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October 3, 2014 reproducibleResearch, opensource, zotero

Your zotero filesystem

The problem

Zotero is a really great tool for organising your scientific and professional documents and their citations, and keeping documents and citations together.

Now usually we want to store documents in some kind of hierarchical or tagged structure. Up to now it has been possible to do that either in zotero, or in your filesystem, but not both.

Zotero gives you the choice of 1) saving your files within zotero or 2) just storing links to files in your filesystem.

If you choose option 1, zotero has great ways to store your docs in a tree structure called “collections” - and you can also store one doc in multiple collections, which is great. But it famously keeps the documents themselves hidden in a weird series of folders with weirder names so basically you have to access your files via zotero, not your filesystem. This is a dealbreaker for me because I want to sync my zotero docs with my large-ish screened phone so I can read an annotate them on the couch in the evening. Even if I sync my whole zotero folder (which is a bit of an overkill) I still can’t easily see which doc is which. Zotfile does have a way of sending docs to your tablet and recovering them after you have read and annotated them but this adds two extra layers of clunk and you have to remember to do it.

If you choose option 2, you are telling zotero not to store your files at all but to just link to existing files. So your docs are stored in whatever Byzantine folder structure you favour. But then you can’t see this structure from within zotero which makes it pretty useless from zotero’s point of view.

The solution: zotfile 4.0

The excellent zotfile plug-in for zotero has just had an update to its rename files functionality including code contributed by simpzan which means you can tell zotero to store attachments as links stored in a folder structure which is the same as the structure of your collections within zotero. To get this functionality, you just have to click “use subfolder defined by” in the preferences and enter /%c/.

There are a few things to think about.

  • If you have saved your doc in more than one collection in zotero, the plug-in asks you which one you want to use for saving the file. This is OK but a bit tiresome as it doesn’t yet remember your previous answer.
  • You still have to remember to select your files in zotero, right-click and choose manage attachments / rename attachments which is a bit of a drag
  • Zotfile renaming won’t work with just files, you have to remember to create parent items first, which is a bit of a drag if you just have a bunch of PDFs which you aren’t intending to create proper references for.

Otherwise, pretty nifty.

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