Upgrade Storage"File not found" error: not syncing, missing files, or false file path; may be ubuntu issue
I am no longer able to access any of the .pdfs in my collection of around 2200 citations. All my citations are unaffected, as well as my attached links and notes. I get the following message when I click on a .pdf or a snapshot:
"The attached file could not be found./It may have been moved or deleted outside of Zotero."
My problem seems to be different from that of other posters on the forums who have had this error message. When I click on one of these faulty .pdfs and check the "deug output", and go to lines such as this on the output...
(2)(+0000001): Attachment file '/home/michael/Documents/Michael PhD/zotero/storage/6DB5UUDD/605217.pdf' not found
...I find that the named file exists at the named file path. For example when I go to /home/michael/Documents/Michael PhD/zotero/storage/6DB5UUDD/ I find the file 605217.pdf.
I can also find the file by clicking on the "locate" button (in the "file not found" error window) and going to the relevant sub-folder (eg. 6DB5UUDD). I can even open and view the .pdf if I go to my file browser and open the file from the relevant sub-folder.
So this does not seem to be a problem with syncing, missing files, or a false file path.
Other info:
When I add new .pdfs to existing citations or to a new citation I do not have this "file not found" error. Nor do I have the error when I take an existing file in a zotero/storage sub-folder and re-attach it to the same citation (ie. by copying the .pdf to the desktop, deleting the .pdf item in zotero, then going "attach stored copy of file" and attaching the .pdf from the desktop).
I have a custom data directory which is (according to the "Advanced" tab in the "Preferences" window) set to home/michael/Documents/Michael PhD/zotero.
I have also done the following to no avail:
--restarted the computer twice
--twice closed all firefox windows then deleted the conpreg.dat and xpti.dat files, then re-opened the firefox windows
--clicked on "check database integrity" and received no-error message
The problem has been happening since 3 weeks ago I copied my zotero folder from an external hard drive onto my current machine, running ubuntu. I had copied the folder directly to the external hard drive from a different machine running Windows XP.
I have earlier backups of the zotero folder, and they create the same problem when I set those backups as the custom directory.
All of my zotero folders (including the backups) have no problems when I use them as data directories on a laptop running Windows Vista, Zotero 2.0.9 and Firefox 3.6.13 (ie. the same Zotero and Firefox versions as on my Ubuntu machine). So the error might have something to do with the switch to Ubuntu, but I know not what.
Details of Ubuntu machine:
zotero version 2.0.9
firefox 3.6.13
Ubuntu 10.04 LTS
Report ID: 1816716211
The Debug ID is D1374131046.
Sorry for the long-winded post, but I hope it helps to solve the problem. Any help much welcome. Thanks.
"The attached file could not be found./It may have been moved or deleted outside of Zotero."
My problem seems to be different from that of other posters on the forums who have had this error message. When I click on one of these faulty .pdfs and check the "deug output", and go to lines such as this on the output...
(2)(+0000001): Attachment file '/home/michael/Documents/Michael PhD/zotero/storage/6DB5UUDD/605217.pdf' not found
...I find that the named file exists at the named file path. For example when I go to /home/michael/Documents/Michael PhD/zotero/storage/6DB5UUDD/ I find the file 605217.pdf.
I can also find the file by clicking on the "locate" button (in the "file not found" error window) and going to the relevant sub-folder (eg. 6DB5UUDD). I can even open and view the .pdf if I go to my file browser and open the file from the relevant sub-folder.
So this does not seem to be a problem with syncing, missing files, or a false file path.
Other info:
When I add new .pdfs to existing citations or to a new citation I do not have this "file not found" error. Nor do I have the error when I take an existing file in a zotero/storage sub-folder and re-attach it to the same citation (ie. by copying the .pdf to the desktop, deleting the .pdf item in zotero, then going "attach stored copy of file" and attaching the .pdf from the desktop).
I have a custom data directory which is (according to the "Advanced" tab in the "Preferences" window) set to home/michael/Documents/Michael PhD/zotero.
I have also done the following to no avail:
--restarted the computer twice
--twice closed all firefox windows then deleted the conpreg.dat and xpti.dat files, then re-opened the firefox windows
--clicked on "check database integrity" and received no-error message
The problem has been happening since 3 weeks ago I copied my zotero folder from an external hard drive onto my current machine, running ubuntu. I had copied the folder directly to the external hard drive from a different machine running Windows XP.
I have earlier backups of the zotero folder, and they create the same problem when I set those backups as the custom directory.
All of my zotero folders (including the backups) have no problems when I use them as data directories on a laptop running Windows Vista, Zotero 2.0.9 and Firefox 3.6.13 (ie. the same Zotero and Firefox versions as on my Ubuntu machine). So the error might have something to do with the switch to Ubuntu, but I know not what.
Details of Ubuntu machine:
zotero version 2.0.9
firefox 3.6.13
Ubuntu 10.04 LTS
Report ID: 1816716211
The Debug ID is D1374131046.
Sorry for the long-winded post, but I hope it helps to solve the problem. Any help much welcome. Thanks.
What happens if you copy that file path above and paste it into the Firefox address bar?
1. Relinking works. That is, if I go "Attach link to file" and then attach the file from the debug file path, the link now works. This would be time-consuming if used as a final solution for all .pdfs.
2. Pasting the debug file path into the firefox address bar does not work. But it *does work* if I just change the file path so that the zotero sub-folder is in lowercase instead of uppercase.
eg. this does not work in address bar:
1) /home/michael/Documents/Michael PhD/zotero/storage/6DB5UUDD/605217.pdf
but this does work:
2) /home/michael/Documents/Michael PhD/zotero/storage/6db5uudd/605217.pdf
I tried changing the name of the zotero sub-folder to uppercase (via my file manager) and then 1) works but 2) does not ie. round the other way. Moreover, zotero then works ie. I can access the .pdf by clicking on it in the zotero window, without a "file not found" error.
Is the case of the sub-folder really the problem and if it is then is there a quick way of getting around it for all my zotero/storage folders?
Thanks a lot.
I changed all the folder-names in zotero/storage to uppercase using the ubuntu terminal.
I just navigated to the zotero/storage directory and then entered this command:
rename 'y/a-z/A-Z/' *
This seems to have solved the problem -- I can now access all the .pdfs and snapshots that I could not access before.
But is this solution going to cause complications in other places? And is there a more elegant solution?
Michael
I just created some new citations with pdfs and indeed the new folders corresponding to them have uppercase names.
I'm still not sure how to explain why the lowercase folders work fine on my Windows machine but not on my ubuntu machine. Also many folder- and file-names on my external drive have uppercase characters, and preserve these uppercases when they are copied from the external drive onto my computer. So the external drive may not be the whole problem.
But now everything works as I need it to work, which is the main thing.
Thanks again, Michael.