ZotFile - Advanced PDF management for Zotero

  • And this is for extracting highlight annotations? Can you copy paste the text correctly manually?
  • Yes, I can copy and paste without issue.
  • I've discovered that if I underline text instead of highlighting it, the extraction function works just fine. I have no idea why this might be so.

    Still, I would appreciate if anyone can answer my poppler question ...
  • @bwiernik Thanks for the suggestion. I deleted the prefs.js file and set up my preferences again, but the problem persists. Sending attachments to my tablet still creates subfolders, despite my Zotfile settings specifying no subfolders.
  • Mozilla has now shut down access to Zotfile. When I try to download, even if I say "allow" it gives me the following message: "This add-on cannot be installed because it has not be verified." Can this be fixed?
  • You need to install Zotfile in Zotero, not Firefox. On Zotfile.com, right-click on the download link, choose Save As, and save the file to your computer. Then, in Zotero, click Tools - Add-ons, and drag the .xpi file you downloaded to the window that pops up.

    @dstillman This comes up a lot. If any headway can be made on switching the extension for Zotero plugins, that would be amazing.
  • So, any thoughts on my poppler question?
  • @bwiernik I added a warning to the Mozilla page with instructions. Pretty clearly visible but I will just take it down in the future. Still addon extension for Zotero so that users can just download and then double click the file would be great.
  • I'm not sure how long this has been a problem, but with the current versions of Zotero and Zotfile, "Extract annotations" only pulls in text box annotations, and not highlights. This may be the same problem that @Bellthorpe has, I'm not clear; but it's rather awkward when I have a lot of papers that I've annotated - including highlighting - on my tablet and want to get them back into Zotero!

    I'm on windows 10, so using pdf.js. Any help appreciated; if I can usefully provide further info, just ask.
  • Hello all,

    I want to use ZotFile to rename tens of thousands of papers into the following format:
    year_issue_pages, which works great with {%y_}{%v_}{%f}.

    I need pages to consist of 4 digits, i.e. 0001-0004 and not 1-4.

    Is there any possibility to create that format?

    Kind regards,
  • answered Yves's question here: https://forums.zotero.org/discussion/71843/zotfile#latest (answer is not possible, though)
  • I'm a bit worried by Zotfile's author's comment at the link below[1] that they won't be working on Zotfile in the near future.
    There's no criticism implied here - obviously they are entitled to not spend their time on it! But a lot of people rely on it, and bits of it are currently broken. So... are others working on it? Is there a prospect of anybody else taking it up?

    (Yes, I realise the probable answer is "if you've volunteering....". No, I don't have the skills. I would contribute to a group effort to employ somebody, if that were viable...)

    [1] https://github.com/jlegewie/zotfile/issues/350#issuecomment-381322477
  • The intention from the Zotero developers is to incorporate many of Zotfile’s features into Zotero itself.
  • Also, I'm pretty sure Joscha just means no major updates; he'll still do maintenance.

    I'm not aware of anything in ZotFile that's currently reliably broken. E.g. I just tested extracting highlights on Windows 10 using Acrobat and that works just fine. I'd try with different annotation software.
  • Just some clarifications from the zotfile author: I am not planing any major update to zotfile right now. I will do some maintenance but I am not going to chase down possible bugs. Most things that get reported here are not easily reproducible either because the user is doing something wrong or because it is related to their specific configuration. The likelihood that I fix something increases when a) I can easily reproduce the problem, b) it affects multiple people and c) it affects myself. I know about some issues (e.g. undefined folder) that I tried to fix in the past but they popped up again. These are things that I hope to fix but don't affects myself and can take time. In the longer term, @bwiernik is right. I hope that zotfile's core features make it into Zotero. Users will lose some of the specific options and workflows they are used to but the payoff is huge in terms of reaching all users, consistent and continuously supported code base etc etc I will support and help in this transition when I can.

    @swaldman Just to give an example. You write "in the current versions of Zotero and Zotfile, 'Extract annotations' only pulls in text box annotations, and not highlights". If this would be a general problem, I would look into it pretty quickly. I rely on this functionality almost every day. But it's not a general problem. It works for me, it works for @adamsmith. I can't even reproduce it. Maybe you are doing something wrong (e.g. maybe you are using the "Pen" annotation tool and not "highlight"), maybe it's related to your specific set-up, maybe you have something else installed that interferes. That is what I mean when I say "I am not going to chase down possible bugs".

    Hope that clarifies my position.
  • @joscha thank you - that is a relief!

    Re my specific problem (in case anybody else can help - I respect your position here): Yes, highlights made in Acrobat work. Highlights made in EzPDF, an Android app, do not work. They used to work - so I don't know whether something has changed in Zotfile/pdf.js, or whether something has changed in EzPDF. Weirdly, if I open the files in Acrobat, the highlights show up as perfectly normal highlights - so presumably they must follow the standard - yet they still don't get imported by Zotfile.
    Hence I'm scratching my head.

    Any insight from those who understand more than me about PDF annotation would be appreciated!
  • edited May 15, 2018
    @swaldman and @Joscha
    I discovered Zotfil three month ago, and it's a fantastic tools for me, but I have the same problem.
    When I used Prewiew : "Extract annotations" only pulled the highlights but not the annotations. Sometimes, my annotations were incomplete, sometimes they were erase and zotefile modified the PDF itself, in the same proportion, so I lost a part of my annotations.

    Now, I use Acrobat Reader. "Extract annotations" seems now to work with the annotations (I am not complete sure). However, I have a problem with the highlights, because it doesn't work correctly. When I use it with "normal" pdf, it's seems to work, but when I want to use it with big pdf like 200 pages e.g (it's why Zotefile can be very helpful for me!) the highlights texts are replace by symbols (like those : "     ")

    N.B : Sorry if my English is not very clear.
  • What exactly do you mean by "annotations"? Which tool do you mean? Zotfile should extract highlights, underlines, and comments entered in the Comment Bubble tool.

    Zotfile doesn't edit PDFs at all, so it would not have caused you to lose any part of your annotations—that would be an issue to investigate with your PDF editor.

    Regarding the highlights being extracted as symbols, are you able to copy-and-paste the text out correctly manually? If so, can you upload the PDF to Dropbox or similar and post a public link here?
  • I don't have an example at hand but I've seen this a ton of times. I think it had to do with a weird typeface being embedded that mapped really strange "text" in the pdf to sensible-looking glyphs in the typeface. I think. It's been a while.
  • @bwiernik sorry, I wanted to say, by "annotations" the comments in the Comment Bubble tool.

    No, Zotfile doesn't edit the PDF itself, but he edit the comments you have wrote. I know it shouldn't make this to that, but it does it.

    I'm not sure I understood. You want me I copy the file generated by Zotefile or the original PDF?

  • No, Zotfile literally cannot edit any part of a pdf file, including annotations. It simply has no ability to interact with a PDF file other than to read it.

    Both of those files (with labels describing each and a description of the exact steps you followed to go from one to the other) would be helpful.
  • edited May 20, 2018
    Problem with Poppler Tool: using MacOS X 10.13, Zotero 5.0.47, Zotfile 5.0.8: After clicking on "Download & Install Poppler Tool" in the Zotfile preferences, Poppler was installed and worked. Then, it is suddenly 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).
  • @swaldman
    Just for the information: I'm using Moon+ Reader for Android and all the highlights (and notes) are extracted by ZotFile without any problems.
  • @studiosus Thanks. I don't especially like Moon Reader's PDF handling, which is why I was with EzPDF, but maybe I'll have to give it another go.
    Incidentally it's not as straightforward as "this app always causes trouble". I tried to reproduce with a sample one-line Word document -> PDF -> EzPDF -> Zotfile, and it worked fine... but it doesn't work with (most?) papers.
    Kinda baffled at the moment, especially as the highlights show up just fine in Firefox, which AIUI also uses PDF.js...
  • Is there a possibility to automatically tag the extracted annotation note with a (static) tag?

    The Preference name would probably be:

    I am just asking in case I overlooked something.
  • Hi, some general questions on functionalities and best practices as I am a newbie and couldn't find easy answers:

    – The moving and renaming of attachments needs to be triggered (either via right-click of the pop-up) – there's no way to do that automatically, right?
    – Same with parsing the annotations. Always needs to be triggered, no automation, right?

    What's the best practice for people that all their attachments to be stored in a Dropbox or similar folder?
    A.) Let Zotero store them directly in dropbox folder, despite of the warning that this may damage the database.
    B.) Let Zotfile move the files to Dropbox folder and link back.
    C.) Something different?
  • Hi, I recently upgraded to Zotero 5.0.47 (and now Zotero has released 5.0.48 as of today). Zotfile is no longer compatible with the recent version of Zotero. Will there be a Zotfile update soon?
  • @ckatzenbach regarding the best practice questions:

    A.) Those warnings are for a reason. Storing your entire Zotero folder in Dropbox is highly *not* recommended.

    B.) If the attachments are added to parent items as "links", then it is safe to store the attachments in Dropbox (or any other cloud sync system).

    @adamsmith What is the recommendation for users wanting to keep only Zotero's "storage" folder in Dropbox? Is that even possible?
  • @gurdas You can symlink the storage folder to a folder in Dropbox. That can work and is safe (though it is rather fiddly to set up):

    @ckatzenbach I would recommend using Zotfile to store your PDFs in Dropbox and manage their locations. That is by far the easiest way to use Zotero with Dropbox. By default, Zotfile will move and rename new attachment files when you add them to Zotero (at least when using the Zotero Browser Connector). If you use Zotfile's Send to Tablet function, you can have annotations automatically extracted when you pull them back from the tablet, but otherwise you need to trigger extraction automatically.
  • Thanks! So the linking option seems the way to go, apparently there's no real downside. (Apart from not having the files in Zotero's online storage.) Full text search works just like with internal storage, right?

    Thanks for the pointer with the Firefox Connector. Right, here renaming and moving works automatically. Not with adding files via drag and drop, though.

This discussion has been closed.