Hello again, i solved the login issue. The main reason for invalid console login was that the keystore.jks being update while the cacerts.jks remained the same. So i took the old bash, then made the same keytool imports to a new file called cacerts.jks and replaced it with the current ones in glassfish domain config backing up the original files
#!/bin/sh
#replace [##] with the correct value
#Alias of the certificate
NAME=[##]
#The current domain registered in letsencrypt
DOMAIN=[##]
#The keystore password, default is (changeit)
KEYSTOREPW=[##]
#Glassfish server location e.g. /home/glassfish/domains/domain1
GFDOMAIN=[##]
LIVE=/etc/letsencrypt/live/$DOMAIN
mkdir etc
cd etc
sudo openssl pkcs12 -export -in $LIVE/cert.pem -inkey $LIVE/privkey.pem -out cert_and_key.p12 -name $NAME -CAfile $LIVE/chain.pem -caname root -password pass:$KEYSTOREPW
sudo keytool -importkeystore -destkeystore keystore.jks -srckeystore cert_and_key.p12 -srcstoretype PKCS12 -alias $NAME -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo keytool -import -noprompt -trustcacerts -alias root -file $LIVE/chain.pem -keystore keystore.jks -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo openssl pkcs12 -export -in $LIVE/fullchain.pem -inkey $LIVE/privkey.pem -out pkcs.p12 -name glassfish-instance -password pass:$KEYSTOREPW
sudo keytool -importkeystore -destkeystore keystore.jks -srckeystore pkcs.p12 -srcstoretype PKCS12 -alias glassfish-instance -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo openssl pkcs12 -export -in $LIVE/fullchain.pem -inkey $LIVE/privkey.pem -out pkcs.p12 -name s1as -password pass:$KEYSTOREPW
sudo keytool -importkeystore -destkeystore keystore.jks -srckeystore pkcs.p12 -srcstoretype PKCS12 -alias s1as -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo openssl pkcs12 -export -in $LIVE/cert.pem -inkey $LIVE/privkey.pem -out cert_and_key.p12 -name $NAME -CAfile $LIVE/chain.pem -caname root -password pass:$KEYSTOREPW
sudo keytool -importkeystore -destkeystore cacerts.jks -srckeystore cert_and_key.p12 -srcstoretype PKCS12 -alias $NAME -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo keytool -import -noprompt -trustcacerts -alias root -file $LIVE/chain.pem -keystore cacerts.jks -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo openssl pkcs12 -export -in $LIVE/fullchain.pem -inkey $LIVE/privkey.pem -out pkcs.p12 -name glassfish-instance -password pass:$KEYSTOREPW
sudo keytool -importkeystore -destkeystore cacerts.jks -srckeystore pkcs.p12 -srcstoretype PKCS12 -alias glassfish-instance -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo openssl pkcs12 -export -in $LIVE/fullchain.pem -inkey $LIVE/privkey.pem -out pkcs.p12 -name s1as -password pass:$KEYSTOREPW
sudo keytool -importkeystore -destkeystore cacerts.jks -srckeystore pkcs.p12 -srcstoretype PKCS12 -alias s1as -srcstorepass $KEYSTOREPW -deststorepass $KEYSTOREPW -destkeypass $KEYSTOREPW
sudo keytool -list -keystore keystore.jks -storepass $KEYSTOREPW
sudo keytool -list -keystore cacerts.jks -storepass $KEYSTOREPW
if [ ! -f $GFDOMAIN/config/keystore-orig.jks ]; then
echo "Backing up original files..."
sudo cp -f $GFDOMAIN/config/keystore.jks $GFDOMAIN/config/keystore-orig.jks
sudo cp -f $GFDOMAIN/config/cacerts.jks $GFDOMAIN/config/cacerts-orig.jks
fi
echo "Updating certificates..."
sudo cp -f keystore.jks $GFDOMAIN/config/keystore.jks
sudo cp -f cacerts.jks $GFDOMAIN/config/cacerts.jks
cd ..
sudo rm -rf etc
service glassfish restart
hope this helps