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Next, download the upgrade script from the SHRINE installer and run it.

$ wget --no-check-certificate https://open.med.harvard.edu/svn/shrine/releases/1.19.2/code/install/i2b2-1.7/shrine/upgrade_tomcat.sh
$ chmod +x upgrade_tomcat.sh
$ ./upgrade_tomcat.sh

The script should cleanly replace an existing Tomcat 6 installation with Tomcat 7, generating a new server.xml (based on tomcat7_server.xml) in the process. If you are already on Tomcat 7 (or newer), the script will exit and do nothing., the script will exit and do nothing.

If Tomcat fails to start, check /opt/shrine/tomcat/logs/catalina.out. An error like this may appear in catalina.out:

java.lang.ClassNotFoundException: org.apache.catalina.mbeans.ServerLifecycleListener

If this appears, comment out the following line in /opt/shrine/tomcat/conf/server.xml:

<Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener"/>

Deploy New shrine.war

Next, we will retrieve the new SHRINE webapp from the HMS Sonatype Nexus server at http://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/shrine-war/. Navigate to the folder for 1.19.2. From there, download the shrine-war-1.19.2.war file to the webapps directory on the SHRINE server and rename it to shrine.war.

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$ cd /opt/shrine/tomcat/webapps
$ wget --no-check-certificate http://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/shrine-war/1.19.2/shrine-war-1.19.2.war -O shrine.war

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$ cd /opt/shrine/tomcat/webapps
$ wget --no-check-certificate https://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/steward/1.19.2/steward-1.19.2.war -O steward.war

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$ cd /opt/shrine/tomcat/webapps
$ wget --no-check-certificate https://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/shrine-proxy/1.19.2/shrine-proxy-1.19.2.war -O shrine-proxy.war

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This step should be handled by install-steward-only.sh, but instructions to manually perform it can be found below:

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1. Start with a sample steward.conf from the installer: https://open.med.harvard.edu/svn/shrine/releases/1.19.2/code/install/i2b2-1.7/shrine/skel/steward.conf
   1. If using the JDBC driver (for example, SQL Server users), make sure slickProfileClassName is set to "scala.slick.driver.JdbcDriver$" (mind the lowercase "dbc"!)
2. Substitute the following variables with their appropriate value. (see common.rc and shrine.rc for reference, as well as the listing of configuration variables in the installer)
   1. SHRINE_ADAPTER_I2B2_DOMAIN
   2. SHRINE_STEWARD_DB_NAME
   3. I2B2_PM_IP
   4. KEYSTORE_FILE
   5. KEYSTORE_PASSWORD
   6. KEYSTORE_ALIAS
3. Save this file to /opt/shrine/tomcat/lib/steward.conf

Make sure that the keystore{} block in steward.conf exactly matches the keystore{} block in shrine.conf!

An important setting in steward.conf which should be manually set by a site administrator is createTopicsMode. By default, this is set to "Pending", which means that topic requests submitted in the Data Steward application will have to be manually approved by a user with DataSteward privileges.

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