ZotFile - Advanced PDF management for Zotero
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To fix, I reinstall Zotfile and it seems to work (for a while at least...). I observed it on Mac OS X (10.6) with Firefox 10 and Win XP with Firefox 3.x.
Thanks - Jacek
jacekg, ZotReader is pretty outdated. It was only a temporary addon, which never made it out of beta. All the ZotReader features and more are part of zotfile 2.x. You should install this version maybe that already answers your question...
Now that everthing is so good, I'm worried that I might lose this. I have zotero on my laptop with zotfile renaming and moving pdfs to a folder in sugar sync so everything is backed up. I also backed up zotero files (preference - advanced - show directory) regularly.
However, if my laptop were to crash, I'm worried that the "links" from the zotero items to the pdfs will no longer be there. How do you guys back up all these?
Meaning I can get all the zotero items back. I can still have my pdfs in sugar sync. But will the links be backed up somehow?
"Inalargeworld, as emphasized by both Savage and Simon, one can no longer assume that “rational” models automaticallyprovidethecorrectanswer." (Gigerenzer and Gaissmaier 2011:453)
I don't know what is the cause of this problem.
I would like to be able to view and save attachments from both Windows and Mac. However, since the paths are hard coded this is not possible.
If Zotero doesn't force a full and valid path (it might not sure) then could the path have an optional prefix added by ZotFile as set in the preferences for each instance of the plugin? So, Zotero would only store the Filename and not the path but ZotFile would add the path when file access was requested. It might require a different menu option or file open (double click) override in Zotero.
If there is another or better way to get the same result please let me know.
Thanks for a great plugin to Zotero!
https://github.com/zotero/zotero/pull/51
Not sure whether this will be integrated soon but you should express your support there...
I've recently been using Zotero with the Zotfile extension, and have been very pleased with the overall system. However, I have been unable to extract annotations from PDF files.
Setup:
Macbook, OSX 10.4.11
Firefox 3.6.28
Running Zotero 3.0.3 (as Firefox Add-on) and ZotFile 2.1
I have tried to extract Annotations added through Preview (ver 3.0.9), however I get an error message:
- "...not supported with Firefox 3.6..." when attempting with pdf.js
or
- "Annotation extraction failed" when attempting with poppler (ver 1.1)
I was hoping for some recommendations to help fix this. I'm afraid that it's going to be "Get a new computer with a current OS" - i'm at the most current version of firefox I can run with 10.4.11
In the meantime, I'm using Skim, which works fine, but as I understand from browsing these forums, won't work with Zotfile for annotation extraction period.
Appreciate any help you can provide.
Thanks,
-J
Thanks for this great extension. I have a little trouble with it.
I had all the attached file stored in a dropbox folder on a D: volume in my hard disk. Unfortunately, my computer was stolen. I bought a new one, but I was unable to re-install the dropbox folder on the same volume (Toshiba apparently reserves the D: volume for system backup files).
Therefore, I have all (1400+) my references back, thanks to Zotero Sync, and all my filed back, thanks to Zotfile and Dropbox. Nevertheless, I'm unable to relink the ones with the others, as the path is not valid anymore.
I tried to replace it manualy, going to my Zotero folder and replacing all the "D:\Dropbox\Bibli-Zotero" (the old location of my dropbox folder) with "C:\Users\Florent\Dropbox\Bibli-Zotero" (the new location of my dropbox folder) inside zotero.sqlite. But once I've done that, Zotero sends me a message indicating the DB was corrupted.
Do you (or other users) have an idea of how I could proceed to have my links back.
Best regards,
Florent
I am not sure whether there is an easy solution to this problem. If you have some programming experience, it's not very hard to write a small script that relinks all files but I don't recommend taking this approach if you don't feel comfortable about it. I would rather bother a friend with this and misuse his/her computer. You could install zotero, sync your database, add dropbox as D (alternatively, you can just copy all the files to an external hard drive and connect it as D), and then use zotfile to relink your files to a location you can also use on your new computer.
Maybe others have better solutions...
I believe the solution your proposing is indeed the most simple and I hadn't thought about it. Thanks a lot !!!
1) For some files it doesn't seem to work at all. The "Extract Annotations" box pops up briefly then disappears, without any note being generated. This has happened with both articles I have scanned, OCR'd, and annotated on my iAnnotate and with articles I have gotten from JSTOR, so I am not sure what the problem would be.
2) In other cases, the extract function hangs. The status bar might get to the just under the r in "Extract" or to the S in "press ESC to Cancel", but then advance no further. It just stays there until I hit ESC and unfreeze it. The file sizes here vary.
I believe I am up to date on the latest releases for Zotfile and Zotero. I have Zotfile's preferences set to use pdf.js as the extraction tool.
Any assistance would be greatly appreciated!
Unfortunately it does not extract PDF annotations as notes. I have checked the forum and configuration as specified - but don't see anything obvious. After selecting 'Extract Annotations', a dialog pops up to say 'Extract PDF annotations (press ESC to cancel), the progress bar moves to the end, then dialog eventually closes without extracting anything.
Thought it may be an issue with pdf.js, so also installed poppler and tried that. This approach doesn't present any dialog and nothing appears to happen.
I have tried a linked PDF file and stored PDF file - no difference.
It doesn't appear that I am doing anything wrong / strange.
Could you please help.
I can send you the PDF file I used if you think it would be helpful.
dazzur, you should check the file above to test the extraction. If the file does not work, try to provide more details following the instructions here. Otherwise, your files are probably the problem or the annotations type you are using.
Is it possible that poppler might work more successfully? I have not tried using that mode of extraction but would try it if it might help.
if I have an attachment opened, e.g. a PDF in a PDF viewer, it is not possible to move the file to the custom location which I have chosen in the settings, because the file is locked (on Windows XP). The corresponding error message in the Javascript console is:
uncaught exception: [Exception... "Component returned failure code: 0x8052000e (NS_ERROR_FILE_IS_LOCKED) [nsIFile.moveTo]" nsresult: "0x8052000e (NS_ERROR_FILE_IS_LOCKED)" location: "JS frame :: chrome://zotfile/content/zotfile.js :: <TOP_LEVEL> :: line 920" data: no]
So, 'cause it is a clear error message, I sticked into the source and wrote a try-catch exception routine around the move (and also the rename) command to treat this error with a well formed error message in the Zotero info window.
Just have a look in the code (also in the comments): https://gist.github.com/2499686
Thanks Joscha for writing this smart and helpful Zotero extension.
Regards,
Dominik
I've incorporated a page numbering ID parameter for renaming in the beta version of zotfile (jlegewie-zotfile-v2.1-0-ge2086ef)(it was actually pretty straightforward!). I have, however, discovered a problem when using customized subdirectories. I'm currently using "\%w PDFs", which should give me subdirectories with "Journal PDFs" or "Publisher PDFs". I've discovered that any characters which match those used in the renaming functions are not used (so that I am getting Journal PDF/Publisher PDF). I've tried a range of different characters, with both capital and lower cases, and these text characters are consistently omitted from the subdirectories. I'm able to recover the correct function by deleting the problematic letters, but this is obviously less than ideal. I'm assuming that characters should only be recognized as parameters if they are preceded by a % character - has anyone else reported a similar error?
I'm very interested about "Extracting annotations" from PDF function, but it doesn't work for me at all, even with different files/computers/systems. Every time I choose to "extract annotations" scale reaches 100% and stays that way for ever. If I press ESC it cancels process correctly, but no annotations or errors appear. I use highlighting of text in PDF and I want to have a summarized text in Zotero. What am I doing wrong?
a) If you ment this one: http://www.columbia.edu/~jpl2136/zotfile-test.pdf it doesn't work either.
b) Error says: zitem.getType is not a function and is related to the code:
// Function replaces wildcard both for filename and subfolder definition
replaceWildcard: function(zitem, rule){
// get item type
var item_type = zitem.getType();
var item_type_string = Zotero.ItemTypes.getLocalizedString(item_type);
c) I am currently on Windows 7 x64, but tried also on Windows 2003 Server x64 and Ubuntu 10.04... all of tested in CZ localization.
I have installed Zotfile but whenever I download a PDF to my specified download folder, neither Zotero nor Zotfile does anything. I wish I could get it to work because it sounds awesome.
Is there any other set up that needs to be done besides identifying the source folder and the location folder. I'm just looking to get automatic renaming working.
This is on Mac Lion.