Profile can't be loaded after installing Zotero 5.0 on Linux

dstillman
This discussion was created from comments split from: [5.0 Beta] Library lost when migrating to Zotero Standalone.
  • antknee
    Hi I am running Linux Mint. Upgrading Firefox I lost all access to my zotero library. Seeing that I could no longer access it through firefox, I tried to run zotero, zotero-standalone. It's been a long time since I used zotero as an application, rather than just adding and editing library data through the browser. \

    So, at this point I'm thinking how am I going to continue my academic work?

    Since Zotero connector is no longer supported I understand I must now rely on the standalone library.

    I therefore followed instructions online and downloaded Zotero 5.

    When I try to launch it from the terminal a pop up says:
    Your Zotero profile cannot be loaded. It may be missing or inaccessible.
    There is no gui to look for or link to the lost profile.

    Therefore

    I've identified a folder, which I am really hoping is my data/reference library at .mozilla/firefox/mwad0hks.default/zotero/zotero.sqlite

    I have tried copying this file using the terminal to
    .zotero/
    .zotero/zotero/
    .zotero/zotero/wf5t0060.default/

    All of this results in the same pop-up: 'Your Zotero profile cannot be loaded. It may be missing or inaccessible.'

    I'm seriously worried that I will lose my library. I use it daily in my academic work. and restoring zotero to functionality on my system is an absolute priority before I can continue with my work.
  • dstillman
    edited November 15, 2017
    I've identified a folder, which I am really hoping is my data/reference library at .mozilla/firefox/mwad0hks.default/zotero/zotero.sqlite
    That's your data directory, not your profile directory, so you definitely don't want to move those files to .zotero/zotero. Zotero 5.0 would normally migrate the data directory out of the Firefox profile automatically, but since I'm guessing this is due to security protections on your system, you can just move .mozilla/firefox/mwad0hks.default/zotero (after restoring those files) to ~/Zotero (capitalized), since that's where Zotero will look for it.

    As for .zotero/zotero/wf5t0060.default, that's your profile directory. What's in there now? If there are files in there, most likely you're running SELinux, AppArmor, or similar and it's preventing Zotero from accessing that directory.
  • antknee
    In the .zotero/zotero/wf5t0060.default folder is the following files:

    8.db key3.db secmod.db
    compatibility.ini mimeTypes.rdf sessionCheckpoints.json
    cookies.sqlite ot11hdea.default SiteSecurityServiceState.txt
    crashes permissions.sqlite times.json
    extensions.ini places.sqlite webappsstore.sqlite
    extensions.json pluginreg.dat xulstore.json
    formhistory.sqlite prefs.js zotero
  • dstillman
    Yeah, that's your profile directory. That's fine, so you should leave it alone (though I'm not sure if that 'zotero' directory is what you just moved there or if that's a separate data directory). So this is either security software or file permissions.
  • antknee
    Ok.

    I tried moving the folder .mozilla/firefox/mwad0hks.default/zotero to a directory I made ~/Zotero (the installation did not automatically make one there). However, I see exactly the same error.

    'Your Zotero profile cannot be loaded. It may be missing or inaccessible.'

    I'm not understanding something about the principle here. What is the profile and what is its purpose? What is the data in relation to the profile? is there anyway I can simply read the data and export it?

    I see the same data files in .zotero .zotero/zotero and .zotero/zotero/wf5t0060.default/zotero

    The first two are definitely there because I copied them there in the hope of restoring the library.

  • dstillman
    I tried moving the folder .mozilla/firefox/mwad0hks.default/zotero to a directory I made ~/Zotero (the installation did not automatically make one there).
    That's expected. (The installation doesn't do it — it happens on a successful Zotero 5.0 startup, but you're not getting that far.)

    The profile contains your settings. The data directory ('zotero', with zotero.sqlite, etc.) used to be stored in either the Zotero or Firefox profile, but in 5.0 that gets moved to ~/Zotero. The 'zotero' in your Zotero profile directory might be from when you used Zotero Standalone previously, if you told it to use a separate data directory at that time — you can check the timestamps. (Zotero 5.0 would automatically migrate the more recent one, and the other could be deleted.)

    But you can ignore all that for now. The first thing you need to do is fix your security settings or permissions so that Zotero can access the profile directory.
  • antknee
    ok. What should the permissions be for Zotero/zotero/
  • dstillman
    Same as any other folders and files — everything just needs to be writable by your user account. Unless stuff is is actually owned by a different user, it's unlikely that permissions are the problem.
  • antknee
    Ok. I've changed the permissions on that folder recursively to read/write just using the file manager rather than chmod:

    ls Zotero/zotero/
    locate storage translators zotero.sqlite.1.bak
    pipes styles zotero.sqlite zotero.sqlite.bak

    ls -lg Zotero/zotero/
    total 16736
    drwxrwxrwx 2 a 4096 Nov 15 18:55 locate
    drwxrwxrwx 2 a 4096 Nov 15 18:55 pipes
    drwxrwxrwx 173 a 28672 Nov 15 18:55 storage
    drwxrwxrwx 2 a 4096 Nov 15 18:55 styles
    drwxrwxrwx 2 a 77824 Nov 15 18:55 translators
    -rw-rw-rw- 1 a 5664768 Nov 14 08:49 zotero.sqlite
    -rw-rw-rw- 1 a 5660672 Nov 12 21:21 zotero.sqlite.1.bak
    -rw-rw-rw- 1 a 5664768 Nov 14 09:12 zotero.sqlite.bak

    I run zotero and the problem persists: 'Your Zotero profile cannot be loaded. It may be missing or inaccessible.'
  • dstillman
    Again, this is likely because of security software. There's really nothing else I can tell you.
  • dstillman
    (But those permissions are now incorrect, also. It doesn't really matter on a personal system, but in general folders should be 775 and files should be 664, not 777/666.)
  • antknee
    Thanks for your help so far. I don't have any security software installed.

    My entire PhD's worth of references is inaccessible.

    What else can I do?
  • dstillman
    You could very easily have SELinux or AppArmor installed and not know it. I'm afraid this is the cost of using Linux — there's much more variability, and you're going to run into problems like this that you'll need to debug (or ask someone to help you with).
  • adamsmith
    though I'll note that the permissions you list above are for your _data_ directory, not the profile directory, which Zotero attempts to create as ~/.zotero/zotero as opposed to ~/Zotero/zotero. The error message refers to the former, not the latter.
  • adamsmith
    I'd try moving the current content in .zotero/zotero out of the way (so you have a copy), deleting that folder, and then trying to run Zotero again.

    I know you're worried about your data, but that's not actually the problem. The data is still there and you'll be able to open it on another computer, restore it locally, etc., so forget about that for the moment. The problem is getting Zotero to run at all.
  • antknee
    Thanks adamsmith. I will do this and report back.
  • antknee
    Wonderful. That allowed the launch of zotero at which point it located my previous directory in .mozilla/zotero I chose to 'switch to the previous directory' and my references are restored and zotero runs fine.

    A very big Thank you
  • adamsmith
    great thanks for reporting back. You can now delete the back-up copy you took of .zotero/zotero in case you haven't already.

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