Zotero standalone won't open, can't access database

eschoolman

Hi,

I've used Zotero for years with no problem. Upgraded to Mavericks 2 weeks ago. Zotero froze this morning. I had to force quit, and when I tried to start Zotero again, I got the message that it can't access the Zotero database, check permissions, etc. I have checked permissions on my Zotero library (/Users/<username>/Library/Application Support/Firefox/Profiles/<randomstring>/zotero) and everything is read/write. One note: there is actually no "zotero" folder inside the <randomstring> folder. All the separate sqlt and so on files are just there inside the <randomstring> folder.

Followed the directions to get an error message from Terminal, and here it is:
-------------
Could not read chrome manifest 'file:///Applications/Zotero.app/Contents/MacOS/chrome.manifest'.

While creating services from category 'profile-after-change', could not create service for entry 'Disk Space Watcher Service', contract ID '@mozilla.org/toolkit/disk-space-watcher;1'

Timestamp: 18/11/2013 15:54:02
Error: [Exception... "Component returned failure code: 0x80520015 (NS_ERROR_FILE_ACCESS_DENIED) [mozIStorageService.openDatabase]" nsresult: "0x80520015 (NS_ERROR_FILE_ACCESS_DENIED)" location: "JS frame :: chrome://zotero/content/xpcom/db.js :: Zotero.DBConnection.prototype._getDBConnection :: line 1109" data: no]
Source File: chrome://zotero/content/xpcom/zotero.js
Line: 821
-------------

dstillman

Have you tried restarting your computer?

eschoolman

Yes. Also restarting Firefox, and making sure the plugin was uptodate, etc.

dstillman

In Terminal, type 'ls -la ' (that's with a space at the end, no quotes) and then drag in the 'zotero' folder from Finder so that it copies the path and hit Return. Paste the output here.

eschoolman

Last login: Mon Nov 18 15:53:43 on ttys000
67-194-7-52:~ eschoolman$ ls -la
total 80
drwxr-xr-x+ 26 eschoolman 501 884 11 Nov 11:48 .
drwxr-xr-x 5 root admin 170 29 Oct 16:42 ..
-rw-r--r-- 1 eschoolman 501 3 11 Jun 2007 .CFUserTextEncoding
-rw-r--r--@ 1 eschoolman 501 24580 18 Nov 15:44 .DS_Store
-rw-r--r--@ 1 eschoolman 501 376 21 May 2011 .JavaPowUpload.properties
drwx------ 123 eschoolman 501 4182 18 Nov 15:35 .Trash
drwxr-xr-x 5 eschoolman 501 170 12 Oct 23:11 .autobahn
-rw-r--r-- 1 eschoolman 501 571 18 Nov 15:58 .bash_history
drwxr-xr-x@ 3 eschoolman 501 102 14 Jul 2009 .cups
drwxr-xr-x 11 eschoolman 501 374 5 Mar 2013 .dropbox
drwxr-xr-x 3 eschoolman 501 102 10 Dec 2007 .qgis
drwxr-xr-x 7 eschoolman 501 238 14 Nov 15:06 .qgis2
-rw-r--r-- 1 eschoolman 501 0 7 Nov 18:04 .st_cmd_hist
drwxr-xr-x 2 eschoolman 501 68 15 Jun 2007 Applications
drwxr-xr-x 3 eschoolman 501 102 31 Dec 2007 Backups
drwxr-xr-x 32 eschoolman 501 1088 13 Nov 22:05 Desktop
drwxr-xr-x 18 eschoolman 501 612 15 Nov 14:51 Documents
drwxr-xr-x 1816 eschoolman 501 61744 18 Nov 15:36 Downloads
drwxr-xr-x@ 9 eschoolman 501 306 23 Feb 2013 Dropbox
drwxr-xr-x@ 61 eschoolman 501 2074 18 Nov 15:58 Library
drwxr-xr-x 7 eschoolman 501 238 29 Oct 21:51 Movies
drwxr-xr-x 7 eschoolman 501 238 29 Oct 21:51 Music
drwxr-xr-x 9 eschoolman 501 306 29 Oct 21:51 Pictures
drwxr-xr-x 5 eschoolman 501 170 7 Dec 2010 Public
drwxr-xr-x 9 eschoolman 501 306 17 Mar 2010 Sites
drwxr-xr-x 3 eschoolman 501 102 28 Oct 15:07 Virtual Machines
67-194-7-52:~ eschoolman$ /Users/eschoolman/Library/Zotero
-bash: /Users/eschoolman/Library/Zotero: is a directory
67-194-7-52:~ eschoolman$

adamsmith

that didn't quite work. Try again with
ls -la /Users/eschoolman/Library/Zotero

eschoolman

67-194-7-52:~ eschoolman$ ls -la /Users/eschoolman/Library/Zotero
total 24
drwxrwxrwx 5 eschoolman 501 170 18 Nov 14:39 .
drwxr-xr-x@ 61 eschoolman 501 2074 18 Nov 15:58 ..
-rwxrwxrwx@ 1 eschoolman 501 6148 18 Nov 15:44 .DS_Store
drwxrwxrwx 4 eschoolman 501 136 18 Nov 11:31 Profiles
-rwxrwxrwx 1 eschoolman 501 103 8 Mar 2013 profiles.ini
67-194-7-52:~ eschoolman$

dstillman

The Zotero data directory is a few levels under that 'Zotero' directory, within the default profile, and is lowercase 'zotero'. See that linked page.

dstillman

And dragging should work — just make sure you don't press Return before dragging the data directory into Terminal.

dstillman

This might work:

ls -la /Users/eschoolman/Library/Zotero/Profiles/*.default/zotero

dstillman

I'm not actually clear how your Zotero files ended up there, though. They normally should be within /Users/<username>/Library/Application Support/Zotero. Did you move these files from another computer by hand? And you mention /Users/<username>/Library/Application Support/Zotero above. Do you have Zotero files in both places?

dstillman

In any case, the Zotero Data page tells you how to show the data directory that's being used.

eschoolman

not quite sure what you mean. There's no lowercase "zotero" folder that I can see inside /Users/eschoolman/Library/Zotero

eschoolman

Is there a way that I can send you a screenshot?

dstillman

See the linked page — it explains all of this.

eschoolman

I don't mean to be argumentative, but I don't think that it does. Specifically:

The linked page says that my Zotero data is stored in the following:

Zotero Standalone
OS X
/Users/<username>/Library/Application Support/Zotero/Profiles/<randomstring>/zotero

But I do not have a lowercase "zotero" folder inside <randomstring>. Instead, I have the following items:

cert8.db
compatibility.ini
content-prefs.sqlite
cookies.sqlite
cookies.sqlite-shm
cookies.sqlite-wal
extensions.ini
extensions.sqlite
extensions.sqlite-journal
formhistory.sqlite
indexedDB
key3.db
localstore.rdf
marionette.log
mimeTypes.rdf
permissions.sqlite
places.sqlite
places.sqlite-shm
places.sqlite-wal
pluginreg.dat
prefs.js
secmod.db
signons.sqlite
webappsstore.sqlite
webappsstore.sqlite-shm
webappsstore.sqlite-wal

As you can see, there is nothing called "zotero" or "zotero.sqlt".

adamsmith

You have been posting two different Zotero data folder paths. It sounds like you have both Standalone and Zotero for Firefox installed, is that correct? If so, you have likely set up Standalone to share the zotero data folder with Zotero for Firefox, so the lowercase zotero folder will only be in one of the profiles. But it is going to be in one of them and you'll need to find it, if need be by searching for zotero.sqlite

My guess, though, would be that
ls -la /Users/eschoolman/Application Support/Firefox/Profiles/*.default/zotero
will actually work.

dstillman

That's the default location for Zotero Standalone, and if you've only used Zotero Standalone, that's where it should be unless you moved the files from another computer or something (which could also explain permissions issues). You seem to also have a /Users/<username>/Library/Zotero folder for some reason, and I'm not sure why. If the 'zotero' directory is under that, it'd be in the same relative location.

If you had Zotero for Firefox installed first, then your data directory may be in the default Zotero for Firefox location, also mentioned on that page (and you would also be able to open Firefox, access the Zotero preferences via the Firefox Add-ons pane, go to the Advanced -> Files and Folders pane, and show the data directory that way).

dstillman

Taking the space into account, it'd be this:

ls -la /Users/eschoolman/Application\ Support/Firefox/Profiles/*.default/zotero

eschoolman

Bingo. I use standalone, but it shares with Firefox, and the zotero folder was in the Firefox profile.

Now what? I can't open Zotero to tell it to look for the data in a different place, because.... well, Zotero won't let me open it.

dstillman

We still need to see the contents of that directory with the ls -la command. You can access the Zotero for Firefox prefs even if you can't open Zotero, but you shouldn't change any settings until we figure out what's actually happening. (Changing Standalone settings if you can't open it is more complicated.)

eschoolman

Okay, I forgot something, which I just re-discovered looking at where Firefox was storing my zotero library. I put it in a folder in my Documents. Here's the path:

67-194-7-52:~ eschoolman$ ls -la
total 80
drwxr-xr-x+ 26 eschoolman 501 884 11 Nov 11:48 .
drwxr-xr-x 5 root admin 170 29 Oct 16:42 ..
-rw-r--r-- 1 eschoolman 501 3 11 Jun 2007 .CFUserTextEncoding
-rw-r--r--@ 1 eschoolman 501 24580 18 Nov 15:44 .DS_Store
-rw-r--r--@ 1 eschoolman 501 376 21 May 2011 .JavaPowUpload.properties
drwx------ 131 eschoolman 501 4454 18 Nov 17:34 .Trash
drwxr-xr-x 5 eschoolman 501 170 12 Oct 23:11 .autobahn
-rw-r--r-- 1 eschoolman 501 571 18 Nov 15:58 .bash_history
drwxr-xr-x@ 3 eschoolman 501 102 14 Jul 2009 .cups
drwxr-xr-x 11 eschoolman 501 374 5 Mar 2013 .dropbox
drwxr-xr-x 3 eschoolman 501 102 10 Dec 2007 .qgis
drwxr-xr-x 7 eschoolman 501 238 14 Nov 15:06 .qgis2
-rw-r--r-- 1 eschoolman 501 0 7 Nov 18:04 .st_cmd_hist
drwxr-xr-x 2 eschoolman 501 68 15 Jun 2007 Applications
drwxr-xr-x 3 eschoolman 501 102 31 Dec 2007 Backups
drwxr-xr-x 33 eschoolman 501 1122 18 Nov 16:55 Desktop
drwxr-xr-x 18 eschoolman 501 612 15 Nov 14:51 Documents
drwxr-xr-x 1817 eschoolman 501 61778 18 Nov 17:34 Downloads
drwxr-xr-x@ 9 eschoolman 501 306 23 Feb 2013 Dropbox
drwxr-xr-x@ 60 eschoolman 501 2040 18 Nov 17:34 Library
drwxr-xr-x 7 eschoolman 501 238 29 Oct 21:51 Movies
drwxr-xr-x 7 eschoolman 501 238 29 Oct 21:51 Music
drwxr-xr-x 9 eschoolman 501 306 29 Oct 21:51 Pictures
drwxr-xr-x 5 eschoolman 501 170 7 Dec 2010 Public
drwxr-xr-x 9 eschoolman 501 306 17 Mar 2010 Sites
drwxr-xr-x 3 eschoolman 501 102 28 Oct 15:07 Virtual Machines
67-194-7-52:~ eschoolman$ /Users/eschoolman/Documents/Articles\ and\ Resources/Zotero
-bash: /Users/eschoolman/Documents/Articles and Resources/Zotero: is a directory
67-194-7-52:~ eschoolman$

dstillman

Sorry, that's still not right. The path has to immediately follow the 'ls -la ' — with a space at the end, not a new line — such that the listing shows 'zotero.sqlite' and other files. You seem to still be pressing Return before dragging in the folder. It should look like our examples above, all in one line.

eschoolman

got it. here we go:

67-194-7-52:~ eschoolman$ ls -la /Users/eschoolman/Documents/Articles\ and\ Resources/Zotero
total 236200
drwxr-xr-x 18 eschoolman 501 612 18 Nov 17:33 .
drwxr-xr-x 12 eschoolman 501 408 8 Mar 2013 ..
-rw-r--r--@ 1 eschoolman 501 6148 18 Nov 17:37 .DS_Store
drwx------ 6 eschoolman 501 204 8 Mar 2013 locate
--wx--xr-x@ 1 eschoolman 501 803236 28 Oct 2008 pdfinfo-MacIntel
--w----r--@ 1 eschoolman 501 4 28 Oct 2008 pdfinfo-MacIntel.version
--wx--xr-x@ 1 eschoolman 501 1080704 28 Oct 2008 pdftotext-MacIntel
--w----r--@ 1 eschoolman 501 4 28 Oct 2008 pdftotext-MacIntel.version
drwx------ 5 eschoolman 501 170 18 Nov 17:37 pipes
d------r-x@ 451 eschoolman 501 15334 18 Nov 11:28 storage
d------r-x@ 19 eschoolman 501 646 15 Nov 14:42 styles
d------r-x@ 423 eschoolman 501 14382 15 Nov 14:42 translators
--w----r--@ 1 eschoolman 501 3165 4 Mar 2010 zotero.moved-files.36.bak
--w----r--@ 4 eschoolman 501 38283264 18 Nov 11:29 zotero.sqlite
--w----r-- 1 eschoolman 501 233744 18 Nov 11:29 zotero.sqlite-journal
--w----r--@ 1 eschoolman 501 29210624 4 Mar 2013 zotero.sqlite.1.bak
--w----r--@ 1 eschoolman 501 22074368 20 Mar 2011 zotero.sqlite.73.bak
--w----r--@ 1 eschoolman 501 29210624 5 Mar 2013 zotero.sqlite.bak
67-194-7-52:~ eschoolman$

adamsmith

nevermind - that's the right one now.

adamsmith

those permissions look off, though - I didn't even know this was possible, but you seem to have write but no read permissions (--w) for zotero.sqlite, which would be one problem (they should start with (-rw).

You also have neither write nor read permissions for the storage, styles, and translators folder (they should start with drw). You should be able to set read and write permissions for the entire folder (/Users/eschoolman/Documents/Articles\ and\ Resources/Zotero) and its contents.
http://www.macinstruct.com/node/415

dstillman

OK, yeah, those permissions are totally messed up. That's not really something Zotero could have done itself, but I couldn't tell you how it happened. So close Firefox and run these commands, on separate lines in Terminal:

sudo chown -R eschoolman /Users/eschoolman/Documents/Articles\ and\ Resources/Zotero

find /Users/eschoolman/Documents/Articles\ and\ Resources/Zotero -type f -exec chmod u+rw,g+r,+X {} \;

find /Users/eschoolman/Documents/Articles\ and\ Resources/Zotero -type d -exec chmod 755 {} \;
You'll have to type your system password after the first one, and you won't see it printed back to you as you type.

I think that should do it.

eschoolman

Done. Whoof, what an afternoon! Thank you both for all your help. Now I'm going to put my pants back on. Just kidding! Seriously, though, thanks.

dstillman

OK, great. And just to avoid future confusion, you might want to figure out which Zotero profile directory is the active one — I would assume the Application Support one, but you can probably tell based on timestamps of files within it — and remove the other one (to the trash or Desktop temporarily, to make sure you're deleting the right one). I'd guess that simply deleting Library/Zotero should be fine, since Zotero should use the Application Support one by default (and I don't even know off-hand how you'd tell it not to).

eschoolman

The only files with "profile" in their name are in Application Support. I actually have deleted that before, and when I start Zotero it just creates a new profile in the same place. Is that OK, to have my library in one location, and my profile in another?

dstillman

That's fine. The data directory (i.e., library, i.e., 'zotero') is made to be configurable. The profile directory (which stores things like preferences) isn't, and should be in Application Support.

But I was referring to what you showed above:

67-194-7-52:~ eschoolman$ ls -la /Users/eschoolman/Library/Zotero
total 24
drwxrwxrwx 5 eschoolman 501 170 18 Nov 14:39 .
drwxr-xr-x@ 61 eschoolman 501 2074 18 Nov 15:58 ..
-rwxrwxrwx@ 1 eschoolman 501 6148 18 Nov 15:44 .DS_Store
drwxrwxrwx 4 eschoolman 501 136 18 Nov 11:31 Profiles
-rwxrwxrwx 1 eschoolman 501 103 8 Mar 2013 profiles.ini
67-194-7-52:~ eschoolman$

That seems to suggests that you have some misplaced 'Zotero' (the parent to 'Profiles', not to be confused with 'zotero') directory directly under Library, separate from whatever you have under Application Support. (And this one shows a date of November 18. Perhaps you were moving files around today and copied 'Zotero' from Library/Application Support to Library by accident?)