Extracting annotations behaves in non comprehensible way

I have a pdf and I tried to extract some annotations from it but I found some issues with this process, or maybe I haven't understood how it works.

Here are the steps that I followed:
1) Highlighted some text on pdf
2) saved pdf with highlights
3) extract annotations

So far so good, then
4) highlight some more text
5) saved pdf
6) extracted annotations

Now this produces a second annotation file, my question is how to have annotations combined into just one file?

The other issue that I faced is that I deleted both annotation files and tried to extract annotations again in hope that it would extract all annotations into one file but this time it only extracts the highlights made in steps 4-6 and not all of them 1-6.

Any ideas on how to get that working or what am I doing wrong?

Also does the hidden setting "extensions.zotfile.tablet.updateExtractAnnotations" have the effect that I'm looking on the tablet, (i.e.) updating the annotations extracted and not creating different files every time you add new annotations?

  • There isn’t currently a way to merge extracted annotations from Zotfile with any manual edits you may have made, so Zotfile takes the cautious route of not overwriting an existing extracted note. You can delete the previous extracted note if it’s not needed.

    That setting is irrelevant for you.
  • @bwiernik thanks, my main issue at the moment is that it keeps generating annotations only from step 4-6, even if I delete all annotations, is there some hidden setting where it somehow cashes stuff and on subsequent extracts it only produces the last cashed element? or somehting like that? Cause I'm not able to generate full extracted annotations from step 1-6 even if I delete all previously extracted annotations in zotero.

    Any ideas about this?
  • No, zotfile extracts all of the annotations from a file each time. Are you sure that the (1-3) annotations are still active and valid in the PDF file?
  • @bwiernik eventually after a lot of trials, deleting and extracting all annotations, now I'm able to see all the annotations extracted, don't know what happened there, hopefully it won't happen again.
  • I would like the option to choose to have only one combined annotation document. The way I see it working is Zotero keeps the original PDF, an annotated copy and an annotations file. If the user chooses to send to tablet a document that has already been anotated, the cersion that is sent is the annotated file so you can just add to the annotations. Upon a get from tablet action the newly modified annotated PDF replaces the one in Zotero and also the annotations file in Zotero is replaced.

    It is left to the user to be sure that they are adding to an existing annotated file and that it will overwrite the previous annotated version.
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