Suppose that you want to access the key store in the var/security folder directly, the following file should be helpful for you :

https://svn.apache.org/repos/asf/geronimo/server/trunk/framework/modules/geronimo-security/src/main/java/org/apache/geronimo/security/keystore/FileKeystoreInstance.java

2011/3/1 KHAksnes <khaksnes@gmail.com>
How do I access a Geronimo KeyStore from a Stateless EJB?
I need a way of specifiing the KeyStore name, then getting a named private
key. The provider field could be used, but I haven't found any documentation
on how to do this in Geronimo.
The available documentation is mainly related to https and security realms.
Not decryption of stored data as I need the key for.
Something like the following could be correct:
KeyStore keyStore =
KeyStore.getInstance(KeyStore.getDefaultType(),"MyKeyStoreName");

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Ivan