edu.dfci.cccb.mev.deseq.domain.cli.CliRDESeqTest.java Source code

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Here is the source code for edu.dfci.cccb.mev.deseq.domain.cli.CliRDESeqTest.java

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package edu.dfci.cccb.mev.deseq.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 java.io.ByteArrayOutputStream;
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.Ignore;
import org.junit.Test;

import edu.dfci.cccb.mev.dataset.domain.contract.Dataset;
import edu.dfci.cccb.mev.dataset.domain.contract.Selection;
import edu.dfci.cccb.mev.dataset.domain.mock.MapBackedValueStoreBuilder;
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.deseq.domain.contract.DESeq;
import edu.dfci.cccb.mev.deseq.domain.contract.DESeq.Entry;
import edu.dfci.cccb.mev.deseq.domain.simple.StatelessScriptEngineFileBackedDESeqBuilder;

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

    @Test
    @Ignore
    public void test() throws Exception {
        try (InputStream inp = getClass().getResourceAsStream("/test_data.tsv");
                ByteArrayOutputStream copy = new ByteArrayOutputStream()) {
            IOUtils.copy(inp, copy);
            Dataset dataset = new SimpleDatasetBuilder().setParserFactories(asList(new SuperCsvParserFactory()))
                    .setValueStoreBuilder(new MapBackedValueStoreBuilder())
                    .build(new MockTsvInput("mock", copy.toString()));
            Selection experiment = new SimpleSelection("experiment", new Properties(),
                    asList("SA1_06_25_14", "SA2_06_25_14", "SA3_06_25_14", "SA4_006_25_14", "SA5_06_25_14"));
            Selection control = new SimpleSelection("control", new Properties(),
                    asList("SA10-06-25-14", "SA11_06_25_14", "SA12_06_25_14"));
            dataset.dimension(COLUMN).selections().put(experiment);
            dataset.dimension(COLUMN).selections().put(control);
            DESeq result = new StatelessScriptEngineFileBackedDESeqBuilder()
                    .r(new ScriptEngineManager().getEngineByName("CliR"))
                    .composerFactory(new SuperCsvComposerFactory()).dataset(dataset).control(control)
                    .experiment(experiment).build();
            for (Entry e : result.full())
                log.debug("Full DESeq entry: " + e);
        }
    }
}