Paperclip CLI

Paperclip by GXL exposes scientific documents through a virtual filesystem and server-side search and readers. This is GXL Paperclip at paperclip.gxl.ai, not the unrelated Paperclip agent-company application. Use the source requested by the user; other providers have their own skills.

This revision checks official docs, the public API schema, and installed CLI/SDK 0.7.92. Local help, SDK request construction, and public metadata were checked. Authenticated retrieval, LLM readers, uploads, and repository mutations were not run during this review; their examples are illustrative. Server behavior can change independently of the CLI version.

Preflight and authentication

command -v paperclip
paperclip --version
paperclip --help

If installed, use the existing account or a key configured privately at https://paperclip.gxl.ai/keys. Do not ask for a key in chat or print credential files. Paperclip does not automatically load a project .env. If the user has supplied a trusted, shell-compatible .env, export it in the same shell invocation as the command:

if [ -f .env ]; then
  set -a
  . ./.env
  set +a
fi
paperclip config 2>&1 | grep -E 'Auth:|Health:'

Sourcing .env executes shell code: use only a trusted file, and keep it out of Git. Repeat the export when a tool starts a fresh shell; an already-exported environment needs no prefix. A bearer token can take precedence over an API key, and absent environment credentials may fall back to a stored OAuth identity. Check the intended account rather than assuming any OAuth login is wrong. Auth reports credential presence; Health probes public reachability. Neither proves the credential is valid. Check authentication on the next task-authorized request.

Use browser paperclip login when the user is available to complete sign-in. Installation and paperclip install also contain prompts; see installation.md. Do not run update, uninstall, account changes, or uploads merely to test documentation.

Choose the retrieval operation

Always pass a source or virtual directory to search. Comma-separated sources work, but separate targeted queries are easier to interpret when mixing papers, trials, and regulatory evidence. Use paperclip skill proteins before protein queries and paperclip skill patents before patents.

Find, read, and cite

paperclip search -s pmc "CRISPR base editing delivery" -n 5
paperclip cat /papers/PMC10945750/meta.json
paperclip head -40 /papers/PMC10945750/content.lines
paperclip ls /papers/PMC10945750/sections/
paperclip grep -n "lipid nanoparticle" /papers/PMC10945750/content.lines
paperclip scan /papers/PMC10945750/content.lines "IC50" "off-target" "efficiency"

Capture the returned result ID; do not reuse the illustrative IDs in this skill. s_ IDs identify saved search/grep/filter cohorts, m_ map runs, and r_ reduce artifacts. Recover recent IDs with paperclip results --list. Terminal output can be a truncated preview, so use saved results or SDK result.papers for structured hits, not a regex over rendered paper titles. See search-and-retrieval.md and python-sdk.md.

Use absolute virtual paths. Prefer head, sections, grep, and scan to dumping a whole paper. A failed read or empty, bounded grep result does not establish scientific absence.

Multi-paper extraction

paperclip search -s pmc "lipid nanoparticle mRNA delivery" -n 5
# Substitute the actual search ID below.
paperclip filter --from s_ID "in vivo delivery with quantified efficiency"
paperclip map --from s_ID "Report delivery vector, target cell type, efficiency, and supporting lines. State 'not reported' when absent."
paperclip results m_ID --save map.txt

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