"Profile Missing" after Firefox update

BPawson
Mac OS Sierra 10.12.5
Firefox 56.0.2 (64 bit)
Zotero 5 (just now) with the Connector for Firefox

After updating Firefox this eve I discovered that the Zotero add-on had become a "legacy" item. At this point I had no access to my 2k odd references, and a paper due... not an inspiring moment.

I therefore proceeded to update Zotero, downloading and installing version 5.0, and then the Zotero Connector (but after installing the Connector and restarting Firefox, the 'Z' button seems to have permanently disappeared after being available for a single click to apparently give me a warning which I now don't recall...? how do I use the connector). Moreover, when I try to load the standalone Zotero 5 I get:
"Profile Missing - Your profile cannot be loaded. It may be missing or inaccessible." The application then quits (or more accurately, never loads).
I've looked in my user Library and don;t see anything named Zotero, however doing a search in that directory for zotero turns up a number of seemingly invisible loose files (including zotero.sqlite at 140MB). I have done no recent modification to this directory, and recently have run a virus check that turned up nothing.

Version 4 of Zotero still exists (renamed) in my applications folder.

At this point I'm extremely concerned about losing my research references. There's years of work in that database. And I don't think I've ever actually synced this to the online version, at least not for years. Does that happen automatically/transparently? (I checked my library at zotero.org and it seems to have at least some very recent items in it, so maybe that's good news).

I'm desperate here. but have faith Zotero is more organized than I seem to be right now.

I look forward to being guided back to sanity.
  • bwiernik
    edited October 30, 2017
    Do you have a Zotero folder at ~/Zotero (Mac) or C:/Users/<username>/Zotero (Windows)? If so, what is in it?

    If not, start by checking if you have an “Old Firefox Data” folder on your desktop and see if your Zotero database is in there.
    https://www.zotero.org/support/kb/restore_after_firefox_reset
  • dstillman
    After updating Firefox this eve I discovered that the Zotero add-on had become a "legacy" item. At this point I had no access to my 2k odd references, and a paper due... not an inspiring moment.
    First, Zotero 4.0 for Firefox still works in Firefox 56 — you just need to be running the latest version. (The "legacy" label is just there to warn you that it won't work starting in Firefox 57.) So if you haven't yet started 5.0 successfully, you can try just reinstalling Zotero 4.0 for Firefox from the download page to finish the paper. If there's still a problem in the latest version of Zotero 4.0, you should explain exactly what that is.

    We can work on the profile issue for Zotero 5.0 when you have more time.

    (Note that a profile directory is different from the data directory bwiernik is referring to, so that question may not be relevant here.)
  • BPawson
    @bwiernik
    There is no Zotero folder in my user directory (Mac), which I thought was strange as I've done nothing that should be deleting information...in ~/Library/Application Support there is an apparently invisible folder called (lowercase) "zotero" which does not display a size and which the Finder's Get info: Sharing and Permissions reports I have "unknown access" to. The Application Support folder/directory also contains a number of loose zotero items, notably the aforementioned zotero.sqlite (140MB).

    I never performed a Firefox "Refresh" (I have only just done a normal update on reload) and so there is no "Old Firefox Data" on my desktop.

    @dstillman
    I simply renamed the old installation to "Firefox 4". Will this corrupt the installation? Because attempting to load it (the standalone version 4) now gives me the same Profile Missing error message as the standalone version 5 installation is giving. I'll try a fresh install of Zotero for Firefox version 4 next, so leaving the browser now - will report back in a bit.

    Also, I do see now that the 'Z' button is simply now a page icon, so it hasn't "disappeared" - my mistake.

    Many thanks to you both for helping :)
  • BPawson
    @dstillman OK now I'm back to where I started from: the Zotero for Firefox add-on (post Firefox update) reports:

    Error
    The Zotero data directory could not be found.
    Previous directory: /Users/my_name/Library/Application Support/Zotero/Profiles/hppskl8x.default/zotero

    response choices are:

    I've been choosing OK just to leave the status unchanged (I hope).
  • BPawson
    apparently angle brackets don't save...
    choices are:
    Locate...
    Use Firefox profile directory
    OK
  • BPawson
    btw, my preference, despite the anxious situation, is to move forward and use Zotero 5 standalone, with the Connector - as long as I can recover my database...
  • dstillman
    edited October 30, 2017
    There is no Zotero folder in my user directory (Mac), which I thought was strange as I've done nothing that should be deleting information
    That's fine. Zotero 5 moves the data directory there on upgrade, but if you haven't successfully started Zotero 5, you won't have that.
    n ~/Library/Application Support there is an apparently invisible folder called (lowercase) "zotero" which does not display a size and which the Finder's Get info: Sharing and Permissions reports I have "unknown access" to.
    That sounds like a potential problem. If /Users/my_name/Library/Application Support/Zotero/Profiles/hppskl8x.default/zotero exists, you'll need to fix the permissions (click the lock icon in that dialog) on the ~/Library/Application Support/Zotero folder and all folders and files within so that your user has read and write access. That should also fix the profile error in the standalone version.

    (I'm not sure why you're getting those specific messages — normally permissions errors are displayed differently — but the "unknown access" part is weird, so something else might be going on here.)
  • BPawson
    Here's some more weirdness. Apparently that 'folder' ("zotero", lower case, unknown size, unknown access) is an alias; although it does not say that in 'get info' -- but if I try to open it I get 'the alias can't be opened because the original item can't be found'. In 'icon view' it does not look like an alias either - just a blank page icon. However get info not only doesn't tell me it is in fact an alias, and says 'you have unknown access' but there is no lock icon in the dialog. The small 'locked' checkbox in the general panel shows an 'x' if I click on it (it comes up empty) but the 'x' goes away after releasing the mouse key, i.e. I can't change its value.

    I swear I have altered nothing in my system since all this was working perfectly well with the previous version of Firefox a couple of days ago. The Firefox update was apparently automatic on a recent restart, because I generally avoid any changes when I have deadlines approaching..
  • dstillman
    Open Terminal via Spotlight and paste in this command:

    ls -la ~/Library/Application\ Support/Zotero ~/Library/Application\ Support/Zotero/Profiles ~/Library/Application\ Support/Zotero/Profiles/hppskl8x.default ~/Library/Application\ Support/Zotero/Profiles/hppskl8x.default/zotero

    Then press Return and paste the output here. (You can redact the username wherever it appears.)
  • BPawson
    edited November 1, 2017
    I _wish_ I could do this...things have gone from bad to much worse. It seems the drive was failing (perhaps files were corrupted in some early phase of this?) at any rate, I'm now hoping that I may just have backed up enough information that I can restore my database whenever I can get a machine up and running again. I'm working on an old PC I have kicking around with most of my source materials missing, but fortunately a copy of the actual document, which at least is in revision stage, not research. Sigh.

    If it is possible to explore this rebuilding with Windows 7 I could try it on my current machine, but I suspect anything that survived the data recovery is Mac oriented.

    So, it would be better to resume this conversation in a week or two when/if I get past the crisis. One final question then; can I recover using the version that seems to have been saved online at zotero.org? I'm not sure I ever (consciously) synced to the zotero servers, but perhaps I had it set to do that automatically? At any rate when I checked a few days back, recent references seemed to be there, so at least some of my database must have been synced (?) or am I misunderstanding the entire procedure/interface?

    Many thanks for all the help at a very critical moment. I will remember that and am deeply appreciative even though it seems I am beyond hope at the moment ;)
  • dstillman
    edited November 1, 2017
    If you have a copy of the Zotero data directory (the lowercase 'zotero' directory), that's platform-agnostic. You would just need to restore that in the default location for Windows (see the linked page) and install Zotero 5.0.
    Can I recover using the version that seems to have been saved online at zotero.org?
    Sure — you just need to set up syncing again on the new computer. You were at your file quota, though, so some attached files would be missing. So if you do have a copy of your old data directory, that'd be the first thing to try. (And if it's a little bit out of date, Zotero will just pull down any recent data that's available.)
  • BPawson
    Thanks again, you've been a fantastic help. I installed Zotero 5.0 for Windows and the Connector for Opera, synced everything up starting from a recovered 2016 back-up I had (the recent disaster did not allow me to recover the much more complete zotero data directory). More recent data was pulled down just fine (thank God I had automatic syncing turned on), and I _will_ be upgrading my storage allotment in the next few days. Lesson learned.
  • BPawson
    Something else has come up. I have a backup of C:\user_name\Library\Application Support\Zotero that in this location \Profiles\hppskl8x.default\zotero contains a number of 8 character named folders (e.g. 2NZHWMUB) some of which windows reports are 'corrupted'. This back-up was from the Mac that died and I'm not sure there is even a reason to maintain these folders; they appear to contain information related to each items saved in my Zotero library - can I just delete this Zotero directory entirely or will this back-up be useful when I rebuild the Mac? The other issue here is at least the folder that reports being corrupted I do not seem to be able to delete...so garbage accumulates on the drive.
  • dstillman
    I'm not totally clear on your current situation, but files within 'storage' are the files associated with attachments in Zotero. You can delete them, but those files will no longer be accessible if you try to open the attachments in Zotero unless they've been synced to the online library (in which case they'll just sync down).
  • BPawson
    Thank you, that alleviates my worry. I now have more storage on Zotero.org and have synced recently. I was concerned, I think, that if I restore my Mac with/without these back-ups that perhaps when next synced it might somehow corrupt/or flush the material backed-up on the Zotero server. Sounds like the best policy is not to keep this back-up. Now to figure out how to delete corrupted directories...
Sign In or Register to comment.