| name | hmdb-skill |
| description | Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries |
Operating rules
- hmdb.ca publishes no JSON API and sits behind a Cloudflare interactive challenge: every path, including
/, /downloads, /metabolites/<id> and /unearth/q, answers a scripted request with HTTP 403 and cf-mitigated: challenge. scripts/rest_request.py cannot retrieve HMDB content. Say so rather than reporting an empty result.
- To act on an HMDB accession, map it to a database that does serve an API: UniChem source 18 is HMDB, and
POST https://www.ebi.ac.uk/unichem/api/v1/compounds with {"type":"sourceID","compound":"<HMDB id>","sourceID":18} returns the ChEBI, ChEMBL, PubChem and DrugBank identifiers for the same structure. Hand those to chebi-skill, chembl-skill, or pubchem-pug-skill.
- Bulk HMDB XML is distributed from https://hmdb.ca/downloads, which a person can fetch in a browser; there is no scripted route to it.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed
... in tool previews as UI truncation, not literal request content.
Execution behavior
- Return concise markdown summaries from the script JSON by default.
- If the user needs the full payload, set
save_raw=true and report the saved file path.
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
- Identifier cross-reference pattern:
{"base_url":"https://www.ebi.ac.uk/unichem/api/v1","path":"compounds","method":"POST","json_body":{"type":"sourceID","compound":"HMDB0000259","sourceID":18},"record_path":"compounds.0.sources","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/unichem/api/v1","path":"compounds","method":"POST","json_body":{"type":"sourceID","compound":"HMDB0000259","sourceID":18},"record_path":"compounds.0.sources","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.
