mgnify-skill

name: mgnify-skill description: Submit compact MGnify API requests for microbiome studies, samples, and biome metadata. Use when a user wants concise MGnify summaries

Operating rules

• Use scripts/rest_request.py for all MGnify calls.
• Use base_url=https://www.ebi.ac.uk/metagenomics/api/v1.
• MGnify uses JSON:API-style responses. Prefer record_path=data for collection endpoints.
• Keep requests narrow by study accession, sample accession, or biome whenever possible.
• Re-run requests in long conversations instead of relying on older tool output.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return raw JSON only if the user explicitly asks for machine-readable output.
• Prefer these paths: studies, samples, and biomes.

Input

• Read one JSON object from stdin.
• Required fields: base_url, path
• Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
• Common MGnify patterns:
  • {"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"studies","params":{"page_size":10},"record_path":"data","max_items":10}
  • {"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"biomes","params":{"page_size":10},"record_path":"data","max_items":10}

Output

• Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
• Use raw_output_path when save_raw=true.
• Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"studies","params":{"page_size":10},"record_path":"data","max_items":10}' | python scripts/rest_request.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.