--- /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.assertNull;\r
+import static org.testng.AssertJUnit.assertTrue;\r
+import static org.testng.AssertJUnit.fail;\r
+\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.metadata.AllTestSuit;\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 DrmaaAsyncClusterEngineTester {\r
+\r
+ public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+ + "TO1381.fasta";\r
+ public static String large_test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+ + "1000x3000Dna.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
+ try {\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal);\r
+ AsyncExecutor runner = new AsyncClusterRunner();\r
+ assertNotNull("Runner is NULL", runner);\r
+ String jobId = runner.submitJob(confClustal);\r
+ assertEquals("Input was not set!", test_input, clustal.getInput());\r
+ assertNotNull("JobId is null", jobId);\r
+ JobStatus status = runner.getJobStatus(jobId);\r
+ assertTrue("Status of the process is wrong!",\r
+ status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
+ JobStatus info = runner.getJobStatus(jobId);\r
+ assertNotNull("JobInfo is null", info);\r
+ Executable<?> result = runner.getResults(jobId);\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(expectedExceptions = ResultNotAvailableException.class, groups = {\r
+ AllTestSuit.test_group_cluster, AllTestSuit.test_group_engine })\r
+ // expectedExceptions = ResultNotAvailableException.class,\r
+ public void testCancel() throws ResultNotAvailableException {\r
+ ClustalW clustal = new ClustalW();\r
+ assertFalse("Cluster execution can only be in unix environment",\r
+ SysPrefs.isWindows);\r
+ clustal.setInput(large_test_input).setOutput(cluster_test_outfile);\r
+\r
+ try {\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal);\r
+ AsyncClusterRunner runner = new AsyncClusterRunner();\r
+ String jobId = runner.submitJob(confClustal);\r
+ assertNotNull("Runner is NULL", runner);\r
+ // assertNotNull("JobId is null", jobId1);\r
+ Thread.sleep(200);\r
+ JobStatus status = runner.getJobStatus(jobId);\r
+ assertTrue("Status of the process is wrong!",\r
+ status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
+ assertFalse("Status of the process is wrong!",\r
+ status == JobStatus.FINISHED);\r
+ runner.cancelJob(jobId);\r
+ // This is never NULL as long as the job has started!\r
+ ConfiguredExecutable<?> exec = runner.getResults(jobId);\r
+ assertNull(exec.getResults());\r
+ } catch (JobSubmissionException 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
+ @Test(groups = { AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_engine })\r
+ public void testGetJobStatus() {\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
+ AsyncClusterRunner runner = new AsyncClusterRunner();\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal);\r
+ String jobId = runner.submitJob(confClustal);\r
+ assertNotNull("Runner is NULL", runner);\r
+ AsyncClusterRunner runner2 = new AsyncClusterRunner();\r
+\r
+ boolean hasRun = false;\r
+ boolean hasPended = false;\r
+ Thread.sleep(500); \r
+ JobStatus status = runner2.getJobStatus(jobId);\r
+ while (status != JobStatus.FINISHED) {\r
+ if (status == JobStatus.CANCELLED) {\r
+ fail("Job is not cancelled!");\r
+ }\r
+ if (status == JobStatus.FAILED) {\r
+ fail("Job should not fail!");\r
+ }\r
+ if (status == JobStatus.RUNNING) {\r
+ hasRun = true;\r
+ }\r
+ if (status == JobStatus.PENDING) {\r
+ hasPended = true;\r
+ }\r
+ if (status == JobStatus.UNDEFINED) {\r
+ System.out.println("Wrong status (UNDEFINED) reported by cluster engine!");\r
+ break;\r
+ }\r
+ status = runner2.getJobStatus(jobId);\r
+ }\r
+ assertTrue(hasRun);\r
+ assertTrue(hasPended);\r
+ assertTrue(hasRun);\r
+ // Bear in mind that if the task were not put in the queue\r
+ // immediately\r
+ // the status could be UNDEFINED!\r
+ // assertFalse(hasUndefined);\r
+ AsyncClusterRunner runner3 = new AsyncClusterRunner();\r
+ Executable<?> exec = runner3.getResults(jobId);\r
+ assertNotNull(exec);\r
+ // Now try collecting result for the second time\r
+ exec=null;\r
+ Thread.sleep(1000);\r
+ exec = runner3.getResults(jobId);\r
+ assertNotNull(exec);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+}\r
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