MetricsFileTest.java

/*
 * The MIT License
 *
 * Copyright (c) 2009 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package htsjdk.samtools.metrics;

import htsjdk.samtools.SAMException;
import htsjdk.samtools.util.FormatUtil;
import htsjdk.samtools.util.Histogram;
import org.testng.Assert;
import org.testng.annotations.Test;

import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.util.Date;

/**
 * Tests for the various classes in the metrics package.  Constructs a MetricsFile,
 * populates it with various items and then ensure that it can be written to disk
 * and read back without altering any values.
 *
 * @author Tim Fennell
 */
public class MetricsFileTest {
    public static enum TestEnum {One, Two, Three}

    public static class TestMetric extends MetricBase implements Cloneable {
        public String   STRING_PROP;
        public Date     DATE_PROP;
        public Short    SHORT_PROP;
        public Integer  INTEGER_PROP;
        public Long     LONG_PROP;
        public Float    FLOAT_PROP;
        public Double   DOUBLE_PROP;
        public TestEnum ENUM_PROP;
        public Boolean  BOOLEAN_PROP;
        public short    SHORT_PRIMITIVE;
        public int      INT_PRIMITIVE;
        public long     LONG_PRIMITIVE;
        public float    FLOAT_PRIMITIVE;
        public double   DOUBLE_PRIMITIVE;
        public boolean  BOOLEAN_PRIMITIVE;

        public TestMetric clone()  {
            try { return (TestMetric) super.clone(); }
            catch (CloneNotSupportedException cnse) { throw new SAMException("That's Unpossible!"); }
        }
    }

    @Test
    public void testWriteMetricsFile() throws Exception {
        MetricsFile<TestMetric,Integer> file = new MetricsFile<TestMetric,Integer>();
        TestMetric metric = new TestMetric();
        metric.STRING_PROP       = "Hello World";
        metric.DATE_PROP         = new FormatUtil().parseDate("2008-12-31");
        metric.SHORT_PROP        = 123;
        metric.INTEGER_PROP      = null;
        metric.LONG_PROP         = Long.MAX_VALUE;
        metric.FLOAT_PROP        = 456.789f;
        metric.DOUBLE_PROP       = 0.713487;
        metric.ENUM_PROP         = TestEnum.Two;
        metric.BOOLEAN_PROP      = false;
        metric.SHORT_PRIMITIVE   = 123;
        metric.INT_PRIMITIVE     = 919834781;
        metric.LONG_PRIMITIVE    = Long.MAX_VALUE - Integer.MAX_VALUE;
        metric.FLOAT_PRIMITIVE   = 0.55694f;
        metric.DOUBLE_PRIMITIVE  = 0.229233;
        metric.BOOLEAN_PRIMITIVE = true;
        file.addMetric(metric);

        MetricsFile<TestMetric,Integer> file2 = writeThenReadBack(file);
        Assert.assertEquals(file, file2);

        // Now add some headers and run the test again
        StringHeader stringHeader = new StringHeader();
        stringHeader.setValue("Hello, I'm a String Header!");
        file.addHeader(stringHeader);

        VersionHeader version = new VersionHeader();
        version.setVersionedItem("MetricsFileTest");
        version.setVersionString("1.0");
        file.addHeader(version);

        version = new VersionHeader();
        version.setVersionedItem("Nada");
        version.setVersionString("0.0alpha1");
        file.addHeader(version);

        file2 = writeThenReadBack(file);
        Assert.assertEquals(file, file2);

        // Now add a Histogram and make sure it still works
        Histogram<Integer> histo = new Histogram<Integer>();
        histo.setBinLabel("small_number");
        histo.setValueLabel("big_number");
        histo.increment(1, 101);
        histo.increment(2, 202);
        histo.increment(3, 4000);
        histo.increment(5, 123981);
        histo.increment(1000, 10981982);
        file.setHistogram(histo);

        file2 = writeThenReadBack(file);
        Assert.assertEquals(file, file2);

        // And lastly add some more metrics rows to the file
        TestMetric metric2 = metric.clone();
        metric2.ENUM_PROP = TestEnum.One;
        metric2.FLOAT_PROP = 0.998f;
        metric2.STRING_PROP = "Wheeeee!";
        file.addMetric(metric2);

        metric2 = metric.clone();
        metric2.ENUM_PROP = TestEnum.Three;
        metric2.DOUBLE_PRIMITIVE = 1.299d;
        file.addMetric(metric2);

        file2 = writeThenReadBack(file);
        Assert.assertEquals(file, file2);
   }

    /** Helper method to persist metrics to file and read them back again. */
    private MetricsFile<TestMetric, Integer> writeThenReadBack(MetricsFile<TestMetric,Integer> in) throws Exception {
        File f = File.createTempFile("test", ".metrics");
        f.deleteOnExit();
        FileWriter out = new FileWriter(f);
        in.write(out);

        MetricsFile<TestMetric,Integer> retval = new MetricsFile<TestMetric,Integer>();
        retval.read(new FileReader(f));
        return retval;
    }
}