cbioportal-skill

Operating rules

• Use scripts/rest_request.py for all cBioPortal API calls.
• Use base_url=https://www.cbioportal.org/api.
• Collection endpoints are better with pageSize=10 and max_items=10; single study or profile lookups usually do not need max_items.
• Use method=POST plus json_body for fetch-style endpoints such as mutation fetches.
• Send Accept: application/json in headers.
• 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: studies, studies/<studyId>/molecular-profiles, molecular-profiles/<profileId>/mutations/fetch, and study-level clinical or sample 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 cBioPortal patterns: