+++ /dev/null
-/* Copyright (c) 2010 Peter Troshin\r
- * Copyright (c) 2013 Alexander Sherstnev\r
- * \r
- * Java Bioinformatics Analysis Web Services (JABAWS)\r
- * (JABAWS) @version: 2.5 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under \r
- * the terms of the Apache License version 2 as published\r
- * by the Apache Software Foundation This library is distributed in the hope\r
- * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
- * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * Apache License for more details. A copy of the license is in\r
- * apache_license.txt. It is also available here:\r
- * \r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt \r
- * \r
- * Any republication or derived work distributed in source code form must include \r
- * this copyright and license notice.\r
- */\r
-package compbio.runner.conservation;\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.Arrays;\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.Preset;\r
-import compbio.metadata.PresetManager;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.runner.RunnerUtil;\r
-import compbio.util.FileWatcher;\r
-import compbio.util.SysPrefs;\r
-\r
-public class AAConTester {\r
-\r
- public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;\r
- public static String test_outfile = "TO1381.aacon.out";\r
- public static String test_alignment_input = CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata" + File.separator + "TO1381.fasta.aln";\r
- private AACon aacon;\r
-\r
- @BeforeMethod(alwaysRun = true)\r
- void init() {\r
- aacon = new AACon();\r
- aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_runner})\r
- public void RunOnCluster() {\r
- assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
- try {\r
- ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
- ClusterRunner runner = ClusterRunner.getInstance(confAAcon);\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
-\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 test 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_runner, AllTestSuit.test_group_cluster})\r
- public void RunOnClusterAsync() {\r
- assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
- try {\r
- ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
- AsyncExecutor aengine = Configurator.getAsyncEngine(confAAcon);\r
- String jobId = aengine.submitJob(confAAcon);\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<AACon> result = (ConfiguredExecutable<AACon>) aengine.getResults(jobId);\r
- assertNotNull(result);\r
- System.out.println("RES:" + result);\r
- // Some times the job could be removed from the cluster accounting \r
- // before 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<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
-\r
- // For local execution use relative\r
- LocalRunner lr = new LocalRunner(confAAcon);\r
- lr.executeJob();\r
- ConfiguredExecutable<?> al1 = lr.waitForResult();\r
- assertNotNull(al1.getResults());\r
- ScoreManager annotations = confAAcon.getResults();\r
- assertNotNull(annotations);\r
- assertEquals(annotations.asSet().size(), 18);\r
- assertEquals(al1.getResults(), annotations);\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 RunLocallyWithPreset() {\r
- try {\r
- PresetManager<AACon> aaconPresets = RunnerUtil.getPresets(AACon.class);\r
- assert aaconPresets != null;\r
- ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
- Preset<AACon> quick = aaconPresets.getPresetByName("Quick conservation");\r
- confAAcon.addParameters(quick.getOptions());\r
- // For local execution use relative\r
- LocalRunner lr = new LocalRunner(confAAcon);\r
- lr.executeJob();\r
- ConfiguredExecutable<?> al1 = lr.waitForResult();\r
- assertNotNull(al1.getResults());\r
- ScoreManager annotations = confAAcon.getResults();\r
- assertNotNull(annotations);\r
- assertEquals(annotations.asSet().size(), 13);\r
- assertEquals(al1.getResults(), annotations);\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
- aacon = new AACon();\r
- aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
-\r
- aacon.setNCore(2);\r
- ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
- confAAcon.addParameters(Arrays.asList("-m=KABAT,JORES"));\r
- confAAcon.addParameters(Arrays.asList("-m=TAYLOR_GAPS"));\r
- // For local execution use relative\r
- LocalRunner lr = new LocalRunner(confAAcon);\r
-\r
- lr.executeJob();\r
- ConfiguredExecutable<?> al1 = lr.waitForResult();\r
- assertNotNull(al1.getResults());\r
- ScoreManager annotations = confAAcon.getResults();\r
- assertNotNull(annotations);\r
- assertEquals(annotations.asSet().size(), 3);\r
- assertEquals(al1.getResults(), annotations);\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<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
- // For local execution use relative\r
-\r
- AsyncExecutor sexec = Configurator.getAsyncEngine(confAAcon);\r
- String jobId = sexec.submitJob(confAAcon);\r
- String file = confAAcon.getWorkDirectory() + File.separator + AACon.getStatFile();\r
- FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
- int count = 0;\r
- long position = 0;\r
- fw.waitForFile(2);\r
- JobStatus status = sexec.getJobStatus(jobId);\r
- do {\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
- fail("job failed!");\r
- break;\r
- }\r
- Thread.sleep(300);\r
- status = sexec.getJobStatus(jobId);\r
- } while (status != JobStatus.FINISHED || fw.hasMoreData());\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
- AACon aacon = new AACon();\r
- aacon.setError("errrr.txt");\r
- aacon.setInput(test_alignment_input);\r
- aacon.setOutput("outtt.txt");\r
- assertEquals(aacon.getInput(), test_alignment_input);\r
- assertEquals(aacon.getError(), "errrr.txt");\r
- assertEquals(aacon.getOutput(), "outtt.txt");\r
- ConfiguredExecutable<AACon> cAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
-\r
- SyncExecutor sexec = Configurator.getSyncEngine(cAAcon);\r
- sexec.executeJob();\r
- ConfiguredExecutable<?> al = sexec.waitForResult();\r
- assertNotNull(al.getResults());\r
-\r
- // Save run configuration\r
- assertTrue(cAAcon.saveRunConfiguration());\r
-\r
- // See if loaded configuration is the same as saved\r
- RunConfiguration loadedRun = RunConfiguration\r
- .load(new FileInputStream(new File(cAAcon\r
- .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
- assertEquals(((ConfExecutable<AACon>) cAAcon).getRunConfiguration(),loadedRun);\r
-\r
- // Load run configuration as ConfExecutable\r
- ConfiguredExecutable<AACon> resurrectedCAAcon = (ConfiguredExecutable<AACon>) cAAcon\r
- .loadRunConfiguration(new FileInputStream(new File(cAAcon\r
- .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
- assertNotNull(resurrectedCAAcon);\r
- assertEquals(resurrectedCAAcon.getExecutable().getInput(), test_alignment_input);\r
- assertEquals(resurrectedCAAcon.getExecutable().getError(), "errrr.txt");\r
- assertEquals(resurrectedCAAcon.getExecutable().getOutput(), "outtt.txt");\r
-\r
- // See in details whether executables are the same\r
- assertEquals(resurrectedCAAcon.getExecutable(), aacon);\r
-\r
- ConfiguredExecutable<AACon> resAAcon = Configurator.configureExecutable(resurrectedCAAcon.getExecutable(),\r
- Executable.ExecProvider.Local);\r
-\r
- sexec = Configurator.getSyncEngine(resAAcon, 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<AACon> aaconConfig = ConfExecutable.getRunnerOptions(AACon.class);\r
- assertNotNull(aaconConfig);\r
- assertTrue(aaconConfig.getArguments().size() > 0);\r
-\r
- PresetManager<AACon> aaconPresets = ConfExecutable.getRunnerPresets(AACon.class);\r
- assertNotNull(aaconPresets);\r
-\r
- LimitsManager<AACon> aaconLimits = ConfExecutable.getRunnerLimits(AACon.class);\r
- assertNotNull(aaconLimits);\r
- assertTrue(aaconLimits.getLimits().size() > 0);\r
- aaconLimits.validate(aaconPresets);\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