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erikringmar

Hi,

I have a very large Zotero database on an external hard disk. For some reason it is no longer accessible. I copied it to the internal hard disk, but the problem persists. I have 10 years worth of work here. It would be great to get access to it.

Any ideas?

Erik

dstillman

database disk image is malformed

Your database is corrupted. This might happen if, say, the drive was unmounted while Zotero was open.

You can try the DB Repair Tool (though if your database is very large you might need to try the manual steps).

erikringmar

Thanks. Yeah, that's what happened. I removed the hard disk while keeping Zotero open. Sigh ... I have 19,000 entries -- over 10 years of work. I'll try the manual recovery, although I'm slightly daunted by "Advanced (or adventurous) users can repair their databases without uploading them."

dstillman

If this just happened, you can also try swapping in one of the last automatic backups or another recent backup. (Be sure to make a backup of all the zotero.sqlite* files before doing anything.) If you're using syncing, Zotero would then just download any changes you made since that backup was made.

erikringmar

I do use sync, and I can download that for the last version. Problem is that this doesn't include pdfs of all the files. Will the "last automatic backup" look for the files?

dstillman

Only the database itself is corrupted, so any PDFs you have locally wouldn't be affected. As long as you were fully in sync before this happened, once you sync you'd end up with your latest data, and that applies whether you start with a new database or a backup. The backup would just be a way to avoid having to pull down all your items by starting with a snapshot from a few hours/days ago.

erikringmar

Thanks for helping me out with this!

The database is syncing and it looks up to date, but how can I return all the PDFs that are stored locally? They seem to be in the wrong directories.

I suppose I should upgrade my storage. That would make it possible to sync the files too ...

dstillman

how can I return all the PDFs that are stored locally? They seem to be in the wrong directories.

I'm not sure what you mean by that. Simply syncing from either a recent database or an empty database wouldn't have any effect on your stored files.

erikringmar

Hmm ... The PDFs show up in the database, but when I click on them I get "the attached file could not be found."

dstillman

For all files or just some?

If your database has an attachment with key "ABCD2345", it looks in that folder in your data directory for the file. If you had synced before the DB corruption, the item would be on the server with the same key. If you then synced down to an empty database, the key would still be "ABCD2345" and it would still look in the same directory. If you restored to a version from a few days ago, the attachment may or may not have existed, but if not then it would reappear once you synced. In all cases, the key is still "ABCD2345" and it's going to look in the same place.

The only ways you'd have missing files would be if 1) you created them on another computer and they didn't sync, likely because you're over your storage quota, but that would've been the same before this or 2) you somehow lost files when your drive was corrupted, but that's pretty unlikely.

erikringmar

I understand what you are saying. I am indeed over the storage quota, and for that reasons I haven't synced the PDFs themselves. But that was OK as long as the files were stored locally. Now I can't locate them.

erikringmar

Not all files actually, but very many of them ...

erikringmar

I think I'm sorting it out ... I had Zotero in a different directory. Zotero_master. The database synced to the default. Now I'm simply copying all the directories in "storage" from Zotero_master to the new default directory. Seems to work.

I could have thought of this myself really. I never looked very deeply into the Zotero directories.

Thanks for your help.

Erik