au.org.ala.delta.confor.ToNexTest.java Source code

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Here is the source code for au.org.ala.delta.confor.ToNexTest.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.confor;

import java.io.BufferedReader;
import java.io.File;
import java.io.StringReader;

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

/**
 * Tests the TRANSLATE INTO NEXUS FORAMT directive in the context of the sample
 * tonex directives file.
 */
public class ToNexTest extends ConforTestCase {

    /**
     * Because of ISSUE 66 the output from the original CONFOR has been
     * modified by chaning some inappicables to unknowns (and vice versa) 
     * to allow this test to be run as a part of the build.
     */
    @Test
    public void testSampleToNex() throws Exception {
        runConfor();

        File expectedFile = new File(FilenameUtils.concat(_samplePath, "expected_results/nexdata"));
        String expected = FileUtils.readFileToString(expectedFile, "utf-8");

        System.out.println(expected);

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

        System.out.print(actual);

        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"));
        }
        // The heading contains the date so will be different.
        String heading = "Grass Genera 14:43 20-OCT-11"; // <Date>, eg. 11:32 05-OCT-11

        actual = actual.replaceAll("Grass Genera.*[0-9]{2}-[a-zA-Z]{3}-[0-9]{4}", heading);

        for (int i = 0; i < expected.length(); i++) {
            if (expected.charAt(i) != actual.charAt(i)) {
                System.out.println("Difference @ char: " + i + " Expected: " + expected.charAt(i)
                        + (int) expected.charAt(i) + ", Actual: " + actual.charAt(i) + (int) actual.charAt(i));
                break;
            }
        }
        BufferedReader expectedReader = new BufferedReader(new StringReader(expected));
        BufferedReader actualReader = new BufferedReader(new StringReader(actual));
        String expectedLine = expectedReader.readLine();
        String actualLine = actualReader.readLine();
        /*while (expectedLine != null) {
           assertEquals(expectedLine.trim(), actualLine.trim());
           expectedLine = expectedReader.readLine();
           actualLine = actualReader.readLine();
               
        }*/

        assertEquals(expected.trim(), actual.trim());
    }

    @Override
    protected String directivesFileName() {
        return "tonex";
    }

}