Comments

• msteffens

  January 2019

  @ndpi, I've written a few scripts that extract PDF highlight annotations from Papers 3:

  • export note+highlight annotations to individual files
  • copy note+highlight annotations to the clipboard
  • export note+highlight annotations to DEVONthink Pro

  These could maybe serve as examples or starting points for you. For more info on how to script Papers 3, see Scripting Papers 3 for Mac with AppleScript – A Getting Started Guide.
• msteffens

  January 2019

  @ndpi, and here's a script that copies formatted references and citekeys (in MultiMarkdown format) to the clipboard:

  -- For all publications selected in Papers 3, copies their citekey and
  -- formatted reference to the clipboard
  tell application id "com.mekentosj.papers3"
      set selectedPubs to selected publications of front library window
  
      set outList to {}
      repeat with aPub in selectedPubs
          set pubCitekey to citekey of aPub
          set pubReference to formatted reference of aPub
          copy "[#" & pubCitekey & "]: " & pubReference to end of outList
      end repeat
  
      set the clipboard to my mergeTextItems(outList, linefeed & linefeed)
      display dialog "Copied info for " & (count of selectedPubs) & " publications to the clipboard." buttons {"OK"} default button "OK" with icon 1
  end tell
  
  -- Merges the given list of text items using the given separator string
  on mergeTextItems(textItemList, aSeparator)
      considering case
          set prevTIDs to text item delimiters of AppleScript
          set text item delimiters of AppleScript to aSeparator
          set mergedText to textItemList as text
          set text item delimiters of AppleScript to prevTIDs
      end considering
      return mergedText
  end mergeTextItems
  
• ndpi

  January 2019

  @msteffens This is very helpful, thank you! AppleScript is still somewhat of a strange beast to me - and I've worked as a professional software engineer.
• achamess

  January 2019

  @ndpi I highlight in Skim.app and then extract to Sublime ZK.
  Here is the script. I can't promise it still works. But give it a try. It's pretty amateurish but it gets the job done for me.

  https://github.com/achamess/skim_to_md_script
• magnus

  February 2019

  Suggestions for Emacs from various sources in this thread https://www.reddit.com/r/emacs/comments/7yxg1t/extracting_pdf_highlights_and_linking_back_to_pdf/