csv), clearly defining its purpose. It distinguishes from siblings like upload_genome_chunk and upload_genome_start by explaining the different modes (remote vs local) and the required workflow.

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?

Provides explicit guidance: for remote server, use get_upload_command, execute in sandbox, then call load_profile; for local, use file_path. Warns against reading genome files inline, which prevents common mistakes. Covers both modes and gives step-by-step instructions.

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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