Get the Latest Code
Make sure that you have cloned the last code, and make sure you are on the
git clone https://github.com/cBioPortal/cbioportal.git git checkout master
Prepare the log4j.properties File
This file configures logging for the portal. An example file is available within GitHub:
cd src/main/resources cp logback.xml.EXAMPLE logback.xml
If you don't create your own
logback.xml, maven will copy the EXAMPLE file to that location when it builds.
logback.xml already exists, it will just use that. This allows us to give you a working, versioned
log config, which you can then override easily.
To modify the logging during tests the same EXAMPLE file can be copied to the relevant test resources folder.
Create the cBioPortal MySQL Databases and User
You must create a
cbioportal database and a
cgds_test database within MySQL, and a user account with rights to access both databases. This is done via the
> mysql -u root -p Enter password: ******** Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 64 Server version: 5.6.23 MySQL Community Server (GPL) Copyright (c) 2000, 2015, Oracle and/or its affiliates. All rights reserved. mysql> create database cbioportal; Query OK, 1 row affected (0.00 sec) mysql> create database cgds_test; Query OK, 1 row affected (0.00 sec) mysql> CREATE USER 'cbio_user'@'localhost' IDENTIFIED BY 'somepassword'; Query OK, 0 rows affected (0.00 sec) mysql> GRANT ALL ON cbioportal.* TO 'cbio_user'@'localhost'; Query OK, 0 rows affected (0.00 sec) mysql> GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost'; Query OK, 0 rows affected (0.00 sec) mysql> flush privileges; Query OK, 0 rows affected (0.00 sec)