Metadata-Version: 2.4
Name: cli-anything-zotero
Version: 1.3.0
Summary: Zotero CLI and Python package for AI-assisted local library workflows.
Home-page: https://github.com/PiaoyangGuohai1/cli-anything-zotero
Author: cli-anything contributors
Author-email: 
License: Apache-2.0
Project-URL: Issues, https://github.com/PiaoyangGuohai1/cli-anything-zotero/issues
Project-URL: Documentation, https://github.com/PiaoyangGuohai1/cli-anything-zotero#installation
Project-URL: Changelog, https://github.com/PiaoyangGuohai1/cli-anything-zotero/releases
Keywords: zotero,cli,reference-manager,bibliography,ai-agents,ai,llm,academic,research-tools,bibtex,citation-manager,claude-code,cursor,python
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Text Processing :: General
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click>=8.0.0
Requires-Dist: prompt-toolkit>=3.0.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
Dynamic: author
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: project-url
Dynamic: provides-extra
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

# cli-anything-zotero

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**Let AI manage your Zotero library.**

[中文文档](docs/README_zh.md) | English | [Roadmap](docs/ROADMAP.md) | [TODO](docs/TODO.md) | [Commands](docs/COMMANDS.md)

> **MCP legacy notice:** `v0.9.5` is the final release with the `zotero-mcp` command and `cli-anything-zotero[mcp]` extra. New releases are CLI/SDK-first. Existing MCP users should pin `pip install "cli-anything-zotero[mcp]==0.9.5"` or use the `legacy/mcp` branch.

---

## 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](#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](https://github.com/HKUDS/CLI-Anything) by [HKUDS](https://github.com/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.

**Prerequisite:** the **Zotero desktop app must be running**. This is intentional — we automate the local client (Connector, Local API, CLI Bridge), not a cloud-only API substitute.

**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
- **DOCX citations** — turn `{{zotero:ITEMKEY}}` placeholders into static text or refreshable Zotero fields (see below)
- **Advanced** — execute arbitrary Zotero JS, semantic search with local embeddings, AI analysis

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

### DOCX citations: static vs dynamic

AI-authored drafts should use placeholders such as `{{zotero:ITEMKEY}}` or
`{{zotero:KEY1,KEY2}}`, then convert them with the `docx` commands.

| Mode | Command | Output | Extra software |
|------|---------|--------|----------------|
| **Static** (default for simple finals) | `docx render-citations` or `docx cite --mode static` | Plain-text citations + static bibliography | **No.** Only `pip install` + JS Bridge + running Zotero (Local API). |
| **Dynamic** (refreshable fields) | `docx insert-citations` or `docx cite --mode dynamic` | Real Zotero fields in Word/LibreOffice + refreshable bibliography | **Yes — extra stack required** (see table below). |
| **Auto** | `docx cite --mode auto` | Picks dynamic if the stack is ready, else static | Same as dynamic when available |

**Dynamic mode is optional and is not installed by `pip` alone.** You also need:

| Requirement | Why |
|-------------|-----|
| Zotero Desktop (running) | Source library + word-processor integration |
| CLI Bridge plugin (`zotero-cli app install-plugin`) | Local privileged bridge used by conversion |
| [LibreOffice](https://www.libreoffice.org/) | Opens/saves the DOCX during field insertion |
| [Zotero LibreOffice plugin](https://www.zotero.org/support/word_processor_plugin_installation) | Creates refreshable citation/bibliography fields |

Check the machine before relying on dynamic mode:

```bash
zotero-cli --json docx doctor
```

If `doctor` reports missing LibreOffice / the LO add-in / Bridge, use **static**
mode (or install the missing pieces). On macOS the full dynamic path is tested
end-to-end; on Windows/Linux, `doctor` works but auto open/save may still need
manual LibreOffice interaction until verified.

One-shot when you are unsure:

```bash
zotero-cli --json docx cite draft.docx --output draft-cited.docx --mode auto --force
```

---

## CLI-First Usage

`cli-anything-zotero` is now maintained as a CLI/SDK-first tool. The primary interface is the `zotero-cli` shell command, which works well for Codex, Claude Code, Cursor, shell scripts, and other agents that can run terminal commands.

For legacy MCP users, install the frozen MCP release explicitly:

```bash
pip install "cli-anything-zotero[mcp]==0.9.5"
```

The `legacy/mcp` branch and the `v0.9.5` release remain available, but MCP receives no new feature maintenance after that line.

---

## Installation

**Prerequisites:** Python 3.10+, Zotero 7+ (running).

### Step 1: Install the package

```bash
pip install cli-anything-zotero
```

This installs the `zotero-cli` command. The old `cli-anything-zotero` command remains as a compatibility alias.

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

```bash
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.

> **Upgrading to Zotero 10:** bridge versions up to 1.2.1 only declare support for Zotero 7–9, so Zotero 10 disables them. Upgrade to 1.2.2 or later and repeat the manual install above once; automatic upgrades work again afterwards.

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

```bash
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

No client-specific setup is required. Tell your AI assistant that `zotero-cli` is available; it can run `zotero-cli --help` to discover commands.

Verify it works:

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

### 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 |
| `No endpoint found` after a Zotero major upgrade | Zotero disabled the bridge as incompatible; `zotero-cli app doctor` reports `app_disabled`. Upgrade cli-anything-zotero, run `zotero-cli app install-plugin`, then install the printed `.xpi` once by hand (**Tools → Plugins → gear → Install Plugin From File...**) and restart Zotero. Automatic upgrade cannot work here because it needs the live bridge |
| Windows: `pip` not recognized | Close and reopen PowerShell after installing Python |

---

## Usage (CLI Mode)

**Search & Browse**
```bash
zotero-cli item find "machine learning"
zotero-cli item search-fulltext "CRISPR"
zotero-cli collection tree
```

**Import**
```bash
# Preferred agent ingest
zotero-cli --json add doi "10.1038/s41586-024-07871-6" --tag "review" --fetch-pdf
zotero-cli --json add arxiv 2602.02093 --collection COLLECTION_KEY
zotero-cli --json add file ./paper.pdf
zotero-cli --json add bibtex ./refs.bib --collection COLLECTION_KEY

# Lower-level import still available
zotero-cli import doi "10.1038/s41586-024-07871-6" --no-translator
zotero-cli --json item fetch-pdf ITEM_KEY --sources zotero,unpaywall,arxiv
zotero-cli --json collection fetch-pdfs COLLECTION_KEY --limit 20 --jsonl-progress

# DOCX one-shot citations
zotero-cli --json docx cite draft.docx --output draft-cited.docx --mode auto --force

# Audit recent write ops
zotero-cli --json audit tail --limit 20
```

**Library hygiene**
```bash
# Find duplicate clusters. Matches on DOI, and on normalized title confirmed by
# a shared creator surname and an agreeing year. Each copy reports its
# attachment counts and its Better BibTeX citation key.
zotero-cli --json item duplicates --limit 20
zotero-cli --json item duplicates --year-tolerance 0   # exact year agreement only
zotero-cli --json item merge KEEP OTHER1               # dry-run; --confirm applies
```

Clusters whose copies carry more than one *pinned* citation key are flagged with
`citation_key_conflict: true`. Merging those silently orphans whichever key your
manuscript already cites, so resolve the key before merging.

**Deleting things**
```bash
zotero-cli item delete ITEM_KEY --confirm     # -> trash. Reversible.
zotero-cli item restore ITEM_KEY              # <- back out of the trash
zotero-cli collection delete COLLECTION_KEY --confirm   # with its subcollections
zotero-cli collection restore COLLECTION_KEY            # brings the subcollections back too
```

`delete` moves things to the Zotero trash, exactly as the Delete key does in the
Zotero UI. Trashed items keep their keys and stay recoverable until you empty the
trash, which the CLI never does for you. `collection delete --delete-items` also
trashes the items of the collection and of every subcollection; `collection restore`
leaves those items in the trash, as the Zotero UI does, so restore them with
`item restore`.

Permanent erasure is a separate path and bypasses the trash entirely:

```bash
zotero-cli item delete ITEM_KEY --permanent --yes-erase
```

`--permanent` prompts before erasing **even when `--confirm` is given**; only the
explicit `--yes-erase` suppresses that prompt. `--confirm` is the flag people
paste into scripts out of habit, so it is deliberately not the flag that can
destroy anything.

**Read & Export**
```bash
zotero-cli item get ITEM_KEY
zotero-cli item find "keyword" --scope fields
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 (details and **extra software requirements** are under
[DOCX citations: static vs dynamic](#docx-citations-static-vs-dynamic)):

- Static citations: `docx render-citations` replaces placeholders with ordinary citation text and appends a static bibliography. Easiest path; **no LibreOffice**. 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. Needs **LibreOffice + Zotero LO add-in + Bridge** on top of Zotero Desktop.

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. Always run `docx doctor` before promising
dynamic conversion.

Recommended AI protocol:

1. `zotero-cli --json docx validate-placeholders <input.docx>`
2. If the user wants editable references / refresh support:
   - `zotero-cli --json docx doctor`
   - `zotero-cli --json docx insert-citations <input.docx> --output <final.docx> --force`
   - If conversion fails, report the failing layer from `doctor` and ask the user for next steps.
3. If the user wants static output or dynamic is unavailable:
   - `zotero-cli --json docx render-citations <input.docx> --output <final.docx> --force`

Keep these files only as handoff artifacts:
- Placeholder draft (`<input.docx>`)
- Final converted draft (`<final.docx>`)
- No intermediate DOCX should be exposed unless `--debug-dir` is explicitly requested.

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.
`docx insert-citations` and `docx render-citations` are the two supported outputs
for AI-authored citation insertion.
`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**
```bash
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**
```bash
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](docs/COMMANDS.md)**

---

## Optional Features

These require extra services. Everything else works without them.

### Semantic Search

Any OpenAI-compatible `/v1/embeddings` endpoint ([Ollama](https://ollama.com), [LM Studio](https://lmstudio.ai), OpenAI, etc.).

```bash
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

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

---

## Legacy MCP Users

MCP support is frozen at `v0.9.5`. To keep using the previous MCP server, install:

```bash
pip install "cli-anything-zotero[mcp]==0.9.5"
```

You can also use the `legacy/mcp` branch for source installs. Starting with `v1.0.0`, the maintained package installs only CLI/SDK surfaces and no longer provides the `zotero-mcp` command.

## 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](https://github.com/54yyyu/zotero-mcp) | [zotero-cli-cc](https://github.com/Agents365-ai/zotero-cli-cc) | [pyzotero-cli](https://github.com/chriscarrollsmith/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** | Legacy via v0.9.5 | 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](LICENSE)
