edu.umn.msi.tropix.proteomics.test.ProteomicsInputTest.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.test.ProteomicsInputTest.java

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.proteomics.test;

import java.io.File;

import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.testng.annotations.Test;

import edu.umn.msi.tropix.proteomics.BiomlWriter;

public class ProteomicsInputTest {

    @Test(groups = { "unit" })
    public void testProteomicsInput() throws Exception {
        testProteomicsInput(false);
    }

    @Test(groups = { "unit" })
    public void testProteomicsInputFromFile() throws Exception {
        testProteomicsInput(true);
    }

    public void testProteomicsInput(final boolean readFromFile) throws Exception {
        BiomlWriter input = null;
        if (readFromFile) {
            final File tempFile = File.createTempFile("tpxtest", "");
            tempFile.deleteOnExit();
            FileUtils.writeStringToFile(tempFile,
                    IOUtils.toString(getClass().getResourceAsStream("proteomicsInput1.xml")));
            input = new BiomlWriter(tempFile.getAbsolutePath());
        } else {
            input = new BiomlWriter(getClass().getResourceAsStream("proteomicsInput1.xml"));

        }
        boolean wasException = false;
        try {
            input.addVariable("test heading", "test");
        } catch (final IllegalArgumentException e) {
            wasException = true;
        }
        assert wasException;
        input.addHeader("test heading 2");
        input.addVariable("test heading 2", "param1", "param1 value again");
        input.addVariable("test heading 2", "param2", "param2 value");
        final String xml = input.toString();
        assert xml.contains("label=\"test heading 2\"") : "XML did not contain heading 2 label";
        assert xml.contains("label=\"test heading 2, param1\"") : "XML did not contain param1 input";
        assert xml.contains("label=\"test heading 2, param2\"") : "XML did not contain param2 input";
        assert xml.contains(">param1 value again<") : "XML did not contain param1 value";
        assert xml.contains(">param2 value<") : "XML did not contain param2 value";
        assert xml.contains("label=\"test heading, param1\"") : "XML did not contain old param1 value";
        assert xml.contains(">param1 value<") : "XML did not contain old param1 value";
    }
}