proteomexchange-skill

## Operating rules - Use `scripts/rest_request.py` for all ProteomeXchange PROXI calls. - Use `base_url=https://proteomecentral.proteomexchange.org/api/proxi/v0.1`. - Collection endpoints are better with `max_items=10`; targeted identifier lookups usually do not need `max_items`. - Keep requests narrow by identifier, spectrum, or dataset whenever possible. - 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: `datasets`, `datasets/<identifier>`, `libraries`, `peptidoforms`, `proteins`, `psms`, `spectra`, and `usi_examples`. - 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 PROXI patterns: - `{"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets","max_items":10}` - `{"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets/PXD000001"}` - `{"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"usi_examples","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://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets","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`.