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
compbio.engine.EngineConfiguratorTester	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
compbio.engine.client.PathValidatorTester	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
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester	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
compbio.metadata.OptionCombinatorTester	testgetAllParameters	1	3
compbio.metadata.OptionMarshallerTester	testMarshalling	1	33
compbio.metadata.OptionMarshallerTester	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
compbio.runner._impl.OBTester	testGetTestCommand	1	0
compbio.runner._impl.RPSBlastTester	testGetTestArgsCommand	1	0
compbio.runner._impl.RPSBlastTester	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
compbio.runner.msa.LimitTester	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

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compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames

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compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames

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compbio.data.sequence.FastaReaderTester:test

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compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration

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compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta

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compbio.data.sequence.SequenceUtilTester:loadJronnFile

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compbio.data.sequence.SequenceUtilTester:testCleanProteinSequence

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compbio.data.sequence.SequenceUtilTester:testCleanSequence

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compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence

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compbio.data.sequence.SequenceUtilTester:testReadAAConResults

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compbio.data.sequence.SequenceUtilTester:testReadDisemblResults

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compbio.data.sequence.SequenceUtilTester:testReadGlobPlotResults

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compbio.data.sequence.SequenceUtilTester:testReadIUPredForGlobDomain

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compbio.data.sequence.SequenceUtilTester:testReadIUPredForShortAndLongDisorder

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compbio.data.sequence.SequenceUtilTester:testReadWriteFasta

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compbio.data.sequence.SequenceUtilTester:testisNonAmbNucleotideSequence

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compbio.data.sequence.SequenceUtilTester:testisProteinSequence

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compbio.engine.EngineConfiguratorTester:testGetAsyncEngine

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compbio.engine.EngineConfiguratorTester:testGetSyncEngine

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compbio.engine.FilePullerTester:testCache

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compbio.engine.FilePullerTester:testGet

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compbio.engine.FilePullerTester:testGetDelay

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compbio.engine.FilePullerTester:testPull

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compbio.engine.LoadBalancerTester:testLoadBalance

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compbio.engine.PulledFileCacheTester:test

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compbio.engine.client.CommandBuilderTester:testCommandBuilding

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compbio.engine.client.CommandBuilderTester:testOptionsToCommand

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compbio.engine.client.CommandBuilderTester:testSpaceDelimiterExecutable

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compbio.engine.client.PathValidatorTester:testGetClassPath

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compbio.engine.client.PathValidatorTester:testIsAbsolutePath

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compbio.engine.cluster.drmaa.ClusterSessionTester:testTaskList

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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

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compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus

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compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testSubmit

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compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testCancel

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compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testSubmit

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compbio.engine.cluster.drmaa.UtilTester:testParser

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compbio.engine.cluster.dundee._QueueTester:testQueue

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compbio.engine.conf.DirectoryManagerTester:testGetDirectory

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compbio.engine.conf.PropertyHelperManagerTester:testClusterEngineConf

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compbio.engine.conf.PropertyHelperManagerTester:validateClustalConfiguration

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compbio.engine.conf.PropertyHelperManagerTester:validateMafftConfiguration

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compbio.engine.conf.PropertyHelperManagerTester:validateMuscleConfiguration

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compbio.engine.conf.PropertyHelperManagerTester:validateTcoffeeConfiguration

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compbio.engine.conf.RunnerConfigMarshallerTester:testMarshalling

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compbio.engine.conf.RunnerConfigMarshallerTester:testSchemaFromCodeGeneration

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compbio.engine.conf.RunnerConfigMarshallerTester:testUnMarshalling

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compbio.engine.conf.RunnerConfigMarshallerTester:testValidation

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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

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compbio.engine.local.AsyncLocalRunnerTester:testAsyncCancelOperation

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compbio.engine.local.AsyncLocalRunnerTester:testAsyncRetrievOperation

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compbio.engine.local.AsyncLocalRunnerTester:testCancelCompletedTaskLocally

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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

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compbio.engine.local.AsyncLocalRunnerTester:testGetStatus

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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

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compbio.engine.local.AsyncLocalRunnerTester:testSubmitLocally

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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

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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

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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

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compbio.metadata.OptionCombinatorTester:testgetAllOptions

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compbio.metadata.OptionCombinatorTester:testgetAllParameters

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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

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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