encode-skill

## Operating rules - Use `scripts/rest_request.py` for all ENCODE API calls. - Use `base_url=https://www.encodeproject.org`. - Object lookups usually do not need `max_items`; portal-style search endpoints are better with `limit=10` and `max_items=10`. - Send `Accept: application/json` in `headers` and add `format=json` in `params` when needed. - Keep request volume modest and avoid large unfiltered searches. - 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 accession paths such as `biosamples/<accession>/` and search paths such as `search/`. - 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 ENCODE patterns: - `{"base_url":"https://www.encodeproject.org","path":"biosamples/ENCBS000AAA/","params":{"frame":"object","format":"json"},"headers":{"Accept":"application/json"}}` - `{"base_url":"https://www.encodeproject.org","path":"search/","params":{"type":"Experiment","assay_term_name":"RNA-seq","limit":10,"format":"json"},"record_path":"@graph","headers":{"Accept":"application/json"},"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 ```bash echo '{"base_url":"https://www.encodeproject.org","path":"search/","params":{"type":"Experiment","assay_term_name":"RNA-seq","limit":10,"format":"json"},"record_path":"@graph","headers":{"Accept":"application/json"},"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`.