258 lines
10 KiB
Java
Executable File
258 lines
10 KiB
Java
Executable File
/*
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* Copyright (c) 2010 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.broad.tribble.Tribble;
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import org.broad.tribble.index.IndexFactory;
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import org.broad.tribble.vcf.VCFCodec;
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import org.broadinstitute.sting.gatk.CommandLineExecutable;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import org.testng.Assert;
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import java.io.File;
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import java.util.*;
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public class WalkerTest extends BaseTest {
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// the default output path for the integration test
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private File outputFileLocation = null;
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private static final boolean ENABLE_REPORTING = false;
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public void setOutputFileLocation(File outputFileLocation) {
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this.outputFileLocation = outputFileLocation;
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}
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public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
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return assertMatchingMD5(name, resultsFile, expectedMD5, parameterize());
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}
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public void maybeValidateSupplementaryFile(final String name, final File resultFile) {
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File indexFile = Tribble.indexFile(resultFile);
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//System.out.println("Putative index file is " + indexFile);
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if ( indexFile.exists() ) {
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if ( resultFile.getAbsolutePath().contains(".vcf") ) {
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// todo -- currently we only understand VCF files! Blow up since we can't test them
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throw new StingException("Found an index created for file " + resultFile + " but we can only validate VCF files. Extend this code!");
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}
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System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
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Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(resultFile, indexFile, new VCFCodec()));
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}
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}
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public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) {
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List<String> md5s = new ArrayList<String>();
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for (int i = 0; i < resultFiles.size(); i++) {
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String md5 = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i));
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maybeValidateSupplementaryFile(name, resultFiles.get(i));
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md5s.add(i, md5);
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}
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return md5s;
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}
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public class WalkerTestSpec {
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String args = "";
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int nOutputFiles = -1;
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List<String> md5s = null;
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List<String> exts = null;
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Class expectedException = null;
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protected Map<String, File> auxillaryFiles = new HashMap<String, File>();
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public WalkerTestSpec(String args, List<String> md5s) {
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this(args, -1, md5s);
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}
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public WalkerTestSpec(String args, int nOutputFiles, List<String> md5s) {
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this.args = args;
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this.nOutputFiles = md5s.size();
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this.md5s = md5s;
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}
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public WalkerTestSpec(String args, List<String> exts, List<String> md5s) {
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this(args, -1, exts, md5s);
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}
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public WalkerTestSpec(String args, int nOutputFiles, List<String> exts, List<String> md5s) {
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this.args = args;
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this.nOutputFiles = md5s.size();
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this.md5s = md5s;
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this.exts = exts;
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}
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public WalkerTestSpec(String args, int nOutputFiles, Class expectedException) {
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this.args = args;
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this.nOutputFiles = nOutputFiles;
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this.expectedException = expectedException;
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}
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public boolean expectsException() {
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return expectedException != null;
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}
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public Class getExpectedException() {
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if ( ! expectsException() ) throw new ReviewedStingException("Tried to get expection for walker test that doesn't expect one");
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return expectedException;
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}
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public void addAuxFile(String expectededMD5sum, File outputfile) {
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auxillaryFiles.put(expectededMD5sum, outputfile);
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}
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}
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protected boolean parameterize() {
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return false;
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}
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protected Pair<List<File>, List<String>> executeTestParallel(final String name, WalkerTestSpec spec) {
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return executeTest(name, spec, Arrays.asList(1, 4));
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}
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protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec, List<Integer> parallelThreads) {
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String originalArgs = spec.args;
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Pair<List<File>, List<String>> results = null;
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for ( int nt : parallelThreads ) {
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String extra = nt == 1 ? "" : (" -nt " + nt);
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spec.args = originalArgs + extra;
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results = executeTest(name + "-nt-" + nt, spec);
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}
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return results;
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}
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protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec) {
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ensureMd5DbDirectory(); // ensure the md5 directory exists
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List<File> tmpFiles = new ArrayList<File>();
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for (int i = 0; i < spec.nOutputFiles; i++) {
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String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i);
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File fl = createTempFile(String.format("walktest.tmp_param.%d", i), ext);
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tmpFiles.add(fl);
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}
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final String args = String.format(spec.args, tmpFiles.toArray());
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System.out.println(Utils.dupString('-', 80));
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if ( spec.expectsException() ) {
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// this branch handles the case were we are testing that a walker will fail as expected
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return executeTest(name, null, tmpFiles, args, spec.getExpectedException());
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} else {
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List<String> md5s = new LinkedList<String>();
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md5s.addAll(spec.md5s);
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// check to see if they included any auxillary files, if so add them to the list
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for (String md5 : spec.auxillaryFiles.keySet()) {
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md5s.add(md5);
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tmpFiles.add(spec.auxillaryFiles.get(md5));
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}
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return executeTest(name, md5s, tmpFiles, args, null);
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}
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}
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/**
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* execute the test, given the following:
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* @param name the name of the test
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* @param md5s the list of md5s
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* @param tmpFiles the temp file corresponding to the md5 list
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* @param args the argument list
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* @param expectedException the expected exception or null
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* @return a pair of file and string lists
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*/
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private Pair<List<File>, List<String>> executeTest(String name, List<String> md5s, List<File> tmpFiles, String args, Class expectedException) {
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if (outputFileLocation != null)
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args += " -o " + this.outputFileLocation.getAbsolutePath();
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executeTest(name, args, expectedException);
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if ( expectedException != null ) {
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return null;
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} else {
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// we need to check MD5s
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return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, md5s));
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}
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}
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/**
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* execute the test, given the following:
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* @param name the name of the test
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* @param args the argument list
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* @param expectedException the expected exception or null
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*/
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public static void executeTest(String name, String args, Class expectedException) {
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CommandLineGATK instance = new CommandLineGATK();
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String[] command = Utils.escapeExpressions(args);
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// add the logging level to each of the integration test commands
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command = Utils.appendArray(command, "-l", "WARN", "-et", ENABLE_REPORTING ? "STANDARD" : "NO_ET");
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// run the executable
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boolean gotAnException = false;
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try {
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System.out.println(String.format("Executing test %s with GATK arguments: %s", name, Utils.join(" ",command)));
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CommandLineExecutable.start(instance, command);
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} catch (Exception e) {
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gotAnException = true;
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if ( expectedException != null ) {
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// we expect an exception
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System.out.println(String.format("Wanted exception %s, saw %s", expectedException, e.getClass()));
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if ( expectedException.isInstance(e) ) {
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// it's the type we expected
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System.out.println(String.format(" => %s PASSED", name));
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} else {
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e.printStackTrace();
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Assert.fail(String.format("Test %s expected exception %s but got %s instead",
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name, expectedException, e.getClass()));
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}
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} else {
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// we didn't expect an exception but we got one :-(
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throw new RuntimeException(e);
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}
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}
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// catch failures from the integration test
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if ( expectedException != null ) {
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if ( ! gotAnException )
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// we expected an exception but didn't see it
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Assert.fail(String.format("Test %s expected exception %s but none was thrown", name, expectedException.toString()));
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} else {
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if ( CommandLineExecutable.result != 0) {
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throw new RuntimeException("Error running the GATK with arguments: " + args);
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}
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}
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}
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protected File createTempFileFromBase(String name) {
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File fl = new File(name);
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fl.deleteOnExit();
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return fl;
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}
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}
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