[Solved] Library gone after update to Zotero 5

danielrschmidt

I just updated to Zotero 5 and cannot see my library anymore. I had both Zotero 4 standalone and a recent version of the Zotero Firefox plugin installed. Standalone being installed was an artifact from me trying out Zotero some time ago, I never used it. Running on Ubuntu with Firefox 54.0.

Now, in my Firefox, the Zotero plugin no longer exists; instead, the connector was installed automatically without my doing. I started the existing standalone installation, but it only shows an empty library; I then updated to Zotero 5 standalone with the same result. I am aware of the FAQ; it basically says "everything should work automatically after the upgrade".

What do I do now?

Btw.: Auto-removing an existing plugin and replacing it by another without user interaction is not cool... It wasn't necessary either, given that I am not on FF 57. I really would have liked a chance to migrate my data in a sane fashion before upgrading FF/Zotero.

dstillman

https://www.zotero.org/support/kb/data_missing_after_zotero_5_upgrade

(When this applies, there should be a warning in Zotero pointing to this page, but it's possible that's not happening for some reason in your situation.)

Auto-removing an existing plugin and replacing it by another without user interaction is not cool...

There was no alternative. If we didn't push the connector, everyone who upgraded to 57 would've just lost Zotero altogether. Other non-ESR versions are no longer receiving security updates and shouldn't be used (in general — not sure if there are patches for Linux packages). Firefox 52 ESR is OK until June 2018, but Zotero 4.0 is no longer supported here, 4.0 syncing will be shut off in early 2018, and, most importantly, we started offering the 5.0 Standalone upgrade, and Zotero 4.0 for Firefox can't be used with Zotero 5.0, so we had to push the connector update at the same time, since many people used both.

Firefox doesn't offer prompting for extension updates, but there was a warning for a week in Zotero before this happened, and many months of warnings here, in multiple blog posts, and on Twitter.

I really would have liked a chance to migrate my data in a sane fashion before upgrading FF/Zotero.

Installing the connector has no effect on your data. If you're not using Firefox 57, there's nothing stopping you from reinstalling 4.0 from the download page, as explained in the FAQ. As for whatever happened with 5.0 for you, see the page linked above, but it should be easy to resolve.

dstillman

I started the existing standalone installation, but it only shows an empty library; I then updated to Zotero 5 standalone with the same result.

Oh, that's the reason this happened, by the way. First, when you originally installed Zotero Standalone and Zotero for Firefox, you told it not to share a data directory (it does by default). And then you started Zotero 4.0 before installing 5.0. When there are multiple data directories to choose from, Zotero 5.0 chooses the one that was more recently used, which in your case was the Standalone one. So you should be able to just delete that data directory (probably at ~/Zotero now, but you can check in the Advanced → Files and Folders pane of the Zotero preferences) with Zotero closed. It should then pick up your Firefox one and migrate it to ~/Zotero automatically, if your security settings allow it (or you can manually move the Firefox one to ~/Zotero).

(You might actually still get a warning on subsequent startups about the presence of a second data directory in the Firefox profile, but that too depends on your security settings.)

danielrschmidt

That was quick and kind help, thank you! The library is back again and Zotero 5 is working fine. I hadn't seen that I can reinstall the firefox plugin, so thanks for that advice, too. Somehow, my settings got lost in the process, but I should be able to restore them manually from the Firefox plugin now that it's working again.

As for the plugin push: The connector plugin could in theory show some popup on first start. Just some information on what's happening and maybe offer an "Export data" button. I know the export is technically not necessary because the upgrade does not touch the data; but it would be a lot less scary that way ;-) As far as I can tell, it would have been possible to install the connector plugin on top of an existing Zotero plugin; FF57 would have disabled the Zotero plugin automatically and it would have kept working on older FF installations. But well, it did work this way, too.

Anyway, Zotero is a great software and I would not want to miss it!

Edit: Yes, I guess the Standalone had an empty library at some point and that one got imported for some reason. I now found all the directories (thanks to your help) and set up everything in a good way for me.

dstillman

Somehow, my settings got lost in the process, but I should be able to restore them manually from the Firefox plugin now that it's working again.

Yeah, that only works when Zotero migrates the Firefox data directory over, I'm afraid. But you can copy them from the prefs.js file in the Firefox profile to the same file in the Zotero profile directory.

The connector plugin could in theory show some popup on first start. Just some information on what's happening

It does, actually — it shows a special message specifically for Firefox users (with a line for 4.0 upgraders looking for their data) linking to the blog post. But only once (because we don't know for sure that you're an upgrader and can't be too unpleasant for new users), so it's somewhat easy to miss.

and maybe offer an "Export data" button

The connector has no access to the filesystem, so that wouldn't have been possible (and there's not really anywhere to export it to, since 5.0 just picks it up in the same place).

it would have been possible to install the connector plugin on top of an existing Zotero plugin

That wouldn't work either — the only thing that lets us push it to users is that it's an update with the same addon id.

Anyway, glad it's working for you now.

danielrschmidt

Hum, yes, I seem to have missed the message. Makes sense to not show it more often since it would get pretty annoying.

Thanks for all your insights, in any case; seems things are a little more difficult than I imagined with the new Firefox-Addon system. I can imagine that it can be quite a pain to deal with!

maechtel

i lost all my entries - but have not upgraded my zotero version yet using 4.029.15
how to get my data back???

bwiernik

First, install Zotero 5 from http://zotero.org/download. Then, if your library is empty when you open the Zotero 5 app, see https://www.zotero.org/support/kb/data_missing_after_zotero_5_upgrade

If you are still having problems, please start a new thread and describe exactly what is happening.