Zotfile Reader - Zotero plugin to work with tablet (iPad, Android tablets etc)

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  • ajlyon
    I'm still hoping to see about compiling this for Linux, but I'm preparing for another big trans-oceanic move again and won't be able to sit down and struggle with it for another week or two.
  • Joscha
    ajlyon: Let me know before you do... I made some small changes to the script and maybe some other bug comes up... Good luck for the move!
  • mark
    edited August 26, 2011
    Joscha: have you thought about using a Dropbox variable instead of hardcoded file locations? That would solve my issue in working with multiple computers where Dropbox is not always on the same drive letter or even in the same folder structure.

    See here, here and here for how to find the Dropbox path on Windows systems.
  • Joscha
    @mark: yes, that's on my list too. But the list is long...
    As you suggested earlier, I actually thought about saving the location of the files on the reader with a wildcard for the base folder ({basefolder}/project/file.pdf). The advantage of that solution would be that it is more general and useful for dropbox and other syncing methods. Any advantages of a dropbox variable?
  • mark
    edited August 26, 2011
    No you're quite right. If you can set the base folder in every instance of Zotero, your wildcard covers that case too.
  • Joscha
    Version 0.5 final is now under review at Mozilla and can already be downloaded from here:

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


    New Features in 0.5
    - Extraction of annotations and highlights from PDFs (currently only on Mac)
    - Compatible with Zotero Standalone
    (for instructions see here and remember to first install zotfile 1.6.4)
    - user-defined sub-folder configuration is now in a separate window
    - empty folders are deleted after changing user-defined subfolders
    - BUG: pop-up menu now works in second FF window

    Changes compared to last beta
    - remove hyphens from highlighted text in zotero note
    - BUG resolved: note was created even when the PDF did not contain any annotations
  • Jeff Sinn
    Wow. This is an amazingly useful tool. It works beautifully.

    In a previous version I tried, the "Scan Reader" option recognized highlights I had made to files on my reader (in a dropbox folder) but this one doesn't, so that the one in Zotero is out of date. It does get updated, but only after I remove the copy from the reader. Is is possible to get back that Scan Reader functionality?

    I'm very impressed. Going to donate now... :) Thank you!!! -js
  • Joscha
    @Jeff: I just tried the 'Scan Reader' and it works in foreground but not background mode. I will fix that in the next couple of days...
  • Joscha
    @Jeff: Actually, I was just using the scan reader function and it seems to work both in foreground and background mode. And you check again and provide more details? I made a mistake earlier because I moved the file in background mode, double-clicked on attachment in Zotero, annotated that file and then used the scan reader function. Scan Reader does not react to this because the file on the reader was not modified. Only the Zotero copy. So double-checking and more details would be helpful.
  • Jeff Sinn
    @Joscha: It's working now. I probably was doing something wrong. Very slick!!
  • Joscha
    I have resolved some serious bugs in the annotation extraction tool (it didn't work with the updated pdf expert 3, for example) and added one feature (line breaks in note annotations now carry over from the pdf to the zotero note).
    The update mechanism for the extraction tool still needs some work though and it will take some time until I get to do that. The new version is already on the server though so that you can update manually. In order to do that, you first have to go to your Zotero library directory and delete the folder 'ExtractPDFAnnotations'. When you now restart Zotero, you should be able to reinstall the extraction tool through the zotfile preference window. (I haven't tried the updated version at a different Mac. So let me know if it does not work)
  • Joscha
    edited September 18, 2011
    Here is a beta of the next version. A lot of the new features are currently only implemented as hidden options (accessible through 'about:config') and have not been tested thoroughly. So any reports about testing them (unsuccessfully OR successfully) are appreciated (please also mention the mode you are using). The fact that a lot of these features are hidden right now is probably going to change (I am also running into space problem, though).

    www.columbia.edu/~jpl2136/zotreader_06b1.xpi

    New Features in 0.6
    - background mode: option to save copy of annotated file with suffix (hidden options: storeCopyOfFile, storeCopyOfFile_suffix)
    - background mode: option to use relative reader paths in zotero, which makes it possible to use different base folders on different computers (hidden option: dest_dir_relativePath)
    - deleting a subfolder prompts user to remove files from reader, move files to base folder, or cancel
    - tagging: option to tag parent item when file is moved and removed from reader, which might be very useful when colored tags get implemented in zotero (hidden option: tagParentPush,tagParentPush_tag,tagParentPull,tagParentPull_tag)
    - right click menu in 'Configuration of Subfolders' window with option to open folder
    - option to add html tag to extracted highlights and notes. By default, notes from pdfs are now formatted in italic (hidden options: pdfExtractionNoteRemoveHtmlNote, pdfExtractionNoteRemoveHtmlHighlight)
    - BUG fix: remove hyphens made extraction fail if note annotation was present
    - BUG fix: annotations are now only extracted if the file on the reader was modified

    Extraction of Annotations
    - new version of annotation extraction tool with major bug fixes
    - update mechanism: zotreader checks for updates when you open the zotfile preference window, and enables the update button if a newer version is available
  • mat-in
    edited September 20, 2011
    Hi there!
    I just installed Zotero 2.x not the beta) /Zotfile (latest) and ZotfileReader (last file beta mentioned here in above post) on my Linux Tablet. Looked like a great Idea to test along with testing different software for their annotation and pdf manipulation qualities.

    The Plugin does move the PDF from my collection to the folder specified, does pull it back, asking to replace the old pdf in zotero, etc. but does do nothing like importing. I did highlight a line of text and add a comment textbox to the PDF in different applications and saved back to PDF.

    Guess linux import is still not implemented? Or did I miss some step?
  • Joscha
    Annotation extraction is currently only supported on mac (for which you need to install a separate program from the zotfile preference pane). I neither have a linux nor a windows pc so that I rely on others to compile the extractions tools for these platforms...
  • mat-in
    I did not do any coding since the glorious days of the C64, but if it can be easily done, I would install a C++ compiler for OpenSuse and compile that code, mail it to you, so you can integrate it and then I would test the extraction on Linux?
  • Joscha
    I don't think it's that easy or at least for someone who doesn't have compiling experience. It took me pretty long to get the mac version running (I don't have compiling experience). ajlyon already gave it a shot for linux and didn't succeed. He might try again later though.

    If you are still willing to try, I suggest that you start with the poppler library (http://poppler.freedesktop.org/) . If you manage to compile one of the utility functions (preferably, pdftotext in the utils folder), it should be relatively easy to compile my little script.

    In any case, I will integrate this for other platforms as soon as someone manages to compile it.
  • mat-in
    OpenSuse does have a Build Service to develop software for different distributions and platforms. I got no idea how "service" it is, if you got code that has to be compiled for Linux, but it was very helpful for finding packages of linux software which I would have been forced to compile by hand otherwise.

    https://build.opensuse.org/
  • Joscha
    edited September 23, 2011
    I finally decided to integrate zotfile and zotfile reader. You can download the first test version of this effort below. Another goal was to make things easier and reduce clutter. So I cleaned up the preference pane and integrated all zotfile functions in the 'Manage Attachments' menu. Any comments about the redesign are welcome including suggestions to improve the description of the different options in the pref pane. I want to make this much easier to use and set up...
    This version also fixes some bugs from the last 0.6 beta.

    http://www.columbia.edu/~jpl2136/zotfile_200b2.xpi


    ps: Updated to run with FF 3.6. Automatic transfer of zotreader preferences still does not work for 3.6 (zofile reader has to be uninstalled manually)!

    ps: Your ZotFile Reader preferences are mostly copied over but it requires a second restart to uninstall zotfile reader. You don't have to do that manually. Just go ahead and install this version as usually.
  • Joscha
    edited September 25, 2011
    Some bug fixes, code cleaning, and new features later...

    http://www.columbia.edu/~jpl2136/zotfile_200b3.xpi

    This should be much better! A saved search is also now created automatically (and can be done manually from the pref window).


    New Features in Zotfile 2.0
    - Zotfile and Zotfile reader are now integrated into one plugin
    (in FF 4+, the reader preferences are automatically transfered and zotfile reader uninstalled)
    - cleaned and improved preference window
    - saved search for tablet item is also now created automatically
    - option to save copy of annotated file with suffix (background mode only)
    - option to save copy of annotated file with suffix (background mode only)
    - zotfile uses relative paths for files on the tablet, which makes it possible to use different base folders on different computers
    - changing the base folder creates a warning if there are files in the old location
    - deleting a subfolder prompts user to remove files from reader, move files to base folder, or cancel
    - tagging: option to tag parent item when file is moved and removed from reader, which might be very useful when colored tags get implemented in zotero (hidden option: tagParentPush,tagParentPush_tag,tagParentPull,tagParentPull_tag)
    - right click menu in 'Configuration of Subfolders' window with option to open folder
    - option to add html tag to extracted highlights and notes. By default, notes from pdfs are now formatted in italic (hidden options: pdfExtractionNoteRemoveHtmlNote, pdfExtractionNoteRemoveHtmlHighlight)
    - lots of bug fixes

    Extraction of Annotations
    - new version of annotation extraction tool with major bug fixes
    - update mechanism: zotreader checks for updates when you open the zotfile preference window, and enables the update button if a newer version is available
  • erica haugtvedt
    Hi, I'm new to Zotero and to zotfile and zotfile reader. I'm a Mac user who's not extremely tech literate, so forgive me if I'm missing something obvious. I've installed the zotfile and zotfile reader addons and I've tried pushing files to my dropbox folder by right clicking and selecting "Manage Reader Files --> Move to Reader." My source folder for Zotfiles is my Downloads folder and my destination folder for Zotfile Reader is my dropbox folder. However, once I "push" these files--I don't see them anywhere in my dropbox. It doesn't seem to be working. Am I missing something obvious?

    Help would be much appreciated. I'm really excited about this add-on, since I prefer annotating my PDFs on my iPad and then writing major papers on my laptop. I really want this to work.
  • erica haugtvedt
    Never mind, got it to work. Apparently what I thought was a PDF file was not really a PDF file, so it didn't sync. I'm an idiot.
  • zanger
    Hi,
    I just installed zotfile 1.6.5 and zotfile reader 0.5 and basically got it to sync with dropbox. It should really be a great app to help me with my ipad.
    Problem is when I delete a previously added subfolder such that it is not shown in dropbox anymore, I'm unable to reload any of the pdf's in this subfolder, even when I try to reload them out of the main library. A question pops up asking if already existing files on the reader should be replaced, which I agreed to, of course.
    May be I'm overlooking something in the settings?
    Thanks in advance
    Uli
  • Joscha
    @ zanger: I am not completely sure what you are doing so can you be more specific? How did you set up zotfile reader? Are you using the background mode? Are you using sub-folders and which option exactly (collection based or user-defined)? How did you exactly proceed? Here is what I understood:
    1) Move pdf to sub-folder on dropbox using zotfile reader
    2) delete folder with files on dropbox
    3) Try to move the same pdf to a different folder, which doesn't work
    Is that correct? If it is, i think I know what the problem is and I can fix it. But in general, I would recommend that you delete at least user-defined sub-folders from zotfile reader and not from dropbox directly. At least the most recent version (I am not sure about 0.5) will ask you what to do with the files in that folder.
  • tom7320
    Hi!

    I really like this plugin because it helps me to read my literature on my iPad. But unfortunately it does not rename the files when I choose "Manage reader files -> Move to reader"?!? It just copies the files with the original name. I want my original zotero library unchanged. Only the copied file should be renamed according to the ZotFile renaming settings.

    TIA for help!

    Tom
  • Joscha
    @tom7320: You should take a look at the 2.0 beta:
    http://www.columbia.edu/~jpl2136/zotfile_200b3.xpi
    Someone else reported that files did not get renamed but I think I solved that problem. I am not sure right now what happens with the file in zotero though. Can you check out the zotfile 2.0 beta and tell me whether that solves your problem?
  • JitM
    Great work! You got my money!
    However I've setup using Zotfile 2.0b3 exporting to a folder in dropbox and checked "Create subfolders using zotero collections" but the attachments all endup in the base folder. Also the folder path is not shown in the textbox.
    I'm using Firefox 7.0.1 on Windows 7 and Zotero 2.1.10 and all my attachments are stored copies on Zotero.

    It's a small nuance in a otherwise stable beta.

    /jonas
  • Joscha
    @jones: When you use subfolders based on zotero collections, your 'Manage Att.' menu should look something like this:
    http://www.columbia.edu/~jpl2136/zotfile_files/subfolder.png
    (with the stuff below 'Move to Subfolder' reflecting the subfolder your zotero item is in. Note that this list is currently only based on the first selected item)
    The files are only moved to subfolders when you click on one of the menu items below 'Move to Subfolder'. Do you see this list for items that are in sub collections and can you confirm that clicking on one of them does not move the file to the appropriate folder?
  • Joscha
    edited October 26, 2011
    No one followed up on any of the bug reports so I assume that the problems are solved. I was going to move forward with zotfile 2.0 and submit it for review at mozilla. Just wanted to check in with the about 60 users of 2.0 whether they have any issues?
  • theed
    Hi,
    this is a great solution. Many thanks.
    Using v2.0b3 downloaded from here, I have these problems on Win7, FF7.0.1:
    1. when scanning the folder, a changed pdf is found, but clicking the option to move it back to zotero is without effect.
    2. I cannot find the option for the background mode anymore. Currently, all exported files appear as links in zotero, and when moving them back, are attached, but I'd like to get a second file with (in addition to the file without) annotations. This seems like the foreground mode (or what the name was) behavior...
  • Joscha
    @theed: I will look into the first point. Just have to find a windows pc. About the second point: The foreground/background option is now hidden (you can access it through 'about:config' 'extensions.zotfile.tablet.mode'. 1 is background and 2 is foreground). Background is the default but when you were using zotfile before 2.0, your old preference was copied. That might be the reason why it's currently running in foreground mode. So change this preference to 1, and then enable 'Save copy of annotated file with suffix' in the zotfile preference dialog (this option only works in background mode). Let me know whether this works for you.

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