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

$ wget https://open.med.harvard.edu/svn/shrine/releases/1.19.12/code/install/i2b2-1.7/shrine/upgrade_tomcat.sh
$ chmod +x upgrade_tomcat.sh
$ ./upgrade_tomcat.sh

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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/. Choose the version that you are upgrading to (for example, 1.19.12) and navigate to that folder. From there, download the appropriate shrine-war-[VERSION].war file shrine-war-[VERSION].war file to the webapps directory on the SHRINE server and rename it to shrine.war.

For example:

$ cd /opt/shrine/tomcat/webapps
$ wget 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

Deploy New shrine-proxy.war

Like other SHRINE artifacts, the SHRINE proxy can be found on the HMS Sonatype Nexus server at https://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/shrine-proxy/. Navigate to the folder for 1.19.2. From there, download the shrine-proxy-1.19.2.war to the webapps directory on the SHRINE server and rename it to shrine-proxy.war.

For example:

$ cd /opt/shrine/tomcat/webapps
$ wget httphttps://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/shrine-warproxy/1.19.12/shrine-warproxy-1.19.12.war -O shrine-proxy.war

[Optional] Deploy New steward.war

Much like shrine.war, steward.war can be found on the HMS Sonatype Nexus server at http://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/steward/. Navigate to the folder for 1.19.12. From there, download the appropriate steward-[VERSION].war file to the webapps directory on the SHRINE server and rename it to steward.war.

...

$ cd /opt/shrine/tomcat/webapps
$ wget https://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/steward/1.19.12/steward-1.19.12.war -O steward.war

Deploy New SHRINE Webclient

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$ cd /opt/shrine/tomcat/webapps
$ svn export https://open.med.harvard.edu/svn/shrine/releases/1.19.12/code/shrine-webclient/

After this, restore the previous i2b2_config_data.js and cell_config_data.js file from your backup and place it in the new shrine-webclient folder:

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1. Create a database (typically stored in MySQL alongside the existing shrine_query_history database, but this is just a suggestion). The installer by default calls it stewardDB.
2. Grant a shrine/steward-specific user full access to this database. The installer by default uses the same credentials as it does for the SHRINE query history database, but you are welcome to (and encouraged to!) change this.
3. Run the appropriate schema script included with the steward application
   1. For MySQL, this is https://open.med.harvard.edu/svn/shrine/releases/1.19.12/code/steward/src/main/sql/mysql.ddl
   2. For SQL Server, this is https://open.med.harvard.edu/svn/shrine/releases/1.19.12/code/steward/src/main/sql/sqlserver.ddl

steward.conf - Application config

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1. Start with a sample steward.conf from the installer: https://open.med.harvard.edu/svn/shrine/releases/1.19.12/code/install/i2b2-1.7/shrine/skel/steward.conf
   1. If using the JDBC driver, 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

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1. Start with a sample steward.xml from the installer: https://open.med.harvard.edu/svn/shrine/releases/1.19.12/code/install/i2b2-1.7/shrine/skel/steward.xml
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_STEWARD_MYSQL_USER
   2. SHRINE_STEWARD_MYSQL_PASSWORD
   3. SHRINE_STEWARD_MYSQL_HOST
   4. SHRINE_STEWARD_DB_NAME
3. Save this file to /opt/shrine/tomcat/conf/Catalina/localhost/steward.xml

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It may take a few seconds for the page to load, but after it does load, verify that the value for <shrineVersion> matches the version that was just deployed. If it is still displaying an old version, repeat steps 1 and 4 to redeploy the shrine.war file and start SHRINE again. Example output from this report for SHRINE 1.19.1 2 can be seen below:

<versionInfo>
  <shrineVersion>1.19.1<2</shrineVersion>
  <ontologyVersion>UNKNOWN</ontologyVersion>
  <adapterMappingsVersion>Unknown</adapterMappingsVersion>
  <scmRevision>(not available)</scmRevision>
  <scmBranch>UNKNOWN_BRANCH</scmBranch>
  <buildDate>2015-06-0430 0918:2103:05<57</buildDate>
</versionInfo>