Upgrade Zotero under Linux

Gabriel_p

I'm using a beta version of Zotero (5.0.35-beta.22+e72da417) and I want to switch to the latest stable version 5.0.35.1.

I'm running elementary OS (a Linux distro) and I have a '/home/Zotero/' folder and a hidden './zotero' folder.

Should I delete everything inside the '/home/Zotero/' folder except the 'zotero.sqlite' file and paste here the contents of the .tar.bz2 file I downloaded with the 5.0.35.1 version?

Should I do that but *also* delete the sqlite file?

Should I keep another file in addition to the sqlite file?

Should I delete the './zotero' folder folder?

adamsmith

Where exactly is the zotero (the bin file) that you're actually running when you start Zotero? There are various ways to set this up on linux, but generally do _not_ delete ~/Zotero or any of its contents.

emilianoeheyns

I use this script for initial install (which puts it in ~/bin/zotero and adds a menu shortcut to it), but after that, the built-in upgrade system has worked without problems for me.

Gabriel_p

Thank you both.

Since I use Zotfile+Dropbopx to organize and sync my PDFs, what I did was:

1. Remove both ~/Zotero and ~/.zotero folders
2. Paste the extracted folder with the latest version in ~/Zotero
3. Launch (new) Zotero, log in and let it sync
4. Install Zotfile
5. Point the base folder to the Dropbox folder where all the PDFs are located
6. Change the options in Zotero and Zotfile to what they were in the old installation

Worked with no issues, now I have the stable version properly installed.

dstillman

OK, first, it was completely unnecessary to remove ~/Zotero or ~/.zotero, which is why adamsmith cautioned you against that. It's probably fine, but there was no reason to do it, and it would be possible to lose data if you weren't fully in sync, and you at the very least lost your settings.

Second, what do you mean by "Paste the extracted folder with the latest version in ~/Zotero"? What folder? If you mean the tarball, you absolutely don't want to store that in either ~/Zotero or ~/.zotero. Those are program files and should go wherever you store your program files (e.g., /usr/local, /opt, ~/.local/share/applications). ~/Zotero is your data directory. ~/.zotero is the profile (settings) directory.

We're happy to help you here, but if you're going to post it's much better to let us actually help you before you just start trying things.

Gabriel_p

I checked that everything was fully synced before attempting anything. I use Dropbox+Zotero to sync the PDFs, so the bulk of the syncing is done outside of Zotero. I did lose my settings, but: a) I use mostly all default settings, b) I stored a copy of the prefs.js file just in case.

Yes, I mean the extracted tarball. The program files are indeed stored in the ~/Zotero folder. My installation steps are rather simple: extract the tarball, copy that folder to home using the name 'Zotero'. That's it.

As far as I am aware, there is no installation file in the downloaded tarball. What other installation steps would recommend I follow?

dstillman

I use Dropbox+Zotero to sync the PDFs, so the bulk of the syncing is done outside of Zotero.

But all of your metadata would still sync via Zotero and would've been deleted along with ~/Zotero. Again, you shouldn't lose data as long as you're fully in sync, but there's still no reason to do a full sync when simply changing versions.

Instructions are here. We don't specify a location to put the files because distros and people have different conventions and preferences. It just shouldn't be in the data directory. Any of the other locations I mention above would be fine.

Gabriel_p

I understand the metadata syncs via Zotero, which is why I made sure it was completely synced before I attempted anything.

The instructions for Linux users are:

> Linux users may wish to use a package for their distro rather than using the tarball directly.

A package? What does this mean? A PPA? Is there one available? The default download option gives you the tarball, nothing else.

> If you download the tarball, unzip it and run zotero from that directory to start Zotero.

This is even more basic than what I do.

> Alternatively, on Ubuntu, move the directory to a location of your choice, run the bundled set_launcher_icon script (which will update the included desktop file with the full path to the bundled Zotero icon), and then double-click Zotero (which may display as zotero.desktop initially). You can also symlink zotero.desktop to ~/.local/share/applications/ to add it to your launcher.

This is precisely what I do.

I only resorted to delete+copy+sync because I was moving from beta to stable and I didn't want garbage left behind. As it is not very clear how this "downgrade" should be made, and the install instructions describe precisely what I do when installing a brand new Zotero, I just did that.

Cheers.

dstillman

A package? What does this mean? A PPA? Is there one available? The default download option gives you the tarball, nothing else.

We don't provide these packages. You'd have to check with your distro.

I only resorted to delete+copy+sync because I was moving from beta to stable and I didn't want garbage left behind.

Right, but this would only be an issue because you've combined your installation files with your data directory.

So what you'll want to do is delete everything from ~/Zotero except for the following: zotero.sqlite*, storage, styles, translators, pdfinfo*, pdftotext*, locate, pipes. Then download the tarball again and extract it somewhere else.

Gabriel_p

Got it, I'll keep it in mind for the next time I need to do a re-install. Thank you @dstillman

in_the_long_run

Hi everybody, I wanted to upgrade zotero under Ubuntu in order to check out the new google docs integration. I extracted the content of the new .tar.bz2 file into a second folder next to the old Zotero_linux-x86_64 folder. Both are located in the documents folder. If I run the zotero file in the new Zotero_linux-x86_64 folder the synced new beta version opens and if I click on the (apparently old) icon in my sidebar which is just a "?" the old version of zotero opens. Now my question is if I can safely delete the complete old Zotero_linux-x86_64 folder since the new beta Version seems to be perfectly in sync.

Or is there any important data stored in the old Zotero_linux-x86_64 folder? The new version didn't seem to download anything from the cloud, because it was in sync instantaneously. That leads me to the assumption that the actual library-data is locally stored in the "zotero" folder I have in my home folder (+ in the cloud) and that it should be no problem to delete the old Zotero_linux-x86_64 folder and replace the icon with the one from the new Zotero_linux-x86_64 folder. Is that correct?

The zotero folder in my home folder contains the files that are mentioned by @Gabriel_p above. I would leave this folder untouched.

Does that sound right?

Thanks alot!

adamsmith

That leads me to the assumption that the actual library-data is locally stored in the "zotero" folder I have in my home folder (+ in the cloud) and that it should be no problem to delete the old Zotero_linux-x86_64 folder and replace the icon with the one from the new Zotero_linux-x86_64 folder. Is that correct?

yes, that's exactly right. That folder only contains the program files, no data.

in_the_long_run

thank you @adamsmith !