In most cases, upgrading an existing instance of SHRINE is a relatively quick process. Exceptions to this rule include older versions of SHRINE that contained substantial changes to configuration files and other portions of the file structure. The instructions here specifically describe an upgrade path from SHRINE 1.25.4 to SHRINE 2.0.0.
SHRINE 2.0.0 is not backwards-compatible with any previous version!
This guide makes the following assumptions of a current 1.25.4 system. Make sure all of these conditions are satisfied before proceeding:
- i2b2 1.7.09c is installed and operational.
- SHRINE 1.25.4 is installed and operational.
- The SHRINE Data Steward has been installed and configured properly.
- The SHRINE Dashboard has been installed and configured properly.
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, especially with unpacking new .war files. Simply run the following command:
Backup your current SHRINE configuration
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.
Start by creating a folder to contain these backups:
Make especially sure that the shrine-webclient/ folder is backed up. If you choose not to make any backups, make sure to at least keep a copy of i2b2_config_data.js and js-i2b2/cells/SHRINE/cell_config_data.js!
Make especially sure that the shrine.keystore is backed up. If you lose the private side of a cert you may not be able to recover it.
Remove old SHRINE components
SHRINE will use new components, so to avoid conflicts with older files, you can remove the old .war files with this command:
Also, you can remove all the existing folders from the /webapps directory:
Deploy New .war Files
Deploy New SHRINE Core
Next, we will retrieve the new SHRINE war files from the HMS Sonatype Nexus server at: https://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/shrine-war/2.0.0/. From there, download shrine-war-2.0.0.war to the webapps/ directory on the SHRINE server and rename it to shrine.war.
Deploy New SHRINE API Service
Like other SHRINE artifacts, the SHRINE API Service can be found on the HMS Sonatype Nexus server at https://repo.open.med.harvard.edu/nexus/content/groups/public/net/shrine/shrine-api-war/2.0.0/. From there, download shrine-api-war-2.0.0.war to the webapps/ directory on the SHRINE server and rename it to shrine-api.war.
Changes to SHRINE's Configuration File - shrine.conf
Since SHRINE 1.25.4, there are a couple of changes to SHRINE's configuration file. If you want to, skip ahead to the sample shrine.conf section and copy the entire contents of the file for use (replacing with your own site specific values).
Part of the new data service allows a node to look up information about itself
Each node can ask the hub about itself and the hub. To ask about itself it needs a shared key with the hub. This will be a unique identifier, ie. "HarvardProdNode". Add that to shrine.conf:
Remove the QEP user from the PM cell, and corresponding section from shrine.conf
Shrine now accesses the DSA's database directly from inside shrine-api.war. It no longer needs a special QEP user to authenticate to the Data Steward service. Delete that user from the PM cell, and remove this section from shrine.conf:
Remove the formerly required "includeAggregateResults = false" from shrine.conf .
Configure the webclient in shrine.conf
In SHRINE 2.0.0, you will need additional parameters to configure the behavior of the webclient. Please add this section in shrine.conf:
The webclient has hard-coded default values for the userNameLabel, passwordLabel, and defaultNumberOfOntologyChildren fields if they are not configured; userNameLabel defaults to "SHRINE User", passwordLabel defaults to "SHRINE Password", and defaultNumberOfOntologyChildren defaults to 10000.
Remove Human-Readable node name property from shrine.conf
The nodeKey property is used by SHRINE internally instead, and the node structure (stored at the hub) holds a real human-readable name with a good assortment of punctuation and spaces, therefore, you will not need this line in shrine.conf anymore.
Redirect webclient, steward, and dashboard to old URL links
Before you perform these steps, please make sure your Tomcat version is at least 8.5.x, but please do not install Tomcat version 9!
The URL to the SHRINE Webclient has changed from https://shrine_url:6443/shrine-webclient to https://shrine_url:6443/shrine-api/shrine-webclient.
The URL to the SHRINE Dashboard has changed from https://shrine_url:6443/shrine-dashboard to https://shrine_url:6443/shrine-api/shrine-dashboard.
To redirect the old URL and preserve existing bookmarks and history in browsers, specify a URL rewrite in Tomcat.
1. Add rewrite valve to conf/server.xml inside the Host configuration section
<Host name="localhost" appBase="webapps"
<Valve className="org.apache.catalina.valves.rewrite.RewriteValve" />
2. Create a file name rewrite.config in conf/Catalina/localhost with the following contents
RewriteRule ^/shrine-webclient/* /shrine-api/shrine-webclient
RewriteRule ^/steward/* /shrine-api/shrine-steward
RewriteRule ^/shrine-dashboard/* /shrine-api/shrine-dashboard
No need to specify a slick driver anymore
Now the system can select the slick driver based on the shrineDatabaseType property in shrine.conf.
If the selected slick driver causes problems it is OK to use the old properties - which will override the one chosen via shrineDatabaseType.
Sample SHRINE configuration file (for a downstream node)
Here's a sample shrine.conf for a 2.0.0 downstream node (it might be helpful to copy the entire contents of this file and then replace with your own institution's specific values):
New nodeKey parameter
The nodeKey parameter will be used to identify your node from the Hub, so we advise that it should be a relatively unique identifier along with the network in which you are in, ie. HarvardProdNode or similar. If you have any questions, please contact the network administrator for more information.
Changes to SHRINE databases
In SHRINE 2.0.0, there are a couple of database changes that you will need to perform to accommodate the new tables and structures needed for SHRINE to work properly.
Remove the PRIVILEGED_USER table and associated constraints and sequences from your database
Drop the column of actual patient counts from the adapter's COUNT_RESULT table
Shrine no longer needs to store the actual (and mildly sensitive) actual count of patients from the CRC in its COUNT_RESULT table. In mysql remove it from the shrine_query_history database with
Drop the column of actual patient counts from the adapter's BREAKDOWN_RESULT table
Shrine no longer needs to store the actual (and mildly sensitive) actual count of patients from the CRC in its BREAKDOWN_RESULT table. In mysql remove it from the shrine_query_history database with
Add a status column for queries at the QEP
Add a status column to qepAuditDB's previousQueries table to support updates in query status with :
Added table QUERY_PROBLEM_DIGESTS
Added table RESULTS_OBSERVED
Make sure you have setenv.sh defined for Tomcat startup
For SHRINE 2.0.0 in addition to the 2.0.1 ACT ontology, we will need to make sure that Tomcat has enough resources to load the ontology and its larger Adapter Mappings file. To do this, you will need to define a setenv.sh file within the tomcat/bin directory:
At this time, please reach out to the network hub administrator so that they can add your individual node to the network with the "nodeKey" that was identified in shrine.conf. Once added to the hub, your node should then start sending and receiving queries. You'll also need to tell the admin your domain parameter, so that the domain will be associated with the nodeKey on the hub.
The only thing left to do at this point is start SHRINE back up. Simply do the following:
Verify SHRINE Upgrade
After starting SHRINE up, verify that the upgrade was properly deployed by checking the SHRINE Dashboard for the version number. The exact address you will need to go to depends on your configuration, but the general format looks like the following:
This is a sample screenshot of the upgraded 2.0.0 dashboard:
You should check to see if you are able to execute a query and see results come back from your own site as well as others on the network. If you do not see your own site and/or other sites, please submit a JIRA ticket with the issue and notify your network administrator.