Zotero

Zotero

Windows Runtime Commands

On native Windows, use the managed Windows runner and the native runtime command target. Set $runtime to the installed runtime root. Multi-agent installs usually use %LOCALAPPDATA%\ai-agents-skills\runtime. Then run:

$runtime = if ($env:AAS_RUNTIME_ROOT) { $env:AAS_RUNTIME_ROOT } else { "$env:LOCALAPPDATA\ai-agents-skills\runtime" }
& "$runtime\run_skill.ps1" "skills/zotero/zot.py" <args>

POSIX examples below use run_skill.sh and .sh command targets; use the Windows command target above on native Windows.

This uses the managed ai-agents-skills runtime copy of the Zotero workflow.

Routing rule

Use this skill first for any paper request involving:

• "send me"
• "get me"
• "retrieve"
• "find"
• "fetch"
• "share"
• "add to Zotero"
• "search my library"
• "my papers"
• "my collections"

Prefer this over getscipapers-requester whenever the request involves the user's library.

Base path

All live commands come from:

• $AAS_RUNTIME_WORKSPACE/skills/zotero/

Use the managed runtime runner rather than invoking run_zot.sh directly. The runner sets the vendored workspace path, PYTHONPATH, secrets, and workspace-local binaries for the migrated workflow.

Shared runner:

• bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh"

Local Library Profile Gate

Do not assume Zotero settings, database, storage, Translation Server, or WebDAV paths. Before library-changing work, run or rely on a profile-aware audit from the canonical installer:

cd ~/ai-agents-skills && make library-profile-audit ARGS="--profile library --json"

The audit is read-only. Discovery does not make a path authoritative. A Zotero database/storage path becomes mutation-eligible only after validation and explicit profile selection.

Supported system profiles:

• linux-local
• windows-mounted for Linux-side inspection of /windows/Users/...
• windows-native for native Windows execution

Mounted Windows and cloud-backed SQLite databases are read-only by default from Linux. If no local Zotero database is found, mark the profile local-db-missing; do not create a database and do not use runtime caches as authoritative state. Remote-only Zotero API/WebDAV workflows may continue only when credentials are configured and the result is labeled remote-only.

Default Zotero mutation must use this order:

1. selected local DB/storage diagnostic preflight
2. Translation Server metadata resolution when metadata is needed
3. Zotero API mutation bound to explicit library scope
4. WebDAV sync for attachment-affecting changes
5. API/WebDAV/local diagnostic verification

Direct zotero.sqlite writes are expert repair only. They require Zotero to be closed, DB/WAL/SHM/storage backups, a copied working DB, integrity checks before and after, a transaction journal, and explicit confirmation.

Storage checks must report local storage/, linked files, API attachment records, and WebDAV zips separately.

Read-only local access is allowed when it is labeled correctly:

• normal search uses the Zotero API first and remains the source of truth
• search --local-db may inspect discovered zotero.sqlite candidates in read-only mode for offline/diagnostic use
• local DB results are degraded when SQLite integrity checks are not clean and must not be used as the only evidence that Zotero lacks an item
• get may return a PDF from local Zotero storage/ before falling back to WebDAV, because this is read-only and uses the API attachment key
• use get --no-local-storage when WebDAV retrieval needs to be forced

Translation Server

The local Translation Server should be available at:

• http://localhost:1969

Linux startup uses architecture-specific, immutable OCI references:

• arm64: zotero/translation-server@sha256:a80abfaaab0d84c8cc4b0ef79e4fde94b391420ee3a1e69d680fc89a18bff115
• amd64: ghcr.io/hoanganhduc/translation-server@sha256:6bb209778e0403d81285404fc9ca5bd142f91e090d14a5541ac33018531c1329
• fork repo for the amd64 image: https://github.com/hoanganhduc/translation-server
• container: zotero-translation-server
• port mapping: 1969:1969
• restart policy: unless-stopped

Do not replace these with tags such as latest. The startup helper accepts a ZOTERO_TS_IMAGE override only when it is an untagged image name followed by an exact lowercase @sha256: digest. Its runtime directory must contain a regular, non-symlink docker-compose.yml with exactly one image declaration:

image: ${ZOTERO_TS_IMAGE:?ZOTERO_TS_IMAGE must be set}

The helper rejects a missing Compose file, static/tagged/defaulted image values, extra image declarations, and Compose builds before starting Docker. The Compose file is supplied by the system-restoration layer rather than this portable runtime manifest. The helper creates no cron or systemd registration.

Status checks:

docker ps --filter name=zotero-translation-server --format '{{.Names}} {{.Image}} {{.Status}} {{.Ports}}'

curl -s -o /dev/null -w '%{http_code}\n' http://localhost:1969/

404 from the root endpoint is acceptable. For a functional metadata smoke test, POST a DOI or URL to /web and confirm Zotero JSON is returned.

curl -s -X POST -H 'Content-Type: text/plain' --data 'https://doi.org/10.1038/nphys1170' http://localhost:1969/web

When starting or repairing the local server, prefer the runtime helper:

bash $AAS_RUNTIME_WORKSPACE/skills/zotero/scripts/start-translation-server.sh

Then run doctor before metadata-dependent add/update workflows. A reachable Translation Server is preferred. If it is unreachable, DOI/arXiv/ISBN metadata may still resolve through the direct fallback when runtime dependencies are installed, and generic URL metadata may use the configured WSL helper path. Treat other failed doctor checks as blockers unless the user explicitly asks for a degraded diagnostic path:

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh doctor

Core commands

Use functions.exec_command.

Common patterns:

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh --json get "<query>"

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh --json get --link "<query>"

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh --json get "<query>" --index 0

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh add "<DOI or arXiv or URL>" --collection "<name>"

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh add "/path/to/file.ext" --collection "<name>"

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh update <key> --item-type manuscript

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh update <key> --attach-file "/path/to/file.pdf"

cd "$AAS_RUNTIME_WORKSPACE" && PYTHONPATH="$AAS_RUNTIME_WORKSPACE/.local:${PYTHONPATH:-}" python3 skills/zotero/zot.py search "<query>" --json

cd "$AAS_RUNTIME_WORKSPACE" && PYTHONPATH="$AAS_RUNTIME_WORKSPACE/.local:${PYTHONPATH:-}" python3 skills/zotero/zot.py search --local-db "<query>" --json

bash "${AAS_RUNTIME_ROOT:-$HOME/.local/share/ai-agents-skills/runtime}/run_skill.sh" skills/zotero/run_zot.sh --json get "<query>" --no-local-storage

cd "$AAS_RUNTIME_WORKSPACE" && PYTHONPATH="$AAS_RUNTIME_WORKSPACE/.local:${PYTHONPATH:-}" python3 skills/zotero/zot.py list-collections --tree --json

cd "$AAS_RUNTIME_WORKSPACE" && PYTHONPATH="$AAS_RUNTIME_WORKSPACE/.local:${PYTHONPATH:-}" python3 skills/zotero/zot.py notes <key>

cd "$AAS_RUNTIME_WORKSPACE" && PYTHONPATH="$AAS_RUNTIME_WORKSPACE/.local:${PYTHONPATH:-}" python3 skills/zotero/zot.py doctor

cd "$AAS_RUNTIME_WORKSPACE" && PYTHONPATH="$AAS_RUNTIME_WORKSPACE/.local:${PYTHONPATH:-}" python3 skills/zotero/zot.py sync-cache

Most important behaviors imported from OpenClaw

• Always search Zotero first before trying other retrieval paths.
• For chapters, @incollection entries, proceedings articles, and older no-DOI sources, search at both levels before reporting an absence: the chapter title/author and the parent container title/editor/ISBN. Clearly distinguish "standalone chapter item not found" from "parent book or proceedings item found."
• For review tasks that need a paper/book, if Zotero does not have it, route next to calibre before any online retrieval.
• If get returns multiple results, show the numbered candidates and ask the user to pick.
• Do not guess the intended paper when results are ambiguous.
• Prefer the default get local-storage check before WebDAV. Treat it as a read-only file lookup, not a DB mutation.
• Use search --local-db only as an explicit offline/diagnostic fallback; label malformed SQLite results as degraded.
• For link sharing, use the Zotero workflow rather than ad hoc file browsing.
• Use --index only after showing the user the numbered candidate list.
• For library-mutating or outward-facing actions (add, update, attachment changes, trash/delete/remove, sync-affecting operations, send, or share), run the relevant dry-run/preview/search first when available, state the exact item/library/collection/channel to be affected, and get explicit confirmation unless the user's latest request already approved that exact action.

Add-paper rules imported from the bot

• Preprints and arXiv papers should end up as manuscript, not preprint.
• Different versions of the same paper are intentionally allowed unless they are DOI-identical duplicates.
• Do not silently add papers without collection assignment unless the user explicitly says to skip that.
• add accepts DOI, arXiv ID, URL, ISBN, or a local file path; keep the collection-assignment workflow in front unless the user explicitly opts out.

Collection workflow

If the user asks to add a paper and does not specify a collection:

1. List the collection tree.
2. Suggest likely collections.
3. Ask the user to choose one or more.
4. Then run the add command.

High-value maintenance actions

• doctor for end-to-end health checks
• sync-cache before heavy library inspection if the cache may be stale
• notes <key> when the user wants child-note context for an item
• update <key> --attach-file ... when a retrieved or local file should be attached to an existing Zotero item

Fallback rule

Only route to getscipapers-requester if:

• the paper is not in Zotero; for chapters and @incollection entries, this means both the chapter-level query and the parent book/proceedings query failed or cannot provide the needed text
• the Calibre library also does not satisfy the request when the task is a review that needs the document
• the user explicitly says not to check/use the library, or confirms external retrieval after the library-first result is reported
• or the Zotero workflow clearly cannot satisfy the request