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Windows Certificate Store vs Java KeyStore: which is preferred for java server application?

We have server application developed in Java to which agent connects. We need to secure network connection with Certificates signed by Trusted CAs.
Customers can use their own Certificate Authority to sign the certificates. So we need to add root certificates in truststore. We need to decide whether to use Java Keystore (cacerts) or Windows store.
What is the standard practice?
There are few points to consider
Java do not have standard library to read windows store. We need to use JNI
If we use java truststore then customer will have to explicitly add their certificates
We need to store public certificates and private keys.

SSL Certificate X.509 Export

I'm trying to use a Web Service but I have many doubts about the certificates, I'm quite a novice in this topic, The team that developed the web services sent me a document where explains how to use it but to enable the connection, I need to USE a certificate (X.509), I generated p7b certificate from they website and I imported that certificate in my local environment, Using Keytool -import it generate a JKS file but they warn that I should install "Entrust" (Root and Intermediate) certificates that they provide me I used keytool -import with these .cer files and the command generated one .JKS for each file, I installed those cer too, my question is:
To use that web service Which certificate file I need to attach in my implementation logic in java, the jks or p7b ?
How I can use this certificate in all the Test environment? (I don't know if this certificate can be use only in the PC that generates the CSR).
I'm trying to simulate the call with the SOAPUI app i'm getting the authentication error so Probably something is worng with the certificate.
He implemented all using windows certificate store and .NET they can't give me support for keytool.

To do client authentication (also called mutual authentication) in SSL/TLS you (your program) needs not just a certificate but a certificate PLUS PRIVATE KEY and usually intermediate/chain certs. There are canonically 5 steps in the process:
On your computer generate a key PAIR which consists of a privatekey and a publickey, and a Certificate Signing Request (CSR) which contains the publickey. These steps may be done separately, or combined in a way that you don't notice there are both a CSR and a privatekey.
Submit the CSR to a Certificate Authority (CA) along with evidence of your identity and authorization as appropriate, and payment if the CA requres it.
The CA issues an 'end-entity' certificate (in this case a client cert) containing your publickey and identity(ies) plus some other information and gives you this certificate, usually along with an intermediate certificate or sometimes a few intermediate certs that form(s) a 'chain' from the entity cert to a trusted CA root or anchor cert. A 'p7b' file is one fairly common way, though not the only one, of transporting a group of related certs, such as your entity cert plus your chain cert(s).
You return the entity cert and the chain cert(s) to your computer and combine with your privatekey from step 1.
You use the combination of privatekey PLUS certificate chain with various program(s) such as a browser, a utility like curl, or a custom application.
Details of steps 1 and 4 (and 5) depend on the systems and software you use, which you don't specify in any recognizable way, although it sounds like you are ending up in the Windows certificate store. If that is the case, and it is specifically the Personal section of the current-user store (as opposed to a machine account like SYSTEM), then when you run MMC (aka Administrative Tools) and select the Cert Mgr addin, or directly run certmgr.msc, the icon for the cert should have a yellow key at the left:
Contrary to your Q, Java JCE (at least Oracle-was-Sun Java on Windows) can handle this; run keytool -list -storetype Windows-MY -keystore NONE and see for yourself.
However, some (probably many) Java programs cannot. For those, you need a keystore file containing the privatekey PLUS certificates; to create that run the Export wizard and select 'Yes, export private key', then format PKCS 12 (aka PFX) with 'include ... path'.
Recent updates of Java 8 by default can automatically handle a PKCS12 keystore (look for keystore.type.compat=true in JRE/lib/security/java.security) and older versions can do so if the program configures the store type (I don't know if SoapUI does that). For older versions that require JKS, after exporting to PKCS12 to let's say mykey.p12 convert with
keytool -importkeystore -srcstoretype pkcs12 -srckeystore mykey.p12 -destkeystore mykey.jks

What you try to archivee is something called a mutual-authentication. In order to understand the basics you need to understand that the humans have simply concepted a password to lock and unlock informations by the same (symetric) password. Everyone who knows the one password can
read the message
rewrite the message to send false informations
this is dangerous. So they have invented two different passwords, one for writing (private) and a compleatly different one for receive(public), we call them asymetric. The problem in asymetric encryption was, that you can choose free only one password, the opposite password is calculated and can not be choosen freely.
Finally they invented certificates to simplify the process. Certificates contains strong Passwords packed into files. Without looking into the certificates you dont know if the passwords are private or public, that means p7b(pkcsv7b) and jks can contain the absolute same informations. The difference is the format only, like the difference between .doc and .docx.
The second problem
In the big japaneese war's spionage was a big thing, the agents gathered informations about the opposite at the point of tactics and send theese informations to their real lords to find weaknesses in the tactics/strategys. Whenever a spoin has been uncovered he has been turned into a double-agent faking honeypots to let the warlord make wrong decisions and fall into traps.
So as an warlord you must trust your agent ... but, how to be sure? Well, you can ask the other agents about the agent you have the informations from to have the guarantee that the message can be trusted. So the first agent must ask other agents to sign the message too, this question between agents is the CSR! If the other agent(s) sign too, we have a "chain of trust". Ok we have four parties now, the agent, the signing-agent(s) the enemy(hacker) and you.
What must be placed where? Well, assuming you are a warlord (server),
you need the public passwords of all your clients(agents) in a truststore to send them messages(download),
you need to know your private password to encode messages(posts, requests, uploads) your agents sent.
Assuming you are a agent(client/browser) of a warlord inside the enemys lines (open field of world-wide-web), you must store:
your private key, to send messages and sign messages of other agents
the public key of the warlord to encode orders of your master.
You have learned now that a certificate can contain aswell private keys as public keys. How to technically use them?
You lucky, the keytools is open source, download the sources from grepcode (click here) and you will have your implementations by copy-and-paste.
Some hints for mutual-authentication:
The server should not offer its public certificate because all authenticated clients already have the public certificate(key) in their truststore.
The client's certificate should be sent in a non-electronic way (printed as rf-code or whatever).
The client should presented the server's public key and the clients private key in two seperate physical letters (you may noticed if you use the electronic-cash-card (ec-card) you had two letters, one for the PIN and one for the ec-card).

Generating Certificates for Windows Azure

I would like to generate a certificate, public key, private key and all other things needed in order to connect Windows Azure via java code. I prefer using only keytool.
How do I do that?
The java code requires a JKS file with private key in it.
Thx!

Keytool can help you up to certain extent however combination of Keytool and OpenSSL will give you everything you need to have your Java based application connect to Windows Azure (both management portal as well as SSL enabled Web Application.
Please follow the documentation as Migrating Keys from 'keytool' to 'OpenSSL'
Using "keytool" to generate a private and public key pair.
Using "keytool" to export the self-signed certificate from PrivateKeyEntry.
Using "keytool" to display details of a certificate.
Using "OpenSSL" to view certificate exported by "keytool".
Writing "DumpKey.java" to dump key pair out of "keytool" keystore files.
Using "OpenSSL" to convert dumped key pair from binary to Base64 encoding.
Using "OpenSSL" to view key pair dumped and converted from "keytool" keystore files.

JBoss/Java and SSL

Hi I'm a bit lost and hope you'll get me out of here. I'll try to be as clear as possible since I don't really understand/know how I should use certificates.
I've got an application that is supposed to communicate with another one using webservices and SSL. We both asked our main "Certificate Authority" to get certificates.
They sent us 4 files and a password for the .P12 file:
.csr, .cer, .key, .P12
Here is what I did :
* Configure JBoss to use SSL on 8443 and used the P12 file as the keystore
To test this I did a small Java class that call a webservices on this server, using :
props.setProperty("javax.net.ssl.trustStore", "/.../.../certif.p12");
props.setProperty("javax.net.ssl.trustStorePassword", "XXXXXXXXX");
props.setProperty("javax.net.ssl.trustStoreType", "PKCS12");
The connection works, but I think I'm missing something as I did not use the other files.
If I send my .P12 file and the password to the application that is supposed to call my Webservices will it be ok/enough ?
Edit :
I forgot to mention that I should call a Webservice on the other application too, so it should be the other way around, do I only need a .P12 and pass ?
I've read a lot of thing about public key, private key, keytool but it's a bit messy in my head right now.
Thanks for any information !

They sent us 4 files and a password for the .P12 file: .csr, .cer,
.key, .P12
Ideally, you should have generated the private key (in .key) and CSR (in .csr) yourself and the CA should have come back with the certificate (typically in .cer) based on the CSR, which you would have assembled together to build your PKCS#12 file (.p12).
At this stage, you can discard the CSR. The PKCS#12 file should now contain the private key, its associated certificate and possibly the certificate chain attached. You could extract the .key and .cer files from that .p12 file later again. I guess you were given all these files because of the way they have been generated (using intermediate files), or for convenience, not to have to convert them yourself.
The Java terminology isn't ideal, but keystore and truststore are two entities of type keystore, but with a different purpose. The difference between the KeyManager and TrustManager (and thus between javax.net.ssl.keyStore and javax.net.ssl.trustStore) is as follows (quoted from the JSSE ref guide):
TrustManager: Determines whether the remote authentication credentials (and thus the connection) should be trusted.
KeyManager: Determines which authentication credentials to send to the remote host.
The javax.net.ssl.trustStore* properties are one way of configuring the TrustManager. The javax.net.ssl.keyStore* properties are one way of configuring the KeyManager.
Typically, there is no need for private key material in a trust store (unless you also use the same as a keystore). It's often better to use a separate truststore, which you'd be able to copy freely across machine, without worrying about leaking private key material.
What would make sense would be to build a new keystore (JKS) that you would use as a truststore, using the CA certificates (not sure if you've been provided with them).
You're not doing mutual authentication by setting the truststore only (there are no default values for the keystore, so they need to specify these parameters explicitly). If you want to use your client-certificate to connect to a remote party, you need to set it in the keystore (for example, using the javax.net.ssl.keyStore* properties in the same way you've done it for the trust store).
You could point both the keystore and truststore to the same .p12 file. The side effect is that other connections made by your service to other places (e.g https://www.google.com) would not be trusted, since it wouldn't contain the CA for those. That's why it might be better to create a separate "truststore keystore" (JKS might be easier) for the CA certificates. You could make a copy of the default cacerts (in the JRE directory), import your CA's certificate into it and use that.

I've got an application that is supposed to communicate with another
one using webservices and SSL.
Ok, stop here. Communicate how? I mean is it only server authentication i.e. your client application will authenticate the web service or mutual authentication and the web service will also request your applications certificate?
This is important as the files you present by the names seem to suggest the latter i.e. that mutual authentication is expected while your code you show is only setting SSL library for server authentication.
Since you are not providing context here I would say that:
.key has your private key
.p12 has your private key along with your signed certificate or perhaps the CA's root certificate (?)
cer could have your signed certificate or perhaps the root's CA
signing certificate that is considered as trusted in the domain and
has probably also signed the web service you want to communicate with
certificate (well that is a possibility/guess here since you don't
say much)
csr is your certificate signing request
I did a small Java class that call a webservices on this server, using
What you do in the code is setting the p12 as the truststore.
If you say this works then there is no mutual authentication only server side authentication and you are authenticating the web service using whatever is in the p12.
In this case the rest are not needed for communication.It is for you to keep especially the key file since this could be your private key and if you lose/someone steals this then your private certificate is useless/compromised.
I am not sure what your requirements on security are here, but it seems to me that you should probably look into it more.
Even for this question I just tried to do an educated guess based on the file names.....
I hope this puts you in some track to read.

How to use PEM file to create a SSL socket in Java?

See related question.
I have a PEM file provided to me and was told that it will be needed in establishing a SSL socket that connects to a c++ server for some API calls. Does anyone know how I can read in the PEM file and connect? I was also given the parapharse password.

It sounds like the PEM file is a client cert for you to use to login to the server. If it is the client cert, and it sounds like it is, you will likely need a ca cert file also to use in validating the servers certificate in order to establish a connection.
The CA certs need to go into a truststore and your client certs need to go into a keystore. In Java, both of these will be JKS (although it has limited support for PKCS12.) There are default keystore/truststore locations for the JRE as well as for each user. You can also specify external locations for these files in your code, as in the examples below. The commons-ssl library seems to be able to support PEM directly, without the need for JKS, but I haven't used it.
The default passphrase for these keystores in Java is "changeit" without the quotes.
This page shows you have to read the PEM into your keystore/truststore. Here is another example.
Once you have your truststore and keystore set up properly, you need to pass the following JSSE system properties to your JVM:
javax.net.ssl.keyStore
javax.net.ssl.keyStoreType
javax.net.ssl.keyStorePassword
javax.net.ssl.trustStore
javax.net.ssl.trustStoreType
javax.net.ssl.trustStorePassword
You may specify them as -D parameters to the JRE or, as in the examples below, programatically.
Once you finish that, heres a commons-ssl example of creating a socket. Also, heres the Java api for SSLSocket. Heres also an example that doesn't use any apache commons.

You need a library that handles SSL. As John Ellinwood noted, some frameworks (such as Java 2 SE) offers these built-in, for others you'd need to use 3rd party libraries.
C developers often use openssl directly, but it can't be said to be easy and when using C++ there are several "gotchas" that are easy to fall into.
I suggest you use a C++ network library with support for SSL, such as QT's network library, or Poco NetSSL. See here for some tutorial documentation and here for the API documentation - you probably want to take a look at initializeClient which takes a PEM file directly.