Creating My Own File Structure for Zotero

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  • edited February 4, 2015
    So if I correctly understand what you're saying about #5, these things are true:

    1. Everything that resides on ZFS also resides on every client.

    2. If one changes the server from ZFS to a WebDAV server, sync will automatically store everything, including all copied attachments, on the WebDAV.

    From the above, it follows that the way to move attachments from ZFS to WebDAV so that they can also be accessed outside Zotero is:

    1. In Zotero, search the library for items with attached PDF's. (Is there a way to search for items with non-PDF attachments?)

    2. Open each copied attached pdf individually.

    3. Save it in a suitable location on the (mounted) WebDAV server.

    4. Add the saved file to the original item as a linked attachment.

    5. In the item, delete the original, copied version of the attachment (which resides on ZFS).

    6. Repeat for all items with copied attachments, except "active" items whose copied attachments should remain on ZFS, and then sync the library.

    7. If the above works, there really is not much need to use ZFS for groups and WebDAV for My Library since only the "active" attachments will reside as copies on ZFS.

    8. OTOH, the linked attachments on the WebDAV server may not always be accessible because mounting via WebDAV is often temperamental. Nonetheless, as long as all the critical "active" attachments are stored as copies on ZFS, they should be accessible through Zotero.

  • you can do all of 1-5 in batch with ZotFile, but note that you can't use linked attachments in groups. Beyond that, this sounds awfully complicated and I can't really help you much.
    Just try it out and keep good back-ups.
  • edited May 7, 2015
    Thank you guys for all these useful and elaborate explanations. I do have an issue that has been bothering me for some time. I have been using zotfile to sync my pdf attachments to a folder located on google drive and then accessing then as linked files. However, am considering investing in zotero storage and for this, I would like to move back all my files in google drive to zotero without creating any duplicates whatsoever.

    The reason, I am saying without creating duplicates is that I think zotfile or zotero created duplicate sub folders in my "storage" folder located in the main zotero folder which I moved from Firefox to a location in my documents. In this "storage" folder located my "my documents" (not the one on google drive), I have over 1204 sub folders; yet I only have 914 files (references) both in my online and standalone libraries. Now I am wondering where the 1024 sub folders could have come from??? It makes be believe that I might have done something wrong; thereby creating duplicate folders (to a tune of 1024) and yet, they are too many for me to check each one of them independently and delete any duplicates manually.

    The other thing is that when I moved my files to google drive using zotfile, some folders created there are empty (By this, I mean I commanded zotfile to rename my attachments using a folder structure, but some of the folders it created are empty without any attachments and yet I can see those attachments when I check my library. This also seems to suggest that when I eventually move those files to the zotero storage space I wish to purchase, I might as well lose those attachments since the folders created on google drive are empty (although I see some of the files in my library).
  • edited May 7, 2015
    Lastly, since I have been modifying my library by deleting certain references I don't want anymore, would I be right to assume that these would also be deleted from the folder zotfile created on my google drive or they are still existing??? And just to be sure, would I be right to say that zotfile only moves pdf and not the other attachments such as snapshots, notes etc (because I don't see these in the folder on google drive). I would assume that these other attachments are contained in the same sub folders I have been talking about (the ones in the main zotero folder in my documents).

    Many thanks to you all for the guidance provided on this forum. Your ideas are increasing my capacity to conduct research with less and less pain :)
  • edited May 7, 2015
    Zotero would have a separate folder for each attachment, i.e. if an item has a PDF and a WebPage Snapshot attached, that'd be 2 folders in zotero/storage.

    so yes to this,
    would I be right to say that zotfile only moves pdf and not the other attachments such as snapshots, notes etc (because I don't see these in the folder on google drive).
    with the exception of notes, which aren't files but part of your database.
  • Hey, I wonder if someone can give me a hand with this. I'm using Zotfile, set up to allow a portable library as described here.

    In several instances, I've scanned edited collections and stored each contribution as a single pdf file within a common folder. For example, a single folder contains several contributions in the book "Money, Power and Space" edited by Stuart Corbridge, Nigel Thrift, and Ron Martin.

    This creates two issues. First, each individual contributions needs its own reference item in Zotero, but this creates two logical places for pdf attachments: associated with the book or associated with the individual reference. I'd like to share the individual pdf files between the reference item for the book and the reference item for the individual book section. This way all the pdf files associated with the book would be attached to the book record, but so too would be each individual pdf and the record containing reference information for the specific item. Is there any way to do this?

    Second, some of the individual pdfs pertain to the book itself. For instance, one pdf may contain front matter and another, back matter. If a book has multiple parts, each with a brief introduction, there may be pdf files for each part. So sometimes a book may have a half-dozen or so separate pdfs. When I import these files into Zotero, Zotfile renames them, and Zotero's "Rename file from parent metadata" option will too. I want to use uniform naming conventions so this is not bad, except for one thing. It would be nice to be able to edit the names of each of the multiple attachments so that one can tell what the attachment is. For example, instead of "Corbridge et al 1994 Money, Power and Space 4.pdf" I'd like the name to be "Corbridge et al 1994 Money, Power and Space - Backmatter.pdf." But I don't see any way to edit the name of the file manually within Zotero.

    Thanks for your help.
  • 1. Linking the same file to multiple items -- if you're using ZotFile to move your files outside of the Zotero storage folder, treating them as links, you can just link to the same file from multiple Zotero items. I wouldn't do that into the storage folder, though, even though it may appear to work (I'd expect issues when syncing).

    2. You can simply click on the bolded filename on the right to change it.
  • Thanks. Works like a charm!
  • Hello,
    I transferred my default zotero database to MEGA "C:\Users\ok\MEGA\data_zotero" including all files and folders (locate, storage, styles, translators) zotero.sqlite etc. My PDFs were as "linked attachment" and I was using both standalone+Firefox(+Zotfile) with the same database.

    Now that I have an extra desktop, I installed MEGA (this time "D:\MEGA\data_zotero") + Zotero (both standalone+Firefox(+Zotfile). When I define my Data Directory Location in my new desktop (Preferences > Advanced > Files and Folders > Data Directory Location "custom") to MEGA\data_zotero, my database is uploaded ok (~8,000 records), but all the linked attachments are not working, even if I define the Base Directory ("D:\MEGA\data_zotero\storage") Any idea about how to correct this problem? Thanks in advance, max
  • Please start a new thread--your issue is a different one from the original problem.
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