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Shut Down SHRINE

Before starting the upgrade process, make sure SHRINE's Tomcat is not running. Leaving it running during this process can cause problems. Simply run the following command:

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$ /opt/shrine/tomcat/bin/shutdown.sh

Create Backups

Now that SHRINE is stopped, it is a good idea to back up the current versions of the components we will be upgrading. The exact method for making this backups may vary, but these instructions will place the backups in a folder called /opt/shrine/upgrade-backups.

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$ mv /opt/shrine/tomcat/webapps/shrine-webclient /opt/shrine/upgrade-backups/shrine-webclient

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 1.21.1. From there, download shrine-war-1.21.1.war to the webapps/ directory of the Tomcat installation that SHRINE uses and rename it to 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/shrine-war/1.21.1/shrine-war-1.21.1.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 1.21.1. From there, download shrine-proxy-1.21.1.war to the webapps/ directory of the Tomcat installation that SHRINE uses and rename it to shrine-proxy.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/1.21.1/shrine-proxy-1.21.1.war -O shrine-proxy.war

Deploy New SHRINE Webclient

NOTE: Installation procedures for this component have changed after 1.19.x! Please be careful. Starting with 1.20.x, the SHRINE webclient is packaged as a zip file, and no longer requires a checkout from the old SHRINE SVN repository.

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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-webclient/1.21.1/shrine-webclient-1.21.1-dist.zip -O shrine-webclient.zip
$ unzip shrine-webclient.zip

Restore Webclient Backups

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

$ cp /opt/shrine/upgrade-backups/shrine-webclient/i2b2_config_data.js /opt/shrine/tomcat/webapps/shrine-webclient/i2b2_config_data.js
$ cp /opt/shrine/upgrade-backups/shrine-webclient/js-i2b2/cells/SHRINE/cell_config_data.js /opt/shrine/tomcat/webapps/shrine-webclient/js-i2b2/cells/SHRINE/cell_config_data.js

Deploy New SHRINE Dashboard

NOTE: This component is a working prototype, and simply mirrors information from the existing SHRINE Happy module in its current state. Additional functionality is coming in a future release.

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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/dashboard-war/1.21.1/dashboard-war-1.21.1.war -O shrine-dashboard.war

(Optional) For Users of Oracle or SQL Server

If you experience issues in getting the audit logging functionality working with Oracle or SQL Server, please try the instructions in this article written by a SHRINE developer: Using SHRINE Data Steward with Oracle or SQL Server (the instructions within also apply to the audit logging functionality).

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Replace "freeslick.driverNameHere$" with the name of the driver you are using ("freeslick.OracleProfile$" for Oracle, and "freeslick.MSSQLServerProfile$" for SQL Server).

Update PRIVILEGED_USER Table Structure

The PRIVILEGED_USER table now allows a user's query threshold to be set to NULL to allow it to fall back to the current value in shrine.conf. Run the following queries on your SHRINE query history database:

alter table PRIVILEGED_USER modify column threshold int null;

Create Additional QEP Audit Database Tables

Additional tables have been added to the qepAuditDB database to support storing query results at the QEP level. Run the following queries on your QEP audit database:

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These SQL statements are for MySQL. If you are using Oracle or SQL Server, use either oracle.ddl or mssql.ddl instead: https://open.med.harvard.edu/stash/projects/SHRINE/repos/shrine/browse/qep/service/src/main/sql?at=refs%2Ftags%2F1.21.1

Modify shrine.conf

The default configuration has changed in SHRINE 1.21 to no longer create a hub unless explicitly asked to. This mirrors the most common installation scenario: a member site connecting to an already established hub. However, on the HMS network, every site is its own hub that broadcasts out to all other sites on its own.

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hub {
  create = true
  [...]
}

Migrate Query History to QEP

This step is crucial if you wish to preserve your previous queries!

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Depending on the size of your database, this process may take a few minutes.

Start SHRINE

The only thing left to do at this point is start SHRINE back up. Simply do the following:

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$ /opt/shrine/tomcat/bin/startup.sh

Verify SHRINE Upgrade

After starting SHRINE up, verify that the upgrade was properly deployed by checking the SHRINE Dashboard. The exact address you will need to go to depends on your configuration, but the general format looks like the following:

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