--- /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.runner.msa;\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.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.Alignment;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.FilePuller;\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.ChunkHolder;\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.Muscle;\r
+import compbio.util.FileWatcher;\r
+import compbio.util.SysPrefs;\r
+\r
+public class MuscleTester {\r
+\r
+ public static String test_outfile = "TO1381.muscle.out"; // homes/pvtroshin/TO1381.clustal.out\r
+ public static String cluster_test_outfile = "TO1381.muscle.cluster.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
+\r
+ private Muscle muscle;\r
+\r
+ @BeforeMethod(alwaysRun = true)\r
+ void init() {\r
+ muscle = new Muscle();\r
+ muscle.setInput(AllTestSuit.test_input).setOutput(cluster_test_outfile);\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<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle,\r
+ Executable.ExecProvider.Cluster);\r
+ ClusterRunner runner = ClusterRunner.getInstance(confMuscle);\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(enabled = false, 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<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle,\r
+ Executable.ExecProvider.Cluster);\r
+ AsyncExecutor aengine = Configurator.getAsyncEngine(confMuscle);\r
+ String jobId = aengine.submitJob(confMuscle);\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 || status !=JobStatus.UNDEFINED) {\r
+ System.out.println("Job Status: " + status);\r
+ Thread.sleep(1000);\r
+ status = aengine.getJobStatus(jobId);\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
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_runner })\r
+ public void testRunLocally() {\r
+ try {\r
+ ConfiguredExecutable<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle, Executable.ExecProvider.Local);\r
+ confMuscle.getParameters().setParam("-matrix", "BLOSUM62");\r
+\r
+ // For local execution use relative\r
+ LocalRunner lr = new LocalRunner(confMuscle);\r
+ lr.executeJob();\r
+ ConfiguredExecutable<?> al1 = lr.waitForResult();\r
+ assertNotNull(al1.getResults());\r
+ Alignment al2 = confMuscle.getResults();\r
+ assertNotNull(al2);\r
+ assertEquals(al1.getResults(), al2);\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 readStatistics() {\r
+ try {\r
+ ConfiguredExecutable<Muscle> confMuscle = Configurator\r
+ .configureExecutable(muscle, Executable.ExecProvider.Local);\r
+ // For local execution use relavive\r
+\r
+ AsyncExecutor sexec = Configurator.getAsyncEngine(confMuscle);\r
+ String jobId = sexec.submitJob(confMuscle);\r
+ FilePuller fw = FilePuller.newFilePuller(confMuscle\r
+ .getWorkDirectory()\r
+ + File.separator + Muscle.getStatFile(),\r
+ FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
+ int count = 0;\r
+ long position = 0;\r
+ fw.waitForFile(4);\r
+ while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || sexec\r
+ .getJobStatus(jobId) == JobStatus.FAILED || sexec\r
+ .getJobStatus(jobId) == JobStatus.UNDEFINED)\r
+ || fw.hasMoreData()) {\r
+ ChunkHolder ch = fw.pull(position);\r
+ String chunk = ch.getChunk();\r
+ position = ch.getNextPosition();\r
+ System.out.print(chunk);\r
+ count++;\r
+ }\r
+ assertTrue(count > 1);\r
+ ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
+ assertNotNull(al.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_runner })\r
+ public void testPersistance() {\r
+ try {\r
+ Muscle muscle = new Muscle();\r
+ muscle.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
+ .setOutput("outtt.txt");\r
+ assertEquals(muscle.getInput(), AllTestSuit.test_input);\r
+ assertEquals(muscle.getError(), "errrr.txt");\r
+ assertEquals(muscle.getOutput(), "outtt.txt");\r
+ ConfiguredExecutable<Muscle> cmuscle = Configurator\r
+ .configureExecutable(muscle, Executable.ExecProvider.Local);\r
+\r
+ SyncExecutor sexec = Configurator.getSyncEngine(cmuscle);\r
+ sexec.executeJob();\r
+ ConfiguredExecutable<?> al = sexec.waitForResult();\r
+ assertNotNull(al.getResults());\r
+ // Save run configuration\r
+ assertTrue(cmuscle.saveRunConfiguration());\r
+\r
+ // See if loaded configuration is the same as saved\r
+ RunConfiguration loadedRun = RunConfiguration\r
+ .load(new FileInputStream(new File(cmuscle\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertEquals(((ConfExecutable<Muscle>) cmuscle)\r
+ .getRunConfiguration(), loadedRun);\r
+ // Load run configuration as ConfExecutable\r
+ ConfiguredExecutable<Muscle> resurrectedCMuscle = (ConfiguredExecutable<Muscle>) cmuscle\r
+ .loadRunConfiguration(new FileInputStream(new File(cmuscle\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertNotNull(resurrectedCMuscle);\r
+ assertEquals(resurrectedCMuscle.getExecutable().getInput(),\r
+ AllTestSuit.test_input);\r
+ assertEquals(resurrectedCMuscle.getExecutable().getError(),\r
+ "errrr.txt");\r
+ assertEquals(resurrectedCMuscle.getExecutable().getOutput(),\r
+ "outtt.txt");\r
+ // See in details whether executables are the same\r
+ assertEquals(resurrectedCMuscle.getExecutable(), muscle);\r
+\r
+ ConfiguredExecutable<Muscle> resmuscle = Configurator\r
+ .configureExecutable(resurrectedCMuscle.getExecutable(),\r
+ Executable.ExecProvider.Local);\r
+\r
+ sexec = Configurator.getSyncEngine(resmuscle,\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<Muscle> muscleConfig = ConfExecutable\r
+ .getRunnerOptions(Muscle.class);\r
+ assertNotNull(muscleConfig);\r
+ assertTrue(muscleConfig.getArguments().size() > 0);\r
+\r
+ PresetManager<Muscle> musclePresets = ConfExecutable\r
+ .getRunnerPresets(Muscle.class);\r
+ assertNotNull(musclePresets);\r
+ assertTrue(musclePresets.getPresets().size() > 0);\r
+ musclePresets.validate(muscleConfig);\r
+\r
+ LimitsManager<Muscle> muscleLimits = ConfExecutable\r
+ .getRunnerLimits(Muscle.class);\r
+ assertNotNull(muscleLimits);\r
+ assertTrue(muscleLimits.getLimits().size() > 0);\r
+ muscleLimits.validate(musclePresets);\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
git://source.jalview.org / proteocache.git / blobdiff