Zotero standalone and dropbox storage

simonho213
I'd like to give reference managers another shot after a few failed attempts with mendeley a couple of years ago, but I'd like some advice on how to fit zotero into my current workflow

All of my research papers are organized in a dropbox folder, with subdirectories for different projects and research topics. This is so I always have access to the files regardless of which computer I'm on. I often add, delete, and move pdfs around in this folder to keep things up to date, and this process works for me as far as keeping my papers organized across different computers

Is it possible to set up zotero to hook into that workflow? The most important thing to me is that the link between reference/notes and a pdf on disk is persistent, even if I reformat my computer or move files around in dropbox

I've tried zotero briefly but I dont think I'm using it correctly. Heres what I've tried:

1. Create collections and drag my pdfs into a collection so zotero stores them internally. Then place the entire zotero data directory on dropbox. This will ensure that zotero always knows which pdf is associated with which reference, but I've now lost the folder structure I typically use when I browse on disk (everything is in directories with random names)

2. Keep pdfs in their current dropbox directories, and have zotero create a relative link to each file. This ensures my folder structure on disk but the file-reference association is broken as soon as I manually move a file on dropbox

3. I've read that the zotero data directory should not be synced on dropbox. But if I leave it in its default place then wouldn't all of my notes/links to pdfs disappear if I ever reformat my computer? (yes I know I can back it up, but just trying to understand how zotero works)

4. Ive heard people mention zotfile but there isnt much documentation online about it. IS it possible to set that up for my use case?

At the end of the day I just want 2 things: 1) retain a flexible directory structure on disk that I can browse, edit, move around, and sync with dropbox (no zotero internal storage) and 2) keep references and associations with specific pdf files even if I reformat my computer, or move files/folders around on dropbox outside of zotero
  • dstillman
    Yes, you probably want to use ZotFile together with Zotero's attachment base directory functionality. I can't help you with the former, but here's some info on the latter:

    https://www.zotero.org/support/preferences/advanced#linked_attachment_base_directory

    https://zotero-manual.github.io/zotero-manual/adding-files#file-copies-and-file-links
  • adamsmith
    For Zotfile, the basic instructions are to set a custom location of files under "Location of Files" in the general tab of the preferences (and, should you want to, set up a subdirectory structure).
    The subfolder option is great to create (or recreate) a folder structure, but I'm pretty sure it won't play well with an existing structure: it'll just try to duplicate that instead of placing files into already existing subfolders.
  • simonho213
    Do these methods allow me to manually move pdfs between folders though? It seems a lot of this would be based on using relative links, which would break if I were to move the files?

    Or, could I move the files to different collections using zotfile, and have it move it on disk for me, while also updating the relative link to the new file location?
  • adamsmith
    right, you never would want to move the files yourself, but you can move them using Zotero and then use ZotFile --> Manage Attachments --> Rename (which also moves files if set up to do so).
    (The relative link base directory, though, should never change, so you want to pick this at a low level -- typically just you Dropbox folder.
  • simonho213
    OK so I've started playing around with this...

    Ive set the zotero base directory do Dropbox/Zotero

    zotfile source folder: Dropbox/Zotero/Watch

    zotfile location of files: Dropbox/Zotero

    Is that the correct setup for my files?

    I've tried dragging my existing files into the Zotero interface and it seems that the files are copied to internal storage as soon as I do that. I dont want that because 1) I want them to be stored in Dropbox/Zotero and I dont want anything to sync to the Zotero servers

    Will files always be stored in internal storage as well as my intended location?
  • adamsmith
    The setup works, yes.

    Files stored internally don't have to sync to Zotero. Just disable file sync in the sync tab of the preferences.
    Initially, I think it'll be easiest to just do this. Once you actually have those files attached to metadata, ZotFile will move them (and they'll disappear from storage folder)
  • simonho213
    so whenever I add new files (by dragging them) into Zotero they will always be stored in internal storage first until I ask zotfile to rename/move them?

    Will this setup hold if I reformatted my computer and have to reinstall zotero? So lets say I lose my entire zotero data directory due to reformat, will all of my notes, metadata, relative links all be synced back down from the zotero servers without me losing anything?
  • adamsmith
    edited October 7, 2016
    I'm a little confused by you coming back to that point. You can and should have full and automated back-ups of all your important data, including your Zotero data directory, and shouldn't just rely on Zotero sync for back-up.
    But yes, the information on the Zotero server will recreate your entire library, including links to files.

    You can use shift+drag (or maybe a different key combination--I'd have to look that up) to create links rather than copies stored in Zotero, but since you'll move them with ZotFile anyway, I don't really see the point (and I'm actually not 100% sure how ZotFile handles linked files, though I think it'd move those, too).
  • simonho213
    If I have an item with a relative link in one of my collections, and zotfile has renamed and moved it, whats the correct way to then move it to another collection?

    I've tried dragging it from one collection to another. Now it shows up in both collections and the file is still located in its original location on disk. How do I move it so that 1) its removed from the old collection and 2) its moved, on disk, to the new directory (and gone from the old directory)?
  • adamsmith
    By default, dragging an item between collections copies it. You can use Cmd + drag on OS X, Shift + drag on Windows/Linux to move items instead.

    You'll have to re-use rename attachments to also move it in your file system. (Generally speaking, you'll have noted that Zotero isn't designed with the idea of simultaneously organizing your files in two places -- Zotero and your file system -- at once. You can do it using ZotFile, but it's a bit clumsy if you want that organization to auto-update. To me, one of the principle advantages of using a reference manager is that I don't have to worry about where a file is on my harddisk. I can just find it in Zotero).
  • simonho213
    Is there a way to delete a file in zotero and have zotfile delete the file on disk as well?

    I tried moving the item to trash, but the item is still on disk

    The reason I want zotero and my disk structure to match is because I often have to email people collections of files and I want to know that the file structure on disk matches what I'm seeing in zotero so I know I'm sending the correct set of files
  • bwiernik
    An alternative to trying to continuously manage files in two locations would be to use the Zotfile plugin's Send to Tablet feature. What this feature really does is copy the selected attachments to a specified folder on you computer. You could compile the collection of articles you want to send in Zotero, select them all and use Zotfile's Send to Tablet, go to the designated folder on your OS, and send the files from there. You can then use Zotfile's Retrieve from Tablet feature to remove the extra copies of the files.
  • bwiernik
    As for deleting the files from a dropbox folder when they are deleted in Zotero, no Zotfile cannot currently do that:
    https://github.com/jlegewie/zotfile/issues/96
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