add general certificate information

Client Certificate


add client cert info

Server Certificate

See also [[Connectivity and Certificates|CN_connectivity]]

Install Certbot

Install the cerbot tool to generate LetsEncrypt certificates.

See [[LetsEncrypt]] for installation details.

Adjust node.properties

Two additional properites need to be added to /etc/dataone/node.properties:

Key Description
environment.hosts Space delimited list of host names for CNs participating in the environment
cn.rsyncuser Username of account to use when syncing content across CNs.

For example, on cn-stage-ucsb-1.test.dataone.org:

environment.hosts=cn-stage-ucsb-1.test.dataone.org cn-stage-unm-1.test.dataone.org cn-stage-orc-1.test.dataone.org

Create Account for rsyncuser

sudo adduser ${RUSER} --disabled-password
sudo su - ${RUSER}
mkdir .ssh
chmod 0700 .ssh
cd .ssh
ssh-keygen -N "" -f id_rsa
cp id_rsa.pub authorized_keys
chmod 0600 *
cd ~
mkdir bin
nano bin/rsync-wrapper.sh
chmod u+x bin/rsync-wrapper.sh



echo "$(date) " $@ >> ${LOG}
/usr/bin/sudo /usr/bin/rsync $@

Prepare for Verification

Before running the certificate generation command it is necessary to create the working folder that will be used for the verifications. Do the following on each CN:

RSUSER=$(grep "^cn.rsyncuser=" ${PROPERTIES} | cut -d'=' -f2)
sudo mkdir -p /var/www/.well-known/acme-challenge
sudo chown -R ${RSUSER}:${RSUSER} /var/www/.well-known/acme-challenge
sudo setfacl -Rdm g:${RSUSER}:rw /var/www/.well-known/acme-challenge/
sudo chmod g+s /var/www/.well-known/acme-challenge/

Apache must be configured to not redirect the verification address in the .well-known folder. The following example is for cn-stage-ucsb-1.test.dataone.org. Adjust ServerName, ServerAlias, and RedirectMatch with appropriate values for the respective environment and host:

<VirtualHost *:80>
  # This config only comes into play when DNS for cn-stage.test.dataone.org
  # is pointing to this server
  ServerName cn.dataone.org
  ServerAlias cn-stage-ucsb-1.dataone.org
  ServerAdmin administrator@dataone.org
  DocumentRoot /var/www/
  ErrorLog ${APACHE_LOG_DIR}/error.log
  CustomLog ${APACHE_LOG_DIR}/access.log combined

  # Redirect all traffic except certbot to HTTPS
  RedirectMatch ^/(?!.well-known)(.*) https://cn-stage.test.dataone.org/$1

Supporting Scripts

The certificate generation process relies on the following authentication and cleanup hooks to copy verification information to other nodes participating in the environment and to cleanup afterwards.


RSUSER=$(grep "^cn.rsyncuser=" ${PROPERTIES} | cut -d'=' -f2)
HOSTS=$(grep "^environment.hosts=" ${PROPERTIES} | cut -d'=' -f2)
THIS_HOST=$(hostname -f)
for TARGET_HOST in ${HOSTS}; do
  if [ "${TARGET_HOST}" != "${THIS_HOST}" ]; then
    echo "Copying verification to ${TARGET_HOST}"


RSUSER=$(grep "^cn.rsyncuser=" ${PROPERTIES} | cut -d'=' -f2)
HOSTS=$(grep "^environment.hosts=" ${PROPERTIES} | cut -d'=' -f2)
THIS_HOST=$(hostname -f)
for TARGET_HOST in ${HOSTS}; do
  if [ "${TARGET_HOST}" != "${THIS_HOST}" ]; then
    echo "Removing verification from ${TARGET_HOST}"
    ssh -i ${CREDS} ${RSUSER}@${TARGET_HOST} "rm ${FNVALID}"

After a certificate is renewed, it is necessary to notify administrators that some action is required. Place the following notify-administrators.sh in the renew-hook.d folder. Any scripts in that folder will be called on a successful certificate renewal.

THIS_HOST=$(hostname -f)
THIS_ENVIRONMENT=$(grep "^cn.router.hostname=" ${PROPERTIES} | cut -d'=' -f2)

cat <<EOF | mail -s "Certificate Renewal on ${THIS_ENVIRONMENT}" ${ADMIN}
certbot running on ${THIS_HOST} has generated a new server certificate for the
${THIS_ENVIRONMENT} environment.

Some manual steps must be taken to complete the installation of the new
certificate. The process for this is documented at:


but basically entails running:


then restarting services on each CN in the ${THIS_ENVIRONMENT} environment.


Account for Synchronization

  • Create account, disable password
  • Create ssh keys
  • Distribute ssh public keys
  • Verify ssh to other hosts
  • Enable rsync for account

Certificate Generation

The server certificate must have a primary subject of the primary CN name and must also include as subject alternative names the host names of each CN participating in the environment. For example, the stage environment would include: cn-stage.test.dataone.org, cn-stage-ucsb-1.test.dataone.org, cn-stage-orc-1.test.dataone.org, and cn-stage-unm-1.test.dataone.org.

Certificate generation is performed by certbot with the following command run on the primary host only (remove the --dry-run parameter to do an actual request):

HOSTS=$(grep "^environment.hosts=" ${PROPERTIES} | cut -d'=' -f2)
THIS_ENVIRONMENT=$(grep "^cn.router.hostname=" ${PROPERTIES} | cut -d'=' -f2)
for DHOST in ${HOSTS}; do DOMAINS="${DOMAINS} -d ${DHOST}"; done

sudo certbot certonly --dry-run --manual \
  --preferred-challenges=http \
  --manual-auth-hook=/etc/letsencrypt/renewal/manual-auth-hook.sh \
  --manual-cleanup-hook=/etc/letsencrypt/renewal/manual-cleanup-hook.sh \
  --cert-name ${THIS_ENVIRONMENT} ${DOMAINS}

After a successful first time certificate generation, is is necessary to configure various services to use the new certificates. This procedure should only need to be done once.

Adjust Apache Configuration

Apache HTTPS configuration is straight forward:

<VirtualHost *:443>
  ServerName cn.dataone.org
  # Change the following for the respective host
  ServerAlias cn-ucsb-1.dataone.org

  SSLCACertificateFile /etc/ssl/certs/DataONECAChain.crt

  SSLCertificateKeyFile  /etc/letsencrypt/live/cn.dataone.org/privkey.pem
  SSLCertificateFile  /etc/letsencrypt/live/cn.dataone.org/fullchain.pem
  SSLCertificateChainFile /etc/letsencrypt/lets-encrypt-x3-cross-signed.pem

Adjust Postgres Certificate References

Postgres is configured to use the server certificate and expects the certificate and key to be located in /var/lib/postgresql/9.3/main/ (Note that “9.3” is the current version of postgres installed. The actual location may change in the future).

Symbolic links may be used to refer to the actual certificate location. Replace the existing server.crt and server.key for postgress with:

THIS_ENVIRONMENT=$(grep "^cn.router.hostname=" ${PROPERTIES} | cut -d'=' -f2)
sudo mv /var/lib/postgresql/9.3/server.crt "/var/lib/postgresql/9.3/server.crt.$(date +%Y%m%d)"
sudo mv /var/lib/postgresql/9.3/server.key "/var/lib/postgresql/9.3/server.key.$(date +%Y%m%d)"
sudo ln -s "${CERTS}/cert.pem" /var/lib/postgresql/9.3/server.crt
sudo ln -s "${CERTS}/privkey.pem" /var/lib/postgresql/9.3/server.key

The linked files will survive a refresh of the certificates, so this only needs to be done once.

cn.server.publiccert.filename=/etc/letsencrypt/live/cn-dev-2.test.dataone.org/cert.pem cn.rsyncuser=rsync_user environment.hosts=cn-stage-ucsb-2.test.dataone.org cn-stage-unm-2.test.dataone.org

Configure the DataONE Portal Application

  • portal.properties
  • set permissions
  • restart tomcat

Certificate Renewal

LetsEncrypt certificates are relatively short lived (three months), so an automated mechanism to check and update the certificates is needed. Since restarting services on the DataONE Coordinating Nodes requires some coordination across the servers, this process is not yet entirely automated, though all that should be necessary is for an administrator to execute a script to distribute the certificate and then manually restart services on each CN. Basically:

  1. certbot generates a new certificate from a cron job
  2. DataONE administrators are notified of the need for action
  3. An administrator distributes the certificate to each CN
  4. An administrator restarts services as necessary

The certificate renewal process is performed by cron using the task /etc/cron.weekly/certbot-renew listed below:

set -e
logger "Checking for LetsEncrypt certificate renewal"
/usr/bin/certbot renew -n --quiet \
  --renew-hook "/bin/run-parts /etc/letsencrypt/renew-hook.d/"

The tasks in /etc/letsencrypt/renew-hook.d/ are executed when certificates are successfully renewed. For the CNs, a successful renewal results in a notification being sent to administrators requesting that the next steps of the certificate renewal are followed.

The following script will ensure the certificates have the correct permissions and synchronize the certificates to other servers using rsync.


RSUSER=$(grep "^cn.rsyncuser=" ${PROPERTIES} | cut -d'=' -f2)
HOSTS=$(grep "^environment.hosts=" ${PROPERTIES} | cut -d'=' -f2)
THIS_HOST=$(hostname -f)
THIS_ENVIRONMENT=$(grep "^cn.router.hostname=" ${PROPERTIES} | cut -d'=' -f2)

function synchronize_certs() {
  logger "INFO: Synchronizing letsencrypt certificates to other CNs..."
  #Set permissions for ssl-cert group access
  echo "Setting permissions on certificates..."
  chgrp -R ssl-cert /etc/letsencrypt/archive
  chmod g+rx /etc/letsencrypt/archive
  chgrp -R ssl-cert /etc/letsencrypt/live
  chmod g+rx /etc/letsencrypt/live
  #This is needed for Postgres to start:
  chmod 0640 /etc/letsencrypt/archive/${THIS_ENVIRONMENT}/privkey*

  #Synchronize with other servers
  for TARGET_HOST in ${HOSTS}; do
    if [ "${TARGET_HOST}" != "${THIS_HOST}" ]; then
      echo "Syncing certificate info to ${TARGET_HOST}"
      rsync -avu --rsync-path="/home/${RSUSER}/bin/rsync-wrapper.sh" \
        -e "ssh -i /home/${RSUSER}/.ssh/id_rsa -l ${RSUSER}" \
        /etc/letsencrypt/*  \

echo "Using variables:"
echo "RSUSER = ${RSUSER}"
echo "HOSTS = ${HOSTS}"
read -p "Does this look OK (y/N)?" -n 1 -r
if [[ $REPLY =~ ^[Yy]$ ]]; then
  exit 0
echo "Aborted."

Service Restarts

After a new certificate has been distributed it is necessary to restart apache2, postgresql, and tomcat7 to pick up the change:

# Verify apache configuration is OK
sudo apache2ctl -t
sudo service apache2 restart
sudo service postgres restart

TODO: refer to procedure for tomcat restart on CNs


Verification that the new certificate basically comes down to three checks:

  1. Check service is running
  • Is the service running?

    sudo service apache2 status
    sudo service postgres status
    sudo service tomcat7 status
  • Is a listener on the expected port?

    sudo netstat -tulpn
  1. Verify the new certificate is being used

    The following command run from the command line will show the certificate being used by the server in its plain text form:

    echo "Q" | openssl s_client -connect ${TARGET} | openssl x509 -text -noout
  2. Verify that a client can connect as expected

    Use a web browser to check the server responds as expected. Use a DataONE client to interact with the server.