-/*\r
- * Copyright (c) 2010 Peter Troshin JAva Bioinformatics Analysis Web Services\r
- * (JABAWS) @version: 2.0 \r
+/* 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
import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\r
-import compbio.conservation.Method;\r
-import compbio.data.sequence.MultiAnnotatedSequence;\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.client.ConfiguredExecutable;\r
import compbio.engine.client.Executable;\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.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.PresetManager;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.metadata.RunnerConfig;\r
-import compbio.runner.Util;\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\r
- .getCurrentDirectory() + File.separator;\r
-\r
- public static String test_outfile = "TO1381.aacon.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
- public static String test_alignment_input = CURRENT_DIRECTORY + "testsrc"\r
- + File.separator + "testdata" + File.separator + "TO1381.fasta.aln";\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
aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
}\r
\r
- @Test()\r
- public void testRunOnCluster() {\r
- assertFalse(SysPrefs.isWindows,\r
- "Cluster execution can only be in unix environment");\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\r
- .configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
- JobRunner runner = JobRunner.getInstance(confAAcon);\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
- // 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
+ 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
-\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
+ int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();\r
assertEquals(0, exitsInt);\r
System.out.println(sm.getAllStats());\r
\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
}\r
\r
/**\r
- * This tests fails from time to time depending on the cluster load or some\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()\r
- public void testRunOnClusterAsync() {\r
- assertFalse(SysPrefs.isWindows,\r
- "Cluster execution can only be in unix environment");\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\r
- .configureExecutable(aacon, Executable.ExecProvider.Cluster);\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
System.out.println("Job Status: " + status);\r
Thread.sleep(1000);\r
status = aengine.getJobStatus(jobId);\r
- ConfiguredExecutable<AACon> result = (ConfiguredExecutable<AACon>) aengine\r
- .getResults(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\r
- // accounting\r
- // before it has been reported to finish. Make sure\r
- // to stop waiting in such case\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
}\r
\r
- @Test()\r
- public void testRunLocally() {\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void RunLocally() {\r
try {\r
- ConfiguredExecutable<AACon> confAAcon = Configurator\r
- .configureExecutable(aacon, Executable.ExecProvider.Local);\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
- MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+ ScoreManager annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 1);\r
+ assertEquals(annotations.asSet().size(), 18);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
}\r
}\r
\r
- @Test()\r
- public void testRunLocallyWithPreset() {\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void RunLocallyWithPreset() {\r
try {\r
- PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);\r
+ PresetManager<AACon> aaconPresets = RunnerUtil.getPresets(AACon.class);\r
assert aaconPresets != null;\r
- ConfiguredExecutable<AACon> confAAcon = Configurator\r
- .configureExecutable(aacon, Executable.ExecProvider.Local);\r
- Preset<AACon> quick = aaconPresets\r
- .getPresetByName("Quick conservation");\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
- MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+ ScoreManager annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 13);\r
+ assertEquals(annotations.asSet().size(), 13);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
}\r
}\r
\r
- @Test()\r
- public void testRunLocallyOnTwoCpu() {\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\r
- .configureExecutable(aacon, Executable.ExecProvider.Local);\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
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+ ScoreManager annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 3);\r
+ assertEquals(annotations.asSet().size(), 3);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
}\r
}\r
- @Test()\r
+ \r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void readStatistics() {\r
try {\r
- ConfiguredExecutable<AACon> confAAcon = Configurator\r
- .configureExecutable(aacon, Executable.ExecProvider.Local);\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
- FilePuller fw = FilePuller.newFilePuller(\r
- confAAcon.getWorkDirectory() + File.separator\r
- + AACon.getStatFile(),\r
- FileWatcher.MIN_CHUNK_SIZE_BYTES);\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
- ChunkHolder ch = fw.pull(position);\r
- String chunk = ch.getChunk();\r
- position = ch.getNextPosition();\r
- // System.out.println(chunk);\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
Thread.sleep(300);\r
status = sexec.getJobStatus(jobId);\r
} while (status != JobStatus.FINISHED || fw.hasMoreData());\r
-\r
assertTrue(count >= 1);\r
ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
assertNotNull(al.getResults());\r
}\r
}\r
\r
- @Test()\r
- public void testPersistance() {\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void Persistance() {\r
try {\r
AACon aacon = new AACon();\r
- aacon.setError("errrr.txt").setInput(test_alignment_input)\r
- .setOutput("outtt.txt");\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\r
- .configureExecutable(aacon, Executable.ExecProvider.Local);\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
RunConfiguration loadedRun = RunConfiguration\r
.load(new FileInputStream(new File(cAAcon\r
.getWorkDirectory(), RunConfiguration.rconfigFile)));\r
- assertEquals(\r
- ((ConfExecutable<AACon>) cAAcon).getRunConfiguration(),\r
- loadedRun);\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(),\r
- test_alignment_input);\r
- assertEquals(resurrectedCAAcon.getExecutable().getError(),\r
- "errrr.txt");\r
- assertEquals(resurrectedCAAcon.getExecutable().getOutput(),\r
- "outtt.txt");\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\r
- .configureExecutable(resurrectedCAAcon.getExecutable(),\r
+ ConfiguredExecutable<AACon> resAAcon = Configurator.configureExecutable(resurrectedCAAcon.getExecutable(),\r
Executable.ExecProvider.Local);\r
\r
- sexec = Configurator.getSyncEngine(resAAcon,\r
- Executable.ExecProvider.Local);\r
+ sexec = Configurator.getSyncEngine(resAAcon, 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
}\r
}\r
\r
- @Test()\r
- public void testConfigurationLoading() {\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void ConfigurationLoading() {\r
try {\r
- RunnerConfig<AACon> aaconConfig = ConfExecutable\r
- .getRunnerOptions(AACon.class);\r
+ RunnerConfig<AACon> aaconConfig = ConfExecutable.getRunnerOptions(AACon.class);\r
assertNotNull(aaconConfig);\r
assertTrue(aaconConfig.getArguments().size() > 0);\r
\r
- PresetManager<AACon> aaconPresets = ConfExecutable\r
- .getRunnerPresets(AACon.class);\r
+ PresetManager<AACon> aaconPresets = ConfExecutable.getRunnerPresets(AACon.class);\r
assertNotNull(aaconPresets);\r
\r
- LimitsManager<AACon> jronnLimits = ConfExecutable\r
- .getRunnerLimits(AACon.class);\r
- assertNotNull(jronnLimits);\r
- assertTrue(jronnLimits.getLimits().size() > 0);\r
- jronnLimits.validate(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
fail(e.getLocalizedMessage());\r
}\r
}\r
-\r
}\r
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