Operating rules
- Use
scripts/rest_request.py for all PharmGKB API calls.
- Use
base_url=https://api.pharmgkb.org/v1/data.
- Single object lookups usually do not need
max_items; list and search endpoints are better with max_items=10.
- 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.
- Prefer these paths:
gene/<id>, variant/<id>, clinicalAnnotation, dosingGuideline, and search endpoints.
- 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
- Common PharmGKB patterns:
{"base_url":"https://api.pharmgkb.org/v1/data","path":"gene/PA36679"}{"base_url":"https://api.pharmgkb.org/v1/data","path":"clinicalAnnotation","params":{"relatedChemicals.accessionId":"PA449726","limit":10},"max_items":10}{"base_url":"https://api.pharmgkb.org/v1/data","path":"variant/PA166158545"}
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://api.pharmgkb.org/v1/data","path":"gene/PA36679"}' | 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.
