cBioPortal at UHN

Local deployment and usage guide

Developer Guide

How to spin up a portal with Maven

1. Use a Maven settings.xml like this:

<?xml version="1.0" encoding="UTF-8"?>
<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
      xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
                          http://maven.apache.org/xsd/settings-1.0.0.xsd">
  <servers>
    <server>
      <id>cbioportal_test</id>
      <username>xxxx</username>
      <password>xxxx</password>
    </server>
  </servers>

  <profiles>
    <profile>
    <id>env-test</id>
      <properties>
        <db.test.serverkey>settingsKey</db.test.serverkey>
        <db.test.driver>com.mysql.jdbc.Driver</db.test.driver>
        <db.test.url>jdbc:mysql://xxxx:3306/xxxx?sessionVariables=sql_mode=ansi</db.test.url>
        <db.test.username>xxxx</db.test.username>
        <db.test.password>xxxx</db.test.password>
      </properties>
    </profile>
  </profiles>

  <activeProfiles>
    <activeProfile>env-test</activeProfile>
  </activeProfiles>
</settings>

But use your database server server host and credentials instead of the xxxxs.

2. Check out and run the portal

git clone https://github.com/pughlab/cbioportal.git
cd cbioportal
cp src/main/resources/portal.properties.EXAMPLE portal.properties
cp src/main/resources/log4j.properties.CONSOLE log4j.properties
mvn verify -P test-portal

How to spin up a portal in Eclipse

First do everything above, checking out the server and setting up the Maven settings, as Maven writes these into a few files in a way that Eclipse doesn’t. Then:

3. From a command line

mvn process-test-resources eclipse:eclipse

4. Within Eclipse

Select server/src/main/java/org/mskcc/cbio/server/httpd/CBioPortalJettyServer
Run as application…

The following settings are needed too. You can set these under Run Configurations...

In Program Arguments, set: -Dorg.eclipse.jetty.webapp.LEVEL=DEBUG
In Environment, add a variable PORTAL_HOME with the value: ${git_dir}/..

Now when you run the application, it should spin up a complete portal, with the mini data set, on the URL: http://localhost:8080