Sonny Software

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-- PubMed to Bookends import applescript
-- Created by Kevin Sanderson on 23/09/06

property refresh_delay : 120 -- wait loop for page refresh - increase if slow connection
property UI_delay : 1 -- delay in seconds to let the UI scripting actions happen - increase/decrease if required

-- check that UI scripting is available and turned on - if not then exit
-- NOTE: it's only the second part (actually importing into Bookends that needs this)
if not my check_can_run() then return

tell application "Safari"
	-- get the URL of the frontmost page/tab in Safari
	set theURL to URL of document 1
	
	-- check to see if the URL makes sense ie it's a PubMed page
	if theURL does not contain "www.ncbi.nlm.nih.gov" then
		display dialog "Unable to proceed. The chosen page does not appear to be PubMed or the format has changed." & return with icon caution buttons {"Quit"} default button "Quit"
		return
	end if
	-- doble check it's an AbstractPlus view
	if theURL does not contain "dopt=AbstractPlus" then
		display dialog "Unable to proceed. The chosen page does not appear to be a PubMed AbstractPlus view or the format has changed." & return with icon caution buttons {"Quit"} default button "Quit"
		return
	end if
	
	-- format is http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16973271&query_hl=1&itool=pubmed_docsum
	-- replace "AbstractPlus" with "medline" and reload the URL to get the medline view
	set theURL to my replace_chars(theURL, "AbstractPlus", "medline")
	set URL of document 1 to theURL
	
	-- wait until the page has loaded
	my page_loaded(refresh_delay)
	
	--get just the data we want from the page using the DOM tree. Info we want is in a <pre></pre> tag
	set this_script to "var myNode=document.getElementsByTagName('pre');" & return & ¬
		"myNode[0].lastChild.nodeValue"
	set medline_source to do JavaScript this_script in document 1
	
	(* Begin munge the end of line marks *)
	-- NOTE if we don't do this Bookends crashes which would be bad
	-- (taken from http://www.macosxhints.com/article.php?story=20031018164326986)
	-- first we ask to put all the lines into a list (fParagraphs). AppleScript doesn't care if it is Unix, Mac or Windows.
	set fParagraphs to paragraphs of medline_source
	-- now we tell AppleScript that lists will be concatenated using return characters when the list is converted to a string 	
	set AppleScript's text item delimiters to return
	-- here we convert the list of paragraphs to strings using the text item delimiters
	set fContentsNew to fParagraphs as string
	-- here we reset the text item delimiters to "" which is default.
	set AppleScript's text item delimiters to ""
	-- finally copy the data onto the clipboard
	set the clipboard to fContentsNew
	(* end of munge the end of line marks *)
end tell

-- make sure Bookends is running and bring it to the front
activate application "Bookends"
tell application "System Events"
	tell process "Bookends"
		--bring up the import dialog
		keystroke "I" using {command down, shift down}
		delay UI_delay * 2 -- slower action so increase the delay a bit
		
		tell window "Import References"
			-- 1) select pubMed import
			click pop up button 1 --first select the menu
			pick menu item "PubMed" of menu of pop up button 1 --then select PubMed import
			delay UI_delay
			
			-- 2) select the clipboard button
			click radio button 1
			delay UI_delay
			
			--3) select the OK button
			click button "OK"
			delay UI_delay * 2 -- slower action so increase the delay a bit 
		end tell
		
		-- finally click OK in the result window
		tell window "Importing References"
			click button "OK"
		end tell
	end tell
end tell

-- utility functions taken from http://www.apple.com/macosx/features/applescript/resources.html
on replace_chars(this_text, search_string, replacement_string)
	set AppleScript's text item delimiters to the search_string
	set the item_list to every text item of this_text
	set AppleScript's text item delimiters to the replacement_string
	set this_text to the item_list as string
	set AppleScript's text item delimiters to ""
	return this_text
end replace_chars

on page_loaded(timeout_value)
	delay 2
	repeat with i from 1 to the timeout_value
		tell application "Safari"
			if (do JavaScript "document.readyState" in document 1) is "complete" then
				return true
			else if i is the timeout_value then
				return false
			else
				delay 1
			end if
		end tell
	end repeat
	return false
end page_loaded

on check_can_run()
	set check to true
	
	tell application "System Events"
		if not ((system attribute "sysv") ? 4144) then -- not Mac OS X 10.3.0+
			beep
			display dialog "This computer can't run this script" & return & return & "The script uses Apple's GUI Scripting technology, which requires an upgrade to Mac OS X 10.3 \"Panther\" or newer." with icon caution buttons {"Quit"} default button "Quit"
			set check to false
		else if not (UI elements enabled) then
			beep
			display dialog "GUI Scripting is not enabled" & return & return & "Open System Preferences and check \"Enable access for assistive devices\" in the Universal Access preference pane, then run this script again." with icon caution buttons {"Quit"} default button "Quit"
			set check to false
		end if
	end tell
	return check
end check_can_run