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.