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Get rid of Signed Java Applet Security Dialog

this might be a ridiculous question.
I have a signed applet which only read and write on the client's computer file system.
I can purchase a digital certificate from the Well known authority like Verysign or Thawte etc. to sign the applet.
If i sign applet using above mentioned authority can i get rid of this ambiguous Security verification held by Java Plug-in ?
someone says in SO that you can configure policy file and you can get
rid of this. may i know how ?
Thanks

The best way to get rid of the dialog is to import the certificate into the JRE trusted certificate store. Another solution is to modify the Java policy file.
Just have a look into Oracle's documentation: http://docs.oracle.com/javase/7/docs/webnotes/tsg/TSG-Desktop/html/plugin.html#gcexdl

Professionally sign an applet

I've made a Java applet and I self signed it before, but due to security changes in recent Java updates, self signing no longer gives the applet the necessary permissions.
I need the applet to be able to read the local file system to use images and to be able to connect to a MYSQL database.
The applet used to work with the database when I self signed it, but not anymore.
In addition, many unknown users will be using the applet, so I won't have control over their machines.
Where can I get my applet professionally signed and if possible, is there another way to self sign that will make the applet work?

Purchase a certificate from any reputable certificate authority. Use that to sign your code. List of CAs
Or, some companies also do this: Sign the jars themselves, but pre-populate the JDK trust store with your (self created) CA cert. If you have control over the JRE that is installed on all user machines, you can place your certificate in JRE/lib/security/cacerts so that is trusted ahead of time.
update: This page (Java Control Panel Documentation) describes what type of signature is required for various client side security level settings:

As long as the applet 'phones home' to the DB & this demo. of the JNLP API file services1 works for the problem machines you should be set to go for a Plug-In 2 JRE (1.6.0_10+) JRE. And if the client has less than that, they should seriously look to update. The Deployment Toolkit Script can assist with that.
It is relevant in that:
It uses a self signed certificate
It allows a sand-boxed app. to read/write to the local file system.
An applet launched using JWS has access to the API.
This should only be considered a work-around. The correct way to solve the problem is to heed the advice offered to get a certified code certificate. Oracle seems to be heading towards making it so that unsigned or self-signed code will not just be sand-boxed, but entirely forbidden (& that is for the best).
As an aside re. DB access: For the protection of the DB. The applet should be forced to go through a 'public interface' (via the site that hosts the applet). Do not give the applet direct access to the DB. Otherwise hackers also have direct DB access.

A straight forward way to open self-signed HTTPS SSL URLs in java?

I'm building an application that needs to open self-signed HTTPS SSL URLs in java. I've learned that you can bypass the SSL problems by adding a call to HttpsURLConnection.setDefaultHostnameVerifier() where you say what hostnames are allowed.
However, I have a second problem where my servers are running self-signed certs. So even with the hostname bypass I'm getting exceptions like:
javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
I've looked around and the only solutions I've found is to add the certificate to the java key store, but this is a problem for me because I have no control over when or how they update java, and I've read that the keystore isn't preserved between updates, and I have no access to the system outside of the JVM.
My application will only make calls to a single server so if there was a way to bypass the self-signed restrictions, and never consult keystores, it wouldn't be a security problem, but is there a way to do this?

I'm building an application that needs to open self-signed HTTPS SSL
URLs in java. I've learned that you can bypass the SSL problems by
adding a call to HttpsURLConnection.setDefaultHostnameVerifier() where
you say what hostnames are allowed.
There are some misconceptions from your question:
Hostname verification is unrelated to whether the certificate is self-signed or not.
It is a verification that matches the domain you are trying to access with the certificate info (CN or Subject Alt Name).
You would need to configure the verifier if you needed to accept a certificate that did not match the url (not recommended at all!!!)
Concerning the self-signed.
This is irrelevant.
You can configure your application to load your custom truststore which would include the certificate your application will trust. In fact this is the best approach (than using Java's cacerts).
All you have to do is import the certificate in a keystore (JKS or PKCS12) and load it in your custom TrustManagers in your application.
Just google arround, plenty of examples E.g. self-signed-ssl

As much as I hate to say this, sometimes it's better to just go with the flow.
Java is attempting to make applications more secure through the use of proper SSL verification practices. In this case, it is succeeding: had you been able to tell the program "it's okay, accept the untrusted self-signed certificate", your program would have been vulnerable to a man-in-the-middle attack where Mallory puts his server (with its own self-signed certificate, just as valid as yours!) in between the host and the target it's attempting to communicate with. Then he proceeds to read all the traffic you thought was nice and safe, and you don't even notice.
So, your assertion that telling Java to "trust any self-signed certificate when connecting to this host" is secure is, regrettably, not correct.
You can get free, totally valid SSL certificates from StartSSL. They're good folks.

That's how PKI is supposed to work - you must have complete chain of trust from some trusted certificate stored in you keystore to your certificate. So you can
set you certificate as trusted
ask somebody already trusted (i.e. with trusted certificate in the keystore) to sign you certificate
Trying to bypass that is not good bad idea. You can install you certificate in some Java post-install hook, you may have some cron job checking it periodically or do it in exception handling. You can even download this way a certificate from the server and install it everytime it changes (extracting the cert with openssl is easy). But for god's sake, if you decide to do such thing, at least write some audit log about it to some third machine a make sure somebody reads it.
You can also write "hacker-friendly" on you doors. :)

(Note that when you're talking about "keystore" in your question, you're in fact talking about the trust store (which is a keystore). More details on this unfortunately confusing Java terminology are in this answer.)
My application will only make calls to a single server so if there was
a way to bypass the self-signed restrictions, and never consult
keystores, it wouldn't be a security problem, but is there a way to do
this?
Actually, it would be a security problem. Your application may indeed be intended to call only a single server, but the trust store is precisely there to help make sure you're connecting to the machine you intended to connect to. Without it, you wouldn't be able to know whether you're connecting to that server or a MITM server.
If you want the security provided by SSL/TLS, don't bypass these rules. (In particular, don't use a trust manager that will accept any certificate.)
I've looked around and the only solutions I've found is to add the
certificate to the java key store, but this is a problem for me
because I have no control over when or how they update java, and I've
read that the keystore isn't preserved between updates, and I have no
access to the system outside of the JVM.
Quoting myself from this answer (to a more specific question):
The right way is to import this self-signed certificate into the client's trust store, using keytool for example:
keytool -import -file server-cert.pem -alias myserver -keystore mytruststore.jks
You can either do it directly in the JRE's trust store (lib/security/cacerts), which may lack some flexibility, or do it in your own copy of this file, which you then set as the trust store (the default password is changeit or changeme on OSX). You configure this truststore globally for your application using the usual javax.net.ssl.trustStore* system properties (e.g. -Djavax.net.ssl.trustStore=mytruststore system property (and -Djavax.net.ssl.trustStorePassword`). [...]
You don't actually have to use the trust store provided by the JRE (and which may be updated regularly). You could import your self-signed cert into a new empty keystore, which you'll use as a trust store within your application (don't import the private key with it). How to discuss trust store management was in fact discussed in this question: nothing prevents you from using a different trust store specifically for your application or part of it (and in fact Sun/Oracle make no guarantee as to the suitability of the default trust store).
I'm building an application that needs to open self-signed HTTPS SSL
URLs in java. I've learned that you can bypass the SSL problems by
adding a call to HttpsURLConnection.setDefaultHostnameVerifier() where
you say what hostnames are allowed.
While it may indeed by slightly less of a problem if you only have a single self-certificate in your trust store, host name verification is also an essential component of the security provided by SSL/TLS. Don't bypass it, verify that the certificate you're connecting to matches the name you're trying to connect to. (To make an analogy, if you want to check someone's identity, you not only want to check the their passport was emitted by a country whose passports you trust, but you'll also want to check they have the right name inside, otherwise you could be in front of anyone from that country.)
Making the CN= RDN of the Subject Distinguished Name of your self-signed certificate be the host name of the server should be enough, although it's the legacy way of doing it. You may also want to add the Subject Alternative Name extension. More on this in this answer.
Generally speaking do not bypass the SSL "problems". These mechanisms are precisely in place to make the usage of SSL/TLS secure.

How to install own certificates into system certificates storage?

I would like to develop an own API for Android that will request "Signature" protection level and will be accessible for 'my" applications.
Idea is following:
"install" my own certificate into system certificates storage
sign "trusted" application with my own certificate
As a result during request from any application to my API system will check if this application is signed with an appropriate certificate. If my sertificate is installed into Android everything should be fine.
I'm going to prototype that approach, but if there is something obvious that can prevent me from doing that - please let me know.
The question:
how to install own certificate into system certificates storage (assuming we will build Android ourselves and can modify system (in a reasonable borders))?
Thank you very much.
P.S. I'm not very familiar with Java/Android development, so please don't mind if you see something strange.
UPDATE:
As I wrote in a comment to zeetoobiker's answer, If I sign my API with my own certificate then it will be accessible for all my applications (signed by my certificate), but it won't have any system permissions. And I don't want all my 'customers' to navigate to the "realmb.com/droidCert/" web site. Instead I want manufacturer to add my certificate into an OS, now I'm working on making a proof of concept.

I don't think you need to install the certificate.
From the permission docs for signature:
A permission that the system grants only if the requesting application is signed with the same certificate as the application that declared the permission. If the certificates match, the system automatically grants the permission without notifying the user or asking for the user's explicit approval.
This means that it's the certificate you use to sign the apps that matter (not any installed certificates) - if you sign App 1 and App 2 with the same certificate then it will have permission. If App 3 which is signed with a different certificate attempts to access the API then it will get a no permission exception.
According to the docs (I have to admit I've not done it although I'm looking at for some of my apps) it should work on vanilla Android without any necessary customisations / access to the device / root.
If you really need to install the root certificate, this may help but I don't think you do for your stated aim.

Can I create self-signed certificate in Java which will be automatically trusted by web browsers?

I've generated a self-signed certificate for my Java app using keytool. However, when I go to the site in a browser it always pops up with a warning - saying this site does not own the certificate - is there a way to self-sign/doctor a certificate so I won't get these warnings in a browser? Both server and browser are located on the same host and I navigate to the site using "http://localhost/". I do not want to add an exception to the browser because I have tests which run on a big build farm so it is excessive to add an exception to all browsers on all build machines.

No, you can't. You might as well ask "How can I make a fake certificate for hsbc.com?"
There are two ways to get a browser to accept a certificate:
Buy a certificate for a domain from a trusted authority (which means proving to that authority that you own that domain) and then use that domain as the name of your test servers
Install your signing certificate into the browsers, so that you effectively become a trusted authority for that browser.
Without touching the browsers, there's no other way to do it - how could there be, if the internet is to remain secure?

You could also setup a self-signed Certificate Authority (CA) using OpenSSL or possibly your Java tool. You can then use that CA to sign a number of server certs.
You are still going to need to manually trust your self-signed CA on all clients that access your test servers, but at least you only have to trust one root CA, rather than a bunch of individual self-signed server certs.
Another option is to check out CAcert.

Is the certificate you created for localhost or for test.textbox.com? If you create a certificate for the FQDN test.textbox.com, that's how you need to be reaching the server to not get those errors, as long as the certificate is properly signed. You can't generate a certificate for the FQDN and then use an IP or an alias (localhost) to access it without being warned that things aren't matching up properly. Or am I misunderstanding your problem?

Make the certificate for "localhost" instead. It needs to match the hostname you have in the URL.
You will still be bothered as the certificate is not trusted, but that is another issue.