| Test | Methods
Passed | Scenarios
Passed | # skipped | # failed | Total
Time | Included
Groups | Excluded
Groups |
|---|
| Ant test | 154 | 165 | 0 | 0 | 524.4 seconds | | performance |
| Class | Method | # of
Scenarios | Time
(Msecs) |
|---|
| Ant test — passed |
|---|
| compbio.data.sequence.ClustalAlignmentUtilTester | testReadClustalFile | 1 | 22 |
| testReadClustalFileLongNames | 1 | 52 |
| testReadClustalFileShortNames | 1 | 54 |
| compbio.data.sequence.FastaSequenceGeneratorTester | testProteinSequenceGeneration | 1 | 8 |
| compbio.data.sequence.FastaSequenceTester | testGetFormattedFasta | 1 | 0 |
| compbio.data.sequence.SequenceUtilTester | testCleanSequence | 1 | 0 |
| testDeepCleanSequence | 1 | 0 |
| testReadWriteFasta | 1 | 16 |
| testisNonAmbNucleotideSequence | 1 | 0 |
| testisProteinSequence | 1 | 0 |
| compbio.engine.EngineConfiguratorTester | testGetAsyncEngine | 1 | 296 |
| testGetSyncEngine | 1 | 0 |
| compbio.engine.FilePullerTester | testCache (engine) | 1 | 6006 |
| testGet | 1 | 46 |
| testGetDelay (engine) | 1 | 0 |
| testPull (engine) | 1 | 450 |
| compbio.engine.PulledFileCacheTester | test | 1 | 5187 |
| compbio.engine.client.CommandBuilderTester | testCommandBuilding | 1 | 1 |
| testOptionsToCommand | 1 | 567 |
| testSpaceDelimiterExecutable | 1 | 0 |
| compbio.engine.client.PathValidatorTester | testGetClassPath | 1 | 234 |
| testIsAbsolutePath | 1 | 0 |
| compbio.engine.cluster.drmaa.ClusterSessionTester | testTaskList (engine, cluster) | 1 | 8964 |
| compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester | testCancel (engine, cluster) | 1 | 1273 |
| testGetJobStatus (engine, cluster) | 1 | 20778 |
| testSubmit (engine, cluster) | 1 | 18714 |
| compbio.engine.cluster.drmaa.DrmaaClusterEngineTester | testCancel (engine, cluster) | 1 | 1587 |
| testSubmit (engine, cluster) | 1 | 17835 |
| compbio.engine.cluster.drmaa.UtilTester | testParser | 1 | 0 |
| compbio.engine.cluster.dundee._QueueTester | testQueue | 1 | 0 |
| compbio.engine.conf.DirectoryManagerTester | testGetDirectory | 4 | 111 |
| compbio.engine.conf.PropertyHelperManagerTester | testClusterEngineConf (cluster) | 1 | 104 |
| validateClustalConfiguration | 1 | 43 |
| validateMafftConfiguration | 1 | 1 |
| validateMuscleConfiguration | 1 | 4 |
| validateTcoffeeConfiguration | 1 | 4 |
| compbio.engine.conf.RunnerConfigMarshallerTester | testMarshalling | 1 | 20 |
| testSchemaFromCodeGeneration | 1 | 504 |
| testUnMarshalling | 1 | 580 |
| testValidation | 1 | 636 |
| testValidationOnMarshalling | 1 | 11 |
| compbio.engine.local.AsyncLocalRunnerTester | testAsyncCancelOperation (engine) | 1 | 48 |
| testAsyncRetrievOperation (engine) | 1 | 560 |
| testCancelCompletedTaskLocally (engine) | 1 | 3053 |
| testCancelLocally (engine) | 1 | 27 |
| testGetStatus (engine) | 5 | 41735 |
| testMultipleCancelLocally (engine) | 1 | 267 |
| testSubmitLocally (engine) | 5 | 634 |
| compbio.engine.local.LocalRunnerTester | testCancelCompletedTaskLocally (engine) | 1 | 336 |
| testCancelLocally (engine) | 1 | 20 |
| testMultipleCancelLocally (engine) | 1 | 58 |
| compbio.metadata.OptionCombinatorTester | testgetAllOptions | 1 | 1 |
| testgetAllParameters | 1 | 3 |
| compbio.metadata.OptionMarshallerTester | testMarshalling | 1 | 58 |
| testUnMarshalling | 1 | 386 |
| compbio.metadata.PresetTester | marshallPreset | 1 | 899 |
| validatePresets | 1 | 1 |
| compbio.metadata.RunnerConfigTester | testCreateNumParameterWithoutValidValue | 1 | 1 |
| testCreateParameter | 1 | 0 |
| testCreateParameterWithValidValueConstrain | 1 | 0 |
| testOptionNoDefaultValidate | 1 | 0 |
| testOptionSetInvalidValue | 1 | 1 |
| testOptionToCommand | 1 | 0 |
| testParameterToCommand | 1 | 0 |
| testValidate | 1 | 0 |
| testValidateBoundaryConstrainCheck | 1 | 1 |
| testValidateLowerBoundaryConstrainCheck | 1 | 0 |
| testValidateUpperBoundaryConstrainCheck | 1 | 0 |
| testValidateValueConstrain | 1 | 0 |
| compbio.runner._impl.MclTester | testGetTestCommand | 1 | 1 |
| compbio.runner._impl.NetNglycTester | testGetTestCommand | 1 | 0 |
| 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.msa.ClustalWParametersTester | testArguments (runner) | 1 | 3518 |
| testConfiguration | 1 | 1 |
| testConstrainedParametersMaxValues (runner) | 1 | 1835 |
| testConstrainedParametersMinValues (runner) | 1 | 1232 |
| testConstrainedParametersRandomValues (runner) | 1 | 3105 |
| testDefaultParameters (runner) | 1 | 502 |
| testOptions (runner) | 1 | 2109 |
| testParameters (runner) | 1 | 2680 |
| testPresets (runner) | 1 | 177 |
| compbio.runner.msa.ClustalWTester | readStatistics (runner) | 1 | 1178 |
| readStatisticsClusterExecution (cluster, runner) | 1 | 8121 |
| testConfigurationLoading (runner) | 1 | 688 |
| testOptionsLocally (runner) | 1 | 1932 |
| testPersistance (runner) | 1 | 431 |
| testRunLocally (runner) | 1 | 171 |
| testRunOnCluster (cluster, runner) | 1 | 15937 |
| testRunWithMatrix (runner) | 1 | 824 |
| compbio.runner.msa.LimitTester | testLoadLimits | 1 | 0 |
| compbio.runner.msa.MafftParametersTester | testArguments (runner, non_windows) | 1 | 6103 |
| testConfiguration | 1 | 1 |
| testConstrainedParametersMaxValues (runner, non_windows) | 1 | 3235 |
| testConstrainedParametersMinValues (runner, non_windows) | 1 | 1326 |
| testConstrainedParametersRandomValues (runner, non_windows) | 1 | 7672 |
| testDefaultParameters (runner, non_windows) | 1 | 20463 |
| testOptions (runner, non_windows) | 1 | 4449 |
| testParameters (runner, non_windows) | 1 | 2422 |
| testPresets (runner, non_windows) | 1 | 2136 |
| compbio.runner.msa.MafftTester | readStatistics (runner, non_windows) | 1 | 639 |
| testClusterExecute (cluster, runner, non_windows) | 1 | 11340 |
| testConfigurationLoading (runner) | 1 | 435 |
| testExecute (runner, non_windows) | 1 | 428 |
| testPersistance (runner, non_windows) | 1 | 1033 |
| testRunOnClusterAsyncCheckStatusLongPoolingTime (cluster, runner, non_windows) | 1 | 21418 |
| testSetInputTester (runner, non_windows) | 1 | 0 |
| compbio.runner.msa.MuscleParametersTester | testArguments (runner) | 1 | 7798 |
| testConfiguration | 1 | 0 |
| testConstrainedParametersMaxValues (runner) | 1 | 1534 |
| testConstrainedParametersMinValues (runner) | 1 | 845 |
| testConstrainedParametersRandomValues (runner) | 1 | 7603 |
| testDefaultParameters (runner) | 1 | 622 |
| testOptions (runner) | 1 | 2481 |
| testParameters (runner) | 1 | 4773 |
| testPresets (runner) | 1 | 856 |
| compbio.runner.msa.MuscleTester | readStatistics (runner) | 1 | 932 |
| testConfigurationLoading (runner) | 1 | 313 |
| testPersistance (runner) | 1 | 241 |
| testRunLocally (runner) | 1 | 101 |
| testRunOnCluster (cluster, runner) | 1 | 8142 |
| compbio.runner.msa.ProbconsParametersTester | testArguments (runner, non_windows) | 1 | 2874 |
| testConfiguration | 1 | 1 |
| testConstrainedParametersMaxValues (runner, non_windows) | 1 | 38416 |
| testConstrainedParametersMinValues (runner, non_windows) | 1 | 768 |
| testConstrainedParametersRandomValues (runner, non_windows) | 1 | 61881 |
| testDefaultParameters (runner, non_windows) | 1 | 14704 |
| testOptions (runner, non_windows) | 1 | 433 |
| testParameters (runner, non_windows) | 1 | 1321 |
| compbio.runner.msa.ProbconsTester | readStatistics (runner, non_windows) | 1 | 441 |
| testClusterExecute (cluster, runner, non_windows) | 1 | 19326 |
| testConfigurationLoading (runner) | 1 | 107 |
| testExecute (runner, non_windows) | 1 | 436 |
| testPersistance (runner, non_windows) | 1 | 509 |
| testSetInputTester (runner, non_windows) | 1 | 0 |
| compbio.runner.msa.TcoffeeParametersTester | testArguments (runner, non_windows) | 1 | 8765 |
| testConfiguration | 1 | 0 |
| testConstrainedParametersMaxValues (runner, non_windows) | 1 | 11166 |
| testConstrainedParametersMinValues (runner, non_windows) | 1 | 5507 |
| testConstrainedParametersRandomValues (runner, non_windows) | 1 | 21942 |
| testDefaultParameters (runner, non_windows) | 1 | 10988 |
| testOptions (runner, non_windows) | 1 | 891 |
| testParameters (runner, non_windows) | 1 | 12717 |
| testPresets (runner, non_windows) | 1 | 1094 |
compbio.runner.msa.TcoffeeTester
"Ant test" | readStatistics (runner, non_windows) | 1 | 876 |
| testClusterExecute (cluster, runner, non_windows) | 1 | 5526 |
| testConfigurationLoading (runner) | 1 | 99 |
| testExecute (runner, non_windows) | 1 | 868 |
| testNcore (runner, non_windows) | 1 | 1 |
| testPersistance (cluster, runner, non_windows) | 1 | 1771 |
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.FastaSequenceGeneratorTester:testProteinSequenceGeneration
back to summary
compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta
back to summary
compbio.data.sequence.SequenceUtilTester:testCleanSequence
back to summary
compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence
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.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/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
23 lines not shown
Caused by Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
compbio.runner.Util.readClustalFile(Util.java:126)
at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
23 lines not shown
back to summary
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus
back to summary
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:328)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
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:258)
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:124)
at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
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:258)
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:328)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
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:124)
at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
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
back to summary
compbio.metadata.OptionMarshallerTester:testUnMarshalling
back to summary
compbio.metadata.PresetTester:marshallPreset
back to summary
compbio.metadata.PresetTester:validatePresets
back to summary
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)
23 lines not shown
back to summary
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)
23 lines not shown
back to summary
compbio.metadata.RunnerConfigTester:testCreateParameterWithValidValueConstrain
back to summary
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)
23 lines not shown
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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.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: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
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compbio.runner.msa.ProbconsTester:testSetInputTester
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compbio.runner.msa.TcoffeeParametersTester:testArguments
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compbio.runner.msa.TcoffeeParametersTester:testConfiguration
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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
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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
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