name: cellxgene-skill
description: Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries
Operating rules
- Use
scripts/rest_request.py for all CELLxGENE Discover calls.
- Use
base_url=https://api.cellxgene.cziscience.com/curation/v1.
- Prefer targeted collection detail lookups rather than full archive dumps by default.
- The public
collections list can be large and may require a higher timeout_sec; collection detail lookups are usually the better first call.
- Re-run requests in long conversations instead of relying on older tool output.
Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer these paths:
collections/<collection_id> first, then collections when the user explicitly wants broad archive discovery.
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 CELLxGENE patterns:
{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections","timeout_sec":60,"max_items":5}
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
echo '{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}' | 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.