Test that stdout redirects and log files do not affect output

public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/RuntimeUtils.java

@@ -28,6 +28,8 @@ package org.broadinstitute.sting.utils.runtime;
 import org.apache.commons.lang.StringUtils;
 
 import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
 
 public class RuntimeUtils {
     public static final String[] PATHS;
@@ -56,4 +58,20 @@ public class RuntimeUtils {
         }
         return null;
     }
+
+    /**
+     * Return the current classpath as a list of absolute paths
+     * @return
+     */
+    public static List<String> getAbsoluteClassPaths() {
+        final String[] relativeClassPaths = System.getProperty("java.class.path").split(File.pathSeparator);
+        final List<String> absoluteClassPaths = new ArrayList<>(relativeClassPaths.length);
+        for (String classPath : relativeClassPaths) {
+            File cp = new File(classPath);
+            if (cp.exists())
+                absoluteClassPaths.add(cp.getAbsolutePath());
+        }
+
+        return absoluteClassPaths;
+    }
 }

public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/LoggingIntegrationTest.java

@@ -0,0 +1,135 @@
+/*
+* 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.commandline;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.log4j.Level;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.MD5DB;
+import org.broadinstitute.sting.MD5Mismatch;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.runtime.*;
+
+public class LoggingIntegrationTest {
+    private final MD5DB md5db = new MD5DB();
+
+    private class LoggingTestProvider extends BaseTest.TestDataProvider {
+
+        private final String baseCmdLine;
+
+        private final Level logLevel;
+        private final String logFileStr;
+        public final File argumentOutputFile;
+        public final File pipedOutputFile;
+
+        private LoggingTestProvider(final Level logLevel, final boolean explicitLogfile) throws IOException {
+            super(LoggingTestProvider.class);
+
+            // TODO: a better command line that exercises log levels besides INFO
+            this.baseCmdLine = String.format("java -cp %s %s -T SelectVariants -R %s -V %s -L 1:1000000-2000000 --no_cmdline_in_header",
+                    StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
+                    CommandLineGATK.class.getCanonicalName(), BaseTest.b37KGReference, BaseTest.b37_NA12878_OMNI);
+
+            this.logLevel = logLevel;
+            this.logFileStr = explicitLogfile ? " -log " + BaseTest.createTempFile(logLevel.toString(), "log") : "";
+            this.argumentOutputFile = BaseTest.createTempFile(logLevel.toString(), "vcf");
+            this.pipedOutputFile = BaseTest.createTempFile(logLevel.toString(), "vcf");
+        }
+
+        public final String getCmdLine(boolean redirectStdout) {
+            String command = String.format("%s -l %s %s", baseCmdLine, logLevel, logFileStr);
+            return redirectStdout ? command : command + " -o " + argumentOutputFile;
+        }
+
+        public String toString() {
+            return String.format("LoggingTestProvider logLevel=%s", logLevel);
+        }
+    }
+
+    @DataProvider(name = "LoggingTest")
+    public Object[][] makeLoggingTestProvider() throws IOException {
+        for (Boolean explicitLogFile : Arrays.asList(true, false)) {
+            // TODO: enable other logging levels when tests for those exist
+            new LoggingTestProvider(Level.DEBUG, explicitLogFile);
+        }
+
+        return LoggingTestProvider.getTests(LoggingTestProvider.class);
+    }
+
+    /**
+     * test that using an output argument produces the same output as stdout
+     */
+    @Test(dataProvider = "LoggingTest")
+    public void testStdoutEquivalence(final LoggingTestProvider cfg) throws IOException {
+
+        ProcessController pc = ProcessController.getThreadLocal();
+
+        // output argument
+
+        ProcessSettings ps = new ProcessSettings(cfg.getCmdLine(false).split("\\s+"));
+        execAndCheck(pc, ps);
+        String output_argument_md5 = md5db.calculateFileMD5(cfg.argumentOutputFile);
+
+        // pipe to stdout
+
+        ps = new ProcessSettings(cfg.getCmdLine(true).split("\\s+"));
+        ps.setStdoutSettings(new OutputStreamSettings(cfg.pipedOutputFile));
+        execAndCheck(pc, ps);
+
+        MD5DB.MD5Match result = md5db.testFileMD5("LoggingIntegrationTest", "LoggingIntegrationTest", cfg.pipedOutputFile, output_argument_md5, false);
+        if(result.failed) {
+            final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
+            Assert.fail(failure.toString());
+        }
+    }
+
+    /**
+     * Execute a process, and throw an IOException if the exit code is nonzero
+     *
+     * @param pc
+     * @param ps
+     * @throws IOException
+     */
+    private void execAndCheck(ProcessController pc, ProcessSettings ps) throws IOException {
+        ProcessOutput po = pc.exec(ps);
+        if (po.getExitValue() != 0) {
+            String message = String.format("Process exited with %d\nCommand Line: %s",
+                    po.getExitValue(),
+                    Utils.join(" ", ps.getCommand()));
+            throw new IOException(message);
+        }
+    }
+}