cli-anything-zotero 0.9.0

Zotero CLI and MCP server package — installs zotero-cli and zotero-mcp for AI-assisted library workflows.

cli-anything-zotero

Let AI manage your Zotero library.

中文文档 | English

---

For Non-Programmers

This tool is designed to be used by AI, not memorized by you. After a simple install (~3 minutes), just talk to your AI assistant in plain language:

"Find papers about diabetes and kidney disease in my Zotero library"

"Import this DOI into my CKM collection: 10.1038/s41586-024-07871-6"

"Export all papers in my thesis collection as BibTeX"

"Find PDFs for items in my review collection that are missing them"

All you need to do:

1. Follow the Installation steps below
2. Tell your AI assistant (Claude Code, Cursor, etc.) what you need
3. That's it

---

What It Does

Built on CLI-Anything by HKUDS, this tool gives AI agents full access to your local Zotero library through a JS Bridge — a lightweight Zotero plugin that exposes a privileged JavaScript endpoint.

Key capabilities:

• Search & browse — keyword search, full-text PDF search, collection tree, tags
• Import — from DOI, PMID, RIS/BibTeX files, or JSON
• Export — BibTeX, CSL-JSON, RIS, CSV, formatted citations
• PDF management — attach files, auto-find PDFs online, search annotations
• Write operations — update metadata, manage tags, add notes, trigger sync
• Advanced — execute arbitrary Zotero JS, semantic search with local embeddings, AI analysis
• MCP server — 56 tools for Claude Desktop, Cursor, LM Studio, and other MCP clients

All write operations run locally through the JS Bridge — no API key or internet connection required.

---

Choose Your Mode

This tool supports two modes. Pick the one that fits your AI client:

	CLI Mode	MCP Mode
How AI calls it	Shell commands (zotero-cli item find ...)	Structured tool calls (no command-line needed)
Works with	Any AI that can run shell commands (Claude Code, ChatGPT, Cursor, Windsurf, Cline, etc.)	AI clients with MCP support (Claude Desktop, Cursor, Claude Code, LM Studio, etc.)
AI learning curve	AI runs --help once to discover all 70+ commands	Zero — 56 tools are auto-registered with typed parameters
Error rate	Occasional typos by AI (self-corrects)	Near-zero (parameters are type-constrained)
Install	pip install cli-anything-zotero	pip install 'cli-anything-zotero[mcp]' + client config

Not sure? If your AI client supports MCP, choose MCP — it's more reliable. Otherwise, CLI works everywhere.

---

Installation

Prerequisites: Python 3.10+, Zotero 7/8/9 (running).

Step 1: Install the package

CLI Mode (for any AI assistant):

pip install cli-anything-zotero

MCP Mode (for Claude Desktop, Cursor, Claude Code, etc.):

pip install 'cli-anything-zotero[mcp]'

Both modes are included in the same package. The [mcp] extra just adds MCP protocol dependencies. The package name stays cli-anything-zotero; the user-facing commands are zotero-cli for CLI workflows and zotero-mcp for MCP clients. The old cli-anything-zotero command remains as a compatibility alias.

Step 2: Install the JS Bridge Plugin (one-time, both modes)

zotero-cli app install-plugin

First install requires manual steps in Zotero:

1. The command generates a .xpi file and prints its path
2. In Zotero: Tools → Plugins → gear icon → Install Plugin From File...
3. Select the .xpi file, then restart Zotero

After the first install, future upgrades via app install-plugin are automatic.

For existing users upgrading to the dynamic DOCX citation workflow, update both the Python package and the Zotero bridge plugin:

python -m pip install -U cli-anything-zotero
zotero-cli app install-plugin
# restart Zotero
zotero-cli app plugin-status
zotero-cli docx doctor

Step 3: Set up your AI client

CLI Mode — No extra setup needed

Just tell your AI assistant the tool is available. It will run zotero-cli --help to discover all commands automatically.

Verify it works:

zotero-cli app ping
zotero-cli js "return Zotero.version"

MCP Mode — Configure your AI client

Claude Code:

claude mcp add zotero --scope user -- zotero-mcp

Claude Desktop / Cursor / LM Studio — add to your MCP config file:

{
  "mcpServers": {
    "zotero": {
      "command": "zotero-mcp"
    }
  }
}

After restarting your AI client, 56 Zotero tools will be available automatically.

Full MCP reference: docs/MCP.md

Troubleshooting

Problem	Solution
Cannot resolve Zotero profile directory	Launch Zotero at least once first
Plugin not appearing	Restart Zotero after installing the .xpi
endpoint_active: false	Plugin failed to load — reinstall via Zotero UI
Windows: pip not recognized	Close and reopen PowerShell after installing Python

---

Usage (CLI Mode)

Search & Browse

zotero-cli item find "machine learning"
zotero-cli item search-fulltext "CRISPR"
zotero-cli collection tree

Import

zotero-cli import doi "10.1038/s41586-024-07871-6" --tag "review"
zotero-cli import pmid "37821702" --collection FMTCPUWN
zotero-cli import file ./refs.ris

Read & Export

zotero-cli item get ITEM_KEY
zotero-cli item export ITEM_KEY --format bibtex
zotero-cli export bib --items KEY1,KEY2 --output refs.bib
zotero-cli item citation ITEM_KEY
zotero-cli item context ITEM_KEY              # LLM-ready context
zotero-cli docx inspect-citations draft.docx  # detect Zotero/EndNote/static citation fields
zotero-cli docx validate-placeholders draft.docx
zotero-cli docx render-citations draft.docx --output draft-static.docx --force
zotero-cli docx doctor
zotero-cli docx insert-citations draft.docx --output draft-zotero.docx --force

For AI-authored DOCX workflows, use Zotero-bound placeholders such as {{zotero:ITEMKEY}} or {{zotero:KEY1,KEY2}}, then choose the final output mode:

• Static citations: docx render-citations replaces placeholders with ordinary citation text and appends a static bibliography. It only needs Zotero's Local API, so it is the easiest path for lightweight reports or one-off documents. Static output cannot be refreshed by the Zotero word processor plugin.
• Dynamic citations: docx insert-citations converts placeholders into real Zotero/LibreOffice fields and creates or updates a refreshable bibliography field. This is the better path for theses, manuscripts, and documents that will be edited or restyled later.

AI agents should ask the user which mode they want when the request is ambiguous. If the user only wants a simple final DOCX and has not installed LibreOffice, prefer static citations. Dynamic DOCX citation insertion is an optional LibreOffice-backed workflow: it requires Zotero Desktop, LibreOffice, the Zotero LibreOffice Add-in, and the CLI Bridge plugin. Run docx doctor when setting up a machine or when an AI agent needs to decide whether the workflow is installed.

Platform support for this optional workflow:

• macOS: tested end-to-end with automatic open, conversion, save, and Word-compatible DOCX output.
• Windows/Linux: the base CLI works, and docx doctor can report missing dependencies. Full automatic LibreOffice open/save for dynamic DOCX citations still needs real Windows/Linux desktop validation; users may need to open or save the LibreOffice document manually until platform automation is verified.

validate-placeholders, zoterify-preflight, and zoterify-probe are diagnostics for setup or failure cases. Add --debug-dir only when you want JSON artifacts for troubleshooting. docx prepare-zotero-import exists only as an experimental debugging command; it is not a supported writing workflow after Zotero 9 + LibreOffice testing. item citation and item bibliography render static previews; they are not refreshable Word/LibreOffice Zotero fields. BIB export is a separate export feature and is not part of the DOCX writing workflow.

Write & Manage

zotero-cli item update KEY --field title="New Title"
zotero-cli item tag KEY --add "important"
zotero-cli item attach KEY ./paper.pdf
zotero-cli item find-pdf KEY
zotero-cli note add KEY --text "My note"
zotero-cli sync

Advanced

zotero-cli item search-annotations "risk"
zotero-cli item annotations KEY
zotero-cli item metrics KEY                   # NIH citation metrics
zotero-cli collection stats COLLECTION_KEY
zotero-cli js "return await Zotero.Items.getAll(1).then(i => i.length)"

Full command reference: docs/COMMANDS.md

---

Optional Features

These require extra services. Everything else works without them.

Semantic Search

Any OpenAI-compatible /v1/embeddings endpoint (Ollama, LM Studio, OpenAI, etc.).

zotero-cli item build-index                            # one-time
zotero-cli item semantic-search "cardiovascular risk"
zotero-cli item similar ITEM_KEY

Variable	Default	Description
ZOTERO_EMBED_API	http://127.0.0.1:8080/v1/embeddings	Embedding API endpoint
ZOTERO_EMBED_MODEL	nomic-embed-text	Model name
ZOTERO_EMBED_KEY	(empty)	API key (if needed)

AI Analysis

export OPENAI_API_KEY=sk-...
zotero-cli item analyze ITEM_KEY --question "What are the main findings?"

---

Upgrading to 0.4.0

Breaking change for MCP users: All MCP tool names have been renamed from mixed conventions to a consistent group_action pattern matching the CLI. If you have agent prompts or configs referencing old tool names, update them:

MCP tool rename table (click to expand)

Old name (0.3.x)	New name (0.4.0)
list_libraries	library_list
list_collections	collection_list
find_collections	collection_find
get_collection	collection_get
create_collection	collection_create
delete_collection	collection_delete
update_collection	collection_rename
find_pdfs_in_collection	collection_find_pdfs
remove_from_collection	collection_remove_item
list_items	item_list
find_items	item_find
get_item	item_get
export_item	item_export
citation_item	item_citation
bibliography_item	item_bibliography
manage_tags	item_tag
update_item_fields	item_update
delete_item	item_delete
find_pdf	item_find_pdf
attach_pdf	item_attach
add_to_collection	item_add_to_collection
get_annotations	item_annotations
search_annotations	item_search_annotations
search_fulltext	item_search_fulltext
semantic_search	item_semantic_search
find_similar	item_similar
build_index	item_build_index
find_duplicates	item_duplicates
get_citation_metrics	item_metrics
analyze_item	item_analyze
get_note	note_get
add_note	note_add
list_tags	tag_list
list_searches	search_list
list_styles	style_list
import_from_doi	import_doi
import_from_pmid	import_pmid
trigger_sync	sync
execute_js	js

New tools in 0.4.0: search_get, search_items, item_move_to_collection

CLI users: No breaking changes. The --help output now shows all commands at once.

---

Related Projects

There are several great tools in the Zotero ecosystem. Each has different strengths depending on your use case:

	cli-anything-zotero	zotero-mcp	zotero-cli-cc	pyzotero-cli
Approach	Local JS Bridge	Web API + MCP	Web API + CLI	Web API + CLI
Best for	Local-first, full control	MCP-native workflows	Agent-driven research	Scripting & automation
Write ops	Local (no API key)	Via Web API	Via Web API	Via Web API
MCP support	56 tools	Yes	45 tools	No
Terminal CLI	Yes	No	Yes	Yes
Zotero JS access	Yes	No	No	No
License	Apache 2.0	MIT	CC BY-NC 4.0	MIT

---

License

Apache 2.0