Definitely not a Zotero problem, but it's certainly conceivable that ZotFile might get stuck.

You've annotated the PDF with the same software you used in tests?

It's not Zotero because the only part of Zotero involved is the ability to create notes for ZotFile and that either works or it doesn't.

ZotFile is able to extract standard annotations on PDF. Most tools use standard annotations, but some don't. There's no list of tools, no. A rule of thumb is, if you can see the annotations when viewing the annotated PDF in Firefox, ZotFile should be able to extract them.

@adamsmith so if I understand well Zotero is not able to extract certain highlights. Would it help if those highlights were in green instead of yellow?

@DWL-SDCA thanks for your reply. So, if the highlight colour is irrelevant, how come Zotero is not extracting, as I described in the beginning?
@adamsmith makes a point of the software used. Now, I am not a Zotero expert, but it seems strange that Zotero would only extract highlights done with certain software. This is even stranger considering there is not approved software list.

@fbennett thanks for clearing that up.

Sure, a list is fine, but the basic rule is that ZotFile will recognize annotations according the the PDF standard and won't recognize annotations that don't follow the standard (it uses the same tool to recognize them that Firefox uses to display PDFs. That's why the above rule of thumb, btw.). That means the majority of pdf readers/annotators are supported. Probably the most notable tool ZotFile doesn't work with is Skim for Mac, but there are others.*

It does sound like, though, that the problem may well be something different than the tool used for annotating. Simplest way to tell would be for @KlaasVaak to use the same method on a very simple document. If extraction works there, the problem is elsewhere. Could be a problem with the document, e.g. document security properties that prevent copying text, or could be a ZotFile bug, e.g. related to the long document. I'd do this simple troubleshooting before spending a lot of time thinking about supported and not supported annotation tools. If you're using a common tool for annotating, you could also just tell us and we'll likely know.


* There is one other slight quirk to this in that ZotFile doesn't recognize all _types_ of annotations. It does recognize standard highlighting (indeed, regardless of color) and it recognizes standard comments, but e.g. I don't think it recognizes text that you associate with highlighting, nor does it recognize other textbox formats you can generate in some tools including Acrobat.

@KlaasVaak One thing to try, if you haven't already, is to print the Okular-annotated file to PDF. That will change its internal structure, and possibly (although only possibly) put the annotations into a form that ZotFile can extract. I've seen that work with Okular files in other contexts, it's worth a try.

@fbennett unfortunately that did not work. As soon as I set Zotfile to extract the annotations from the secondary PDF file, the rectangular Zotfile pop-up in the bottom right corner showed the name of the file with a red cross before it, nothing at all was extracted.

I then tried an older file with 200 pages that I knew for sure I had annotated in Foxit, and that worked. Ironically, the Windows version of Foxit has its built-in annotations export feature, but not in the Linux version :-(((

So, the take away for me is that I should not use Okular anymore (I always apply annotations to PDFs) and reinstall Foxit, which I had installed and uninstalled because of the lack of this feature. Zotfile has "saved" me :-)

A big thanks to you and @adamsmith for your help, as well as your time.

Stumbled on this because I'm using Okular and created a bunch of Inline Notes. Is there a way to convert these annotations to regular annotations? I tried Save As pdf but it didn't work.