Noah’s Zotero Setup

A step-by-step on how to set up Zotero with your favorite cloud storage solution

There’s an abundance of Zotero setup guides available on the web, and even more discussion within the Zotero forums. However, no single guide included everything that I wanted Zotero to do. Resultingly, this page aims to serve as an initial, all-encompassing, setup guide to get your Zotero working with full cloud-sync functionality.

Once set up, you will be able to use the Zotero browser extension to download and organise reference metadata and .pdf files to your Zotero library with a single click and without having to deal with pesky enterprise logins (provided you’re okay with breaking a copyright law or two).

Note that this guide assumes that you are a first time user without a library already within Zotero. I had success bulk re-adding all my references after set up but I can’t guarantee it’ll be that simple for everyone.

Download and install Zotero. Run once and install the browser plugin by clicking Tools > Install Browser Connector.

Navigate to the Zotero Plugins page and download and install ZotFile, Zotero Memento and Zotero Citation Counts Manager.

ZotFile serves as a way for us to organise and rename our .pdfs automatically as well as gives us the option to pull out any pdf annotations we make in the future, Zotero Memento will ensure that none of our imported links will degrade and Zotero Citation Counts Manager will allow us to automatically fetch citation counts for our imported references. Check the respective documentation on each of these plugins for more info.

To install plugins, download and save the .xpi file and then, within Zotero, click Tools > Add-Ons. Click the gear symbol in the top right of the popup window and Install Add-on From File. Navigate to the saved .xpi and click open. You will need to restart Zotero after each individual plugin is installed.

After all plugins are installed, open Zotero again and navigate to Edit > Preferences. We’ll now update the Zotero sync-settings (so you’re not using their webserver) and designate where your pdf library will be stored.

First, click the Sync tab and link your Zotero account. Ensure that you uncheck all boxes under File Syncing. Leave the Sync Automatically and Sync Full-text Content boxes checked.

Now, navigate to the Advanced Tab and click on the Files and Folders subtab. First, set your Linked Attachment Base Directory to a root folder on your Google drive (or other cloud-based mounted drive) where you want all your Zotero-related files to be stored. You can leave the Data Directory Location as default or move wherever you please just make sure that this folder is not being synced across multiple locations (i.e. not on your Cloud drive) as that can lead to corruption of the Zotero library.

Now, we need to set up ZotFile. Within Zotero, click Tools > ZotFile Preferences.

In the General Settings tab we want to first set up a place where we will save our manually downloaded, unorganised files (for instances where the browser connector fails). This folder can be wherever but I like to keep it within my Google Drive in a folder named Unsorted.

We also want to designate a custom Location of Files. This will be where ZotFile saves our organised pdfs. This is the same directory as the Linked Attachment Base Directory we designated earlier. You can also now implement some subfolders where your pdfs will automatically be sorted to. My settings result in pdfs being sorted by Journal (%w) and then subsorted by Year (%y). A full list of sorting wildcards is available at the ZotFile homepage.
Note that you must use backslashes (\) on Windows and forward-slashes (/) on Mac OS.

Next, navigate to the Renaming Rules tab within the ZotFile preferences. Uncheck ‘Use Zotero to Rename’ and then define your desired renaming style. My settings result in pdfs being saved as {Journal} {Year} {Author}. A full list of renaming wildcards is available at the ZotFile homepage.

At this point, Zotero is now fully set up with your cloud server. You should be able to use the browser connector to download a reference and, provided you have access, the pdf. This reference metadata will be saved to your Zotero account and synced via Zotero to any other devices you have Zotero set up on. The downloaded pdf will be renamed and organised automatically by ZotFile following the rules we have set above. Once you’ve update the root cloud directories on your other installations of Zotero to the ones you’ve created here, the .pdfs saved there by ZotFile will also be available on your other devices.

To implement Sci-Hub Functionality we can follow Medium user Simon’s guide to create a custom pdf resolver. This will result in the Zotero browser extension downloading from Sci-Hub in instances where the article is not freely available.

Navigate to the Advanced tab within the Zotero Preferences window and click the ‘Config Editor’ button. A warranty warning will pop up, click okay.

Now search for the line :

extensions.zotero.findPDFS.resolvers

Click modify and in the text input delete everything and paste the following code. Note that you can update the sci-hub url in the future if the .st domain ever goes down.

{"name":"Sci-Hub","method":"GET","url":"https://sci-hub.st/{doi}","mode":"html","selector":"#pdf","attribute":"src","automatic":true}

An enormous thankyou to Alexandra Elbakyan for creating, and supporting Sci-Hub.

Scientific knowledge should be free.

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