au.org.ala.delta.dist.DISTTest.java Source code

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Here is the source code for au.org.ala.delta.dist.DISTTest.java

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/*******************************************************************************
 * Copyright (C) 2011 Atlas of Living Australia
 * All Rights Reserved.
 * 
 * The contents of this file are subject to the Mozilla Public
 * License Version 1.1 (the "License"); you may not use this file
 * except in compliance with the License. You may obtain a copy of
 * the License at http://www.mozilla.org/MPL/
 * 
 * Software distributed under the License is distributed on an "AS
 * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or
 * implied. See the License for the specific language governing
 * rights and limitations under the License.
 ******************************************************************************/
package au.org.ala.delta.dist;

import java.io.File;
import java.net.URL;

import junit.framework.TestCase;

import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.junit.Before;
import org.junit.Test;

/**
 * This is an integration test for the DIST program.
 */
public class DISTTest extends TestCase {

    private String _path;

    @Before
    public void setUp() throws Exception {
        File dataSetDirectory = urlToFile("/dataset");
        File dest = new File(System.getProperty("java.io.tmpdir"));
        FileUtils.copyDirectory(dataSetDirectory, dest);
        _path = dest.getAbsolutePath();
    }

    @Test
    public void testDISTWithSample() throws Exception {
        String path = FilenameUtils.concat(_path, "sample");

        runDIST(FilenameUtils.concat(path, "dist"));
        checkResults(path, "grass.nam", false);
        checkResults(path, "grass.dis", true);
    }

    /**
     * Still uses the sample data as input, but tests the PHYLIP FORMAT,
     * MATCH OVERLAP and EXCLUDE ITEMS directives.
     */
    @Test
    public void testDISTPhylipFormatMatchOverlap() throws Exception {
        String path = FilenameUtils.concat(_path, "sample");

        runDIST(FilenameUtils.concat(path, "dist2"));
        checkResults(path, "grass2.dis", false);
    }

    private void checkResults(String path, String resultFileName, boolean compareAsFloats) throws Exception {

        java.io.File expectedFile = new File(FilenameUtils.concat(path, "expected_results/" + resultFileName));
        String expected = FileUtils.readFileToString(expectedFile, "cp1252");

        System.out.println(expected);

        File actualFile = new File(FilenameUtils.concat(path, resultFileName));
        String actual = FileUtils.readFileToString(actualFile, "cp1252");

        System.out.print(actual);
        expected = replaceNewLines(expected);

        if (compareAsFloats) {
            String[] actualFloats = actual.trim().split("\\s+");
            String[] expectedFloats = expected.trim().split("\\s+");
            for (int i = 0; i < expectedFloats.length; i++) {
                float float1 = Float.valueOf(actualFloats[i]);
                float float2 = Float.valueOf(expectedFloats[i]);
                assertEquals("index " + i, float2, float1, 0.001f);
            }
        }

        assertEquals(expected, actual);
    }

    protected String replaceNewLines(String expected) {
        boolean dosEol = expected.contains("\r\n");
        String expectedLineSeparator = "\n";
        if (dosEol) {
            expectedLineSeparator = "\r\n";
        }

        if (!System.getProperty("line.separator").equals(expectedLineSeparator)) {
            expected = expected.replaceAll(expectedLineSeparator, System.getProperty("line.separator"));
        }
        return expected;
    }

    private void runDIST(String... args) throws Exception {
        DIST.main(args);
    }

    private File urlToFile(String urlString) throws Exception {
        URL url = DISTTest.class.getResource(urlString);
        File file = new File(url.toURI());
        return file;
    }
}