--- /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.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
+import java.util.ArrayList;\r
+import java.util.Collections;\r
+import java.util.List;\r
+\r
+import javax.xml.bind.JAXBException;\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.ggf.drmaa.DrmaaException;\r
+import org.ggf.drmaa.JobInfo;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.FastaSequence;\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.Executable.ExecProvider;\r
+import compbio.engine.client.RunConfiguration;\r
+import compbio.engine.cluster.drmaa.ClusterUtil;\r
+import compbio.engine.cluster.drmaa.JobRunner;\r
+import compbio.engine.cluster.drmaa.StatisticManager;\r
+import compbio.engine.conf.RunnerConfigMarshaller;\r
+import compbio.engine.local.AsyncLocalRunner;\r
+import compbio.engine.local.LocalExecutorService;\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.OptionCombinator;\r
+import compbio.runner.Util;\r
+import compbio.util.FileWatcher;\r
+import compbio.util.SysPrefs;\r
+\r
+public class ClustalOTester {\r
+\r
+ static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH\r
+ + "ClustalParameters.xml";\r
+ public static String test_outfile = "TO1381.clustal.out";\r
+ public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
+\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnCluster() {\r
+ ClustalW clustal = new ClustalW();\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ clustal.setInput(AllTestSuit.test_input)\r
+ .setOutput(cluster_test_outfile);\r
+\r
+ try {\r
+\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal);\r
+ JobRunner runner = JobRunner.getInstance(confClustal);\r
+ // ClusterSession csession = JobRunner.getSession();\r
+ assertNotNull(runner);\r
+ runner.executeJob();\r
+ // assertNotNull("JobId is null", jobId1);\r
+ JobStatus status = runner.getJobStatus();\r
+ assertTrue(status == JobStatus.PENDING\r
+ || status == JobStatus.RUNNING);\r
+ JobInfo info = runner.getJobInfo();\r
+ assertNotNull(info);\r
+ StatisticManager sm = new StatisticManager(info);\r
+ assertNotNull(sm);\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 = ClusterUtil.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
+ // At present the task directory could not be completely removed\r
+ // @see JobRunner.cleanup()\r
+ assertFalse(runner.cleanup(),\r
+ "Could not remove some files whilst cleaning up ");\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
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testRunLocally() {\r
+ ClustalO clustal = new ClustalO();\r
+ clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
+ try {\r
+\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<ClustalO> confClustal = Configurator\r
+ .configureExecutable(clustal, Executable.ExecProvider.Local);\r
+ LocalRunner lr = new LocalRunner(confClustal);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalO>) lr.waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testConfigurationLoading() {\r
+ try {\r
+ RunnerConfig<ClustalW> clustalConfig = ConfExecutable\r
+ .getRunnerOptions(ClustalW.class);\r
+ assertNotNull(clustalConfig);\r
+ assertTrue(clustalConfig.getArguments().size() > 0);\r
+\r
+ PresetManager<ClustalW> clustalPresets = ConfExecutable\r
+ .getRunnerPresets(ClustalW.class);\r
+ assertNotNull(clustalPresets);\r
+ assertTrue(clustalPresets.getPresets().size() > 0);\r
+ clustalPresets.validate(clustalConfig);\r
+\r
+ LimitsManager<ClustalW> clustalLimits = ConfExecutable\r
+ .getRunnerLimits(ClustalW.class);\r
+ assertNotNull(clustalLimits);\r
+ assertTrue(clustalLimits.getLimits().size() > 0);\r
+ clustalLimits.validate(clustalPresets);\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
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testOptionsLocally() {\r
+ try {\r
+\r
+ RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(\r
+ RunnerConfig.class);\r
+\r
+ RunnerConfig<ClustalW> clustalConfig = clustalmarsh.read(\r
+ new FileInputStream(new File(clustalConfigFile)),\r
+ RunnerConfig.class);\r
+\r
+ OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
+ List<String> options = clustalOpc.getOptionsAtRandom();\r
+ for (int i = 0; i < options.size(); i++) {\r
+ System.out.println("Using options: " + options);\r
+ ClustalW clustal = new ClustalW();\r
+ clustal.setInput(AllTestSuit.test_input)\r
+ .setOutput(test_outfile);\r
+\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal, ExecProvider.Local);\r
+\r
+ // Add options to the executable\r
+ confClustal.addParameters(options);\r
+\r
+ LocalRunner lr = new LocalRunner(confClustal);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalW>) lr\r
+ .waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+ Collections.shuffle(options);\r
+ }\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JAXBException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ public static final void main(String[] args) throws JobSubmissionException,\r
+ JobExecutionException, InterruptedException {\r
+ ClustalW clustal = new ClustalW();\r
+ clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal);\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ lr.submitJob(confClustal);\r
+ Thread.sleep(3000);\r
+ LocalExecutorService.shutDown();\r
+ }\r
+\r
+ @Test(enabled = false)\r
+ public void testAddParameters() {\r
+ ArrayList<FastaSequence> seqs = new ArrayList<FastaSequence>();\r
+ FastaSequence fs = new FastaSequence("tests1",\r
+ "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
+ FastaSequence fs2 = new FastaSequence("tests2",\r
+ "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
+ FastaSequence fs3 = new FastaSequence("tests3",\r
+ "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
+ seqs.add(fs);\r
+ seqs.add(fs2);\r
+ seqs.add(fs3);\r
+ ClustalW cl = new ClustalW();\r
+ cl.setInput("input.txt").setOutput("output.txt");\r
+ ConfiguredExecutable<ClustalW> confClustal;\r
+ try {\r
+ confClustal = Configurator.configureExecutable(cl);\r
+ Util.writeInput(seqs, confClustal);\r
+\r
+ LocalRunner lr = new LocalRunner(confClustal);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+\r
+ assertTrue(confClustal.saveRunConfiguration());\r
+ ConfiguredExecutable<ClustalW> cexec = (ConfiguredExecutable<ClustalW>) confClustal\r
+ .loadRunConfiguration(new FileInputStream(new File(\r
+ confClustal.getWorkDirectory(),\r
+ RunConfiguration.rconfigFile)));\r
+ assertNotNull(cexec);\r
+\r
+ lr = new LocalRunner(cexec);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+\r
+ System.out.println("CE:" + cexec);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (FileNotFoundException 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
+ } 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
+ ClustalW clustal = new ClustalW();\r
+ clustal.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
+ .setOutput("outtt.txt");\r
+ assertEquals(clustal.getInput(), AllTestSuit.test_input);\r
+ assertEquals(clustal.getError(), "errrr.txt");\r
+ assertEquals(clustal.getOutput(), "outtt.txt");\r
+ ConfiguredExecutable<ClustalW> cClustal = Configurator\r
+ .configureExecutable(clustal, Executable.ExecProvider.Local);\r
+\r
+ SyncExecutor sexec = Configurator.getSyncEngine(cClustal);\r
+ sexec.executeJob();\r
+ cClustal = (ConfiguredExecutable<ClustalW>) sexec.waitForResult();\r
+ assertNotNull(cClustal.getResults());\r
+ // Save run configuration\r
+ assertTrue(cClustal.saveRunConfiguration());\r
+\r
+ // See if loaded configuration is the same as saved\r
+ RunConfiguration loadedRun = RunConfiguration\r
+ .load(new FileInputStream(new File(cClustal\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertTrue(((ConfExecutable<ClustalW>) cClustal)\r
+ .getRunConfiguration().equals(loadedRun));\r
+ // Load run configuration as ConfExecutable\r
+ ConfiguredExecutable<ClustalW> resurrectedCclustal = (ConfiguredExecutable<ClustalW>) cClustal\r
+ .loadRunConfiguration(new FileInputStream(new File(cClustal\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertNotNull(resurrectedCclustal);\r
+ // See in details whether executables are the same\r
+ assertEquals(resurrectedCclustal.getExecutable(), clustal);\r
+\r
+ // Finally rerun the job in the new task directory\r
+ ConfiguredExecutable<ClustalW> resclustal = Configurator\r
+ .configureExecutable(resurrectedCclustal.getExecutable(),\r
+ Executable.ExecProvider.Local);\r
+\r
+ sexec = Configurator.getSyncEngine(resclustal,\r
+ Executable.ExecProvider.Local);\r
+ sexec.executeJob();\r
+ cClustal = (ConfiguredExecutable<ClustalW>) sexec.waitForResult();\r
+ assertNotNull(cClustal.getResults());\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 readStatistics() {\r
+ try {\r
+ ClustalW clustal = new ClustalW().setInput(AllTestSuit.test_input)\r
+ .setOutput(test_outfile);\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal, Executable.ExecProvider.Local);\r
+\r
+ AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);\r
+ String jobId = sexec.submitJob(confClustal);\r
+ FilePuller fw = FilePuller.newFilePuller(\r
+ confClustal.getWorkDirectory() + File.separator\r
+ + ClustalW.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\r
+ || sexec.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_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void readStatisticsClusterExecution() {\r
+ try {\r
+ ClustalW clustal = new ClustalW().setInput(AllTestSuit.test_input)\r
+ .setOutput(test_outfile);\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal,\r
+ Executable.ExecProvider.Cluster);\r
+\r
+ AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);\r
+ String jobId = sexec.submitJob(confClustal);\r
+ FilePuller fw = FilePuller.newFilePuller(\r
+ confClustal.getWorkDirectory() + File.separator\r
+ + ClustalW.getStatFile(),\r
+ FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
+ int count = 0;\r
+ long position = 0;\r
+ fw.waitForFile(200);\r
+ /*\r
+ * Under certain circumstances DRMAA could report the status wrongly\r
+ * thus this loop never ends TODO deal with this!\r
+ */\r
+ while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || sexec\r
+ .getJobStatus(jobId) == JobStatus.FAILED)\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
+ if (sexec.getJobStatus(jobId) == JobStatus.UNDEFINED) {\r
+ System.out.println("DRMAA reported wrong status for job + "\r
+ + jobId + " continue anyway!");\r
+ break;\r
+ }\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
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