/*
Adding Postgenomic comments to Connotea 

Based very heavily on Pedro's script at http://wiki.nodalpoint.org/projects_postgenomic

There's almost certainly a much better way to do this using the Postgenomic API, JSON and a callback function:

http://www.postgenomic.com/api.php?type=paper&format=json&ids_only=1

However, as a proof of concept this'll do!

*/

// ==UserScript==
// @name			Connotea / Postgenomic mashup
// @namespace		http://www.postgenomic.com/userscripts
// @description		Papers that are in the Postgenomic index get a wee link next to them in Connotea.
// @include			http://www.connotea.org*
// ==/UserScript==

var d = new Date();
var curr_date = d.getDate();
var stored_date=0;
var DOI_list="";
var stored_date= GM_getValue("postgenomics_data_date", 0);
// Check for new DOIs in Postgenomic only once per day
if (stored_date != curr_date)
{
	get_DOI_list();
	GM_setValue("postgenomics_data_date", curr_date);
}
var test_list = GM_getValue("postgenomics_DOI_list",0);

GM_log("Starting Postgenomic / Connotea mashup : DOI list is " + test_list.length + " chars long.");

var allLinks, thisLink;
allLinks = document.evaluate(
	"//a[@class='dblink']",
    document,
    null,
    XPathResult.UNORDERED_NODE_SNAPSHOT_TYPE,
    null);
for (var i = 0; i < allLinks.snapshotLength; i++) {
    thisLink = allLinks.snapshotItem(i);
    // do something with thisLink
	GM_log("Found a DB link " + thisLink.textContent);
	
	// strip out the "DOI:" or "PMID:" bits of the text
	var reg = /(?:.*?):(?:\s*)(.+)/i;
	var ar = reg.exec(thisLink.textContent);
	var doi_found = RegExp.$1;
	
	if (ar && doi_found) {
		var reg = new RegExp(doi_found, "i");
		if (reg.exec(test_list)) {	

			newanchor = document.createElement("a");
			newanchor.setAttribute("title","Comments from Postgenomic");
			newanchor.setAttribute("href","http://postgenomic.com/paper.php?doi=" + doi_found);
			//var linkText = document.createTextNode("pg");
			//newanchor.appendChild(linkText);

			img = document.createElement("img");
			img.setAttribute("alt","Comments at Postgenomic");
			img.setAttribute("src","http://www.postgenomic.com/images/comments.png");
			img.setAttribute("border","0");
			newanchor.appendChild(img);	

			thisLink.parentNode.insertBefore(newanchor, thisLink.nextSibling);
		}
	}
}

function get_DOI_list(){
	GM_log("GETTING DOI LIST");
	GM_xmlhttpRequest({
		method: 'GET',
		url: "http://www.postgenomic.com/api.php?type=paper&ids_only=1&format=text",
		headers: {
			'User-agent': 'Mozilla/4.0 (compatible) Greasemonkey',
			'Accept': 'application/xml,text/html',
		},
		onload: function(responseDetails) {
			var response_status=responseDetails.status;
			var response_text=null;
			if (response_status==200){
				GM_log("Get Doi List: response ok");
				response_text=responseDetails.responseText;
			}
			var count_doi=0;
			var reg_test = /(10\.[0-9\.]+\/\S+)\s/ig;
			while (reg_test.exec(response_text))
			{
				count_doi++;
				//The DOIs are kept in a simple string
				DOI_list=DOI_list+";"+RegExp.$1;
			}
//			GM_log("LIST:"+DOI_list);
//			GM_log(count_doi);
			GM_setValue("postgenomics_DOI_list", DOI_list);
 
		}
	});
}