| 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.
