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Javascript not getting loaded

I added a custom jquery function to my wordpress site. The code was to open a popup window on every alternative clicks. This doesn't work if I add to my wordpress theme header.php
This is what I added <script src="/alternateclicks.js"></script>
The js file was added to the wordpress root location public_html. I don't see any popup whatsoever.
jQuery(document).ready(function( $ ){
var canClick = 2;
$("body").click(function () {
if (canClick%2==0) {
window.open("https://example.com/").blur();
window.focus();
canClick = canClick+1;
}
else {
canClick=canClick+1;}
});
});
The solutions I tried, I tried adding the code to footer.php. Didn't work. I added them using wp_enqueue. Didn't work.
UPDATE
In console am seeing that jquery is not defined. But I added the code only in footer.

Seems like, a Plugin interfered with my loading. The plugin disabled jquery.
Found that the code worked in some pages and didn't work in some pages.
Found out using the console.
Then later when disabling the plugin perfmatters, jquery worked fine.

How do I call a LightBox on a click action?

Please bear with me but I was giving some code to launch a lighbox. I need to display a lightbox when a user clicks on my link. The lightbox coded is in place already and is launched using a unique id. My example below uses (1111)
<script src="bootstrap.js" type="text/javascript"></script>
<script type="text/javascript">
lightbox = new fusepump.lightbox.buynow(1111);
var callToActionElement = document.getElementById( "unique-btn");
callToActionElement.addEventListener("click", function()
{ lightbox.show(); //Show the lightbox } );
</script>
My link code is:
Buy
For some reason it's not working. I think that the syntax is wrong.

EDIT: you commented out the last part of your code //Show the lightbox } );
The brackets never get closed and the semicolon won't be at the end of your code but in the comment. Make the comment like this /*Show the lightbox*/
You can also set an onClick attribute in which you can call the function name of your javascript function. It will look like this:
Buy

Auto Loading HTML in a Div with Javascript

I'm looking to use this code in JS Fiddle http://jsfiddle.net/syE7s/ to load some content into a div.
It's exactly what I need but I want link A to auto load when the page loads. My knowledge of Javascript is fairly minimal so if someone could get it working in jsfiddle I would be very greatful.
I've tried googling everything but I just can't seem to make it work.
It is essential I use the HTML as the links I use parse tokens that use {} to identify them as tokens but it obviously gets confused with Javascript when they are sat together.
enter code here
thanks

Here is a working JS Fiddle, I added a function to load the first link :
function launch() {
var link = $('#A').attr("href");
$('#target').load(link);
}
launch();
http://jsfiddle.net/dhmLjme6/

You can add just one line to your javascript.
It will look like this (line 3):
$(document).ready(function(){
$('#target').load($('.trigger').attr("href"));
$('.trigger').click(function(e){
e.preventDefault();
var link = $(this).attr("href");
$('#target').load(link);
});
});

Link + on(pagecontainershow) fail

I have a simple app done with jQuery Mobile, in some point I have this:
Start!
which loads a new HTML with a lot of jquery mobile pages:
<div data-role="page">
I have defined, in my external JS file, an global variable:
var startTimeQuestion;
And this method, which is inside my HTML (test_es.html):
<script>
$(document).on('pagecontainershow', function() {
console.log("Storing time..");
startTimeQuestion = new Date().getTime();
});
</script>
The problem is that when I click on the button it loads correctly the file but it seems like it don't load the JS or the function or I don't know, because when I'm going to use my startTimeQuestion variable it says UNDEFINED and it don't show in the console the 'Storing time..'. If a reload the page, it works fine.
I have tried to do an '$.(document).ready()' function for the first time I load the page but still not working. It looks like test_es.html it isn't loading my custom.css and my test.js file until I reload completely the page. So I supposed that the error is in how I call my test_es.html, it isn't this:
Start!
the correct way to do it?
Thanks.

Thanks to the comment before I found the solution, it was as simple as put the 'data-ajax' attribute to false this way:
Start!

How to make this grid work

I purchased a html5 theme that I am customizing for my church website. It has two cool features:
A tab script that allows for multiple items to displayed on one page.
a grid that will allow me to display sermons in a series in a neat and orderly way.
Both of these work well when used alone, but when I try to use the grid inside the tabs, no dice.
I am a design guy and know very little about Javascript functions and need help. Here is what the developer, who has not got back with me said to do:
"The grid function is built to run on page load and when you put it inside a tab it doesn’t initialize on page load so don’t work when you change tabs. A custom function needs to be built for this which will run the isotope grid on tabs change. Like:"
$(".nav-tabs li")click(function(e){
ADORE.IsoTope();
e.preventDefault();
}
I do not know where to add this or even if something else needs to be added. I have also attached a link where you can download my code (html/php and .js file) so you can see what is going on. Any help would be appreciated. Remember, I know very little about Javascript.
https://www.dropbox.com/s/jypfjz3a89soxh7/example.zip?dl=0

Add:
$(".nav-tabs li a").click(function(e){
$('a[href="' + $(this).attr('href') + '"]').tab('show');
var IsoTopeCont = $(".isotope-grid");
IsoTopeCont.isotope({
itemSelector: ".grid-item",
layoutMode: 'sloppyMasonry'
});
});
at Line 469 of your init.js and it should work for you. Thanks

You can try the following: inside your init.js add the following:
$(".nav-tabs li").click(function(e){
e.preventDefault();
ADORE.IsoTope();
});
e.g. in the first line after var ADORE = window.ADORE || {};
As you mentioned that you don't know much about javascript: the first line starts with
jQuery(function($){ ...
This takes care about that everything inside the { will get executed when jQuery is loaded.
I'm not sure if the e.preventDefault(); is necessary - this is used e.g. to prevent links from getting executed and attach a different function to the click() event, so it could be possible that Isotope is working when a tab is clicked, but the tab is not working anymore.
If this won't work, you can check with web dev tools if there are any script errors. In case you're unfamiliar with web dev tools, find some details for Firefox here: https://developer.mozilla.org/en-US/docs/Tools/Web_Console and for Chrome here: https://developer.chrome.com/devtools/docs/console