biostudies-arrayexpress-skill

Operating rules

• Use scripts/rest_request.py for all BioStudies and ArrayExpress calls.
• Use base_url=https://www.ebi.ac.uk/biostudies/api/v1.
• Search pages are better with pageSize=10 and max_items=10; accession lookups usually do not need max_items.
• 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: search, ArrayExpress/search, studies/<accession>, and studies/<accession>/info.
• If the user needs the full payload, set save_raw=true and report the saved file path instead of pasting large study records into chat.

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 BioStudies patterns:
  • {"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"search","params":{"query":"rna","page":1,"pageSize":10},"record_path":"hits","max_items":10}
  • {"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"ArrayExpress/search","params":{"query":"single cell","page":1,"pageSize":10},"record_path":"hits","max_items":10}
  • {"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"studies/E-MTAB-6701"}

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://www.ebi.ac.uk/biostudies/api/v1","path":"search","params":{"query":"rna","page":1,"pageSize":10},"record_path":"hits","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.