ZotFile: Zotero Plugin to rename, move, and attach PDFs, send them to iPad & extract PDF annotations

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  • Thanks for your effort, Joscha.
  • It took me some time but I finally tried FF5 beta. Everything worked for me. Can you try this version and let me know whether it works?

    http://www.columbia.edu/~jpl2136/zotfile_files/zotfile_158b1.xpi


    Joscha
  • Thanks Joscha,
    everything seems to work nicely with firefox 5b4 and zotero 2.1.7.
    SiGi
  • The version is under review now...
  • The plugin is now compatible with FF 5 and 6...
  • edited June 30, 2011
    Here is the beta of a new zotfile version. Can anyone test this?

    http://www.columbia.edu/~jpl2136/zotfile_160b6.xpi


    New in 1.6

    ATTENTION: Some preference default values have changed so that might have to change their preferences or get prompted by zotfile.

    - Preference dialog (Actions -> Zotfile Preferences) with preview of renaming rules
    - User can now set the filetypes that are considered by zotfile (default: pdf,doc,txt,rtf)
    - Zotfile can now attach all files in source folder (available through preferences)
    - New preference for attaching a new file: Use FF download folder
    - New preference for renaming option: truncation after . , ?
    - New preference for renaming option: add user input to automatically generated filename
    - renaming behavior: smart tuncation does not cut of word
  • Feature request: item-type based subfolder name

    Thank you for ZotFile. I am testing the new version with the customization dialog. Although I can live with about:config, this dialog makes the documentation page almost redundant. It's a pity that about:config does not suport in place documentation for the options!

    I have a suggestion for the subfolder feature, that I'd like to use.

    Ideally I would like to have all my files linked and with the subfolder structure based on item type:

    BaseFolder/Articles/
    BaseFolder/Books/
    BaseFolder/Presentations/

    and so on...

    as far as I could understand, there's no replacement token
    (%something) for item type. That would do it, pretty much.

    It occurs to me that one may want to define also naming policies depending on the item type. This would speak for dedicated handlers for each item type that use the default naming policy unless a preference option has been set. Maybe those item-specific options could be left to the advanced customization in about:config if it is too time-consuming to build a tab for them in the new preferences dialog.

    The ability to control names very finely helps when migrating away from Mendeley. In fact it enables one to use Mendeley for highlighting and leave the pdf in place for Zotero.
  • Problems with preview filename in 1.6b6

    I noticed that the customization pane has problems with the filename preview:

    1. The preview gets two underscores prepended
    2. It doesn't react to changing e.g. the max number of authors to 1
    3. I hanged ZotFile and thus Firefox by changing the max. title length to 10.
    -á.
  • Images, css, etc belonging to an html file

    I used ZotFile to relocate to my 'link directory' a webpage that I had downloaded by dragging the wikipedia icon into the middle column. The auxiliary files that live with the html file in the zotero storage folder do not come with it to the link directory (and it would be a mess if they would, because they'd highly clutter the directory where I hold also pdfs from articles, etc.).

    What is the recommended way to deal with this? should I leave downloaded html pages where Zotero puts them, i.e., in the storage directory, or is there any easy workaround that I've overlooked?

    If Joscha's plans for ZotFile include handling this use case, I'd argue that providing item-specific subfolders and naming policies may help - in this case WebPages would have their own subfolder and within this folder they may be organized by domain, so in this particular case this webpage (Receiver_Operating_Characteristic.html) would have landed e.g. at

    Base/WebPages/en.wikipedia.org/Receiver_Operating_Characteristic

    together with all auxiliary files.

    Dos this make sense?
  • edited July 5, 2011
    not the same here... I tried the new version too.
  • @ alv: Can you post the citation of the item and send a screenshot of the wrong preview? Do these problem occur regardless of the item you pick for preview? Can you reproduce the hanging?

    Thanks!
  • About the feature request, I will look into using the file type for the subfolder. I don't think that I will do something about handling webpages. So far now the best practice would be to leave them in the Zotero storage folder.

    Another question: did you have to change your 'link directory' after installing 1.6 or did zotfile automatically carry it over? Or were you prompted for input (which should only happen on macs under certain conditions).
  • Great news about the subfolder! thanks!

    I migrated from the previous version without having configured it, i.e. I got prompted to give input on the link directory, and other stuff (I am on Ubuntu).

    This is an example article:

    1.Leibold, C. & Kempter, R. Memory Capacity for Sequences in a Recurrent Network with Biological Constraints. Neural computation 18, 904–941 (2006).

    Regarding the hanging I could reproduce it (press on Update after setting max title length to 10; script becomes unresponsive at line 184). I am sending three screenshots per e-mail, as I am having trouble lately to post to a public Drobpox url.

    Another caveat: when there's no author or year, ZotFile still emits the separator character (here '_') so that the filename looks like __Title.ext
  • edited July 6, 2011
    I wasn't able to reproduce the crash but it's certainly the 'smart truncation' code. I have changed that. Can you check out whether this version also crashes?

    http://www.columbia.edu/~jpl2136/zotfile_160b7.xpi

    I haven't changed anything about the author thing...

    ps: I added a for option for turning smart truncation off and on...
  • actually, try

    http://www.columbia.edu/~jpl2136/zotfile_160b8.xpi

    and %T for item type... I think it should work. It's based on the localized string so that it differs depending on the language you use.
  • Feature Request

    Great tool!

    I'd also like to suggest a feature for naming subfolders: using the 1st alphabet of the 1st author's last name as the name of a subfolder (something like %a[0] perhaps?), just because that's how my current collections are organized.

    Thanks!
  • here you go
    http://www.columbia.edu/~jpl2136/zotfile_160b9.xpi

    Use %A for the first char of the author string. So "Einstein et al" becomes "E". I haven't tested it but it should work. Can you confirm?
  • Hi Joscha,

    I've been trying to batch-rename and move all my pdfs stored from the subfolders of zotero/storage/... into a single folder, so I marked all my entries and did a rename. However, despite asking me whether I was sure I wanted to do this for the ~2000 items, it only processed the first item. Is this a known bug?

    Cheers
    Stan
  • no, it's not. Can you tell my which version you are using (both zotero and zotfile)? Try the beta from my last post if you are using 1.5.7. I resolved a bug from an earlier version but I am not sure whether it is connected to your issue. So maybe the new version will just work (and please report if it does).
    Can you also check whether the FF error console spits our any errors (Tools->Error Console)? Does it also happen when you just select a couple of items?
    I have never tried to use the batch rename with such a large database but it should work in principle. Still, you should make sure to backup your data before you do this.
  • Thanks for the quick reply!
    I tried with both with 1.5.7 and zotfile_160b9.xpi. I'm running Zotero 2.1.8 on FF 5.0 in Ubuntu 11.04. I just noticed that the import stops when it hits an entry with a broken link, i.e. where the pdf file went missing. I have lots of them in my library since I moved libraries from a different computer. Don't quite understand why. Could broken references be removed by default?
  • edited July 11, 2011
    okay, I see. Here is a version that should take care of the issue:

    http://www.columbia.edu/~jpl2136/zotfile_160b10.xpi

    Does it work?

    ps: it just skips broken references for now. Maybe I will change that in the future but for now batch renaming is not stopped by broken references.
  • It works indeed, thank you! Amazing.
    Just one more thing, it also moves and renames html files, although they are not on the list of file types in the zotfile preferences. Is this intended?
  • Release of zotfile 1.6.0

    https://addons.mozilla.org/en-US/firefox/addon/zotfile/

    New features

    ATTENTION: Some preference default values have changed so that might have to change their preferences or get prompted by zotfile.

    - New Preference dialog (Actions -> Zotfile Preferences)
    - zotfile just works after first installation (changed default settings that usually do not require ANY changes from the user before using zotfile)
    - User can now set the filetypes that are considered by zotfile (default: pdf,doc,txt,rtf)
    - Zotfile can now attach all files in source folder (available through preferences)
    - New preference for attaching a new file: Use FF download folder
    - New preference for renaming option: truncation after . , ?
    - New preference for renaming option: add user input to automatically generated filename
    - renaming behavior: smart tuncation does not cut of word
  • edited July 14, 2011
    For those who installed the beta over the last couple of days: Please install 1.6.2 !!

    I strewed up the version numbers a little so that the current 1.6.0 version on mozilla DOES NOT contain some of the features I recently added. 1.6.2 is already under review and contains these features. You can install it from here:

    https://addons.mozilla.org/en-US/firefox/addon/zotfile/versions/

    New Features in 1.6.2 (note reviewed yet!)

    - preview of renaming rules in preference pane
    - %A for first letter of author (useful for subfolders)
    - %T for item type (localized)
    - option to turn smart truncation off
    - option to only batch rename attachments from life of file types (default is true)
    - Bug: Rename Existing attachments skips broken attachments
    - Bug: improved smart truncation of title


    ps: @schymans: there is an option for this in 1.6.2
  • Beautiful. Very happy with this version. Unlike (perhaps) many users, I use it not to organize my PDFs into folders (I don't mind Zotero doing that), but mainly as a way to cope with imperfect or missing translators. Get the reference into my library, download the PDF, and let Zotfile put them together. This works very nicely.
  • I have just released a new add-on that streamlines the process to work with Zotero and your pdf reader applications on tablet computers (iPad, Android tablets etc):

    http://forums.zotero.org/discussion/18737/zotfile-reader-zotero-plugin-to-work-with-tablet-ipad-android-tablets-etc/

    I am also taking donations now. So please consider a donation if you have been happily using zotfile! Just go here and press 'donate': http://www.columbia.edu/~jpl2136/zotfile.html

    Reviews on mozilla are also appreciated!
  • Thank you so much Joscha for all your work on Zotfile.
    Some time has passed since I intensively used Zotero for the last time, and I now find out all the very much appreciated improvements of your plugin. Especially the directly accessible preferences. I didn't go through each of them yet and I will surely discover more.
    Did you consider using Flattr as a mean for social micro-payments?
  • Testing http://www.columbia.edu/~jpl2136/zotfile_160b10.xpi here

    Title truncation works. Author number = 1 and 3 work. Author number = 2 results in only one author. Et al. works.
  • Thierry.C, Flattr is added to the webpage... Let's see how that works...
  • Hi, I'm using zotfile 1.6.0

    The new options interface looks great, and I'm excited about future plans for working with readers. Great work.

    I'm experiencing the following with Zotfile after upgrading to 1.6.0:
    I use zotfile to move items from my downloads folder to the folder that is the repository for all of my PDFs. I use links attached to item entries in zotero. since upgrading, when zotfile looks in my downloads folder for an item, it returns the following confirmation query:

    Do you want to rename and link the file 'undefined' to the currently selected Zotero item?

    It should have the filename, rather than "undefined" It was working fine previously, so I wonder if perhaps this is a bug. BTW, when I confirm (I took a chance), it does indeed move and link the appropriate file.

    Thanks.
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