zotero-fulltext-mcp

Convert a Zotero library's linked PDF attachments to Markdown, build a full-text search index, and expose it to LLM tools (Claude Code, Codex, etc.) through an MCP server — so an assistant can search and read your papers' full text, not just their metadata.

The pipeline is read-only with respect to Zotero: it never writes to your live zotero.sqlite except through the optional, approval-gated zotero-write workflow. Everything else reads Zotero's data and writes only to a separate converted_text output folder that you control.

Prerequisites

• Python 3.11+.

• A Zotero library that uses linked attachments (Zotero.Attachments.linkFromFile, i.e. PDFs stay in a folder you choose rather than Zotero's internal storage/). Stored/managed attachments are not the tested path for this project.

• Windows is the primary, verified platform. macOS/Linux are supported in the code (path resolution, process detection) but not yet verified end-to-end — see "Cross-platform notes" below.

Related MCP server: mcp-zotero

Install

Create a virtual environment outside this repository — a venv contains a machine-specific absolute Python path and compiled dependencies, so keeping it inside a folder you might sync or re-clone elsewhere just produces a broken venv there.

py -3.11 -m venv C:\Users\you\.venvs\zotero_fulltext_mcp
C:\Users\you\.venvs\zotero_fulltext_mcp\Scripts\python.exe -m pip install -U pip
cd C:\path\to\zotero_fulltext_mcp
C:\Users\you\.venvs\zotero_fulltext_mcp\Scripts\python.exe -m pip install -e .[mcp]
$python = C:\Users\you\.venvs\zotero_fulltext_mcp\Scripts\python.exe

macOS/Linux:

python3.11 -m venv ~/.venvs/zotero_fulltext_mcp
~/.venvs/zotero_fulltext_mcp/bin/python -m pip install -U pip
cd /path/to/zotero_fulltext_mcp
~/.venvs/zotero_fulltext_mcp/bin/python -m pip install -e '.[mcp]'
python=~/.venvs/zotero_fulltext_mcp/bin/python

Optional extras: [zotero-write] (write-plan workflow via pyzotero), [marker] (marker-pdf, needed for reconvert-math/reconvert_with_math_ocr, GPU-bound), [test] (pytest, needed to run the test suite — pip install -e .[mcp,test]). A plain pip install -e . with no extras gets you the conversion pipeline and CLI but not the MCP server.

Configure

Copy the template and fill in your own paths:

Copy-Item config.example.json config.json

Edit config.json:

• zotero_root — a working folder for this project's own outputs/reports.

• zotero_data_directory — your local, non-synced Zotero data directory (where zotero.sqlite lives). Never point this at a cloud-synced folder (Dropbox, Nextcloud, OneDrive, etc.) — see docs/architecture.md for why.

• linked_attachments — the folder your Zotero library links PDFs from (baseAttachmentPath in Zotero's settings).

• output_root — where converted Markdown and the search index get written.

If you run this from more than one machine, name each machine's config config.<hostname>.json (Python's platform.node()) instead of hand-maintaining separate files — zotero-pdf-text picks the right one automatically. You can also point at any config file explicitly via the ZOTERO_PDF_TEXT_CONFIG environment variable, which takes priority over both the hostname-based file and the plain config.json fallback. This is the mechanism to use when your config/data live somewhere other than next to this repo checkout.

Build the index

& $python -m zotero_pdf_text ensure-zotero
& $python -m zotero_pdf_text dry-run --config .\config.json
& $python -m zotero_pdf_text convert-new --config .\config.json

convert-new runs mapping, conversion, and index updates together for newly linked verified PDFs, and is the incremental command you'll run repeatedly as you add papers. See docs/operations.md for the full command reference (sampling, manual review of unverified matches, rebuilding vs. appending to the index, etc.) and docs/architecture.md/ docs/data-dictionary.md for how the pipeline and schema fit together.

Smoke-test the index directly:

& $python -m zotero_pdf_text search-fts --db .\converted_text\index\zotero_text_index.sqlite --query "some topic" --limit 3

Register the MCP server

& $python -m zotero_pdf_text install-mcp --config .\config.json

This resolves the current venv's zotero-fulltext-mcp executable, your config, and the FTS database path, then prints a ready-to-paste claude mcp add command and a Codex config.toml block — no manual path editing. Add --apply to also run the Claude Code registration for you (falls back to printing the command if claude isn't on PATH). Codex's config.toml is never edited automatically; paste the printed block in yourself.

Verify:

claude mcp get zotero-fulltext

Expected status: Connected.

Tool contract

The server exposes:

• ensure_zotero_running — check/start the Zotero application.

• search_fulltext(query) — ranked full-text search with bounded snippets.

• get_fulltext_chunk(attachment_key) — full converted text for one paper.

• get_item_context(parent_key | attachment_key) — sidecar metadata (title, authors, DOI, citation key, file paths).

• coverage_report() — how many items are indexed vs. total, including has_math counts.

• export_bibtex_entries_by_key(citation_keys) — Better BibTeX/BibLaTeX entries by citation key (requires Zotero + Better BibTeX running locally).

• reconvert_with_math_ocr(attachment_key) — re-extract one paper with marker-pdf when equations/figures look garbled; blocking, GPU-bound, just-in-time only (see the server's own tool description for the reasoning against bulk use).

Companion MCP server: pairing with the official Zotero MCP

This server is deliberately scoped to offline full-text search over a pre-built index — it works even when Zotero and its connector are closed, and it never talks to Zotero's live API. It does not expose collections, tags, notes, or other live metadata.

For that, install the official Zotero MCP server alongside this one — the two are meant to be used together, not merged:

• This server (zotero-fulltext-mcp): full-text search and retrieval from the sidecar index.

• Official Zotero MCP: live collections, tags, notes, child attachments, Zotero URIs. Requires Zotero running.

If the official server's connector is down, zotero-fulltext-mcp tools remain fully functional since they never depend on it.

Optional: write-side workflows (debug-bridge, ZotMoov)

import-doi, find-pdf, and link-pdf (CLI commands, also documented in the MCP server's own instructions for use mid-conversation) drive Zotero's UI-equivalent actions through the debug-bridge plugin — see docs/debug-bridge-setup.md for setup, including generating your own bridge token. link-pdf additionally uses the ZotMoov plugin to relocate linked files into your managed linked_attachments folder. Both are optional; core search/conversion works without them.

Cross-platform notes

• Zotero executable auto-detection (--zotero-exe default) and process-name checks (ensure_zotero_running) are Windows-verified. macOS (/Applications/Zotero.app/...) and Linux (/usr/lib/zotero/zotero) defaults are best-effort, untested guesses — pass --zotero-exe explicitly if the default doesn't match your install.

• Dependencies (pyproject.toml) are minimum-pinned (>=) only, with no lockfile and no tested upper bounds.

License

MIT — see LICENSE.