File Not Found error

dstillman
This discussion was created from comments split from: I can't open PDF's.
  • clcastanedar
    Please help me!

    Every time that I tried to open my PDFs I receive this message: “File not Found The attached file could not be found. It may have been moved or deleted outside of Zotero… it may not yet have been synced to Zotero.org. this message”

    This problem happened after I upgraded to Zotero 5.0.74 and I installed Zotero standalone to a second computer (PC desktop).

    Originally, I did all my work on my laptop (MacBook Pro) using the standalone version of Zotero. For security purposes, I synced all my files to the online version of Zotero but I only used the standone version.

    At this point I had tried pretty much everything except resetting and, still, I cannot open my PDFs in any of the two versions (standalone and online). Since then I unstalled Zotero from my PC and I only use my PC for my work.

    Standalone version: All my documents show/have PDF icons. However, about one-third have light blue dots and others light blue circles. I can only open files with blue dots but when I click the files with blue circles the aforementioned message appears.

    Online version: Like in the standalone version I can only open about one-third of my documents. Other files showed the PDF icon along with the message (attachment details) that takes me to the journal’s website.

    Thank you very much.
  • dstillman
    See Files Not Syncing, which is linked from that error dialog. The files just haven't synced from the computer where they were created.
  • clcastanedar

    Thank you for your prompt response.

    1. Before updating Zotero to 5.0.74 I had accessed to all PDF files on my laptop (standalone) and online. After the update, I only have access to one third of my PDFs which are stored within my Zotero data directory. This is the path: Macintosh HD>Users>XXX>Zotero>storage .I checked each of the folders in the storage file and I am missing 2/3 of my documents.

    2. I am using Zotero storage; currently, I have used 30% of the quota and the subscription expires on June/2020. I am not getting a sync error.

    3. I followed Step 5 instructions: I went to the Sync-Reset pane of the Zotero preferences on Computer A and select Reset File Sync History. I got this message: Success The file sync history for “My Library” has been cleared. Unfortunately, I still can’t access my PDFs.

    4. Next step, I am submitting a Debug ID. I will keep you updated.
    Thank you
  • clcastanedar
    This is the Debug ID: D810340441

    Thank you, again
  • clcastanedar
    I sent the Debug ID 3 days ago. There has been no changes. I still cant open my PDFs.

    What is the next step after sending the debug ID?

    I am working on my dissertation and I need access to the documents. Please help!!

  • dstillman
    edited October 7, 2019
    That appears to just be for a few seconds of the sync, not the whole thing, and it doesn't include an attempt to open a missing file, as requested in the instructions.

    But just to be clear, files would never disappear on the computer where they were created unless 1) you somehow ended up with Zotero pointed at a different Zotero data directory, which would also result in a completely empty library until you synced, or 2) you deleted them outside of Zotero.

    So the answer here is almost certainly just that you're trying to open files that were created elsewhere and haven't yet been synced to the online library on the computer where they were created.
  • emilianoeheyns
    The open blue dots are on the PC desktop? Or also on the Macbook?
  • clcastanedar
    The blue dots are on both PC desktop and on the Macbook.

    "1) you somehow ended up with Zotero pointed at a different Zotero data directory," -- Undertood but How do I find the misplaced files? So far I located the storage file in both PC and Macbook but the file in both computers only shows 189 files out of 520.

    "which would also result in a completely empty library until you synced,"-- Yes, but what do i do if the sycing is not working.

    "So the answer here is almost certainly just that you're trying to open files that were created elsewhere and haven't yet been synced to the online library on the computer where they were created."-- I read some of the documents that Zotero has availble but so far I have not located any more files. Please, could you walk me thru the steps? 1. How do i locate the missing files?


  • dstillman
    edited October 7, 2019
    We still need the Debug ID as requested in the instructions.
    How do i locate the missing files?
    https://www.zotero.org/support/zotero_data#locating_missing_zotero_data

    First, go to a computer where you first added a file that's now missing — ignore any other synced computers. What are the filenames, sizes, and timestamps of zotero.sqlite* files in the current Zotero data directory? If you look in 'storage', how many folders are there, and are the folder modification times all from a given time (suggesting that you synced them all down from the online library at once) or are they spread out throughout the time period that you were working with Zotero?
  • clcastanedar
    This is the Debug ID: D810340441 that I sent 4 days ago. Do I need to generate another one?

    I will follow directions you sent to locate missing files.

    Thank you for your assistance.

  • dstillman
    edited October 8, 2019
    As I said, the Debug ID didn’t cover the requested operations.
    That appears to just be for a few seconds of the sync, not the whole thing, and it doesn't include an attempt to open a missing file, as requested in the instructions.
  • clcastanedar
    Hi, this is the more recent Debug ID: D364756484. I followed Debug Output Logging directions. But it seems to be a problem because like the first time the syncing lasted less than 30seconds.


  • dstillman
    edited October 9, 2019
    That's still not what we need.

    1) Start debug logging with Zotero already started. Don't use "Restart with Logging Enabled…".

    2) Reset File Sync History.

    3) Sync and wait for the sync to finish.

    4) Try to open a file that's still missing.

    5) Submit the output.
  • clcastanedar
    Thank you so much for your time and help. I will follow the Debug ID directions.

    Per your suggestion, I tried to locate the missing data here: > Library >Application support >Zotero>Profiles> 56oasylq.default>storage.sqlite (Document 512 bytes ; created and modified 6/20/19 6:21 pm)

    Because I had trouble locating my previous data I am sending the following information:

    1. Your current data directory location from the Advanced → Files and Folders pane of the Zotero preferences: User/myname/Zotero

    2. The timestamp and sizes of zotero.sqlite* files within that directory
    a. zotero.sqlite 12.7 MB Created 4/28/2019 Modified: Today (10/8/2019) 9:00 pm
    b. zotero.sqlite-journal 91KB Created today (10/8/2019) at 9:00 PM Modified: Today (10/8/2019) 9:00 pm
    c. zotero.sqlite.1.bak 12.6 MB Created 10/3/2019 at 10:20 AM
    d. zotero.sqlite.bak 12.7 MB Created Yesterday 10/7/2019 at 12:40 PM

    3. Which version of Zotero you were using previously
    not sure
    4. The names of a few files you see in your Firefox profile directory
    I do not use Firefox


  • dstillman
    edited October 9, 2019
    Per your suggestion, I tried to locate the missing data here: > Library >Application support >Zotero>Profiles> 56oasylq.default>storage.sqlite
    storage.sqlite isn't something in any instructions. You would be looking for a 'zotero' directory within '56oasylq.default'. (That wouldn't be there unless you previously used Zotero Standalone 4.0 on this computer.)
    a. zotero.sqlite 12.7 MB Created 4/28/2019 Modified: Today (10/8/2019) 9:00 pm
    So it looks this database was created in April. Is that when you first started using Zotero on this computer?

    You didn't answer the questions about the 'storage' directory within /Users/user/Zotero:
    If you look in 'storage', how many folders are there, and are the folder modification times all from a given time (suggesting that you synced them all down from the online library at once) or are they spread out throughout the time period that you were working with Zotero?
  • clcastanedar
    I have been using Zotero Standalone for sometime now. I renewed Zotero storage on 4/6/2019.

    Storage directory:
    I have 195 folders but my library had 550 documents. The folder modification times are spread out throughout the time period that I have been working with Zotero. The oldest that I could located is from October 2017 and latest one is from 10/3/2019.

    -- I am about to cry. Please help!!
    I just tried to open zotero and it says that "Profile missing Your Zotero profile cannot be loaded. It may be missing or inaccessible"
  • dstillman
    edited October 9, 2019
    I just tried to open zotero and it says that "Profile missing Your Zotero profile cannot be loaded. It may be missing or inaccessible"
    This would happen if you changed the permissions on your Zotero profile directory or made some other change to it. There's a small chance that restarting your computer would fix it. Otherwise, you'll need to fix the permissions or just move it to your desktop as a backup and let Zotero create a new profile directory.

    To be clear, this is about the profile directory, not the data directory.
  • clcastanedar
    I already restated my computer and it did not work.

    Yes it is the profile directory.

    Move the Zotero profile directory to my desktop?

    I have not idea how to fix the permissions so i guess I will move it to my desktop.
  • clcastanedar
    Great!

    I moved "Zotero profile directory to my desktop" It worked. I am back in business.

    Next, I will follow new directions to generate Debug ID.

  • clcastanedar
    edited October 9, 2019
    This time the syncing last longer but still I do not have access to most of my PDFs.

    This is the Debug ID D608086188.

    This is what I did:

    1) Start debug logging with Zotero already started. Don't use "Restart with Logging Enabled…".
    In the Help menu, go to Debug Output Logging and select Enable,

    2) Reset File Sync History.
    I got this message: Success. The file sync history for "My Library" has been
    cleared.

    If the file hasn't been uploaded correctly but syncing completes on Computer A without a sync error, go to the Sync→Reset pane of the Zotero preferences on Computer A and select Reset File Sync History. (Do not use the other options in the Reset pane.) Resetting file sync history shouldn't be necessary under normal usage, but it will cause Zotero to check every attachment to make sure that it has been uploaded to the server.

    If the file becomes available online, continue to the next step.
    No files became available online.

    If not, provide a Debug ID for the first sync after performing Reset File Sync History, followed by a successful opening of the file locally, and post it to the Zotero Forums.

    3) Sync and wait for the sync to finish.
    Done, lasted at least one minute this time.

    4) Try to open a file that's still missing.
    I could not open any file that was still missing (blue circle as opposed to blue dot)

    5) Submit the output.
    D787428090
  • dstillman
    Attachment file '/Users/[…]/Zotero/storage/Z43JSP86/[…].pdf' not found
    OK, so that file doesn't exist on this computer, and it doesn't exist online either, which likely means it was created on another computer in 2016 and never uploaded. You need to find the computer where it was created and sync files on that computer. The same goes for all other missing files.

    Given that the 'storage' directory on this computer shows folders dating back to October 2017, it's possible you created it on this computer in 2016 and then ended up with Zotero pointing at a different data directory, so you could search for a 'Z43JSP86' directory. If you previously used Zotero for Firefox on this computer, you'd want to check the Firefox profile directory location for a 'zotero' directory, as explained on the support page, whether or not you're using Firefox now. But that folder would normally be migrated automatically, so there's a good chance you were just using another computer back then.
  • clcastanedar
    edited October 9, 2019
    This is the only computer that I have used.

    The first time I encountered this problem was when I downloaded Zotero in my Desktop (PC) and upgraded Zotero storage. That was back in June 21, 2019. Before that, I had access to all 550 PDFs. I wrote my QE using Zotero and never had a problem.

    Do you think downloading Zotero to my desktop (Computer B) might have been the problem?

    I will check Firefox profile directory. If this does not work. Do you have any other suggestions?

  • dstillman
    edited October 9, 2019
    The first time I encountered this problem was when I downloaded Zotero in my Desktop (PC) and upgraded Zotero storage. That was back in June 21, 2019. Before that, I had access to all 550 PDFs.
    No, you're almost certainly mistaken about this. You may have first noticed this when you installed Zotero on the PC, because these files never existed in the online library and therefore wouldn't have synced down to the PC, so if you then tried to verify that files had synced, they wouldn't be there. But installing Zotero elsewhere wouldn't cause these files to go missing on your Mac. Zotero never deletes files on disk separately from the attachment items in the library. The only possibilities are that something deleted them outside of Zotero or you created them in another data directory, either on this computer or another.
  • clcastanedar
    I know that I did not create them in another directory or computer -- I do not make any changes to programs and this is the only computer that I have used for the last 4 years.

    It is possible that the missing files never existed in the online library. I mainly use the standalone version; so, maybe they were not properly synced.

    But failure to sync should not affect files in the standalone version, right? And, what could had happened that only deleted Zotero files. This is a mystery!

    Do you have any other suggestion? or I just cut my losses and move on?














  • dstillman
    The suggestions are on the page I linked to above. You need to search your computer for the missing files, and you should also look specifically for a Firefox profile. There’s no other answer. They’re elsewhere on this computer, they were deleted by something outside of Zotero, or they were created on another computer.
  • clcastanedar
    Thank you for your time and patience.

    1. You need to search your computer for the missing files: "Done"
    2. you should also look specifically for a Firefox profile: "Unlikely but I have nothing to lose at these point"
    3. There’s no other answer. - Yes, it seems like you are right :(
    4. They were deleted by something outside of Zotero: "This will remain an unsolved mystery"
    5. They were created on another computer: "Not possible"

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