Your entire Zotero research library, searchable offline — version-based incremental sync into SQLite with full-text search no other Zotero tool has.
zotero-research-library-pp-cli mirrors your library into a local SQLite cache using the API's version cursors, then answers research-grounding questions offline: ranked full-text search with snippets, collection trees, recent-additions triage, and Better BibTeX citekey lookups. What the Web API meters at 100 items a page, your cache answers in milliseconds.
Authentication
Create an API key at zotero.org/settings/keys and set ZOTERO_API_KEY (or run auth set-token). The CLI resolves your numeric userID automatically via /keys/current and stores the library-prefixed base URL in config — you never need to look up your user ID.
Quick Start
# Verify config shape without touching the API
zotero-research-library-pp-cli doctor --dry-run
# First full mirror of items, collections, tags, and full text
zotero-research-library-pp-cli sync --full
# The grounding ritual: what does my library say about this?
zotero-research-library-pp-cli ground "velocity based training" --limit 10
# What did I add this week
zotero-research-library-pp-cli items recent --days 7 --agent
# The library's shape at a glance
zotero-research-library-pp-cli collections tree --counts
Unique Features
These capabilities aren't available in any other tool for this API.
Research grounding that compounds
-
ground — Ranked full-text search over your synced library — title, abstract, creators, tags, and attachment full text — answered offline in under a second, with snippets and citation-ready metadata.
Reach for this when asked what the user's own library says about a topic.
zotero-research-library-pp-cli ground "hamstring injury prevention" --limit 10 --agent
-
items recent — What landed in the library recently, sorted by dateAdded from the local cache, with a --days cutoff and pipeable keys.
Use for weekly triage of new additions.
zotero-research-library-pp-cli items recent --days 7 --agent
-
collections tree — Renders the full collection hierarchy with per-node item counts in one command — a shape the flat API cannot return in one call.
Use for a hierarchical overview of how the library is organized.
zotero-research-library-pp-cli collections tree --counts --agent
Manuscript plumbing
-
cite — Resolves a Better BibTeX citekey to its item from the local cache and exports citekey-faithful BibTeX; sync backfills citekeys via the desktop's local JSON-RPC when available.
Use when a manuscript needs a citation by its Better BibTeX citekey.
zotero-research-library-pp-cli cite smithHamstring2024 --format bibtex
Agent-native plumbing
-
cache status — Sync cursors, row and FTS counts, and last-sync age from the local cache; 'cache reindex' rebuilds the FTS index from base tables with zero network.
Use to check cache freshness offline before trusting search results.
zotero-research-library-pp-cli cache status --agent
Recipes
Research-grounding query
zotero-research-library-pp-cli ground "return to play criteria" --limit 10 --agent --select key,title,creators,date,DOI
Offline ranked search with citation-ready fields; the first step of the grounding workflow.
Full-text deep search
zotero-research-library-pp-cli ground "nordic hamstring" --fulltext --agent
Extends the search into attachment full text and resolves hits to their parent papers.
Weekly additions to BibTeX
zotero-research-library-pp-cli items recent --days 7 --agent --select key,title
Fresh additions ready to pipe into an export.
Scope a search to a collection
zotero-research-library-pp-cli ground "acl injury" --collection HAMSTRING --limit 5
Collection-scoped grounding using the local join table.
Live server-side search fallback
zotero-research-library-pp-cli items list --q "tendon" --qmode everything --limit 10 --json
When you need unsynced server state, the generated endpoint carries the API's full search grammar.
Usage
Run zotero-research-library-pp-cli --help for the full command reference and flag list.
Paths & environment variables
This CLI separates local files into four path kinds:
| Kind | Contents |
|---|
config | User-editable settings such as config.toml and saved profiles |
data | Durable local data: credentials.toml, data.db, cookies, browser-session proof files, and other auth sidecars |
state | Runtime state such as persisted queries, jobs, and teach.log |
cache | Regenerable HTTP/cache files |
Each kind resolves independently. The ladder is:
- Per-kind env var:
ZOTERO_RESEARCH_LIBRARY_CONFIG_DIR, ZOTERO_RESEARCH_LIBRARY_DATA_DIR, ZOTERO_RESEARCH_LIBRARY_STATE_DIR, or ZOTERO_RESEARCH_LIBRARY_CACHE_DIR
--home <dir> for this invocationZOTERO_RESEARCH_LIBRARY_HOME for a flat relocated root- XDG env vars:
XDG_CONFIG_HOME, XDG_DATA_HOME, XDG_STATE_HOME, XDG_CACHE_HOME
- Platform defaults matching existing installs
For containers and agent sandboxes, prefer a single relocated root:
export ZOTERO_RESEARCH_LIBRARY_HOME=/srv/zotero-research-library
zotero-research-library-pp-cli doctor
Under ZOTERO_RESEARCH_LIBRARY_HOME=/srv/zotero-research-library, the four dirs resolve to /srv/zotero-research-library/config, /srv/zotero-research-library/data, /srv/zotero-research-library/state, and /srv/zotero-research-library/cache.
MCP servers do not receive CLI flags from the host. Put relocation in the host env block:
{
"mcpServers": {
"zotero-research-library": {
"command": "zotero-research-library-pp-mcp",
"env": {
"ZOTERO_RESEARCH_LIBRARY_HOME": "/srv/zotero-research-library"
}
}
}
}
Precedence matters in fleets: an ambient per-kind variable such as ZOTERO_RESEARCH_LIBRARY_DATA_DIR overrides an explicit --home for that kind. Use ZOTERO_RESEARCH_LIBRARY_HOME or the per-kind variables for durable fleet relocation; treat --home as the weaker per-invocation lever.
Relocation is one-way. Unsetting ZOTERO_RESEARCH_LIBRARY_HOME does not move files back to platform defaults, and doctor cannot find credentials left under a former root. Move the files manually before unsetting relocation variables.
Existing installs keep working because the platform-default rung matches the legacy layout. On the first auth write, stored secrets leave config.toml and are consolidated into credentials.toml under the data directory. Run zotero-research-library-pp-cli doctor --fail-on warn to check path and credential-location warnings in automation.
Commands
collections
Hierarchical collections organizing the library
zotero-research-library-pp-cli collections get - One collection by keyzotero-research-library-pp-cli collections items - Items in a collection (including children)zotero-research-library-pp-cli collections list - All collectionszotero-research-library-pp-cli collections subcollections - Subcollections of a collectionzotero-research-library-pp-cli collections top - Top-level collections
deleted
Deletion tombstones for sync
zotero-research-library-pp-cli deleted - Keys of items/collections/searches/tags deleted since a library version
fulltext
Full-text content index
zotero-research-library-pp-cli fulltext - Attachment keys whose full-text content changed since a version
items
Bibliographic items in the library
zotero-research-library-pp-cli items children - Child notes and attachments of an itemzotero-research-library-pp-cli items fulltext - Full-text content of an attachment itemzotero-research-library-pp-cli items get - Get one item by keyzotero-research-library-pp-cli items list - List items. Supports q (phrase search), qmode=everything (includes fulltext), tag filters with || OR and - negation, itemType, and since=zotero-research-library-pp-cli items top - Top-level items only (no child notes/attachments)zotero-research-library-pp-cli items trash - Items in the trash
keys
API key introspection
zotero-research-library-pp-cli keys - Resolve the current API key to userID, username, and access scopes (doctor probe + userID discovery)
searches
Saved searches
zotero-research-library-pp-cli searches get - One saved searchzotero-research-library-pp-cli searches list - All saved searches
tags
Tags across the library
zotero-research-library-pp-cli tags - All tags in the library
Self-learning loop
This CLI caches per-question discovery so repeat queries skip the walk and structurally similar queries get answered via entity substitution. The loop also self-captures: every invocation is journaled locally, and failed-flag corrections plus fresh teaches surface as candidates on the next recall for confirm/reject judgment. Agents call recall before discovery and fire teach & after answering. See the ## Automatic learning section in SKILL.md for the full protocol.
zotero-research-library-pp-cli recall <query> - Look up cached resources for a query before running discoveryzotero-research-library-pp-cli teach - Record a query -> resource mapping (silent on success, safe to background with &)zotero-research-library-pp-cli learnings list - Inspect taught rowszotero-research-library-pp-cli learnings forget <query> - Undo a teachzotero-research-library-pp-cli learnings candidates - List auto-captured candidates awaiting confirm/rejectzotero-research-library-pp-cli learnings stats - Local loop metrics: recall hit rate, teach-to-reuse, playbook resolution, candidate countszotero-research-library-pp-cli teach-pattern - Install a query/resource template up frontzotero-research-library-pp-cli teach-lookup - Add an entity mapping (e.g. country code, team alias) for pattern substitution
Pass --no-learn or set ZOTERO_RESEARCH_LIBRARY_NO_LEARN=true to disable the loop for deterministic flows.
The local store's schema version stamp is one-way: once this version of zotero-research-library-pp-cli opens the database, older binaries refuse it with a version error — upgrade the binary rather than downgrading.
Output Formats
# Human-readable table (default in terminal, JSON when piped)
zotero-research-library-pp-cli collections list
# JSON for scripting and agents
zotero-research-library-pp-cli collections list --json
# Filter to specific fields
zotero-research-library-pp-cli collections list --json --select id,name,status
# Dry run — show the request without sending
zotero-research-library-pp-cli collections list --dry-run
# Agent mode — JSON + compact + no prompts in one flag
zotero-research-library-pp-cli collections list --agent
Agent Usage
This CLI is designed for AI agent consumption:
- Non-interactive - never prompts, every input is a flag
- Pipeable -
--json output to stdout, errors to stderr
- Filterable -
--select id,name returns only fields you need
- Previewable -
--dry-run shows the request without sending
- Read-only by default - this CLI does not create, update, delete, publish, send, or mutate remote resources
- Offline-friendly - sync/search commands can use the local SQLite store when available
- Agent-safe by default - no colors or formatting unless
--human-friendly is set
Exit codes: 0 success, 2 usage error, 3 not found, 4 auth error, 5 API error, 7 rate limited, 10 config error.
Freshness
This CLI owns bounded freshness for registered store-backed read command paths. In --data-source auto mode, covered commands check the local SQLite store before serving results; stale or missing resources trigger a bounded refresh, and refresh failures fall back to the existing local data with a warning. --data-source local never refreshes, and --data-source live reads the API without mutating the local store.
Set ZOTERO_RESEARCH_LIBRARY_NO_AUTO_REFRESH=1 to disable the pre-read freshness hook while preserving the selected data source.
Covered command paths:
zotero-research-library-pp-cli collectionszotero-research-library-pp-cli collections getzotero-research-library-pp-cli collections listzotero-research-library-pp-cli collections searchzotero-research-library-pp-cli deletedzotero-research-library-pp-cli deleted getzotero-research-library-pp-cli deleted listzotero-research-library-pp-cli deleted searchzotero-research-library-pp-cli itemszotero-research-library-pp-cli items getzotero-research-library-pp-cli items listzotero-research-library-pp-cli items searchzotero-research-library-pp-cli searcheszotero-research-library-pp-cli searches getzotero-research-library-pp-cli searches listzotero-research-library-pp-cli searches searchzotero-research-library-pp-cli tagszotero-research-library-pp-cli tags getzotero-research-library-pp-cli tags listzotero-research-library-pp-cli tags search
JSON outputs that use the generated provenance envelope include freshness metadata at meta.freshness. This metadata describes the freshness decision for the covered command path; it does not claim full historical backfill or API-specific enrichment.
Health Check
zotero-research-library-pp-cli doctor
Verifies configuration, credentials, and connectivity to the API.
Configuration
Run zotero-research-library-pp-cli doctor to see the resolved config, data, state, and cache directories. The platform-default config path is ~/.config/zotero-research-library-pp-cli/config.toml; --home, ZOTERO_RESEARCH_LIBRARY_HOME, and per-kind env vars can relocate it.
Static request headers can be configured under headers; per-command header overrides take precedence.
Environment variables:
| Name | Kind | Required | Description |
|---|
ZOTERO_API_KEY | per_call | Yes | Set to your API credential. |
agentcookie (optional)
If you use agentcookie to sync secrets across machines, this CLI auto-adopts agentcookie-managed credentials with no extra setup. When the daemon writes to this CLI's config, zotero-research-library-pp-cli doctor reports agentcookie: detected and auth-status labels the source as agentcookie. Skip this section if you don't use agentcookie - the CLI works the same as any other.
Troubleshooting
Authentication errors (exit code 4)
- Run
zotero-research-library-pp-cli doctor to check credentials
- Verify the environment variable is set:
echo $ZOTERO_API_KEY
Not found errors (exit code 3)
- Check the resource ID is correct
- Run the
list command to see available items
API-specific
- 403 Forbidden on every call — Key lacks library access — regenerate at zotero.org/settings/keys with 'Allow library access' checked
- ground returns nothing — The cache is empty — run 'sync --full' first; check 'cache status' for cursors and row counts
- cite finds no citekeys — Citekeys come from the Better BibTeX plugin via the desktop app — open Zotero desktop and re-run 'sync'