paperclip

Paperclip CLI

Paperclip exposes roughly 11M full-text papers, 217K+ regulatory documents, 110K+ clinical trial protocols, and 574K+ protein entries as a read-only virtual filesystem navigated with Unix commands, backed by server-side semantic search and LLM readers.

Every document is line-numbered, and that is the point of the tool: you cite #L45 and a reader jumps to the exact sentence. Read the lines you cite, do not paraphrase past what they say, and never present a semantic-search snippet as if you had read the paper.

Step 1 — preflight

Run this before anything else. It answers "is it installed" and "who am I" in one call.

command -v paperclip >/dev/null || echo "paperclip NOT INSTALLED"
command -v paperclip >/dev/null && { paperclip --version; [ -f .env ] && { set -a; . ./.env; set +a; }; paperclip config 2>&1 | grep -E "Auth|Health"; }

Read the Auth: line — it decides everything that follows:

Output	Meaning	Do this
✓ API key (env)	The API key loaded. Correct state.	Proceed, using the auth prefix below
✓ [email protected]	The key did not load — this is stored OAuth, a different identity	If .env holds a key, you forgot the prefix. Fix it
✗ (run: paperclip login)	No credential at all	Ask the user to authenticate — see Installing
paperclip NOT INSTALLED	No binary	See Installing

Health: ✓ server reachable is an unauthenticated probe, and Auth: ✓ only means a credential is present, not valid. A junk key produces the same two lines. Prove the credential with a real query:

[ -f .env ] && { set -a; . ./.env; set +a; }; paperclip search -s pmc "test" -n 1
# invalid key → "[error] Authentication failed (API key invalid)." and exit 1

Step 2 — operating rules

These are the rules that make the difference between working and silently-wrong. They matter more than any individual command.

1. Put the auth prefix in every command

Shell state does not survive between tool calls. Exporting the key in one call and running paperclip in the next means the key is gone — and Paperclip does not error, it silently falls back to stored OAuth, i.e. a different identity and possibly a different account.