Hippocamplus My Second Memory

Syncing Mendeley and PDFs across devices

20 March 2019 Edit: I switched to Zotero (yeay open-source, bye Elsevier), using Google Drive to store the PDF files. See the Internet section and the blog post that inspired the change.

Recently, I’ve been setting up new computers from scratch as I moved from Montreal to Santa Cruz. Like for spring cleaning, it might be a good idea to clarify the system I’ve been using to manage bibliography and PDF annotation.

Briefly I use Mendeley Desktop and also put all PDF files in a Google Drive. Both are synced with my Android tablet. On the tablet, I use the Mendeley app to get information, search etc, but I read/annotate the PDFs from the Google Drive. On a computer I use a custom Python script to update the PDFs if necessary.

The updateMendeley.py script

I wrote a Python script that checks the Google Drive folder and Mendeley’s local folder, matches PDF files and syncs them. The updateMendeley.py script is on the GitHub repo.

I needed something slightly better than a rsync because it’s possible that the filenames are not the same between the two folders. This might not be a big problem for new files but at some point Mendeley Desktop and the app I used on the tablet produced slightly different file names for the same article. I don’t use the Android app to download PDFs anymore but I still have old PDFs that I didn’t take the time to rename.

The matching part of the script compares each file name in the Google Drive with the file names in the local Mendeley folder. It uses the SequenceMatcher function from the difflib module. If two file names have more than 90% match, it assumes that it’s the same article. The result of the matching step is saved locally in a “cache” file to speed up future runs.

Then it’s just a question of copying the new articles to the Google Drive or updating the local Mendeley folder (if files have different sizes).

In practice, I run the following command when I feel a sync is needed (first a dry run, then without the -dry):

python updateMendeley.py -local PATH/TO/MendeleyDesktop -remote PATH/TO/GoogleDrive/ArticlesPDF -dry

Why Mendeley?

  1. That’s what I started using a while ago (before Elsevier acquired it).
  2. It has an Android app (I have an Android tablet).
  3. It does what I need: tagging system, export to BibTeX, search in PDFs, online portal.

Maybe I could find a good system with EndNote or Zotero but that would take some time and work. The idea of Zotero is appealing and I would prefer an open-source software (not owned by Elsevier). I tried to make the switch but it froze when importing my entire library. I should try again. There is still the problem of the Android app: I don’t know what they are worth for Zotero. There are two unofficial apps. Maybe I could pay the $2 and test them.

Why not use the PDF syncing mechanism from Mendeley?

  1. Google Drive is more user-friendly: quickly access from different devices, easy to share PDF with others.
  2. Control over the files.
  3. Easy to update PDFs annotated on the tablet. Useful because I prefer to use a separate Android application to annotate PDFs (RepliGo).
  4. Bad experience this summer with a bug in Mendeley (blocked for more than a month and lost many PDFs, some of which were annotated).

Syncing the Google Drive folder