--- /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.local;\r
+\r
+import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertFalse;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.assertNotSame;\r
+import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.util.concurrent.CancellationException;\r
+\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.Alignment;\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.engine.client.EngineUtil;\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.runner.msa.Muscle;\r
+import compbio.util.SysPrefs;\r
+\r
+public class AsyncLocalRunnerTester {\r
+\r
+ // Input path must be absolute to avoid coping input in working directory\r
+ public static String unix_test_input = AllTestSuit.CURRENT_DIRECTORY\r
+ + File.separator + AllTestSuit.TEST_DATA_PATH + "TO1381.fasta";\r
+\r
+ public static String unix_test_AVG_input = AllTestSuit.CURRENT_DIRECTORY\r
+ + File.separator + AllTestSuit.TEST_DATA_PATH\r
+ + "50x500Protein.fasta";\r
+\r
+ public static String unix_test_LARGE_input = AllTestSuit.CURRENT_DIRECTORY\r
+ + File.separator + AllTestSuit.TEST_DATA_PATH\r
+ + "200x500Protein.fasta";\r
+\r
+ // Output file will be located in the task working directory, thus only name\r
+ // is required\r
+ public static String unix_test_outfile = "TO1381.alignment.out";\r
+ public static String cluster_test_outfile = "TO1381.alignment.cluster.out";\r
+\r
+ // Input path must be absolute to avoid coping input in working directory\r
+ public static String win_test_input = AllTestSuit.CURRENT_DIRECTORY\r
+ + File.separator + AllTestSuit.TEST_DATA_PATH + "TO1381.fasta";\r
+\r
+ public static String win_test_LARGE_input = AllTestSuit.CURRENT_DIRECTORY\r
+ + File.separator + AllTestSuit.TEST_DATA_PATH\r
+ + "200x500Protein.fasta";\r
+\r
+ public static String win_test_AVG_input = AllTestSuit.CURRENT_DIRECTORY\r
+ + File.separator + AllTestSuit.TEST_DATA_PATH\r
+ + "50x500Protein.fasta";\r
+\r
+ // Output file will be located in the task working directory, thus only name\r
+ // is required\r
+ public static String win_test_outfile = "TO1381.alignment.out";\r
+\r
+ @Test(expectedExceptions = { CancellationException.class,\r
+ ResultNotAvailableException.class }, groups = { AllTestSuit.test_group_engine })\r
+ public void testCancelLocally() throws ResultNotAvailableException {\r
+ System.out.println("Running testCancelLocally");\r
+ ClustalW clustal = new ClustalW();\r
+\r
+ if (SysPrefs.isWindows) {\r
+ System.out.println("Working in WINDOWS environment");\r
+ clustal.setInput(win_test_input).setOutput(win_test_outfile);\r
+ } else {\r
+ System.out.println("Working in UNIX environment");\r
+ clustal.setInput(unix_test_input).setOutput(unix_test_outfile);\r
+ }\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ try {\r
+ ConfiguredExecutable<ClustalW> confClust = Configurator\r
+ .configureExecutable(clustal);\r
+ String jobId = lr.submitJob(confClust);\r
+ // Thread.sleep(10); //wait for 100ms\r
+ assertNotSame(lr.getJobStatus(jobId), JobStatus.FINISHED,\r
+ "Job has finished already. Too late to test cancel!");\r
+ lr.cancelJob(jobId);\r
+ // This call causes CancellationException to be thrown\r
+ Executable<?> clustalr = lr.getResults(jobId);\r
+ // @see AsyncLocalRunner.cleanup documents\r
+ // assertTrue(lr.cleanup(jobId));\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(invocationCount = 5, threadPoolSize = 4, groups = { AllTestSuit.test_group_engine })\r
+ public void testSubmitLocally() {\r
+ System.out.println("Running testSubmitLocally()");\r
+ Muscle muscle = new Muscle();\r
+\r
+ if (SysPrefs.isWindows) {\r
+ System.out.println("Working in WINDOWS environment");\r
+ muscle.setInput(win_test_input).setOutput(win_test_outfile);\r
+ } else {\r
+ System.out.println("Working in UNIX environment");\r
+ muscle.setInput(unix_test_input).setOutput(unix_test_outfile);\r
+ }\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ try {\r
+ ConfiguredExecutable<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle);\r
+ String jobId = lr.submitJob(confMuscle);\r
+ // Thread.sleep(10); //wait for 100ms\r
+ // assertNotSame("Job has finished already. Too late to test cancel!",\r
+ // JobStatus.FINISHED, lr.getJobStatus(jobId));\r
+ // This call causes CancellationException to be thrown\r
+ Executable<?> muscler = lr.getResults(jobId);\r
+ Alignment al = confMuscle.getResults();\r
+ assertNotNull(al);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(invocationCount = 5, threadPoolSize = 4, groups = { AllTestSuit.test_group_engine })\r
+ public void testGetStatus() {\r
+ System.out.println("Running testGetStatus");\r
+ Muscle muscle = new Muscle();\r
+\r
+ if (SysPrefs.isWindows) {\r
+ System.out.println("Working in WINDOWS environment");\r
+ muscle.setInput(win_test_AVG_input).setOutput(win_test_outfile);\r
+ } else {\r
+ System.out.println("Working in UNIX environment");\r
+ muscle.setInput(unix_test_AVG_input).setOutput(unix_test_outfile);\r
+ }\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ try {\r
+ ConfiguredExecutable<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle);\r
+ String jobId = lr.submitJob(confMuscle);\r
+ // Thread.sleep(10); //wait for 100ms\r
+ JobStatus status = lr.getJobStatus(jobId);\r
+ while (status == JobStatus.UNDEFINED) {\r
+ assertTrue(status == JobStatus.UNDEFINED);\r
+ Thread.sleep(100);\r
+ status = lr.getJobStatus(jobId);\r
+ }\r
+ while (status != JobStatus.FINISHED) {\r
+ Thread.sleep(500);\r
+ assertTrue(status == JobStatus.RUNNING);\r
+ status = lr.getJobStatus(jobId);\r
+ }\r
+ // assert that we get here, means that the job reached FINISHED\r
+ // status\r
+ // This call causes CancellationException to be thrown\r
+ Executable<?> muscler = lr.getResults(jobId);\r
+ /*\r
+ * After results were obtained the task were removed for the queue,\r
+ * and it status could not be determined\r
+ */\r
+ // Make sure list has been updated\r
+ Thread.sleep(200);\r
+ status = lr.getJobStatus(jobId);\r
+ assertTrue(status == JobStatus.FINISHED);\r
+\r
+ Alignment al = confMuscle.getResults();\r
+\r
+ assertNotNull(al);\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(expectedExceptions = CancellationException.class, groups = { AllTestSuit.test_group_engine })\r
+ public void testMultipleCancelLocally() {\r
+ System.out.println("Running testMultipleCancelLocally()");\r
+ ClustalW clustal = new ClustalW();\r
+ ClustalW clustal2 = new ClustalW();\r
+ if (SysPrefs.isWindows) {\r
+ System.out.println("Working in WINDOWS environment");\r
+ clustal.setInput(win_test_input).setOutput(win_test_outfile);\r
+ clustal2.setInput(win_test_input).setOutput(win_test_outfile);\r
+ } else {\r
+ System.out.println("Working in UNIX environment");\r
+ clustal.setInput(unix_test_input).setOutput(unix_test_outfile);\r
+ clustal2.setInput(unix_test_input).setOutput(unix_test_outfile);\r
+ }\r
+ try {\r
+ ConfiguredExecutable<ClustalW> confClustal1 = Configurator\r
+ .configureExecutable(clustal);\r
+ ConfiguredExecutable<ClustalW> confClustal2 = Configurator\r
+ .configureExecutable(clustal2);\r
+ AsyncLocalRunner lr = new AsyncLocalRunner();\r
+ AsyncLocalRunner lr2 = new AsyncLocalRunner();\r
+\r
+ String jobId1 = lr.submitJob(confClustal1);\r
+ String jobId2 = lr2.submitJob(confClustal2);\r
+\r
+ // Thread.sleep(10); //wait for 100ms\r
+ assertNotSame(lr.getJobStatus(jobId1), JobStatus.FINISHED,\r
+ "Job has finished already. Too late to test cancel!");\r
+ lr.cancelJob(jobId1);\r
+ // Thread.sleep(10);\r
+ assertNotSame(lr2.getJobStatus(jobId2), JobStatus.FINISHED,\r
+ "Job has finished already. Too late to test cancel!");\r
+ lr2.cancelJob(jobId2);\r
+ // This call causes CancellationException to be thrown\r
+ Executable<?> clustalr = lr.getResults(jobId1);\r
+ Executable<?> clustalr2 = lr2.getResults(jobId2);\r
+\r
+ assertTrue(lr.cleanup(jobId1));\r
+ assertTrue(lr2.cleanup(jobId2));\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_engine })\r
+ public void testCancelCompletedTaskLocally() {\r
+ System.out.println("Running testCancelCompletedTaskLocally");\r
+ ClustalW clustal = new ClustalW();\r
+ if (SysPrefs.isWindows) {\r
+ System.out.println("Working in WINDOWS environment");\r
+ clustal.setInput(win_test_input).setOutput(win_test_outfile);\r
+ } else {\r
+ System.out.println("Working in UNIX environment");\r
+ clustal.setInput(unix_test_input).setOutput(unix_test_outfile);\r
+ }\r
+ try {\r
+ ConfiguredExecutable<ClustalW> confClustal1 = Configurator\r
+ .configureExecutable(clustal);\r
+ AsyncLocalRunner lr = new AsyncLocalRunner();\r
+ String jobId = lr.submitJob(confClustal1);\r
+ Thread.currentThread();\r
+ Thread.sleep(3000); // wait for 100ms\r
+ assertEquals(lr.getJobStatus(jobId), JobStatus.FINISHED,\r
+ "Job has not finished!");\r
+ lr.cancelJob(jobId);\r
+ // This call causes CancellationException to be thrown\r
+ Executable<?> clustalr = lr.getResults(jobId);\r
+ assertNotNull(clustalr);\r
+\r
+ assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
+ JobStatus.CANCELLED));\r
+ assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
+ JobStatus.STARTED));\r
+ assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
+ JobStatus.COLLECTED));\r
+ assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
+ JobStatus.FINISHED));\r
+ assertFalse(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
+ JobStatus.SUBMITTED));\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_engine })\r
+ public void testAsyncRetrievOperation() {\r
+ System.out.println("Running testAsyncOperation()");\r
+ Muscle muscle = new Muscle();\r
+\r
+ if (SysPrefs.isWindows) {\r
+ System.out.println("Working in WINDOWS environment");\r
+ muscle.setInput(win_test_input).setOutput(win_test_outfile);\r
+ } else {\r
+ System.out.println("Working in UNIX environment");\r
+ muscle.setInput(unix_test_input).setOutput(unix_test_outfile);\r
+ }\r
+\r
+ try {\r
+ ConfiguredExecutable<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle);\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ String jobId = lr.submitJob(confMuscle);\r
+ AsyncLocalRunner as = new AsyncLocalRunner();\r
+ ConfiguredExecutable<Muscle> muscler = (ConfiguredExecutable<Muscle>) as\r
+ .getResults(jobId);\r
+ assertNotNull(muscler);\r
+ Alignment al1 = muscler.getResults();\r
+\r
+ assertTrue(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
+ JobStatus.STARTED));\r
+ assertTrue(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
+ JobStatus.COLLECTED));\r
+ assertTrue(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
+ JobStatus.FINISHED));\r
+ assertFalse(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
+ JobStatus.CANCELLED));\r
+ assertFalse(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
+ JobStatus.SUBMITTED));\r
+ Alignment al2 = confMuscle.getResults();\r
+ assertNotNull(al1);\r
+ assertNotNull(al2);\r
+ assertTrue(al1.equals(al2));\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_engine })\r
+ public void testAsyncCancelOperation() {\r
+ System.out.println("Running testAsyncOperation()");\r
+ Muscle muscle = new Muscle();\r
+\r
+ if (SysPrefs.isWindows) {\r
+ System.out.println("Working in WINDOWS environment");\r
+ muscle.setInput(win_test_input).setOutput(win_test_outfile);\r
+ } else {\r
+ System.out.println("Working in UNIX environment");\r
+ muscle.setInput(unix_test_input).setOutput(unix_test_outfile);\r
+ }\r
+\r
+ try {\r
+ ConfiguredExecutable<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle);\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ String jobId = lr.submitJob(confMuscle);\r
+ // This call causes CancellationException to be thrown\r
+ AsyncLocalRunner as = new AsyncLocalRunner();\r
+ assertTrue(as.getJobStatus(jobId) != JobStatus.FINISHED);\r
+ as.cancelJob(jobId);\r
+ assertTrue(as.getJobStatus(jobId) == JobStatus.CANCELLED);\r
+\r
+ assertTrue(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
+ JobStatus.CANCELLED));\r
+ // could be both\r
+ // assertFalse(Util.isMarked(confMuscle.getWorkDirectory(),\r
+ // Util.StatFileType.STARTED));\r
+ assertFalse(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
+ JobStatus.COLLECTED));\r
+ assertFalse(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
+ JobStatus.FINISHED));\r
+ assertFalse(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
+ JobStatus.SUBMITTED));\r
+ // Executable<?> muscler = as.getResult(jobId);\r
+ // assertNotNull(muscler);\r
+ // Alignment al = muscle.getResults();\r
+ // assertNotNull(al);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / proteocache.git / blobdiff