513 lines
24 KiB
Java
513 lines
24 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting;
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import org.apache.log4j.AppenderSkeleton;
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import org.apache.log4j.Level;
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import org.apache.log4j.Logger;
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import org.apache.log4j.PatternLayout;
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import org.apache.log4j.spi.LoggingEvent;
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import org.broad.tribble.readers.LineIterator;
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import org.broad.tribble.readers.PositionalBufferedStream;
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import org.broadinstitute.sting.commandline.CommandLineUtils;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.crypt.CryptUtils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.io.IOUtils;
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import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
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import org.broadinstitute.variant.bcf2.BCF2Codec;
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import org.broadinstitute.variant.variantcontext.Genotype;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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import org.broadinstitute.variant.vcf.VCFCodec;
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import org.broadinstitute.variant.vcf.VCFConstants;
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import org.broadinstitute.variant.vcf.VCFHeader;
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import org.broadinstitute.variant.vcf.VCFHeaderLine;
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import org.testng.Assert;
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import org.testng.Reporter;
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import org.testng.SkipException;
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import java.io.File;
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import java.io.IOException;
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import java.util.*;
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/**
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*
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* User: aaron
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* Date: Apr 14, 2009
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* Time: 10:24:30 AM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date Apr 14, 2009
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* <p/>
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* Class BaseTest
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* <p/>
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* This is the base test class for all of our test cases. All test cases should extend from this
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* class; it sets up the logger, and resolves the location of directories that we rely on.
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*/
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@SuppressWarnings("unchecked")
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public abstract class BaseTest {
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/** our log, which we want to capture anything from org.broadinstitute.sting */
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public static final Logger logger = CommandLineUtils.getStingLogger();
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public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
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public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
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public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
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//public static final String b37KGReference = "/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta";
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public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
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public static final String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
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public static final String validationDataLocation = GATKDataLocation + "Validation_Data/";
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public static final String evaluationDataLocation = GATKDataLocation + "Evaluation_Data/";
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public static final String comparisonDataLocation = GATKDataLocation + "Comparisons/";
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public static final String annotationDataLocation = GATKDataLocation + "Annotations/";
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public static final String b37GoodBAM = validationDataLocation + "/CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
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public static final String b37GoodNA12878BAM = validationDataLocation + "/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam";
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public static final String b37_NA12878_OMNI = validationDataLocation + "/NA12878.omni.vcf";
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public static final String dbsnpDataLocation = GATKDataLocation;
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public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
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public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf";
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public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
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public static final String hg18dbSNP132 = dbsnpDataLocation + "dbsnp_132.hg18.vcf";
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public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
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public static final String b37hapmapGenotypes = hapmapDataLocation + "genotypes_r27_nr.b37_fwd.vcf";
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public static final String b37hapmapSites = hapmapDataLocation + "sites_r27_nr.b37_fwd.vcf";
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public static final String intervalsLocation = GATKDataLocation;
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public static final String hg19Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list";
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public static final String hg19Chr20Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list";
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public static final boolean REQUIRE_NETWORK_CONNECTION = false;
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private static final String networkTempDirRoot = "/broad/hptmp/";
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private static final boolean networkTempDirRootExists = new File(networkTempDirRoot).exists();
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private static final String networkTempDir;
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private static final File networkTempDirFile;
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private static final String privateTestDirRelative = "private/testdata/";
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public static final String privateTestDir = new File(privateTestDirRelative).getAbsolutePath() + "/";
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protected static final String privateTestDirRoot = privateTestDir.replace(privateTestDirRelative, "");
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private static final String publicTestDirRelative = "public/testdata/";
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public static final String publicTestDir = new File(publicTestDirRelative).getAbsolutePath() + "/";
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protected static final String publicTestDirRoot = publicTestDir.replace(publicTestDirRelative, "");
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public static final String keysDataLocation = validationDataLocation + "keys/";
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public static final String gatkKeyFile = CryptUtils.GATK_USER_KEY_DIRECTORY + "gsamembers_broadinstitute.org.key";
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public static final String exampleFASTA = publicTestDir + "exampleFASTA.fasta";
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public final static String NA12878_PCRFREE = privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam";
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public final static String NA12878_WEx = privateTestDir + "CEUTrio.HiSeq.WEx.b37_decoy.NA12878.20_10_11mb.bam";
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public static final boolean pipelineTestRunModeIsSet = System.getProperty("pipeline.run").equals("run");
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/** before the class starts up */
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static {
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// setup a basic log configuration
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CommandLineUtils.configureConsoleLogging();
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// setup our log layout
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PatternLayout layout = new PatternLayout();
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layout.setConversionPattern("TEST %C{1}.%M - %d{HH:mm:ss,SSS} - %m%n");
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// now set the layout of all the loggers to our layout
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CommandLineUtils.setLayout(logger, layout);
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// Set the Root logger to only output warnings.
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logger.setLevel(Level.WARN);
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if (networkTempDirRootExists) {
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networkTempDirFile = IOUtils.tempDir("temp.", ".dir", new File(networkTempDirRoot + System.getProperty("user.name")));
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networkTempDirFile.deleteOnExit();
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networkTempDir = networkTempDirFile.getAbsolutePath() + "/";
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} else {
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networkTempDir = null;
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networkTempDirFile = null;
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}
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if ( REQUIRE_NETWORK_CONNECTION ) {
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// find our file sources
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if (!fileExist(hg18Reference) || !fileExist(hg19Reference) || !fileExist(b36KGReference)) {
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logger.fatal("We can't locate the reference directories. Aborting!");
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throw new RuntimeException("BaseTest setup failed: unable to locate the reference directories");
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}
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}
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}
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/**
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* Simple generic utility class to creating TestNG data providers:
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*
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* 1: inherit this class, as in
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*
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* private class SummarizeDifferenceTest extends TestDataProvider {
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* public SummarizeDifferenceTest() {
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* super(SummarizeDifferenceTest.class);
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* }
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* ...
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* }
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*
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* Provide a reference to your class to the TestDataProvider constructor.
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*
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* 2: Create instances of your subclass. Return from it the call to getTests, providing
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* the class type of your test
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*
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* @DataProvider(name = "summaries"
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* public Object[][] createSummaries() {
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* new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
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* new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
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* return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
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* }
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*
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* This class magically tracks created objects of this
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*/
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public static class TestDataProvider {
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private static final Map<Class, List<Object>> tests = new HashMap<Class, List<Object>>();
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protected String name;
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/**
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* Create a new TestDataProvider instance bound to the class variable C
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* @param c
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*/
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public TestDataProvider(Class c, String name) {
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if ( ! tests.containsKey(c) )
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tests.put(c, new ArrayList<Object>());
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tests.get(c).add(this);
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this.name = name;
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}
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public TestDataProvider(Class c) {
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this(c, "");
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}
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public void setName(final String name) {
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this.name = name;
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}
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/**
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* Return all of the data providers in the form expected by TestNG of type class C
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* @param c
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* @return
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*/
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public static Object[][] getTests(Class c) {
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List<Object[]> params2 = new ArrayList<Object[]>();
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for ( Object x : tests.get(c) ) params2.add(new Object[]{x});
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return params2.toArray(new Object[][]{});
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}
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@Override
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public String toString() {
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return "TestDataProvider("+name+")";
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}
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}
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/**
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* test if the file exists
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*
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* @param file name as a string
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* @return true if it exists
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*/
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public static boolean fileExist(String file) {
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File temp = new File(file);
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return temp.exists();
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}
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/**
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* this appender looks for a specific message in the log4j stream.
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* It can be used to verify that a specific message was generated to the logging system.
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*/
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public static class ValidationAppender extends AppenderSkeleton {
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private boolean foundString = false;
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private String targetString = "";
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public ValidationAppender(String target) {
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targetString = target;
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}
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@Override
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protected void append(LoggingEvent loggingEvent) {
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if (loggingEvent.getMessage().equals(targetString))
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foundString = true;
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}
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public void close() {
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// do nothing
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}
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public boolean requiresLayout() {
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return false;
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}
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public boolean foundString() {
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return foundString;
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}
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}
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/**
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* Creates a temp file that will be deleted on exit after tests are complete.
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* @param name Prefix of the file.
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* @param extension Extension to concat to the end of the file.
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* @return A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.
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*/
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public static File createTempFile(String name, String extension) {
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try {
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File file = File.createTempFile(name, extension);
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file.deleteOnExit();
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return file;
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} catch (IOException ex) {
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throw new ReviewedStingException("Cannot create temp file: " + ex.getMessage(), ex);
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}
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}
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/**
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* Creates a temp file that will be deleted on exit after tests are complete.
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* @param name Name of the file.
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* @return A file in the network temporary directory with name, which will be deleted after the program exits.
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* @throws SkipException when the network is not available.
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*/
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public static File tryCreateNetworkTempFile(String name) {
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if (!networkTempDirRootExists)
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throw new SkipException("Network temporary directory does not exist: " + networkTempDirRoot);
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File file = new File(networkTempDirFile, name);
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file.deleteOnExit();
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return file;
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}
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/**
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* Log this message so that it shows up inline during output as well as in html reports
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*
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* @param message
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*/
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public static void log(final String message) {
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Reporter.log(message, true);
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}
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private static final double DEFAULT_FLOAT_TOLERANCE = 1e-1;
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public static final void assertEqualsDoubleSmart(final Object actual, final Double expected) {
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Assert.assertTrue(actual instanceof Double, "Not a double");
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assertEqualsDoubleSmart((double)(Double)actual, (double)expected);
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}
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public static final void assertEqualsDoubleSmart(final Object actual, final Double expected, final double tolerance) {
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Assert.assertTrue(actual instanceof Double, "Not a double");
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assertEqualsDoubleSmart((double)(Double)actual, (double)expected, tolerance);
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}
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public static final void assertEqualsDoubleSmart(final double actual, final double expected) {
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assertEqualsDoubleSmart(actual, expected, DEFAULT_FLOAT_TOLERANCE);
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}
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public static final <T> void assertEqualsSet(final Set<T> actual, final Set<T> expected, final String info) {
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final Set<T> actualSet = new HashSet<T>(actual);
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final Set<T> expectedSet = new HashSet<T>(expected);
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Assert.assertTrue(actualSet.equals(expectedSet), info); // note this is necessary due to testng bug for set comps
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}
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public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance) {
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assertEqualsDoubleSmart(actual, expected, tolerance, null);
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}
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public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance, final String message) {
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if ( Double.isNaN(expected) ) // NaN == NaN => false unfortunately
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Assert.assertTrue(Double.isNaN(actual), "expected is nan, actual is not");
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else if ( Double.isInfinite(expected) ) // NaN == NaN => false unfortunately
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Assert.assertTrue(Double.isInfinite(actual), "expected is infinite, actual is not");
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else {
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final double delta = Math.abs(actual - expected);
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final double ratio = Math.abs(actual / expected - 1.0);
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Assert.assertTrue(delta < tolerance || ratio < tolerance, "expected = " + expected + " actual = " + actual
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+ " not within tolerance " + tolerance
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+ (message == null ? "" : "message: " + message));
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}
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}
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public static void assertVariantContextsAreEqual( final VariantContext actual, final VariantContext expected ) {
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Assert.assertNotNull(actual, "VariantContext expected not null");
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Assert.assertEquals(actual.getChr(), expected.getChr(), "chr");
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Assert.assertEquals(actual.getStart(), expected.getStart(), "start");
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Assert.assertEquals(actual.getEnd(), expected.getEnd(), "end");
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Assert.assertEquals(actual.getID(), expected.getID(), "id");
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Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "alleles for " + expected + " vs " + actual);
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assertAttributesEquals(actual.getAttributes(), expected.getAttributes());
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Assert.assertEquals(actual.filtersWereApplied(), expected.filtersWereApplied(), "filtersWereApplied");
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Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "isFiltered");
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assertEqualsSet(actual.getFilters(), expected.getFilters(), "filters");
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assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual());
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Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes");
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if ( expected.hasGenotypes() ) {
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assertEqualsSet(actual.getSampleNames(), expected.getSampleNames(), "sample names set");
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Assert.assertEquals(actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "sample names");
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final Set<String> samples = expected.getSampleNames();
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for ( final String sample : samples ) {
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assertGenotypesAreEqual(actual.getGenotype(sample), expected.getGenotype(sample));
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}
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}
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}
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public static void assertVariantContextStreamsAreEqual(final Iterable<VariantContext> actual, final Iterable<VariantContext> expected) {
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final Iterator<VariantContext> actualIT = actual.iterator();
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final Iterator<VariantContext> expectedIT = expected.iterator();
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while ( expectedIT.hasNext() ) {
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final VariantContext expectedVC = expectedIT.next();
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if ( expectedVC == null )
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continue;
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VariantContext actualVC;
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do {
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Assert.assertTrue(actualIT.hasNext(), "Too few records found in actual");
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actualVC = actualIT.next();
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} while ( actualIT.hasNext() && actualVC == null );
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if ( actualVC == null )
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Assert.fail("Too few records in actual");
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assertVariantContextsAreEqual(actualVC, expectedVC);
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}
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Assert.assertTrue(! actualIT.hasNext(), "Too many records found in actual");
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}
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public static void assertGenotypesAreEqual(final Genotype actual, final Genotype expected) {
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Assert.assertEquals(actual.getSampleName(), expected.getSampleName(), "Genotype names");
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Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "Genotype alleles");
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Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString(), "Genotype string");
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Assert.assertEquals(actual.getType(), expected.getType(), "Genotype type");
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// filters are the same
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Assert.assertEquals(actual.getFilters(), expected.getFilters(), "Genotype fields");
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Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "Genotype isFiltered");
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// inline attributes
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Assert.assertEquals(actual.getDP(), expected.getDP(), "Genotype dp");
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Assert.assertTrue(Arrays.equals(actual.getAD(), expected.getAD()));
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Assert.assertEquals(actual.getGQ(), expected.getGQ(), "Genotype gq");
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Assert.assertEquals(actual.hasPL(), expected.hasPL(), "Genotype hasPL");
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Assert.assertEquals(actual.hasAD(), expected.hasAD(), "Genotype hasAD");
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Assert.assertEquals(actual.hasGQ(), expected.hasGQ(), "Genotype hasGQ");
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Assert.assertEquals(actual.hasDP(), expected.hasDP(), "Genotype hasDP");
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Assert.assertEquals(actual.hasLikelihoods(), expected.hasLikelihoods(), "Genotype haslikelihoods");
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Assert.assertEquals(actual.getLikelihoodsString(), expected.getLikelihoodsString(), "Genotype getlikelihoodsString");
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Assert.assertEquals(actual.getLikelihoods(), expected.getLikelihoods(), "Genotype getLikelihoods");
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Assert.assertTrue(Arrays.equals(actual.getPL(), expected.getPL()));
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Assert.assertEquals(actual.getPhredScaledQual(), expected.getPhredScaledQual(), "Genotype phredScaledQual");
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assertAttributesEquals(actual.getExtendedAttributes(), expected.getExtendedAttributes());
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Assert.assertEquals(actual.isPhased(), expected.isPhased(), "Genotype isPhased");
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Assert.assertEquals(actual.getPloidy(), expected.getPloidy(), "Genotype getPloidy");
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}
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public static void assertVCFHeadersAreEqual(final VCFHeader actual, final VCFHeader expected) {
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Assert.assertEquals(actual.getMetaDataInSortedOrder().size(), expected.getMetaDataInSortedOrder().size(), "No VCF header lines");
|
|
|
|
// for some reason set.equals() is returning false but all paired elements are .equals(). Perhaps compare to is busted?
|
|
//Assert.assertEquals(actual.getMetaDataInInputOrder(), expected.getMetaDataInInputOrder());
|
|
final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaDataInSortedOrder());
|
|
final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaDataInSortedOrder());
|
|
for ( int i = 0; i < actualLines.size(); i++ ) {
|
|
Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
|
|
}
|
|
}
|
|
|
|
public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException {
|
|
final Pair<VCFHeader, GATKVCFUtils.VCIterable<LineIterator>> vcfData = GATKVCFUtils.readAllVCs(vcfFile, new VCFCodec());
|
|
final Pair<VCFHeader, GATKVCFUtils.VCIterable<PositionalBufferedStream>> bcfData = GATKVCFUtils.readAllVCs(bcfFile, new BCF2Codec());
|
|
assertVCFHeadersAreEqual(bcfData.getFirst(), vcfData.getFirst());
|
|
assertVariantContextStreamsAreEqual(bcfData.getSecond(), vcfData.getSecond());
|
|
}
|
|
|
|
private static void assertAttributeEquals(final String key, final Object actual, final Object expected) {
|
|
if ( expected instanceof Double ) {
|
|
// must be very tolerant because doubles are being rounded to 2 sig figs
|
|
assertEqualsDoubleSmart(actual, (Double) expected, 1e-2);
|
|
} else
|
|
Assert.assertEquals(actual, expected, "Attribute " + key);
|
|
}
|
|
|
|
private static void assertAttributesEquals(final Map<String, Object> actual, Map<String, Object> expected) {
|
|
final Set<String> expectedKeys = new HashSet<String>(expected.keySet());
|
|
|
|
for ( final Map.Entry<String, Object> act : actual.entrySet() ) {
|
|
final Object actualValue = act.getValue();
|
|
if ( expected.containsKey(act.getKey()) && expected.get(act.getKey()) != null ) {
|
|
final Object expectedValue = expected.get(act.getKey());
|
|
if ( expectedValue instanceof List ) {
|
|
final List<Object> expectedList = (List<Object>)expectedValue;
|
|
Assert.assertTrue(actualValue instanceof List, act.getKey() + " should be a list but isn't");
|
|
final List<Object> actualList = (List<Object>)actualValue;
|
|
Assert.assertEquals(actualList.size(), expectedList.size(), act.getKey() + " size");
|
|
for ( int i = 0; i < expectedList.size(); i++ )
|
|
assertAttributeEquals(act.getKey(), actualList.get(i), expectedList.get(i));
|
|
} else
|
|
assertAttributeEquals(act.getKey(), actualValue, expectedValue);
|
|
} else {
|
|
// it's ok to have a binding in x -> null that's absent in y
|
|
Assert.assertNull(actualValue, act.getKey() + " present in one but not in the other");
|
|
}
|
|
expectedKeys.remove(act.getKey());
|
|
}
|
|
|
|
// now expectedKeys contains only the keys found in expected but not in actual,
|
|
// and they must all be null
|
|
for ( final String missingExpected : expectedKeys ) {
|
|
final Object value = expected.get(missingExpected);
|
|
Assert.assertTrue(isMissing(value), "Attribute " + missingExpected + " missing in one but not in other" );
|
|
}
|
|
}
|
|
|
|
private static final boolean isMissing(final Object value) {
|
|
if ( value == null ) return true;
|
|
else if ( value.equals(VCFConstants.MISSING_VALUE_v4) ) return true;
|
|
else if ( value instanceof List ) {
|
|
// handles the case where all elements are null or the list is empty
|
|
for ( final Object elt : (List)value)
|
|
if ( elt != null )
|
|
return false;
|
|
return true;
|
|
} else
|
|
return false;
|
|
}
|
|
}
|