Firefox freeze when attaching document

Hi there,
firefox crashes when I attach a pdf to a reference (linked or copied) from my computer or when I add a reference through a website. The document is often attached successfully after I restart firefox.
I have firefox 3 and zotero 1.0.7. I have tried to use the db rebuilder as it found errors when zotero analyzed it. But zotero still finds errors and the bug still occurs.

What should I do?

By the way, apart for that new issue, Zotero rocks and I'm advising it to everyone around me.
thanks!
Emmanuel
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  • Are you using the latest FireFox build, 3.0.4?
  • Yes: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.0.4) Gecko/2008102920 Firefox/3.0.4
  • By "crash" do you mean a real crash—as in, Firefox quits unexpectedly—or is there an error message?
  • more precisely firefox gets stuck with the "wait" cursor and the only way to get it back is to restart it.

    Actually, I think I've found the more precise situation in which it happens: there is some incompatibility with Quartz PDF plugin (which allows to display pdf within firefox on the mac). Firefox crashes when a pdf is open within firefox (with Quartz) and I try to attach a pdf.

    This happens pretty often when I do a literature search (as I skim a lot of documents and only add a few).
  • It might not really be hanging. If you have the PDF converter tools installed, it may just be indexing the imported PDF. Currently, this can look like a hang with a large PDF, particularly with slower computers, though you should hear disk activity. I haven't seen any conflict with Quartz.

    You might want to run Zotero with debug output enabled to see if it's actually doing anything.
  • edited December 8, 2008
    I have a similar problem, but have not tracked as above. My problem is that Zotero on my Mac system reports an error quite frequently and asks me to restart firefox. Sometimes, the reference I am adding is lost, sometimes it is there in part. I will try to track my actions when it happens. I have not found it to cause the same problem when I am using portable firefox and this is why I now have two separate databases.

    The error has occurred again. I have sent an error report 1563739586.
  • Cherry:
    [JavaScript Error: "uncaught exception: [Exception... "Component returned failure code: 0x8052000b (NS_ERROR_FILE_CORRUPTED) [mozIStorageStatement.execute]" nsresult: "0x8052000b (NS_ERROR_FILE_CORRUPTED)" location: "JS frame :: chrome://zotero/content/xpcom/fulltext.js :: indexWords :: line 250" data: no]"]"
    Use the DB Repair Tool. Assuming you originally upgraded from Firefox 2, which had database instability problems, this shouldn't happen again.
  • What is the DB repair tool. Is it part of Zotero or Firefox?
  • Cherry,

    The phrase "DB Repair Tool" in Dan's post is a link. Click it and it takes you to a page that explains how to use it.
  • Thanks
    Got it.
  • Hi there,
    Zotero worked well for a while but started to crash again like above when I add documents (either online or from HD). Sometimes it works (i.e. usually when I have the debug output on!) but often it freezes. I can email the debug to someone because it's too big to insert here. I've included only the end of it below.
    Thanks,
    Emmanuel


    zotero(5): SELECT creatorTypeID AS id, creatorType AS name FROM itemTypeCreatorTypes NATURAL JOIN creatorTypes WHERE itemTypeID=? ORDER BY primaryField=1 DESC, name

    zotero(5): Binding parameter 1 of type int: 33

    zotero(3): Notifier.trigger('add', 'item', [15934]) called [observers: 3]

    zotero(4): Calling notify() on observer with hash 'J7'

    zotero(4): Calling notify() on observer with hash 'Ph'

    zotero(4): Calling notify() on observer with hash 'l5'

    zotero(5): SELECT sourceItemID FROM itemAttachments WHERE itemID=15934

    zotero(5): SELECT creatorTypeID AS id, creatorType AS name FROM itemTypeCreatorTypes NATURAL JOIN creatorTypes WHERE itemTypeID=? ORDER BY primaryField=1 DESC, name

    zotero(5): Binding parameter 1 of type int: 33

    zotero(5): Beginning DB transaction

    zotero(3): Beginning Notifier event queue

    zotero(5): SELECT linkMode, path FROM itemAttachments WHERE itemID=15934

    zotero(5): SELECT mimeType FROM itemAttachments WHERE itemID=15934

    zotero(5): SELECT charsetID FROM itemAttachments WHERE itemID=15934

    zotero(5): SELECT linkMode FROM itemAttachments WHERE itemID=15934

    zotero(3): Running pdfinfo "/Users/emmanuelfreudental/Documents/readings/zotero/storage/15934/Niermann and Patel - 1991 - HITEC a test generation package for sequential ci.pdf" "/Users/emmanuelfreudental/Documents/readings/zotero/storage/15934/.zotero-ft-info"

    T
  • PS: I have a feeling it might come from the "tab mix plus" session manager because it bugs more when I "recover" the crashed session after firefox crashed when I added an attachment to Zotero
  • I'm experiencing this same problem after switching to a Mac: anytime I am attaching a PDF (either automatically when adding a citation, or manually by using the add attachment feature) I get the "beach ball of death" and have to force quit. Generally when I restart, the PDF is in fact attached there.

    I thought it might be my "Tab Kit" or "Firefox PDF Plugin for Mac OS X" plugins given what was said above, so I disabled them, but the problem persists.

    My error report is : 374519186

    There was mention of PDF indexing as the problem above, but I don't know how to disable that.

    I would love to get this working, since this makes using Zotero not an option for me at all.

    Thanks,

    Dean
  • I have had the same problem, and clearing my index (save for web pages) seems to have cleared it up. I have not rebuilt the index yet, so cannot say whether or not the problem reappears.
  • edited January 22, 2009
    I am having the same general problem. In some detail:

    I only get a problem when I try to attach a PDF file (as far as I can tell) or drop it into the zotero contents window. The symptoms are that the spinning colorful wheel apperas, Firefox is thus "hung" and unresponsive, and I have to Force Quit. Otherwise, both programs are functioning fine. The interesting thing is that after I quite Firefox and restart, zotero will have attached the PDF file (only when I attach; otherwise it doesn't show up if I drop it into contents or something similar).

    I am using Firefox 3.0.5 on a MacBook with Tiger 10.5.6 and zotero 10.0.9. I have very items in my library (about 10) so this is not an issue of things going slowly because of too many items to index or whatnot.

    I ran firefox in debug mode (i.e. from a terminal) when trying to attach a file and the last line of output is

    zotero(3): Running pdfinfo "/Users/sohrab/Documents/References and papers/LDA+U.pdf" "/Users/sohrab/Library/Application Support/Firefox/Profiles/d44fhovv.default/zotero/storage/12536/.zotero-ft-info"

    I then suspended it and looked about. The only process it has spawned (seen via "ps") is a child called psinfo-MacIntel which is zombied (Z state) and thus hanging. My guess is this is the problem?

    More generally, my guess is that here is some PDF indexing issue. How can I disable pdfinfo from launching?

    My problems are now serious: I though reindexing would help. So I cleared index cache and tried to reindex, but now the reindexing (from Preferences) hangs (with color wheel) and restarting gives me no index. So I have no index anymore! Help!!!
  • If the truth be told, I am now much happier with a clean index. Zotero is much more useful now that it only searches for item metadata and the text of notes. Would be nice (I guess that I should make a new thread about this) if we could have more control over indexing - i.e. turn attachment indexing on and off in a more or less arbitrary manner.
  • It may be an issue with our modified version of pdfinfo (which, unlike the original version, saves output to disk). We'll look into it (unless someone else wants to take a look).

    In the meantime, if you're having this problem, you could try deleting pdfinfo from the Zotero data directory. Zotero won't have data on the number of pages in PDFs but (I believe) should still index them.
  • telesthetic: If you're familiar with gdb and could provide a backtrace for the stalled pdfinfo process, that might be helpful. (If not, don't worry about it.)
  • Dan Stillman: Thanks! deleting pdfinfo from my data directory seems to have fixed the hanging problem.

    Previously, Firefox would hang as described by others in this thread. PDFs do indeed still seem to be indexed (can search for and find unique terms), though Zotero is a bit confused and lists the Indexed stat as "Unknown" even after manually selecting the "Reindex" icon.

    Firefox 3.0.6, Zotero 1.0.9 OSX 10.5.6
  • hi I am a new zotero user -
    I am experiencing the same prob when I try to pull my pdf's into zotero - usually it crashes.

    Has anyone been able to get this to work?

    bryanp - did you delete these 2 files (pdfinfo-MacIntel
    pdfinfo-MacIntel.version) ? and are you able to index your pdf's now in zotero?
    I've been using a great program called PAPERS but I would love to just move completely over to Zotero.

    THANKS!
    tricia

    firefox 3.0.6, zoterzo 1.5, osx 10.5.6
  • Just another datapoint:

    Running zotero 2.0.3, firefox 3.5.9 on ubuntu 9.10 (karmic); pdfinfo and pdftext are 3.02pl1.

    I had this (or at least a similar) problem: when I added a PDF file to zotero it (firefox+zotero) hung with the "Saving item..." popup. Then I had to manually kill firefox. On restart, the PDF file was present in zotero, but attempting to index it or to retrieve metadata for it again caused a hang.

    I tried a wide variety of tests without success; but eventually, moving the pdfinfo and pdftotext binaries out of the zotero directory (in firefox profile), restarting firefox, and reinstalling the binaries (from within zotero) seemed to fix it. This was surprising, as the re-installed binaries exactly matched the ones I moved out; and the previous binaries executed fine "standalone". So the binaries themselves did not seem to be corrupt; rather, something seemed to change in the way zotero invokes them when I deleted and reinstalled.

    Note that before deleting these binaries, I already checked for updates of them from within zotero, and was (correctly) told they were up to date; despite this, it seems that I needed to remove them and reinstall...

    I know this all sounds very unlikely, or even impossible...; maybe there is some crazy race condition in the synchronization between parent and offspring processes such that just having pdfinfo/pdftotext physically elsewhere on the disk was enough to tweak it away... who knows (certainly not I ...).

    (My route to resolution involved first trying the removal of pdfinfo and pdftotext as a workaround; that did indeed "work" in the sense that firefox+zotero no long hung, but at a cost of losing PDF indexing and retrieval of PDF metadata. I was ready to stop then - I really could not see any way that re-installing pdfinfo and pdftotext could help, since those original binaries were not corrupt and worked "standalone"; but just tried the re-install to be sure, and what do you know, everything started working again...)

    Anyway, it took several hours of my time before I finally got to this resolution, so I'm posting here in case it will be helpful to somebody else...
  • So the binaries themselves did not seem to be corrupt; rather, something seemed to change in the way zotero invokes them when I deleted and reinstalled.
    Were you actually getting it every time before? As far as we know it's just an intermittent error that some people sometimes get (though I've never gotten it, which makes it somewhat hard to fix).
    maybe there is some crazy race condition in the synchronization between parent and offspring processes such that just having pdfinfo/pdftotext physically elsewhere on the disk was enough to tweak it away...
    It definitely seems like a race condition of some sort, so this isn't the craziest theory.
    My route to resolution involved first trying the removal of pdfinfo and pdftotext as a workaround; that did indeed "work" in the sense that firefox+zotero no long hung, but at a cost of losing PDF indexing and retrieval of PDF metadata.
    That's not the recommended workaround. As I note above, the recommended workaround is removing just pdfinfo, which means you lose some metadata but indexing still works.

    At any rate, I'm hoping this will go away when we upgrade from Xpdf to Poppler.
  • Dan asks:

    Were you actually getting it every time before?

    Yes: every single action that I tested, that involved either pdfinfo or pdftotext, caused a hang. It was very consistent. As I mentioned, I first suspected some issue specific to the particular PDF file; but I tried two independent files with no change in behaviour.

    [removal of pdfinfo and pdftotext is] not the recommended workaround. As I note above, the recommended workaround is removing just pdfinfo, which means you lose some metadata but indexing still works.

    I did try that at one point - though not all that carefully. The problem was that I was getting a hang not just on invocation of pdfinfo but also on pdftotext - so, in my particular case, it did not seem to be possible to retain indexing. But of course, others' mileage may vary (especially if this is a subtle timing issue).

    Anyway, thanks for the response. I appreciate that it is difficult to do much about when it is so hard to reproduce. Maybe there is some scope to add additional debug output in the code that invokes/syncs with pdfinfo/pdftotext? That might help shed some more light if it happens again.

  • edited May 24, 2010
    I confirm the same behavior (crash on pdfinfo step, reinstalling pdfinfo fixes problem) with Firefox 3.6.3 and Zotero 2.0.3 under Ubuntu 10.04.

    Furthermore, reverting to the original pdfinfo binary after reinstalling does not seem to cause the bug to return.
  • Unfortunately, the proposed solution does not work on my installation (Ubuntu 10.4, Firefox 3.6.6, Zotero 2.0.3, pdfinfo 3.02pl1, pdftotext 3.02pl1). I deleted the binaries and did a re-install of pdfinfo & pdftotext, but Firefox still hangs approximately 1 of 3 times when pdf's are indexed. (I should add, maybe, that I use a custom Zotero-path.)
  • Then remove pdfinfo, which is the real solution (for now).

    There's a chance this is a Mozilla bug and that it'll be fixed in Firefox 4, which has rewritten process-spawning code. If not we'll look into another solution.
  • Thanks! But I wonder: Is your advice to remove pdfinfo _without_ reinstalling it? And does that imply that PDFs will not be indexed then?
  • Me, above:
    In the meantime, if you're having this problem, you could try deleting pdfinfo from the Zotero data directory. Zotero won't have data on the number of pages in PDFs but (I believe) should still index them.
  • Thanks again! I can confirm both that indexing still works and that number of pages is indeed left out. (Sorry for not reading the earlier discussion carefully enough.)
  • ...however, what I cannot confirm is that this actually solves the problem. After removing the pdfinfo from the Zotero data directory, Firefox still hangs frequently when PDF's are indexed...
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