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In a browser environment, is it possible to obtain list of SSL certificates in JavaScript?

In order to connect to a third party application, I have to give my users the capability to select one of their installed SSL client certificates and transfer it to the third party which is used by the application server. (My web application does not require SSL, it is the third party that require SSL certificates).
It seems to me that access to this list of certificates is only possible by the browser itself when connecting to a service that require SSL. Is it possible to launch the same dialog box through Javascript or is there any way for a web application to browse the SSL store of the end-user ?
If it is not possible, can I simply open a file dialog box and upload the client certificate as any standard file ?
I have to support any browser from IE9 and no plug-ins are allowed in our application.
Thanks.

If it is not possible, can I simply open a file dialog box and upload the client certificate as any standard file ?
Firstly, that's not the way SSL/TLS client authentication works at all. It's simply not a matter of uploading the certificate. The private key matching the certificate is used to sign some content (in the CertificateVerify TLS message) during the TLS handshake. That's what performs the authentication.
Coming back to your main question, for security reasons, the SSL/TLS stack is handled outside the scope of the JavaScript code. Selecting the client certificate is part of that.
You could potentially have some sort of API to let the JavaScript code access some of the cryptographic features of the browser (and there has been work in this area). However, there would be security considerations to take into account.
Even if certificates only contain public information to some extent, that doesn't mean it's public information that is to be distributed to anyone in the world, at least not necessarily in conjunction with the act of browsing any website.
If you had the ability to list the user's list of certificate from the JavaScript code sent by your server, you'd certainly have the ability to send that list back to yourself almost transparently with an Ajax call. While some people are concerned about the privacy implications of being tracked by cookies, being tracked by which client certs you may have takes this to another level (e.g. Subject DN with CN=John Smith and Issuer DN with CN=Department/Ministry of Health/Defence: that would be a bit of a giveaway).
My web application does not require SSL, it is the third party that require SSL certificates.
Here, you're not saying whether that third party is accessed directly by the user's browsers, or if you expect the users to delegate their credentials for you to interact with that third party (without direct user involvement).
If the users have direct access to that third party (via another request), their browser should prompt them for the certificate they with to use.
If it's about credential delegations, that's another problem entirely, since users you never give you the private key for their own client certificate to be able to sign in their name. (It's might be technically possible for users to just give you their PKCS#12 file, for example, but it defeats the point of putting up in place this sort of authentication in the first place).
There has been work done about authentication delegation with certificates using proxy certificates (RFC 3820). Essentially, your EEC (End-Entity Certificate) is used as a mini-CA, despite not having the CA flags, to issue a short-lived certificate with the remote party will accept. This sort of mechanism is generally not well integrated in browsers.
Another, more realistic approach, would be to look into the world of SSO, SAML and Shibboleth, for example. That does work with existing browsers, but the overall architecture is a bit different (so you'll need to discuss that with the third party).

The certificate isn't part of the DOM, so no, this won't be possible.

In a browser environment, is it possible to obtain list of SSL certificates in JavaScript?
The WebCrypto API allows you to discover some things, like shared and derived keys. But looking at their charter and use cases, its not clear to me if they allow enumeration and discovery of certificates.
I see it was discussed in the past and an issue was raised. Here's the discussion: Crypto-ISSUE-15: Discovering certificates associated with (private) keys. But I can't find anything on Issue 15 in the WebCrypto Tracker.
Also see Will the WebCrypto API allow discovery/enumeration of certificates? question on the WebCrypto Mailing list. Hopefully there will be a simple, YES/NO answer.
But don't be surprised if its not available through WebCrypto. The browser security engineers have a particular way of looking at things, and that usually does not include client certificates. Client certificates would effectively stop MitM attacks (see, for example, Origin Bound Certificates), and browsers don't make stopping MitM a priority. Instead, they are OK with mishandling credentials like passwords; and they opt for a One Time Password (OTP) using U2F.
In a reality stranger than fiction, the browsers will even (1) use Public Key Pinning for HTTP, and then (2) break a known good pinset because the user was phished! You can't make this stuff up...

How to verify that ssl was not intercepted via proxy etc in browser?

Recently I installed fiddler and it did allow me to view (decrypt) my Ssl requests from any browser.
Although its not legal, some firewalls also allow installing some root certificates and then firewall can monitor and track https protocol.
We provide sensitive information via ssl and how check and prevent such interception via proxy or fiddler kind of tool.
Is there any JavaScript API? There should be something, that I can check on page load.
$( function() {
if(!isSSLValid())
{
alert('Your traffic is monitored...');
location.href = '/SSLInstructions.html';
}
});
Think of it as mobile or tab browser where in iOS there is no way to view certificate, just an icon.

(This is quite similar to this question on Security.SE.)
As a client, you can verify that your SSL/TLS connection was not intercepted by a MITM proxy (Fiddler or other) by checking its certificate. That's the entire purpose of having certificates to authenticate servers.
You were only able to allow Fiddler to look at the traffic because you chose to validate its certificate. Similarly, MITM proxy servers (mostly used in corporate environments) need to install their CA certificate on the client machines. In environment where this happens, the clients are not really in control of the machine they use anyway: they delegate their administration to whoever controls that proxy.
It's ultimately the sole responsibility of the client to check that (a) SSL/TLS is used and (b) it is used correctly (with a certificate they can trust for the machine they intended to communicate with in the first place). (See this longer explanation on Webmasters.SE for more details.)
How to verify that ssl was not intercepted via proxy etc in browser?
Tell your users not to ignore warnings. If there's a corporate proxy with matching CA certificates installed on their machines, they could in principle look at the details of the certificate. If they don't trust the machine they're using for this, they should use their own, from a network that allows them not to be intercepted.
Mobile devices are indeed quite poor for checking those details unfortunately, but as a server there's not much you can do.
One way to check whether the client received the same server certificate as the one the server sent is to require client-certificate authentication, which will make the client sign the handshake (including the server cert) with its own private key, so the server can check if the signature matches what it expects. This requires a bit more infrastructure to deal with client-certificates (and you'd need to show your users how to use them).
EDIT: About your comment.
That's flaw in ssl that we have no way to check if anyone is watching
or not, and it defetes whole purpose of it.
Not really, it's ultimately always the responsibility of the user to check what/who it's talking to, even in real life situation. If you fill the right forms to vote by proxy and delegate this voting power to someone, or if you give your ID and delivery slip to someone to pick up a parcel for you from the post office, it's up to you to make sure that you trust that person. If you give your bank passwords to someone and they phone your bank for you, your bank has no way of telling whether it's you or not: as far as it's concerned you're identified by these credentials.
Only the user is in a position to check that it's talking to the right server: if not, the legitimate server isn't in contact with the user, so it simply can't give any warning that something wrong is happening.
You simply will never be able to force the users to talk to the right server from your server, because you don't control what they do. They could give their passwords to anyone they want, you wouldn't know. (You can teach them not to do so, at best.)
What you can do is to prevent your server to give data to someone who isn't your user. Following the real-life analogies, this can be done by using mechanisms where you insist on the person to be present (you don't allow someone to act for someone else, even if they turn up with the other person's ID). This can be done with SSL/TLS when using client-certificates: only the holder of the private key can be authenticated, no intermediate party. (Of course, from a practical point of view, users would have to make sure they don't give their private keys.)

Checking if a security exception has been accepted by the client

We have a few staging environments for internal testing/dev that do not use "real" SSL certs. Honestly I'm a bit fuzzy on the details, but the bottom line is when accessing a subdomain on those environments, browser would prompt you to add a security exception along the lines of "You have asked Firefox to connect securely to example.com but we can't confirm that your connection is secure":
Could this be detected e.g. by making a request to the url in question and processing the error code/any other relevant information it may come back with? I could not find any specifications to indicate how this is being handled by the browser.
Edit:
I don't mind the error occurring on the landing page itself, it's pretty clear to the user. However some requests fail like this in the background (pulling css/js/other static content from different subdomains) but you don't know they do unless you go to net panel in firebug and open it in new tab and see the error...
The intention is not to circumvent this but rather to detect the issue and say something like "hey, these requests are failing, you can add security exceptions by going to these urls directly: [bunch of links]"

Checking the validity of the certificate is solely the responsibility of the client. Only it can know that it has to use HTTPS, and that it has to use it against a certificate that's valid for that host.
If the users don't make these checks and therefore put themselves in a position where a MITM attack could take place, you wouldn't necessarily be able to know about it. An active MITM attacker could answer perform the tasks you use to try to check the users are doing things correctly, but the legitimate users might not even get to know about it. This is quite similar to wanting to use redirections from http:// to https://: it works as long as there is no active MITM attack downgrading the connection.
(There is an exception to this, to make sure the client has seen the same handshake as you: when using client certificates. In this case, you would at least know that the client that ha authenticated with a cert would have seen your server cert and not a MITM cert, because of the signature at the end of the handshake. This is not really what you're looking for, though.)
JavaScript mechanisms generally won't let you check the certificate themselves. This being said, XHR requests to untrusted websites (with such warnings) will fail one way or another (generally via an exception): this could be a way to detect whether other pages than the landing page have are accessible by background requests (although you will certainly run into issues regarding Same Origin Policies).
Rather than using self-signed certificates for testing/development, you would be in a much better position if you deployed a test Certification Authority (CA). There are a number of tools to help you do this (which one to use would depend on the number of certificates you need). You would then have to import your own CA certificate into these browsers (or other clients), but the overall testing would be more realistic.

No.
That acceptance (or denial) only modifies a behavior in the client's browser (each browser, in a different way). It ACKs nothing to the server and the page is not yet loaded, therefore, there is no chance to catch that event.

Self-signed certs -- helping users know they need to add root CA to trusted cert store

I have a desktop product which uses an embedded webserver which will use self-signed certs.
Is there something that I can put in a web page that would detect that they haven't added the root CA to their trusted list, and display a link or DIV or something directing them how to do it?
I'm thinking maybe a DIV that has instructions on install the CA, and a Javascript that runs some test (tries to access something without internal warnings??), and hides the DIV if the test succeeds. Or something like that...
Any ideas from the brilliant SO community ? :)

Why do you want to do this? It is a bad idea to train users to indiscriminately install root CA certificates just because a web site tells them to. You are undermining the entire chain of trust. A security conscious user would ignore your advice to install the certificate, and might conclude that you are not taking security seriously since you did not bother to acquire a certificate from an existing CA.
Do you really need HTTPS? If so, you should probably bite the bullet and make a deal with a CA to facilitate providing your customers with proper CA signed server certificates. If the web server is only used for local connections from the desktop app, you should either add the self-signed certificate to the trusted list as part of the installation process, or switch to HTTP instead.

Assuming you know C# and you want to install a pfx file.Create a exe that will be run from a url.Follow this URL
and this

The only idea I have is to use frames and some javascript.
The first element of the frame will act as a watchdog waiting x amount of time (javascript setTimeout) before showing your custom ssl failure message to the user with hyperlinks or instructions to download the self-signed cert.
The second frame element attempts the https connection and if successful resets the watchdog frame so that it never fires. If it fails (assume https cert validation failed) the watchdog message would then fire and be presented to the user.
Depending on your browser you will most likely still see some security warning with the approach but you would at least be able to push your own content without requiring users to run untrusted code with no proper trust chain (This would be much much worse from a security POV than accepting the cert validation errors and establishing an untrusted ssl session)
Improvements to the concept may be possible using other testing methods such as XMLHttpRequest et al.

You should not do this. Root certificates are not something you just install, since adding one could compromise any security given to you by https.
However if you are making a desktop app then just only listen to 127.0.0.1. That way the traffic never leaves the users computer and no attacker can listen in.

You might try to add some (hidden) Flex element or Java Applet once per user session.
It will just download any https page of your server and will get all information about connection:
com.sun.deploy.security.CertificateHostnameVerifier.verify()
or
javax.security.cert.X509Certificate.checkValidity()
I suppose Flex (which is more common to users) shoul have similar ways of validating https certificate from user's point of view. It should also share OS' trusted cert. store while Java might have its own.

Since the server is running on the client machine (desktop product) can it not check the supported browsers for installed certs using winapi/os functions? I know Firefox has a cert database in the user's profile directory and IE probably keeps information in the registry. It wouldn't be reliable for all browsers but if the server simply chooses between "Certificate Found" and "Please ensure you have installed the cert before continuing" then no harm is done as the user can choose to continue either way.
You could also simplify matters by providing an embedded browser as well (ie, gecko), this way you only have 1 browser to deal with which simplifies a lot of things (including pre-installing the root CA).

To recap: you are setting up webservers on desktop apps; each desktop will have its own webserver, but you want to use SSL to secure the connection to that webserver.
I guess there are several problems here with certificates, one being that the hostname used to access the desktop has to match the certificate. In this case you have little choice but to generate certificates on the client. You'll need to allow the user some way to specify the host name in case the name used by outsiders can't be detected from the host itself.
I'd also suggest allowing for an admin to install a trusted cert, for those who don't want to rely on self-signed certs. This way you can also offload the cost of trusted cert maintenance to the admins who really want it.
Finally, in my experience browsers either allow or refuse the self-signed cert and there is no way for the server to know if the cert is denied, or temporarily accepted, or permanently accepted. I assume there must be a mechanism somewhere to handle SSL failures but typical web programming doesn't operate at that layer. In any case, the only thing a webserver can do if SSL fails is to fallback to non-SSL, and you've indicated in a comment that you can't have anything non-SSL. I think you should try to have that restriction lifted; a non-SSL start page would be extremely helpful in this situation: it can test (using frames or images or JSON or AJAX) the https connection, and it can link to documentation about how to set up the certificate, or where to download an installer for the cert.
If the browser won't connect because of a self-signed cert, and you're not allowed to use plain HTTP at all, by what other means could you communicate with the user? There are no other channels and you can't establish one because you don't have any communication.
You mentioned in a comment writing a win32 app for installing the cert. You could install a cert at the time you install the application itself, but that doesn't help any remote browsers, and a local browser doesn't need SSL to access localhost.

We've been working on an opensource JavaScript project, called Forge, that's related to this problem. Do you have a website that your users could access? If so, then you could provide a secure connection to those desktop apps via your website using a combination of Flash for cross-domain + JavaScript for TLS. It will require you to implement some web services on your website to handle signing certificates the desktop app certificates (or having your desktop apps upload the self-signed certs so they can be accessed via JavaScript). We describe how it works here:
http://blog.digitalbazaar.com/2010/07/20/javascript-tls-1/
An alternative to setting up a website, but is less secure because it allows for a MiTM attack is to host the JavaScript+Flash directly on the desktop app server. You could have your users hit your desktop app over regular http to download the JS+Flash+SSL cert, but then start using TLS afterwards via the JS. If you're on a localhost connection the MiTM attack might be a little less worrisome -- perhaps enough for you to consider this option.

An ActiveX control could do the trick. But I really didn't chime in to help with the solution, more to disagree with the stance that what you are doing is a security risk.
To be clear, you are needing a secure cipher (hopefully AES and not DES), and are already in control of your endpoints, just not able to completely rule out promiscuous-mode network sniffers that could catch clear-text passwords or other sensitive data.
SSL is a "Secure Socket Layer", and by definition, is NOT dependent upon ANY certificates.
However, all effective modern ciphers require it to authenticate the tunnel endpoints, which is not always a necessity for every application; a frustration I have dealt with in numerous back-end datacenter automation routines using web service APIs to manage nodes, where the "users" were actually processes that needed encrypted key exchange prior to a RESTful command negotiation.
In my case, the VLANs were secured via ACLs, so I really "could" send clear-text authentication headers. But just typing that made me throw up in my mouth a little bit.
I'm sure I'll get flamed for typing this, but I'm extremely battle-hardened and would've made the same comments to you in years 10-15 of my IT career. So I empathize with their worries, and very much appreciate if they are passionate enough about security to flame me. They'll figure it out eventually.....
But I do agree with the fact that it is a BAD idea to "train" users to install root CA's on their own. On the other hand, if you use a self-signed cert, you have to train them to install that. And if a user doesn't know how to determine if a CA Cert is trustworthy, they definitely won't be able to determine a self-signed cert from a CA Cert, and thus either process would have the same effect.
If it were me, I would automate the process instead of having it assist the end-users, so that it becomes as hidden from them as possible, just like a proper PKI would do for an enterprise.
Speaking of which, I just thought of a potential solution. Use the Microsoft PKI Model. With Server 2012 R2, you can deliver trusted keys to endpoints that are not even domain members using "device control" via "workspaces", and the client machines can subscribe to multiple workspaces, so they are not committed solely to yours if they subscribe. Once they do, and authenticate, the AD Certificate Services Role will push all root CA Certs necessary, as are present in active directory, or specified LDAP server. (In case you are using offline CA servers)
Also, I realize this thread is like 7 years old, but am sure it still gets referenced by a good number of people needing similar solutions, and felt obligated to share a contrasting opinion. (Ok Microsoft, where's my kickback for the plug I gave you?)
-cashman

how to prevent JS hijacking in public computers

This problem is regarding a JS hijacking scenario, and here it is :
Say Mr. Good has a website called "iamtooinnocent.com" which loads a "x.js" file to perform some particular tasks, and Mr. Bad is an evil cyber cafe owner, who has set a redirect rule in place that whenever any surfer using his cyber cafe visits Good's website then when the "x.js" file will be requested it will simply redirect it to some other evil domain which serves say a different "x.js" file with evil code in it, this way Good's website will never come to know that it has got a different JS file than what it has requested.
I hope I have explained the scenario properly, so my problem is how can this be prevented? Is there really a way to prevent this? Can this be prevented by serving the JS file using HTTPS, though I am not so sure? Can anybody give me some heads up regarding this?
Thanks in advance.

HTTPS is standard for fighting man-in-the-middle attacks like one you've described. It encrypts all traffic using public certificate of your site. So it's not possible to change it. And the certificate itself is verified by third party certificate authorities.
But it can't guarantee 100% security because it's possible to create a local fake certificate authorities available only in cafe.

If the computer owner is against you....you will have a hard time. The browser guarantees certain security rules, but the computer owner can modify it to his evil heart's content and you would be none the wiser...

Rule #1 in web security boils down to: NEVER trust the client.
Remember that clients can do just about anything with the data you are sending them, and the data they send YOU:
modify cookies for subsequent requests
alter or add/remove other HTTP headers, spoof User Agents
Specify any combination of data in GET/POST
You should assume any data coming IN from HTTP to your application is a malicious, tained, evil mess, and sanitize accordingly.

Is this the sort of cyber cafe where they provide the computers? If so, you just have to trust the owner, because you can't have security on somebody else's machine. If nothing else, they can install a hardware keylogger.
If this is the sort where they provide a wireless connection and you bring your laptop, HTTPS should be a safeguard. If your browser handles certificates and SSL properly, it should be possible to go to a site that has a verified certificate and be safe. If there's any problems in your browser, of course, the cyber cafe owner is in an ideal position to take advantage of it, so you might want to keep an eye on known vulnerabilities.
The best move is not to patronize cyber cafes run by evil owners, but that can be difficult in some parts of the world.