Zotero

--zotero adds the papers of a search, similar or get to your Zotero library, optionally in a named collection. mosaic talks to Zotero desktop on your machine, or to the Zotero web API when you configure a key.

Usage

mosaic search "hall thruster particle-in-cell" --zotero
mosaic search "hall thruster" --zotero --zotero-collection "Hall thrusters"
mosaic similar 10.1063/1.4972269 --zotero --zotero-collection "Related work"
mosaic get --from refs.bib --zotero --zotero-collection "Imported"
mosaic search "hall thruster" --download --zotero      # also link the PDFs (local API only)

• --zotero-collection NAME puts the items in that collection, created on first use (top level).
• --zotero-local uses Zotero desktop even when a web API key is configured.

The two APIs

Configuration	API used
no zotero.api_key	local: Zotero desktop at http://localhost:23119, which must be running
zotero.api_key set	web: https://api.zotero.org/users/<user_id>
zotero.api_key set and --zotero-local	local

To use the web API, create a key with write access at zotero.org/settings/keys, then:

mosaic config --zotero-key YOUR_KEY

mosaic asks Zotero for the user ID that owns the key and saves it as zotero.user_id.

How it works

Each paper becomes a Zotero item: preprint for arXiv, bioRxiv and medRxiv, journalArticle otherwise. The item gets the title, the authors (split into first and last name: "Last, First" at the comma, "First Last" at the last space), the year, the abstract, the DOI, the journal and a URL (the paper's page, or https://doi.org/<doi>). Items are sent 50 at a time, Zotero's limit per request.

With --download, each downloaded PDF is linked to its item as a linked_file attachment: Zotero stores the absolute path, and the file stays in your mosaic library. The web API gets the metadata only; mosaic does not upload files.

mosaic does not look for duplicates in Zotero: running the same export twice adds the items twice.

Configuration

[zotero]
api_key = ""   # web API key; empty means the local API
user_id = 0    # filled in by mosaic config --zotero-key

Troubleshooting

• "Zotero desktop is not running": start Zotero, or configure a web API key.
• "Zotero web API not reachable. Check your API key.": the key was rejected or has no write access; mosaic config --show prints the key mosaic uses.
• A collection is missing on another device: it exists on the server only after Zotero syncs.

See also: tutorial chapter 6, export recipes, mosaic search, mosaic get.