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My supervisor usually requests me to deliver some kind of written reports. I write them in LaTeX, deliver them as PDF, and get them back with lots of comments. She uses Acrobat Professional to create the comments.

I would like to extract a list of all comments from the file so I can in a second step import them into a task management tool. Some simple text format will suffice, I can write a script to add markup if needed. All I want is that single comments are separated somehow, e.g. by two blank rows (I think she sometimes adds newlines into comments).

I strongly prefer a solution which works under Linux, but in the worst case will accept something which requires Windows. I don't have a license for Acrobat professional or other paid PDF readers, so please recommend free software if possible.

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Comments in PDFs can be exported/imported as FDF files. FDF files are usually only a few megabytes in size (unless the comments include images or other files). The comments list can also be exported to Word. Both options are found in the options menu in the comments pane as in the screenshot below (from Acrobat X Professional).

enter image description here

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I think the terminology is Annotations, so that may help in your searches. ;)

Otherwise, perhaps an online solution such as ?

Note: I found this particular link in an answer on another SU question: Print only the annotations of a pdf. I've never used it myself.

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Since you use LaTeX, the texlive-latex-extra package on Ubuntu contains the pdfannotextractor executable that can extract comments for you. This uses libpdfbox-java that you will also need to install.

Another option is to install python-poppler and use this Python script from a similar stackoverflow question (see answer by Enno Gröper): Parse annotations from a pdf

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