I want to undo my profile creation

cl417

On Saturday I experimented with Zotero profiles, but I made a mistake by choosing my home folder as the profile folder and I want to turn back the clock and start over. Here's a link describing the situation:

https://forums.zotero.org/discussion/71560/how-can-i-create-multiple-libraries-in-zotero

Somehow during this profile-creation process my version of Zotero was upgraded from 5.0.20 to 5.0.45 and I believe that the profile information is connected to the 5.0.45 version. I don't want to use the 5.0.45 version connected to the profile mistake, so my plan is to delete 5.0.45 and reinstall 5.0.20 (I still have the 5.0.20 DMG installation file).

My detailed plan is to delete all the files that Zotero put in my home folder (except the folder named Zotero which contains all my attachments and the sqlite databases), delete Zotero 5.0.45 from my applications folder, and then reinstall 5.0.20.

Will this work?

fbennett

Out of curiousity, why do you want to use the earlier version of Z?

cl417

Because I don't think it's connected to the profile problem. Also, I don't like having software installed on my computer without my knowledge.

cl417

I want to do the deletion and reinstallation because I do not know how Zotero maintains profile information. I suspect that the profile information is not maintained in the Zotero data directory (ie. the folder named Zotero containing the following folders and files: locate, pipes, storage, styles, translators, zotero.sqlite, zotero.sqlite.1.bak, and zotero.sqlite.bak).

So I want to keep the data directory, dump the new version of Zotero and start fresh with a reinstallation of the older version that, I hope, will be able to access the old data directory.

fbennett

Reading through the earlier thread, I'm puzzled how the Firefox runtime configuration files ended up in your home directory. When you set up the profile, did you run a command like ./zotero -P in the terminal, and get a popup like this?

https://imgur.com/kwMawIA

cl417

Hi fbennett,

Thanks for your response.

To create the test profile I typed the following into Terminal:

/Applications/Zotero.app/Contents/MacOS/zotero -P

Then I just followed whatever the instructions were. I don't remember exactly what I did. I think it just asked me to choose a folder for the new profile and I guess I wanted all my profiles in one place so I chose the folder where my original Zotero stuff was stored, which was my home folder. I did not get a dialog box like the one you linked to.

Do you know if Zotero keeps any profile information in the data directory?

fbennett

With the command above, in the example shown in the screenshot, the Firefox runtime files would be placed in /home/bennett/.zotero/zotero/6ylfgq2e.Default User—not in the home folder (which would be /home/bennett on my system here).

Did you instead run a command like ./zotero --profile /Users/XXXX? That is not recommended, but it would produce an effect like what you are describing.

cl417

The only command I ever ran from Terminal was:

/Applications/Zotero.app/Contents/MacOS/zotero -P

When I ran that command, Zotero started up and presented me with a dialog box that asked me to choose a folder for the new profile.

I assume that when you used "Firefox" above you meant "Zotero". I am running a stand-alone version of Zotero and my Zotero is not connected to Firefox in any way.

fbennett

Aha. I just tried this on MacOS, and it does indeed offer the option of selecting an arbitrary folder for the new profile. That's a trap for the unwary, and it really shouldn't do that. The data folder and the profile are separate things, and should not be jumbled together like this.

To untangle the two sets of data files, start by figuring out what profiles are installed, and where their respective date folders are located. Running the program with that same command, with the -P option, should show you a list of profiles (likely two of them). Start Zotero in each profile in turn, and note the data directory path by checking Preferences -> Advanced -> Files & Folders.

fbennett

Under the hood, Zotero Standalone is running on an instance of Firefox with the browser stripped away. Those many extraneous files that were added to your data directory are Firefox runtime configuration files. In ordinary operation, they are not visible, but they are always created and maintained (somewhere) by Zotero Standalone.

adamsmith

I gave precise instructions on how to undo this in the thread you link to. Follow those and ask if something isn't clear. Not sure why you opened a new thread?

fbennett

If both the former and the newly created profiles are both set to use the same Zotero data directory, you can delete the newly created profile from the menu, but when it asks whether you want to delete data files, do not delete them. That will remove the profile from the listing, but will leave all of the files in that directory in place (both the Zotero data files and the runtime configuration files).

fbennett

Then confirm that you can run Zotero in the normal way and access your library.

fbennett

After confirming that you can access your library, you can use Finder to move the now-unused runtime files to the trash. After trashing the files, confirm that Zotero still runs normally, and you're done.

fbennett

Those additional files created in your data directory are created for all versions of Zotero. They are not a special product of v5.0.45. You can and should install the most recent version of the client after tidying up.

cl417

fbennett,

I have opened both profiles and the data directory path is the same in both cases. I don't want to delete the new profile because when I start to do so, Zotero says that it will delete the whole folder and I do not want to delete my home folder.

adamsmith,

I stated a new thread because I don't want to just try and repair damage. I want to start over as if I never made a mistake in the first place.

fbennett

(Finally, if you had moved your data files directly into your home directory, it would be worth moving them back to the standard ./Zotero subdirectory. That will reduce clutter, and help avoid accidental deletion of one or more of the files.)

cl417

My assumption is that the Zotero data directory is a self-contained entity that is not inextricably connected to any particular instance of Zotero and that it does not contain any profile information. If I'm correct, then I hope that by reinstalling a virgin copy of Zotero 5.0.20, deleting the stuff added during the profile creation and keeping the data directory, I will be back to where I was before the profile problem.

Related question: can I take my data directory to any computer (Windows, Mac or Linux) and have it work with any version of Zotero?

fbennett

Returning to the topic of the previous thread, if it was me, I would look either at using Saved Search (suggested by @noksagt), or at creating groups online via a Zotero.org account, syncing to add the empty groups to the client, and then disabling sync for them (suggested by @bwiernik). Both of those solutions would allow you to access all sets of files from inside a single session of Zotero, which would be convenient, assuming that it is desirable.

cl417

fbennett,

Thanks for those ideas, but I like the profiles option. I just want to start over and do the profiles right.

bwiernik

The Zotero version has nothing to do with your issue with profiles. Most programs install updates automatically (particularly minor bug fix updates, like the difference between Zotero 5.0.20 and 5.0.45), and it is strongly recommended that you continue to let Zotero do so. The instructions provided by adamsmith in your other thread can fix the issues you are experiencing.

dstillman

It's not just strongly recommend — we don't provide support for outdated versions of Zotero. Whether or not the core issue is related to the version you're running, it's not a good use of people's time to try to help you when you might encounter other issues that have since been fixed, might now show clearer error messages, etc.

fbennett

@adamsmith Apologies for the intrusion.

cl417

bwiernik and dstillman,

When a program works fine for me, I do not like to take a chance that an upgrade will not. I've been burned in the past on this issue with other software and prefer stability to adventure.

to all,

Thanks for your attention and replies. Since nobody has claimed that my plan to start over won't work, I'm going to give it a try.

bwiernik

It won't work. Please follow adamsmith's instructions in your other thread.

cl417

bwiernik,

adamsmith's instructions involve fooling around with profiles and deleting folders. I do not want to take ANY chances with my home folder. I want a do-over.

I think that if my plan wouldn't work, one of you would have said why it won't work.

I assume that a single data directory is portable to other computers and other versions of Zotero without any profile baggage. If that's the case, then all my plan involves is the using of my old data directory with a "new" version of Zotero, (ie. a reinstalled 5.0.20).

dstillman

Given that 5.0.20 was an early release of a major new version and that there've been thirty Zotero point releases since then containing a large number of bug fixes (including various improvements to profile/data-dir handling), you're definitely not choosing stability. You can use whatever version you want, of course, but you shouldn't expect support here for anything but the latest version. Others here might be willing to help you regardless. As the person who wrote most of the code in question, I'm not.

(Support aside, Zotero is also web-connected software, and you're putting yourself and the internet at large at risk by using an outdated version that may contain security vulnerabilities in the underlying Firefox browsing platform. Frankly, not installing point releases is a deeply misguided and dangerous position in the age of web-connected software.)

fbennett

@cl417 I won't post here any further after this, but a few notes to tie things off at my end.

The only reference to "deleting folders" in the instructions from @adamsmith was the suggestion that you can safely remove the newly created profile. Since that profile has been set in your home directory, you obviously do not want to approve deletion of its data files when removing it, since that would remove your entire home directory. But you do need to remove the newly created profile programmatically via the -P option.

You really shouldn't peg your system at a stale version of the client. It may come across as rather blunt, but developers issue upgrades to solve problems, and if you don't want them solved, you may not receive much in the way of support. As several people have explained, there is no relationship between the Zotero version and the oddities you are seeing. The confusion all originates from setting a profile in a non-standard (and sensitive) location.

That's it from me: I'm going to sign off now, as too many cooks spoil the stew.

cl417

dstillman,

Thanks for your response and especially thanks for all your work on Zotero. I love it and I have invested hundreds of hours building libraries for books and papers. My book library has over 600 PDF books and is pushing 30GB. I have hundreds of books waiting to be added to the library and I find new books every week. My papers library has thousands of PDF papers. Zotero is really a wonderful thing for me.

On the other hand, I do not like web-connected software, especially software that does things without telling me. I like to be in control of what happens on my computer. I also like to have the option of reverting to versions of software that I know work if there's a problem with the new version. When Zotero deletes my current version and installs a new version without giving me any choice in the matter or any option to go back, it pisses me off.

I will consider installing a virgin copy of 5.0.45, but I definitely want to delete the currently-installed version because I want to eradicate everything involved with my profile problems.

I'm also thinking about using TimeMachine to restore Zotero to the way it was in the middle of last week, although I'll have to re-add a few dozen books that I'd added between the last backup and the profile problem on Saturday.

cl417

fbennett,

Thanks for your help.

There may not be a connection between the 5.0.45 version of Zotero and my profile problems, but there is definitely a connection between the instance of 5.0.45 installed on my computer right now and my profiles problem. The currently-installed instance of 5.0.45 is the one that got me into the profile mess and I want to get rid of it.

As I mentioned to dstillman, I may download and install a virgin copy of 5.0.45 that doesn't have any vestiges of my profile issues.

dstillman

On the other hand, I do not like web-connected software, especially software that does things without telling me.

To be clear, the "web-connected" part is the fact that there's a browser built in, and when you save items it connects to the open web. That requires security updates to happen safely.

There may not be a connection between the 5.0.45 version of Zotero and my profile problems, but there is definitely a connection between the instance of 5.0.45 installed on my computer right now and my profiles problem.

No, you're misunderstanding this. The application files in the Zotero app that you download from zotero.org are totally separate from your profile directory or your data directory. Uninstalling Zotero — i.e., removing it from /Applications — or reinstalling it has zero effect on your data. You should have the latest version to avoid bugs, but the version you have installed has otherwise nothing to do with this issue.

The issue here is that you specified your home directory as the data directory instead of a subfolder of the home directory. That's it.