Java tutorial
/* * 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.sting; import org.apache.commons.lang.StringUtils; import org.broad.tribble.Tribble; import org.broad.tribble.index.Index; import org.broad.tribble.index.IndexFactory; import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.variant.bcf2.BCF2Utils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.testng.Assert; import org.testng.annotations.AfterSuite; import org.testng.annotations.BeforeMethod; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.PrintStream; import java.text.SimpleDateFormat; import java.util.*; public class WalkerTest extends BaseTest { private static final boolean GENERATE_SHADOW_BCF = true; private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false; private static final boolean ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX = false; private static final boolean ENABLE_AUTO_INDEX_CREATION_AND_LOCKING_FOR_TESTS = false; private static MD5DB md5DB = new MD5DB(); @BeforeMethod public void initializeWalkerTests() { logger.debug("Initializing walker tests"); GenomeAnalysisEngine.resetRandomGenerator(); } @AfterSuite public void finalizeWalkerTests() { logger.debug("Finalizing walker tests"); md5DB.close(); } public static MD5DB getMd5DB() { return md5DB; } public MD5DB.MD5Match assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) { return getMd5DB().assertMatchingMD5(name, resultsFile, expectedMD5, parameterize()); } public void validateOutputBCFIfPossible(final String name, final File resultFile) { final File bcfFile = BCF2Utils.shadowBCF(resultFile); if (bcfFile != null && bcfFile.exists()) { logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile); try { assertVCFandBCFFilesAreTheSame(resultFile, bcfFile); logger.warn(" Shadow BCF PASSED!"); } catch (Exception e) { Assert.fail("Exception received reading shadow BCFFile " + bcfFile + " for test " + name, e); } } } public void validateOutputIndex(final String name, final File resultFile) { if (!ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX) return; File indexFile = Tribble.indexFile(resultFile); //System.out.println("Putative index file is " + indexFile); if (indexFile.exists()) { if (resultFile.getAbsolutePath().contains(".vcf")) { // todo -- currently we only understand VCF files! Blow up since we can't test them throw new StingException("Found an index created for file " + resultFile + " but we can only validate VCF files. Extend this code!"); } System.out.println( "Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile); Index indexFromOutputFile = IndexFactory.createDynamicIndex(resultFile, new VCFCodec()); Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath()); if (!indexFromOutputFile.equalsIgnoreProperties(dynamicIndex)) { Assert.fail(String.format( "Index on disk from indexing on the fly not equal to the index created after the run completed. FileIndex %s vs. on-the-fly %s%n", indexFromOutputFile.getProperties(), dynamicIndex.getProperties())); } } } public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) { List<String> md5s = new ArrayList<String>(); List<MD5DB.MD5Match> fails = new ArrayList<MD5DB.MD5Match>(); for (int i = 0; i < resultFiles.size(); i++) { MD5DB.MD5Match result = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i)); validateOutputBCFIfPossible(name, resultFiles.get(i)); if (!result.failed) { validateOutputIndex(name, resultFiles.get(i)); md5s.add(result.expectedMD5); } else { fails.add(result); } } if (!fails.isEmpty()) { List<String> actuals = new ArrayList<String>(); List<String> expecteds = new ArrayList<String>(); for (final MD5DB.MD5Match fail : fails) { actuals.add(fail.actualMD5); expecteds.add(fail.expectedMD5); logger.warn("Fail: " + fail.failMessage); } final MD5Mismatch failure = new MD5Mismatch(actuals, expecteds); Assert.fail(failure.toString(), failure); } return md5s; } public String buildCommandLine(String... arguments) { String cmdline = ""; for (int argIndex = 0; argIndex < arguments.length; argIndex++) { cmdline += arguments[argIndex]; if (argIndex < arguments.length - 1) { cmdline += " "; } } return cmdline; } public class WalkerTestSpec { // Arguments implicitly included in all Walker command lines, unless explicitly // disabled using the disableImplicitArgs() method below. String args = ""; int nOutputFiles = -1; List<String> md5s = null; List<String> exts = null; Class expectedException = null; boolean includeImplicitArgs = true; boolean includeShadowBCF = true; // the default output path for the integration test private File outputFileLocation = null; protected Map<String, File> auxillaryFiles = new HashMap<String, File>(); public WalkerTestSpec(String args, List<String> md5s) { this(args, -1, md5s); } public WalkerTestSpec(String args, int nOutputFiles, List<String> md5s) { this.args = args; this.nOutputFiles = md5s.size(); this.md5s = md5s; } public WalkerTestSpec(String args, List<String> exts, List<String> md5s) { this(args, -1, exts, md5s); } public WalkerTestSpec(String args, int nOutputFiles, List<String> exts, List<String> md5s) { this.args = args; this.nOutputFiles = md5s.size(); this.md5s = md5s; this.exts = exts; } public WalkerTestSpec(String args, int nOutputFiles, Class expectedException) { this.args = args; this.nOutputFiles = nOutputFiles; this.expectedException = expectedException; } public String getArgsWithImplicitArgs() { String args = this.args; if (includeImplicitArgs) { args = args + (ENABLE_PHONE_HOME_FOR_TESTS ? String.format(" -et %s ", GATKRunReport.PhoneHomeOption.STANDARD) : String.format(" -et %s -K %s ", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile)); if (includeShadowBCF && GENERATE_SHADOW_BCF) args = args + " --generateShadowBCF "; if (!ENABLE_AUTO_INDEX_CREATION_AND_LOCKING_FOR_TESTS) args = args + " --disable_auto_index_creation_and_locking_when_reading_rods "; } return args; } /** * In the case where the input VCF files are malformed and cannot be fixed * this function tells the engine to not try to generate a shadow BCF * which will ultimately blow up... */ public void disableShadowBCF() { this.includeShadowBCF = false; } public void setOutputFileLocation(File outputFileLocation) { this.outputFileLocation = outputFileLocation; } protected File getOutputFileLocation() { return outputFileLocation; } public boolean expectsException() { return expectedException != null; } public Class getExpectedException() { if (!expectsException()) throw new ReviewedStingException("Tried to get expection for walker test that doesn't expect one"); return expectedException; } public void addAuxFile(String expectededMD5sum, File outputfile) { auxillaryFiles.put(expectededMD5sum, outputfile); } public void disableImplicitArgs() { includeImplicitArgs = false; } } protected boolean parameterize() { return false; } public enum ParallelTestType { TREE_REDUCIBLE, NANO_SCHEDULED, BOTH } protected Pair<List<File>, List<String>> executeTestParallel(final String name, WalkerTestSpec spec, ParallelTestType testType) { final List<Integer> ntThreads = testType == ParallelTestType.TREE_REDUCIBLE || testType == ParallelTestType.BOTH ? Arrays.asList(1, 4) : Collections.<Integer>emptyList(); final List<Integer> cntThreads = testType == ParallelTestType.NANO_SCHEDULED || testType == ParallelTestType.BOTH ? Arrays.asList(1, 4) : Collections.<Integer>emptyList(); return executeTest(name, spec, ntThreads, cntThreads); } protected Pair<List<File>, List<String>> executeTestParallel(final String name, WalkerTestSpec spec) { return executeTestParallel(name, spec, ParallelTestType.TREE_REDUCIBLE); } protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec, List<Integer> ntThreads, List<Integer> cpuThreads) { String originalArgs = spec.args; Pair<List<File>, List<String>> results = null; boolean ran1 = false; for (int nt : ntThreads) { String extra = nt == 1 ? "" : (" -nt " + nt); ran1 = ran1 || nt == 1; spec.args = originalArgs + extra; results = executeTest(name + "-nt-" + nt, spec); } for (int nct : cpuThreads) { if (nct != 1) { String extra = " -nct " + nct; spec.args = originalArgs + extra; results = executeTest(name + "-cnt-" + nct, spec); } } return results; } protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec) { List<File> tmpFiles = new ArrayList<File>(); for (int i = 0; i < spec.nOutputFiles; i++) { String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i); File fl = createTempFile(String.format("walktest.tmp_param.%d", i), ext); tmpFiles.add(fl); } final String args = String.format(spec.getArgsWithImplicitArgs(), tmpFiles.toArray()); System.out.println(Utils.dupString('-', 80)); if (spec.expectsException()) { // this branch handles the case were we are testing that a walker will fail as expected return executeTest(name, spec.getOutputFileLocation(), null, tmpFiles, args, spec.getExpectedException()); } else { List<String> md5s = new LinkedList<String>(); md5s.addAll(spec.md5s); // check to see if they included any auxillary files, if so add them to the list for (String md5 : spec.auxillaryFiles.keySet()) { md5s.add(md5); tmpFiles.add(spec.auxillaryFiles.get(md5)); } return executeTest(name, spec.getOutputFileLocation(), md5s, tmpFiles, args, null); } } private void qcMD5s(String name, List<String> md5s) { final String exampleMD5 = "709a1f482cce68992c637da3cff824a8"; for (String md5 : md5s) { if (md5 == null) throw new IllegalArgumentException("Null MD5 found in test " + name); if (md5.equals("")) // ok continue; if (!StringUtils.isAlphanumeric(md5)) throw new IllegalArgumentException( "MD5 contains non-alphanumeric characters test " + name + " md5=" + md5); if (md5.length() != exampleMD5.length()) throw new IllegalArgumentException( "Non-empty MD5 of unexpected number of characters test " + name + " md5=" + md5); } } /** * execute the test, given the following: * @param name the name of the test * @param md5s the list of md5s * @param tmpFiles the temp file corresponding to the md5 list * @param args the argument list * @param expectedException the expected exception or null * @return a pair of file and string lists */ private Pair<List<File>, List<String>> executeTest(String name, File outputFileLocation, List<String> md5s, List<File> tmpFiles, String args, Class expectedException) { if (md5s != null) qcMD5s(name, md5s); if (outputFileLocation != null) args += " -o " + outputFileLocation.getAbsolutePath(); executeTest(name, args, expectedException); if (expectedException != null) { return null; } else { // we need to check MD5s return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, md5s)); } } /** * execute the test, given the following: * @param name the name of the test * @param args the argument list * @param expectedException the expected exception or null */ private void executeTest(String name, String args, Class expectedException) { CommandLineGATK instance = new CommandLineGATK(); String[] command = Utils.escapeExpressions(args); // run the executable boolean gotAnException = false; try { final String now = new SimpleDateFormat("HH:mm:ss").format(new Date()); final String cmdline = Utils.join(" ", command); System.out.println(String.format("[%s] Executing test %s with GATK arguments: %s", now, name, cmdline)); // also write the command line to the HTML log for convenient follow-up // do the replaceAll so paths become relative to the current BaseTest.log(cmdline.replaceAll(publicTestDirRoot, "").replaceAll(privateTestDirRoot, "")); CommandLineExecutable.start(instance, command); } catch (Exception e) { gotAnException = true; if (expectedException != null) { // we expect an exception //System.out.println(String.format("Wanted exception %s, saw %s", expectedException, e.getClass())); if (expectedException.isInstance(e)) { // it's the type we expected //System.out.println(String.format(" => %s PASSED", name)); } else { final String message = String.format( "Test %s expected exception %s but instead got %s with error message %s", name, expectedException, e.getClass(), e.getMessage()); if (e.getCause() != null) { final ByteArrayOutputStream baos = new ByteArrayOutputStream(); final PrintStream ps = new PrintStream(baos); e.getCause().printStackTrace(ps); BaseTest.log(message); BaseTest.log(baos.toString()); } Assert.fail(message); } } else { // we didn't expect an exception but we got one :-( throw new RuntimeException(e); } } // catch failures from the integration test if (expectedException != null) { if (!gotAnException) // we expected an exception but didn't see it Assert.fail(String.format("Test %s expected exception %s but none was thrown", name, expectedException.toString())); } else { if (CommandLineExecutable.result != 0) { throw new RuntimeException("Error running the GATK with arguments: " + args); } } } protected File createTempFileFromBase(String name) { File fl = new File(name); fl.deleteOnExit(); return fl; } }