Zotero Import Workflow

This skill teaches the correct tool-calling sequence for importing papers into Zotero via the zotero_* MCP tools. All Zotero tools are local-only and require Zotero to be running with the Local API enabled (Settings → Advanced → "Allow other applications on this computer to communicate with Zotero").

Writes need the zotero-inspire plugin. Zotero's native Local API is read-only — every POST/DELETE returns 400 "Endpoint does not support method". File attachment (zotero_add + file_path) and deletion (zotero_delete) are performed through the zotero-inspire plugin (≥ 3.0.3), which registers an authenticated POST /connector/zinspireWrite endpoint. The MCP reads the endpoint token from the Zotero profile prefs.js automatically; override with the ZOTERO_WRITE_TOKEN env var. Item/note creation still works without the plugin (via the Connector). If the plugin is missing, item writes succeed and the attachment is reported as file_attached:false with an attach_error (never silently dropped).

Core Pattern: Two-Step Add/Confirm

Every Zotero write operation follows a preview-then-confirm pattern:

zotero_add { source: {...}, ... }     # Step 1: Preview — returns confirm_token
    |
zotero_confirm { confirm_token: "..." } # Step 2: Execute — creates/updates the item

The zotero_add call resolves metadata, checks for duplicates, and returns a confirm_token (valid for 10 minutes). The agent should present the preview to the user, then call zotero_confirm to execute.

Source Types

INSPIRE (HEP papers)

{ "source": { "type": "inspire", "recid": "1234567" } }

DOI (HEP and non-HEP)

{ "source": { "type": "doi", "doi": "10.1103/PhysRevD.110.030001" } }

• HEP DOIs are resolved via INSPIRE first (richer metadata with arXiv IDs, collaborations).
• Non-HEP DOIs automatically fall back to CrossRef (e.g., 10.1063/1.864977).

arXiv

{ "source": { "type": "arxiv", "arxiv_id": "2301.12345" } }

Manual item

{
  "source": {
    "type": "item",
    "item": {
      "itemType": "journalArticle",
      "title": "...",
      "creators": [{ "creatorType": "author", "lastName": "...", "firstName": "..." }],
      "DOI": "10.xxx/yyy",
      "date": "2024"
    }
  }
}

Collection Selection

Option A: Use Zotero UI selection (default)

If collection_keys is omitted, the tool writes to whichever collection is currently selected in Zotero's left sidebar. To check:

zotero_get_selected_collection {}

Before any write, verify that the selected collection is intended for this task. Do not write to personal, reserved, archival, or project-excluded collections just because they happen to be selected in the Zotero UI. If the collection name suggests it is reserved, or if the user has named a collection that must not receive imported papers, stop and ask for an explicit collection key or a different UI selection. A read-only lookup does not require collection confirmation; a write does.

Option B: Explicit collection key

{ "source": {...}, "collection_keys": ["ABCD1234"] }

Library root

By default, writing to the library root (no collection) is rejected. Override with:

{ "source": {...}, "allow_library_root": true }

Existing Zotero Items

When the user provides a Zotero select URI such as zotero://select/library/items/ABCD1234, prefer a read-only inspection of that existing item and its attachments before attempting an import. Use the item key with zotero_local, zotero_find_items, zotero_search_items, or zotero_export_items as appropriate. Do not create a duplicate item from DOI/arXiv metadata unless the user explicitly asks to import another copy or the existing item is confirmed unsuitable.

File Attachment

To attach a local file (e.g., a downloaded PDF) to the created item:

{
  "source": { "type": "doi", "doi": "10.xxx/yyy" },
  "file_path": "/absolute/path/to/paper.pdf",
  "attach_mode": "import"
}

• The path must be absolute and the file must exist.
• Attachment is performed via the zotero-inspire write endpoint (see the note at the top); the native Local API cannot attach files.
• attach_mode (default import):
  • import — copies the file into Zotero storage. Never mutates the source file and is robust to file-management plugins. Recommended default.
  • link — references the file in place (Zotero stores a path, not a copy). ⚠️ File-management plugins (e.g. Attanger, ZotFile) auto-rename/move linked source files based on the parent item's metadata — using link may rename your original file on disk. Prefer import unless you specifically manage linked files yourself.
• On success the confirm result reports file_attached: true, attach_mode, and attachment_key. On failure it reports file_attached: false and a structured attach_error (the item write still succeeds).
• Supported formats: PDF, EPUB, HTML, DJVU, DOC/DOCX, and others.

Deduplication

The dedupe parameter controls behavior when the item already exists in Zotero:

Dedup matches on DOI, arXiv ID, and INSPIRE recid.

Tags and Notes

{
  "source": { "type": "doi", "doi": "10.xxx/yyy" },
  "tags": ["hep-ph", "review"],
  "note": "Key reference for section 3"
}

Complete Example: Import a non-HEP paper with PDF

# 1. Check which collection is selected
zotero_get_selected_collection {}

# 2. Preview the import
zotero_add {
  "source": { "type": "doi", "doi": "10.1063/1.864977" },
  "tags": ["plasma-physics"],
  "file_path": "/path/to/Downloads/hasegawa1983.pdf"
}
# -> Returns confirm_token + preview

# 3. Confirm
zotero_confirm { "confirm_token": "<token from step 2>" }
# -> Item created with PDF attached

Integration with sci-hub

When a paper has been downloaded via sci-hub, the manifest contains the DOI and file path. Use these directly:

zotero_add {
  "source": { "type": "doi", "doi": "<DOI from manifest>" },
  "file_path": "<downloaded PDF path>"
}

Common Pitfalls

1. Token expiry: Confirm tokens expire after 10 minutes. If expired, re-run zotero_add.
2. Collection not selected: If Zotero has no collection selected and no collection_keys given, the call fails. Check with zotero_get_selected_collection first.
3. Native Local API is read-only: The native Local API cannot create attachments or delete items (400 "Endpoint does not support method"). File attachment and zotero_delete route through the zotero-inspire plugin endpoint (see the note at the top). If it is unavailable, item/note creation still works; attachment is reported as file_attached:false + attach_error rather than silently dropped.
4. link attach mutates source files: With attach_mode:"link", file-management plugins (Attanger/ZotFile) may rename or move your source file. Use the default attach_mode:"import".
5. Large metadata: The item source type has a 200KB JSON limit.

Deleting Items

Delete follows the same preview → confirm pattern (destructive, so it is gated):

# 1. Preview — resolves each key's title/type; returns confirm_token
zotero_delete { "item_keys": ["ABCD1234", "EFGH5678"], "mode": "trash" }

# 2. Execute
zotero_confirm { "confirm_token": "<token from step 1>" }

• mode: "trash" (default) moves items to the Zotero trash — recoverable.
• mode: "erase" permanently deletes them — not recoverable; the preview warns accordingly.
• Missing keys are flagged in the preview and skipped on execute; per-item results are returned (succeeded/skipped/failed).
• Deleting a top-level item removes its child attachments/notes too.

Tool Reference