// Released under the GPL license
// http://www.gnu.org/copyleft/gpl.html
// --------------------------------------------------------------------
//
// ==UserScript==
// @name Quotes for Molecules
// @namespace http://wiki.cubic.uni-koeln.de/cb/inchi
// @description Adds Chemical Blogspace and PostGenomic content to InChIs
// @include *
// ==/UserScript==
// Load overlib
var p = unsafeWindow;
function waitForOverlib() {
if (typeof p.olMain=='undefined')
// set to check every 100 milliseconds if the libary has loaded
window.setTimeout(waitForOverlib, 100);
else
main();
}
function loadOverlib() {
// dynamically creates a script tag
var overlib = document.createElement('script');
overlib.type = 'text/javascript';
overlib.src = 'http://www.redbrick.dcu.ie/~noel/Tools/overlib_bubble/all_overlib.js';
document.getElementsByTagName('head')[0].appendChild(overlib);
waitForOverlib();
}
window.addEventListener('load', loadOverlib(), false);
// Finished loading overlib
function main() {
var d = new Date();
var curr_date = d.getDate();
var INCHI_list="";
var cb_stored_date= GM_getValue("chemical_blogspace_data_date", 0);
// Check for new DOIs only once per day
if (cb_stored_date != curr_date)
{
get_INCHI_list("http://wiki.cubic.uni-koeln.de/cb/api_inchi.php?type=inchi&ids_only=1", "chemical_blogspace_ID_list");
GM_setValue("chemical_blogspace_data_date", curr_date);
}
var cb_id_list = eval('(' + GM_getValue("chemical_blogspace_ID_list","{InChI:{}}") + ')'); // check this line
//GM_log("eval:" + GM_getValue("chemical_blogspace_ID_list","{InChI:{}}"));
// PubChem support
GM_log("pubchem support");
allAelems = document.getElementsByTagName('a');
for (var i = 0; i < allAelems.length; i++) {
// GM_log("a href:" + allAelems[i].href);
var reg = /\%22(InChI=1\/.*)\%22\[InChI\]/i;
var ar = reg.exec(allAelems[i].href);
var inchi_found = RegExp.$1;
if (ar && inchi_found) {
if (allAelems[i].firstChild &&
allAelems[i].firstChild.nodeName == "SUP") {
GM_log("Sechemtic created link detected... ");
} else {
GM_log("InChI: " + inchi_found);
//when a DOI is found, check if it is listed in chemical blogspace
if (cb_id_list.InChI[inchi_found])
get_citations_cb(cb_id_list.InChI[inchi_found], allAelems[i]);
}
}
}
// Sechemtic support (microformat: <span class="inchi"/> or RDFa: <span class="chem:inchi"/>)
GM_log("sechemtic support");
allSpanelems = document.getElementsByTagName('span');
for (var i = 0; i < allSpanelems.length; i++) {
// GM_log("span class:" + allSpanelems[i].className);
if (allSpanelems[i].className == "chem:inchi" || allSpanelems[i].className == "inchi") {
thisSpan = allSpanelems[i];
if (!thisSpan.firstChild) {continue;}
for (var k =0;k< thisSpan.childNodes.length;k++) {
// inchi_found = allSpanelems[i].nodeValue;
var reg = /(InChI=1\/[^\s]+)/i;
var ar = reg.exec(thisSpan.childNodes[k].nodeValue);
var inchi_found=RegExp.$1;
if (ar && inchi_found){
GM_log("InChI found: " + inchi_found);
//when a DOI is found, check if it is listed in chemical blogspace
if (cb_id_list.InChI[inchi_found])
get_citations_cb(cb_id_list.InChI[inchi_found], thisSpan);
}
}
}
}
/* var allTextareas, thisTextarea;
allTextareas = document.getElementsByTagName('*');
//For every node in the document
for (var i = 0; i < allTextareas.length; i++) {
thisTextarea = allTextareas[i];
if (!thisTextarea.firstChild){continue;}
//For every child of this node check for the presence of a DOI
for (var k =0;k< thisTextarea.childNodes.length;k++ )
{
var reg = /(InChI=1\/[^\s]+)/i;
var ar = reg.exec(thisTextarea.childNodes[k].nodeValue);
var doi_found=RegExp.$1;
if (ar && doi_found){
GM_log(thisTextarea.childNodes[k].nodeValue+": "+doi_found);
//when a DOI is found, check if it is listed in chemical blogspace
if (cb_id_list.InChI[doi_found])
get_citations_cb(cb_id_list.InChI[doi_found], thisTextarea);
}
}
}*/
}
function get_INCHI_list(myurl, variablename){
GM_log("GETTING InChI LIST");
GM_xmlhttpRequest({
method: 'GET',
url: myurl,
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 InChI List: response ok");
response_text=responseDetails.responseText;
//GM_setValue("chemical_blogspace_ID_list", response_text);
GM_setValue(variablename, response_text);
}
else GM_log("Response not ok!");
},
});
}
function get_citations_cb(doi, textarea) {
//GM_log("param: " + doi);
url = "http://wiki.cubic.uni-koeln.de/cb/api.php?type=post&citing_cbid="+doi+"&format=json";
GM_log("Starting get_citations: " + url);
GM_xmlhttpRequest({
method: 'GET',
url: url,
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){
response_text=responseDetails.responseText;
GM_log("Get InChI List: response ok: " + response_text);
insert_citations_cb( eval('(' + response_text + ')'), doi, textarea );
}
else GM_log("Response not ok!");
}
});
GM_log("Finished get citations");
}
function insert_citations_cb(obj, doi, textarea) {
var bubbletext = "";
for (var i=0; i<obj.length; i++) {
post = obj[i];
bubbletext += "<br /><a href='" + post.url + "'><b>" + post.title + "</b></a> <i>" + post.blog_name + "</i> " + post.summary + "... ";
}
newanchor = document.createElement("a");
newanchor.setAttribute("href","http://wiki.cubic.uni-koeln.de/cb/inchi.php?id="+doi);
newanchor.setAttribute("onmouseover", "return overlib('" + myescape(bubbletext) + "', STICKY, MOUSEOFF, WIDTH, 400, VAUTO, CAPTION, 'Powered by Chemical Blogspace');")
newanchor.setAttribute("onmouseout", "return nd();")
img = document.createElement("img");
img.setAttribute("alt","Comments at Chemical Blogspace");
img.setAttribute("src","http://www.redbrick.dcu.ie/~noel/Tools/overlib_bubble/logo.gif");
img.setAttribute("border","0");
newanchor.appendChild(img);
//insert the created node before the next sibling of the DOI containing node
textarea.parentNode.insertBefore(newanchor, textarea.nextSibling);
}
function hashtableToString(hashtable) { // Useful for debugging purposes
var result = "";
for (var i in hashtable) {
if (hashtable[i] != null)
result += "{" + i + "},{" + hashtable[i] + "}\n";
}
return result;
}
function myescape(text) {
var ans = text.replace(/'/g, "\\'");
// May have to also replace ( and ) with \( and \)
// May have to also replace " with &whatever;
// (see the overLIB FAQ)
return ans;
}
