Infrastructure

1. In order to make java 1.7 client to connect the Metacat through https on Ubuntu 12.04 work, we need this line to the default-ssl on the apache configuration:
   ServerName servername.mydomain.com
   Otherwise, the client should set the system property to false:
   System.setProperty("jsse.enableSNIExtension", "false”);
   java -Djsse.enableSNIExtension=false yourClass

2. In order to make morpho to connect Metacat work, we need add this attribute on the element of "context" in the context.xml file under tomcat7/conf directory:
   useHttpOnly='false'

Upgrade Ubuntu from 10.04 to 12.04

1. Prepare
   sudo apt-get update
   sudo apt-get upgrade
   sudo apt-get install update-manager-core
   sudo vim /etc/update-manager/release-upgrades
   (Verify that the line presents in the file: Prompt=lts)

2. Do upgrade
   sudo do-release-upgrade
   notes:
   Choose Y for newer verion packages.
   GRUB should be installed in /dev/vda (use the space key to select it).

3. Install openjdk 7 and configure it

   a. sudo apt-get install openjdk-7-jdk

b. choose openjdk-7 as default java, javac and javaws:
sudo update-alternatives --config java
sudo update-alternatives --config javac
sudo update-alternatives --config Javaws
sudo update-alternatives --config keytool

1. Install tomcat 7 :
   sudo apt-get install tomcat7

2. Migrate the database data from Postgresql 8.4 to 9.1 (after the upgrade, the system has both 8.4 and 9.1 running):

   a. stop both 8.4 and 9.1 server:
   sudo /etc/init.d/postgresql stop

   b: make some links as the root:
   ln -s /etc/postgresql/9.1/main/postgresql.conf /var/lib/postgresql/9.1/main/
   ln -s /etc/postgresql/8.4/main/postgresql.conf /var/lib/postgresql/8.4/main/

   c. run the upgrade script with the —check option as user postgresql:
   /usr/lib/postgresql/9.1/bin/pg_upgrade --check -b /usr/lib/postgresql/8.4/bin -B /usr/lib/postgresql/9.1/bin -d /var/lib/postgresql/8.4/main -D /var/lib/postgresql/9.1/main

   d. do a real upgrade as user postgresql:
   /usr/lib/postgresql/9.1/bin/pg_upgrade -b /usr/lib/postgresql/8.4/bin -B /usr/lib/postgresql/9.1/bin -d /var/lib/postgresql/8.4/main -D /var/lib/postgresql/9.1/main

   e: remove 8.4:
   sudo apt-get remove postgresql-8.4

   f: edit the file /etc/postgresql/9.1/main/postgresql.conf as the user postgres:
   change the port to 5432

   g: start postgresql 9.1:
   sudo /etc/init.d/postgresql start

   h: vaccum db as the user postgres
   /usr/lib/postgresql/9.1/bin$ ./vacuumdb --all

3. Modify the configuration of Apache:

   a. modify /etc/apache2/site-enabled/knb-ssl:
   ServerName mn-demo-11.test.dataone.org (if this line doesn't exist, please add it)
   DocumentRoot /var/lib/tomcat7/webapps/knb
   ScriptAlias /knb/cgi-bin/ /var/lib/tomcat7/webapps/knb/cgi-bin/

   b.modify apache /etc/apache2/workers.properties:
   workers.tomcat_home=/var/lib/tomcat7
   workers.java_home=/usr/lib/jvm/java-1.7.0-openjdk-amd64

   c. restart apache
   sudo /etc/init.d/apache2 restart

4. Modify the configuration of Tomcat and Metacat:

   a. stop tomcat
   sudo /etc/init.d/tomcat stop

   b. Modify the file /var/lib/tomcat7/conf/context.xml:
   add a new attribute useHttpOnly='false' for the “context" element

   c. change the ownership of /var/metacat to tomcat7:tomcat7 recursively
   sudo chown -R tomcat7:tomcat7 /var/metacat

   d. start tomcat:
   sudo /etc/init.d/tomcat start

5. Install the metacat on tomcat 7.