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Clean up shrine.conf

shrine.conf is considerably more compact than in SHRINE 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.)

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

...
<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"
      //provide the email address of the shrine  url="jdbc:mysql://localhost:3306/shrine_query_history?serverTimezone=UTCnode system admin, to handle bounces and invalid addresses
      to = "shrine-steward@example.com"
      //provide the externally-reachable URL for the data  testOnBorrow="true" validationQuery="SELECT 1" />
...

Override default logging level from info to debug (Optional)

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:Override with environmental override in shrine/apps/shrine-api-war/src/main/resources/logback.xml, and shrine/commons/util/src/main/resources/logback.xml

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

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