Is it possible to rename papers inside folders? Zotfile / Zotero mac

Hi. I just changed from mendeley to zotero and am struggling to make it work with my current library organization on dropbox. My papers are all organized in subfolders by theme. Using zotfile, i managed to link a dropbox folder to zotero that contains all my subfolders and files. However, if I ask it to rename, it will move the file to the root, not the subfolder.
Is it possible to: 1) rename the file without moving it anywhere; 2) use collections as wildcards to keep my current organizing system?

What bothers me is that I don't want zotfile to create new copies of my files. It's pointless.

Thanks :)
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  • Which ZotFile version are you using?
    And so I understand correctly, you currently have your files linked to Zotero items or not?
  • Looks like it's the 3.1.
    No. So I have over a thousand files and since i'm still trying to get it right, i'm testing small chunks. So i have a folder with 12 files that is under papers/theme and i dragged them to zotero, fetched metadata, etc. Then, when i ask it to rename, it will create new files under papers/ and ignore the original files under papers/theme - am I making myself clear? What I managed to do was only to get zotero to use my dropbox folder as base directory (preferences > advanced > base directory). I did not change the data directory location
  • You can shift+drag to Zotero (or use the equivalent "Link to File" under the Green plus) and it will just create links to the files. That should do what you want.
    ZotFile 4.0 (which you can get under "all versions" from the add-on page on mozilla) does have a wildcard for collections for future use. See the ZotFile homepage for details.
  • Tough generally you'll likely make your life better if you export from Mendeley as RIS or Endnote XML and re-import into Zotero. That _will_ create duplicate files, but you could then delete the originals and use ZotFile to re-create essentially the same structure.
  • Do I need extra setup to use shift+file?

    See if that's what I should do: create collections to match my themed folders and then shift+drag them there, without further setup? Do I need to do anything else to keep zotero from creating local copies?

    I'll look at the zotfile 4.0!
  • I never took the time to organize my mendeley. their one-by-one correction feature makes me want to die a little whenever I import new folders. So my mendeley is not organized at al :/
  • it's actually ctrl+shift+drag, sorry about that. No extra set-up for that, though, no.
  • I can't download the 4.1 for the standalone, it just seems to come as a firefox plugin. damn.

    On a mac, would it be ctrl or cmnd? With the links, can I still use the rename feature?
  • just use right-click--> save link as the same way you would for the 3.1 version. Definitely works for Standalone, too.

    It's cmd+shift + drag on Mac I believe. You'll recognize links. They have a little link icon over them.

    You can use Zotero's "Rename from Metadata" for linked files, but I don't think there's a way to use ZotFile's more customizable renaming without moving the file.
  • I will try this and I'll let you know what works best. Thanks :)
    I now see why 'strong online community' is often listed as a zotero advantage over mendeley!
  • and I wish I posted this sooner lol it would save me a lot of time
  • alright. So zotfile 4.1 solves the problem of saving under the themed folder. It still duplicates the file, though, when asked to rename. Ideas? is there anything I can setup to avoid this?
  • No, I don't think so. What's your current workflow? I don't think I fully understand why you need ZotFile at all for files already on your harddisk.
  • I read on the ipad with goodreader, keep my files on dropbox. I mainly work with my macbook so i don't care for a setup that would work for multiple computers. So what you are saying is that i'd be better off with the cmd+shift+drag?
  • (1) I'm also having a hard time understanding what exactly you want to achieve. Can you explain in more detail about where you're starting and what you want to end up with?

    (2) I can't reproduce the duplicating of files based on my understanding of what you're doing. Can you explain in more detail what steps you're taking that result in a duplicate?
  • ok. I am trying to set up zotero for the first time.
    My papers are all organized on dropbox, by theme. I intend to replicate these themes as collections on Zotero to keep the same organization logic.

    The reason I keep my papers on dropbox is because I read pdfs on the ipad, on goodreader, and it syncs perfectly.

    What I want to achieve:

    I want to add the papers i currently have on my dropbox on zotero, folder by folder, creating a collection for each. It would be desirable to rename my files to have a better naming system. I formerly did that manually so not everything is as it should.

    After adding the pdfs, I'll fetch metadata.

    I also want to prevent zotero from creating copies of my files in its root folder under those bizarre random names.

    With ZotFile I managed to rename within the themed folder, but it still duplicates the file - therefore, it doesn't rename it, it creates a duplicated file.
    Is it clearer now?
  • edited January 8, 2015
    So there are two options:
    A
    1. Move the items into Zotero using shift+cmd+drag
    2. Fetch Metadata
    3. Rename using Zotero's Rename function

    B
    1. Just drag the items into Zotero (this will create a duplicate)
    2. Fetch Metadata (and manually add it where automatic fetch was unsuccessful)
    3. Use ZotFile to rename _and_ move (Custom Location in the General Tab) those Files --> They are no longer in the Zotero folder with random folder names, but they're still duplicates
    4. Delete your original files

    I think option B will work better for the long run, as it'll also place new files in the right place.
  • (alternatively, for B 1. you can use shift+drag to Zotero, which will delete the original file, though you may not like that, temporarily, it will only be in Zotero's somewhat cryptic folder.)
  • I guess solution B would work. But then again I'd still have to manually add new papers as I download them, right? Would mendeley be a better solution in my case?
  • no, with B, ZotFile would automatically sort the new papers in the right place.
    One source of confusion could be that the "fetch metadata" workflow really isn't the principal way to get papers into Zotero once you have it set up. You want to use the URL bar icon which in most cases will include the PDF as you download the article metadata.
  • yeah, of course! fetch metadata is for organizing what I already have.
    So this setup would work to exchange papers between zotero and goodreader on my ipad? as a followup, is it worth it to get any client to access zotero on the ipad?
  • you'd be able to read and annotate through the dropbox app, yes.

    As for iOS apps: papership doesn't work with Dropbox, so that's out from the start although it's a very nice app otherwise. ZotPad does work with your set up and is free, so I'd give it a try. I guess the main question would be if you benefit from access to the Zotero data while reading on your iPad. That's something that depends on your workflow.
  • i really don't think i'd need that. goodreader currently fits all my needs.
    Goodreaders syncs with dropbox folders. So, assuming I go with the B setup and have zotfile organize my files directly on dropbox, will it fetch the annotated file (assuming it keeps the name) on its own or do I have to use that tablet feature on zotfile to sync my annotated files?
  • You don't need the tablet feature, that's for a different use case (pushing individual papers to a tablet via dropbox or the like).

    Since Dropbox does the syncing, there's nothing that ZotFile would have to fetch. You do have to run the extract annotation feature manually, though (if you want the annotations in notes).
  • Cool. I'm testing this setup on a small set of folders but it seems like you solved my problem with setting B.
    Oh, I tried but it didn't work to drag files with links using the cmd+shift+drag. is the shortcut correct?

    Thank you so much for helping out!
  • I always get Mac shortcuts wrong: Cmd+Opt+drag
  • Okay. I still have a problem.
    Using solution B, i was able to import files creating collections and then rename them on a new folder on my dropbox. However, Zotero is still saving the files on its data folder - which results in several copies of the same file. How to prevent zotero from saving them?
  • run me through what you're doing step-by-step. ZotFile would move the files out of Zotero's storage folder if you're using that, so I'm not sure what's going on.
  • i first import them by dragging into a folder, then fetch metadata and finally ask zotfile to rename. Then it saves it in the new designated folder on dropbox, but somehow a copy is still on the data directory
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