"Item x in this citation no longer exists in your Zotero database"

jphekman

PROBLEM: When I attempt to add a new Zotero citation, or edit an old one, I get the error "Item X in this citation no longer exists in your Zotero database" with an offer to replace it. This happens for many, but not all, items in the document. I do not wish to replace all the items, as Zotero does not make it clear which item needs replacing, so finding the new citation ID is difficult.

BACKGROUND: Unfortunately, a complicated history! I use Zotero on two different Linux boxes (my desktop and my laptop). My old laptop (on which I used to edit this paper, along with the desktop) recently broke and I purchased a new one. This is the first time I am using Zotero on the new laptop. (I copied my entire home directory from old laptop to new laptop, so that is how the Zotero database got copied over.)

Additionally, since it has been several months since I have last attempted to edit the paper, the Zotero plugin has upgraded in the meantime. When I first opened the document, I was told that it needed to be upgraded "to work with Zotero 2.1 or later." I allowed the upgrade.

Desktop: Firefox 3.6.17, Ubuntu 10.04 (lucid), Zotero 2.1.5
Laptop: Firefox 3.6.17, Ubuntu 10.10 (maverick), Zotero 2.1.6

WHAT I'VE TRIED:
Laptop: using an old version of zotero.sqlite and re-syncing. This actually appeared to work for a while and I was able to add some new references, but then the problem recurred. (I don't know what I did to make the problem recur -- I don't think I did anything!)

I also tried copying zotero.sqlite from the desktop to the laptop. This never seemed to fix the problem.

I also tried editing the file directly on the desktop (the old version, not the version that I had edited on the laptop, so it did ask me to upgrade it again). This never seemed to fix the problem.

I am mailing a copy of the document to support@zotero.org.

I see that there has been a lot of discussion about similar problems on this forum and have tried to follow those suggestions but have had no success so far. Apologies if I did something dumb.

Thanks so much for any help you can give!

jphekman

OK, I am about to dive in to fixing this manually (wish me patience!).

I would love, love, love suggestions on how to keep this from happening again. I have come to dread coming back to any project with Zotero footnotes in it after an appreciable gap, as there always seems to be something unfixably wrong with the document. What am I doing wrong? I am using ODT, not DOC. OpenOffice, not Word. Allowing the plugin to upgrade (maybe that's my problem?).

Any help appreciated! Thanks,
Jessica

dstillman

What's a reference that shows up as missing?

jphekman

Reference 69 is one.

It is possible it actually IS all of them; as I am working through the document, giving it new references to replace the ones it can't find, it just keeps offering me more. It skips some, but then comes back to some -- maybe we are going to go through the whole document, out of order; I can't tell.

As I correct each error, I am offered a new one. Periodically it does not offer me a new one, but instead complains that it can't update the document because a reference is missing (yeah, you think?). If I then try to add a reference or edit a reference, it starts offering me more references to find replacements for -- different ones from before. Since the document still doesn't say it's been edited, I am a little worried that all this work is just going straight down the drain.

Jessica

jphekman

Update: finished "fixing" the document, in that it no longer offers me more missing references. However, when I try to edit a reference that it had asked me to replace, the "edit citation" box now comes up with no citation in it, if that makes sense. Huh! When I go to add the correct citation, it won't let me -- I click on the arrow to move the citation into the list of multiple citations, and nothing happens. I tried just making a brand new reference -- no luck, still can't add a citation to it. ?!

I created a new document and was able to add the same citation to that one, no problem.

Is my document just completely hosed? Do I have to start entirely from scratch? I am trying not to get all stressed out about this, but I can feel myself starting to slide down the slope :)

Jessica

fbennett

Jessica,

If you check your messages on zotero.org, I can supply you with a copy of Zotero 2.1.6 that has the latest version of the citeproc-js processor. I can't guarantee a positive result, but I would be very interested to know whether the problems in your document heal up with the processor revision.

dstillman

Reference 69 does exist in your database on the server, at least, along with all the other ones I checked.

Frank, why would a processor issue affect the ability of Zotero to find an item in the database?

fbennett

That's a very good question. But since the 2.1.6 release, I've done quite a bit of cleanup in the processor, and it would be worth checking, if Jessica is willing to back up and give it a try.

Technical note: One issue I've fixed that might be relevant relates to previewing. If the processor crashed for some reason while generating the preview string, it threw an error that Zotero would step past. This left the processor registry out of harmony with the actual state of the document, which could cause various errors. An empty preview box does suggest, at least, that there may be an issue there in Jessica's document.

(Edit: to clarify, by "step past", I mean that the processor crash would hang the plugin popup, but would not bring down Zotero. Any subsequent edit or insert attempts would then have unpredictable results, because the processor registry contents are incomplete or incorrect.)

dstillman

Has Jessica (or anyone else) verified whether the updated processor addresses this issue?

jphekman

I emailed Frank so that he could send me the link to the version with the updated processor but have not heard back, so I haven't been able to test it.

Would you like to see a copy of the newest version of the document, in which I replaced all the references, which now will not let me edit/add new references? (I should say: it does not let me edit it on my laptop; I tried copying it to my desktop, where I got the old "item X does not exist in your database" error.)

I still wonder if the fact that I got a new laptop a few months ago has anything to do with this. I did try to clean up my database by using an older version of zotero.sqlite. Is there something else I can do? (My desktop has not been changed; I get the same error there; but perhaps syncing with the laptop db broke that.) Can I completely get rid of zotero.sqlite and download a clean db from your server?

dstillman

Here's one way to check whether those errors are legitimate or whether it's due to something else (such as the processor):

1) Hover over a citation bookmark that shows as missing, and you should see a URI that includes an 8-character key, e.g., "AB2G6WBW". (If using fields in Word, you would have to right-click and select Toggle Field Codes.)

2) In your Firefox address bar, paste this URL:

zotero://report/items/0_AB2G6WBW/html/report.html

Replace "AB2G6WBW" with the key from the bookmark.

If the item does exist in your library, you should see a generated report with its data.

jphekman

Testing that on the older version of the document (before I tried to repair the links) I get a page saying "Invalid ID." Testing it on the newer version of the document (after I tried to repair the links) I get a page summarizing the link in question.

It sounds like the item does not exist in my library -- but I see it there, so I guess the ID is just wrong. So then it is NOT a processor problem?

(Dan: btw, sorry about the confusion on the General forum -- I meant to discuss a broader problem, not reopen this one.)

dstillman

What's an example of a missing key from the original document?

And I understood that you were trying to discuss a broader problem, but there's nothing to discuss in the abstract—we can only debug specific, reproducible problems.

jphekman

zotero://report/items/0_FMTQ68GD/html/report.html

ajlyon

I mentioned in the other thread that if you exported and reimported all or part of your library at any point, the linkages the affected items in your library could break. Could that be what happened here?

dstillman

You deleted that item—along with >400 others—from your online library on May 2nd.

My guess is that you manually deleted duplicates or otherwise cleaned out your library a few days ago, and so citation links were lost. That's really all there is to it.

Duplicate detection functionality that preserves citation links is forthcoming.

jphekman

Dan: Yeah, when I saw that I was going to have to rebuild all the links in the file by hand anyways, I figured it was a good time to get rid of all my duplicates (which I had been allowing to remain in order to avoid exactly this problem). This problem started before I removed the duplicates. It does make it hard to debug, though -- sorry; at the time that I did it I was under the impression that I was just going to have to move ahead without more debugging.

I still don't know why the new version of the document won't let me add or edit citations. I guess the way forward there is to just cut and paste and redo that from scratch.

ajlyon: I never exported and reimported my library, but I did move my local database to my new laptop. I am still unsure if that is what broke things. All I did to move it was copy my home directory from old to new laptop. Do you know if there is a different way that I should have copied it over (that I should deal with this the next time I get a new computer)?

adamsmith

no, copying your home directory was exactly the right way to go. That's unlikely to be the problem.

dstillman

When I go to add the correct citation, it won't let me -- I click on the arrow to move the citation into the list of multiple citations, and nothing happens. I tried just making a brand new reference -- no luck, still can't add a citation to it. ?!

Provide a Report ID.

jphekman

Dan! You fixed it magically by requesting a proper report!

I swear to god it was broken yesterday and that I stopped and restarted Oo and Firefox before posting about it.

I seem to be entirely unstuck now and moving forward. Frustrated that this was such a nebulous problem to report and sympathetic that it was a nebulous problem to try to debug. Thanks for all the help.

Jessica