How to create own self-signed root certificate and intermediate CA to be imported in Java keystore?

Just a side note for anyone wanting to generate a chain and a number of certificates. Refining @EpicPandaForce's own answer, here's a script that creates a root CA in root-ca/, an intermediate CA in intermediate/ and three certificates to out/, each signed with the intermediate CA.

#!/bin/bash -x

set -e

for C in `echo root-ca intermediate`; do

  mkdir $C
  cd $C
  mkdir certs crl newcerts private
  cd ..

  echo 1000 > $C/serial
  touch $C/index.txt $C/index.txt.attr

  echo '
[ ca ]
default_ca = CA_default
[ CA_default ]
dir            = '$C'                     # Where everything is kept
certs          = $dir/certs               # Where the issued certs are kept
crl_dir        = $dir/crl                 # Where the issued crl are kept
database       = $dir/index.txt           # database index file.
new_certs_dir  = $dir/newcerts            # default place for new certs.
certificate    = $dir/cacert.pem          # The CA certificate
serial         = $dir/serial              # The current serial number
crl            = $dir/crl.pem             # The current CRL
private_key    = $dir/private/ca.key.pem  # The private key
RANDFILE       = $dir/.rnd                # private random number file
nameopt        = default_ca
certopt        = default_ca
policy         = policy_match
default_days   = 365
default_md     = sha256

[ policy_match ]
countryName            = optional
stateOrProvinceName    = optional
organizationName       = optional
organizationalUnitName = optional
commonName             = supplied
emailAddress           = optional

[req]
req_extensions = v3_req
distinguished_name = req_distinguished_name

[req_distinguished_name]

[v3_req]
basicConstraints = CA:TRUE
' > $C/openssl.conf
done

openssl genrsa -out root-ca/private/ca.key 2048
openssl req -config root-ca/openssl.conf -new -x509 -days 3650 -key root-ca/private/ca.key -sha256 -extensions v3_req -out root-ca/certs/ca.crt -subj '/CN=Root-ca'

openssl genrsa -out intermediate/private/intermediate.key 2048
openssl req -config intermediate/openssl.conf -sha256 -new -key intermediate/private/intermediate.key -out intermediate/certs/intermediate.csr -subj '/CN=Interm.'
openssl ca -batch -config root-ca/openssl.conf -keyfile root-ca/private/ca.key -cert root-ca/certs/ca.crt -extensions v3_req -notext -md sha256 -in intermediate/certs/intermediate.csr -out intermediate/certs/intermediate.crt

mkdir out

for I in `seq 1 3` ; do
  openssl req -new -keyout out/$I.key -out out/$I.request -days 365 -nodes -subj "/CN=$I.example.com" -newkey rsa:2048
  openssl ca -batch -config root-ca/openssl.conf -keyfile intermediate/private/intermediate.key -cert intermediate/certs/intermediate.crt -out out/$I.crt -infiles out/$I.request
done

Based on the following guide, special thanks to Jamie Nguyen for making a guide which made this possible, thank you!

By following the guide on https://jamielinux.com/articles/2013/08/act-as-your-own-certificate-authority/ do the following :

• Install OpenSSL for Windows: http://slproweb.com/products/Win32OpenSSL.html

• Add the bin folder to the environment variable PATH

• Create a directory for the certificates, I will call this cert-test

• Use the following openssl.cfg data for the [ CA_default ] tag:

this

[ CA_default ]
dir        = .    # Where everything is kept
certs        = $dir/certs                # Where the issued certs are kept
crl_dir    = $dir/crl                # Where the issued crl are kept
database    = $dir/index.txt            # database index file.
new_certs_dir    = $dir/newcerts            # default place for new certs.

certificate    = $dir/cacert.pem                # The CA certificate
serial        = $dir/serial                # The current serial number
crl        = $dir/crl.pem                # The current CRL
private_key    = $dir/private/ca.key.pem       # The private key
RANDFILE    = $dir/.rnd     # private random number file

• create the directories in cert_test: certs crl newcerts private

• use following commands to create

Root CA:

openssl genrsa -aes256 -out /etc/pki/CA/private/ca.key.pem 4096

openssl req -new -x509 -days 3650 -key /etc/pki/CA/private/ca.key.pem -sha256 -extensions v3_ca -out /etc/pki/CA/certs/ca.cert.pem

• create folder intermediate

• create folders certs crl newcerts private

• create file index.txt

• create file serial and write a number into it like 1000

• execute following

commands:

openssl genrsa -aes256 -out intermediate/private/intermediate.key.pem 4096

openssl req -config intermediate/openssl.cfg -sha256 -new -key intermediate/private/intermediate.key.pem -out intermediate/certs/intermediate.csr.pem

openssl ca -keyfile private/ca.key.pem -cert certs/ca.cert.pem -extensions v3_ca -notext -md sha256 -in intermediate/certs/intermediate.csr.pem -out intermediate/certs/intermediate.cert.pem

• Create chain file with

cat:

cat intermediate/certs/intermediate.cert.pem certs/ca.cert.pem > intermediate/certs/ca-chain.cert.pem

• Creating JKS file from chain with

keytool:

keytool -importkeystore -srckeystore ia.p12 -srcstoretype PKCS12 -destkeystore ia.jks

keytool -import -noprompt -trustcacerts -alias test_certificate -file ia.crt -keystore ia.jks -storepass helloworld

keytool -importcert -alias test_cert_ca -keystore "c:\Program Files\Java\jdk1.8.0\jre\lib\security\cacerts" -file ca.crt

keytool -importcert -alias test_cert_ia -keystore "c:\Program Files\Java\jdk1.8.0\jre\lib\security\cacerts" -file ia.crt

And you might have to import the CA cert into the ia.jks.