ZotFile - Advanced PDF management for Zotero

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  • Note in the Changelog (for 5.0.2)
    REMOVED FUNCTION: Watching folders is not possible anymore. This was always more a hack and resource intense.
  • Thanks for pointing that out in the changelog. I suggest that the "Features" section on the Zotfile site be corrected, as it currently reads "ZotFile can rename and add the most recently modified file from the Firefox download or a user specified folder as a new attachment to the currently selected Zotero item."

    I would argue that this feature is one of the main benefits of using Zotfile, so if it could be restored without being too resource intense I think many would find it useful.

    I do observe that the renaming does work for files that are dragged onto a Zotero record, however the renaming popup message now persists indefinitely until it is clicked. If the popup behavior could return to disappearing automatically after a few seconds, that would be less annoying.
  • No, ZotFile can still do that: right-click --> Attach New Item.
    What it does no longer do is to add files added to the watch folder automatically to Zotero, and the feature description doesn't say it does.
  • Like cmf5, I also noticed that the 'File has been renamed' popup persists indefinitely until it is clicked. It also is layered on top of all other windows (not tied to Zotero). Seems to be a bug introduced along with the Z 5.0 update (for which thanks!).
  • Is Zotfile fully functional with Zotero 5.x? I cannot create linked attachments and Zotfile does not add the newest download from my firefox download map.

    I suspect that the problem has to do with this: When I try to change the Zotfile options to save the pdfs into a custom location on my computer, the button to choose that location does not work. Clicking on it does not open a menu to select a path. I typed in the path by hand but am not sure if it is correctly recognized by the program.

    I experience these problems when working with Zotero: when I click "manage attachments, rename attachment", the renamed files are only renamed but not changed into linked attachments anymore, and they are saved in the Zotero folder instead of my library folder.
    The option "Attach New File" also does not work. Even when there is a new pdf in the firefox download folder, it just does nothing.

    So questions:
    - Can I still use Zotfile to link all my records to a specific folder (in my case a folder on Dropbox)? (I assumed yes from the Zotfile website).
    - Are there any extra settings that I need to make before Zotfile can create linked attachments with Zotero 5? (I assume not)
    - Any solution for this issue with Zotfile at the moment?

    My setup: Zotero 5.0.18, Zotfile 5.0.4. I want to use Zotfile to link all my records to PDFs in Dropbox. I copied all the settings conscientiously from my other computer so unless there is an extra step in the new program, that should not be the cause of the problems.
  • edited September 15, 2017
    When I try to change the Zotfile options to save the pdfs into a custom location on my computer, the button to choose that location does not work.
    Yes, I'd assume that's the problem. What operating system? And you've made sure that the folder choose option isn't just appearing behind some other Windows or on another screen?
    (edit: so in answer to your questions: everything else in ZotFile still works, or is supposed to work, in exactly the same way)
  • edited September 15, 2017
    Thanks for the quick response, Adam. No, I already checked if the window was open in the background (as far as that was possible because you cannot move the firefox window when the options are open). That was not the case (but a good guess).

    I'm using Windows 7.
  • what part of that isn't working?
  • edited September 16, 2017
    Bug(?) report: When I try to change the Zotfile options (in the Firefox/Add-on settings menu) to save the pdfs into a custom location on my computer (and create a link to those files in Zotero), clicking the button to choose that location has no effect. I do not get a menu to select a path. I typed in the path by hand but I don't think that it is correctly recognized by the program because the files are still placed in the Zotero folder.

    version => 5.0.18, platform => Win32, oscpu => Windows NT 6.1 (Windows 7); WOW64, locale => en-US, appName => Zotero, appVersion => 5.0.18, extensions => Zotero LibreOffice Integration (5.0.6.SA.5.0.18, extension), Zotero Word for Windows Integration (5.0.2.SA.5.0.18, extension), ZotFile (5.0.4, extension), Shockwave Flash (27.0.0.130, plugin) Firefox: 55.0.3 (64-bits)
  • edited September 20, 2017
    ENHANCEMENT REQUEST

    Besides fixing the bug I reported 7 days ago, I'd like to see the following enhancements.

    With the new version of Zotero, I'm finding it more reliably attaches pdf files, for example from publication sites to which I have access to pdfs of individual articles. Hooray!

    But this sometimes causes confusion. I often have scanned versions of the same articles but with my own handwritten underlining and annotations. So, depending on how I intend to use the article, I may want two copies (one marked and one clean to use in a course I teach) or just one (the marked one if I'm only going to use it for my own scholarship).

    This example of use suggests the following enhancements:

    1. An easy way to turn off automatic downloading of pdfs temporarily so that Zotero only scrapes the bibliographic information from a web site but does not download the associated pdf.

    2. A way to rename individual attachments from within Zotero in addition to Zotfile's renaming goodness. For example, Zotero/Zotfile might scrape bibliographic data and download a 2017 article by John Doe entitled "Conundrums," automatically renaming the file as "DoeJ 2017 - Conundrums.pdf." The user might then attach a second, marked version of the same pdf file and use Manage Attachments > Rename Attachments to give the second file a name like the first. But now the user would have a way to modify both the file name and the link to differentiate between the two versions, e.g. by editing and adding "Marked" to the file name.

    3. For cases in which a clean pdf has been downloaded, renamed, and saved unnecessarily, a way to delete both the attachment address from the Zotero item record and the attachment itself by deleting the file stored in Zotfile's "Custom Location." Currently one has to delete the attachment link and, outside of Zotero, use a file navigation app to delete the saved file. Currently this often requires examing the content of two or more files to make sure the right one is being deleted. Of course, this capability would be useful in many other situations too.

    Thanks.

    (BTW, a particularly elegant version of enhancement 2 might use something like Zotero's colored tags. For example, one could establish "attachment tags" such as "clean" and "marked." Then the tags would apply to the individual attachments rather than to the item record as a whole, and a colored tag indicator would appear before the attachment rather than before the item record. There would still need to be a way to rename the files themselves, perhaps by adding the applicable attachment tags to the file name.)
  • That feature was a major problem for computer performance and was always quite buggy. It won’t return. However, you can always attach the most recent item in your old watch folder by right clicking on the item and choosing Attach New File.
  • edited September 26, 2017
    I am having the same problem as marsh reported above: multiple attachments being renamed sequentially, but given the same filename in the Zotero database, and therefore no longer linked properly in the Zotero record (actually I'm using Juris-M 5, but this should be the same).

    In my case, this has happened when I rename existing files in the database. I have a number of books in which each chapter is a separate PDF attachment, e.g., Author, Anne. Concepts and Notions. Townton: Juice Press, 2017. With the following attachments

    • Author_2017_Concepts_and_Notions Intro.pdf
    • Author_2017_Concepts_and_Notions Ch 1.pdf
    • Author_2017_Concepts_and_Notions Ch 2.pdf
    • Author_2017_Concepts_and_Notions Ch 3.pdf
    • Author_2017_Concepts_and_Notions Conclusion.pdf

    Zotfile moves the files to the appropriate folder and renames them to:

    • Author_2017_Concepts_and_Notions.pdf
    • Author_2017_Concepts_and_Notions1.pdf
    • Author_2017_Concepts_and_Notions2.pdf
    • Author_2017_Concepts_and_Notions3.pdf
    • Author_2017_Concepts_and_Notions4.pdf

    Which is fine. But then in the database there's just a series of identical links to the first file:

    • Author_2017_Concepts_and_Notions.pdf
    • Author_2017_Concepts_and_Notions.pdf
    • Author_2017_Concepts_and_Notions.pdf
    • Author_2017_Concepts_and_Notions.pdf
    • Author_2017_Concepts_and_Notions.pdf

    So the remaining files are no longer referenced in the database.

    As the files are being renamed the pop-up briefly shows the filename with the number appended, then the filename without the number.

    I'm using standard renaming rules: {%a_}{%y_}{%t}

  • If you use those renaming rules, I would recommend using Zotero’s native renaming functon, rather than Zotfile’s function.
  • Is there a way of defining renaming rules in Zotfile that will avoid this kind of collision?
  • I don’t believe so currently, no.
  • After the last update, I cannot access to the preferences from the Zotero menu anymore. I need to go in extension, and then option, in order to modify them.

    In addition, is there any chance that the creation of sub-folders (e.s. Author\year\) is repristinated? I really miss that function.

    Thanks
  • What version of Zotero and Zotfile are you using?
  • @bwiernik Hi, I am using zotero 5.0.22 (portable) and zotfile 5.0.5. The issue with the subfolders started when I upgraded to Zotero 5.

    Thanks
  • Okay, the Zotfile preferences are under the Tools menu. I’m not sure if it will help, but you should update to the current version of Zotero (5.0.23).
  • Hi Joscha,

    Thanks for your work on Zotfile. It was exactly what I was looking for. I have a small comment about the "Send to Subfolder on Tablet Feature", which I use to periodically back-up all my pdfs in dropbox so I can read them on my phone:

    Not sure if I am doing something wrong or if someone else already pointed it out to you, but when I select multiple records that are in different collections or subcollections, Zotfile seems to send all files to the subfolder of the one specific file I right-click in order to send the command, instead of sending each file to their respective subfolder (as based on the collections they are in).

    My way around this is to only multi-select and send records that are in the same collection and hence will go to the same sub-folder anyway. Which works fine. But perhaps it would be better if, when for example you select your entire library at once, the files still go to their respective subfolders?

    Not too big a deal, but something I noticed.

    With regards,
    YF
  • edited October 13, 2017
    @bwiernik If I check for updates under zotero help section, no updates have been found...

    ps: I just found out that even the option "change sub-folder" in the Zotfile right click menu is no working anymore :(

    UPDATE: never mind, I uninstalled and re-installed the plug-in and now these two menus are working properly. However, the automatically created sub-folders are still an issue!

    Thanks
  • Hi @YiFongAu. Just out of curiosity, what kind of Zotero are you using? Because I have been having an issue with this feature since I upgraded to Zotero 5. Basically, I cannot create sub-folders based on the article parameters (e.g. year\author) anymore, but I can just send attachments to the main folder (the one that you create from the sub menu "change subfolder".

    Thank you
  • Problem with Poppler Tool, using MacOS X 10.12, Zotero 5.0.23, Zotfile 5.0.5: I clicked on "Download & Install Poppler Tool," and it was installed and worked to extract annotations. Now, it seems to be not installed anymore, the button to Download and Install reappeared, and clicking on it doesn't change anything. Thank you for your help (and for creating such an incredibly useful plug-in).
  • Zotfile is fantastic, thank you devs for working on it.

    I have a feature request, which I think should be quite simple -- I'd like to retain the functionality of pdfExtraction.colorNotes, but not split them into different notes; rather prefix each highlight with its colour, so there's one note with all of the highlights in sequential order. Something like this:

    Green - "This is a quote" (Smith, p. 37)

    Red - "This is another highlighted quote" (Smith, p. 43)

    Green - "This is yet another quote" (Smith, p. 427)

    I thought I could achieve it by putting %(color) in the pdfExtraction.formatAnnotationHighlight option, but it renders as "rgb(0,255,0)", so obviously the conversion using pdfExtraction.colorCategories happens elsewhere (and perhaps only for pdfExtraction.formatNoteTitleColor?)

    If I get time I might dig into the Zotfile code, but if this was an easy fix -- i.e. to enable the parsing of colorCategories in formatAnnotationHighlight, even when colorNotes is disabled -- that would be fantastic :)

    Many thanks again,

    Laurence
  • I managed it by adding the following to line 265 of pdfAnnotations.js:

    if (anno.subtype == "Highlight")
    anno.markup = "(" + color_category + ") - " + anno.markup + "";

    (note that it also adds a highlight to the note, so it's easy to tell the difference between different coloured highlights at-a-glance).

    If/when I get a chance I'll add this as a Zotfile preference, and submit a pull request.
  • Hey everyone.

    Excellent work with the software btw. I have one small feature request/bug/feature that used to work (apparently) before Zotero 5.0 but no longer that I'd like to be (re-)implemented.

    I posted this on the main Zotero forums so you can see there for a full discussion (https://forums.zotero.org/discussion/68517/zotfile-renaming-linked-files-but-not-moving-them)

    Basically, I want to rename linked pdfs but not move their location.

    I've got a load of pdfs in lots of folders for different courses saved across my harddrive. I completely understand how to rename (retreive metadata, manage attachments etc.) files I've copied into Zotero. However, once the linked file is renamed Zotfile moves it to a different directory. I'm aware that one can customise the directory to which these files are saved.

    However, I DO NOT want these renamed files to be moved at all. I've got pdfs in literally hundreds and hundreds of folders. It'd be so much easier if Zotfile will just rename the linked file and leave it in its original source (linked) directory.

    A fellow user, bwiernik, said this feature used to work before Zotero 5.0 by choosing custom location and leaving the field blank.

    Doing this in Zotero 5.0 and following the same renaming process that I'd normally use (which moves the pdfs) - add linked file to the directory, retrieve metadata (which creates top-level item with linked file underneath), Manage Attachments -->, Rename Attachments, the top field in zotero (the field with the item in bold which when clicked displays a command window named 'Prompt' and contains 'New title:') gets renamed with my renaming rules but the Filename field does not change at all.

    I hope it should be a very simple option to have a checkbox implemented in the Zotfile preferences menu saying 'Rename (linked) files in source directory'. Even if that isn't possible, if someone could inform me how to implement this for my Zotfile preferences in the meantime that'd be great. Otherwise I'll just have to wait until the bug's fixed in a future Zotfile release (hopefully not too soon!).

    Thanks all.

  • FYI: Re. above;

    Nothing shows up in the 'Report Errors' help option regarding this. I'm using Win8.1 and I'm not using Zotero through firefox, just the desktop application and the latest version of Zotfile.

    Thanks again
  • Just commenting to echo mark and cmf5, that the added file popup persists indefinitely, which is a new and unfortunate behavior. It would be great to fix this if possible - many thanks, though, for all of the hard work that has already been put in to this project!
  • The software of zotero and zotfile are both wonderful.
    But when I use zotero standalone and zotfile. Use the settlement, I can not link the pdf and the item automatic. I have to drag the document to the item.
  • I’m not sure what you mean. Can you elaborate?
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