+++ /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