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Missing quotes here:

if(href.indexOf(read_today) != -1) 

Should be:

if(href.indexOf('read_today') != -1) 

Also change:

link.setAttribute('onclick', 'alert("Okay")');

To:

link.setAttribute('onclick', function(){ alert("Okay") });

Overall, this is what you should have:

var ourdomainname = "ourdomain.com";
function linkallthelinks(domain) {
 var links = document.getElementsByTagName("a");
 for (var i = 0; i < links.length; i++) {
 var link = links[i];
 var href = link.getAttribute("href");
 if (href.indexOf('read_today') != -1) {
 link.setAttribute('onclick', function(){ alert("Okay") });
 }
 }
}
//function call
linkallthelinks(ourdomainname);​

Missing quotes here:

if(href.indexOf(read_today) != -1) 

Should be:

if(href.indexOf('read_today') != -1) 

Overall, this is what you should have:

var ourdomainname = "ourdomain.com";
function linkallthelinks(domain) {
 var links = document.getElementsByTagName("a");
 for (var i = 0; i < links.length; i++) {
 var link = links[i];
 var href = link.getAttribute("href");
 if (href.indexOf('read_today') != -1) {
 link.setAttribute('onclick', 'alert("Okay")');
 }
 }
}
//function call
linkallthelinks(ourdomainname);​

Missing quotes here:

if(href.indexOf(read_today) != -1) 

Should be:

if(href.indexOf('read_today') != -1) 

Also change:

link.setAttribute('onclick', 'alert("Okay")');

To:

link.setAttribute('onclick', function(){ alert("Okay") });

Missing quotes here:

if(href.indexOf(read_today) != -1) 

Should be:

if(href.indexOf('read_today') != -1) 

Also change:

link.setAttribute('onclick', 'alert("Okay")');

To:

link.setAttribute('onclick', function(){ alert("Okay") });

Overall, this is what you should have:

var ourdomainname = "ourdomain.com";
function linkallthelinks(domain) {
 var links = document.getElementsByTagName("a");
 for (var i = 0; i < links.length; i++) {
 var link = links[i];
 var href = link.getAttribute("href");
 if (href.indexOf('read_today') != -1) {
 link.setAttribute('onclick', function(){ alert("Okay") });
 }
 }
}
//function call
linkallthelinks(ourdomainname);​

Missing quotes here:

if(href.indexOf(read_today) != -1) 

Should be:

if(href.indexOf('read_today') != -1) 

Also change:

link.setAttribute('onclick', 'alert("Okay")');

To:

link.setAttribute('onclick', 'function(){ alert("Okay") }');

Missing quotes here:

if(href.indexOf(read_today) != -1) 

Should be:

if(href.indexOf('read_today') != -1) 

Also change:

link.setAttribute('onclick', 'alert("Okay")');

To:

link.setAttribute('onclick', function(){ alert("Okay") });