258 lines
10 KiB
Java
Executable File
258 lines
10 KiB
Java
Executable File
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.broadinstitute.sting.commandline.CommandLineUtils;
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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 java.io.File;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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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 refseqAnnotationLocation = annotationDataLocation + "refseq/";
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public static final String hg18Refseq = refseqAnnotationLocation + "refGene-big-table-hg18.txt";
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public static final String hg19Refseq = refseqAnnotationLocation + "refGene-big-table-hg19.txt";
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public static final String b36Refseq = refseqAnnotationLocation + "refGene-big-table-b36.txt";
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public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt";
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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 String networkTempDir;
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public static final File networkTempDirFile;
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public static final File testDirFile = new File("public/testdata/");
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public static final String testDir = testDirFile.getAbsolutePath() + "/";
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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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/** 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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networkTempDirFile = IOUtils.tempDir("temp.", ".dir", new File("/broad/shptmp/" + System.getProperty("user.name")));
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networkTempDirFile.deleteOnExit();
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networkTempDir = networkTempDirFile.getAbsolutePath() + "/";
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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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* 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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*/
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public static File createNetworkTempFile(String name) {
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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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