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Clean up shrine.conf

shrine.conf is considerably more compact than in SHRINE 1.25.4, and slightly more compact than in SHRINE 2.3.0.0. Take this opportunity to clean out the file in older installations. See the example file start with a fresh shrine.conf file available in shrine-setup/qep-and-adapter-shrine.conf as a starting point.

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Add password.conf

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file 

Move shrine.keystore.password and shrine.hiveCredentials.password properties Shrine no longer uses broadcasterServiceEndpoint in shrine.conf . Delete that from shrine.conf to save confusion.

Add a Timezone Parameter to mysql URLs in /opt/shrine/tomcat/conf/context.xml (MariaDB only)

Inside /opt/shrine/tomcat/conf/context.xml, add a ?serverTimezone=UTC parameter to each mysql URL. (No change is needed if you are using a different brand of database.)

...
<Context>
    <WatchedResource>WEB-INF/web.xml</WatchedResource>
    <Resource name="jdbc/problemDB" auth="Container" type="javax.sql.DataSource"
              maxTotal="128" maxIdle="32" maxWaitMillis="10000"
              username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/shrine_query_history?serverTimezone=UTC"
              testOnBorrow="true" validationQuery="SELECT 1" />
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New Endpoint for the ACT aim 3 Plugins

If your site uses the ACT aim 3 plugins reconfigure them to use this SHRINE endpoint URL:

https://your.shrine.node:6443/shrine-api/aim3/xml

Remove akka and permgen parameters from setenv.sh

With earlier versions of the JDK SHRINE needed a few arguments involving akka and permgen. Remove these. Set -Xmx to use all but one gigabyte of your system's memory. A typical SHRINE setenv.sh will look like:

# Set Tomcat options
export CATALINA_OPTS="$CATALINA_OPTS -server -Xms1024m -Xmx3072m -Duser.timezone=America/New_York"

Ensure that adapterMappingsFileName exists in shrine.conf

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password.conf. The password.conf file should contain the following properties:

shrine.keystore.password = "<enter your password>"
shrine.hiveCredentials.password = "<enter your password>"

Update shrine.conf

• Remove pmEndpoint.url. Add pmEndpoint.urlPath property to shrine.conf only if different from default value of /i2b2/services/PMService/getServices/. This value will be appended to the i2b2BaseUrl. 
• Remove ontEndpoint.url. Add ontEndpoint.urlPath property to shrine.conf only if different from default value of /i2b2/services/rest/OntologyService/. This value will be appended to the i2b2BaseUrl. 
• Remove adapter.crcEndpoint.url. Add adapter.crcEndpoint.urlPath property to shrine.conf only if different from default value of /i2b2/services/QueryToolService/. This value will be appended to the i2b2BaseUrl. 
• Remove breakdownResultOutputTypes.
• Move shrine.messagequeue element to to shrine.hub.messagequeue.
• Move i2b2BaseUrl and shrinehubBaseUrl into the main shrine{} block.

Updated shrine.conf

shrine {


  shrineHubBaseUrl = "https://shrine-hub.faraway.com:6443" //The shrine hub's URL as observed from this tomcat server
  i2b2BaseUrl = "http://i2b2.example.com:9090" //The local i2b2's URL as observed from this tomcat server
  i2b2Domain = "exampleDomain"
  i2b2ShrineProjectName = "SHRINE"


  nodeKey = "testNode" //node key to get information from the hub about this node.


  //shrineDatabaseType = "mysql" // "mysql" by default. It can be "sqlserver" "mysql" or "oracle"


  webclient {
   siteAdminEmail = "shrine-admin@example.com"
  }
  
  hiveCredentials {
    username = "demo"
    crcProjectId = "Demo"
  }//hiveCredentials


  keystore {
    privateKeyAlias = "shrine-node1"
    caCertAliases = ["shrine-ca"]
  }//keystore


  steward {
    emailDataSteward {
      //provide the email address of the shrine node system admin, to handle bounces and invalid addresses
      from = "shrine-admin@example.com"
      //provide the email address of the shrine node system admin, to handle bounces and invalid addresses
      to = "shrine-steward@example.com"
      //provide the externally-reachable URL for the data steward
      externalStewardBaseUrl = "https://shrine.example.com:6443/shrine-api/shrine-steward"
    }
  }//steward
}//shrine

(Optional) Require a specific project for users

To require users to be a member of a specific PM cell project.

shrine.authenticate.pmProjectName = "ACT"

(Optional) Override default info logging level

Override with environmental override in /opt/shrine/tomcat/webapps/shrine-api/WEB-INF/classes/logback.xml. Below is an example of changing the logging level to debug:

<logger name="net.shrine" additivity="false" level="debug">
 <appender-ref ref="shrine"/>
</logger>

shrine {
...  
  adapter {
...
    adapterMappingsFileName = "AdapterMappings.csv"
...
  }//adapter
...
}//shrine