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How do you convert PKCS#12 String to Certificate and PrivateKey?

I am receiving the following String from a certificate stored in Azure Key Vault. I am using the Secret API in order to retrieve both the certificate and the private key related to this cert.
Initially the certificate was uploaded using a .pfx file to Azure Key vault. Now I need to create a Certificate and a PrivateKey to allow client authentication to a 3rd party system and I am using the given String retrieved from the API, however I am note sure how to get around that in Java.
I took some hints from this link in C# however I am pretty certain that this method doesn't work like that in Java. In particular an X509Certificate or a Certificate in general doesn't hold any information about the PrivateKey in Java, unlike C#, and I am not sure how to extract that information from given String in Java.
This works as expected to retrieve the certificate from the String retrieved from the API
String secret = azureSecret.getValue();
byte[] certkey = Base64.getDecoder().decode(secret);
ByteArrayInputStream inputStream = new ByteArrayInputStream(certkey);
CertificateFactory cf = CertificateFactory.getInstance("X.509");
Certificate cert = cf.generateCertificate(inputStream);
The azureSecret.getValue() format is like the following however I am not sure how to get PrivateKey out of the given String
MIIKvgIBaaZd6Euf3EYwYdHrIIKYzCC...

YES, Java X509Certificate and Certificate is only the certificate. Instead use KeyStore which can contain multiple entries each of which is either a 'trusted' certificate (for someone else), or a privatekey plus certificate plus other chain cert(s) (if applicable) for yourself, or (not relevant here) a 'secret' (symmetric) key. PKCS12 is supported as one type of KeyStore along with others not relevant here, so after the base64-decoding you already have do something like:
KeyStore ks = KeyStore.getInstance("PKCS12");
ks.load(inputstreamfromvaultvalue, password);
// then
PrivateKey pkey = (PrivateKey) ks.getKey(alias, password);
// and
Certificate cert = ks.getCertificate(alias); // if you only need the leaf cert
// or
Certificate[] chain = ks.getCertificateChain(alias); // usually
But if you want to do client authentication in TLS/SSL (including HTTPS), you give the JSSE KeyManager the whole keystore object not the individual pieces (privatekey and certificates). Similarly to verify the peer in TLS/SSL, you give TrustManager a keystore containing trusted certificates, usually root CAs and often defaulted to a built-in set of public root CAs.

Change certificate for private key in keystore

Is it possible to change the certificate and certificate chain for existing entry (private key) in keystore. As I understand, firstly I need to delete existing entry and then store same private key with new certificate and chain. This solution is not an option since I don't know the password for that entry in keystore.
Solution so far:
Key generation and initial storage:
KeyPair kp = generateRSAKeyPair();
X509Certificate selfSignedCert = makeSelfSignedCert(kp);
ks.load(...);
ks.setKeyEntry("entry1", kp.getPrivate(), PASSWORD, new X509Certificate[]{selfSignedCert});
ks.store(...);
After CA sends certificate I want:
ks.load(...);
ks.setCertificateEntry("entry1", caSignedCert);
ks.store(...);
The main issue is that I don't have the right certificate at the time when the key is being stored to keystore. There is a delay between the generation of keys and when CA sends signed certificates.
Another option would be to not set certificate at all, and after CA signs CSR, add the final signed certificate to keystore. Something like:
KeyPair kp = generateRSAKeyPair();
ks.load(...);
ks.setKeyEntry("entry1", kp.getPrivate(), PASSWORD);
ks.store(...);
// after some time
ks.load(...);
ks.setCertificateEntry("entry1", caSignedCert);
ks.store(...);
But I couldn't find a way to store private key without an associated certificate in keystore. Storing private key elsewhere else is also not an option.
A potential solution is to store signed certificate from CA until a user provides the password to keystore entry and then deleting existing entry & creating new entry with proper certificates. This solution is not ideal and I would like to avoid going down this road.
Any suggestions are welcome.

The solution is to first store key to keystore with the self-signed certificate. At this time, this key cannot be used because CA did not sent the proper certificate for this key yet. If one would use key at this time for signing, the associated self-signed certificate would be used (which is not desirable).
After some time CA sends the proper certificate, which must be stored somewhere (database in my case).
On the first opportunity when the password for key entry is supplied, key is retrieved from keystore and immediately gets stored again with the same password but different alias and proper certificate from CA. Then it is safe to delete original entry with self-signed certificate.
I hope this helps someone. Any better solutions are welcome.

Create signature with bouncycastle api. Key always null

I'm using bouncycastle for generating detached signature for XML's signing. For key initialize I use this code:
Security.addProvider(new BouncyCastleProvider());
KeyStore ks = KeyStore.getInstance(KEYSTORE_INSTANCE);
ks.load(new FileInputStream(KEYSTORE_FILE), KEYSTORE_PWD.toCharArray());
Key key = ks.getKey(CERT_ALIAS, KEYSTORE_PWD.toCharArray());
I have JKS keystore with certificate. But if I do this:
Key key = ks.getKey(CERT_ALIAS, KEYSTORE_PWD.toCharArray());
key stay always null and I have InvalidKeyException
Where's my mistake? I new in crypto

I can't comment due to too low reputation. So I'll answer/edit instead.
The above example works fine, the error is probably in one of the constants being used. What are they, and what is the exact error you're getting?
I mean something like: java.security.InvalidKeyException: Illegal key size
Here is the working example I tried while loading a KeyStore from a file:
'secret1' is the store password, 'secret2' is the key password and 'myKey' is the key alias.
KeyStore keyStore = KeyStore.getInstance(KeyStore.getDefaultType());
keyStore.load(new FileInputStream(keyStoreFile.getAbsolutePath()), "secret1".toCharArray());
Key key = keyStore.getKey("myKey", "secret2".toCharArray());

Storing an X.509 certificate into a keystore using java code

I have an X.509 certificate created using bouncycastle library. How can I store it into a java Keystore?
I tried this code
KeyStore ks = KeyStore.getInstance(KeyStore.getDefaultType());
// get user password and file input stream
char[] password = getPassword();
java.io.FileInputStream fis =
new java.io.FileInputStream("keyStoreName");
ks.load(fis, password);
fis.close();
I found this code here, but the key store created using this way does not work with keytool, it tells me the keystore is corrupted.

Use KeyStore.setCertificateEntry(alias, cert) and give it an alias name of your choice. Then, use KeyStore.store(...) to save the keystore (typically using a FileOutputStream).

loading a certificate from keystore

Load a certificate and keys from keystore which is password protected and then use it for cert verification and digital signing

To read the certificate is really trivial.
CertificateFactory factory = CertificateFactory.getInstance("X.509");
X509Certificate certificate = (X509Certificate) factory.generateCertificate(new FileInputStream("file.pem"));
This is with standard APIs (in try/catch) etc and you have loaded your certificate.
Now the toString method of certificate is not suitable for you since it just captures the "user's" view of the certificate e.g. you would use it for println for instance
Can't you send the certificate object itself?
Not sure what your server expects so you can look into the various methods of certificate
X509Certificate

I use this code
PEMReader pr=new PEMReader(new StringReader(trust_certs));
KeyStore trustStore = KeyStore.getInstance(KeyStore.getDefaultType());
trustStore.load(null, null);
Object o;
int i=0;
while((o=pr.readObject())!=null){
if(o instanceof X509Certificate){
i++;
X509Certificate c=(X509Certificate)o;
trustStore.setCertificateEntry(Integer.toString(i), c);
}
}
http://www.bouncycastle.org/docs/docs1.6/org/bouncycastle/openssl/PEMReader.html

A pem file is read as any other text file. Read the Java tutorial about IO (and concentrate on character streams, since a pem file contains text, and on File IO, since this is what you want to do)