Move execAndCheck() to ProcessController

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

@@ -29,6 +29,7 @@ import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -267,6 +268,25 @@ public class ProcessController {
         return new ProcessOutput(exitCode, stdout, stderr);
     }
 
+    /**
+     * Executes a command line program with the settings and waits for it to return,
+     * processing the output on a background thread.
+     *
+     * Throws an IOException if the ProcessOutput exit code is nonzero
+     *
+     * @param settings Settings to be run.
+     */
+    public ProcessOutput execAndCheck(ProcessSettings settings) throws IOException {
+        ProcessOutput po = exec(settings);
+        if (po.getExitValue() != 0) {
+            String message = String.format("Process exited with %d\nCommand Line: %s",
+                    po.getExitValue(),
+                    Utils.join(" ", settings.getCommand()));
+            throw new IOException(message);
+        }
+        return po;
+    }
+
     /**
      * @return The set of still running processes.
      */

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

@@ -40,7 +40,6 @@ 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 {
@@ -100,14 +99,14 @@ public class LoggingIntegrationTest {
         // output argument
 
         ProcessSettings ps = new ProcessSettings(cfg.getCmdLine(false).split("\\s+"));
-        execAndCheck(pc, ps);
+        pc.execAndCheck(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);
+        pc.execAndCheck(ps);
 
         MD5DB.MD5Match result = md5db.testFileMD5("LoggingIntegrationTest", "LoggingIntegrationTest", cfg.pipedOutputFile, output_argument_md5, false);
         if(result.failed) {
@@ -115,21 +114,4 @@ public class LoggingIntegrationTest {
             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);
-        }
-    }
 }