citation no longer in database

vinatan

Hi there,

Hope you can help. I'm about to have panic attacks soon... (working on lots of writing and Zotero is not cooperating!)

Recently had problems with syncing Zotero Standalone with Zotero Mozilla. Problem resolved by pointing the data directory to the one in Zotero Mozilla. This was on my home PC. Then went to work, Zotero had an 'update' and asked which library to follow. I went with the Zotero Mozilla in my office PC. Not sure what it followed before that. But work PC does not have Zotero bar in Mozilla after that but that issue is for another day.

Now, I'm working on a document (last opened in my work PC) and Zotero won't let me edit citations. "... no longer exists in your database". But it is in my database, well the one that I can see in my Zotero Standalone, home PC. I'm sure it is there in my office PC as well. I don't want to edit each citation again, 100++.

Please advise. I tried changing styles and some citation changed but others didn't. Refresh didn't work as well.

aurimas

Zotero had an 'update' and asked which library to follow

A regular Zotero update will never ask you to point it to a data directory. Can you explain a bit more on how you updated?

work PC does not have Zotero bar in Mozilla after that

See http://www.zotero.org/support/kb/no_status_bar_icon

Zotero won't let me edit citations. "... no longer exists in your database". But it is in my database, well the one that I can see in my Zotero Standalone, home PC. I'm sure it is there in my office PC as well.

If you're having sync issues, then it's likely that while the citation is on both PCs, it is not really the same exact citation (different IDs). Make sure you successfully sync both computers with zotero.org. After you sync, you will probably have duplicate citations (hopefully not too many) that you can merge.

Btw, how have you been transferring citations between work and home PCs?

vinatan

I don't know how I transfer citations between work and home PC. I thought that having one zotero login account handles it all?

That might explain why my recent additions at work didn't show up in my home PC.

But I worked on this same document before in my home PC and never had problems. All these recently popped up this year.

Forgive my ignorance but I don't remember what prompted the 'update' in my office PC but do remember the question of which library to use because of my recent sync issues.

vinatan

What can I do now?

aurimas

So it seems like you're just having issues syncing the two libraries, once you fix the syncing, everything will work. Go through these steps to start: http://www.zotero.org/support/kb/changes_not_syncing

vinatan

I read the link several times and don't know what to do. What is root library? trash? Sync arrow's green, and working...

I just remembered that the sync from my office to my home PC worked because it had folders that I created on SA appear in my home SA. the funny thing was a pdf article that I highlighted and saved in Zotero office was not transferred to my home PC. That was what prompted me to think that these two PC are not syncing.

Will uninstalling and reinstalling Zotero now help?

aurimas

No, do not re-install. This will almost never help resolve issues with Zotero.

Can you add a new item to you home PC for testing and verify that this item syncs to zotero.org? (See My Library link at the top of the page)

vinatan

It syncs.

aurimas

Now you should do the same from your work PC, though I suspect you don't have a way to do that right now.

Have you tried substituting that one reference with one from your home PC's library? (I'm not sure if that's how you decided that you would need to replace 100+ references) My guess is that you will _not_ need to do this for all of your references. This way you could continue working on the document until you can troubleshoot sync issues on your work PC.

Edit: please keep a copy of your original document.

vinatan

I guess I would have to leave it for now. But I have this extra info and not sure if it would help...

When I had my home SA and Mozilla not pointing to the same directory (last week, I think), someone from Zotero made a comment about why my SA directory was pointing to an empty folder. Then I was advised to use the Mozilla directory. This issue cropped up because my saves from Mozilla kept going into the Mozilla Zotero and not my SA. And that also didn't happen before, like a year ago.

Oh, what am I supposed to do when I get to the office? I'm pretty sure it syncs as I only used it two days ago and it synced the new folders to my home PC. Only thing fishy is the article that was highlighted didn't appear as highlighted at home.

aurimas

The reference that Zotero claims is no longer in your database, when was it inserted into the document? Was it before pointing SA to Mozilla directory?

vinatan

Yes, it was inserted before pointing SA to Mozilla.

aurimas

Could you search your whole computer for "zotero.sqlite" files? Post here the file sizes and last modified dates for each file.

Your references may be left in your old database if they did not sync to zotero.org before changing the data directory for SA. The idea would be to find the old database, point SA to that location, sync (it will not delete new references already on zotero.org), then change SA back to the current directory (make sure you make note of what that is) and sync again. Your databases would then be merged.

vinatan

I think my computer is still searching but have a feeling that these two are it. The data directory looks familiar.

First one,
C:\Users\user\AppData\Roaming\Mozilla\Firefox\Profiles\vsyteg5c.default-1391294546871\zotero
Size: 34.6 MB (36,360,192 bytes)
Created: Monday, ‎3 ‎February, ‎2014, ‏‎8:57:13 PM
Modified: ‎Today, ‎8 ‎February, ‎2014, ‏‎14 minutes ago
Accessed: Monday, ‎3 ‎February, ‎2014, ‏‎8:57:13 PM

Second,
C:\Users\user\AppData\Roaming\Mozilla\Firefox\Profiles\31rbtr5f.default\zotero
Size: 26.4 MB (27,774,976 bytes)
Created: ‎Friday, ‎25 ‎October, ‎2013, ‏‎10:17:27 AM
Modified: ‎Friday, ‎24 ‎January, ‎2014, ‏‎12:09:50 PM
Accessed: ‎Friday, ‎25 ‎October, ‎2013, ‏‎10:17:27 AM

vinatan

Yup, those two are it. The search just ended.

Should I carry out the change directory, sync, etc.?

aurimas

I assume your SA is currently pointing to C:\Users\user\AppData\Roaming\Mozilla\Firefox\Profiles\vsyteg5c.default-1391294546871\zotero

In that case, you can change it to point to C:\Users\user\AppData\Roaming\Mozilla\Firefox\Profiles\31rbtr5f.default\zotero

After the change and restarting SA, go to Preferences -> Sync and make sure that your username is correct. Then, click the green circular arrow to sync. Make sure that it completes successfully. After the sync (with Firefox closed), open up your Word document and see if you still get that message. Hopefully you will no longer see it.

Now point SA back at C:\Users\user\AppData\Roaming\Mozilla\Firefox\Profiles\vsyteg5c.default-1391294546871\zotero restart and sync

If everything synced correctly and you are concerned about wasted hard drive space (otherwise, I would not do this), you can probably delete C:\Users\user\AppData\Roaming\Mozilla\Firefox\Profiles\31rbtr5f.default\zotero Though I would hold onto it at least for a week or so, until you're sure everything is ok.

Edit: sync after restoring SA data directory at the end.

vinatan

I will report back after all this. Before that, I want to let you know that you saved my tears from falling... Lump in throat nearly gone. Thank you for troubleshooting.

vinatan

Hi again,

It didn't work. I checked a whole bunch on citations in the document and some were blank although I have the file in my SA.

I will leave it for now and try it when in the office. Will report back. Meantime, I am still open to suggestions.

I am working on my thesis and unless someone has it real bad for me, I hope this will not happen in that document.

Thanks again.