OncoKB Core

Repository for OncoKB, a precision oncology knowledge base.

The core of OncoKB Annotation service.

Status

Info

Running Environment

Please confirm your running environment is:

• Java version: 8
• MySQL version: 5.7.28

MySQL db dump

oncokb_v3_11_db_dump.sql.gz

Prepare properties files

cp -r core/src/main/resources/properties-EXAMPLE core/src/main/resources/properties

Properties file

1. database.properties
   • jdbc.driverClassName : We use mysql as database. Here, it will be com.mysql.jdbc.Driver
   • jdbc.url: Database url
   • jdbc.username & jdbc.password: MySQL user name and password
2. config.properties
   • oncotree.api: OncoTree service. Default: http://oncotree.info/api/
   • google.username & google.password(Optional) : Google account info. It is used to send email

Build the WAR file

mvn clean && mvn package -P curate -DskipTests

The WAR file is under /web/target/

Deploy with frontend

Please choose one of the profile when building the war file

• curate - core + API + curation website
• public - core + API + public website (deprecated)

You could find specific instructions in curate or public repo,

Questions?

The best way is to send an email to contact@oncokb.org so all our team members can help.