--- /dev/null
+/* Copyright (c) 2009 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.engine.cluster.drmaa;\r
+\r
+import static org.testng.AssertJUnit.assertEquals;\r
+import static org.testng.AssertJUnit.assertFalse;\r
+import static org.testng.AssertJUnit.assertNotNull;\r
+import static org.testng.AssertJUnit.assertTrue;\r
+import static org.testng.AssertJUnit.fail;\r
+\r
+import java.text.ParseException;\r
+\r
+import org.ggf.drmaa.DrmaaException;\r
+import org.ggf.drmaa.JobInfo;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.Alignment;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.EngineUtil;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobExecutionException;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.msa.ClustalW;\r
+import compbio.util.SysPrefs;\r
+\r
+public class DrmaaClusterEngineTester {\r
+\r
+ public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+ + "TO1381.fasta";\r
+ public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
+\r
+ /**\r
+ * This test uses ClustalW executable as runnable to testing, thus depends\r
+ * on its correct functioning\r
+ */\r
+ @Test(groups = { AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_engine })\r
+ public void testSubmit() {\r
+ ClustalW clustal = new ClustalW();\r
+ assertFalse("Cluster execution can only be in unix environment",\r
+ SysPrefs.isWindows);\r
+ clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
+\r
+ try {\r
+ ConfiguredExecutable<ClustalW> confClust = Configurator\r
+ .configureExecutable(clustal,\r
+ Executable.ExecProvider.Cluster);\r
+ assertNotNull(confClust.getWorkDirectory());\r
+\r
+ ClusterRunner runner = ClusterRunner.getInstance(confClust);\r
+ assertEquals("Input was not set!", test_input, clustal.getInput());\r
+ assertNotNull("Runner is NULL", runner);\r
+ runner.executeJob();\r
+ // assertNotNull("JobId is null", jobId1);\r
+ JobStatus status = runner.getJobStatus();\r
+ assertTrue("Status of the process is wrong!",\r
+ status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
+ JobInfo info = runner.getJobInfo();\r
+\r
+ assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.CANCELLED));\r
+ assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.STARTED));\r
+ assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.COLLECTED));\r
+ assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.FINISHED));\r
+ assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.SUBMITTED));\r
+\r
+ ConfiguredExecutable<?> confExec = runner.waitForResult();\r
+ // At this point results are marked as collected\r
+ assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.COLLECTED));\r
+\r
+ assertNotNull("JobInfo is null", info);\r
+ StatisticManager sm = new StatisticManager(info);\r
+ assertNotNull("Statistics manager is null", sm);\r
+\r
+ try {\r
+\r
+ String exits = sm.getExitStatus();\r
+ assertNotNull("Exit status is null", exits);\r
+ // cut 4 trailing zeros from the number\r
+ int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
+ .intValue();\r
+ assertEquals("Exit status is not 0", 0, exitsInt);\r
+ System.out.println(sm.getAllStats());\r
+\r
+ } catch (ParseException e) {\r
+ e.printStackTrace();\r
+ fail("Parse Exception: " + e.getMessage());\r
+ }\r
+ assertTrue("Process exited:", sm.hasExited());\r
+ assertFalse("Process aborted:", sm.wasAborted());\r
+ assertFalse("Process hasdump:", sm.hasDump());\r
+ assertFalse("Process signaled:", sm.hasSignaled());\r
+\r
+ Alignment al = confExec.getResults();\r
+ assertNotNull(al);\r
+ assertFalse("Could not remove some files whilst cleaning up ",\r
+ runner.cleanup());\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (DrmaaException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_engine })\r
+ public void testCancel() {\r
+ ClustalW clustal = new ClustalW();\r
+ assertFalse("Cluster execution can only be in unix environment",\r
+ SysPrefs.isWindows);\r
+ clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
+\r
+ try {\r
+\r
+ ConfiguredExecutable<ClustalW> confClust = Configurator\r
+ .configureExecutable(clustal,\r
+ Executable.ExecProvider.Cluster);\r
+ assertNotNull(confClust.getWorkDirectory());\r
+\r
+ ClusterRunner runner = ClusterRunner.getInstance(confClust);\r
+ assertNotNull("Runner is NULL", runner);\r
+\r
+ runner.executeJob();\r
+ // assertNotNull("JobId is null", jobId1);\r
+ Thread.sleep(500);\r
+ JobStatus status = runner.getJobStatus();\r
+ assertTrue("Status of the process is wrong!",\r
+ status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
+ runner.cancelJob();\r
+ Thread.sleep(200); // give fs time to write a file\r
+ JobInfo info = runner.getJobInfo();\r
+ assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.CANCELLED));\r
+ assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.STARTED));\r
+ assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.COLLECTED));\r
+ assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.FINISHED));\r
+ assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
+ JobStatus.SUBMITTED));\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail("Interupted exception caught:" + e.getMessage());\r
+ }\r
+ }\r
+\r
+}\r
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