Installed 5.0 - can't access a 2nd Firefox profile and q. about synching

EileenClancy

[Mac Sierra] After updating to 5.0, I have these issues. I was using the affordances of the the Zotero ecosystem to keep my research projects separate. I had one set of materials in Standalone, and two in separate Firefox profiles. So, 3 separate data directories.

Since you removed the option to keeping files separately in Firefox, I don't have a way to keep my files, workflows and storage separate. It's very important to me that my research be stored locally, never to the cloud, except in the instance that I have to share something with my boss.

It used to be set up like this:

Remote contract work shared (always synched) Standalone 2000 items
Main (never synched) Firefox profile - 7000 items
Writing a book (never synched) Firefox profile - 1200 items

What happened when I updated to 5.0:

Standalone 5.0 connected to the data directory for my "Main" Firefox profile. But not the others.

Problems:
1) I can't access my second Firefox profile "Writing a book"
2) I want to keep these research files separate but still have the ability to synch one subset. (or by using a separate account).

dstillman

Zotero supports the same profile flags that Firefox does. Each profile can point to a different data directory.

(There's not currently a way to have the connector talk to different running instances of Zotero — it'll save to the one you opened first — but we might add that in a future version.)

Since you removed the option to keeping files separately in Firefox

Just to be clear, we didn't have a choice here — Firefox extensions can no longer access the filesystem.

EileenClancy

I wasn't asking about having different running instances of Zotero Standalone open at the same time. Is that possible? Because it would be very helpful.)

You wrote "Each profile can point to a different data directory." I know how to do this in Firefox; but not in the new Zotero Standalone. And I don't see documentation for how to connect to multiple profiles.

Would you please explain how to do this?

adamsmith

Zotero Standalone uses the same profile manage as Firefox. Just run Zotero from the terminal once with the -ProfileManager flag and you can set up profiles exactly as you previously did for Firefox.

dstillman

It's the same as the Firefox instructions I linked to, but you use /Applications/Zotero.app/Contents/MacOS/zotero for the executable instead of /Applications/Firefox.app/Contents/MacOS/firefox-bin.

I wasn't asking about having different running instances of Zotero Standalone open at the same time. Is that possible?

Yes. If you start Zotero from the command line with a different profile, a second copy will open (at least on macOS and Linux — you might need the -no-remote flag on Windows). I'm not sure off-hand what the best way to set that up via the GUI is — you could add a shell script to the files section of your Dock (though that opens a Terminal window each time) or maybe do something with AppleScript.

EileenClancy

Huh, so it does. I created a second profile. When I open the second profile, this dialog box popped up "Other Data Directory Found". It's asking me if I want to switch to the previous directory or use the current directory.

But, I can't see what they look like. Should I pick "Previous" or "Current"? (Maybe they are both the same anyway?)

dstillman

You can ignore that and say Current.

But you should move all the 'zotero' directories out of your Firefox profiles and put them somewhere else. Zotero 5.0 defaults to "Zotero" in your home directory for its data directory, so you could have "Zotero", "Zotero Book", etc.

Once you have those, create your three profiles and point each at the right data directory from the Advanced → Files and Folders pane of the Zotero preferences.

EileenClancy

When you say "move all the 'zotero' directories out of your Firefox profiles" does that mean I should move each folder in the Firefox Profiles directory that looks like "randomstring.default" elsewhere?

INO, move the entire folder or just the contents of that folder?
And what should the name of the folder be? Do I have to retain the "randomstring.default" naming convention?

Is the folder (on a Mac) "/Users//Zotero" is what you are calling the profile?

Do I understand you to recommend making a series of folders that act as profiles like this :
/Users//Zotero
/Users//Zotero-book
/Users//Zotero-remote

dstillman

No, those are your Firefox profiles — you certainly don't want to move those. We're just talking about your Zotero data directory here, which by default in Zotero 4.0 was the 'zotero' directory within your Zotero profile directory or Firefox profile directory. Zotero 5.0 automatically migrates the data directory to "Zotero" in your home directory, so one of your old ones is likely already there.

EileenClancy

I appreciate that you are trying to be helpful, but sorry, that is super unclear. It's not your fault; the lack of documentation for the update is making this unnecessarily complicated. It's also not helpful that all the terms are almost identical. Like "zotero" and "Zotero."

Right now, I have one folder containing my PDFs and other data named in this way:
/Users/username/Zotero

When I started the new 5.0 Zotero Standalone, that folder is the one it automatically found.

My problem is: I have 2 other profiles that can Zotero data.
My question is: what *exactly* do I move from the 3 folders now named?

"1randomstring.default"
"2randomstring.default"
"3randomstring.default"

Do I open them and copy/move zotero.sqlite and the "storage" folder?
Or do I move the entire folder?

And, where in the file system should they go?

Thank you.

adamsmith

the relevant folder is not "1randomstring.default" but "1randomstring.default/zotero" That's your old Zotero data directory.
What Dan is telling you to do is to take the _entire content_ of that directory (which includes zotero.sqlite and the storage folder and its content), place it in a new folder, say, /Users/Zotero-book
Then create a new Zotero profile and in the preferences select /Users/Zotero-book as the custom data directory location.
Repeat for the "remote" profile. It sounds like the main profile is already moved.

EileenClancy

That's more clear, thanks.

But (on my Mac) there is no folder "1randomstring.default/zotero"
Just "1randomstring.default" and its contents

Its seems weird to me that the only place for my new profiles is one level away from root. That's why I keep asking about "where." I was wondering if the structure should look like:

/Users/username/Zotero/Zotero-book

But, you're saying it should look like:

/Users/username/Zotero
/Users/username/Zotero-book
/Users/username/Zotero-remote

Thanks.

dstillman

That's entirely up to you. The default directory is /Users/username/Zotero. If you want to put it somewhere else, such as /Users/username/Zotero/Zotero-book, you can set a custom data directory location in the preferences. You've always been able to set a custom data directory in Zotero, and this is no different. The only thing that's changed is the default location.

What Dan is telling you to do is to take the _entire content_ of that directory (which includes zotero.sqlite and the storage folder and its content), place it in a new folder, say, /Users/Zotero-book

That would work, but that's not really what I said, because you shouldn't leave a 'zotero' directory behind that might lead to confusion. What I said was quite precise:

But you should move all the 'zotero' directories out of your Firefox profiles and put them somewhere else. Zotero 5.0 defaults to "Zotero" in your home directory for its data directory, so you could have "Zotero", "Zotero Book", etc.

Once you have those, create your three profiles and point each at the right data directory from the Advanced → Files and Folders pane of the Zotero preferences.

Just move 'zotero' and put it wherever you want, call it whatever you want, and point Zotero to it. I didn't say to move "1randomstring.default", and you shouldn't do that.

I appreciate that you are trying to be helpful, but sorry, that is super unclear. It's not your fault; the lack of documentation for the update is making this unnecessarily complicated.

Using multiple profiles and data directories is a fairly advanced and rare practice, so I've assumed you were familiar with the basics of profile directories, data directories, command-line flags, etc. And very little here has actually changed other than the default location of the data directory. But we can obviously explain further as necessary.

dstillman

Its seems weird to me that the only place for my new profiles is one level away from root.

Just to reiterate, they're not profiles — they're data directories.

Profiles contain settings (prefs.js and such), exist for both Firefox and Zotero, and stay within ~/Library/Application Support.

Data directories contain your library data, with zotero.sqlite and 'storage', and can exist anywhere. In 4.0 the default location was within the Firefox or Zotero profile directory as 'zotero'. In Zotero 5.0 the default is /Users/username/Zotero.

EileenClancy

Dan, I really appreciate your clarifications.

Also, you wrote: <<Using multiple profiles and data directories is a fairly advanced and rare practice, so I've assumed you were familiar with the basics of profile directories, data directories, command-line flags.>>

It's true that I am a little more advanced than the average academic. But everyone I know who works on the CL frequently prefers to see a line of bash script written out when possible.

But, probably the main reason is my feeling that Zotero databases seem somewhat fragile. Usually when you are working on the CL, you aren't going to "break" anything unless you get sloppy with "rm." But, the impression I have from reading this forum over several years is that it's pretty easy to do something unorthodox and break your Zotero data directory or certainly to lose access to it for a while. And, that because users are working in such different hardware and software environments, it can be frustrating for both the users and you folks doing support to fix.

Hence my cautious, tedious and step-by-step approach.

Thanks for talking me thru each step of this.

And, while I have technical skills in a variety of areas, I know very little about browsers, including profile directories. My impression is that it's a fairly arcane area.

It took me several years to figure out that I could work with multiple directories. It was only necessity that drove me to it. ;-) In the meanwhile, I have collected "guides" to Zotero written by faculty and librarians all over the country. Do you know there is a 60-page guide to doing legal referencing with Zotero? ;-)

I would like to see Zotero have more voluminous documentation. I wish I was in a position to write it for you; because I think it would be helpful to many people.

And, one final word, my first look at Zotero 5.0 makes me think that it is much improved for my purposes. My biggest data directory is more than 20 GBs. So, it had gotten impossible to use Zotero and I had started using other types of storage.

But, the new Zotero is really speedy!! Congratulations to all of you for getting it done.

And, thanks again.

dstillman

(There's not currently a way to have the connector talk to different running instances of Zotero — it'll save to the one you opened first — but we might add that in a future version.)

Correction: This is already possible. extensions.zotero.httpServer.port hidden pref in Zotero, connector.url in the connector. So you could change the port in each profile (just incrementing the number by one should be fine) and then make the same change for the connector in different Firefox profiles or different browsers to save to each.