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Clearing a cookie via JS and yet PHP still detects it

I'm setting a "SESSION" cookie via JS:
var d = new Date();
d.setTime(d.getTime() + (2*24*60*60*1000));
var expires = "expires="+ d.toUTCString();
document.cookie = cookie.name + "=" + cookie.value +";"+ expires + ";
path="+cookie.path+";domain="+data.shared_domain+";";
Then I'm deleting the cookie by making it expire, via JS:
document.cookie = "SESSION=; expires=Thu, 01 Jan 1971 00:00:01 UTC; path=/;domain="+domain;
After doing this, console.log(document.cookie) will return all other cookies except this one, which is what I would expect.
On the other hand, I am doing session checks via PHP, trying to read the cookie by doing $_COOKIE["SESSION"].
isset($_COOKIE["SESSION"]) will return true, and I can read the old value of the cookie. No matter how many times I refresh the page, it still reads it.
Am I misunderstanding how cookies work? Is there another way to check if a cookie has expired in PHP?
Update:
Yes, the problem is that the cookie has an HttpOnly flag.
So now I'm trying to delete it via PHP. Based on this other question, I do:
setcookie("SESSION", "", time()-3600);
if (isset($_COOKIE['SESSION'])) unset($_COOKIE['SESSION']);
When I'm done, I check that it's gone with a quick var_dump($_COOKIE), and yes, it is nowhere to be seen.
Except that Chrome still sees it (expired in 1969), and when I navigate to another part of the site, checking for that cookie will return a value.
I will add one extra piece of information, in case it makes a difference: This cookie is shared by sub.domain.com and app.sub.domain.com. When I set it, I set it for .domain.com. And I unset it for .domain.com as well.
How can I get rid of that cookie for good?

It's not clear how you're creating the cookie in the first place; I assume using PHP's session handler, but you haven't specified.
Either way, it is likely being generated with cookie security settings that limit access to it from the JavaScript. This setting is called httpOnly and is typically used on session cookies and other similar cookie data that is intended for use only by the server-side code.
If this cookie setting has been set (and any good session handler will have set it), then you simply won't be able to set or unset this cookie from the browser; you will have to do it from your PHP code.
For more info on this topic, see this wikipedia article: https://en.wikipedia.org/wiki/Secure_cookie

Cookies across sub-domains

I have two subdomains foo.example.com and bar.example.com, I am setting javascript cookies on the foo.example.com, but not able access it on bar.example.com, please suggest a way to access the cookie created on the foo.example.com on bar.example.com

In php I set a persistent cookie to do something similar, if it can be accessed from separate browsing sessions it can be accessed cross-domain i'd imagine.
I have "borrowed" this javascript from #pete because I'm not a JS expert, and barely even a novice, but I think something along these lines could work, set a cookie to expire after a year or other time period, as opposed to when browser session closes or the page has been left.
You'll need to do some messing about with it but hey, that's the fun part!
// Build the expiration date string:
var expiration_date = new Date();
var cookie_string = '';
expiration_date.setFullYear(expiration_date.getFullYear() + 1);
// Build the set-cookie string:
cookie_string = "test_cookies=true; path=/; expires=" +
expiration_date.toUTCString();
// Create or update the cookie:
document.cookie = cookie_string;

document.cookie returns only PHPSESSID=*random number*

I'm trying to get a cookie I have set but all I'm getting is the PHPSESSID.
I set my cookie in a separate PHP page with:
setcookie("username", $sentname, time()+(60*60*24*30),NULL,NULL,NULL,false);
I can then find it through firefox settings.
When I try to access it using JavaScript on a different page I use:
<script>
$(document).ready(function(){
var cookie = document.cookie;
alert(cookie);
});
</script>
which then returns:
PHPSESSID=gvjsgfd8etlbdq43lndni3o0g4
It should return all the cookies, only "username" so far, I have set in a key paired string. I tried using the jquery plugin for cookies and it returned the same thing. I also couldn't find this problem elsewhere online.

Not sure if I should delete the question but one of the related links gave me the answer.
The cookie path must be set to '/' to be accessible from all subdomains. so I changed it too:
setcookie("username", $sentname, time()+(60*60*24*30),'/',NULL,NULL,false);
which gives me:
PHPSESSID=gvjsgfd8etlbdq43lndni3o0g4; username=asdf

Reload page with javascript only one time for load cookies

I have a function that request a data for the user one time. I need reload the page after save these data in a cookie and server read these cookie, but i dont know if these cookie are defined or not. ¿How i reload only one time if i dont have a counter and dont like use parameter? the referrer dont change with reload.
I now have this methot, but i like change for remove parameters:
function getURLParameter(name) {
return decodeURIComponent((new RegExp('[?|&]' + name + '=' + '([^&;]+?)(&|#|;|$)').exec(location.search) || [, ""])[1].replace(/\+/g, '%20')) || null
}
if (getURLParameter('reload') != 'true') {
//here have function for load cookie
window.location = window.location.href + '?reload=true';
}

HTTP is a stateless protocol, which mean there is not way - within the protocol - to know the state of a request. For instance : is it the first time it's launched or the second time ?
Usual workarounds are adding a parameter to the request, as you suggests or using a cookie on the browser's side. This is how sessions are implemented in platforms like Java EE or PHP.
Why don't you test for another cookie like 'never been reloaded', if it does not exists : create this cookie and reload the page.
The tricky part is when should you delete the cookie, ie : when does your business logic wants you to reload the page again ? That's up to you to decide.

PHP: Reading a cookie set with Javascript

Using Javascript & Jquery, I'm creating a cookie on a click event, and then redirecting the user to another page. I'm doing that like this:
<script type="text/javascript">
$(".my-div").click(function() {
document.cookie ="answers=:" + myAnswers + "; path=/; domain=.mydomain.com;";
setTimeout("location.href = '/my-destination-page.php/';", 5000);
});
</script>
When I reach my-destination-page.php, I can see the cookie is set correctly in Google Developer Tools. However, PHP doesn't detect that it's set:
<?php
var_dump($_COOKIE['answers']);
?>
The above returns a big fat NULL.
Any ideas why this is happening?

try to change,
document.cookie ="answers=:" + myAnswers + "; path=/; domain=.mydomain.com;";
to
document.cookie ="answers=:" + myAnswers + "; expires=Thu, 12 Aug 2015 20:47:11 UTC;path=/; domain=.mydomain.com;";
and check

I didn't test your specific code -- but I know building raw cookie strings manually is a finicky, error prone thing. If you get something wrong the cookie processing code on the server (won't recognize your cookies).
Since you're already using jQuery, I'd try using the jQuery cookie plugin. Even if you don't want to deploy with this plugin, you can use it to set your cookie, examine the request headers, and determine where your cookie string is incorrect (or determine that your cookie strings is correct, and that your problem lies elsewhere)