cellxgene-skill

Imported from openai/plugins (plugins/life-science-research/skills/cellxgene-skill/SKILL.md). Install upstream with npx skills add openai/plugins --skill cellxgene-skill. Copyright stays with the author.

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.