Integration test for the file extensions CatVariants should handle

public/gatk-framework/src/test/java/org/broadinstitute/sting/tools/CatVariantsIntegrationTest.java

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+/*
+* 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.tools;
+
+import org.apache.commons.lang.StringUtils;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.MD5DB;
+import org.broadinstitute.sting.MD5Mismatch;
+import org.broadinstitute.sting.utils.runtime.ProcessController;
+import org.broadinstitute.sting.utils.runtime.ProcessSettings;
+import org.broadinstitute.sting.utils.runtime.RuntimeUtils;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+
+public class CatVariantsIntegrationTest {
+    private final MD5DB md5db = new MD5DB();
+    private final File CatVariantsDir = new File(BaseTest.privateTestDir, "CatVariants");
+
+    private class CatVariantsTestProvider extends BaseTest.TestDataProvider {
+        private final File file1;
+        private final File file2;
+        public final File outputFile;
+        public final String md5;
+
+        private CatVariantsTestProvider(final String file1, final String file2, final File outputFile, final String md5) {
+            super(CatVariantsTestProvider.class);
+
+            this.file1 = new File(CatVariantsDir, file1);
+            this.file2 = new File(CatVariantsDir, file2);
+            this.outputFile = outputFile;
+            this.md5 = md5;
+        }
+
+        public final String getCmdLine() {
+            return String.format("java -cp %s %s -R %s -V %s -V %s -out %s",
+                    StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
+                    CatVariants.class.getCanonicalName(), BaseTest.b37KGReference, file1, file2, outputFile);
+        }
+
+        public String toString() {
+            return "CatVariantsTestProvider " + outputFile;
+        }
+    }
+
+    @DataProvider(name = "ExtensionsTest")
+    public Object[][] makeExtensionsTestProvider() {
+        new CatVariantsTestProvider("CatVariantsTest1.vcf", "CatVariantsTest2.vcf", BaseTest.createTempFile("CatVariantsTest", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
+        new CatVariantsTestProvider("CatVariantsTest1.bcf", "CatVariantsTest2.bcf", BaseTest.createTempFile("CatVariantsTest", ".bcf"), "6a57fcbbf3cae490896d13a288670d83");
+
+        for (String extension : VariantContextWriterFactory.BLOCK_COMPRESSED_EXTENSIONS)
+            new CatVariantsTestProvider("CatVariantsTest1.vcf" + extension, "CatVariantsTest2.vcf" + extension, BaseTest.createTempFile("CatVariantsTest", ".vcf" + extension), "33f728ac5c70ce2994f3619a27f47088");
+
+        return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
+    }
+
+    @Test(dataProvider = "ExtensionsTest")
+    public void testExtensions(final CatVariantsTestProvider cfg) throws IOException {
+
+        ProcessController pc = ProcessController.getThreadLocal();
+        ProcessSettings ps = new ProcessSettings(cfg.getCmdLine().split("\\s+"));
+        pc.execAndCheck(ps);
+
+        MD5DB.MD5Match result = md5db.testFileMD5("testExtensions", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
+        if(result.failed) {
+            final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
+            Assert.fail(failure.toString());
+        }
+    }
+
+    @Test(expectedExceptions = IOException.class)
+    public void testMismatchedExtensions1() throws IOException {
+
+        String cmdLine = String.format("java -cp %s %s -R %s -V %s -V %s -out %s",
+                StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
+                CatVariants.class.getCanonicalName(),
+                BaseTest.b37KGReference,
+                new File(CatVariantsDir, "CatVariantsTest1.vcf"),
+                new File(CatVariantsDir, "CatVariantsTest2.vcf"),
+                BaseTest.createTempFile("CatVariantsTest", ".bcf"));
+
+        ProcessController pc = ProcessController.getThreadLocal();
+        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
+        pc.execAndCheck(ps);
+    }
+
+    @Test(expectedExceptions = IOException.class)
+    public void testMismatchedExtensions2() throws IOException {
+
+        String cmdLine = String.format("java -cp %s %s -R %s -V %s -V %s -out %s",
+                StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
+                CatVariants.class.getCanonicalName(),
+                BaseTest.b37KGReference,
+                new File(CatVariantsDir, "CatVariantsTest1.vcf"),
+                new File(CatVariantsDir, "CatVariantsTest2.bcf"),
+                BaseTest.createTempFile("CatVariantsTest", ".vcf"));
+
+        ProcessController pc = ProcessController.getThreadLocal();
+        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
+        pc.execAndCheck(ps);
+    }
+}