ZotFile - Advanced PDF management for Zotero

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  • OK, kindly forget that I mentioned importing from another reference manager.

    I'm not sure of your terminology: I am guessing that "linked attachments" means pointers to a pdf somewhere or the other, and "import attachments" means pdfs in Zotero's own storage area. Is that right?

    In any case, suppose I have a lot of entries in Zotero with pointers to pdf's in various places, not in Zotero's own storage area. How can I make zotfile import the pdf's into Zotero's own storage and rename them? Can I also get the files organized, for example with a folder for each author and subfolders by year of publication, or some such scheme?
  • You are right about linked and imported attachments. Zotfile can change attachments from linked to imported (apparently what you want to do) but zotero does not allow you to organize imported attachments into subfolders. If you want that, you have to use linked attachments. That's how Zotero's attachments work and zotfile can do this stuff (also with batch processing just by selecting multiple items).
  • edited July 7, 2014
    NEVER MIND! I FOUND WHAT I WAS OVERLOOKING.
    I have been successfully using zotfile to place files in a folder that is backed up to the cloud and that I access from my tablet. However, I want to switch to a different cloud service, and need to place this folder in a virtual drive for it to synch. I tried to change the "location of files" to a different custom location(in Zotfile preferences. However, Zotfile continues to place files in the old location. (For now, I left a copy of the folder in the old location. If I remove it, Zotfile will not show a folder to which I can move the files.)
  • Hi mates,

    I would like to know if ZotFile would be interested in a kind of versioning system ?
    I mean be able to follow modification and action on files with a kind of #Hashtag system.

    You could read more on this topic : https://forums.zotero.org/discussion/38338/

    Thank you for your kind collaboration.

    A.
  • Hi,
    Using Zotfile I've switched the location of the pdf files to a custom location so that all attached files appear in zotero as links.
    What I didn't know before is that all links refer to absolute paths and not relative one (I don't know if zotfile supports relative paths but in any case I accidentally set the path as absolute).
    This had a disastrous outcome for me since I'm using several computers to access my zotero library (which is synced via dropbox) and I've essentially lost the ability to access my files on my other computer (which I actually use for work).
    Is there a way to revert this?
    Alternatively (and preferably) is there a way to batch edit all the links to replace their base directory?

    Thanks in advance,
    Roey
  • You can set relative paths in the Advanced tab of the Zotero preferences.
  • Hi bwiernik,
    I have relative paths set in zotero.
    Both base directory and data directory locations point to ~/Dropbox/Literature/Zotero (within it I have a directory called PDF which contain all pdf files).
    The relative paths worked great between the two computer *until* I asked zotfile to move and link the files.
  • edited August 10, 2014
    I've just installed zotfile on osx, and I must be doing something wrong, because annotations are not coming through. I've configured the input folder for zotfile and I can attach pdfs just fine. But the annotations I create using skim don't seem to import. This applies whether I save the annotations in skim format, or by exporting a new pdf from skim. I've tried a variety of plain-vanilla PDFs and none of them work. I've also tried with and without poppler.

    What I do (one example)
    Open a PDF using skim
    confirm that the text highlight works fine and that skim knows the text contents
    create some annotations - a variety of highlights and text notes
    export to PDF, ensuring that notes are included
    take the new PDF that is created, put it in zotfile source folder
    attach it to an item ("zotero quick start guide"). The PDF shows up fine, I can open it and see the annotations, but no notes are attached to the item in zotero
    right-click the pdf, manage attachments, extract annotations.
    Still no notes on either the parent item or the pdf in zotero.

    What am I doing wrong?

    My name is Jxaxmxexsxoxn Qxuxixnxn, without the x's, and I have a gmail address with my first name, a dot, and my last name. I'd be happy to try out any troubleshooting you need from me.
  • edited October 12, 2014
    homunq, Skim uses it's own annotations standard (not the adobe's pdf standard for annotations). Zotfile doesn't support this standard so that you won't be able to extract the annotations. It should be possible to add support for skim annotations but I won't do it so that a community member would have to do it. Here is a [ticket](https://github.com/jlegewie/zotfile/issues/77) for it.

    roey.angel, I never worked with or tried the relative path feature for linked attachments. It's something that should work though but I don't have the time to get into it right now. For now, you can use imported attachments, which work on both computers.
  • Hi,
    Could it be that a bug is present (or perhaps re-introduced) in ZotFile 3.1, which I see mentioned in the very beginning of this forum thread (Jan 2009)? It concerns the case when the file extension is uppercase, and ZotFile does not (move and) rename such files.
  • I am not having the problem with the current development version from github...
  • Joscha (and others), I'm wondering if someone can help me make sense of this in the 3.1 changelog:
    watch folder now adds an attachment and retrieves metadata if no file is selected (change message, change version)
    this sounds like it'd be possible to automatically add new files saved to, say, the download folder into Zotero and have it run retrieve metadata. However, I can't find a way to do that. The only thing I manage to do with the watch folder is attach PDFs to existing items.
    Am I misunderstanding that sentence or could someone tell me how to do this?
  • Yes, it pretty much does what you are think but only if no item is selected (if an item is selected, the file is added to that item). I think the only way to select no item is to select a different collection. Does that work for you?

    By the way, zotfile calls zotero's retrieve metadata function but does not rename the attachment. There is no callback for retrieve metadata so that implementing the automatic renaming would have required changes to zotero. So the process is still not optimal (also with the different behavior for item selected or no item selected).
  • You can deselect items with Ctrl/Cmd
  • Regarding the uppercase extension problem, then maybe this is in 3.1 only (the current stable version). I encountered it in Zotero Standalone with Zotfile 3.1 in both Windows 7 and Bodhi Linux 2.4.0, for different profiles.
  • 3.2 is stable and downloadable from the version history on mozilla add-ons. Joscha is just struggling to get it through review.
  • @Joscha, @bwiernik - thanks, I finally got it too work. The trigger seems unreliable for me on both Windows and Linux, but at least I have this working in general.
  • Yes, the feature is not really working consistently. Or probably, the implementation makes it only work in certain situation... :(
  • Hi, I am using Zotfiles to extrract annotations from PDF files.
    To annotate I use Foxit. Extracting highlighted text as notes worked just fine.

    But, when I use Foxit to enter a comment on the highlighted text, Zotfile will stay stuck in the "Copying annotations"-loading bar and I cannot stop it pushing ESC. To use Zotero again, I have to restart it.

    If Zotfiles is not capable of copying comments from the file, that would be OK, but crashing in this manner is not acceptable. Can someone help me on this?

    cheers
  • I tried it again on a fresh new file (another copy of the same pdf) and everything works, seems like something went wrong with that particular file while processing it with zotfile.
  • Hi there,
    I have not clear how to allow to zotfile (version 3.1) to watch a directory. In the preferences, in "Source folder ..." I have put my custom directory. But Zotero does not include automatically. Am I missing something?
  • I'm pretty new to zotero. I am using zotero standalone on my Dell laptop with Windows 7 (also web-based at work) and Papership on my Ipad to review and annotate articles. I'm ready to write and attempted to extract the annotations into standalone so that I could have everything side by side. I'm finding that zotero is hanging and I have to restart it - nothing is being extracted, although the highlighting and comments have synced. I cannot figure out how to proceed. please help!
  • After a looooong review time, zotfile 3.2 was rejected by mozilla (again). I started a new and final attempt. Zotfile 4.0 is now under review at mozilla. This version basically includes all the changes from 3.2 and 3.3 as well as an update to the most recent version of pdf.js. The change log is here: http://zotfile.com/#changelog

    Experienced users can already download it from github: https://github.com/jlegewie/zotfile/releases/tag/4.0
    It's already under review but some testing would be great!



    calmateen, you have to include more detail. Look at the zotfile webpage for information about "EXTRACT PDF ANNOTATIONS" and "REPORTING A BUG".
  • Hello Joscha,

    I wonder if you might consider automatically truncating titles after an exclamation mark. I've encountered a few papers lately whose over-zealous authors have decided to separate their title and subtitle with a ! rather than the more typical . : or ?.

    Thanks for your work on Zotfile!

    Devin
  • Hi everyone,

    I would like to report a bug.

    I don't use the storage feature of Zotero. When I downloading a pdf, I would like Zotero to copy this file into a specific folder, to create a new entry in my library and to link the file to the new entry.

    I understood Zotfile could achieve this three steps goal (download pdf > create entry > link pdf).

    However, when I download a pdf from firefox and choose "save in Zotero", the pdf is copied to the Zotero storage service (inside the "storage" folder of Zotero). This is a bug because I specified in zotero settings I don't want Zotero to save pdf and I choose a precise folder in Zotfile settings.

    When downloading a pdf, I would like Zotfile to save it in the folder I specified in Zotfile settings.
  • That's not a bug.

    Since ZotFile is designed to use the information of the parent item for both renaming and, if you want to, the exact location to move an item to, it doesn't move PDFs that you drag or save into Zotero (which at that point aren't attached to any item). Also, there is not setting in Zotero to tell it to not store PDFs (not sure what you are referring to). The two things that ZotFile does is:

    1.) It _automatically_ moves PDFs to a specified folder when they are downloaded as attachments to an item, i.e. via the URL bar icon and
    2.) If you attach a PDF to an item at a later point, you can have Zotfile move that by using Manage Attachments --> Rename Files.

    Just as a reminder, while saving PDFs to Zotero certainly works, it is in most cases not the intended way of importing items to Zotero. Most workflows, including ZotFile's are optimized for using the URL bar icon.
  • edited October 6, 2014
    Ok thanks for these precisions.

    But I didn't get everything. I would like to achieve 1.) (that is to say using the URL bar icon to add an entry to my library and have the pdf automatically moved and renamed).

    I visited springer website. I am connected with my university so I have access to pdfs. I use the URL bar icon and I have a new entry in my library with the pdf *but* the pdf is stored on zotero "storage" folder (and not renamed: the title is "FULL TEXT") and not in my specific folder. So there is a bug: according to my zotfile settings, the pdf should be moved to my specific folder. Indeed, in the main tab of zotfile settings (the first one) I set a specifi location for files and there is a green tick saying zotfile see this folder.

    Why my pdf aren't moved in this folder?
  • edited October 6, 2014
    Could you take a screenshot of the general tab of your ZotFile preferences, upload it to a free image hosting site (dropbox, imgur.com) and link to it here. That should definitely work and I've never seen it not work.

    Edit: actually the first option there is irrelevant for what you're trying to do. That's the folder that ZotFile is monitoring, not where it's saving. That's done in the second option on that tab.
  • edited October 6, 2014
    I created a screencast you can download at the following url (I will delete it after ~1 day)

    http://urlgone.com/d40a75/ (sorry for the add : don't know any other url shortener with expiration date)

    In this screencast you can see me:

    1. showing my zotfile settings (Sorry it's in French but you can see I did set a specific folder and the "always rename" option exactly like in the screenshot posted by aurimas).

    2. visiting the springer website and adding a article to my zotero library with the URL bar icon.

    3. Result: the article is added but the file is stored in zotero "storage" folder and not renamed...

    Maybe the problem is related to linux which has a different folder structure (not C://... but /home/user/...?
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