gatk-3.8/public/java/test/org/broadinstitute/variant/VariantBaseTest.java

/*
* Copyright (c) 2012 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 AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

package org.broadinstitute.variant;

import org.testng.Assert;

import java.io.File;
import java.io.IOException;
import java.util.*;

/**
 * Base class for test classes within org.broadinstitute.variant
 */
public class VariantBaseTest {

    public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
    public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";

    // TODO: change this to an appropriate value once the move to the Picard repo takes place
    public static final String variantTestDataRoot = new File("private/testdata/").getAbsolutePath() + "/";

    /**
     * Simple generic utility class to creating TestNG data providers:
     *
     * 1: inherit this class, as in
     *
     *      private class SummarizeDifferenceTest extends TestDataProvider {
     *         public SummarizeDifferenceTest() {
     *           super(SummarizeDifferenceTest.class);
     *         }
     *         ...
     *      }
     *
     * Provide a reference to your class to the TestDataProvider constructor.
     *
     * 2: Create instances of your subclass.  Return from it the call to getTests, providing
     * the class type of your test
     *
     * @DataProvider(name = "summaries"
     * public Object[][] createSummaries() {
     *   new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
     *   new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
     *   return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
     * }
     *
     * This class magically tracks created objects of this
     */
    public static class TestDataProvider {
        private static final Map<Class, List<Object>> tests = new HashMap<Class, List<Object>>();
        protected String name;

        /**
         * Create a new TestDataProvider instance bound to the class variable C
         * @param c
         */
        public TestDataProvider(Class c, String name) {
            if ( ! tests.containsKey(c) )
                tests.put(c, new ArrayList<Object>());
            tests.get(c).add(this);
            this.name = name;
        }

        public TestDataProvider(Class c) {
            this(c, "");
        }

        public void setName(final String name) {
            this.name = name;
        }

        /**
         * Return all of the data providers in the form expected by TestNG of type class C
         * @param c
         * @return
         */
        public static Object[][] getTests(Class c) {
            List<Object[]> params2 = new ArrayList<Object[]>();
            for ( Object x : tests.get(c) ) params2.add(new Object[]{x});
            return params2.toArray(new Object[][]{});
        }

        @Override
        public String toString() {
            return "TestDataProvider("+name+")";
        }
    }

    /**
     * Creates a temp file that will be deleted on exit after tests are complete.
     * @param name Prefix of the file.
     * @param extension Extension to concat to the end of the file.
     * @return A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.
     */
    public static File createTempFile(String name, String extension) {
        try {
            File file = File.createTempFile(name, extension);
            file.deleteOnExit();
            return file;
        } catch (IOException ex) {
            throw new RuntimeException("Cannot create temp file: " + ex.getMessage(), ex);
        }
    }

    private static final double DEFAULT_FLOAT_TOLERANCE = 1e-1;

    public static final void assertEqualsDoubleSmart(final Object actual, final Double expected) {
        Assert.assertTrue(actual instanceof Double, "Not a double");
        assertEqualsDoubleSmart((double)(Double)actual, (double)expected);
    }

    public static final void assertEqualsDoubleSmart(final Object actual, final Double expected, final double tolerance) {
        Assert.assertTrue(actual instanceof Double, "Not a double");
        assertEqualsDoubleSmart((double)(Double)actual, (double)expected, tolerance);
    }

    public static final void assertEqualsDoubleSmart(final double actual, final double expected) {
        assertEqualsDoubleSmart(actual, expected, DEFAULT_FLOAT_TOLERANCE);
    }

    public static final <T> void assertEqualsSet(final Set<T> actual, final Set<T> expected, final String info) {
        final Set<T> actualSet = new HashSet<T>(actual);
        final Set<T> expectedSet = new HashSet<T>(expected);
        Assert.assertTrue(actualSet.equals(expectedSet), info); // note this is necessary due to testng bug for set comps
    }

    public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance) {
        assertEqualsDoubleSmart(actual, expected, tolerance, null);
    }

    public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance, final String message) {
        if ( Double.isNaN(expected) ) // NaN == NaN => false unfortunately
            Assert.assertTrue(Double.isNaN(actual), "expected is nan, actual is not");
        else if ( Double.isInfinite(expected) ) // NaN == NaN => false unfortunately
            Assert.assertTrue(Double.isInfinite(actual), "expected is infinite, actual is not");
        else {
            final double delta = Math.abs(actual - expected);
            final double ratio = Math.abs(actual / expected - 1.0);
            Assert.assertTrue(delta < tolerance || ratio < tolerance, "expected = " + expected + " actual = " + actual
                    + " not within tolerance " + tolerance
                    + (message == null ? "" : "message: " + message));
        }
    }
}