Zotero beta hangs importing 6GB Mendeley library

molivo
edited July 7, 2021
Now that Zotero has a native viewer and can import Mendeley highlights, I am trying to switch from Mendeley. My library is around 6GB. I first tried switching using the online method. Things seemed to be fine until at the very end, when the importing process froze up with just a little left to go. I blamed that on my internet connection and tried to import locally using an old version of Mendeley. However, the same thing happened. There is only a little left on the importing process progress bar and it has been like that for 12 hours. One thing I noticed is that I no longer get notifications of ZotFile renaming files, so I suppose the problem arises after writing the files. What can I do? I'm interested in keeping my Mendeley highlights.
This happens with 5.0.97-beta.33+fdcd4e51c.
  • dstillman
    You should disable all plugins before trying to import.
  • molivo
    edited July 7, 2021
    Still hangs at the same point, with only a little left in the progress bar.
  • dstillman
    Can you provide a Debug ID for an attempt that hangs? (If you can't access the menus once it freezes, use the View Output window so that there's a separate window you can submit the output from.)
  • molivo
    edited July 7, 2021
    I'll do that, but first, how can I "reset" Zotero? When I forcibly quit Zotero when it hangs, still some entries show up in the library. I can delete those manually, but I can't delete the group libraries, even though I am not syncing.
  • dstillman
    edited July 7, 2021
    Not sure what you mean by that. You don't need to delete entries each time. A repeated import just skips previously imported entries. And group libraries have no relation to this.

    (If you've done the import with ZotFile enabled, though, you should close Zotero and delete the Zotero data directory before trying again, since otherwise you may end up with something of a mess. You can run ZotFile on imported items later if you want to.)
  • molivo
    Alright, I sent an email to support@zotero.org.
  • dstillman
    Does it always hang running pdfinfo on the same PDF?
  • dstillman
    (And if so, running the import again without deleting anything should work, because it would just skip that file, which is already imported.)
  • dstillman
    Actually, it looks like that's just the first PDF it's trying to process, and running pdfinfo is just freezing for you.

    Is this an institutional computer? Are there any third-party system utilities that might interfere with running certain programs? If you open Terminal via Spotlight, copy and paste this line, and press Return, what happens?

    /Applications/Zotero.app/Contents/MacOS/pdfinfo
    ~/Zotero/storage/5JLHSLAF/*.pdf ~/Zotero/storage/5JLHSLAF/.zotero-ft-info

    If it seems to complete without error, what's the output of this command?

    ls -la ~/Zotero/storage/5JLHSLAF/.zotero-ft-info
  • molivo
    edited July 7, 2021
    This is the output (how do I format it?)
    First command:
    This is a custom xpdf pdfinfo build. Please use the original version!
    4.02
    Copyright 1996-2019 Glyph & Cog, LLC
    pdfinfo
    zsh: no matches found: /Users/mmm/Zotero/storage/5JLHSLAF/*.pdf

    Second command:
    ls: /Users/mmm/Zotero/storage/5JLHSLAF/.zotero-ft-info: No such file or directory

    It's my personal computer.
  • dstillman
    Did you delete your Zotero data directory before running that? Does storage/5JLHSLAF not exist with a PDF inside it?
  • molivo
    Ah, I was going to run the whole thing again. I tried with that specific file:
    /Applications/Zotero.app/Contents/MacOS/pdfinfo ~/Desktop/zoterotest/*.pdf ~/Desktop/zoterotest/.zotero-ft-info
    It's been frozen for a while, I suppose that task should be completed quickly, so there is no .zotero-ft-info output.
  • molivo
    I also noticed several instances of pdfinfo in Activity Monitor, I suppose those remained lingering from the several times I tried importing the Mendeley library.
  • molivo
    I tried with another PDF and it completed fine. I can send you the problematic PDF if you want.
  • dstillman
    Sure.
  • molivo
    The pdf document was corrupted (perhaps on the way to/from Mendeley servers), so pdfinfo couldn't process it. I hope there aren't many of those.

    Perhaps it'd be good to have the program raise a warning and go on with the rest?
  • dstillman
    We'll look into why our bundled pdfinfo version hangs on the corrupted file — thanks.
  • dstillman
    @molivo: This should be fixed in the latest beta.
This discussion has been closed.