blue attachment dot

YvBa
Hi,
we do currently have some problems with our group library.
Since we have the nice new feature of the blue dot, indicating whether there is a file attached to an entry or not, there are error messages when opening certain files. So references that once definitely had a file attached now show an unfilled blue dot and when attempting to open the file it says:
"The attached file could not be found. It may have been moved or deleted outside of zotero." It also offers the opportunity to locate the file, which does not work.
Does anybody have an idea how this could be solved?
Thanks!
  • dstillman
    Start here: http://www.zotero.org/support/kb/files_not_syncing
  • YvBa
    The problem is, that I can see the attachment on the server, but I am unable to open it -- even there.
    Is this also a syncing issue then?
  • dstillman
    Where was the file added originally?
  • YvBa
    Files are added by several group members from several computers and locations. All of them sync before and after working with the group library. Sharing the files like that used to work quite well.
  • adamsmith
    Can _they_ access the PDF from the server? If not, something isn't working wrt to their file syncing.
  • YvBa
    Once everyone could open those files in question, also from the server, yes. This changed, in my opinion, since we have the blue dot. I don´t know if this really is the reason, but it seemed to be connected. We now have the situation that some entries do have more than one PDF attached, with at best, one working, and others not.
    However, this also means that the markings in the original PDFs are lost and there is a huge amount of entries for which we would have to add a new attachment.
  • fbennett
    I think adamsmith would like to know whether, at present, the user that uploaded an attachment that currently shows an empty dot on your system can (a) still access the file on their own computer, and (b) if so, whether they can access the file in the online library when they are logged in.
  • adamsmith
    what fbennett says. In general it sounds like file syncing isn't working for you at all at the moment and you'll want to troubleshoot that.
    The link by Dan above gives you specific steps for that and tells you what type of information we need if none of those steps work.
  • Brown Biomechanics
    We are having a similar problem and as best I can tell its not related to syncing as described above.

    Once upon a time all PDF were available to our group. Then over the past few weeks the blue dots started showing up unfilled. Clinking on the attached PDF says the file cant be found. But it is there, it is in its Zotero folder. Whats stranger is this: I locate it and click on the file but Zotero still cant locate it.

    If I delete the PDF and reattach it then it seems to be working, but this is really frustrating to go and manually fix all these. Additionally, Zotero seems to create a new folder so I am not sure how its handling the now orphaned folder.
  • adamsmith
    Dan will want a debug ID for an unsuccessful attempt to open a PDF:
    http://www.zotero.org/support/debug_output
    It would likely help if you also provide the file-path of the PDF (i.e. it's actual location in the Zotero folder).
  • Brown Biomechanics
    Debug ID is D641668100
    PDF is stored here - H:\Zotero References\storage\UFTT5MF8
    Even after I located the PDF, Zotero says attached file cant be found.


    Thanks!
  • dstillman
    edited June 3, 2013
    Locating is meant for linked files that were moved/renamed or for stored files that were renamed outside of Zotero. You can't locate a file in another subdirectory of 'storage'—that file belongs to another item, according to the item key that makes up the directory name.

    According to your debug output, the file needs to exist here:

    H:\Zotero References\storage\4HXRAGN7\

    There's no reference to the item "UFTT5MF8" in your debug output. (To try to find that item in your Zotero library, paste that (without quotes) into the quick search bar. Note that it could exist in any of your libraries or their respective trashes, or it could not exist at all if you did something to get your 'storage' directory out of sync with the Zotero database.)
  • dstillman
    I checked—both 4HXRAGN7 and UFTT5MF8 exist in the same library of yours. Only UFTT5MF8 has a synced file on the server.
  • Brown Biomechanics
    The reference PDF existed as an attachment, then the blue dot turned open. Clicking on the PDF in Zotero gave the error that the file could not be located.
    A search outside Zotero located the correct PDF in ...\UFTT5MF8.
    I just checked and I am pretty confident there is no folder called ...4HXRAGN7\

    I also just noticted that for some references the open blue dot is showing up for SNAP SHOTS, but not for PubMed Entry under the same refs.
  • adamsmith
    H:\ isn't a network drive, is it?
  • Brown Biomechanics
    Yes H:\ is one our servers. Its been setup that way since we starting using Zotero, a few years ago.
  • adamsmith
    I'm not sure I completely understand the set-up, but having your Zotero database on a shared network drive can (and likely will) cause exactly these types of issues - you're using two types of syncing - via the server and via Zotero - at the same time and that causes exactly those types of problems. None of the internals have changed - the blue dot is just a display change.
  • Brown Biomechanics
    Hi, not sure i am following you about the two syncing. Under Preferences, I simply have the Data Directory Location set to CUSTOM and specify H:\Zotero References. I do this because H:\ is backed up while C:\ is not. I understand the blue dot is a new display,bu t we haven't noticed this problem until recently.

    Solution? Should we only be using local drives? Is there a way to clean this up ?
  • dstillman
    4HXRAGN7 doesn't have a file associated with it on the server, and it also hasn't been updated in over a year, which suggests the file was never synced to the server. There's no way in Zotero for a storage subdirectory to disappear without the associated attachment item being deleted. If the folder disappeared, it did so on your network drive, but the file also wouldn't have been synced to anyone else.

    Bear in mind that the blue attachments dots have only existed since Zotero 4.0, so you quite easily could've just not noticed that some files were missing in earlier versions.

    Also note that those two items, while by the same author, are actually completely different, so trying to associated the PDF from one to the other made no sense anyway.
  • adamsmith
    as for the network drive - the problem would be simultaneous access from multiple locations - I assume that's possible? Or do you just access that drive from one computer?
  • Brown Biomechanics
    We have a about 10 people in my lab all using Zotero. This "Brown Biomechanics" is the lab account. Each person has there own account. That network storage is only for my account and I only access that drive from one computer.

    On a quick look we are all missing the same files.

    How do we solve this and keep it from happening again? Thanks!
  • dstillman
    edited June 3, 2013
    Again, the file in your example—from the item 4HXRAGN7—is not on the Zotero server, and there's no indication that it ever was. And if not, that's why it wouldn't be on anyone's computer, because it was never synced. It should have been on the computer where it was originally added, but if it was deleted somehow, it's highly unlikely that that was through Zotero, since the attachment item still exists.

    I'm happy to look at another example, but the one you've provided doesn't seem to be indicative of a problem with Zotero.
  • Brown Biomechanics
    edited June 3, 2013
    Here is another one - thanks!
    Debug ID is D1895591090.

    It says this PDF was uploaded August 23, 2012. Clicking on it gives the cant locate file error.
  • dstillman
    That file also isn't on the server, with no record of its ever being synced. As I said above, the file should be on at least one computer—the one where it was added—but without its being synced it wouldn't be on multiple computers.

    The local folder would be H:\Zotero References\storage\23CABTF6\.

    I'm pretty sure there's no code in Zotero that could delete just the storage folder of an attachment without deleting the attachment itself, so I don't think this is a Zotero bug.
  • dstillman
    It looks like one admin in that group—username beginning with 'e'—did try to upload that file on 5/28 and hit a quota error (did you recently increase your storage space or transfer the group between users?). Does the file exist on the computer belonging to that user?
  • Brown Biomechanics
    Yes we did recently upgrade space.

    The PDFs are listed as attached files. If were never uploaded why do they show up as being attached ?

    The other strange thing is that there are some references, that I know never had PDFs. For these often they had SnapShots. Now for a few of these the SnapShots cant be located (open blue dots) - the the same symptom as the lost PDFs.
  • dstillman
    The PDFs are listed as attached files. If were never uploaded why do they show up as being attached ?
    An attachment item is separate from the file on disk, and a file on disk wouldn't be on the server until a file sync completed successfully.

    Best I can tell you is to read Files Not Syncing. There could be an issue with your network drive causing some storage folders to disappear—you'd have to answer my question above about that user in question—but beyond that I think you're just misunderstanding some of the fundamentals here.
  • Brown Biomechanics
    I think this may be related. A question:

    I click on a PDF that says is attached and it tells me it cant locate it. I have the option of locating it. I do. I find the PDF in another folder on my computer and select it. The window closes, everything looks okay, but when I click on PDF attachment again it still cant find it.

    ID is D174143747
  • dstillman
    edited June 5, 2013
    See what I said above about locating files in different directories:
    Locating is meant for linked files that were moved/renamed or for stored files that were renamed outside of Zotero. You can't locate a file in another subdirectory of 'storage'—that file belongs to another item, according to the item key that makes up the directory name.
    For your latest example, Zotero is looking for this file:

    /Users/[...]/Documents/Zotero Data Folder/storage/7HGHZA47/Salem.pdf

    You can see this yourself if you look at the bottom of the debug output.

    Also, the file for that item has never been synced to the server, so it wouldn't be on anyone else's computer.
  • dstillman
    edited June 5, 2013
    Just to be a bit clearer, if you try to locate a file in a different 'storage' directory from the one the file was originally in, I think Zotero will probably just use the filename of the selected file but look for it in the attachment's original directory, which obviously won't work. And when you go to locate a missing file Zotero will place you in the proper 'storage' subdirectory if it exists, so you should never need to click on a 'storage' directory yourself. If you do, you're doing something wrong. We should really display a proper error if you try to do that, but, basically, you're not supposed to navigate the 'storage' directories yourself, and you shouldn't really be trying to locate a file at all unless you know that you renamed it outside of Zotero.

    I can't tell you what happened to the original files, but you still haven't answered my question above about whether the file you were looking for above exists on the computer of the user who was previously trying to upload it, so I'm not convinced that you're even looking on the right computer for the files.

    Given that none of the files you've given as examples so far have existed on the server, I doubt there's anything going on here other than someone's files not having been synced to the server, as explained on Files Not Syncing. That's pretty much all I can say about this.
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