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:
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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
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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 |
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<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" />
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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.
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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
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<logger name="net.shrine" additivity="false" level="debug">
<appender-ref ref="shrine"/>
</logger>
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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:
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# Set Tomcat options
export CATALINA_OPTS="$CATALINA_OPTS -server -Xms1024m -Xmx3072m -Duser.timezone=America/New_York"
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Ensure that adapterMappingsFileName exists in shrine.conf
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language | js |
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theme | RDark |
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title | shrine.conf |
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shrine {
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adapter {
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adapterMappingsFileName = "AdapterMappings.csv"
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}//adapter
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}//shrine |