Given :
path to JKS,
password for the JKS,
alias of the cert
how can I get the serial number of the cert from the JKS, programmatically ?
You can load a certificate from a Java keystore like that:
char[] pwdArray = "password".toCharArray();
KeyStore ks = KeyStore.getInstance("JKS");
ks.load(new FileInputStream("myKeyStore.jks"), pwdArray);
Certificate cert = ks.getCertificate("MyAlias");
The base Certificate class has no method to access serial numbers, but I assume that you are using X.509 certificates. The you can use the X509Certificate class like that:
X509Certificate xcert = (X509Certificate) cert;
BigInteger serial = xcert.getSerialNumber();
You can see details in the API docs at https://docs.oracle.com/javase/7/docs/api/java/security/cert/X509Certificate.html