Attachments were saved (into storage/) but db was not updated so work is effectively gone?

andrew.nguyen

I have been doing quite a bit of research and collecting new papers and references over the past few hours. They were all appearing in the Zotero pane as expected, and I even renamed most of the downloaded attachments based on the parent metadata. Everything was working as expected and I was able to update abstracts and everything.

I hit Command-Q and quit Firefox, no big deal, right?

However, when opening FF and opening the Zotero pane, it seems all of my updates were not saved into the SQLite DB. I can verify that all of the attachments are in the Zotero storage directory, as expected. However, none of the references I've been downloading this morning are in the Zotero pane. I had also created a new collection and relocated an old one. These "changes" were lost also.

I must've pulled in at least a hundred papers and I really don't want to have to recreate my work.

My questions are:

* Has anyone else experienced this and been able to retrieve the metadata without redoing all of the research?
* What could the underlying cause be?

I don't want to continue to invest more time using Zotero (which has been great so far) only to lose my work again.

ETA: Based on seeing some other threads, I opened the SQLite db on the commandline and the data itself is not in the db (as opposed to a lack of updating the information on the Zotero pane properly)

noksagt

I have not seen this & the most likely ways I can think that this would happen are either that: you are now looking at some other sqlite file (possibly an automatic backup) or that some sync went awry (particularly if you are using third-party syncing). Have you inspected your zotero directory for other database files and what syncing (if any) do you use?

andrew.nguyen

I have checked the various *.bak files in my directory, and they don't have the expected metadata either (via sqlite cmd line).

I have Zotero syncing to my Zotero account with webdav to my own server. I did notice that the Zotero sync icon (spinny arrow) was going continuously before I happened to quit FF. It does this often (takes a while to sync) so I didn't think anything of it.

dstillman

No one else has reported anything like this. Are you sure you're not using a third-party syncing tool (such as Dropbox)? What's the date of the most recent item in the database?

andrew.nguyen

Yes, not using any third-party syncing tools. The problem is that I imported a bunch of new papers via Zotero and FF. Zotero saved all of the PDF's but none of the metadata was saved into the sqlite database.

In the database, the most recent item was from a few days before (the last time I had added more papers to the database).

In an effort to not have to redo my research, is there any way to have Zotero pull the metadata from the PDF? I'm now using Mendeley since it was able to reconstruct the majority of my metadata straight from the PDF combined with title-based searches on google scholar.

adamsmith

Zotero also has a "retrieve metadata" function for pdfs:
http://www.zotero.org/support/retrieve_pdf_metadata
it only works for pdfs that aren't attached to any parent item.

Last time I looked my impression was that the equivalent function worked better in Mendeley than in Zotero.

I think we pretty much understand what you say happened - the problem is that an error that is not-reproducible and only occurred to one user once is basically impossible to diagnose or fix. And quite honestly, in most cases where it can be diagnosed somehow it turns out to be caused by some type of user behavior or misunderstanding - might not be the case here, but from a programmer's point of view that's the most plausible starting point.