The following assumes that you are in the SSH terminal connected to your EC2 instance.

1. Stop the running tomcat instance

1. Go to the tomcat directory

   • cd /opt/apache-tomcat-7.0.39/

2. Stop tomcat using the shutdown wrapper script

   • sudo -su tomcat bin/shutdownwrapper.sh

3. Verify tomcat has been shutdown

   • ps aux | grep tomcat

[root@ip-172-31-54-208 log]# cd /opt/apache-tomcat-7.0.39/
[root@ip-172-31-54-208 apache-tomcat-7.0.39]# sudo -su tomcat bin/shutdown.sh
Using CATALINA_BASE:   /opt/apache-tomcat-7.0.39
Using CATALINA_HOME:   /opt/apache-tomcat-7.0.39
Using CATALINA_TMPDIR: /opt/apache-tomcat-7.0.39/temp
Using JRE_HOME:        /opt/jdk1.8.0_66
Using CLASSPATH:       /opt/apache-tomcat-7.0.39/bin/bootstrap.jar:/opt/apache-tomcat-7.0.39/bin/tomcat-juli.jar
[root@ip-172-31-54-208 apache-tomcat-7.0.39]# ps aux | grep tomcat
root      1646  0.0  0.0 103312   876 pts/0    S+   13:02   0:00 grep tomcat
 
#### The following means that tomcat is still running ####
tomcat    1674 93.2 11.4 3599164 116800 pts/0  Sl   13:08   0:03 /opt/jdk1.8.0_66/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.39/conf/logging.properties 
-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xmx1536m -XX:+PrintGCDetails 
-Xloggc:/opt/apache-tomcat-7.0.39/logs/tomcat-gc.log -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.39/endorsed 
-classpath /opt/apache-tomcat-7.0.39/bin/bootstrap.jar:/opt/apache-tomcat-7.0.39/bin/tomcat-juli.jar 
-Dcatalina.base=/opt/apache-tomcat-7.0.39 -Dcatalina.home=/opt/apache-tomcat-7.0.39 
-Djava.io.tmpdir=/opt/apache-tomcat-7.0.39/temp org.apache.catalina.startup.Bootstrap start

2. Modify configuration.properties for the repository

1. Go to the repository home directory
   • cd ${REPO_HOME}
2. Open configuration.properties file in a text editor of your choice
   • vim configuration.properties
3. The following property must be be set for your eagle-i node
   • eaglei.repository.namespace
4. The following properties should be set for proper display of the interface
   • eaglei.repository.title
   • eaglei.repository.logo

5. Save the changes.
   
   

   [root@ip-172-31-54-208 ~]# cd ${REPO_HOME} [root@ip-172-31-54-208 repo]# vim configuration.properties   ##### configuration.properties file #### eaglei.repository.namespace = http://ec2-54-175-59-6.compute-1.amazonaws.com/i/ eaglei.repository.title = AMI Test Repository eaglei.repository.logo = https://alaska.qa.eagle-i.net:8443/sweet/images/eaglei-medium-blue.png

3. Prepare the repository for customization

1. Go to the repository home directory
   • cd ${REPO_HOME}
2. Delete the existing derby database
   • rm -fr db/
3. Run the prepare-install script in the etc directory.  Replace REPOADMIN and REPOADMINPW with the credentials for the repository administrator.
   • bash etc/prepare-install.sh REPOADMIN REPOADMINPW ${REPO_HOME}

4. Modify the ownership of the derby database to be owned by the tomcat user

   • chown -R tomcat:tomcat db/

    

   [root@ip-172-31-54-208 sparqler]# cd ${REPO_HOME} [root@ip-172-31-54-208 repo]# rm -r db/ [root@ip-172-31-54-208 repo]# bash etc/prepare-install.sh ami-admin-user ami-admin-pw ${REPO_HOME} _RUNJAVA set to "/opt/jdk1.8.0_66/jre/bin/java" java version "1.8.0_66" Java(TM) SE Runtime Environment (build 1.8.0_66-b17) Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode) ---all superuser logins--- ami-admin-user [root@ip-172-31-54-208 repo]# chown -R tomcat:tomcat db/

4. Start tomcat

1. Go to the tomcat directory

   • cd /opt/apache-tomcat-7.0.39/

2. Start tomcat using the startup wrapper script

   • sudo -su tomcat bin/startupwrapper.sh

3. Wait for tomcat to finish startup.

   [root@ip-172-31-54-208 opt]# cd apache-tomcat-7.0.39/ [root@ip-172-31-54-208 apache-tomcat-7.0.39]# sudo -su tomcat bash bin/startupwrapper.sh Waiting for Tomcat to startup ... Tomcat startup finished in ~120 seconds

5. Finish the repository customization

1. Go to the repository home directory
   • cd ${REPO_HOME}
2. Run the finish install script in the etc directory.  Replace REPOADMIN and REPOADMINPW with the credentials for the repository administrator.
   • bash etc/finish-install.sh REPOADMIN REPOADMINPW repository-url-prefix

3. Run the upgrade script in the etc directory. Replace REPOADMIN and REPOADMINPW with the credentials for the repository administrator.

   • bash etc/upgrade.sh REPOADMIN REPOADMINPW repository-url-prefix 

   [root@ip-172-31-54-208 sparqler]# cd ${REPO_HOME} [root@ip-172-31-54-208 repo]# bash etc/finish-install.sh ami-admin-user ami-admin-pw https://ec2-54-175-59-6.compute-1.amazonaws.com User metadata created. Updating data model ontology from jar, please wait... Updated data model ontology from jar. [root@ip-172-31-54-208 repo]# bash etc/upgrade.sh ami-admin-user ami-admin-pw https://ec2-54-175-59-6.compute-1.amazonaws.com ***** Checking and Upgrading Repository's Internal Graphs INFO: Skipping, internal graph is already up to date: http://eagle-i.org/ont/repo/1.0/ INFO: Skipping, internal graph is already up to date: http://eagle-i.org/ont/repo/1.0/NG_Query .....lots of output and stuff here .....   OK - specials all succeeded. rm -rf /tmp/repo-upgrade-9784

6. Verify repository has been customized correctly

In a browser, navigate to the repository admin console and log in using the repository administrator credentials.