Associate an existing certificate


The openssl software package needs to be installed in your system and inside the $PATH variable (login with the same user account that runs the ioChem-BD software and try to execute openssl version command to check its properly installed).

iochembd$  openssl version
OpenSSL 1.0.2h  3 May 2016  (or another version)
The update process also needs these certificate files
- A file with the public certificate
- A file with the certificate private key
- A file with the intermediate certificates (optional)
Now we will detail the file names and the format of every file enumerated previously.
The file with the public certificate must be encoded on X.509 PEM format and with extension .crt. Example:

The file with the private certificate must be encoded on unencrypted PKCS#8 PEM format and with extension .key. Example:


Under some circumstances the certificate also has some intermediate certificates that contain its upper level certificates (the ones that the certificate trusts). In this special case you must concatenate all that certificates into a single file on X509 PEM format , ordered from them most local to most global and must have .bundle extension. Example file content with three intermediate certificates:


Final checks: To ensure our certification chain is valid before we update ioChem-BD certificates, we will run the following command:

iochembd$   openssl verify -CAfile additional.bundle  certificate.crt
certificate.crt : OK

Any different response from previous command except OK should be analyzed and it’s not advised to continue this certificate update procedure until the certification chain is totally valid.

Update process

From now on we will talk about BASE_PATH when we refer to the path where the software has been installed, please replace it for the real full path

We will run the update process with the same user account that runs the software (in this case iochembd), all previous certificate files must also be owned by this user.

We will initially stop the web service:

iochembd$  BASE_PATH/apache-tomcat/bin/

Once the service has stopped, we will copy copy all certificate files inside BASE_PATH/ssl/new folder:

iochembd$  cp certificate.crt    BASE_PATH/ssl/new    #Only file extensions are fixed, filenames can be arbitrary
iochembd$  cp certificate.key    BASE_PATH/ssl/new
iochembd$  cp additional.bundle  BASE_PATH/ssl/new    #Optional file

With the requested files inside the ssl folder, we will launch the tool that replaces self-signed certificates for the new ones.

iochembd$  cd BASE_PATH/updates
iochembd$  ./ -p ReplaceDomainCertificate


If you get an error retrieving the patch files similar to this one:

Error retrieving patch files on!
Please contact ioChem-BD development team at:
Please replace the update script with the latest version from:

The output of this patch will enumerate all steps performed and which files are backed up and replaced:

16:13:40 [main] INFO  utils.Utils - Running command:[/bin/pgrep, -a, -f, tomcat]
16:13:40 [main] INFO  update.UpdatePatch -      Running update vxxx.ReplaceDomainCertificate
16:13:40 [main] INFO  update.UpdatePatch - Generating pkcs12 certificate file from certs + key
16:13:40 [main] INFO  utils.Utils - Running command:[openssl, pkcs12, -export, -in, /home/user/iochem-bd/ssl/new/cert.crt, -inkey, /home/user/iochem-bd/ssl/new/cert.key, -out, /home/user/iochem-bd/ssl/new/certificate.p12, -name, iochem-bd, -chain, -CAfile, /home/user/iochem-bd/ssl/new/cert.bundle, -caname, root, -passin, pass:changeit, -passout, pass:changeit]
16:13:40 [main] INFO  update.UpdatePatch - Generating keystore from pkcs12 certificate
16:13:40 [main] INFO  utils.Utils - Running command:[keytool, -importkeystore, -deststorepass, changeit, -destkeypass, changeit, -destkeystore, /home/user/iochem-bd/ssl/new/keystore.jks, -srckeystore, /home/user/iochem-bd/ssl/new/certificate.p12, -srcstoretype, PKCS12, -srcstorepass, changeit, -alias, iochem-bd]
16:13:40 [main] INFO  update.UpdatePatch - Replacing keystore with the newly generated one.
16:13:40 [main] INFO  update.UpdatePatch -

End update successfully
16:13:40 [main] INFO  update.UpdateProcess - ioChem-BD updated with patch ReplaceDomainCertificate.

If the result of the update process is successful, we can start the service.

iochembd$    BASE_PATH/apache-tomcat-7.0.37/bin/

Once started, we can check that the ioChem-BD service is running with a valid HTTPS certificate, green lock indicates a valid certificate.

Green lock on navigation bar

Green lock on navigation bar


If an exception raises during the certification replacement process, you can undo the entire process by restoring previous certificates and contact reporting your errors