Blank library after update

rickus
edited March 18, 2019
After the latest update to Zotero 5.0.63 (March 15, 2019), the library is completely blank and the middle pane shows a 'Welcome to Zotero' screen.

I am using a custom path for my base directories. These are still set correctly in 'Zotero Preferences > Advanced > Files and Folders', but the content of the data directory does not load.

(System: Win 10)
  • dstillman
    Are you using a custom data directory? Are you saying that you have the base directory and the data directory set to the same thing? (That should never be the case, and the data directory also should never be in a cloud storage folder.)

    If you click Show Data Directory, what do you see in there in terms of zotero.sqlite* files and their sizes and timestamps, and what do you see in 'storage' if it exists in terms of creation times?
  • rickus
    The base directory is 'D:\Articles' and the custom data directory 'D:\Articles\ZOTERO'. This has worked for many years. I did not change anything to the setup, just let Zotero run its automatic update.

    Show Data Directory: Aha, strange things are happening here:
    - zotero.sqlite (last modified 18/03/2019 11:56) has been turned into a 4,960 KB file. This was well over half a GB last time I checked
    - zotero.sqlite.1.bak (last modified 22/10/2018 12:03) 972,672 KB
    - zotero.sqlite.bak (last modified 18/03/2019 09:44) is 904KB
    - zotero.sqlite-1.tmp (last modified 20/10/2018 17:11) is 715,676 KB
    - zoter.sqlite-journal (last modified 18/03/2019 11:56) is 417 KB

    My online library appears to be intact, so i unlinked it from offline Zotero to preserve the data.

    Storage:
    11,723 folders, the latest modified 05/03/2019 20:43
  • dstillman
    The data directory shouldn't be within the base directory, but that shouldn't matter here.

    Is this an external drive? Network drive? How much free space is available? Your database seems to have somehow been deleted, and the normal automatic daily backups that Zotero makes don't seem to have been made either (since zotero.sqlite.1.bak is from last October). I also don't know how you ended up with zotero.sqlite-1.tmp.

    Do you have a recent backup of this directory? If so, you'd want to restore zotero.sqlite from there. Otherwise, you can try swapping in the zotero.sqlite.1.bak file to recover the database you had last October, but you wouldn't have the items you created since if you haven't been syncing. If you're not able to restore those items, you can move all storage directories created since October out of there and add the PDFs back to Zotero (which you can do in batch), and Zotero may be able to retrieve metadata for many of them.
  • rickus
    Just local hard drive with a single partition with 430GB of free space.

    My hard disk is automatically backed up to an external RAID system, but the error had already percolated through the system. However, I discovered a file named:

    zotero__Mar-13-103439-2019_Conflict.sqlite

    ... and two similar files from earlier dates on the backup system. Renamed it and that did the trick.

    Any idea what happened here, how the conflict file was generated and why the normal Zotero backup process stopped? (I would like to avoid this from happening in the future.)
  • dstillman
    That's not a file Zotero creates, so I couldn't tell you how you got that. Something on your system is doing some kind of sync operation in your data directory, and you should figure out what it is and stop it or else you'll get further data loss.
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