# Introduction

This page is about how to run and debug, in an IDE agnostic way, any test classes added to the backend (Java layer).

# Steps

# Set up test instance of MySQL server

# System installed (assumes Linux OS)

Start mysql:

sudo systemctl start mysql

Log into database:

sudo mysql -u root

mysql -u root -p

In the MySQL console run:

SET GLOBAL local_infile=1;
CREATE DATABASE cgds_test;
CREATE USER 'cbio_user'@'localhost' IDENTIFIED BY 'somepassword';
GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost';
FLUSH PRIVILEGES;
SET default_storage_engine=InnoDB;
SET SESSION sql_mode = 'ANSI_QUOTES';

(Optional) Load schema and seed:

When running tests through Maven this step can be skipped. In MySQL console run:

source <path-to-file>/cgds-test.sql
source <path-to-file>/seed_mini.sql

# Note

Cgds-test.sql should be generated with /db-scripts/src/main/resources/gen-cgds-test-schema.sh.

# Docker container

Create file init.sql with the following contents:

SET GLOBAL local_infile=1;
CREATE DATABASE cgds_test;
CREATE USER 'cbio_user'@'localhost' IDENTIFIED BY 'somepassword';
GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost'";
FLUSH PRIVILEGES;
SET default_storage_engine=InnoDB;
SET SESSION sql_mode = 'ANSI_QUOTES';

Run (making sure the file paths are correct):

 docker run -ti --rm \
  --name testdb \
  --env MYSQL_ROOT_PASSWORD=root \
  --env MYSQL_USER=cbio_user \
  --env MYSQL_PASSWORD=somepassword \
  --env MYSQL_DATABASE=cgds_test \
  -v <path-to-file>/init.sql:/docker-entrypoint-initdb.d/first_file.sql \
  -v <path-to-file>/cgds-test.sql:/docker-entrypoint-initdb.d/second_file.sql \
  -v <path-to-file>/seed_mini.sql:/docker-entrypoint-initdb.d/third_file.sql \
  -p 3306:3306 mysql:5.7
  --ssl=0

# Notes

When running tests through Maven, the line with volume mounts (starting with -v) to the schema (cgds-test.sql) and seed (seed_mini.sql) should be skipped.
Cgds-test.sql should be generated with /db-scripts/src/main/resources/gen-cgds-test-schema.sh.

# Running the tests with Maven

Make sure you have built the project once with e.g. mvn clean install -DskipTests
Run integration tests with

mvn integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword

This will create the tables in cgds_test and populate your schema with test data.

you can run all other tests with

mvn test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword

you can run a specific test with

mvn test -pl core -Dtest=TestIntegrationTest -Ddb.test.username=cbio -Ddb.test.password= <your_db_password>

where -pl is the name of the module (in this example core) and -Dtest is the name of the Java test class (in this example TestIntegrationTest).

you can debug a specific test with

mvn integration-test -Dmaven.surefire.debug -pl core test -Dtest=TestIntegrationTest -Ddb.test.username=cbio -Ddb.test.password=<your_db_password> 

where -pl is the name of the module (in this example core) and -Dtest is the name of the Java test class (in this example TestIntegrationTest). This command will pause execution and wait for you to connect your IDE to the listening port, reporting something like below:

[INFO] Surefire report directory: /cbioportal/core/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Listening for transport dt_socket at address: 5005

Once you connected your IDE (after setting a breakpoint in the code), the execution will continue in your debugger view.