Most files can no longer be located

SimonPek
Hello everyone,

I use Zotero for Firefox and recently had to reboot Windows. Upon re-downloading Zotero for Firefox I can no longer open many of the files: I constantly get an error message saying "The attachment could not be found" when I click on the PDF. In some cases I can open an article and then the next time I try opening it I get that error message! It seems to be very sporadic and I have no clue how to solve this. I checked online in my Zotero library and many of the PDFs are no longer there either. Any tips on how I can resolve this to get my PDFs back?
«1
  • dstillman
    By "reboot Windows" do you mean reinstall Windows?

    If so, and this is a clean install of Zotero that pulled down your server data — which is what it looks like from your sync history — it's more likely that some of your files were never uploaded to zotero.org. If the files aren't on zotero.org, it's unlikely they ever were.
    In some cases I can open an article and then the next time I try opening it I get that error message!
    That's extremely unlikely. I'd guess that you're misremembering this.

    Do you have a backup of your Zotero data directory from before you wiped your computer?
  • SimonPek
    Hi Dan,

    I am referring to not a total reinstallation but just a reset (all files were retained - just apps and programs had to be reinstalled). I couldn't see why some files would not have been uploaded to zotero.org as I always synched on a regular basis. I don't hav ea copy of the data directory, unfortunately. And I know it is strange but I in fact was able to open a PDF document this morning and later couldn't open it...

    Simon
  • dstillman
    edited January 27, 2014
    Your sync history shows a full download of your library on January 20th. If that's when you did this reset, then you accidentally ended up with a new Zotero data directory, and that's why you're missing all files that weren't uploaded to zotero.org. (Why they weren't uploaded I can't tell you, but if you can provide the eight-character item keys — which you can find by right-clicking on an attachment, generating a report, and copying the item key (which will look something like 0_ABCD2345) from the end of the URL — for some attachments in question I can look into it.)
    And I know it is strange but I in fact was able to open a PDF document this morning and later couldn't open it...
    Can you provide a Debug ID for an attempt to open such a file?
  • dstillman
    Anyhow, I'm not sure how you did the reset, but you should look on your hard drive for other copies of your Zotero data directory.
  • SimonPek
    Just sent the de-bug to Zotero using that process.
  • SimonPek
    Just realized another potential clue: I created a custom directory last year that was likely being used until this reset. Since I downloaded Z for F again, the standard default storage location is being used. Could be that most of the old files are still in the original directory. Is there a way to merge these without losing them?
  • dstillman
    We need the Debug ID to look at the output.
  • dstillman
    Could be that most of the old files are still in the original directory. Is there a way to merge these without losing them?
    Just point Zotero at the original directory. Any changes you've made locally will have synced to the server (assuming you've synced) and will sync back to the other directory.
  • dstillman
    (And obviously you should make a backup of both directories before changing anything.)
  • SimonPek
    Hi Dan,

    What do you mean by point zotero to the original library? Would this be for the linked attachment or data directory part? And which sub-folder of the generic Zotero folder should be used as the main folder when linking?

    Thanks again,

    Simon
  • dstillman
    The same way you did it originally.
    Would this be for the linked attachment or data directory part?
    Data directory
    And which sub-folder of the generic Zotero folder should be used as the main folder when linking?
    It's the directory with zotero.sqlite and 'storage' in it. See Zotero Data for details.
  • SimonPek
    I connected it to the original database on the advanced pane, it synced the data, but several articles are still missing. Is there a way to merge the two database folders to have a complete list of all PDFs that could have been in either database? I'm just at a loss as to what I can do to have my original library back and wouldn't want to have to manually download all the articles again if there is any way to restore what was once there.
  • dstillman
    There shouldn't be any need to merge the two data directories if you properly selected the old directory, which from the looks of it you didn't — I see another full download from your account from a few hours ago.
  • dstillman
    To make sure you're doing this right, I would start by temporarily disabling auto-sync in the Sync pane of the preferences.

    If you look in the original directory, you should see a zotero.sqlite file with a timestamp from before the reset (unless you've used it since). Select the 'zotero' folder that contains it as the data directory.
  • SimonPek
    When I added linked Zotero to my original custom directory, Zotero was completely empty. I synced and then I guess I synced with the account contents. I don't know how I can properly link it other than following the directions we noted earlier:

    Advanced > Files and Folders > Selected the overarching "Zotero" folder of my previous, custom directory and contains the sqlite file and the storage folder, among others.
  • adamsmith
    if you selected that folder you should most definitely not have gotten an empty library. Disable auto-sync, try this again, and restart Zotero/Firefox.
  • SimonPek
    Just tried again with a the backed up version of my old directory. As I linked that file I got this error: The directory you selected is not empty and does not appear to be a Zotero data directory. Like last time I continued, restarted, and then got an empty library again. I'm not sure what the problem is with the old directory... it contains the storage folder, sqlite, etc.
  • dstillman
    edited January 28, 2014
    If you get that message, don't continue, because it means you're doing something wrong, and it's just going to leave a trail of empty zotero.sqlite files around.

    I'm not sure what you mean by "overarching". You want to select the folder that directly contains those files, which means actually navigating into that directory — such that you can see zotero.sqlite and 'storage' — and pressing Open or Choose (or whatever the button is on your OS). I'd guess that you're accidentally selecting the parent directory.
  • SimonPek
    I chose the entire "Zotero" folder such that, when I now click on the "Show Data Directory" button I see all of the sub-folders which include locate, styles, storage, translate, zotero.sqlite, etc. Still nothing in my library.

    When I go into that folder manually in my documents I can see some PDF files in individual subfolders in the storage tab; however, they don't show up in Zotero now...
  • dstillman
    edited January 28, 2014
    Zotero only shows the "The directory you selected is not empty" message if zotero.sqlite doesn't exist in the directory you're choosing. You may be past that now, but whichever directory you were choosing that triggered that message was not correct (or contained everything but a zotero.sqlite file, perhaps, if you somehow deleted/moved it).

    How large are the various zotero.sqlite.* files in that directory, and what are their timestamps?
  • adamsmith
    did you check the timestamp on the zotero.sqlite? What's its file size?
  • SimonPek
    984 KB (1,007,616 bytes)
    Created and Accessed: ‎January ‎27, ‎2014, ‏‎10:27:39 PM
  • dstillman
    Right, that's an empty, just-created database.
  • SimonPek
    The storage folder is full of all hundreds of articles, though, which still have all of the PDFs, etc. Any way to get at those or is this a lost cause?
  • dstillman
    Not without the accompanying zotero.sqlite database.
  • dstillman
    edited January 28, 2014
    Well, but since the database isn't actually the problem in your case, if those are your old files, you can actually copy the folders from the 'storage' directory into your other, mostly working data directory (after pointing Zotero back to there) and Zotero will be able to open the files. The unique strings that make up the folder names within 'storage' are named after the internal identifiers of Zotero items and don't change, so as long as they're where Zotero expects them within the 'storage' directory, they should work.
  • SimonPek
    Right so just copy all of the files from the storage subfolder of my backed up database and paste them into the storage folder of the profile directory directory?
  • adamsmith
    yes
  • dstillman
    Yes. Be sure you have a backup of your profile directory directory first, though.
  • SimonPek
    By backup do you mean just copying the original folder and pasting in another location as a reserve? That's what I gathered from other posts on the forum. The reason I ask is that, when I just copied and pasted, the sqlite file in the newly created folder was time stamped with today's date and has a size of 53,000 kb. Maybe this is also why my old sqlite didn't work.

This is an old discussion that has not been active in a long time. Before commenting here, you should strongly consider starting a new discussion instead. If you think the content of this discussion is still relevant, you can link to it from your new discussion.

Sign In or Register to comment.