REQUIRED PROGRAMS: - Skim (pdf viewer and annotator) - Evernote (cloud based note app) - works with PDFPen for iPad and iPhone This script will (as the title suggests) export all of you Skim notes directly to Evernote with hyperlinks.

Export Skim Annotations with PDFPen urls

(* EXPORT ALL SKIM NOTES TO EVERNOTE WITH IOS HYPERLINKS

-- Stephen Margheim
-- 10/16/13
-- open source

REQUIRED PROGRAMS:
- Skim (pdf viewer and annotator)
- Evernote (cloud based note app)
- works with PDFPen for iPad and iPhone

This script will (as the title suggests) export all of you Skim notes directly to Evernote with hyperlinks. 

When launched, the script will ask you a series of questions:
* where you want the current PDF to be moved to finally reside,
* what the relation of the Printed page number is relative to Skim's indexed page number, 
* if the PDF is a Primary Source or a Secondary Source. 

Your choices will determine (1) the file path used in the URL Handler, (2) the key to generating the hyperlinked printed page numbers, (3) the text values for the 6 different highlight colors. 

NOTE: YOU MUST SAVE YOUR PDFS TO THE SAME FOLDER AS THE FOLDER THAT THE URL HANDLER SEARCHES
*)



(* PROPERTIES *)
property LF : (ASCII character 10)
property LF1 : (ASCII character 32) & (ASCII character 32) & (ASCII character 10)
property tid : AppleScript's text item delimiters
property theHome : path to home folder as string



(* THE SCRIPT *)
tell application "Skim"
  
	(* ///
	PRE-PROCESSING: 
	Check if annotated on iOS. If yes, convert annotations 
	/// *)
	
	if every note of document 1 = {} then convert notes document 1
	
	(* ///
	PART 1: 
	Dialog Boxes 
	/// *)
	
	--move PDF file to its proper place
	set theFile to name of document 1 as string
	set theFolder to choose folder default location (theHome & "Dropbox:" as alias) with prompt "Whither save the PDF?"
	set theFolder to theFolder as string
	
	--get relation of printed page number to Skim's indexed page number
	set pageRelation to text returned of (display dialog ¬
		"Subtract printed page number from Skim's indexed page number" with title "Relation of Printed page # to indexed page #" default answer "") as number
	
	--determine type of PDF
	set theTextStatus to display dialog "Is the PDF a Primary or Secondary text?" buttons {"Primary", "Secondary"} default button {"Secondary"}
	
	(* ///
	PART 2: 
	Generate Top 3 Notes with relevant Meta-Data 
	/// *)
	
	--URL encode pdf's title
	set pdfTitle to name of document 1
	set PdfName to my encode_text(pdfTitle, true, false)
	
	--create Custom URL with partial file path
	set customurl to "pdfpen:///" & pdfTitle & "?pg="
	
	--create the three opening notes
	tell page 1 of document 1
		make note with properties {type:anchored note, bounds:{579, 842, 595, 826}, text:customurl, extended text:pdfTitle}
		delay 0.1
		make note with properties {type:anchored note, bounds:{579, 826, 595, 810}, text:"[" & pdfTitle & "](" & customurl}
		delay 0.1
		make note with properties {type:anchored note, bounds:{579, 810, 595, 794}, text:pageRelation, extended text:"pr# - sk#"}
	end tell
	
	
	(* /// 
	PART 3: 
	Get all Annotation Information 
	/// *)
	
	--get info for all notes
	set allNotes to every note of document 1
	set allNotes_types to every type of notes of document 1
	set allNotes_text to text of every note of document 1
	set allNotes_pages to index of every page of every note of document 1
	
	--get info for all notes except top 3
	set selNotes to items 1 through -4 of allNotes
	set selNotes_types to items 1 through -4 of allNotes_types
	set selNotes_text to items 1 through -4 of allNotes_text
	set selNotes_pages to items 1 through -4 of allNotes_pages
	
	--get info from top 3 notes
	set PDFLink to customurl
	set Markdownlink to (get text of note -2 of page 1 of document 1) as string
	set number_of_Note3 to (get text of note -1 of page 1 of document 1) as string
	
	--prepare Headers for all of the various note types
	set notesText_text to "<hr />" & LF & LF & "<h2>The ToC</h2>" & LF1 & LF & LF
	set notesText_anchor to "<hr />" & LF & LF & "<h2>All of my Text Notes</h2>" & LF1 & LF & LF
	set notesText_highlight to "<hr />" & LF & LF & "<h2>All of the Highlighted Text </h2>" & LF1 & LF & LF
	set notesText_underline to "<hr />" & LF & LF & "<h2>All of the Underlined Text</h2>" & LF1 & LF & LF
	set notesText_strikethru to "<hr />" & LF & LF & "<h2>All of the Strike-Through Text</h2>" & LF1 & LF & LF
	
	
	(* ///
	PART 4:
	The Meat-n-Potatoes of the Script 
	/// *)
	
	repeat with i from 1 to count of selNotes_types
		
		--prepare Skim page # and actual page #
		set notePage to item i of selNotes_pages
		set theRealPage to notePage + number_of_Note3 as string
		
		--collect Text Notes
		if item i of selNotes_types is text note then
			set noteText to item i of selNotes_text
			set notesText_text to notesText_text & "<p>" & noteText & " (<a href=\"" & PDFLink & notePage & "\">" & "p." & theRealPage & "</a>)" & LF & LF
			
			--collect Anchor Notes	
		else if item i of selNotes_types is anchored note then
			set titleText to item i of selNotes_text
			set noteText to extended text of item i of selNotes
			
			--precaution for running script multiple times
			repeat 1 times
				if titleText contains "customurl://" or noteText contains "pr# - sk#" then exit repeat
				set notesText_anchor to notesText_anchor & "<p><strong>" & titleText & ":</strong> " & noteText & " (<a href=\"" & PDFLink & notePage & "\">p." & theRealPage & "</a>)" & LF & LF
			end repeat
			
			--collect Underline Notes	
		else if item i of selNotes_types is underline note then
			set noteText to item i of selNotes_text
			set notesText_underline to notesText_underline & "<p>\"" & noteText & "\"" & " (<a href=\"" & PDFLink & notePage & "\">" & "p." & theRealPage & "</a>)" & LF & LF
			
			--collect Strike-Thru Notes	
		else if item i of selNotes_types is strike out note then
			set noteText to item i of selNotes_text
			set notesText_strikethru to notesText_strikethru & "<p>\"" & noteText & "\"" & " (<a href=\"" & PDFLink & notePage & "\">" & "p." & theRealPage & "</a>)" & LF & LF
			
			--collect Highlight Notes	
		else if item i of selNotes_types is highlight note then
			set theColor to color of item i of selNotes
			set titleText to my color2text(theColor, theTextStatus)
			set noteText to item i of selNotes_text
			
			set notesText_highlight to notesText_highlight & "<p><strong>" & titleText & ":</strong> " & LF1 & "\"" & noteText & "\"" & " (<a href=\"" & PDFLink & notePage & "\">p." & theRealPage & "</a>)" & LF & LF
		end if
	end repeat
	
	(* ///
	PART 5:
	Extract Summary Annotations 
	/// *)
	
	--extract "Summary" notes from the collection of all highlight notes
	set theSummary to {}
	set theParas to paragraphs of notesText_highlight
	repeat with i from 1 to count of theParas
		if item i of theParas contains "<p><strong>Summary:" then
			set theTitle to item i of theParas
			set theText to item (i + 1) of theParas
			set theSumm to theTitle & LF & theText & LF & LF
			copy theSumm to the end of theSummary
		end if
	end repeat
	
	--remove "Summary" highlight notes from collection of highlight notes
	if (not (theSummary is {})) then
		set SumText to theSummary as string
		set SumList to paragraphs of SumText
		set empty to {""}
		set FinalSum to my cleanmyList(SumList, empty)
		
		set HighList to paragraphs of notesText_highlight
		set finalHighlights to my cleanmyList(HighList, FinalSum)
		set AppleScript's text item delimiters to LF
		set notesText_highlight to (finalHighlights as string)
		set theSummary to "<hr />" & LF & LF & "<h2>Text Summary</h2>" & LF1 & LF & LF & SumText
	end if
	--ALWAYS RETURN TEXT ITEM DELIMITERS TO NORMAL
	set AppleScript's text item delimiters to tid
	
	(* ///
	PART 6:
	Remove any Empty Annotation Sections
	/// *)
	
	--remove any note sections that are empty
	set FinalList to my textCheck(notesText_text, notesText_anchor, notesText_highlight, notesText_underline, notesText_strikethru, theSummary)
	
	--prepare the final collection of notes, with MetaData
	set FinalText to FinalList
	
	(* ///
	PART 7:
	Create the Evernote Note
	/// *)
	
	tell application "Evernote"
		
		--create new "PDF Notes" notebook if necessary
		if (not (notebook named "PDF Notes" exists)) then
			make notebook with properties {name:"PDF Notes"}
		end if
		
		--create the HTML note
		set theTitle to "Notes: " & pdfTitle
		set newNote to create note title theTitle with html FinalText notebook "PDF Notes"
		
		set noteTags_list to {"notes", "pdfpen"}
		repeat with i from 1 to count of noteTags_list
			set x to item i of noteTags_list
			if (not (tag named x exists)) then
				set tag1 to make tag with properties {name:x}
			else
				set tag1 to tag x
			end if
			assign tag1 to newNote
		end repeat
		
		--synchronize Evernote
		repeat until isSynchronizing is false
			synchronize
		end repeat
		repeat until isSynchronizing is false
		end repeat
	end tell
	
	(* ///
	PART 8:
	Display Growl Notifications
	/// *)
	
	--save as flattened pdf to be viewed by iOS app
	save front document as "PDF With Embedded Notes" in (theFolder & theFile)

	--is Growl installed?
	set Growl_ to my Growl_Check()
	
	--notify on Success or Failure
	if Growl_ is true then
		tell application "Growl"
			set allNotificationsFiles to {"Success Notification", "Failure Notification"}
			set enabledNotificationsFiles to {"Success Notification", "Failure Notification"}
			register as application ¬
				"Skim Annotations to Evernote" all notifications allNotificationsFiles ¬
				default notifications enabledNotificationsFiles ¬
				icon of application "URL Handler"
		end tell
		
		--on Success
		tell application "Growl"
			if newNote exists then
				notify with name ¬
					"Success Notification" title ¬
					"Import Success!" description "Successfully Exported All Skim Annotations to Evernote" application name "Skim Annotations to Evernote" icon of application "Custom URL Handler"
			else
				notify with name ¬
					"Failure Notification" title ¬
					"Import Failed" description "The script failed to export all Skim notes to Evernote" application name "Skim Annotations to Evernote" icon of application "Custom URL Handler"
			end if
		end tell
	end if
end tell




(* HANDLERS *)

--URL encode text
on encode_text(this_text, encode_URL_A, encode_URL_B)
	set the standard_characters to "abcdefghijklmnopqrstuvwxyz0123456789"
	set the URL_A_chars to "$+!'/?;&@=#%><{}[]\"~`^\\|*"
	set the URL_B_chars to ".-_:"
	set the acceptable_characters to the standard_characters
	if encode_URL_A is false then set the acceptable_characters to the acceptable_characters & the URL_A_chars
	if encode_URL_B is false then set the acceptable_characters to the acceptable_characters & the URL_B_chars
	set the encoded_text to ""
	repeat with this_char in this_text
		if this_char is in the acceptable_characters then
			set the encoded_text to (the encoded_text & this_char)
		else
			set the encoded_text to (the encoded_text & encode_char(this_char)) as string
		end if
	end repeat
	return the encoded_text
end encode_text

on encode_char(this_char)
	set the ASCII_num to (the ASCII number this_char)
	set the hex_list to {"0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "A", "B", "C", "D", "E", "F"}
	set x to item ((ASCII_num div 16) + 1) of the hex_list
	set y to item ((ASCII_num mod 16) + 1) of the hex_list
	return ("%" & x & y) as string
end encode_char

on replaceString(theText, oldString, newString)
	-- ljr (http://applescript.bratis-lover.net/library/string/)
	local ASTID, theText, oldString, newString, lst
	set ASTID to AppleScript's text item delimiters
	try
		considering case
			set AppleScript's text item delimiters to oldString
			set lst to every text item of theText
			set AppleScript's text item delimiters to newString
			set theText to lst as string
		end considering
		set AppleScript's text item delimiters to ASTID
		return theText
	on error eMsg number eNum
		set AppleScript's text item delimiters to ASTID
		error "Can't replaceString: " & eMsg number eNum
	end try
end replaceString

--convert highlights into text values
on color2text(noteColor, theTextStatus)
	set colorText to {}
	if theTextStatus is {button returned:"Secondary"} then
		if noteColor is {64634, 900, 1905, 65535} then
			set end of colorText to "Disagree"
		else if noteColor is {64907, 32785, 2154, 65535} then
			set end of colorText to "Agree"
		else if noteColor is {65535, 65531, 2689, 65535} then
			set end of colorText to "Summary"
		else if noteColor is {8608, 65514, 1753, 65535} then
			set end of colorText to "Reference"
		else if noteColor is {8372, 65519, 65472, 65535} then
			set end of colorText to "Quotable"
		else if noteColor is {64587, 1044, 65481, 65535} then
			set end of colorText to "Technique"
		end if
	else if theTextStatus is {button returned:"Primary"} then
		if noteColor is {64634, 900, 1905, 65535} then
			set end of colorText to "Key Quote"
		else if noteColor is {64907, 32785, 2154, 65535} then
			set end of colorText to "Key Theme"
		else if noteColor is {65535, 65531, 2689, 65535} then
			set end of colorText to "Summary Passage"
		else if noteColor is {8608, 65514, 1753, 65535} then
			set end of colorText to "Key Motif"
		else if noteColor is {8372, 65519, 65472, 65535} then
			set end of colorText to "Confusing Passage"
		else if noteColor is {64587, 1044, 65481, 65535} then
			set end of colorText to "\"Purple\" Passage"
		end if
	end if
	return colorText
end color2text

--remove any empty note sections
on textCheck(notesText_text, notesText_anchor, notesText_highlight, notesText_underline, notesText_strikethru, theSummary)
	if notesText_text is "<hr />

<h2>The ToC</h2>  


" then
		set notesText_text to ""
	else
		set notesText_text to notesText_text & LF & LF
	end if
	if notesText_anchor is "<hr />

<h2>All of my Text Notes</h2>  


" then
		set notesText_anchor to ""
	else
		set notesText_anchor to notesText_anchor & LF & LF
	end if
	if notesText_highlight is "<hr />

<h2>All of the Highlighted Text </h2>  


" then
		set notesText_highlight to ""
	else
		set notesText_highlight to notesText_highlight & LF & LF
	end if
	if notesText_underline is "<hr />

<h2>All of the Underlined Text</h2>  


" then
		set notesText_underline to ""
	else
		set notesText_underline to notesText_underline & LF & LF
	end if
	if notesText_strikethru is "<hr />

<h2>All of the Strike-Through Text</h2>  


" then
		set notesText_strikethru to ""
	else
		set notesText_strikethru to notesText_strikethru & LF & LF
	end if
	if theSummary is {} then
		set theSummary to ""
	else
		set theSummary to theSummary & LF & LF
	end if
	return notesText_text & theSummary & notesText_anchor & notesText_highlight & notesText_underline & notesText_strikethru
end textCheck

--remove items from a list
on cleanmyList(theList, itemsToDelete)
	set cleanList to {}
	repeat with i from 1 to count theList
		if {theList's item i} is not in itemsToDelete then set cleanList's end to theList's item i
	end repeat
	return cleanList
end cleanmyList

--Check For Growl 
on Growl_Check()
	if appIsRunning("Growl") then
		set growl_Running to true
		tell application "Growl"
			set allNotificationsFiles to {"Import To Evernote", "Success Notification", "Failure Notification"}
			set enabledNotificationsFiles to {"Import To Evernote", "Success Notification", "Failure Notification"}
			register as application ¬
				"Skim Annotations to Evernote" all notifications allNotificationsFiles ¬
				default notifications enabledNotificationsFiles ¬
				icon of application "Custom URL Handler"
		end tell
		return growl_Running
	else
		error
	end if
end Growl_Check

--App Detect
on appIsRunning(appName)
	tell application "System Events" to (name of processes) contains appName
end appIsRunning