please help--references lost from zotero database

waisman

I desperately need help. I am using openoffice 2.41 and firefox 2.0017 with Mandriva 2008.1. I have written a paper and Zotero worked brilliantly. However I have written most of a second paper which I saved. After opening the manuscript and trying to add another reference Zotero told me that "this citation no longer exists in the Zotero database." The reference was in the database but is now gone. I then added the reference and after saving the document tryed again. Now most of the references are now longer in the database and I have many of the no longer exists errors. This is a huge, huge problem and I desperately need help. I love zotero but unless this problem is solved I cannot use the program. I hate the thought of going back to Refman.

Hope someone can help.

waisman

Forgot to mention that my database size is 23M. Is there a limit to the size??

dstillman

Did you by any chance use import/export to move references between multiple libraries?

waisman

Hi Dan,
Thank you for the reply. First, let me say that Zotero is an amazing program. You should be congratulated for an amazing effort. I am a former user of Reference manager. I used that program when it was first available in DOS so I am quite familiar with that program. I like Linux and use openoffice whenever possible. I have been looking for an excuse to break the Microsoft addition but could not find a linux program that would substitute for Refman. When I read about your program I decided to take the plunge. When I wrote the first paper (I am a professor of biochemistry and molecular biology) with zotero and openoffice I really tortured the program. It was indestructible. I couldn't believe how easy it was to use. I could tell you horror stories about Refman and corrupt databases that I experienced. Zotero is a remarkable achievement and I wouldn't hesitate to recommend it.
I backup the database on a stick using rsync and have never had any problems. My database is enormous--at least 23 M and growing. I like to attach pdfs to the papers so the database grows rapidly. When I was writing the second paper (which has over 200 references) I experienced the problem with references disappearing from the database. It took me an hour to correct the problem and re-enter the references. Since the bibliography at the end of the paper still had the references it wasn't a huge problem. When I used it again I again lost some references from the database and got the citation no longer in the database message--the citation was present in the manuscript but for some reason the reference was deleted. I also noticed that if I deleted a reference that it was immediately removed--no popup about am I sure I want to remove the entry. Then I read on the forum that some users were having problems with Firefox 20017. I upgraded Firefox to 3 and now I get the question about am I sure that I want to remove the entry. Most importantly, no more problems.
What is amazing to me is after all this messing around with the database everything is just fine.It look like the old Firefox allows entries to be removed but this does not happen with Firefox 3.--If I am correct then you should warn your users about this problem.

Thanks for a great program.
ps. is there a limit to the size of the database.

waisman

Sorry but the problem is back but I also got have another problem. It is specific to the document as everything is OK with other documents. I submitted report 705972729.

inadmissable value or data type. Index out of defined range.

The basic script stops at


The program has cut my references again.

Can you help.

waisman

the problem seems specific to my current document (the paper )as I tried another document and it is OK. I am really worried as the paper is due shortly.--Please help.

The basic script stops at
' Update bibliography data
If mResultArray(1) = "X" Then
For i = 0 To (j - 1)
Set mMarks(mBibliographies(i)) = fnRenameMark(mMarks(mBibliographies(i)), "ZOTERO_BIBL")
Next i
ElseIf mResultArray(1) <> "!" Then
For i = 0 To (j - 1)
Set mMarks(mBibliographies(i)) = fnRenameMark(mMarks(mBibliographies(i)), "ZOTERO_BIBL " & mResultArray(1))
Next i
End If

waisman

I cannot figure this out. If I cut the first four pages of the document into a fresh document the references are fine. If I add the fifth page then I get the inadmissable message. If I put the fifth page into a fresh document the references are OK. If I put it back into the 4 page document I get the same error message. The problem must be specific to the document---any ideas??

waisman

Wow. The previous document that worked perfectly does not work either. Same error message about inadmissable value.

must be a problem with the script but i cannot figure out why the problem has developed. I reloaded the addon but no luck.

dstillman

[I've removed your other two posts. There's no need to create new threads for the same problem.]

OK, so, to clarify, is this happening in all your documents, including new documents, or only certain documents?

When the script stops, what line is highlighted in the above code?

Have you tried removing the bibliography and re-inserting it?

waisman

Hi Dan,
Thanks for the response. It seems that all my documents are now affected. Also, occasionally, I notice that a reference is missing from the database. I tried deleting the bibliography and reinserting but it doesn't work. The script stops at
If mResultArray(1)= "x" Then.

I am a total loss to figure this out. My database is OK as it passes the integrity test and can be converted to RIS format and imported into Reference Manager where it works fine.

dstillman

It seems that all my documents are now affected.

New documents as well?

waisman

new documents seem OK.

dstillman

If you send one of the broken documents to support@zot....org, we'll take a look.

waisman

I have sent it to you this morning.

dmedelstein

Just wondering if there's any update on this case that could be publicly shared. I'm considering switching to zotero, but this user's story really frightens me.

waisman

Nope. I am waiting to hear from Dan. I hope he can figure it out because it has really worried me.

dstillman

waisman: Assuming you're still seeing this problem, could you upload your database to the DB Repair Tool and send us the Upload ID via e-mail? (You can ignore the download links it provides.) The citations in the documents you sent appear to be OK. A new copy of a file that triggers the error would probably also be helpful.

waisman

Hi Dan--I am still having the problem and my documents are unworkable. I have sent the database via the repair tool and sent support an email. The database has also been imported into Refman 10 and works OK with that program. I really cannot use zotero for any documents until this problem is identified as I cannot trust that it will not happen on new documents. I am still using Zotero to keep track of my PDFs. Hope you can solve this problem.

Thanks
David

dstillman

David: I tested the document you sent with the database you uploaded, and it appears to work just fine for me with Firefox 2, Zotero 1.0.7, OpenOffice 2.4.1, and 1.0b4 of the OO plugin. I was able to add a few citations and refresh the bibliography without triggering any errors.

Can you provide (here or via e-mail) explicit steps to reproduce the error?

waisman

Dan: I tried it again and have the same problem--the basic script stops at "If mResultArray(1) = "X" Then"
I have used both the rebuilt and original database. Can you tell me what that error means.Based on your results it looks like the problem is with the extension. I will try again to load the extension into OO and see if that makes any difference. Meanwhile do you have any other suggestions??

Thanks
David

waisman

Dan--I had an idea. I will send you my plugin since there is an export function.

David

dstillman

What exact steps are you taking, with the document you sent us, to reproduce the error?

The plugin is just the file you downloaded from our site, so that doesn't help, unfortunately.

waisman

I load the document into OO then hit the refresh button and immediately get the error message and a stop at the script at -my macros and dialog.zotero-. Same problem if I try to add a reference into the document. I tried to delete the existing extension and load a new extension but still get the same problem. What does the error code mean??

I plan to reinstall OO so lets see if that helps.

waisman

Interesting--I reinstalled OO writer and it refreshed the document. However when I attempted to insert a reference it gave me the same error message--This is a really tough problem!!

waisman

Hi Dan--I have also tried the document on another computer with a similar setup. Same problem. Do you know what can cause the zotero extension--my macros and dialog.zotero- to hang up at this point??

Thanks.

sunnyalley

I am having a similar problem, though perhaps with different causes.

I wanted to run my database from Dropbox so that it continuously updates and is available from other computers. When I went through the process of changing where my browser saves the database, it simply wiped it out. I recreated the database using a backup I had created by exporting to an rdf file. However, when I open a document created before I did this, I get the message saying this "citation no longer exists in the Zotero database" (the citation IS still in my database). These citations then no longer appear in my bibliography.

sunnyalley

Sorry - I should have mentioned - I am using the updated version of Firefox and Microsoft Word 2002

noksagt

RDF import/export does not preserve item IDs.

If you used the recommended backup method (keeping a full copy of your zotero data directory), restore that.

If you only have the RDF, you'll have to replace citations in that Word file.

dstillman

sunnyalley: It's highly unlikely that anything got "wiped out". Zotero doesn't move your data when you change the data directory setting—you have to copy it yourself. See Troubleshooting Zotero Data to understand how this works. Please start a new thread if you're still having trouble.

waisman

Hi Dan--I had an idea. Could you email me the document that you made from my original that you have added references to. I will see if it works on my system.

Thanks.

dstillman

"Index out of defined range" issue continued on another thread.