Zotero library empty after deleting the zotero.dmg (& online not up to date)

mado_sharp

Hello
I ahve opened up my zotero library and it is completely empty.
They only thing I can think of that hapened since I alast openened it (yesterday) is that I deleted the zotero.dmg file while cleaning up my computer.

I can find the zotero.sqitle file but it is dated today, so presumably reflect the empty library.

My online library is not up to date (separate issue, not sure why, presumably because my syncing had been turned off at some point)

Please help! Thanks!

mado_sharp

For added info:
- there are only a current version of zotero.sqlite and zotero.sqlite.bak files, that are 1.1MB in size. No older versions of this file in my ZOtero data directory
- In that same directory, I do have a Zotero/storage filder, and it does contain entries up until yesterday, confirming that this is indeed the location of my ZOtero data directory

adamsmith

Disk cleaning software on Mac has been known to delete the zotero.sqlite, so if that happens, there's not much we can do. You don't have a back-up in time machine or so?

mado_sharp

Unfortunately I do not have a backup on the disk or timemachine. I have restored part of my library from the web library (but it was pnly up to date until about a year ago when I exceeded my storage limit).

(and I did not run any disk cleaning software that I am aware of!)

So my next question: is there a way to back up from the files from the Storage folder, that contains all the pdfs and the html files?

Thanks!

adamsmith

It's certainly worth doing another thorough search for zotero.sqlite anywhere else on your computer (the 1.1MB databases are definitely new and empty indeed).

Honestly, there's not much you can do with the storage folder: it's no different that if you had a pile of files anywhere else: for the PDFs, you can use Zotero's retrieve metadata and that may work reasonably well, but that's about it.

Being above the storage quota wouldn't have stopped metadata sync, btw., so something else went wrong with that.

dstillman

and I did not run any disk cleaning software that I am aware of!

Note that this would include the built-in macOS storage management tool (rather inappropriately named "Reduce Clutter"). You definitely did something like this — there's just no other way for the SQLite files to disappear while leaving everything in 'storage' in place. It's definitely not related to deleting the .dmg — that is totally standard and has nothing whatsoever to do with your data.

So if you have no other backup, the best you can do is sync to pull down your outdated data from the online library. (You probably realize this now, but there was no need to turn off syncing altogether just because you were at your file storage quota.) Attached files will be a little tricky, though. If you leave the existing 'storage' folder in place, you'll likely have a lot of orphaned files mixed in, whereas if you move it out of the way, you'll only have the 300 MB of files that you uploaded before you hit your quota.

Probably I'd suggest moving the old 'storage' folder out of the way, syncing down what's online, and then creating a smart folder in macOS to show all PDFs within the old 'storage' folder as a flat list. Then when Zotero can't find an attachment, you can re-locate it from that list, which will cause Zotero to automatically copy it into the new 'storage' folder. When an item is missing altogether (because you added it within the last year), you can go to that folder and drag the file into Zotero and let it try to retrieve metadata.

Any notes or Zotero annotations you made in the last year would be gone, though.