Refactoring: rename duplicated Util classes

[jabaws.git] / engine / compbio / engine / cluster / drmaa / JobRunner.java

diff --git a/engine/compbio/engine/cluster/drmaa/JobRunner.java b/engine/compbio/engine/cluster/drmaa/JobRunner.java
index a3f002a..516c3eb 100644 (file)
--- a/engine/compbio/engine/cluster/drmaa/JobRunner.java
+++ b/engine/compbio/engine/cluster/drmaa/JobRunner.java
@@ -39,7 +39,7 @@ import compbio.engine.client.ConfiguredExecutable;
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PathValidator;\r
 import compbio.engine.client.PipedExecutable;\r
-import compbio.engine.client.Util;\r
+import compbio.engine.client.EngineUtil;\r
 import compbio.engine.client.Executable.ExecProvider;\r
 import compbio.metadata.JobExecutionException;\r
 import compbio.metadata.JobStatus;\r
@@ -195,7 +195,7 @@ public class JobRunner implements SyncExecutor {
                        log.trace("Setting job environment to:" + env_variables);\r
                        Map<String, String> sysEnv = jobtempl.getJobEnvironment();\r
                        if (sysEnv != null && !sysEnv.isEmpty()) {\r
-                               Util.mergeEnvVariables(sysEnv, env_variables);\r
+                               EngineUtil.mergeEnvVariables(sysEnv, env_variables);\r
                        } else {\r
                                sysEnv = env_variables;\r
                        }\r
@@ -231,14 +231,11 @@ public class JobRunner implements SyncExecutor {
                        ClusterJobId clusterJobId = ClusterSession.getClusterJobId(jobId);\r
                        switch (clustSession.getJobStatus(clusterJobId)) {\r
                        case Session.DONE:\r
-                               compbio.engine.client.Util.writeStatFile(Configurator.getWorkDirectory(jobId),\r
-                                               JobStatus.FINISHED.toString());\r
-\r
+                               EngineUtil.writeStatFile(Configurator.getWorkDirectory(jobId), JobStatus.FINISHED.toString());\r
                                return compbio.metadata.JobStatus.FINISHED;\r
-                       case Session.FAILED:\r
-                               compbio.engine.client.Util.writeMarker(Configurator.getWorkDirectory(jobId),\r
-                                               JobStatus.FAILED);\r
 \r
+                       case Session.FAILED:\r
+                               EngineUtil.writeMarker(Configurator.getWorkDirectory(jobId), JobStatus.FAILED);\r
                                return compbio.metadata.JobStatus.FAILED;\r
 \r
                        case Session.RUNNING:\r
@@ -285,14 +282,14 @@ public class JobRunner implements SyncExecutor {
                 * cancelled, finished or failed.\r
                 */\r
                String workDir = Configurator.getWorkDirectory(jobId);\r
-               if (Util.isMarked(workDir, JobStatus.FINISHED)\r
-                               || Util.isMarked(workDir, JobStatus.COLLECTED)) {\r
+               if (EngineUtil.isMarked(workDir, JobStatus.FINISHED)\r
+                               || EngineUtil.isMarked(workDir, JobStatus.COLLECTED)) {\r
                        return JobStatus.FINISHED;\r
                }\r
-               if (Util.isMarked(workDir, JobStatus.CANCELLED)) {\r
+               if (EngineUtil.isMarked(workDir, JobStatus.CANCELLED)) {\r
                        return JobStatus.CANCELLED;\r
                }\r
-               if (Util.isMarked(workDir, JobStatus.FAILED)) {\r
+               if (EngineUtil.isMarked(workDir, JobStatus.FAILED)) {\r
                        return JobStatus.FAILED;\r
                }\r
                return JobStatus.UNDEFINED; \r
@@ -315,13 +312,13 @@ public class JobRunner implements SyncExecutor {
        }\r
 \r
        JobInfo waitForJob(String jobId) throws JobExecutionException {\r
-               assert Util.isValidJobId(jobId);\r
-               return ClusterUtil.waitForResult(clustSession, jobId);\r
+               assert EngineUtil.isValidJobId(jobId);\r
+               return ClusterEngineUtil.waitForResult(clustSession, jobId);\r
        }\r
 \r
        boolean cancelJob(String jobId) {\r
-               assert Util.isValidJobId(jobId);\r
-               return compbio.engine.cluster.drmaa.ClusterUtil.cancelJob(jobId,\r
+               assert EngineUtil.isValidJobId(jobId);\r
+               return compbio.engine.cluster.drmaa.ClusterEngineUtil.cancelJob(jobId,\r
                                clustSession);\r
        }\r
 \r