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

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Here is the source code for au.org.ala.delta.confor.ToKeyTest.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.File;
import java.net.URL;
import java.util.List;

import junit.framework.TestCase;

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

import au.org.ala.delta.io.BinFileMode;
import au.org.ala.delta.io.BinaryKeyFile;
import au.org.ala.delta.key.ItemsFileHeader;

/**
 * Tests the CONFOR tokey process.
 */
public class ToKeyTest extends TestCase {

    @Test
    public void testSampleToKey() throws Exception {

        File tointDirectory = urlToFile("/dataset/");
        File dest = new File(System.getProperty("java.io.tmpdir"));
        FileUtils.copyDirectory(tointDirectory, dest);

        String tokeyFilePath = FilenameUtils.concat(dest.getAbsolutePath(), "sample/tokey");

        CONFOR.main(new String[] { tokeyFilePath });

        String expectedKCharsFilename = FilenameUtils.concat(dest.getAbsolutePath(),
                "sample/expected_results/kchars");
        String expectedKItemsFilename = FilenameUtils.concat(dest.getAbsolutePath(),
                "sample/expected_results/kitems");

        BinaryKeyFile expectedKChars = new BinaryKeyFile(expectedKCharsFilename, BinFileMode.FM_READONLY);
        BinaryKeyFile expectedKItems = new BinaryKeyFile(expectedKItemsFilename, BinFileMode.FM_READONLY);

        String actualKCharsFilename = FilenameUtils.concat(dest.getAbsolutePath(), "sample/kchars");
        String actualKItemsFilename = FilenameUtils.concat(dest.getAbsolutePath(), "sample/kitems");

        BinaryKeyFile kchars = new BinaryKeyFile(actualKCharsFilename, BinFileMode.FM_READONLY);
        BinaryKeyFile kitems = new BinaryKeyFile(actualKItemsFilename, BinFileMode.FM_READONLY);

        int numRecords = expectedKChars.getLength() / BinaryKeyFile.RECORD_LENGTH_BYTES;
        int actualNumRecords = kchars.getLength() / BinaryKeyFile.RECORD_LENGTH_BYTES;

        int count = Math.min(numRecords, actualNumRecords);

        for (int i = 1; i <= count; i++) {
            List<Integer> expectedRecord = expectedKChars.readIntegerList(i, BinaryKeyFile.RECORD_LENGTH_INTEGERS);
            List<Integer> actualRecord = kchars.readIntegerList(i, BinaryKeyFile.RECORD_LENGTH_INTEGERS);

            System.out.println("Record: " + i);
            System.out.println(expectedRecord);
            System.out.println(actualRecord);

            System.out.println("Expected as string: ");
            System.out.println(expectedKChars.readString(i, BinaryKeyFile.RECORD_LENGTH_BYTES));

            System.out.println();
            assertEquals(expectedRecord, actualRecord);

        }

        numRecords = expectedKItems.getLength() / BinaryKeyFile.RECORD_LENGTH_BYTES;
        System.out.println("**** Items File (" + numRecords + ")*****");

        List<Integer> header = expectedKItems.readIntegerList(1, BinaryKeyFile.RECORD_LENGTH_INTEGERS);
        ItemsFileHeader itemsHeader = new ItemsFileHeader();
        itemsHeader.fromInts(header);

        for (int i = 1; i < numRecords; i++) {

            System.out.println("Record: " + i);

            if ((i >= itemsHeader.getCharcterReliabilitiesRecord() && i < itemsHeader.getTaxonMaskRecord())
                    || i >= itemsHeader.getItemAbundancesRecord()) {
                List<Float> expectedFloats = expectedKItems.readFloatList(i, BinaryKeyFile.RECORD_LENGTH_INTEGERS);
                List<Float> actualFloats = kitems.readFloatList(i, BinaryKeyFile.RECORD_LENGTH_INTEGERS);
                System.out.println(expectedFloats);
                System.out.println(actualFloats);

                for (int f = 0; f < expectedFloats.size(); f++) {
                    // Note sure if this is a difference in encoding or precision
                    // but our floats are quite different.
                    assertEquals(expectedFloats.get(f), actualFloats.get(f), 0.021f);
                }
            } else if (i >= itemsHeader.getHeadingRecord() && i < itemsHeader.getCharacterMaskRecord()) {
                // The header has the date in it so will be different.
            } else {
                List<Integer> expectedRecord = expectedKItems.readIntegerList(i,
                        BinaryKeyFile.RECORD_LENGTH_INTEGERS);
                List<Integer> actualRecord = kitems.readIntegerList(i, BinaryKeyFile.RECORD_LENGTH_INTEGERS);
                System.out.println(expectedRecord);
                System.out.println(actualRecord);

                System.out.println("Expected as string: ");
                char[] chars = expectedKItems.readString(i, BinaryKeyFile.RECORD_LENGTH_BYTES).toCharArray();
                for (int c = 0; c < chars.length; c++) {
                    System.out.print(chars[c]);
                }
                if (i != 1) {
                    assertEquals(expectedRecord, actualRecord);
                }
            }
            System.out.println();

            char[] actualChars = kitems.readString(i, BinaryKeyFile.RECORD_LENGTH_BYTES).toCharArray();
            for (int c = 0; c < actualChars.length; c++) {
                System.out.print(actualChars[c]);
            }
            System.out.println();

            System.out.println();
        }

    }

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