edu.dfci.cccb.mev.limma.domain.cli.CliRLimmaTest.java Source code

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Here is the source code for edu.dfci.cccb.mev.limma.domain.cli.CliRLimmaTest.java

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package edu.dfci.cccb.mev.limma.domain.cli;

/**
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

import static edu.dfci.cccb.mev.dataset.domain.contract.Dimension.Type.COLUMN;
import static java.util.Arrays.asList;
import static org.hamcrest.Matchers.any;
import static org.hamcrest.Matchers.closeTo;
import static org.hamcrest.core.Is.is;
import static org.junit.Assert.assertThat;

import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Properties;

import javax.script.ScriptEngineManager;

import lombok.extern.log4j.Log4j;

import org.apache.commons.io.IOUtils;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;

import edu.dfci.cccb.mev.dataset.domain.contract.Dataset;
import edu.dfci.cccb.mev.dataset.domain.contract.DatasetException;
import edu.dfci.cccb.mev.dataset.domain.contract.Selection;
import edu.dfci.cccb.mev.dataset.domain.fs.FlatFileValueStoreBuilder;
import edu.dfci.cccb.mev.dataset.domain.mock.MockTsvInput;
import edu.dfci.cccb.mev.dataset.domain.simple.SimpleDatasetBuilder;
import edu.dfci.cccb.mev.dataset.domain.simple.SimpleSelection;
import edu.dfci.cccb.mev.dataset.domain.supercsv.SuperCsvComposerFactory;
import edu.dfci.cccb.mev.dataset.domain.supercsv.SuperCsvParserFactory;
import edu.dfci.cccb.mev.limma.domain.contract.Limma;
import edu.dfci.cccb.mev.limma.domain.contract.Limma.Entry;
import edu.dfci.cccb.mev.limma.domain.contract.Limma.GoEntry;
import edu.dfci.cccb.mev.limma.domain.contract.Limma.Species;
import edu.dfci.cccb.mev.limma.domain.simple.StatelessScriptEngineFileBackedLimmaBuilder;

/**
 * @author levk
 * 
 */
@Log4j
public class CliRLimmaTest {

    Limma result;

    @Before
    public void setupLimmaResult() throws IOException, DatasetException {
        try (InputStream inp = getClass().getResourceAsStream("/mouse_test_dataset.tsv");
                ByteArrayOutputStream copy = new ByteArrayOutputStream()) {
            IOUtils.copy(inp, copy);
            Dataset dataset = new SimpleDatasetBuilder().setParserFactories(asList(new SuperCsvParserFactory()))
                    .setValueStoreBuilder(new FlatFileValueStoreBuilder())
                    .build(new MockTsvInput("mock", copy.toString()));
            Selection experiment = new SimpleSelection("experiment", new Properties(), asList("A", "B", "C"));
            Selection control = new SimpleSelection("control", new Properties(), asList("D", "E", "F"));
            dataset.dimension(COLUMN).selections().put(experiment);
            dataset.dimension(COLUMN).selections().put(control);
            result = new StatelessScriptEngineFileBackedLimmaBuilder()
                    .r(new ScriptEngineManager().getEngineByName("CliR"))
                    .composerFactory(new SuperCsvComposerFactory()).dataset(dataset).control(control)
                    .experiment(experiment).species(Species.MOUSE).go("BP").test("Fisher test").build();
        }
    }

    //TODO: TopGO part of the analysis is broken. Need to re-enable this test once it is fixed. 
    //For now testNoTopGoResult() tests only the limma portion
    @Test
    @Ignore
    public void test() throws Exception {
        for (Entry e : result.full())
            log.debug("Full limma entry: " + e);
        for (GoEntry e : result.topGo())
            log.debug("topGo entry: " + e);

        assertThat(result.full().iterator().next().averageExpression(), closeTo(12.985, 0.001));
        assertThat(result.topGo().iterator().next().pValue(), any(Double.class));
    }

    @Test
    public void testNoTopGoResult() throws Exception {

        for (Entry e : result.full())
            log.debug("Full limma entry: " + e);
        for (GoEntry e : result.topGo())
            log.debug("topGo entry: " + e);

        assertThat(result.full().iterator().next().averageExpression(), closeTo(12.985, 0.001));
        assertThat(result.topGo().iterator().hasNext(), is(false));

    }
}