Zotero library exports empty folders (RDF and File Hierarchy)

edited July 11, 2023
Hello,

I'm trying to export my library including PDFs. The library contains around 700 items in several collections. However, it would only export a few folders (collections) and a few PDFs. I tried both Zotero RDF and File Hierarchy options but neither returns the expected results. After a couple tests, I suspect whether this has to do with the PDFs not stored on my desktop but only on Zotero web storage. To be able to export the files, do PDF files need to physically exist on my local drive? I've deleted all the PDFs related to this team project from Zotero directory on my desktop to earn 2GB space since they exist on Zotero cloud and will be downloaded when I access them later.

For context, for my personal Zotero use, I configured it so it does not save snapshots or PDFs when I collect an item (journal article, webpage, etc.) because I use Zotfile + my main cloud storage to link PDFs and Zotero.
And now, I'm working with colleagues who use Zotero storage (Zotfile won't work for group library anyway) and want to export the library - I'm not entirely convinced why they would want to export them when they can access PDFs using Zotero as interface. As my Zotero use preferences differ from the rest of the team, I wonder the way I set up my Zotero doesn't support the conventional library export, which makes me anxious because it may mean I have to collect all the items again with the corrected Zotero settings.

Any insights would be very much appreciated!



  • To be able to export the files, do PDF files need to physically exist on my local drive?
    Yes. Otherwise Zotero would need to redownload all the files before the export, which maybe it should do (or do with some kind of warning), but isn't what it does now. So if you wanted to export all files you'd need to use "at sync time" file-sync mode and do a Reset File Sync History in Sync → Reset to force it to re-check all files.

    But I'm not totally sure I'm understanding. You say that you deleted the local files because they're on the Zotero cloud, but also that you're using linked files with ZotFile. Those are mutually exclusive, so I'm not sure what you mean.

    It also sounds like your goal here is maybe just to create a group library with stored files? Currently I believe if you drag an item with a linked-file attachment to a group library, Zotero will just ignore the attachment, but in a future version it may be possible to tell it to convert linked files to stored files in the group.
  • (This probably isn't what you're referring to, but also note that the export dialog doesn't currently wait for files to be exported, so if you choose to include Zotero annotations, which takes a lot longer, additional folders will continue appearing after the export seems to have finished within Zotero.)
  • edited July 12, 2023
    Thanks @distillman. I've followed your instructions re. Sync settings and saw the Success window when I hit the reset for the library in question. I expected this action would redownload files to my drive. However it didn't seem to have done anything. And I found it odd the Success window appearing promptly on the click of the reset button.

    Re. Zotfile, I mentioned this in case it might be relevant. I use this functionality for My Library for my own use. For this team project, I (and the team) use Zotero file attachments. And of course, my Zotero is set up to 'not' auto-download PDFs when collecting bibliographic items, so file attachments in retrospect were done manually. I did this on Zotero Web version. For further context, the team were exploring some other methods for managing and linking PDFs to Zotero, but (after several months) ended up coming back to Zotero storage. So we did have all the PDFs downloaded somewhere (and they were all named in a standardised way for ease of navigation). The task manual linking wasn't too time-consuming.

    Re. the file download time, yes, I kind of guessed that files would download after sometime even if Zotero won't indicate the progress bar in the export dialogue. But, it didn't download after waiting some time. Also, the txt file is blank (when exported with File Hierarchy), indicating something's misconfigured with my Zotero items?
  • I've followed your instructions re. Sync settings and saw the Success window when I hit the reset for the library in question. I expected this action would redownload files to my drive. However it didn't seem to have done anything.
    You have to perform a sync after resetting file sync history.

    But I still don't understand the issue here. You say you're using ZotFile for My Library. Does that mean you're using a group library already for the team use? Why are you performing an export at all if you already have the items in a group library? I just don't understand what you're trying to accomplish here.
  • It doesn't download files even after I performed a sync - by clicking the green circular icon in the top right corner. It spin for 1-2 mins and PDF icons are still greyed out. Should I perhaps contact support?

    Zotfile is just for myself (My Library). I don't use it for group library (it's not compatible). I mentioned it because I felt it may interfere normal Zotero operations in unexpected ways, because I'm using both libraries from the same Zotero desktop app with Zotfile installed.

    Re. why export library, exactly that was my question. I wasn't entirely convinced about why we would export the library when it can be accessed by all group members via cloud and sync. And I asked the other team member and learned that library export (RDF and attachments) is for additional backup in case cloud & sync goes wrong. It's just a part of the process in this project team when completing a lit review phase.
  • Should I perhaps contact support?
    This is support. See Files Not Syncing for what we'd need to debug further.
    I mentioned [ZotFile] because I felt it may interfere normal Zotero operations in unexpected ways, because I'm using both libraries from the same Zotero desktop app with Zotfile installed.
    No, it has no affect on group libraries.
    I asked the other team member and learned that library export (RDF and attachments) is for additional backup in case cloud & sync goes wrong
    An export isn't a backup and shouldn't be used as one. See Backing Up Your Zotero Data for backup steps.
  • Thanks for these resources. I understand that what our team is doing is not a backup that will restore the state of Zotero, but I guess the team's happy with preserving PDFs and bibliographic information just in case.

    I've looked at the Files Not Syncing article, but it doesn't seem to cover the issue I'm experiencing. I am able to access PDFs on server - Zotero downloads the pdf when I double-click on it and the faint pdf icon becomes clear. So I'm seeking a way to download them all on my local drive at once to enable export. I was expecting Reset File Sync History would solve it but it hasn't so far. Is there a resource specifically around this?
  • I guess the team's happy with preserving PDFs and bibliographic information just in case
    But I'm telling you how to make an actual backup. That's what they should do.
    I'm seeking a way to download them all on my local drive at once to enable export. I was expecting Reset File Sync History would solve it but it hasn't so far.
    "at sync time" + Reset File Sync History + sync should do that. If it doesn't, we still need the same info on that page: a Debug ID for the first sync after performing Reset File Sync History, plus an attempt to open a locally missing file (even if it then downloads).
  • Great. Here's the debug id for those steps: D577866202
  • No remote storage changes for d[…] -- skipping file downloads
    You may need to add another file — from another computer or the web library, or possibly this computer — to convince it to re-download remote files. (Resetting file sync history in theory should be sufficient, but it's not currently overriding an optimization that skips unnecessary file syncs.)
  • Files finally synced and exported! Thanks!
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