--- /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
+\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.testng.annotations.BeforeMethod;\r
+import org.testng.annotations.Test;\r
+\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.client.Executable.ExecProvider;\r
+import compbio.engine.cluster.drmaa.ClusterRunner;\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.Mafft;\r
+import compbio.util.SysPrefs;\r
+\r
+public class MafftTester {\r
+\r
+ private Mafft mafft;\r
+\r
+ @BeforeMethod(groups = { AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
+ public void init() {\r
+ mafft = new Mafft();\r
+ // mafft.setParameter("--aamatrix");\r
+ // mafft.setParameter("PAM100");\r
+ mafft.setInput(AllTestSuit.test_input); // .setOutput("Mafft.out").setError("mafft.progress");\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_runner,\r
+ AllTestSuit.test_group_non_windows })\r
+ public void testSetInputTester() {\r
+ Mafft mf = new Mafft();\r
+ // System.out.println(mf.getParameters(null));\r
+ mf.setInput("INNN");\r
+ // System.out.println(mf.getParameters(null));\r
+ mf.setError("ERRR");\r
+ mf.setInput("INN222");\r
+ mf.setOutput("OUT");\r
+ // System.out.println(mf.getParameters(null));\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_runner,\r
+ AllTestSuit.test_group_non_windows })\r
+ public void testExecute() {\r
+ try {\r
+ ConfiguredExecutable<Mafft> cmafft = Configurator\r
+ .configureExecutable(mafft, Executable.ExecProvider.Local);\r
+ cmafft.getParameters().setParam("--aamatrix", "PAM120");\r
+ SyncExecutor sexecutor = Configurator.getSyncEngine(cmafft);\r
+ sexecutor.executeJob();\r
+ cmafft = (ConfiguredExecutable<Mafft>) sexecutor.waitForResult();\r
+ assertNotNull(cmafft.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobExecutionException 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
+ AllTestSuit.test_group_non_windows })\r
+ public void testPersistance() {\r
+ try {\r
+ Mafft mafft = new Mafft();\r
+ mafft.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
+ .setOutput("outtt.txt");\r
+ assertEquals(mafft.getInput(), AllTestSuit.test_input);\r
+ assertEquals(mafft.getError(), "errrr.txt");\r
+ assertEquals(mafft.getOutput(), "outtt.txt");\r
+ ConfiguredExecutable<Mafft> cmafft = Configurator\r
+ .configureExecutable(mafft, Executable.ExecProvider.Local);\r
+\r
+ SyncExecutor sexec = Configurator.getSyncEngine(cmafft);\r
+ sexec.executeJob();\r
+ ConfiguredExecutable<?> al = sexec.waitForResult();\r
+ assertNotNull(al.getResults());\r
+ // Save run configuration\r
+ assertTrue(cmafft.saveRunConfiguration());\r
+\r
+ // See if loaded configuration is the same as saved\r
+ RunConfiguration loadedRun = RunConfiguration\r
+ .load(new FileInputStream(new File(cmafft\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertEquals(\r
+ ((ConfExecutable<Mafft>) cmafft).getRunConfiguration(),\r
+ loadedRun);\r
+ // Load run configuration as ConfExecutable\r
+ ConfiguredExecutable<Mafft> resurrectedCMafft = (ConfiguredExecutable<Mafft>) cmafft\r
+ .loadRunConfiguration(new FileInputStream(new File(cmafft\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertNotNull(resurrectedCMafft);\r
+ // See in details whether executables are the same\r
+ assertEquals(resurrectedCMafft.getExecutable(), mafft);\r
+\r
+ // Finally rerun the job in the new task directory\r
+ ConfiguredExecutable<Mafft> resmafft = Configurator\r
+ .configureExecutable(resurrectedCMafft.getExecutable(),\r
+ Executable.ExecProvider.Local);\r
+\r
+ sexec = Configurator.getSyncEngine(resmafft,\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_cluster,\r
+ AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
+ public void testClusterExecute() {\r
+ try {\r
+ \r
+ ConfiguredExecutable<Mafft> cmafft = Configurator\r
+ .configureExecutable(mafft, Executable.ExecProvider.Cluster);\r
+ ClusterRunner sexecutor = (ClusterRunner) Configurator.getSyncEngine(\r
+ cmafft, Executable.ExecProvider.Cluster);\r
+ sexecutor.executeJob();\r
+ ConfiguredExecutable<?> al = sexecutor.waitForResult();\r
+ assertNotNull(al.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * This test demonstrates the problem with Drmaa which can return UNDEFINED status after Running!\r
+ * enable it to see the problem \r
+ */\r
+ @Test(enabled=false, groups = { AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
+ public void testRunOnClusterAsyncCheckStatusShortPoolingTime() {\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ try {\r
+ ConfiguredExecutable<Mafft> confMafft = Configurator\r
+ .configureExecutable(mafft, Executable.ExecProvider.Cluster);\r
+ AsyncExecutor aengine = Configurator.getAsyncEngine(confMafft);\r
+ String jobId = aengine.submitJob(confMafft);\r
+ assertNotNull(jobId, "Runner is NULL");\r
+ // let drmaa to start\r
+ Thread.sleep(500);\r
+ boolean run = false;\r
+ JobStatus status = aengine.getJobStatus(jobId);\r
+ while (status != JobStatus.FINISHED) {\r
+ if (status == JobStatus.RUNNING) {\r
+ run = true;\r
+ }\r
+ Thread.sleep(500);\r
+ status = aengine.getJobStatus(jobId);\r
+ // Once the job was in the RUNNING state UNDEFINED should not\r
+ // occur\r
+ // Unfortunately with a short pooling time like here\r
+ // this problem occurs. There seems to be a bug in DRMAA SGE\r
+ // implementation\r
+ // Perhaps longer pooling time e.g. 5 second will fix the issue\r
+ // see the next test case for this\r
+ if (run) {\r
+ assertNotSame(status, JobStatus.UNDEFINED);\r
+ }\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
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
+ public void testRunOnClusterAsyncCheckStatusLongPoolingTime() {\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ try {\r
+ ConfiguredExecutable<Mafft> confMafft = Configurator\r
+ .configureExecutable(mafft, Executable.ExecProvider.Cluster);\r
+ AsyncExecutor aengine = Configurator.getAsyncEngine(confMafft);\r
+ String jobId = aengine.submitJob(confMafft);\r
+ assertNotNull(jobId, "Runner is NULL");\r
+ // let drmaa to start\r
+ Thread.sleep(500);\r
+ boolean run = false;\r
+ JobStatus status = aengine.getJobStatus(jobId);\r
+ while (status != JobStatus.FINISHED) {\r
+ if (status == JobStatus.RUNNING) {\r
+ run = true;\r
+ }\r
+ Thread.sleep(5000);\r
+ status = aengine.getJobStatus(jobId);\r
+ // Once the job was in the RUNNING state UNDEFINED should not\r
+ // occur\r
+ // Hopefully with a long pooling time like here\r
+ // this problem should not occur. There seems to be a bug in\r
+ // DRMAA SGE implementation\r
+ if (run) {\r
+ assertNotSame(status, JobStatus.UNDEFINED);\r
+ }\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
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_runner,\r
+ AllTestSuit.test_group_non_windows })\r
+ public void readStatistics() {\r
+ Mafft mafft = new Mafft();\r
+ mafft.setError("errrr.txt").setInput(AllTestSuit.test_input).setOutput(\r
+ "outtt.txt");\r
+ ConfiguredExecutable<Mafft> cmafft;\r
+\r
+ try {\r
+ cmafft = Configurator.configureExecutable(mafft,\r
+ Executable.ExecProvider.Local);\r
+ AsyncExecutor sexec = Configurator.getAsyncEngine(cmafft,\r
+ ExecProvider.Local);\r
+ String jobId = sexec.submitJob(cmafft);\r
+ FilePuller fw = FilePuller.newFilePuller(compbio.engine.client.EngineUtil\r
+ .getFullPath(cmafft.getWorkDirectory(), cmafft.getError()),\r
+ 256);\r
+ int count = 0;\r
+ long position = 0;\r
+ fw.waitForFile(4);\r
+ while (fw.hasMoreData()) {\r
+ ChunkHolder ch = fw.pull(position);\r
+ String chunk = ch.getChunk();\r
+ position = ch.getNextPosition();\r
+ System.out.print("CHUNK:" + 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 testConfigurationLoading() {\r
+ try {\r
+ RunnerConfig<Mafft> mafftConfig = ConfExecutable\r
+ .getRunnerOptions(Mafft.class);\r
+ assertNotNull(mafftConfig);\r
+ assertTrue(mafftConfig.getArguments().size() > 0);\r
+\r
+ PresetManager<Mafft> mafftPresets = ConfExecutable\r
+ .getRunnerPresets(Mafft.class);\r
+ assertNotNull(mafftPresets);\r
+ assertTrue(mafftPresets.getPresets().size() > 0);\r
+ mafftPresets.validate(mafftConfig);\r
+\r
+ LimitsManager<Mafft> mafftLimits = ConfExecutable\r
+ .getRunnerLimits(Mafft.class);\r
+ assertNotNull(mafftLimits);\r
+ assertTrue(mafftLimits.getLimits().size() > 0);\r
+ mafftLimits.validate(mafftPresets);\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
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