Grabbing notes from PDFs

gistfile1.applescript

(*

Script courtesy of Walton Jones, modified slightly 
http://drosophiliac.com/2012/09/an-academic-notetaking-workflow.html

Original script by John Sidiropoulos
http://www.organognosi.com/export-skim-notes-according-to-their-highlight-colors/

*)

tell application "Skim"
    set the clipboard to ""
    set numberOfPages to count pages of document 1
    
    activate
    set myColorCodes to my chooseColor()
    
    set firstPage to "1" as number
    set lastPage to numberOfPages
    set the clipboard to "# Notes #" & return & return
    
    repeat with currentPage from firstPage to lastPage
        set pageNotes to notes of page currentPage of document 1
        exportPageNotes(pageNotes, currentPage, myColorCodes) of me
    end repeat
    
end tell

on exportPageNotes(listOfNotes, pageForProcessing, myColorCodes)
    tell application "Skim"
        
        set currentPDFpage to pageForProcessing
        repeat with coloredNote in listOfNotes
            
            repeat with i from 1 to the count of myColorCodes
                if color of coloredNote is item i of myColorCodes then
                    set categoryColors to ({"Summary", "Methods", "Arguments", "Reference", "Thesis", "Question or connection"})
                    set noteColor to color of coloredNote as string
                    if noteColor is item i of myColorCodes as string then
                        set noteColor to item i of categoryColors
                    end if
                    set noteText to get text for coloredNote
                    set the clipboard to (the clipboard) & "**[" & noteColor & "]" & "(file://" & name of document 1 & "#page=" & pageForProcessing & ")**" & ":   " & return & noteText & return & return
                end if
            end repeat
        end repeat
        
    end tell
end exportPageNotes

on chooseColor()
    set selectedColors to ({"Summary", "Methods", "Arguments", "Reference", "Thesis", "Question or connection"})
    set colorCodes to {}
    set noteColor to ""
    repeat with noteCol in selectedColors
        set noteColor to noteCol as text
        if noteColor is "Summary" then
            set end of colorCodes to {64634, 900, 1905, 65535}
        else if noteColor is "Methods" then
            set end of colorCodes to {64907, 32785, 2154, 65535}
        else if noteColor is "Arguments" then
            set end of colorCodes to {65535, 65531, 2689, 65535}
        else if noteColor is "Reference" then
            set end of colorCodes to {8608, 65514, 1753, 65535}
        else if noteColor is "Thesis" then
            set end of colorCodes to {8372, 65519, 65472, 65535}
        else if noteColor is "Question or connection" then
            set end of colorCodes to {64587, 1044, 65481, 65535}
            
        end if
    end repeat
    
    return colorCodes
end chooseColor