Newbie: should Zotero be saving PDFs to my Linked Attachment Base Directory?

felciano
Hi --

I'm evaluating Zotero as an open replacement to Mendeley and would like to confirm that it is possible to aggregate and store citation-related PDFs in an external folder that can reside on Dropbox. This is to allow synching with other machines, easy searching using other PDF tools, and remote access via the Dropbox apps.

(Please note that this post is only about storage of PDFs associated with citations. I understand from the documentation that storing the Zotero data files in Dropbox is a bad idea. I have left them in their default locations, and have configured Sync to enable updates on multiple machines.)

When adding a citation to Zotero using the Chrome plugin, it nicely captures both citation metadata as well as a PDF if available. However that PDF seems to get stored in the data directory, despite the fact that I have the "Linked Attachment Base Directory" configured. Is there another configuration setting to use to actually instruct Zotero to use this configured directory rather than its default?

In case it matters, this is all running on Mac OSX 10.14 (Mojave).

Thank you in advance for your help,

Ramon
  • adamsmith
    No, you need to install the Zotfile add-on (zotfile.com) to set up turning files into links. The linked attachment base director does not set up where files are stored, it just establishes relative filepaths for linked files.
  • felciano
    Thanks @adamsmith. I tried that but can't figure out how to configure it correctly. I don't see any instructions on the Zotfile page about linked attachments.

    Maybe an example would help. Here's a publication I'm interested in capturing: https://www.nature.com/articles/s41467-019-11952-w. If I visit that page in Chrome with the Zotero extension installed, I can click the little Zot icon and it tells me it is"Saving to" my library, and indicates it is grabbing "Full Text PDF" and "Snapshot".

    When I switch to Zotero, it shows me the PDF has been downloaded to:

    /Users/felciano/Zotero/storage/NI5CR592/

    which is the local data directory. I have installed Zotfile but I don't see any options that would allow me to tell Zotero to instead store this PDF in

    /Users/felciano/Dropbox/MyPDFsFromZotero/

    Is this workflow feasible directly from within Zotero and its plugins?

    Thanks again,
    Ramon
  • adamsmith
    Yes.
    Zotfile Preferences (under Tools)
    Location of Files
    --> Custom Location : /Users/felciano/Dropbox/MyPDFsFromZotero/
  • hgunz
    I'm having the same problem (albeit using OneDrive instead of DropBox). I have the ZotFile Custom Location set to a OneDrive folder (on this machine it's at D:\Data\OneDrive\Zotero\storage). Zotero's base directory is set to the same folder. However, when I import a new reference from a web page using the Zotero Firefox add-on, the file goes to the storage folder in the Zotero data directory. If I drag a file to a reference in Zotero, the attachment is put in the Zotero data directory storage folder, not the OneDrive folder. I'm obviously doing something wrong, but I can't see what it might be.
  • adamsmith
    What happens if you use right-click, manage attachments --> rename attachments?
    Does that move the file to the folder on One Drive?
  • hgunz
    Yes, it does, and thanks for your help. Also, after a good night's sleep Zotero/Zotfile have started to put attachments in the OneDrive folder when they're dragged from e.g. the desktop to a reference in Zotero. Additionally, importing references from EndNote is now putting the attachments in the OneDrive folder.

    However, when importing a pdf from Firefox using Zotero Connector, the attachment is still put in the storage folder in the Zotero data directory. Of course, I can now move it to the OneDrive folder manually in the way you suggest, but it looks like something still isn't working right with my setup.
  • adamsmith
    That sounds like a Zotfile bug rather than a problem with your set-up then.
    This is on Windows 10 with the newest Zotero?
  • hgunz
    Yes, that's right. Zotero 5.0.74 on Windows 10 1903. Where can I find the Zotfile version?
  • hgunz
    I notice, too, that when Zotfile moves an attachment to the OneDrive folder, it leaves the subfolder in the Zotero storage directory that previously held the attachment. This subfolder contains two files (.zotero-ft-cache and .zotero-ft-info). Perhaps this is by design, but it means, of course, that the Zotero storage directory is going to fill up with folders that don't have attachments in them. Is there a way of preventing this, or would preventing it be undesirable?
  • bwiernik
    Those files are the cache for the full text index. You can ignore them—they are expected and fine.
  • hgunz
    Thanks.
  • hgunz
    Zotfile on a different machine is now not moving attachments to the specified custom location (on OneDrive, which is also specified as the linked attachment base directory) when I right-click on the attachment and select Manage Attachments > Rename Attachments. The pop-up "ZotFile: Renamed Attachments" appears, but the file isn't moved from Zotero storage to the linked attachment base directory. Does anyone have any suggestions for what I'm doing wrong?
  • dstillman
    @hgunz: Try upgrading to the latest ZotFile version. There were some bugs in previous versions that should be fixed in 5.0.13.
  • hgunz
    Thank you. That cured the problem.
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