Updated to Firefox 37 and lost Zotero files

teisenman · May 8, 2015

Hello –

I recently updated Firefox to version 37.0.2 and lost the Zotero data on my computer. My data on the web-based Zotero cloud seems to be intact, so all I should need to do is download/sync the cloud data down to my computer. But I am concerned that the sync will go in the opposition direction ... in other words, that the cloud will read the (now) empty zotero folders on my computer, and in so doing I may lose all 3,700 unique zotero entries I've accumulated over the past several years.

How do I do a sync to ensure that only the cloud data downloads to my computer?

Kind Regards,
-Theo

adamsmith · May 8, 2015

There is a Restore from Server option under Reset in the Zotero preferences. YOu don't really need it -- Zotero sync won't delete any items you haven't explicitly deleted -- but it also won't do any harm here.

That said, I'd want to find out what happened to your Zotero data locally. Data doesn't just disappear. Do you see an entirely empty library with just the "Welcome to Zotero" item? Did you re-install Zotero at some point in troubleshooting? Create a new Firefox profile?

dstillman · May 8, 2015

There's almost certainly an Old Firefox Data folder on your desktop with your old Firefox profile, and within that there should be a 'zotero' folder that you can copy into your new Firefox profile directory and restart Firefox. It's still unclear to me whether Firefox in some cases does this on its own or whether people agree to it, but this is Firefox's reset feature at work, and it doesn't actually delete any data. It's better to just restore that folder if you have it rather than using sync to pull down all your data.

Maise Tomlinson1 · May 14, 2015

Hi, I have a similar problem, but the solution above hasn't worked. I refreshed Firefox and lost most (but not all) of my Zotero library, as I hadn't synced since 2012. I have an Old Firefox Data folder on my computer and so I copied the Zotero folder and pasted into my Firefox profile, as per Mozilla Support's instructions (I guessed there might be lots of duplicates, but I hoped it would notify and let me select them out - it didn't). However, on restarting the computer, I click on the zotero icon- and nothing has happened. Same 2012 data as before. Does anyone know why?

dstillman · May 14, 2015

What's the date of the zotero.sqlite file in the 'zotero' folder in Old Firefox Data?

Note that you should remove the 'zotero' folder in your current Firefox profile before copying the folder from Old Firefox Data. (You can also temporarily disable auto-sync in the Sync pane of the Zotero preferences so it doesn't keep trying to pull down the server data while you're looking for the right copy of your database.)

Maise Tomlinson1 · May 17, 2015

Hello Dan, thanks for your reply.

I have done what you suggested - deleted the zotero files in the current Firefox profile and copied over the Old Firefox Data zotero file again but with no success. It copies over fine, but just isn't reflected in the zotero pane, which now shows 0 files since I deleted the zotero file in the current profile. The Old Firefox zotero has not updated into the pane.

I disabled auto-sync.

The date of the zotero.sqlite file is 10th April 2015.

Any more ideas?

adamsmith · May 17, 2015

what's the size of that file?

Maise Tomlinson1 · May 19, 2015

Ah - after some brow-furrowing I realised I had made a silly error and copied zotero over to the overarching Profiles folder instead of the profile itself. Thanks though both for your help!

teisenman · May 28, 2015

Dear Colleagues,

Belated thanks for your timely and detailed feedback. I've been traveling the last few weeks, thus the delayed response. During this period I also upgraded my Macintosh OS + Firefox. The Zotero library is now fully intact within Firefox, and I am much relieved.

The only minor glitch is that attachments are opening in webview, as opposed to the originals that live on my computer. I prefer the latter, as I tend to make highlights and keep notes directly in the PDFs. I'm sure it's probably just a few clicks to revert back to the system I had before where the original articles opened up when I clicked on them in Zotero . . . but I've searched in the help forum + gone through the preference settings directly in Zotero, and I can't find the correct links.

Any assistance you can provide on this matter is appreciated.

Kind Regards,
-Theo

adamsmith · May 28, 2015

what exactly do you mean by "webview"? Firefox's built-in PDF viewer, or the webpage you downloaded the item from originally?

teisenman · May 28, 2015

Instead of the PDF (that lives on my computer, and upon which I've already made comments) opening up as an independent file, it opens up in Firefox's built-in PDF viewer.

adamsmith · May 28, 2015

what does it say in the URL bar when that happens? Do you see a regular URL, or something like zotero://attachments/1234 ?

teisenman · May 28, 2015

It says: "zotero://attachment/6684/"

teisenman · May 28, 2015

I'm using Firefox 38.0.1

adamsmith · May 28, 2015

OK, so that _is_ the file that's on your computer. It just defaults to Firefox's built in viewer. I'm surprised you don't see your comments there--for most PDF viewers except Skim, Firefox should show comments.

You can default to your system's (rather than Firefox's) by toggling the "launchNonNativeFiles" hidden preference https://www.zotero.org/support/preferences/hidden_preferences#general_preferences

teisenman · May 28, 2015

Thanks. I can see comments in the Firefox PDF viewer, but interaction with the document is clumsy, and I'm not sure if/how to make new comments.

I'm trying to follow directions to fix this...and upon clicking on "about:config" Firefox opens up this huge warning window stating that anything I do may jeopardize the security of the system and nullify the warranty. I nevertheless proceeded . . . and got another window with hundreds (thousands?) of rows of technical computer jargon. Is this really the path I should be pursuing? Isn't there any easier solution?

adamsmith · May 28, 2015

you'd just past "launchNonNative" into the filter box, right click the corresponding option and select "toggle," so it's not actually hard to do. The only other choice would be to adjust your Firefox PDF settings, but you may not actually want that.

teisenman · May 28, 2015

Excellent! That helped. I made the change and it worked.

Thanks so much for the assistance. As an academic, Zotero is one of my most important applications, by far, and despite some minor glitches the software works amazing well. I'm a huge fan. :-)

teisenman · June 30, 2016

Hello,

I am picking up on this thread from about a year ago, because I have encountered the same problem again. When updating Firefox (now 47.0.1), I lost all of the Zotero data in the Firefox plug-in.

I followed the directions above: I copied the Zotero folder from the "Old Firefox Data" on my desktop and pasted it into the "Firefox Profile Directory" and then restarted Firefox. But my Zotero data is still not populating within the Firefox plug-in. The only thing showing in the Firefox Zotero window is a "Zotero Quick Start Guide."

I am on deadline for submission of an article and cannot currently add citations...so I'd like to resolve this problem as soon as possible. Any assistance is kindly appreciated.

Kindly,
-Theo

dstillman · June 30, 2016

Theo, see these steps: Restore After Firefox Reset

You may have to adjust them, since you've already moved things around. What matters is that you have a non-1 MB zotero.sqlite file and a populated 'storage' folder within 'zotero' within your active data directory. Obviously, don't delete or overwrite anything.

teisenman · June 30, 2016

Thanks Dan –

Since my previous message, I updated the Java plug-in and restarted Firefox (regarding another problem), and voila, all of sudden the Zotero data was populated in Firefox plug-in. I have no idea if this was related to the Java update or not.

Here's what I currently see in the Zotero folder within the Firefox Profiles folder, as it relates to your directions below:

- zotero.sqlite 19.8 MB
- zotero.sqlite-journal 54KB
- zotero.sqlite.1.bak 1MB
- zotero.sqlite.bak 1.1 MB

Is everything kosher?

adamsmith · June 30, 2016

It definitely wasn't Java (which Zotero doesn't use). From what you describe in addition to the sqlite sizes, I'd guess that what happened was that your Zotero library synced down from the Zotero server. That's perfectly fine and you won't have any problems going forward. The one thing to check is that you are able to open attachments (just test out a couple). If that's the case, you're good to go.

teisenman · June 30, 2016

Yup – I am able to open PDFs from within the Zotero window in Firefox. Excellent!

NOW... there is one problem remaining. I am unable to insert citations from within MSWord. When I click on the Zotero icon in MSWord, I get the following error message: "Zotero could not load the component required to communicate with your word processor. Please ensure that the appropriate extension is installed and try again."

Do I need to reinstall the Zotero plug-in for MSWord?

adamsmith · June 30, 2016

Yes, that'd be the first step.

teisenman · June 30, 2016

Can you please offer direction, i.e. how do I remove the current plug-in and replace with a new one?

Thanks.

adamsmith · June 30, 2016

Just re-install the relevant add-on from https://www.zotero.org/support/word_processor_plugin_installation
no need to remove the old one.

teisenman · June 30, 2016

Thanks Adam – I successfully installed a new plug-in for MSWord and everything seems to be working fine. I appreciate your assistance.

Musaed Aklan · November 30, 2016

I found Firefox updated and don't know how! I couldn't find Zotero icon anymore, should I install it again. what about my files i saved in zotero before? I organized all documents in groups, can i find all files and groups i created before? many thanks

adamsmith · November 30, 2016

It depends on what you're seeing. If this was just a Firefox update and Zotero is no longer compatible, yes, re-installing will do and your data will still be there.

If, on the other hand, Firefox refreshed, see here: https://www.zotero.org/support/kb/restore_after_firefox_reset

Musaed Aklan · July 19, 2017

I have my references in my laptop and have nothing in my online library. Two days ago I opened Firefox and Zotero and found nothing in Zotero library except empty collections. I found all names of my groups and sub-groups (collections and subcollections) but all are empty? can you advice what to do?