Pubmed2connotea updated for Pubmed Beta.

I've updated the greasemonkey script 'pubmed2connotea'. The script alters the content of NCBI pubmed by inserting somes hyperlinks to connotea and it now works for the new pubmed beta.
I also added a hyperlink to http://del.icio.us.

see:

pubmed2connotea

Updated 2010-08-12 source code

// pubmed2connotea
// version 0.4 BETA!
// 2007-04-26
// Copyright (c) 2006, 2007, Pierre Lindenbaum PhD
// Released under the GPL license
// http://www.gnu.org/copyleft/gpl.html
// http://www.integragen.com
// --------------------------------------------------------------------
//
// This is a Greasemonkey user script. To install it, you need
// Greasemonkey 0.6.4 or later: http://greasemonkey.mozdev.org/
// and Firefox 1.5 : http://www.mozilla.com/
// Then restart Firefox and revisit this script.
// Under Tools, there will be a new menu item to "Install User Script".
// Accept the default configuration and install.
//
// To uninstall, go to Tools/Manage User Scripts,
// select "pubmed2connotea", and click Uninstall.
//
// 2006-07: changed for abstract-plus
// 2007-04: pubmed beta
//
// --------------------------------------------------------------------

// ==UserScript==
// @name pubmed2connotea
// @namespace http://www.integragen.com
// @description insert a shortcut link used to add an entry in http://www.connotea.org or http://www.citeulike.org/ when browsing NCBI pubmed
// @include http://www.ncbi.nlm.nih.gov/entrez/*
// @include http://www.ncbi.nlm.nih.gov/sites/*
// @include http://www.ncbi.nlm.nih.gov/pubmed/*

// ==/UserScript==



function gm_xpath(expression,contextNode)
{
return document.evaluate(expression,contextNode,null,XPathResult.ORDERED_NODE_SNAPSHOT_TYPE,null);
}

function getParameter(url,parameter)
{
if(url==null) return null;
parameter=parameter.toLowerCase();
var a= url.indexOf("?");
if(a==-1) return null;
if(url.toLowerCase().indexOf(parameter+"=")==-1) return null;
var params= url.substring(a+1).split("&");
var i=0;
for(i=0;i<params.length;i++)
{
b= params[i].indexOf("=");
if(b==-1) continue;
var key = params[i].substring(0,b).toLowerCase();
if(key!=parameter) continue;
return params[i].substring(b+1);
}
return null;
}

function hasParameter(url,key,value)
{
var s= getParameter(url,key);
return (s!=null && s.toLowerCase() == value.toLowerCase() );
}

function escapeURL(url)
{
var s="";
var i=0;

for(i=0;i< url.length;++i)
{
var c=url.charAt(i)
switch( c )
{
case ':': s+= '%3A'; break;
case '/': s+= '%2F'; break;
case '?': s+= '%3F'; break;
case '=': s+= '%3D'; break;
case '&': s+= '%26'; break;
default : s+= c; break;
}
}
return s;
}


function insertAnchors()
{

if(document.getElementsByTagName)
{
//hack found at http://erik.eae.net/archives/2005/06/10/22.21.42/#comment-5337
var inputElements = document.getElementsByTagName("input");
var i=0;
for (i=0; inputElements[i]!=null; i++)
{
inputElements[i].setAttribute("autocomplete","off");
}
}
}

var prefix="http://www.ncbi.nlm.nih.gov/pubmed/";
var allAnchors = gm_xpath("//a[@href]",document);

var i=0;
var prev=0;

for(i=0; i<allAnchors.snapshotLength; i++)
{
a = allAnchors.snapshotItem(i);
if(a.parentNode==null) continue;
var href=a.href;

var index=href.indexOf(prefix);


var list_uids="null";
if(index==-1){
var templocation=href.indexOf("IdsFromResult");
if(templocation!=-1){
list_uids=getParameter(href,"IdsFromResult");
index=0;
}
}

if(index==-1) continue;

if(href.indexOf("id=Limits")!=-1||
href.indexOf("id=Preview/Index")!=-1||
href.indexOf("id=History")!=-1||
href.indexOf("id=Clipboard")!=-1||
href.indexOf("id=Details")!=-1||
href.indexOf("filter=review&")!=-1
) continue;

if(list_uids=="null"){

qlocation=href.indexOf("?");
if(qlocation!=-1){
list_uids=href.substring(35,qlocation);//pmid starts at 35
}
}

if(list_uids!=prev){

href= "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids="+list_uids;
//href= "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids="+list_uids;
prev=list_uids;

var newanchor = document.createElement("a");
newanchor.setAttribute("title","insert into www.connotea.org");
newanchor.setAttribute("target","connotea"+i+list_uids);
//addpopup?continue=confirm
//newanchor.setAttribute("href","http://www.connotea.org/addpopup?continue=confirm&uri="+escapeURL(href)+"&button=Look%20Up");
newanchor.setAttribute("href","http://www.connotea.org/addpopup?continue=confirm&uri="+escapeURL(href));

var img = document.createElement("img");
img.setAttribute("alt","insert into www.connotea.org");
img.setAttribute("src","http://www.connotea.org/connotea_icon.png");
img.setAttribute("border","0");

newanchor.appendChild(img);
//GM_log(a.href);
a.parentNode.insertBefore(newanchor,a);
a.parentNode.insertBefore(document.createTextNode(" "),a);

//now create link for citeulike

newanchor = document.createElement("a");
newanchor.setAttribute("title","insert into www.citeulike.org");
newanchor.setAttribute("target","citeulike"+i);
newanchor.setAttribute("href","http://www.citeulike.org/posturl?url="+escapeURL(href)+"&title=Entrez%20PubMed");

img = document.createElement("img");
img.setAttribute("alt","insert into www.citeulike.org");
img.setAttribute("src","http://static.citeulike.org/img/note.gif");
img.setAttribute("border","0");

newanchor.appendChild(img);
a.parentNode.insertBefore(newanchor,a);
a.parentNode.insertBefore(document.createTextNode(" "),a);


//now create link for del.icio.us

newanchor = document.createElement("a");
newanchor.setAttribute("title","insert into del.icio.us");
newanchor.setAttribute("target","delicious"+i);
newanchor.setAttribute("href","http://del.icio.us/post?url="+escapeURL(href));

img = document.createElement("img");
img.setAttribute("alt","insert into del.icio.us");
img.setAttribute("src","http://del.icio.us/favicon.ico");
img.setAttribute("border","0");

newanchor.appendChild(img);
a.parentNode.insertBefore(newanchor,a);
a.parentNode.insertBefore(document.createTextNode(" "),a);

}
}


window.addEventListener("load", insertAnchors, false);