X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=engine%2Fcompbio%2Fengine%2Fcluster%2Fdrmaa%2FClusterRunner.java;fp=engine%2Fcompbio%2Fengine%2Fcluster%2Fdrmaa%2FJobRunner.java;h=d36ca899dd36541e24adf518ec15db42f9718ed1;hb=b56011664ec5d11bb5d0cd09395e646586888700;hp=516c3eb3d1a3ae9d09f6fb87ea528b8d2e1a05ab;hpb=1791d2710aba8bf012a83e5d18c5c1988ecc176b;p=jabaws.git

diff --git a/engine/compbio/engine/cluster/drmaa/JobRunner.java b/engine/compbio/engine/cluster/drmaa/ClusterRunner.java
similarity index 92%
rename from engine/compbio/engine/cluster/drmaa/JobRunner.java
rename to engine/compbio/engine/cluster/drmaa/ClusterRunner.java
index 516c3eb..d36ca89 100644
--- a/engine/compbio/engine/cluster/drmaa/JobRunner.java
+++ b/engine/compbio/engine/cluster/drmaa/ClusterRunner.java
@@ -56,17 +56,17 @@ import compbio.metadata.ResultNotAvailableException;
  *       template gets deleted, this needs to be taken into account in this
  *       class design!
  */
-public class JobRunner implements SyncExecutor {
+public class ClusterRunner implements SyncExecutor {
 
 	final JobTemplate jobtempl;
 	static ClusterSession clustSession = ClusterSession.getInstance();
 	static Session session = clustSession.getSession();
-	static final Logger log = Logger.getLogger(JobRunner.class);
+	static final Logger log = Logger.getLogger(ClusterRunner.class);
 	final ConfiguredExecutable<?> confExecutable;
 	private final String workDirectory;
 	String jobId;
 
-	public JobRunner(ConfiguredExecutable<?> confExec)
+	public ClusterRunner(ConfiguredExecutable<?> confExec)
 			throws JobSubmissionException {
 		try {
 			String command = confExec.getCommand(ExecProvider.Cluster);
@@ -84,9 +84,7 @@ public class JobRunner implements SyncExecutor {
 			// Tell the job where to get/put things
 			jobtempl.setWorkingDirectory(this.workDirectory);
 
-			/*
-			 * Set environment variables for the process if any
-			 */
+			// Set environment variables for the process if any
 			Map<String, String> jobEnv = confExec.getEnvironment();
 			if (jobEnv != null && !jobEnv.isEmpty()) {
 				setJobEnvironmentVariables(jobEnv);
@@ -97,20 +95,15 @@ public class JobRunner implements SyncExecutor {
 				jobtempl.setArgs(args);
 			}
 
-			/*
-			 * If executable need in/out data to be piped into it
-			 */
+			//If executable need in/out data to be piped into it
 			if (confExec.getExecutable() instanceof PipedExecutable<?>) {
 				setPipes(confExec);
 			}
 
-			/*
-			 * If executable require special cluster configuration parameters to
-			 * be set e.g. queue, ram, time etc
-			 */
+			// If executable require special cluster configuration parameters to
+			// be set e.g. queue, ram, time etc
 			setNativeSpecs(confExec.getExecutable());
 
-
 			log.trace("using arguments: " + jobtempl.getArgs());
 			this.confExecutable = confExec;
 			// Save run configuration
@@ -368,7 +361,7 @@ public class JobRunner implements SyncExecutor {
 	public ConfiguredExecutable<?> waitForResult() throws JobExecutionException {
 		ConfiguredExecutable<?> confExec;
 		try {
-			confExec = new AsyncJobRunner().getResults(this.jobId);
+			confExec = new AsyncClusterRunner().getResults(this.jobId);
 			if (confExec == null) {
 				log.warn("Could not find results of job " + this.jobId);
 			}
@@ -384,9 +377,9 @@ public class JobRunner implements SyncExecutor {
 		return getJobStatus(this.jobId);
 	}
 
-	public static JobRunner getInstance(ConfiguredExecutable<?> executable)
+	public static ClusterRunner getInstance(ConfiguredExecutable<?> executable)
 			throws JobSubmissionException {
-		return new JobRunner(executable);
+		return new ClusterRunner(executable);
 	}
 
 } // class end