| Tests passed/Failed/Skipped: | 216/0/0 |
| Started on: | Thu Jun 23 10:34:54 BST 2011 |
| Total time: | 453 seconds (453928 ms) |
| Included groups: | |
| Excluded groups: | webservices performance |
| PASSED TESTS | |||
| Test method | Instance | Time (seconds) | Exception |
| loadJronnFile Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| marshallPreset Test class:Ant test |
compbio.metadata.PresetTester@7a4fe91e | 0 | |
| readStatistics Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 1 | |
| readStatistics Test class:Ant test |
compbio.runner.disorder.DisemblTester@5d469658 | 0 | |
| readStatistics Test class:Ant test |
compbio.runner.disorder.GlobPlotTester@45389b3f | 0 | |
| readStatistics Test class:Ant test |
compbio.runner.disorder.JronnTester@3d3b5a3a | 18 | |
| readStatistics Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 0 | |
| readStatistics Test class:Ant test |
compbio.runner.msa.MafftTester@5f0f0625 | 0 | |
| readStatistics Test class:Ant test |
compbio.runner.msa.MuscleTester@63f8247d | 0 | |
| readStatistics Test class:Ant test |
compbio.runner.msa.ProbconsTester@32830122 | 0 | |
| readStatistics Test class:Ant test |
compbio.runner.msa.TcoffeeTester@54a6af6e | 0 | |
| readStatisticsClusterExecution Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 1 | |
| test Test class:Ant test |
compbio.data.sequence.FastaReaderTester@2dc0435 | 0 | |
| test Test class:Ant test |
compbio.engine.PulledFileCacheTester@472462b3 | 5 | |
| testArguments Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 1 | |
| testArguments Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 3 | |
| testArguments Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 4 | |
| testArguments Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 1 | |
| testArguments Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 4 | |
| testAsyncCancelOperation Test class:Ant test |
compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | |
| testAsyncRetrievOperation Test class:Ant test |
compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | |
| testCache Test class:Ant test |
compbio.engine.FilePullerTester@1e670479 | 6 | |
| testCancel Test class:Ant test |
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@57c8b24d | 1 | compbio.metadata.ResultNotAvailableException: 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! at 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) Caused by: 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! at compbio.runner.Util.readClustalFile(Util.java:93) at compbio.runner.msa.ClustalW.getResults(ClustalW.java:70) ... 25 more ... Removed 22 stack frames compbio.metadata.ResultNotAvailableException: 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! at 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) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) Caused by: 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! at compbio.runner.Util.readClustalFile(Util.java:93) at compbio.runner.msa.ClustalW.getResults(ClustalW.java:70) ... 25 more |
| testCancel Test class:Ant test |
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@39320a41 | 1 | |
| testCancelCompletedTaskLocally Test class:Ant test |
compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 3 | |
| testCancelCompletedTaskLocally Test class:Ant test |
compbio.engine.local.LocalRunnerTester@3fde891b | 0 | java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) at java.util.concurrent.FutureTask.get(FutureTask.java:83) at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139) ... Removed 22 stack frames java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$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) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testCancelLocally Test class:Ant test |
compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) at java.util.concurrent.FutureTask.get(FutureTask.java:83) at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130) at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105) ... Removed 22 stack frames java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$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) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testCancelLocally Test class:Ant test |
compbio.engine.local.LocalRunnerTester@3fde891b | 0 | java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) at java.util.concurrent.FutureTask.get(FutureTask.java:83) at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66) ... Removed 22 stack frames java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$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) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testCleanProteinSequence Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testCleanSequence Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testClusterEngineConf Test class:Ant test |
compbio.engine.conf.PropertyHelperManagerTester@4ee14d81 | 0 | |
| testClusterExecute Test class:Ant test |
compbio.runner.msa.MafftTester@5f0f0625 | 1 | |
| testClusterExecute Test class:Ant test |
compbio.runner.msa.ProbconsTester@32830122 | 2 | |
| testClusterExecute Test class:Ant test |
compbio.runner.msa.TcoffeeTester@54a6af6e | 5 | |
| testCollectStat Test class:Ant test |
compbio.stat.collector.ExecutionStatCollectorTester@b478a2d | 0 | |
| testCommandBuilding Test class:Ant test |
compbio.engine.client.CommandBuilderTester@25cbfa42 | 0 | |
| testConfiguration Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 0 | |
| testConfiguration Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 0 | |
| testConfiguration Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 0 | |
| testConfiguration Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 0 | |
| testConfiguration Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.disorder.DisemblTester@5d469658 | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.disorder.GlobPlotTester@45389b3f | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.disorder.JronnTester@3d3b5a3a | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.msa.MafftTester@5f0f0625 | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.msa.MuscleTester@63f8247d | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.msa.ProbconsTester@32830122 | 0 | |
| testConfigurationLoading Test class:Ant test |
compbio.runner.msa.TcoffeeTester@54a6af6e | 0 | |
| testConstrainedParametersMaxValues Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 0 | |
| testConstrainedParametersMaxValues Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 1 | |
| testConstrainedParametersMaxValues Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 1 | |
| testConstrainedParametersMaxValues Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 37 | |
| testConstrainedParametersMaxValues Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 4 | |
| testConstrainedParametersMinValues Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 0 | |
| testConstrainedParametersMinValues Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 0 | |
| testConstrainedParametersMinValues Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 1 | |
| testConstrainedParametersMinValues Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 0 | |
| testConstrainedParametersMinValues Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 2 | |
| testConstrainedParametersRandomValues Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 0 | |
| testConstrainedParametersRandomValues Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 3 | |
| testConstrainedParametersRandomValues Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 2 | |
| testConstrainedParametersRandomValues Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 70 | |
| testConstrainedParametersRandomValues Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 8 | |
| testCreateNumParameterWithoutValidValue Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | java.lang.IllegalStateException: 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! at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234) at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222) ... Removed 22 stack frames java.lang.IllegalStateException: 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! at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234) at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testCreateParameter Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | compbio.metadata.WrongParameterException: 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 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240) at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93) ... Removed 22 stack frames compbio.metadata.WrongParameterException: 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 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240) at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testCreateParameterWithValidValueConstrain Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | |
| testDeepCleanSequence Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testDefaultParameters Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 0 | |
| testDefaultParameters Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 4 | |
| testDefaultParameters Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 0 | |
| testDefaultParameters Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 4 | |
| testDefaultParameters Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 3 | |
| testExecute Test class:Ant test |
compbio.runner.msa.MafftTester@5f0f0625 | 0 | |
| testExecute Test class:Ant test |
compbio.runner.msa.ProbconsTester@32830122 | 0 | |
| testExecute Test class:Ant test |
compbio.runner.msa.TcoffeeTester@54a6af6e | 0 | |
| testGet Test class:Ant test |
compbio.engine.FilePullerTester@1e670479 | 0 | |
| testGetAsyncEngine Test class:Ant test |
compbio.engine.EngineConfiguratorTester@4513e9fd | 0 | |
| testGetClassPath Test class:Ant test |
compbio.engine.client.PathValidatorTester@729b1670 | 0 | |
| testGetDelay Test class:Ant test |
compbio.engine.FilePullerTester@1e670479 | 0 | |
| testGetDirectory | compbio.engine.conf.DirectoryManagerTester@79fcf790 | 0 | |
| testGetDirectory | compbio.engine.conf.DirectoryManagerTester@79fcf790 | 0 | |
| testGetDirectory | compbio.engine.conf.DirectoryManagerTester@79fcf790 | 0 | |
| testGetDirectory | compbio.engine.conf.DirectoryManagerTester@79fcf790 | 0 | |
| testGetFormattedFasta Test class:Ant test |
compbio.data.sequence.FastaSequenceTester@5ec24193 | 0 | |
| testGetJobStatus Test class:Ant test |
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@57c8b24d | 4 | |
| testGetStats Test class:Ant test |
compbio.stat.servlet.util.StatCollectionTester@26c1186f | 0 | |
| testGetStatus | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 19 | |
| testGetStatus | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 19 | |
| testGetStatus | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 19 | |
| testGetStatus | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 19 | |
| testGetStatus | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 19 | |
| testGetSyncEngine Test class:Ant test |
compbio.engine.EngineConfiguratorTester@4513e9fd | 0 | |
| testGetTestArgsCommand Test class:Ant test |
compbio.runner._impl.OBTester@2658dd2d | 0 | |
| testGetTestArgsCommand Test class:Ant test |
compbio.runner._impl.RPSBlastTester@1420c906 | 0 | |
| testGetTestCommand Test class:Ant test |
compbio.runner._impl.MclTester@f35f44e | 0 | |
| testGetTestCommand Test class:Ant test |
compbio.runner._impl.NetNglycTester@1f3a34af | 0 | |
| testGetTestCommand Test class:Ant test |
compbio.runner._impl.OBTester@2658dd2d | 0 | |
| testGetTestCommand Test class:Ant test |
compbio.runner._impl.RPSBlastTester@1420c906 | 0 | |
| testGetTestCommand Test class:Ant test |
compbio.runner._impl.RonnTester@746db33c | 0 | |
| testGetTestCommand Test class:Ant test |
compbio.runner._impl.Tmhmm2Tester@4e1263db | 0 | |
| testHasCompleted Test class:Ant test |
compbio.stat.collector.ExecutionStatCollectorTester@b478a2d | 0 | |
| testIsAbsolutePath Test class:Ant test |
compbio.engine.client.PathValidatorTester@729b1670 | 0 | |
| testLimitExceeded Test class:Ant test |
compbio.runner.msa.LimitTester@2bdafb4e | 0 | |
| testLoadBalance Test class:Ant test |
compbio.engine.LoadBalancerTester@7d56b386 | 0 | |
| testLoadLimits Test class:Ant test |
compbio.runner.msa.LimitTester@2bdafb4e | 0 | |
| testMarshalling Test class:Ant test |
compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c | 0 | |
| testMarshalling Test class:Ant test |
compbio.metadata.OptionMarshallerTester@6087e704 | 0 | javax.xml.bind.MarshalException
- with linked exception:
[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
at 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)
Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
at 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)
... 26 more
... Removed 22 stack framesjavax.xml.bind.MarshalException
- with linked exception:
[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
at 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)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
at org.testng.TestRunner.runWorkers(TestRunner.java:759)
at org.testng.TestRunner.privateRun(TestRunner.java:592)
at org.testng.TestRunner.run(TestRunner.java:486)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
at org.testng.SuiteRunner.run(SuiteRunner.java:204)
at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
at org.testng.TestNG.run(TestNG.java:784)
at org.testng.TestNG.privateMain(TestNG.java:949)
at org.testng.TestNG.main(TestNG.java:922)
Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
at 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)
... 26 more
|
| testMultipleCancelLocally Test class:Ant test |
compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) at java.util.concurrent.FutureTask.get(FutureTask.java:83) at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130) at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239) ... Removed 22 stack frames java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$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) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testMultipleCancelLocally Test class:Ant test |
compbio.engine.local.LocalRunnerTester@3fde891b | 0 | java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) at java.util.concurrent.FutureTask.get(FutureTask.java:83) at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114) ... Removed 22 stack frames java.util.concurrent.CancellationException at java.util.concurrent.FutureTask$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) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testNcore Test class:Ant test |
compbio.runner.msa.TcoffeeTester@54a6af6e | 0 | |
| testOptionNoDefaultValidate Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | javax.xml.bind.ValidationException: 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 at compbio.metadata.Option.validate(Option.java:317) at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149) ... Removed 22 stack frames javax.xml.bind.ValidationException: 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 at compbio.metadata.Option.validate(Option.java:317) at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testOptionSetInvalidValue Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | compbio.metadata.WrongParameterException: 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 at compbio.metadata.Option.setDefaultValue(Option.java:130) at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172) ... Removed 22 stack frames compbio.metadata.WrongParameterException: 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 at compbio.metadata.Option.setDefaultValue(Option.java:130) at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testOptionToCommand Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | |
| testOptions Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 0 | |
| testOptions Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 0 | |
| testOptions Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 1 | |
| testOptions Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 0 | |
| testOptions Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 0 | |
| testOptionsLocally Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 0 | |
| testOptionsToCommand Test class:Ant test |
compbio.engine.client.CommandBuilderTester@25cbfa42 | 0 | |
| testParameterToCommand Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | |
| testParameters Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 1 | |
| testParameters Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 1 | |
| testParameters Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 1 | |
| testParameters Test class:Ant test |
compbio.runner.msa.ProbconsParametersTester@3823bdd1 | 1 | |
| testParameters Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 3 | |
| testParser Test class:Ant test |
compbio.engine.cluster.drmaa.UtilTester@43f4ebd | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.disorder.DisemblTester@5d469658 | 1 | |
| testPersistance Test class:Ant test |
compbio.runner.disorder.GlobPlotTester@45389b3f | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.disorder.JronnTester@3d3b5a3a | 18 | |
| testPersistance Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.msa.MafftTester@5f0f0625 | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.msa.MuscleTester@63f8247d | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.msa.ProbconsTester@32830122 | 0 | |
| testPersistance Test class:Ant test |
compbio.runner.msa.TcoffeeTester@54a6af6e | 0 | |
| testPresetWithMuptiOptions Test class:Ant test |
compbio.metadata.PresetTester@7a4fe91e | 0 | |
| testPresets Test class:Ant test |
compbio.runner.msa.ClustalWParametersTester@74e2ad16 | 0 | |
| testPresets Test class:Ant test |
compbio.runner.msa.MafftParametersTester@35a8d460 | 0 | |
| testPresets Test class:Ant test |
compbio.runner.msa.MuscleParametersTester@535c97e4 | 0 | |
| testPresets Test class:Ant test |
compbio.runner.msa.TcoffeeParametersTester@36bf7916 | 0 | |
| testProteinSequenceGeneration Test class:Ant test |
compbio.data.sequence.FastaSequenceGeneratorTester@3a98350a | 0 | |
| testPull Test class:Ant test |
compbio.engine.FilePullerTester@1e670479 | 0 | |
| testQueue Test class:Ant test |
compbio.engine.cluster.dundee._QueueTester@584a5c78 | 0 | |
| testReadAAConResults Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testReadClustalFile Test class:Ant test |
compbio.data.sequence.ClustalAlignmentUtilTester@44739f3f | 0 | |
| testReadClustalFileLongNames Test class:Ant test |
compbio.data.sequence.ClustalAlignmentUtilTester@44739f3f | 0 | |
| testReadClustalFileShortNames Test class:Ant test |
compbio.data.sequence.ClustalAlignmentUtilTester@44739f3f | 0 | |
| testReadDisemblResults Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testReadGlobPlotResults Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testReadIUPredForGlobDomain Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testReadIUPredForShortAndLongDisorder Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testReadResults Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 0 | |
| testReadWriteFasta Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testRunLocally Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 0 | |
| testRunLocally Test class:Ant test |
compbio.runner.disorder.DisemblTester@5d469658 | 0 | |
| testRunLocally Test class:Ant test |
compbio.runner.disorder.GlobPlotTester@45389b3f | 0 | |
| testRunLocally Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 0 | |
| testRunLocally Test class:Ant test |
compbio.runner.disorder.JronnTester@3d3b5a3a | 18 | |
| testRunLocally Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 0 | |
| testRunLocally Test class:Ant test |
compbio.runner.msa.MuscleTester@63f8247d | 0 | |
| testRunLocallyOnTwoCpu Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 0 | |
| testRunLocallyOnTwoCpu Test class:Ant test |
compbio.runner.disorder.JronnTester@3d3b5a3a | 7 | |
| testRunLocallyWithParams Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 0 | |
| testRunLocallyWithPreset Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 0 | |
| testRunOnCluster Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 3 | |
| testRunOnCluster Test class:Ant test |
compbio.runner.disorder.DisemblTester@5d469658 | 2 | |
| testRunOnCluster Test class:Ant test |
compbio.runner.disorder.GlobPlotTester@45389b3f | 2 | |
| testRunOnCluster Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 3 | |
| testRunOnCluster Test class:Ant test |
compbio.runner.disorder.JronnTester@3d3b5a3a | 13 | |
| testRunOnCluster Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 5 | |
| testRunOnCluster Test class:Ant test |
compbio.runner.msa.MuscleTester@63f8247d | 3 | |
| testRunOnClusterAsync Test class:Ant test |
compbio.runner.conservation.AAConTester@1959e6e8 | 5 | |
| testRunOnClusterAsync Test class:Ant test |
compbio.runner.disorder.DisemblTester@5d469658 | 6 | |
| testRunOnClusterAsync Test class:Ant test |
compbio.runner.disorder.GlobPlotTester@45389b3f | 6 | |
| testRunOnClusterAsync Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 6 | |
| testRunOnClusterAsync Test class:Ant test |
compbio.runner.disorder.JronnTester@3d3b5a3a | 11 | |
| testRunOnClusterAsyncCheckStatusLongPoolingTime Test class:Ant test |
compbio.runner.msa.MafftTester@5f0f0625 | 5 | |
| testRunWithMatrix Test class:Ant test |
compbio.runner.msa.ClustalWTester@3a0b53e | 0 | |
| testSchemaFromCodeGeneration Test class:Ant test |
compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c | 0 | |
| testSetInputTester Test class:Ant test |
compbio.runner.msa.MafftTester@5f0f0625 | 0 | |
| testSetInputTester Test class:Ant test |
compbio.runner.msa.ProbconsTester@32830122 | 0 | |
| testSetParameter Test class:Ant test |
compbio.runner.disorder.IUPredTester@758689a | 0 | |
| testSpaceDelimiterExecutable Test class:Ant test |
compbio.engine.client.CommandBuilderTester@25cbfa42 | 0 | |
| testSubmit Test class:Ant test |
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@57c8b24d | 3 | |
| testSubmit Test class:Ant test |
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@39320a41 | 3 | |
| testSubmitLocally | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | |
| testSubmitLocally | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | |
| testSubmitLocally | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | |
| testSubmitLocally | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | |
| testSubmitLocally | compbio.engine.local.AsyncLocalRunnerTester@31df5f21 | 0 | |
| testTaskList Test class:Ant test |
compbio.engine.cluster.drmaa.ClusterSessionTester@23de4dd8 | 3 | |
| testUnMarshalling Test class:Ant test |
compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c | 0 | |
| testUnMarshalling Test class:Ant test |
compbio.metadata.OptionMarshallerTester@6087e704 | 0 | |
| testUpdateStatTester Test class:Ant test |
compbio.stat.collector.ExecutionStatCollectorTester@b478a2d | 35 | |
| testValidate Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | |
| testValidateBoundaryConstrainCheck Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | |
| testValidateLowerBoundaryConstrainCheck Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | compbio.metadata.WrongParameterException: 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 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248) at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268) ... Removed 22 stack frames compbio.metadata.WrongParameterException: 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 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248) at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testValidateUpperBoundaryConstrainCheck Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | compbio.metadata.WrongParameterException: 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 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248) at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296) ... Removed 22 stack frames compbio.metadata.WrongParameterException: 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 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248) at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testValidateValueConstrain Test class:Ant test |
compbio.metadata.RunnerConfigTester@1451ef4e | 0 | javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208) at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341) ... Removed 22 stack frames javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208) at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609) at org.testng.internal.Invoker.invokeMethod(Invoker.java:532) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.runWorkers(TestRunner.java:759) at org.testng.TestRunner.privateRun(TestRunner.java:592) at org.testng.TestRunner.run(TestRunner.java:486) at org.testng.SuiteRunner.runTest(SuiteRunner.java:332) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299) at org.testng.SuiteRunner.run(SuiteRunner.java:204) at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912) at org.testng.TestNG.runSuitesLocally(TestNG.java:876) at org.testng.TestNG.run(TestNG.java:784) at org.testng.TestNG.privateMain(TestNG.java:949) at org.testng.TestNG.main(TestNG.java:922) |
| testValidation Test class:Ant test |
compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c | 0 | |
| testValidationOnMarshalling Test class:Ant test |
compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c | 0 | javax.xml.bind.MarshalException
- with linked exception:
[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
at 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)
Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
at 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)
... 26 more
... Removed 22 stack framesjavax.xml.bind.MarshalException
- with linked exception:
[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
at 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)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
at org.testng.TestRunner.runWorkers(TestRunner.java:759)
at org.testng.TestRunner.privateRun(TestRunner.java:592)
at org.testng.TestRunner.run(TestRunner.java:486)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
at org.testng.SuiteRunner.run(SuiteRunner.java:204)
at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
at org.testng.TestNG.run(TestNG.java:784)
at org.testng.TestNG.privateMain(TestNG.java:949)
at org.testng.TestNG.main(TestNG.java:922)
Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
at 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)
... 26 more
|
| testVerifyJobsCount Test class:Ant test |
compbio.stat.collector.StatDBTester@5c09624 | 0 | |
| testgetAllOptions Test class:Ant test |
compbio.metadata.OptionCombinatorTester@2afb6c5f | 0 | |
| testgetAllParameters Test class:Ant test |
compbio.metadata.OptionCombinatorTester@2afb6c5f | 0 | |
| testisNonAmbNucleotideSequence Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| testisProteinSequence Test class:Ant test |
compbio.data.sequence.SequenceUtilTester@235f4a7f | 0 | |
| validateClustalConfiguration Test class:Ant test |
compbio.engine.conf.PropertyHelperManagerTester@4ee14d81 | 0 | |
| validateMafftConfiguration Test class:Ant test |
compbio.engine.conf.PropertyHelperManagerTester@4ee14d81 | 0 | |
| validateMuscleConfiguration Test class:Ant test |
compbio.engine.conf.PropertyHelperManagerTester@4ee14d81 | 0 | |
| validatePresets Test class:Ant test |
compbio.metadata.PresetTester@7a4fe91e | 0 | |
| validateTcoffeeConfiguration Test class:Ant test |
compbio.engine.conf.PropertyHelperManagerTester@4ee14d81 | 0 | |