{"id":24691,"plugin_id":"plugins~Plugin_7113e6f705948191bad2d24c30465361","kind":"skill","collection_source":null,"comparison_source":null,"observed_at":"2026-09-30T23:18:35.355Z","digest":"180e188c12b9f7b0ecd16cc82d9214ce876309e129c475e4561044297b819a02","against":null,"payload":{"name":"cbioportal-skill","description":"Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries","included_files":[{"relative_path":"agents/openai.yaml","size_in_bytes":109},{"relative_path":"scripts/rest_request.py","size_in_bytes":10728}],"skill_md_contents":"---\nname: cbioportal-skill\ndescription: Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries\n---\n\n## Operating rules\n- Use `scripts/rest_request.py` for all cBioPortal API calls.\n- Use `base_url=https://www.cbioportal.org/api`.\n- Collection endpoints are better with `pageSize=10` and `max_items=10`; single study or profile lookups usually do not need `max_items`.\n- Use `method=POST` plus `json_body` for fetch-style endpoints such as mutation fetches.\n- Send `Accept: application/json` in `headers`.\n- Re-run requests in long conversations instead of relying on older tool output.\n- Treat displayed `...` in tool previews as UI truncation, not literal request content.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Prefer these paths: `studies`, `studies/<studyId>/molecular-profiles`, `molecular-profiles/<profileId>/mutations/fetch`, and study-level clinical or sample endpoints.\n- If the user needs the full payload, set `save_raw=true` and report the saved file path.\n\n## Input\n- Read one JSON object from stdin.\n- Required fields: `base_url`, `path`\n- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common cBioPortal patterns:\n  - `{\"base_url\":\"https://www.cbioportal.org/api\",\"path\":\"studies\",\"params\":{\"keyword\":\"breast\",\"projection\":\"SUMMARY\",\"pageSize\":10},\"headers\":{\"Accept\":\"application/json\"},\"max_items\":10}`\n  - `{\"base_url\":\"https://www.cbioportal.org/api\",\"path\":\"molecular-profiles/brca_tcga_mutations/mutations/fetch\",\"method\":\"POST\",\"json_body\":{\"sampleListId\":\"brca_tcga_all\",\"entrezGeneIds\":[7157]},\"headers\":{\"Accept\":\"application/json\"},\"max_items\":10}`\n\n## Output\n- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.\n- Use `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` and `error.message`.\n\n## Execution\n```bash\necho '{\"base_url\":\"https://www.cbioportal.org/api\",\"path\":\"studies\",\"params\":{\"keyword\":\"breast\",\"projection\":\"SUMMARY\",\"pageSize\":10},\"headers\":{\"Accept\":\"application/json\"},\"max_items\":10}' | python scripts/rest_request.py\n```\n\n## References\n- No additional runtime references are required; keep the import package limited to this file and `scripts/rest_request.py`.\n"},"changes":[],"summary":"First saved snapshot. No earlier version is available for comparison.","summary_kind":"deterministic","summary_metadata":{}}