+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * Copyright (c) 2013 Alexander Sherstnev\r
- * \r
- * Java Bioinformatics Analysis Web Services (JABAWS) \r
- * @version: 2.5 \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.ScoreManager;\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.util.FileWatcher;\r
-import compbio.util.SysPrefs;\r
-\r
-public class JronnTester {\r
-\r
- public static String test_outfile = "TO1381.jronn.out";\r
- private Jronn jronn;\r
-\r
- @BeforeMethod(alwaysRun = true)\r
- void init() {\r
- jronn = new Jronn();\r
- jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner})\r
- public void RunOnCluster() {\r
- assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
- try {\r
- ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
- ClusterRunner runner = ClusterRunner.getInstance(confJronn);\r
-\r
- assertNotNull(runner, "Runner is NULL");\r
- runner.executeJob();\r
- JobStatus status = runner.getJobStatus();\r
- assertTrue(status == JobStatus.PENDING || status == JobStatus.RUNNING, "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
- 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).intValue();\r
- assertEquals(0, exitsInt);\r
- //System.out.println(sm.getAllStats());\r
- } catch (ParseException e) {\r
- e.printStackTrace();\r
- fail("Parse Exception: " + e.getMessage());\r
- }\r
- assertTrue(sm.hasExited());\r
- assertFalse(sm.wasAborted());\r
- assertFalse(sm.hasDump());\r
- assertFalse(sm.hasSignaled());\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, AllTestSuit.test_group_runner})\r
- public void RunOnClusterAsync() {\r
- assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
- try {\r
- ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
- AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);\r
- String jobId = aengine.submitJob(confJronn);\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<Jronn> result = (ConfiguredExecutable<Jronn>) aengine.getResults(jobId);\r
- assertNotNull(result);\r
- System.out.println("RES:" + result);\r
- // Some times the job could be removed from the cluster accounting before \r
- // it has been reported to finish. Make sure 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
- @Test(groups = {AllTestSuit.test_group_runner})\r
- public void RunLocally() {\r
- try {\r
- ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);\r
-\r
- // For local execution use relative\r
- LocalRunner lr = new LocalRunner(confJronn);\r
- lr.executeJob();\r
- ConfiguredExecutable<?> al1 = lr.waitForResult();\r
- assertNotNull(al1.getResults());\r
- ScoreManager al2 = confJronn.getResults();\r
- assertNotNull(al2);\r
- assertEquals(al2.asMap().size(), 3);\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 RunLocallyOnTwoCpu() {\r
- try {\r
- jronn.setNCore(2);\r
- ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);\r
-\r
- // For local execution use relative\r
- LocalRunner lr = new LocalRunner(confJronn);\r
- lr.executeJob();\r
- ConfiguredExecutable<?> al1 = lr.waitForResult();\r
- assertNotNull(al1.getResults());\r
- ScoreManager al2 = confJronn.getResults();\r
- assertNotNull(al2);\r
- assertEquals(al2.asMap().size(), 3);\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<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);\r
- // For local execution use relavive\r
-\r
- AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);\r
- String jobId = sexec.submitJob(confJronn);\r
- String file = confJronn.getWorkDirectory() + File.separator + Jronn.getStatFile();\r
- FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
- int count = 0;\r
- long position = 0;\r
- fw.waitForFile(4);\r
- JobStatus status = sexec.getJobStatus(jobId);\r
- while (status != JobStatus.FINISHED) {\r
- if (fw.hasMoreData()) {\r
- ChunkHolder ch = fw.pull(position);\r
- String chunk = ch.getChunk();\r
- position = ch.getNextPosition();\r
- }\r
- count++;\r
- // Make sure the loop is terminated if the job fails\r
- if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
- break;\r
- }\r
- Thread.sleep(300);\r
- status = sexec.getJobStatus(jobId);\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
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_runner})\r
- public void Persistance() {\r
- try {\r
- Jronn jronn = new Jronn();\r
- jronn.setError("errrr.txt");\r
- jronn.setInput(AllTestSuit.test_input);\r
- jronn.setOutput("outtt.txt");\r
- assertEquals(jronn.getInput(), AllTestSuit.test_input);\r
- assertEquals(jronn.getError(), "errrr.txt");\r
- assertEquals(jronn.getOutput(), "outtt.txt");\r
- ConfiguredExecutable<Jronn> cJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);\r
- SyncExecutor sexec = Configurator.getSyncEngine(cJronn);\r
- sexec.executeJob();\r
- ConfiguredExecutable<?> al = sexec.waitForResult();\r
- assertNotNull(al.getResults());\r
- // Save run configuration\r
- assertTrue(cJronn.saveRunConfiguration());\r
-\r
- // See if loaded configuration is the same as saved\r
- RunConfiguration loadedRun = RunConfiguration\r
- .load(new FileInputStream(new File(cJronn\r
- .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
- assertEquals(\r
- ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),\r
- loadedRun);\r
- // Load run configuration as ConfExecutable\r
- ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn\r
- .loadRunConfiguration(new FileInputStream(new File(cJronn.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(), jronn);\r
-\r
- ConfiguredExecutable<Jronn> resJronn = Configurator\r
- .configureExecutable(resurrectedCMuscle.getExecutable(),\r
- Executable.ExecProvider.Local);\r
-\r
- sexec = Configurator.getSyncEngine(resJronn, Executable.ExecProvider.Local);\r
- sexec.executeJob();\r
- al = sexec.waitForResult();\r
- assertNotNull(al);\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 ConfigurationLoading() {\r
- try {\r
- RunnerConfig<Jronn> jronnConfig = ConfExecutable.getRunnerOptions(Jronn.class);\r
- assertNull(jronnConfig); // There is no supported parameters for Jronn\r
-\r
- PresetManager<Jronn> jronnPresets = ConfExecutable.getRunnerPresets(Jronn.class);\r
- assertNull(jronnPresets); // there is no presets\r
-\r
- LimitsManager<Jronn> jronnLimits = ConfExecutable.getRunnerLimits(Jronn.class);\r
- assertNotNull(jronnLimits);\r
- assertTrue(jronnLimits.getLimits().size() > 0);\r
- jronnLimits.validate(jronnPresets);\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
git://source.jalview.org / proteocache.git / blobdiff