--- /dev/null
+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \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.runner.disorder;\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.assertNull;\r
+import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.text.ParseException;\r
+\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.ggf.drmaa.DrmaaException;\r
+import org.ggf.drmaa.JobInfo;\r
+import org.testng.annotations.BeforeMethod;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.ScoreManager.ScoreHolder;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.SyncExecutor;\r
+import compbio.engine.client.ConfExecutable;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.RunConfiguration;\r
+import compbio.engine.cluster.drmaa.ClusterEngineUtil;\r
+import compbio.engine.cluster.drmaa.ClusterRunner;\r
+import compbio.engine.cluster.drmaa.StatisticManager;\r
+import compbio.engine.local.LocalRunner;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobExecutionException;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.runner.msa.Mafft;\r
+import compbio.util.SysPrefs;\r
+\r
+public class IUPredTester {\r
+\r
+ private IUPred iupred;\r
+\r
+ @BeforeMethod(alwaysRun = true)\r
+ void init() {\r
+ iupred = new IUPred();\r
+ iupred.setInput(AllTestSuit.test_input);\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnCluster() {\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ try {\r
+ ConfiguredExecutable<IUPred> confIUPred = Configurator\r
+ .configureExecutable(iupred,\r
+ Executable.ExecProvider.Cluster);\r
+ ClusterRunner runner = ClusterRunner.getInstance(confIUPred);\r
+\r
+ assertNotNull(runner, "Runner is NULL");\r
+ runner.executeJob();\r
+ // assertNotNull("JobId is null", jobId1);\r
+ JobStatus status = runner.getJobStatus();\r
+ assertTrue(status == JobStatus.PENDING\r
+ || status == JobStatus.RUNNING,\r
+ "Status of the process is wrong!");\r
+ JobInfo info = runner.getJobInfo();\r
+ assertNotNull(info, "JobInfo is null");\r
+ StatisticManager sm = new StatisticManager(info);\r
+ assertNotNull(sm, "Statictic manager is null");\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(0, exitsInt);\r
+ System.out.println(sm.getAllStats());\r
+\r
+ } catch (ParseException e) {\r
+ e.printStackTrace();\r
+ fail("Parse Exception: " + e.getMessage());\r
+ }\r
+ // assertFalse(runner.cleanup());\r
+ assertTrue(sm.hasExited());\r
+ assertFalse(sm.wasAborted());\r
+ assertFalse(sm.hasDump());\r
+ assertFalse(sm.hasSignaled());\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
+ }\r
+ }\r
+\r
+ /**\r
+ * This tests fails from time to time depending on the cluster load or some\r
+ * other factors. Any client code has to adjust for this issue\r
+ */\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnClusterAsync() {\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ try {\r
+ ConfiguredExecutable<IUPred> confIUPred = Configurator\r
+ .configureExecutable(iupred,\r
+ Executable.ExecProvider.Cluster);\r
+ AsyncExecutor aengine = Configurator.getAsyncEngine(confIUPred);\r
+ String jobId = aengine.submitJob(confIUPred);\r
+ assertNotNull(jobId, "Runner is NULL");\r
+ // let drmaa to start\r
+ Thread.sleep(500);\r
+ JobStatus status = aengine.getJobStatus(jobId);\r
+ while (status != JobStatus.FINISHED) {\r
+ System.out.println("Job Status: " + status);\r
+ Thread.sleep(1000);\r
+ status = aengine.getJobStatus(jobId);\r
+ ConfiguredExecutable<IUPred> result = (ConfiguredExecutable<IUPred>) aengine\r
+ .getResults(jobId);\r
+ assertNotNull(result);\r
+ System.out.println("RES:" + result);\r
+ // Some times the job could be removed from the cluster\r
+ // accounting\r
+ // before it has been reported to finish. Make sure\r
+ // to stop waiting in such case\r
+ if (status == JobStatus.UNDEFINED) {\r
+ break;\r
+ }\r
+ }\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ \r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testSetParameter() {\r
+ assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
+ assertTrue(iupred.getParameters(null).getCommandString().trim().endsWith(AllTestSuit.test_input));\r
+ iupred.setParameter("long");\r
+ assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
+ String cmd = iupred.getParameters(null).getCommandString().trim(); \r
+ assertTrue(cmd.endsWith("long"));\r
+ assertTrue(cmd.contains(AllTestSuit.test_input)); \r
+ }\r
+ \r
+ \r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testReadResults() {\r
+ ScoreManager scoreMan;\r
+ try {\r
+ scoreMan = iupred.getResults(AllTestSuit.TEST_DATA_PATH_ABSOLUTE);\r
+ System.out.println(scoreMan.asMap());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+ \r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testRunLocally() {\r
+ try {\r
+ ConfiguredExecutable<IUPred> confIUPred = Configurator\r
+ .configureExecutable(iupred, Executable.ExecProvider.Local);\r
+\r
+ // For local execution use relative\r
+ LocalRunner lr = new LocalRunner(confIUPred);\r
+ lr.executeJob();\r
+ ConfiguredExecutable<?> al1 = lr.waitForResult();\r
+ assertNotNull(al1.getResults());\r
+ ScoreManager al2 = confIUPred.getResults();\r
+ assertNotNull(al2);\r
+ assertEquals(al2.asMap().size(), 3);\r
+ assertEquals(al2.getNumberOfSeq(),3);\r
+ \r
+ ScoreHolder sch = al2.getAnnotationForSequence("Foobar");\r
+ assertEquals(sch.getNumberOfScores(), 3);\r
+ \r
+ Score sc = sch.getScoreByMethod("Long");\r
+ assertEquals(sc.getMethod(), "Long");\r
+ assertTrue(sc.getRanges().isEmpty());\r
+ assertNotNull(sc.getScores());\r
+ assertEquals(sc.getScores().size(), 481);\r
+ assertEquals(al1.getResults(), al2);\r
+\r
+ \r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testRunLocallyWithParams() {\r
+ try {\r
+ iupred.setParameter("short");\r
+ ConfiguredExecutable<IUPred> confIUPred = Configurator\r
+ .configureExecutable(iupred, Executable.ExecProvider.Local);\r
+\r
+ // For local execution use relative\r
+ LocalRunner lr = new LocalRunner(confIUPred);\r
+ lr.executeJob();\r
+ ConfiguredExecutable<?> al1 = lr.waitForResult();\r
+ assertNotNull(al1.getResults());\r
+ ScoreManager al2 = confIUPred.getResults();\r
+ \r
+ assertNotNull(al2.asMap());\r
+ assertEquals(al2.asMap().size(), 3);\r
+ ScoreHolder sch = al2.getAnnotationForSequence("Foobar");\r
+ assertNotNull(sch);\r
+ assertEquals(sch.getNumberOfScores(), 1); \r
+ \r
+ /*\r
+ assertNotNull(al2);\r
+ assertEquals(al2.asSet().size(), 1);\r
+ assertEquals(al2.getNumberOfSeq(),1);\r
+ Score sc = al2.asSet().iterator().next(); \r
+ assertEquals(sc.getMethod(), "Long");\r
+ assertTrue(sc.getRanges().isEmpty());\r
+ assertNotNull(sc.getScores());\r
+ assertEquals(sc.getScores().size(), 568);\r
+ assertEquals(al1.getResults(), al2);\r
+*/\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testPersistance() {\r
+ try {\r
+ IUPred iupred = new IUPred();\r
+ iupred.setError("errrr.txt").setInput(AllTestSuit.test_input);\r
+ assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
+ assertEquals(iupred.getError(), "errrr.txt");\r
+\r
+ ConfiguredExecutable<IUPred> cIUPred = Configurator\r
+ .configureExecutable(iupred, Executable.ExecProvider.Local);\r
+\r
+ SyncExecutor sexec = Configurator.getSyncEngine(cIUPred);\r
+ sexec.executeJob();\r
+ ConfiguredExecutable<?> al = sexec.waitForResult();\r
+ assertNotNull(al.getResults());\r
+ // Save run configuration\r
+ assertTrue(cIUPred.saveRunConfiguration());\r
+\r
+ // See if loaded configuration is the same as saved\r
+ RunConfiguration loadedRun = RunConfiguration\r
+ .load(new FileInputStream(new File(cIUPred\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertEquals(\r
+ ((ConfExecutable<IUPred>) cIUPred).getRunConfiguration(),\r
+ loadedRun);\r
+ // Load run configuration as ConfExecutable\r
+ ConfiguredExecutable<IUPred> resurrectedCIUPred = (ConfiguredExecutable<IUPred>) cIUPred\r
+ .loadRunConfiguration(new FileInputStream(new File(cIUPred\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertNotNull(resurrectedCIUPred);\r
+ assertEquals(resurrectedCIUPred.getExecutable().getInput(),\r
+ AllTestSuit.test_input);\r
+ assertEquals(resurrectedCIUPred.getExecutable().getError(),\r
+ "errrr.txt");\r
+\r
+ // See in details whether executables are the same\r
+ assertEquals(resurrectedCIUPred.getExecutable(), iupred);\r
+\r
+ ConfiguredExecutable<IUPred> resIUPred = Configurator\r
+ .configureExecutable(resurrectedCIUPred.getExecutable(),\r
+ Executable.ExecProvider.Local);\r
+\r
+ sexec = Configurator.getSyncEngine(resIUPred,\r
+ Executable.ExecProvider.Local);\r
+ sexec.executeJob();\r
+ al = sexec.waitForResult();\r
+ assertNotNull(al);\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testConfigurationLoading() {\r
+ try {\r
+ RunnerConfig<IUPred> iupredConfig = ConfExecutable\r
+ .getRunnerOptions(IUPred.class);\r
+\r
+ assertNotNull(iupredConfig);\r
+\r
+ assertTrue(iupredConfig.getArguments().size() != 0);\r
+\r
+ PresetManager<IUPred> iupredPresets = ConfExecutable\r
+ .getRunnerPresets(IUPred.class);\r
+ assertNull(iupredPresets); // there is no presets\r
+\r
+ LimitsManager<IUPred> iupredLimits = ConfExecutable\r
+ .getRunnerLimits(IUPred.class);\r
+ assertNotNull(iupredLimits);\r
+ assertTrue(iupredLimits.getLimits().size() > 0);\r
+ iupredLimits.validate(iupredPresets);\r
+\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ValidationException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+}\r
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