Upgrade StorageAfter exporting to Mendeley: Attached file not found. Could have been moved or deleted.
Hello everybody,
I usually use Zotero for scientific bibliography retrieval, organization and citation. However, since my colleagues use Mendeley I decided to export my references to Mendeley, from within the later (Mendeley asks to include the Zotero sqlite path for exporting). After doing so I find the topic error message each time I try to open a pdf file.
Zotero shows the attached files as pdf icons in the references list, with their corresponding name, which I usually rename using the container metadata. However, when I either double left click or right click and select show pdf the error message shows up. I searched the storage directory and the pdf files are there, each in a subdirectory under:
.mozilla/firefox/some_name.default/zotero/storage/folder_with_pdf_file.
There are as many folder_with_pdf_file as saved pdf from the internet source (usually NIH Pubmed).
I use the GNU/Linux 64 bit version of Zotero (currently 4.0.28) on an Asus eee pc 1215p dual core netbook with GNU/Linux Debian 8.0 stable version (Kernel version: 3.16.7-ckt20-1+deb8u3).
I would appreciate any help to solve this issue.
Thank you in advance. Regards,
I usually use Zotero for scientific bibliography retrieval, organization and citation. However, since my colleagues use Mendeley I decided to export my references to Mendeley, from within the later (Mendeley asks to include the Zotero sqlite path for exporting). After doing so I find the topic error message each time I try to open a pdf file.
Zotero shows the attached files as pdf icons in the references list, with their corresponding name, which I usually rename using the container metadata. However, when I either double left click or right click and select show pdf the error message shows up. I searched the storage directory and the pdf files are there, each in a subdirectory under:
.mozilla/firefox/some_name.default/zotero/storage/folder_with_pdf_file.
There are as many folder_with_pdf_file as saved pdf from the internet source (usually NIH Pubmed).
I use the GNU/Linux 64 bit version of Zotero (currently 4.0.28) on an Asus eee pc 1215p dual core netbook with GNU/Linux Debian 8.0 stable version (Kernel version: 3.16.7-ckt20-1+deb8u3).
I would appreciate any help to solve this issue.
Thank you in advance. Regards,
https://www.zotero.org/support/debug_output
That should allow us to say more.
The fact that this happened after importing to Mendeley, though, is a bit troubling. Obviously that shouldn't change anything on the Zotero side of things.
This is what I get, but I don't know if this actually refers to the error I receive. Notice that some reference is made to an https address and I am having trouble using the standalone version.
Debug ID 748260766
[JavaScript Error: "no element found" {file: "https://Mendieta:********@api.zotero.org/users/2025772/items/258XT8ZI/file?auth=1&iskey=1&version=1&info=1" line: 1}]
[JavaScript Error: "no element found" {file: "https://Mendieta:********@api.zotero.org/users/2025772/items/28GN9484/file?auth=1&iskey=1&version=1&info=1" line: 1}]
[JavaScript Error: "no element found" {file: "https://Mendieta:********@api.zotero.org/users/2025772/items/292HTMB8/file?auth=1&iskey=1&version=1&info=1" line: 1}]
[JavaScript Error: "no element found" {file: "https://Mendieta:********@api.zotero.org/users/2025772/items/294TP6B2/file?auth=1&iskey=1&version=1&info=1" line: 1}]
version => 4.0.28, platform => Linux x86_64, oscpu => Linux x86_64, locale => en-US, appName => Zotero, appVersion => 4.0.28, extensions => Zotero LibreOffice Integration (3.5.9.SA.4.0.28, extension), iTunes Application Detector (, plugin), IcedTea-Web Plugin (using IcedTea-Web 1.5 (1.5-2+deb8u1)) (, plugin), Gnome Shell Integration (, plugin), Shockwave Flash (11.2.202.559, plugin)
Thank you in advance. Regards,
Gerardo
For some reason Zotero appears to be looking online rather than locally.
@Dan -- could you check the Debug to see if there's anything else that'd plausibly go on?
But are you seeing this on the same computer where they were added, and in the same data directory? It's much more likely that the files simply weren't synced properly. Note that you're at your file sync quota, so your files likely haven't all synced. Even if it is the same computer, if you changed your data directory and didn't move the existing files properly, Zotero would download all server data to repopulate your database, but files in your previous data directory that hadn't been uploaded wouldn't come back down to the new data directory.
Answers to Adam:
1) I can see the pdf in the directories when I check them.
2) Strange enough, the path to the data directory is as follows:
/home/germ/.mozilla/firefox/60076pwx.default/zotero/storage/storage
Notice that the subdir storage appears twice (but data files are only in the last path of the chain)
3) The subdirs where the pdf files are (within the "storage" subdir") may be duplicated, e.g., two 258XT8ZI or similar may be present.
4) Within these duplicated subdirs, besides the pdf file which is always present, there is always a .zotero-ft-cache file. However, a .zotero-ft-info file may be present in one of the subdirs but not in the other.
Answers to Dan:
1) I am seeing this on the same computer where they were added and in the same data directory.
2) Regarding syncing I kept the local system syncing with the Zotero server last night (I also thought it was a syncing matter because of a problem with my university server this weekend). However, after full syncing with the Zotero server the problem persisted. In fact, I have the same number of pdf files in my standalone version and in the Zotero server.
I eagerly wait for your further comments and directions. Thank you both,
Best regards,
Gerardo
One thing I forgot to tell is that, if I go to Preferences and check for db integrity, the db doesn't show any errors.
The path to the data directory shown in the Files and Folders tab is:
/home/germ/.mozilla/firefox/60076pwx.default/zotero/storage/storage
That is, the same as commented in my previous message and the base directory is:
/home/germ/Research/References
Thanks again. Best regards,
Gerardo
Following there may be a clue about what's going on. But I don't know how to solve it.
When I position the cursor at a line containing a pdf file in the Zotero main window (where I have the columns "Author", "Year" and "Title") I find the right side panel shows file info. One of the lines states: Indexed (Yes/No). I found that I can open the pdf files as far as the line shows Indexed: Yes. But not when it shows Indexed: No.
So the problem is in indexing. I don't know when the indexing mess came out but it is obviously that which is causing trouble.
pdftotex and pdfinfo version 3.04 are installed. So, I've just pressed the "Rebuild index" button (I don't know if the English version of the button is this, just a literal translation from my Spanish version). It takes long for the whole index to be rebuilt (even for my 4-core micro, 2 GB RAM netbook working at 1.5 GHz). I'll comment what happened in my next post.
Thank you in advance. Best regards,
Gerardo
First, let me tell that rebuilding the index had no effect. Second, regarding my previous comment on the possibility to open pdf files provided the rightmost panel showed Indexed: YES. It is only partially true. Some of the files with the YES tag would open but others would not.
Last, I never set the data directory manually. I just let Zotero set the directories during the installation process. The weird thing is that the double zotero/storage/storage/... directory path appeared after an installation from a .tar.bz2 file I downloaded from Zotero, since the package from my Debian distribution was outdated and no newer version appeared in the repositories. This forced me to download the latest Zotero version, because I couldn't handle the pdf files for some reason, but everything went ok so far. At least until I did the "famous" export to Mendeley, which I understand may be a coincidence and not the cause for the currently observed problem.
Last, regarding your previous comment, "For some reason Zotero appears to be looking online rather than locally", what I found is that I can open the pdf files when I call them from the Zotero version opened from a firefox tab (the famous "Z" symbol in Firefox tools. But this is not possible when I use the standalone version. In line with yor comment above, although syncing with Zotero server fails because I reached my storage quota, I can still save references when using the firefox tabbed version Zotero and retrieve the pdf files when I right click con "View pdf" or "View online". The references and pdf files appear in the "off line" Zotero version too, though I cannot open them. And the pdf files are in my HD because I find the directory where they are saved under the data directory. Moreover, pdf files appearing with Indexed = YES in the tabbed version, show Indexed = NO in the off line version. May be this is something that may help you understand what's going on.
Thanks again Adam and Dan for the help you are providing to solve the bug (if it is really one). Besides this, Zotero is awesome. And I will go on sticking to it in spite of my colleagues preference for Mendeley (hehe).
Best regards,
Gerardo
See https://www.zotero.org/support/kb/sharing_data_directory
Thank you for the link. This is what I found.
When I first open the Zotero tab for Firefox and then open the standalone version, a message appears stating I cannot see the db in the Zotero Firefox tab because the standalone version is open. On the other hand, if I open the standalone version, the Zotero tab for Firefox won't open at all. Moreover a message appears when I put my mouse on the "Z" icon (not necessary to press any button). The literal translation from Spanish to English would be something like:
"Autonomous Zotero was launched, but it's not accessible. If you have expeerienced and error opening autonomous Zotero, reinitialize Firefox." When I go to Zotero standalone (I didn't reinitialize Firefox yet) I find a yellow triangle to the left side of the syncing icon (the green curved arrow). If I press the left mouse button on this triangle the following message pops up (literal translation): "You have reached your Zotero files storing quota. Some files were not loaded. Other Zotero data will continue to be synced with the server. Check your accound configuration at zotero.org for additional storage options".
Continuing with the journey to somewhere lands...
When I call the data directory with "Show data directory" from the standalone version, it shows:
/home/germ/.mozilla/firefox/60076pwx.default/zotero/storage/storage
When I do the same from the Firefox tabbed version, it shows:
/home/germ/.mozilla/firefox/60076pwx.default/zotero/storage/storage
Therefore data directories accessed by both the standalone and tabbed version seem to be the same. However, I still suspect there is a syncing problem. Am I wrong?
Thank you again for your help.
Best regards,
Gerardo