How to run cbioportal tomcat war using heroku's webapp-runner.jar

Question

I've been following the tutorial from Heroku ( https://devcenter.heroku.com/articles/java-webapp-runner ) to learn how to run a war file using webapp-runner.jar. Now I would like to run cbioportal ( https://github.com/cbioportal/cbioportal ) on heroku. I've managed to add the webapp-runner.jar as a dependency, see: https://github.com/inodb/cbioportal/tree/heroku .

When I run the following from the repo directory:

java -Djava.naming.factory.initial=org.apache.naming.java.javaURLContextFactory \
    -jar portal/target/dependency/webapp-runner.jar --port 9099 portal/target/portal

I get an error like this:

SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityMapper' defined in class path resource [applicationContext-business.xml]: Cannot resolve reference to bean 'sqlSessionFactory' while setting bean property 'sqlSessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sqlSessionFactory' defined in class path resource [applicationContext-business.xml]: Cannot resolve reference to bean 'businessDataSource' while setting bean property 'dataSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'businessDataSource' defined in class path resource [applicationContext-business.xml]: Invocation of init method failed; nested exception is javax.naming.NameNotFoundException: Name [java:comp/env/jdbc/mydb] is not bound in this Context. Unable to find [java:comp].

I've tried passing the context.xml of my local Tomcat install and setting the mysql connection string directly in the file but to no avail.

Answer 1

I think you'll need to register the DB URL as a JNDI resource in a context.xml file, maybe like this:

<Context>
  <Resource name="jdbc/cbioportal" auth="Container" type="javax.sql.DataSource"
               maxTotal="100" maxIdle="30" maxWaitMillis="10000"
               username="user" password="pass" driverClassName="com.mysql.jdbc.Driver"
               url="jdbc:mysql://localhost:3306/dbname"/>
</Context>

Then you'd need to add that context XML as an option to the java command like this:

$ java ... \
    -jar portal/target/dependency/webapp-runner.jar \
    --context-xml context.xml --port 9099 \
    portal/target/portal

For the url in the context.xml , you'll have to get that from your $ heroku config and convert it into a jdbc url. It is available at runtime as $JDBC_DATABASE_URL , but I'm not sure how to get that into the context.xml dynamically.

For that reason, I think you're better off not using JNDI if possible. Can you configure the DB params directly in your app?

I got the JNDI name from this line in your config

For more on JNDI with Tomcat see the Tomcat docs .

For more on webapp-runner options see the project readme .