RnaSeqDgeExampleTest.java

/**
 * Copyright 2014 VU University Medical Center.
 * Licensed under the Apache License version 2.0 (see http://www.apache.org/licenses/LICENSE-2.0.html).
 */

package nl.vumc.biomedbridges.examples;

import com.google.inject.Guice;

import nl.vumc.biomedbridges.core.Constants;
import nl.vumc.biomedbridges.core.DummyWorkflow;
import nl.vumc.biomedbridges.core.TestGuiceModule;
import nl.vumc.biomedbridges.core.Workflow;
import nl.vumc.biomedbridges.core.WorkflowFactory;
import nl.vumc.biomedbridges.core.WorkflowType;

import org.junit.Test;

import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;

/**
 * Unit tests for the RnaSeqDgeExample class.
 *
 * @author <a href="mailto:f.debruijn@vumc.nl">Freek de Bruijn</a>
 */
public class RnaSeqDgeExampleTest {
    /**
     * Test the RNA-Seq differential gene expression example under normal circumstances.
     */
    @Test
    public void testRnaSeqDgeExampleNormal() {
        final RnaSeqDgeExample example = Guice.createInjector(new TestGuiceModule()).getInstance(RnaSeqDgeExample.class);
        addDummyOutput(example.workflowFactory, 7);
        assertTrue(example.runExample(Constants.THE_HYVE_GALAXY_URL));
    }

    /**
     * Test the RNA-Seq differential gene expression example with a workflow returning false.
     */
    @Test
    public void testRnaSeqDgeExampleReturningFalse() {
        final RnaSeqDgeExample example = Guice.createInjector(new TestGuiceModule()).getInstance(RnaSeqDgeExample.class);
        addDummyOutput(example.workflowFactory, 0);
        DummyWorkflow.setReturnedResult(false);
        assertFalse(example.runExample(Constants.THE_HYVE_GALAXY_URL));
    }

    /**
     * Test the RNA-Seq differential gene expression example with a workflow throwing an exception.
     */
    @Test
    public void testRnaSeqDgeExampleThrowingException() {
        final RnaSeqDgeExample example = Guice.createInjector(new TestGuiceModule()).getInstance(RnaSeqDgeExample.class);
        addDummyOutput(example.workflowFactory, 7);
        DummyWorkflow.setThrowException(true);
        assertFalse(example.runExample(Constants.THE_HYVE_GALAXY_URL));
    }

    /**
     * Add dummy output files that could have been generated by the dummy workflow.
     *
     * @param workflowFactory the workflow factory.
     * @param outputCount     the number of dummy output files.
     */
    private void addDummyOutput(final WorkflowFactory workflowFactory, final int outputCount) {
        final Workflow workflow = workflowFactory.getWorkflow(WorkflowType.DEMONSTRATION, null, Constants.WORKFLOW_RNA_SEQ_DGE);
        for (int outputIndex = 0; outputIndex < outputCount; outputIndex++)
            workflow.addOutput("dummy-output-" + (outputIndex + 1), "dummy");
    }
}