Test | Methods Passed | Scenarios Passed | # skipped | # failed | Total Time | Included Groups | Excluded Groups |
Ant test | 205 | 216 | 0 | 0 | 453.9 seconds | | webservices performance |
Class | Method | # of Scenarios | Time (Msecs) |
Ant test — passed |
compbio.data.sequence.ClustalAlignmentUtilTester | testReadClustalFile | 1 | 12 |
testReadClustalFileLongNames | 1 | 19 |
testReadClustalFileShortNames | 1 | 14 |
compbio.data.sequence.FastaReaderTester | test | 1 | 18 |
compbio.data.sequence.FastaSequenceGeneratorTester | testProteinSequenceGeneration | 1 | 7 |
compbio.data.sequence.FastaSequenceTester | testGetFormattedFasta | 1 | 0 |
compbio.data.sequence.SequenceUtilTester | loadJronnFile | 1 | 27 |
testCleanProteinSequence | 1 | 1 |
testCleanSequence | 1 | 0 |
testDeepCleanSequence | 1 | 0 |
testReadAAConResults | 1 | 269 |
testReadDisemblResults | 1 | 125 |
testReadGlobPlotResults | 1 | 104 |
testReadIUPredForGlobDomain | 1 | 6 |
testReadIUPredForShortAndLongDisorder | 1 | 36 |
testReadWriteFasta | 1 | 8 |
testisNonAmbNucleotideSequence | 1 | 1 |
testisProteinSequence | 1 | 0 |
compbio.engine.EngineConfiguratorTester | testGetAsyncEngine | 1 | 12 |
testGetSyncEngine | 1 | 1 |
compbio.engine.FilePullerTester | testCache (engine) | 1 | 6008 |
testGet | 1 | 2 |
testGetDelay (engine) | 1 | 0 |
testPull (engine) | 1 | 14 |
compbio.engine.LoadBalancerTester | testLoadBalance | 1 | 57 |
compbio.engine.PulledFileCacheTester | test | 1 | 5011 |
compbio.engine.client.CommandBuilderTester | testCommandBuilding | 1 | 1 |
testOptionsToCommand | 1 | 40 |
testSpaceDelimiterExecutable | 1 | 0 |
compbio.engine.client.PathValidatorTester | testGetClassPath | 1 | 1 |
testIsAbsolutePath | 1 | 0 |
compbio.engine.cluster.drmaa.ClusterSessionTester | testTaskList (engine, cluster) | 1 | 3953 |
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester | testCancel (engine, cluster) | 1 | 1257 |
testGetJobStatus (engine, cluster) | 1 | 4765 |
testSubmit (engine, cluster) | 1 | 3976 |
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester | testCancel (engine, cluster) | 1 | 1538 |
testSubmit (engine, cluster) | 1 | 3508 |
compbio.engine.cluster.drmaa.UtilTester | testParser | 1 | 1 |
compbio.engine.cluster.dundee._QueueTester | testQueue | 1 | 0 |
compbio.engine.conf.DirectoryManagerTester | testGetDirectory | 4 | 105 |
compbio.engine.conf.PropertyHelperManagerTester | testClusterEngineConf (cluster) | 1 | 1 |
validateClustalConfiguration | 1 | 0 |
validateMafftConfiguration | 1 | 2 |
validateMuscleConfiguration | 1 | 0 |
validateTcoffeeConfiguration | 1 | 0 |
compbio.engine.conf.RunnerConfigMarshallerTester | testMarshalling | 1 | 4 |
testSchemaFromCodeGeneration | 1 | 130 |
testUnMarshalling | 1 | 17 |
testValidation | 1 | 82 |
testValidationOnMarshalling | 1 | 10 |
compbio.engine.local.AsyncLocalRunnerTester | testAsyncCancelOperation (engine) | 1 | 17 |
testAsyncRetrievOperation (engine) | 1 | 124 |
testCancelCompletedTaskLocally (engine) | 1 | 3017 |
testCancelLocally (engine) | 1 | 13 |
testGetStatus (engine) | 5 | 38622 |
testMultipleCancelLocally (engine) | 1 | 54 |
testSubmitLocally (engine) | 5 | 229 |
compbio.engine.local.LocalRunnerTester | testCancelCompletedTaskLocally (engine) | 1 | 49 |
testCancelLocally (engine) | 1 | 17 |
testMultipleCancelLocally (engine) | 1 | 44 |
compbio.metadata.OptionCombinatorTester | testgetAllOptions | 1 | 1 |
testgetAllParameters | 1 | 3 |
compbio.metadata.OptionMarshallerTester | testMarshalling | 1 | 33 |
testUnMarshalling | 1 | 65 |
compbio.metadata.PresetTester | marshallPreset | 1 | 14 |
testPresetWithMuptiOptions | 1 | 1 |
validatePresets | 1 | 1 |
compbio.metadata.RunnerConfigTester | testCreateNumParameterWithoutValidValue | 1 | 0 |
testCreateParameter | 1 | 0 |
testCreateParameterWithValidValueConstrain | 1 | 0 |
testOptionNoDefaultValidate | 1 | 0 |
testOptionSetInvalidValue | 1 | 0 |
testOptionToCommand | 1 | 0 |
testParameterToCommand | 1 | 0 |
testValidate | 1 | 0 |
testValidateBoundaryConstrainCheck | 1 | 0 |
testValidateLowerBoundaryConstrainCheck | 1 | 0 |
testValidateUpperBoundaryConstrainCheck | 1 | 1 |
testValidateValueConstrain | 1 | 0 |
compbio.runner._impl.MclTester | testGetTestCommand | 1 | 0 |
compbio.runner._impl.NetNglycTester | testGetTestCommand | 1 | 1 |
compbio.runner._impl.OBTester | testGetTestArgsCommand | 1 | 0 |
testGetTestCommand | 1 | 0 |
compbio.runner._impl.RPSBlastTester | testGetTestArgsCommand | 1 | 0 |
testGetTestCommand | 1 | 0 |
compbio.runner._impl.RonnTester | testGetTestCommand | 1 | 0 |
compbio.runner._impl.Tmhmm2Tester | testGetTestCommand | 1 | 0 |
compbio.runner.conservation.AAConTester | readStatistics (runner) | 1 | 1493 |
testConfigurationLoading (runner) | 1 | 113 |
testPersistance (runner) | 1 | 775 |
testRunLocally (runner) | 1 | 827 |
testRunLocallyOnTwoCpu (runner) | 1 | 289 |
testRunLocallyWithPreset (runner) | 1 | 653 |
testRunOnCluster (runner) | 1 | 3640 |
testRunOnClusterAsync (cluster, runner) | 1 | 5018 |
compbio.runner.disorder.DisemblTester | readStatistics (runner) | 1 | 0 |
testConfigurationLoading (runner) | 1 | 44 |
testPersistance (runner) | 1 | 1297 |
testRunLocally (runner) | 1 | 579 |
testRunOnCluster (cluster, runner) | 1 | 2047 |
testRunOnClusterAsync (cluster, runner) | 1 | 6011 |
compbio.runner.disorder.GlobPlotTester | readStatistics (runner) | 1 | 0 |
testConfigurationLoading (runner) | 1 | 43 |
testPersistance (runner) | 1 | 980 |
testRunLocally (runner) | 1 | 454 |
testRunOnCluster (cluster, runner) | 1 | 2503 |
testRunOnClusterAsync (cluster, runner) | 1 | 6021 |
compbio.runner.disorder.IUPredTester | testConfigurationLoading (runner) | 1 | 69 |
testPersistance (runner) | 1 | 308 |
testReadResults (runner) | 1 | 25 |
testRunLocally (runner) | 1 | 196 |
testRunLocallyWithParams (runner) | 1 | 71 |
testRunOnCluster (cluster, runner) | 1 | 3308 |
testRunOnClusterAsync (cluster, runner) | 1 | 6025 |
testSetParameter (runner) | 1 | 0 |
compbio.runner.disorder.JronnTester | readStatistics (runner) | 1 | 18639 |
testConfigurationLoading (runner) | 1 | 45 |
testPersistance (runner) | 1 | 18613 |
testRunLocally (runner) | 1 | 18541 |
testRunLocallyOnTwoCpu (runner) | 1 | 7131 |
testRunOnCluster (cluster, runner) | 1 | 13058 |
testRunOnClusterAsync (cluster, runner) | 1 | 11022 |
compbio.runner.msa.ClustalWParametersTester | testArguments (runner) | 1 | 1649 |
testConfiguration | 1 | 1 |
testConstrainedParametersMaxValues (runner) | 1 | 678 |
testConstrainedParametersMinValues (runner) | 1 | 682 |
testConstrainedParametersRandomValues (runner) | 1 | 672 |
testDefaultParameters (runner) | 1 | 129 |
testOptions (runner) | 1 | 396 |
testParameters (runner) | 1 | 1074 |
testPresets (runner) | 1 | 129 |
compbio.runner.msa.ClustalWTester | readStatistics (runner) | 1 | 518 |
readStatisticsClusterExecution (cluster, runner) | 1 | 1640 |
testConfigurationLoading (runner) | 1 | 46 |
testOptionsLocally (runner) | 1 | 429 |
testPersistance (runner) | 1 | 303 |
testRunLocally (runner) | 1 | 132 |
testRunOnCluster (cluster, runner) | 1 | 5003 |
testRunWithMatrix (runner) | 1 | 130 |
compbio.runner.msa.LimitTester | testLimitExceeded | 1 | 14 |
testLoadLimits | 1 | 0 |
compbio.runner.msa.MafftParametersTester | testArguments (runner, non_windows) | 1 | 3027 |
testConfiguration | 1 | 0 |
testConstrainedParametersMaxValues (runner, non_windows) | 1 | 1461 |
testConstrainedParametersMinValues (runner, non_windows) | 1 | 886 |
testConstrainedParametersRandomValues (runner, non_windows) | 1 | 3530 |
testDefaultParameters (runner, non_windows) | 1 | 4507 |
testOptions (runner, non_windows) | 1 | 971 |
testParameters (runner, non_windows) | 1 | 1179 |
testPresets (runner, non_windows) | 1 | 965 |
compbio.runner.msa.MafftTester | readStatistics (runner, non_windows) | 1 | 516 |
testClusterExecute (cluster, runner, non_windows) | 1 | 1264 |
testConfigurationLoading (runner) | 1 | 62 |
testExecute (runner, non_windows) | 1 | 162 |
testPersistance (runner, non_windows) | 1 | 305 |
testRunOnClusterAsyncCheckStatusLongPoolingTime (cluster, runner, non_windows) | 1 | 5535 |
testSetInputTester (runner, non_windows) | 1 | 0 |
compbio.runner.msa.MuscleParametersTester | testArguments (runner) | 1 | 4387 |
testConfiguration | 1 | 1 |
testConstrainedParametersMaxValues (runner) | 1 | 1977 |
testConstrainedParametersMinValues (runner) | 1 | 1112 |
testConstrainedParametersRandomValues (runner) | 1 | 2749 |
testDefaultParameters (runner) | 1 | 100 |
testOptions (runner) | 1 | 1360 |
testParameters (runner) | 1 | 1919 |
testPresets (runner) | 1 | 242 |
compbio.runner.msa.MuscleTester | readStatistics (runner) | 1 | 520 |
testConfigurationLoading (runner) | 1 | 43 |
testPersistance (runner) | 1 | 233 |
testRunLocally (runner) | 1 | 100 |
testRunOnCluster (cluster, runner) | 1 | 3867 |
compbio.runner.msa.ProbconsParametersTester | testArguments (runner, non_windows) | 1 | 1819 |
testConfiguration | 1 | 0 |
testConstrainedParametersMaxValues (runner, non_windows) | 1 | 37102 |
testConstrainedParametersMinValues (runner, non_windows) | 1 | 768 |
testConstrainedParametersRandomValues (runner, non_windows) | 1 | 70319 |
testDefaultParameters (runner, non_windows) | 1 | 4845 |
testOptions (runner, non_windows) | 1 | 443 |
testParameters (runner, non_windows) | 1 | 1344 |
compbio.runner.msa.ProbconsTester | readStatistics (runner, non_windows) | 1 | 455 |
testClusterExecute (cluster, runner, non_windows) | 1 | 2710 |
testConfigurationLoading (runner) | 1 | 89 |
testExecute (runner, non_windows) | 1 | 455 |
testPersistance (runner, non_windows) | 1 | 527 |
testSetInputTester (runner, non_windows) | 1 | 0 |
compbio.runner.msa.TcoffeeParametersTester | testArguments (runner, non_windows) | 1 | 4098 |
testConfiguration | 1 | 0 |
testConstrainedParametersMaxValues (runner, non_windows) | 1 | 4319 |
testConstrainedParametersMinValues (runner, non_windows) | 1 | 2887 |
testConstrainedParametersRandomValues (runner, non_windows) | 1 | 8762 |
testDefaultParameters (runner, non_windows) | 1 | 3850 |
testOptions (runner, non_windows) | 1 | 377 |
testParameters (runner, non_windows) | 1 | 3800 |
testPresets (runner, non_windows) | 1 | 214 |
compbio.runner.msa.TcoffeeTester | readStatistics (runner, non_windows) | 1 | 516 |
testClusterExecute (cluster, runner, non_windows) | 1 | 5084 |
testConfigurationLoading (runner) | 1 | 39 |
testExecute (runner, non_windows) | 1 | 364 |
testNcore (runner, non_windows) | 1 | 0 |
testPersistance (cluster, runner, non_windows) | 1 | 769 |
compbio.stat.collector.ExecutionStatCollectorTester | testCollectStat | 1 | 271 |
testHasCompleted | 1 | 1 |
testUpdateStatTester | 1 | 35012 |
compbio.stat.collector.StatDBTester | testVerifyJobsCount | 1 | 412 |
compbio.stat.servlet.util.StatCollectionTester "Ant test" | testGetStats | 1 | 22 |
Ant test
compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFile
back to summary
compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames
back to summary
compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames
back to summary
compbio.data.sequence.FastaReaderTester:test
back to summary
compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration
back to summary
compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta
back to summary
compbio.data.sequence.SequenceUtilTester:loadJronnFile
back to summary
compbio.data.sequence.SequenceUtilTester:testCleanProteinSequence
back to summary
compbio.data.sequence.SequenceUtilTester:testCleanSequence
back to summary
compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence
back to summary
compbio.data.sequence.SequenceUtilTester:testReadAAConResults
back to summary
compbio.data.sequence.SequenceUtilTester:testReadDisemblResults
back to summary
compbio.data.sequence.SequenceUtilTester:testReadGlobPlotResults
back to summary
compbio.data.sequence.SequenceUtilTester:testReadIUPredForGlobDomain
back to summary
compbio.data.sequence.SequenceUtilTester:testReadIUPredForShortAndLongDisorder
back to summary
compbio.data.sequence.SequenceUtilTester:testReadWriteFasta
back to summary
compbio.data.sequence.SequenceUtilTester:testisNonAmbNucleotideSequence
back to summary
compbio.data.sequence.SequenceUtilTester:testisProteinSequence
back to summary
compbio.engine.EngineConfiguratorTester:testGetAsyncEngine
back to summary
compbio.engine.EngineConfiguratorTester:testGetSyncEngine
back to summary
compbio.engine.FilePullerTester:testCache
back to summary
compbio.engine.FilePullerTester:testGet
back to summary
compbio.engine.FilePullerTester:testGetDelay
back to summary
compbio.engine.FilePullerTester:testPull
back to summary
compbio.engine.LoadBalancerTester:testLoadBalance
back to summary
compbio.engine.PulledFileCacheTester:test
back to summary
compbio.engine.client.CommandBuilderTester:testCommandBuilding
back to summary
compbio.engine.client.CommandBuilderTester:testOptionsToCommand
back to summary
compbio.engine.client.CommandBuilderTester:testSpaceDelimiterExecutable
back to summary
compbio.engine.client.PathValidatorTester:testGetClassPath
back to summary
compbio.engine.client.PathValidatorTester:testIsAbsolutePath
back to summary
compbio.engine.cluster.drmaa.ClusterSessionTester:testTaskList
back to summary
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testCancel
java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
compbio.runner.msa.ClustalW.getResults(ClustalW.java:73)
at compbio.runner.msa.ClustalW.getResults(ClustalW.java:34)
at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:207)
at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
23 lines not shown
Caused by Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
compbio.runner.Util.readClustalFile(Util.java:93)
at compbio.runner.msa.ClustalW.getResults(ClustalW.java:70)
at compbio.runner.msa.ClustalW.getResults(ClustalW.java:34)
at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:207)
at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
23 lines not shown
back to summary
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus
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compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testSubmit
back to summary
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testCancel
back to summary
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testSubmit
back to summary
compbio.engine.cluster.drmaa.UtilTester:testParser
back to summary
compbio.engine.cluster.dundee._QueueTester:testQueue
back to summary
compbio.engine.conf.DirectoryManagerTester:testGetDirectory
back to summary
compbio.engine.conf.PropertyHelperManagerTester:testClusterEngineConf
back to summary
compbio.engine.conf.PropertyHelperManagerTester:validateClustalConfiguration
back to summary
compbio.engine.conf.PropertyHelperManagerTester:validateMafftConfiguration
back to summary
compbio.engine.conf.PropertyHelperManagerTester:validateMuscleConfiguration
back to summary
compbio.engine.conf.PropertyHelperManagerTester:validateTcoffeeConfiguration
back to summary
compbio.engine.conf.RunnerConfigMarshallerTester:testMarshalling
back to summary
compbio.engine.conf.RunnerConfigMarshallerTester:testSchemaFromCodeGeneration
back to summary
compbio.engine.conf.RunnerConfigMarshallerTester:testUnMarshalling
back to summary
compbio.engine.conf.RunnerConfigMarshallerTester:testValidation
back to summary
compbio.engine.conf.RunnerConfigMarshallerTester:testValidationOnMarshalling
null
com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:259)
23 lines not shown
Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:259)
23 lines not shown
back to summary
compbio.engine.local.AsyncLocalRunnerTester:testAsyncCancelOperation
back to summary
compbio.engine.local.AsyncLocalRunnerTester:testAsyncRetrievOperation
back to summary
compbio.engine.local.AsyncLocalRunnerTester:testCancelCompletedTaskLocally
back to summary
compbio.engine.local.AsyncLocalRunnerTester:testCancelLocally
null
java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
23 lines not shown
back to summary
compbio.engine.local.AsyncLocalRunnerTester:testGetStatus
back to summary
compbio.engine.local.AsyncLocalRunnerTester:testMultipleCancelLocally
null
java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
23 lines not shown
back to summary
compbio.engine.local.AsyncLocalRunnerTester:testSubmitLocally
back to summary
compbio.engine.local.LocalRunnerTester:testCancelCompletedTaskLocally
null
java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
23 lines not shown
back to summary
compbio.engine.local.LocalRunnerTester:testCancelLocally
null
java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
23 lines not shown
back to summary
compbio.engine.local.LocalRunnerTester:testMultipleCancelLocally
null
java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
23 lines not shown
back to summary
compbio.metadata.OptionCombinatorTester:testgetAllOptions
back to summary
compbio.metadata.OptionCombinatorTester:testgetAllParameters
back to summary
compbio.metadata.OptionMarshallerTester:testMarshalling
null
com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
23 lines not shown
Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
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compbio.metadata.OptionMarshallerTester:testUnMarshalling
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compbio.metadata.PresetTester:marshallPreset
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compbio.metadata.PresetTester:testPresetWithMuptiOptions
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compbio.metadata.PresetTester:validatePresets
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compbio.metadata.RunnerConfigTester:testCreateNumParameterWithoutValidValue
Attempting to set default value for parameter: Option name: Matrix
Description: DNA weight matrix
URL: null
Is required: false
Without possible values! Please define possible value first!
compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
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compbio.metadata.RunnerConfigTester:testCreateParameter
Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
Description: Protein weight matrix
URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
Is required: true
Option Names:
--AAMATRIX
POSSIBLE VALUES:
BLOSUM
GONNET
ID
PAM
compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
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compbio.metadata.RunnerConfigTester:testCreateParameterWithValidValueConstrain
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compbio.metadata.RunnerConfigTester:testOptionNoDefaultValidate
Default value is required as multiple optionNames are defined for option: Option name: Matrix1
Description: Protein weight matrix
URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
Is required: true
Option Names:
--AAMATRIX
--ABMAT
--BBBB
compbio.metadata.Option.validate(Option.java:317)
at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
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compbio.metadata.RunnerConfigTester:testOptionSetInvalidValue
Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
Description: Protein weight matrix
URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
Is required: true
Option Names:
--AAMATRIX
--ABMAT
--BBBB
compbio.metadata.Option.setDefaultValue(Option.java:130)
at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
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compbio.metadata.RunnerConfigTester:testOptionToCommand
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compbio.metadata.RunnerConfigTester:testParameterToCommand
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compbio.metadata.RunnerConfigTester:testValidate
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compbio.metadata.RunnerConfigTester:testValidateBoundaryConstrainCheck
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compbio.metadata.RunnerConfigTester:testValidateLowerBoundaryConstrainCheck
Attempting to set default value outside boundaries defined by the constraint: Type: Float
Min: -10.12
Max: 0
For parameter: Option name: Matrix1
Description: Protein weight matrix
URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
Is required: true
Option Names:
--AAMATRIX
Type: Float
Min: -10.12
Max: 0
compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
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compbio.metadata.RunnerConfigTester:testValidateUpperBoundaryConstrainCheck
Attempting to set default value outside boundaries defined by the constraint: Type: Float
Min: -10.12
Max: 0
For parameter: Option name: Matrix1
Description: Protein weight matrix
URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
Is required: true
Option Names:
--AAMATRIX
Type: Float
Min: -10.12
Max: 0
compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
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compbio.metadata.RunnerConfigTester:testValidateValueConstrain
Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
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compbio.runner._impl.MclTester:testGetTestCommand
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compbio.runner._impl.NetNglycTester:testGetTestCommand
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compbio.runner._impl.OBTester:testGetTestArgsCommand
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compbio.runner._impl.OBTester:testGetTestCommand
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compbio.runner._impl.RPSBlastTester:testGetTestArgsCommand
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compbio.runner._impl.RPSBlastTester:testGetTestCommand
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compbio.runner._impl.RonnTester:testGetTestCommand
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compbio.runner._impl.Tmhmm2Tester:testGetTestCommand
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compbio.runner.conservation.AAConTester:readStatistics
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compbio.runner.conservation.AAConTester:testConfigurationLoading
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compbio.runner.conservation.AAConTester:testPersistance
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compbio.runner.conservation.AAConTester:testRunLocally
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compbio.runner.conservation.AAConTester:testRunLocallyOnTwoCpu
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compbio.runner.conservation.AAConTester:testRunLocallyWithPreset
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compbio.runner.conservation.AAConTester:testRunOnCluster
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compbio.runner.conservation.AAConTester:testRunOnClusterAsync
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compbio.runner.disorder.DisemblTester:readStatistics
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compbio.runner.disorder.DisemblTester:testConfigurationLoading
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compbio.runner.disorder.DisemblTester:testPersistance
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compbio.runner.disorder.DisemblTester:testRunLocally
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compbio.runner.disorder.DisemblTester:testRunOnCluster
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compbio.runner.disorder.DisemblTester:testRunOnClusterAsync
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compbio.runner.disorder.GlobPlotTester:readStatistics
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compbio.runner.disorder.GlobPlotTester:testConfigurationLoading
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compbio.runner.disorder.GlobPlotTester:testPersistance
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compbio.runner.disorder.GlobPlotTester:testRunLocally
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compbio.runner.disorder.GlobPlotTester:testRunOnCluster
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compbio.runner.disorder.GlobPlotTester:testRunOnClusterAsync
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compbio.runner.disorder.IUPredTester:testConfigurationLoading
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compbio.runner.disorder.IUPredTester:testPersistance
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compbio.runner.disorder.IUPredTester:testReadResults
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compbio.runner.disorder.IUPredTester:testRunLocally
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compbio.runner.disorder.IUPredTester:testRunLocallyWithParams
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compbio.runner.disorder.IUPredTester:testRunOnCluster
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compbio.runner.disorder.IUPredTester:testRunOnClusterAsync
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compbio.runner.disorder.IUPredTester:testSetParameter
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compbio.runner.disorder.JronnTester:readStatistics
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compbio.runner.disorder.JronnTester:testConfigurationLoading
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compbio.runner.disorder.JronnTester:testPersistance
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compbio.runner.disorder.JronnTester:testRunLocally
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compbio.runner.disorder.JronnTester:testRunLocallyOnTwoCpu
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compbio.runner.disorder.JronnTester:testRunOnCluster
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compbio.runner.disorder.JronnTester:testRunOnClusterAsync
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compbio.runner.msa.ClustalWParametersTester:testArguments
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compbio.runner.msa.ClustalWParametersTester:testConfiguration
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compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMaxValues
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compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMinValues
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compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersRandomValues
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compbio.runner.msa.ClustalWParametersTester:testDefaultParameters
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compbio.runner.msa.ClustalWParametersTester:testOptions
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compbio.runner.msa.ClustalWParametersTester:testParameters
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compbio.runner.msa.ClustalWParametersTester:testPresets
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compbio.runner.msa.ClustalWTester:readStatistics
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compbio.runner.msa.ClustalWTester:readStatisticsClusterExecution
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compbio.runner.msa.ClustalWTester:testConfigurationLoading
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compbio.runner.msa.ClustalWTester:testOptionsLocally
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compbio.runner.msa.ClustalWTester:testPersistance
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compbio.runner.msa.ClustalWTester:testRunLocally
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compbio.runner.msa.ClustalWTester:testRunOnCluster
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compbio.runner.msa.ClustalWTester:testRunWithMatrix
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compbio.runner.msa.LimitTester:testLimitExceeded
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compbio.runner.msa.LimitTester:testLoadLimits
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compbio.runner.msa.MafftParametersTester:testArguments
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compbio.runner.msa.MafftParametersTester:testConfiguration
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compbio.runner.msa.MafftParametersTester:testConstrainedParametersMaxValues
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compbio.runner.msa.MafftParametersTester:testConstrainedParametersMinValues
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compbio.runner.msa.MafftParametersTester:testConstrainedParametersRandomValues
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compbio.runner.msa.MafftParametersTester:testDefaultParameters
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compbio.runner.msa.MafftParametersTester:testOptions
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compbio.runner.msa.MafftParametersTester:testParameters
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compbio.runner.msa.MafftParametersTester:testPresets
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compbio.runner.msa.MafftTester:readStatistics
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compbio.runner.msa.MafftTester:testClusterExecute
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compbio.runner.msa.MafftTester:testConfigurationLoading
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compbio.runner.msa.MafftTester:testExecute
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compbio.runner.msa.MafftTester:testPersistance
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compbio.runner.msa.MafftTester:testRunOnClusterAsyncCheckStatusLongPoolingTime
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compbio.runner.msa.MafftTester:testSetInputTester
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compbio.runner.msa.MuscleParametersTester:testArguments
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compbio.runner.msa.MuscleParametersTester:testConfiguration
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compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMaxValues
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compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMinValues
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compbio.runner.msa.MuscleParametersTester:testConstrainedParametersRandomValues
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compbio.runner.msa.MuscleParametersTester:testDefaultParameters
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compbio.runner.msa.MuscleParametersTester:testOptions
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compbio.runner.msa.MuscleParametersTester:testParameters
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compbio.runner.msa.MuscleParametersTester:testPresets
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compbio.runner.msa.MuscleTester:readStatistics
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compbio.runner.msa.MuscleTester:testConfigurationLoading
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compbio.runner.msa.MuscleTester:testPersistance
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compbio.runner.msa.MuscleTester:testRunLocally
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compbio.runner.msa.MuscleTester:testRunOnCluster
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compbio.runner.msa.ProbconsParametersTester:testArguments
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compbio.runner.msa.ProbconsParametersTester:testConfiguration
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compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMaxValues
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compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMinValues
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compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersRandomValues
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compbio.runner.msa.ProbconsParametersTester:testDefaultParameters
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compbio.runner.msa.ProbconsParametersTester:testOptions
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compbio.runner.msa.ProbconsParametersTester:testParameters
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compbio.runner.msa.ProbconsTester:readStatistics
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compbio.runner.msa.ProbconsTester:testClusterExecute
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compbio.runner.msa.ProbconsTester:testConfigurationLoading
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compbio.runner.msa.ProbconsTester:testExecute
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compbio.runner.msa.ProbconsTester:testPersistance
back to summary
compbio.runner.msa.ProbconsTester:testSetInputTester
back to summary
compbio.runner.msa.TcoffeeParametersTester:testArguments
back to summary
compbio.runner.msa.TcoffeeParametersTester:testConfiguration
back to summary
compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMaxValues
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compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMinValues
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compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersRandomValues
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compbio.runner.msa.TcoffeeParametersTester:testDefaultParameters
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compbio.runner.msa.TcoffeeParametersTester:testOptions
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compbio.runner.msa.TcoffeeParametersTester:testParameters
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compbio.runner.msa.TcoffeeParametersTester:testPresets
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compbio.runner.msa.TcoffeeTester:readStatistics
back to summary
compbio.runner.msa.TcoffeeTester:testClusterExecute
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compbio.runner.msa.TcoffeeTester:testConfigurationLoading
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compbio.runner.msa.TcoffeeTester:testExecute
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compbio.runner.msa.TcoffeeTester:testNcore
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compbio.runner.msa.TcoffeeTester:testPersistance
back to summary
compbio.stat.collector.ExecutionStatCollectorTester:testCollectStat
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compbio.stat.collector.ExecutionStatCollectorTester:testHasCompleted
back to summary
compbio.stat.collector.ExecutionStatCollectorTester:testUpdateStatTester
back to summary
compbio.stat.collector.StatDBTester:testVerifyJobsCount
back to summary
compbio.stat.servlet.util.StatCollectionTester:testGetStats
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