Working with PKCS #1 PEM based certificates in Java is an itch. Here is the scratch.

Include the project into your application (e.g. with Maven):

<dependency>
  <groupId>de.dentrassi.crypto</groupId>
  <artifactId>pem-keystore</artifactId>
  <version>3.0.0</version> <!-- check for most recent version -->
</dependency>

The project acts as a Java security provider. Providing only a KeyStore implementation. However, you need to make Java aware of the security provider. There are several ways to do this:

You can manually specify the security provider:

KeyStore keyStore = KeyStore.getInstance("PEM", new PemKeyStoreProvider() );

This way the security provider will only be used for this single call.

You can manually register the security provider at the start of your application:

Security.addProvider(new PemKeyStoreProvider());
KeyStore keyStore = KeyStore.getInstance("PEM");

This will make the provider available to the whole application. As this provider currently is the only provider supporting PEM at the moment, the order is not important. But you can always use Security.insertProviderAt instead:

Security.insertProviderAt(new PemKeyStoreProvider(), 10);

It is also possible to configure the provider in <JRE>/conf/security/java.security file. Also see: https://docs.oracle.com/javase/10/security/howtoimplaprovider.htm#GUID-831AA25F-F702-442D-A2E4-8DA6DEA16F33

The basic usage of the PEM KeyStore is:

KeyStore keyStore = KeyStore.getInstance("PEM");
try ( InputStream in = … ) {
  keyStore.load ( in, null );
}

// Use X509Certificates from the KeyStore

But the reality is more complex of course ;-)

Sometimes, like when using OpenShift, key and certificate come in two different files. However the whole "KeyStore" construct is built around the idea that only one file/resource exists, which stores the information.

For this case, or also for Let's Encrypt, you can use the PEMCFG KeyStore type. It is variation of the PEM store and initially loads a Java properties while, which then points towards the different files to load.

A properties file looks like:

alias=alias-name
source.key=/etc/tls/tls.key
source.cert=/etc/tls/tls.crt

The alias property defines under which alias the key/cert will be provided. Every property key starting with source. will be used a file system path to load an additional source. Certificates will be chained together and presented alongside the key.

The remainder of the key, the part after the source., will be ignored.

Java keystores can either store one or more certificate chains. Java only uses the tip of the chain as a trusted certificate. So when you have a PKCS #1 PEM file, it is not clear if this is a chain of certificates, or a set of root certificates to trust.

By default, certificates get chained together when read. However, the PEMCA Keystore will store certificates individually:

KeyStore keyStore = KeyStore.getInstance("PEMCA");
try ( InputStream in = … ) {
  keyStore.load ( in, null );
}

// Use X509Certificates from the KeyStore

In this case the alias will be used as a prefix, and the entries will be named <alias>-#, where # is an increasing index, starting with 0 (zero).