Restoring Data from a dual Linux-Windows PC to a new Windows PC

edited February 17, 2020

I was using laptop in my last job with Linux (Ubuntu) and a Windows Virtual Machine. I used to browse the web using Firefox in Linux and add all the articles and notes from there, so all my the pdfs are stored in the Zotero for Linux version. On the other hand I used Zotero in Windows VM mainly for using the Office word plug-in for writing. So in my Zotero for Windows version I didn't have all the pdfs (possibly some of them were synced from the server, but I have a limit on the amount of storage, so not all files are in the Windows version).

I want now to install Zotero in my personal laptop and restore my data. In this laptop I have only Windows. I have read this but I still have some doubts.

I have gone into my old Zotero directories in Linux and Windows.

In Linux I have 2 zotero folders.

1) First a "/.zotero" directory which only had a "profiles" file and a directory witih a wird name ended in .default. In that file there are other directories like "crashes", "gmp" and "storage" and plenty of files like "storage.sqlite", "formhistory.sqlite", "cookies.sqlite"...

2) I also have a user\Profil_Firefox\zotero directory. This seems to be the proper one with the files "zotero.sqlite", "zotero.sqlite.1.bak", "zotero.sqlite.bak"... and directories like "storage", "styles", "locate"... and I will refer later to this one . I guess it is inside Profil_Firefox as I started with the zotero for firefox version, although after a firefox updated I had to migrate to a desktop zotero version.

In Windows I have a Zotero directory with similar files and folders.

The point is that there are some differences between the Zotero directory in Windows and Linux. First, the sqlite files have different modification dates. Second, I have more styles in the Windows version (as it is the version I was using for writing in Office), and as I said in the beginning the Linux "Storage" folder is the one with all the pdfs. Second, there are some OS specific files in the Zotero directory. In Linux I have "", "pdfinfo-Linux-x86_64", "pdfinfo-Linux-x86_64.version", "pdftotext-Linux-x86_64" and "pdftotext-Linux-x86_64.version", while in Windows I have "pdfinfo-Win32", "pdfinfo-Win32.exe.version", "pdftotext-Win32" and "pdftotext-Win32.version".

So now, I am not sure what I should do to restore my data in my personal Windows laptop. I don't know if should use the method of using one of the old Zotero folders as my new Zotero folder. The most recent sqlite files are those in my old Windows version (although I don´t think there would be significant differences as I used to sync regularly). I would like to keep my more complete "Styles" folder from my old Windows. On the other hand, my complete "Storage" folder is the Linux one. In addition, I have done recently some changes to my library in the server, so any of these folders represent my most recent libraries. But I guess this last point could be solved by sincyng after restoring.

Can I combine folders from my old Windows and Linux Zotero folders to construct my new Windows Zotero folder? For example, by copying the entire old Zotero folder from the old Windows and overwriting the "Storage" folder with the "Storage" folder from my old Linux Zotero version? even if the sqlite files have different modified dates, and could potentially refer to different versions of the library? or better to import, somehow, later all the pdfs from this "Storage" Linux folder?

I have assumed that in Linux I have to look at the Profil_Firefox\zotero folder and that I don't need the other ".zotero" folder first mentioned. Is this correct? or there is important data that I need to consider also there?

Side question: Are notes added to the library items stored in both Windows and Linux versions?

Any clue on the best way of solving this?


  • You don't need the ~/.zotero folder. That contains your Zotero profile directory, which just has some settings that can be easily recreated.

    The Profil_Firefox\zotero folder is your Zotero data directory, and if you used that one you would rename that 'zotero' to 'Zotero' and put it in your home directory on the new Windows computer, the same way it is on the old one.

    Styles are easily reinstallable from the preferences or (if they're custom styles) by copying the .csl files over to the new 'styles' directory, so don't worry about that.
    For example, by copying the entire old Zotero folder from the old Windows and overwriting the "Storage" folder with the "Storage" folder from my old Linux Zotero version?
    I wouldn't recommend overwriting 'storage'. I would just choose one of the two Zotero data directories and copy that to the new computer, and then use syncing to bring it up to date with any additional date. If you have all the storage files locally on one computer, use that one, since data syncing is unlimited even if you're at your file storage quota.
    Are notes added to the library items stored in both Windows and Linux versions?
    Yes. Those are just in your database.
  • edited February 18, 2020
    Thank you very much for your help @dstillman

    So if choose to use my old Linux Zotero folder as my new Windows Zotero folder, What would happen with the OS specific files?

    I refer to those "", "pdfinfo-Linux-x86_64", "pdfinfo-Linux-x86_64.version", "pdftotext-Linux-x86_64" and "pdftotext-Linux-x86_64.version" in Linux vs "pdfinfo-Win32", "pdfinfo-Win32.exe.version", "pdftotext-Win32" and "pdftotext-Win32.version" in Windows.

    Will it cause problems to have the Linux related files in my new Windows instead of the Windows related ones? Or should I replace those files with the ones from my old Windows Zotero folder?
  • Those files are no longer used — they just haven't been cleaned up automatically yet. They won't cause any problems either way, but there's no harm in deleting them.
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