Zotero from the shell

zotero-cli reaches a Zotero library directly. Prefer it over the Zotero MCP server when you have shell access: the MCP server's tool schemas cost ~14k tokens of context on every request whether or not you use them, while this costs only what you actually run.

Check it is set up before the first real call:

zotero-cli config          # prints the resolved Zotero settings

If that fails, Zotero is not reachable. Local mode needs the Zotero desktop app running with its local API enabled; web mode needs ZOTERO_API_KEY and ZOTERO_LIBRARY_ID. Say so rather than guessing at library contents.

Always pass --json when you will read the output

Default output is markdown for humans. --json gives you one object per invocation with a stable shape, so you never parse prose:

{"ok": true, "command": "search", "schema": 1, "data": {...}}
{"ok": false, "command": "search", "schema": 1, "error": {"message": "...", "code": "..."}}

Both go to stdout; [INFO]/[WARN] diagnostics go to stderr. Check ok before using data. Run zotero-cli --json-schema for the full contract.

The core loop

Almost every task is: find keys → act on keys. Item keys are 8 characters and are the currency of every command.

# 1. find - use --detail keys_only to keep the result small while browsing
zotero-cli --json search "attention mechanisms" --limit 10 --detail keys_only

# 2. act - metadata, full text, or a page range
zotero-cli --json get metadata ABCD1234
zotero-cli --json get fulltext ABCD1234
zotero-cli --json read ABCD1234 --start-page 3 --end-page 8

Pipe keys straight into the next call:

zotero-cli --json search "diffusion models" --limit 5 --detail keys_only \
  | jq -r '.data.items[].key' \
  | while read -r key; do zotero-cli --json get metadata "$key"; done

Choosing a search mode

Mode	Use it for	Command
items (default)	a title, author or phrase you know	search "Vaswani attention"
semantic	a topic or idea, no exact wording	search --mode semantic "why transformers scale"
tag	items you filed under a tag	search --mode tag "to-read,important"
advanced	structured field conditions	search --mode advanced --conditions '[...]'
citekey	a BibTeX citation key	search --mode citekey smith2020
notes	text inside your notes, not item fields	search --mode notes "research question"

semantic needs the search index built (zotero-cli db status to check, zotero-cli db update to build). If it is empty, fall back to items and say why rather than reporting no results.

Every search covers one library — the active one. When you don't know which library holds something, or a search comes up empty and the item might live in a group library, add --all-libraries:

zotero-cli search "Cladder-Micus" --all-libraries

Each result is then labelled **Library:** <name>. It needs the SQLite backend, the default in local mode, and errors clearly if it is not in use, so try it once and fall back to per-library searches if it is refused. Tag filters work with it; --collection does not, because a collection lives inside one library.

Reading efficiently

get fulltext on a book-length PDF returns a great deal of text. When you need one section, use the outline to find it and read only those pages. To locate a passage by its words, --find returns the matching pages with short snippets instead of the pages themselves:

zotero-cli --json outline ABCD1234
zotero-cli --json read ABCD1234 --find "robustness check"
zotero-cli --json read ABCD1234 --start-page 42 --end-page 55

For "what does my library say about X", prefer search --mode semantic followed by targeted get metadata over reading whole papers.

Paging

Listings cap at --limit. When more exists, the response says so and names the next offset:

zotero-cli --json get collection-items QS7TQPPA --limit 100 --offset 100

Keep going until data.count is less than --limit.

Writing

Write commands report what they did as text under data.text.

zotero-cli add doi 10.1038/s41586-021-03819-2 -c "Reading List"
zotero-cli edit ABCD1234 --title "Corrected Title" --add-tags reviewed
zotero-cli notes create --item-key ABCD1234 --text "Key finding: ..."
zotero-cli batch --item-keys A1B2C3D4,E5F6G7H8 --add-tags screened

Note text is Markdown, converted to Zotero's note format: headings, lists, tables, code, links (zotero:// ones stay clickable), $math$ and $$display$$, plus <u>, <s>, <sub>, <sup>, <mark> and <span style="color: red"> or background-color (red, orange, yellow, green, purple, magenta, blue, gray, or #hex). Pipe long text with --text -. HTML starting with <p>/<div> is kept to the note editor's tags, so a note read with notes list --raw-html, edited and written back with notes update keeps its citations and images; notes update --append adds to the end.

add is idempotent by default: re-running files the existing item into the named collection rather than creating a duplicate. Use --if-exists skip to never touch an existing item.

Before a destructive change (delete, duplicates merge, a batch over many items), confirm with the user and show what will be affected. delete item refuses notes unless --allow-note is passed.

Reading and annotating a paper

zotero-cli get children ITEM_KEY                          # the PDF's attachment key
zotero-cli read ITEM_KEY --start-page 1 --end-page 99     # end page clamps to the last page
zotero-cli path ATTACHMENT_KEY                            # the PDF file on disk
zotero-cli open ITEM_KEY --page 7                         # show that page in the Zotero reader
zotero-cli open --annotation ANNOTATION_KEY               # jump to one annotation and select it

When the user is reading along in Zotero and asks where something is, point the reader at it with open rather than only quoting a page number. annotations create --open does both in one step.

Extracted text is reliable for prose and unreliable for math, figures and tables: symbols drop out and table cells run together. read flags each page where that happens ("Garbled in this text: Equation (1), Table 2"). For those pages, look at the page itself if you can view images:

zotero-cli read ITEM_KEY --start-page 4 --format image                         # PNG per page, up to 10
zotero-cli read ITEM_KEY --start-page 4 --format image --rect 0.35,0.49,0.3,0.05   # zoom into one region

To annotate, plan everything, check it, then write it in one run:

1. zotero-cli --json layout ATTACHMENT_KEY lists figure, table and equation boxes with their captions and a paste-ready rect_arg.
2. Write one JSON object per line: {"page": 4, "text": "exact words", "comment": "...", "color": "yellow"} for a highlight, or {"page": 3, "rect": "x,y,w,h", "comment": "..."} for a box, or {"page": 1, "note": "x,y", "comment": "..."} for a sticky note centered on a point (its text is the comment). Copy highlight text exactly from read; it is searched for on that page and two pages either side.
3. zotero-cli annotations batch --attachment-key ATTACHMENT_KEY --file plan.jsonl --dry-run shows the words each highlight would cover. Fix every miss.
4. Run it again without --dry-run. Anything that did not land is listed under data.results with ok: false, and the exit code is 1.

Colors take Zotero's names: yellow, red, green, blue, purple, magenta, orange, gray. Three or four colors with fixed meanings read better than eight; say what they mean in a note on the item.

Writes in local mode need a one-time zotero-mcp authorize-local (Zotero 10 or newer) or web API credentials. A write refused for that reason says so.

When something looks wrong

• Empty search results: check zotero-cli config and, for semantic mode, zotero-cli db status. Do not report "you have no papers on X" until you know the library is actually reachable and indexed.
• ok: false: read error.message. It names the cause.
• A partial-results note on a search means the scan was cut short, not that nothing else matched. Narrow the query and re-run.
• An item marked "deleted": true is in the trash. Do not treat it as part of the live library.

Full command reference

reference.md in this skill directory lists every command and flag. Read it when you need something not covered above. zotero-cli <command> --help also works for any single command.