The Zotero data directory could not be found at ..., but a data directory was found at...

mkery

Hello,

I create a new Zotero profile, add a lot of data to it (hours of work). I quit the profile.

next time I open the profile, I am shown this:

"The Zotero data directory could not be found at (/home/user/my_profile_name), but a data directory was found at (/home/user/Zotero). Use this directory instead?"

1)Locate
2) Quit
3) Use New Location

when I select (1), Zotero is closed.
when I select (3), the above profile will be populated with the data of the other profile that is stored at (/home/user/Zotero).

under my home folder (/home/user) I see the latter "Zotero" folder, but no other folder named following Zotero's typical folder naming convention, like "Zotero my_profile_name".

The hidden ".zotero" folder under the home folder contains a folder with the said new profile name, but there is no database file in it. (/home/user/.zotero/zotero/somerandomlettersandnumbers.my_profile_name).

What is all this? Where is all the data that I created in Zotero?`Why is this happening?

mkery

when tried with a test profile, it seems there is no single way to create a custom folder path. one gets a warning that says the folder is empty (what were a newly created folder supposed to have been?) or else the default /home/user/Zotero is selected, which is not empty and belongs to another profile, as aforementioned.

mkery

looks like one of those software version upgrades that wreaks havoc without prior notice.

perhaps you could be kind enough to let me know where I'd find my lost data?

dstillman

It sounds like you did something to move or delete the new data directory. Zotero certainly didn't delete it — there's literally no code to do so. You can search for other zotero.sqlite files on your system.

when tried with a test profile, it seems there is no single way to create a custom folder path

I don't know what you mean by this.

When you create a new secondary profile, and ~/Zotero already exists and is linked to by an existing profile, it automatically creates a data directory named after the new profile (e.g., "~/Zotero Test").

dstillman

The Zotero data directory could not be found at (/home/user/my_profile_name)

Also, presumably this said "/home/user/Zotero my_profile_name", not "/home/user/my_profile_name", right?

mkery

correct

mkery

When you create a new secondary profile, and ~/Zotero already exists and is linked to by an existing profile, it automatically creates a data directory named after the new profile (e.g., "~/Zotero Test").

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definitely not. this is the problem. I see no folder named "Zotero my_profile_name" under my home dir.

mkery

"It sounds like you did something to move or delete the new data directory. Zotero certainly didn't delete it — there's literally no code to do so. You can search for other zotero.sqlite files on your system. "

--

definitely done nothing. I wrote what happened. I worked in the profile, closed it, and the next time I opened it I got the above warning.

dstillman

definitely not. this is the problem. I see no folder named "Zotero my_profile_name" under my home dir.

No, you're misunderstanding this.

If you were using Zotero, you had a data directory. It's now missing. But if Zotero is looking for it, it definitely existed previously, and Zotero didn't delete it. It literally has no way of doing so.

The only time Zotero deletes a data directory is if you switch sync accounts, and then it 1) warns you very clearly it's going to clear the data directory and makes you confirm it and 2) creates a new, empty data directory. So that's not what happened here.

I have no way of telling you what happened on your system. I can just tell you that Zotero didn't delete your data directory. It can't do something that there's literally no code to do.

The only other way you wouldn't have had a "~/Zotero my_profile_name" would be if you had actually been using ~/Zotero in the new profile, but then you would've seen your original library to begin with in the new profile, and Zotero wouldn't have then told you it was looking for "~/Zotero my_profile_name".

mkery

If you were using Zotero, you had a data directory. It's now missing. But if Zotero is looking for it, it definitely existed previously, and Zotero didn't delete it. It literally has no way of doing so.

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so you are telling me that the warning is the proof that a proper data file has been created during my very first session that is now lost, and that it must be somewhere in my system saved as "zotero.sqlite" file.

I am searching through the files with this name.

dstillman

I'm saying it existed. Whether it still exists I couldn't tell you.

Note that if you're using a third-party Zotero package that uses sandboxing, all bets are off. We can only provide support for the tarball from our site, which isn't sandboxed. If you're using a snap or similar, you could easily have trouble with non-whitelisted directories. I don't know what happens if you try to use another directory in a sandboxed version of the app.

mkery

When you create a new secondary profile, and ~/Zotero already exists and is linked to by an existing profile, it automatically creates a data directory named after the new profile (e.g., "~/Zotero Test").

--

I created a test profile, and there is no folder created "~/Zotero Test".

also no sqlite file with the lost content anywhere in the system.

and let me add one more thing. this is not the first time. as soon as the upgrade of a month or so ago came, none of the additional profiles under the home folder have been recognized by Zotero.

I think this IS a problem that occured after the said upgrade, update or whatever. because of this, I had to recreate the folders of all my profiles elsewhere, except the one at ~/Zotero.

For the same reason, I cant see the folder of a newly created test profile under the home dir.

and possibly for the same reason, I worked for hours but no data was saved because no data folder was created under the home dir.

dstillman

It sounds like you're using a sandboxed package, as I explained above. Again, we can only provide support for the Zotero tarball from this site. You're not using "Zotero" — you're using a third-party package that we have nothing to do with.

dstillman

(That's also likely why Locate crashes the program.)

mkery

yes, Zotero I used is installed from flatpak.

I checked inside the related folder (home/user/.var/app(org.zotero.Zotero), but there is no hint of data there except the cache folder which I didnt further try. (the data there is a heap of randomly named files and thumbnails).

regardless, when other profiles have their own sqlite files in their own respective folders on other locations, the question still ends up being why the data file is not there for this profile.

dstillman

Again, we can't provide support for this. Zotero is obviously using a database when it's running. What some sandboxed environment does with non-whitelisted folders is not something we have anything to do with.

mkery

seems like you did in the past:

https://forums.zotero.org/discussion/72022/move-database-to-another-drive-device-on-linux

dstillman

No, I asked those people if they were running a third-party package, and I said if they were that was likely the problem.

We have never supported third-party packages. We can't support something that we don't have anything to do with creating.

mkery

you tell me you are submitting your software to third parties and telling them "do what you want with it, including the disruption of its proper functioning" ?

the mentioned disruption here being data loss through such a grave error as the failure to create the data folder.

I doubt flatpak (or any other such party) would do anything that would cause a database file to disappear - and that for more than a month by now. (that would already have damaged loads of people, not only me, right?)

dstillman

I don't know what you think you're accomplishing here by arguing with us, but you are wasting people's time, and you are going to get banned from posting here if you keep this up.

We don't "submit" our software to third parties. Zotero is open source, we provide a tarball that we vouch for, and third parties create packages for various Linux distributions and configurations. That's how most Linux software works.

A sandbox is a sandbox. It's going to break any functionality that can't work within the sandbox, and that's obviously the case for arbitrary folder locations. We don't distribute a sandboxed version of Zotero for that reason.

There was no "failure to create the data folder" by Zotero. Zotero can't work without a data folder. It created one, in whatever virtualized filesystem environment that was made available to it, and used it for as long as you were using Zotero. We can't vouch for anything beyond that.

Most third-party packages presumably work fine in a default configuration, with ~/Zotero whitelisted. Creating a secondary profile is an advanced feature, and if you don't know how to make it work with the third-party sandboxed package you chose to use, you shouldn't use it. Or you can switch to the tarball (or the minimal repackaging of the tarball done by a trusted community member), which works the way we intend for Zotero to work.

mkery

I don't know what you think you're accomplishing here by arguing with us, but you are wasting people's time, and you are going to get banned from posting here if you keep this up.

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hardly the way to talk to people who come here with problems and ask questions concerning them.

you should seriously reconsider these remarks.

DWL-SDCA

@dstillman please feel free to delete this comment if you believe that I have overstepped.

First, I want to say that Dan Stillman, the lead developer of Zotero, has demonstrated time and again on this forum that he is wise, competent, and kind. You are misinterpreting his remarks here.

Zotero is open source software. The Zotero obtained from Zotero.org works within several Linux environments as well as Mac and Windows. At least tens of thousands (hundreds of thousands?) of users have no problems with Zotero unless they make unusual changes to their operating environment. Please reread the attempts to help you. There is something unusual about how you obtained Zotero or how you have your operating system configured. Perhaps, both. Instead of accepting the suggestions made that should solve your problems you have argued that your issues are not internal to your system but the fault of Zotero. Clearly, you are frustrated that things are not working as you desire. However, your refusal to consider much less follow the advice given is misplaced and frustrating to those who are genuinely trying to help.

dstillman

hardly the way to talk to people who come here with problems and ask questions concerning them.

@mkery: No, that's not what you're doing. I have explained, over and over again, that the problem is not with Zotero but a result of using a third-party sandboxed package coupled with an advanced, non-standard configuration that is inherently incompatible with sandboxing. You've refused to accept what I've been saying to you and have continued to insist that this is somehow a problem in Zotero that we're responsible for, which is both obnoxious and a waste of our time that we could spend helping other people. So yes, I am genuinely warning you that you will be banned from posting further if you continue arguing about this.

If you're having problems with Flatpak sandboxing, go ask in Flatpak support forums. Someone might be able to tell you where you might look for files created within the sandbox that you can no longer find. If you want to keep using that package going forward, I believe there are command line flags that can be used to trivially grant access to other directories. But this has nothing to do with us, and we can't help you with this further here.