Zotero frequently hangs & transferred files do not show up

iainC
I installed Zotero standalone & FF add-in last week and began adding the large number of PDFs already stored on my laptop to my new Zotero collection. It was a little slow when transferring a large number of files in one go (>100) so I began dragging them across in batches. Once I got used to what worked reliably it was working OK.

After some transfers I then practiced retrieving metadata (although I deal with many reports as well as journal articles, and Zotero is almost never able to find metadata... hey ho). Once I was used to how that worked and manually updated some articles I decided to embark on getting the rest of my articles into Zotero.

Yesterday and today I made several attempts to transfer across the rest of my PDFs. Since then Zotero has frequently crashed and the zotero-bin process just sits there eating all my CPU time. It's also not showing PDFs in the database, even though I can see they have been written to the storage folder. I have had to resort to force-quitting Zotero several times, so I decided to start afresh and reinstall.

I uninstalled the application by dragging it from my Applications folder to the Trash, and I removed the FF add-in through the FF Tools menu. On reinstalling Zotero standalone it weirdly immediately restored all my previous settings, which makes me suspect the uninstall wasn't performed correctly. I am also having exactly the same problem as before with Zotero just hanging, and making my whole OS run strangely (other apps hang too, or become unaccessible in the dock).

Some quick notes, as these might be related to the problem:

1) Zotero is almost guaranteed to hang when I attempt a drag and drop of a large PDF, approx. 20 MB or more. Is there a limit to what it can cope with?
2) The storage folder – and only the storage folder, none of the other Zotero files – has a symlink so that the PDFs are written to Dropbox. I have way too many PDFs to make use of Zotero's free 300 MB, plus I already have the Dropbox account acting as a useful backup since many of my PDFs are annotated.
3) I am using an Intel Macbook Pro running OS X ver. 10.6.8.

I find the constant crashes make Zotero unusable for me, and I am concerned the database is more likely to be corrupted if I am constantly forced to shut down (force quit) the program. I do not want to transfer any more files until I can work out what's causing this problem, as it's GBs worth of PDFs (many annotated with my own notes). I would really like to get Zotero to work so I can have a much better organized system of references than I do now, not to mention the added benefits in generating citations, etc. Any suggestions on what is causing this? Do I need to go nuclear and scourge everything Zotero from my computer before reinstalling?
  • dstillman
    edited February 6, 2013
    (although I deal with many reports as well as journal articles, and Zotero is almost never able to find metadata... hey ho)
    There are some bugs with the metadata retrieval in the current version, including not notifying you when you're blocked by Google Scholar (which is the most likely cause of chronic metadata retrieval failures). They're fixed in 3.0.12, which will be out in the next day or so.
    It's also not showing PDFs in the database, even though I can see they have been written to the storage folder.
    If you force-quit Zotero during an import attempt, that would happen. Changes to your database would be rolled back, but not file writes. Someone might have written a tool to clear orphaned 'storage' directories—I don't remember off-hand. Zotero can't clear those up itself right now, though we might add that eventually. (It could also be written as a plugin.)
    On reinstalling Zotero standalone it weirdly immediately restored all my previous settings, which makes me suspect the uninstall wasn't performed correctly.
    Uninstalling doesn't clear your settings or data, and almost never fixes anything. Don't bother.
    1) Zotero is almost guaranteed to hang when I attempt a drag and drop of a large PDF, approx. 20 MB or more. Is there a limit to what it can cope with?
    It's likely just indexing. Note that there's a good chance it's just freezing temporarily while it indexes—have you let it go for a few minutes? You can run Zotero with real-time debug output to see if it's actually doing anything. If not, that's a problem.

    In what other situations is it hanging? Just when adding large PDFs?
    Do I need to go nuclear and scourge everything Zotero from my computer before reinstalling?
    No, don't do that. We'll help you.
  • iainC
    Dan, first of all, thank you for taking the time to respond so promptly yesterday. One thing that convinced me to plump for Zotero was that many people said the support was great. You've allayed my fears that something was inherently wrong with my sqlite file, which I thought I may have caused by force quitting and corrupting it. Good to know there's no point in uninstalling too.

    I appreciate the explanation as to why the PDFs appeared in the \storage folder and not in the library itself. After transferring problem PDFs one at a time successfully, I then tracked down the duplicate PDFs in the /storage directory and deleted them after first quitting Zotero and FF. I assume this is OK to do in the absence of a handy tool to clear orphan storage files?
    In what other situations is it hanging? Just when adding large PDFs?
    As far as I can tell, it was only hanging when dealing with large (or a large number) of files at once. I had tried leaving the program for a while, 30 to 45 minutes in several cases, and it was still sitting there with the rainbow wheel of doom spinning. That's what prompted me to force quit. I ran Zotero with the real-time debug and tried a few transfers today. Typically, nothing caused it to hang for more than 3 or 4 minutes at a time, and I could see that during these pauses Zotero was busy indexing. Your diagnosis seems to be correct. At least now I know what to look for, so thanks.

    Is there a cut-off for the time it takes to index files? I have some very large reports (>900 pages) and I wondered how long Zotero might sit there indexing, or will it give up at some point? I did change the 'max pages to index' setting in Preferences > Search when I first installed the program to allow for these large reports.
  • dstillman
    I assume this is OK to do in the absence of a handy tool to clear orphan storage files?
    Yes, that's fine.
    Is there a cut-off for the time it takes to index files?
    There's not, but we'll be changing the way full-text indexing works in the near future, which will hopefully make indexing large PDFs much faster.

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