Zotero startup error, even after reboot

Gracile

I've restarted my computer several times but I can't start Zotero (FF or Standalone) anymore.

I was switching between Standalone and Firefox (several times actually, because of the differences in the way proxies are handled, and in order to use Zutilo "attach the current page to the current Zotero item" firefox-only function). I knew it could be risky… My database is probably locked, what can I do?

Here's the content of the Error console window for Zotero Standalone (just after having restarted Windows):

Could not read chrome manifest 'file:///C:/Program%20Files%20(x86)/Zotero%20Standalone/xulrunner/chrome.manifest'.

Timestamp: 18/06/2015 15:43:46
Warning: mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial [[Prototype]] value using Object.create
Source File: resource://gre/modules/Preferences.jsm
Line: 381

While creating services from category 'profile-after-change', could not create service for entry 'MobileConnection Service', contract ID '@mozilla.org/mobileconnection/mobileconnectionservice;1'

Timestamp: 18/06/2015 15:43:47
Warning: mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial [[Prototype]] value using Object.create
Source File: chrome://zotero/content/xpcom/xregexp/xregexp.js
Line: 109

Timestamp: 18/06/2015 15:43:47
Error: [Exception... "Component returned failure code: 0x80630001 (NS_ERROR_STORAGE_BUSY) [mozIStorageService.openDatabase]" nsresult: "0x80630001 (NS_ERROR_STORAGE_BUSY)" location: "JS frame :: chrome://zotero/content/xpcom/db.js :: Zotero.DBConnection.prototype._getDBConnection :: line 1119" data: no]
Source File: chrome://zotero/content/xpcom/zotero.js
Line: 801

dstillman

There's no problem switching between Standalone and Firefox — it's designed to do that — but is your Zotero data directory on a network hard drive, in a server-mirrored home directory, in Dropbox, or something similar?

Gracile

No…

dstillman

Well, if there's a SQLite -journal file in your data directory, you can try deleting that, but make sure you have a backup of your data directory, since that risks corrupting your database. Generally when this happens there's some other sort of problem — security software or a filesystem issue — that's the root cause, so if you're running security software, try disabling that first. If deleting the journal file does work, check your database integrity from the Advanced → Files and Folders pane of the Zotero preferences afterward.

Gracile

I've disabled temporarily Microsoft Security Essentials Real-Time Protection. No change.
I, while MSE was still disabled, deleted zotero.sqlite-journal. No change.

Gracile

Content of my data dir (zotero.sqlite-journal has been recreated)

locate\
storage\
styles\
translators\
abbreviations-for-zotero.sqlite
abbreviations-for-zotero.sqlite-journal
abbreviations-for-zotero.sqlite.bak
abbreviations-for-zotero.sqlite.1.bak
abbreviations-for-zotero.sqlite.12.bak
abbreviations-for-zotero.sqlite.13.bak
lyz.sqlite
lyz.sqlite.bak
pdfinfo.vbs
pdfinfo-Win32.exe
pdfinfo-Win32.exe.version
pdftotext.vbs
pdftotext-Win32.exe
pdftotext-Win32.exe.version
zotero.sqlite
zotero.sqlite-journal
zotero.moved-files.36.bak
zotero.sqlite.bak
zotero.sqlite.damaged
zotero.sqlite.1.bak
zotero.sqlite.73.bak
zotero.sqlite.76.bak
zotero-item-history.sqlite
zotero-item-history.sqlite-journal
zotero-item-history.sqlite.bak
zotero-item-history.sqlite.1.bak

adamsmith

have you tried disabling the other add-ons?

Gracile

with Standalone, no… (edit: just to be clear, I mean, I can't disable them if I can't start Standalone)
with Z for Firefox, disabling the other add-ons didn't change anything.

Gracile

Dan, could the Zotero Database Repair Tool be helpful ?

dstillman

Sure, you could certainly try that.

Gracile

It doesn't change anything unfortunately.

Gracile

And no more luck if I rename zotero.sqlite.bak or zotero.sqlite.1.bak

Gracile

I decided to go the sync route because my db backups were a bit old. Everything is fine but a couple of questions: 

One of my attachments was not on the server, and thus not downloaded (it was the only one with an empty blue circle). I added it thanks to my backup, reset the file sync history. It worked well and the missing attachment is now on the server. But it seems that after having reset the file sync history, Zotero uploaded 1000 MB (or did it check them on the server?) 1000 MB, that's not the weight of my complete library (1530 MB), nor that of the missing file (2,64 MB).

How can I be sure that files I delete locally (with Finder/Explorer) on my computer are not uploaded to the server? Before zotero 3.0, each time I took a snapshot of a webpage, zotero stored a lot of superflous files with @22 extension. I deleted them at that time but I realize now that they were still on the server… and now locally.

dstillman

But it seems that after having reset the file sync history, Zotero uploaded 1000 MB (or did it check them on the server?)

It checked them on the server.

How can I be sure that files I delete locally (with Finder/Explorer) on my computer are not uploaded to the server?

Modifying files other than the main file in an HTML snapshot doesn't affect anything unless you modify the main file too.

Gracile

1.Did it check all the files? Still don't understand why I only saw "1000MB remaining" (mouse over the green sync arrow).

[edit: 1b. is there a way to check that the server has sync all my files, ie to avoid what happened here?]

2.Resetting the File Sync History won't do anything if I understand correctly. Sync relies on the modification date of the main file, right?

BTW, I've just understood why I couldn't open Zotero… I had modified manually engines.json (was adding other engines manually) and made a syntax error in the json. That prevented Zotero to start… Pff, sorry for the hassle and thanks for your answers.

dstillman

It checks all (main) files after a reset, yes. Counter sum can be different for various reasons.

2. Resetting the File Sync History won't do anything if I understand correctly. Sync relies on the modification date of the main file, right?

Correct.

dstillman

[edit: 1b. is there a way to check that the server has sync all my files, ie to avoid what happened here?]

Not currently, but we'll be able to do more with API syncing.