From: pvtroshin Date: Thu, 23 Jun 2011 09:47:41 +0000 (+0000) Subject: Adding latest test results X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d508522d082c3cbf7aaf970aee044d3aae68415c;p=jabaws.git Adding latest test results git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4313 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/website/tests/Ant suite/Ant test.html b/website/tests/Ant suite/Ant test.html new file mode 100644 index 0000000..4ad5419 --- /dev/null +++ b/website/tests/Ant suite/Ant test.html @@ -0,0 +1,1876 @@ + + +TestNG: Ant test + + + + + + + + +

Ant test

+ + + + + + + + + + + +

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

+(Hover the method name to see the test class name)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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
Click to show all 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$Sync.innerGet(FutureTask.java:220) + at java.util.concurrent.FutureTask.get(FutureTask.java:83) + at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) + at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) + at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139) +... Removed 22 stack frames
Click to show all stack frames +
java.util.concurrent.CancellationException + at java.util.concurrent.FutureTask$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$Sync.innerGet(FutureTask.java:220) + at java.util.concurrent.FutureTask.get(FutureTask.java:83) + at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) + at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130) + at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105) +... Removed 22 stack frames
Click to show all stack frames +
java.util.concurrent.CancellationException + at java.util.concurrent.FutureTask$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$Sync.innerGet(FutureTask.java:220) + at java.util.concurrent.FutureTask.get(FutureTask.java:83) + at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) + at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) + at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66) +... Removed 22 stack frames
Click to show all stack frames +
java.util.concurrent.CancellationException + at java.util.concurrent.FutureTask$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
Click to show all 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
Click to show all 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 frames
Click to show all stack frames +
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) + 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$Sync.innerGet(FutureTask.java:220) + at java.util.concurrent.FutureTask.get(FutureTask.java:83) + at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) + at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130) + at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239) +... Removed 22 stack frames
Click to show all stack frames +
java.util.concurrent.CancellationException + at java.util.concurrent.FutureTask$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$Sync.innerGet(FutureTask.java:220) + at java.util.concurrent.FutureTask.get(FutureTask.java:83) + at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) + at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) + at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114) +... Removed 22 stack frames
Click to show all stack frames +
java.util.concurrent.CancellationException + at java.util.concurrent.FutureTask$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
Click to show all 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
Click to show all 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
Click to show all 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
Click to show all 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
Click to show all 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 frames
Click to show all stack frames +
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) + 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

+ + \ No newline at end of file diff --git a/website/tests/Ant suite/Ant test.properties b/website/tests/Ant suite/Ant test.properties new file mode 100644 index 0000000..688741c --- /dev/null +++ b/website/tests/Ant suite/Ant test.properties @@ -0,0 +1 @@ +[SuiteResult Ant test] \ No newline at end of file diff --git a/website/tests/Ant suite/Ant test.xml b/website/tests/Ant suite/Ant test.xml new file mode 100644 index 0000000..1182c37 --- /dev/null +++ b/website/tests/Ant suite/Ant test.xml @@ -0,0 +1,220 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/tests/Ant suite/classes.html b/website/tests/Ant suite/classes.html new file mode 100644 index 0000000..2ff1808 --- /dev/null +++ b/website/tests/Ant suite/classes.html @@ -0,0 +1,2009 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Class name Method name Groups
compbio.engine.client.CommandBuilderTester
@Test
testOptionsToCommand
testSpaceDelimiterExecutable
testCommandBuilding
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.NetNglycTester
@Test
testBuildCommand cluster runner
testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.EngineConfiguratorTester
@Test
testGetAsyncEngine
testGetSyncEngine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.disorder.GlobPlotTester
@Test
testRunOnCluster cluster runner
testPersistance runner
testRunOnClusterAsync cluster runner
testConfigurationLoading runner
readStatistics runner
testRunLocally runner
@BeforeClass
@BeforeMethod
init
@AfterMethod
@AfterClass
compbio.stat.collector.ExecutionStatCollectorTester
@Test
testHasCompleted
testHasTimedOut
testCollectStat
testUpdateStatTester
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.local.AsyncLocalRunnerTester
@Test
testCancelLocally engine
testMultipleCancelLocally engine
testAsyncCancelOperation engine
testAsyncRetrievOperation engine
testSubmitLocally engine
testCancelCompletedTaskLocally engine
testGetStatus engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MafftTester
@Test
testExecute runner non_windows
testRunOnClusterAsyncCheckStatusShortPoolingTime cluster runner non_windows
testPersistance runner non_windows
testClusterExecute cluster runner non_windows
testSetInputTester runner non_windows
testConfigurationLoading runner
readStatistics runner non_windows
testRunOnClusterAsyncCheckStatusLongPoolingTime cluster runner non_windows
@BeforeClass
@BeforeMethod
init cluster runner non_windows
@AfterMethod
@AfterClass
compbio.data.sequence.ClustalAlignmentUtilTester
@Test
testReadClustalFile
testReadClustalFileLongNames
testReadClustalFileShortNames
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.disorder.IUPredTester
@Test
testRunOnCluster cluster runner
testReadResults runner
testPersistance runner
testRunOnClusterAsync cluster runner
testSetParameter runner
testConfigurationLoading runner
testRunLocally runner
testRunLocallyWithParams runner
@BeforeClass
@BeforeMethod
init
@AfterMethod
@AfterClass
compbio.engine.client.PathValidatorTester
@Test
testIsAbsolutePath
testGetClassPath
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.stat.collector.StatDBTester
@Test
testReadOneMonthData
testVerifyJobsCount
testReadYearData
testGetEarliestRecord
@BeforeClass
init
@BeforeMethod
@AfterMethod
@AfterClass
compbio.stat.servlet.util.StatCollectionTester
@Test
testGetStats
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester
@Test
testSubmit engine cluster
testCancel engine cluster
testGetJobStatus engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester
@Test
testSubmit engine cluster
testCancel engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.conservation.AAConTester
@Test
testRunOnCluster runner
testRunLocallyWithPreset runner
testPersistance runner
testRunOnClusterAsync cluster runner
testRunLocallyOnTwoCpu runner
testConfigurationLoading runner
readStatistics runner
testRunLocally runner
@BeforeClass
@BeforeMethod
init
@AfterMethod
@AfterClass
compbio.runner._impl.RPSBlastTester
@Test
testBuildCommand cluster runner
testGetTestCommand
testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.PulledFileCacheTester
@Test
test
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.disorder.DisemblTester
@Test
testRunOnCluster cluster runner
testPersistance runner
testRunOnClusterAsync cluster runner
testConfigurationLoading runner
readStatistics runner
testRunLocally runner
@BeforeClass
@BeforeMethod
init
@AfterMethod
@AfterClass
compbio.runner._impl.MclTester
@Test
testBuildCommand cluster runner
testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.dundee._QueueTester
@Test
testQueue
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.LoadBalancerTester
@Test
testLoadBalance
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ProbconsParametersTester
@Test
testConstrainedParametersMaxValues runner non_windows
testConstrainedParametersRandomValues runner non_windows
testConstrainedParametersMinValues runner non_windows
testArguments runner non_windows
testOptions runner non_windows
testDefaultParameters runner non_windows
testParameters runner non_windows
testConfiguration
@BeforeClass
@BeforeMethod
setup runner non_windows
@AfterMethod
@AfterClass
compbio.metadata.RunnerConfigTester
@Test
testValidateUpperBoundaryConstrainCheck
testOptionSetInvalidValue
testValidateBoundaryConstrainCheck
testValidateValueConstrain
testCreateParameterWithValidValueConstrain
testValidateLowerBoundaryConstrainCheck
testOptionNoDefaultValidate
testCreateParameter
testOptionToCommand
testParameterToCommand
testCreateNumParameterWithoutValidValue
testValidate
@BeforeClass
@BeforeMethod
setup
@AfterMethod
@AfterClass
compbio.runner.disorder.JronnTester
@Test
testRunOnCluster cluster runner
testPersistance runner
testRunOnClusterAsync cluster runner
testRunLocallyOnTwoCpu runner
testConfigurationLoading runner
readStatistics runner
testRunLocally runner
@BeforeClass
@BeforeMethod
init
@AfterMethod
@AfterClass
compbio.runner.msa.MafftParametersTester
@Test
testConstrainedParametersMaxValues runner non_windows
testConstrainedParametersRandomValues runner non_windows
testConstrainedParametersMinValues runner non_windows
testArguments runner non_windows
testOptions runner non_windows
testDefaultParameters runner non_windows
testParameters runner non_windows
testPresets runner non_windows
testConfiguration
@BeforeClass
@BeforeMethod
setup runner non_windows
@AfterMethod
@AfterClass
compbio.runner._impl.RonnTester
@Test
testBuildCommand cluster runner
testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ProbconsTester
@Test
testExecute runner non_windows
testPersistance runner non_windows
testClusterExecute cluster runner non_windows
testSetInputTester runner non_windows
testConfigurationLoading runner
readStatistics runner non_windows
@BeforeClass
@BeforeMethod
init cluster runner non_windows
@AfterMethod
@AfterClass
compbio.engine.conf.PropertyHelperManagerTester
@Test
testClusterEngineConf cluster
validateClustalConfiguration
validateTcoffeeConfiguration
validateMuscleConfiguration
validateMafftConfiguration
@BeforeClass
testLoadResources
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.OptionCombinatorTester
@Test
testgetAllParameters
testgetAllOptions
@BeforeClass
@BeforeMethod
setup
@AfterMethod
@AfterClass
compbio.engine.FilePullerTester
@Test
testGet
testCache engine
testGetDelay engine
testPull engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleTester
@Test
testRunOnCluster cluster runner
testPersistance runner
testRunOnClusterAsync cluster runner
testConfigurationLoading runner
readStatistics runner
testRunLocally runner
@BeforeClass
@BeforeMethod
init
@AfterMethod
@AfterClass
compbio.runner.msa.TcoffeeTester
@Test
testExecute runner non_windows
testPersistance cluster runner non_windows
testNcore runner non_windows
testClusterExecute cluster runner non_windows
testConfigurationLoading runner
readStatistics runner non_windows
@BeforeClass
@BeforeMethod
init cluster runner non_windows
@AfterMethod
@AfterClass
compbio.runner._impl.OBTester
@Test
testBuildCommand cluster runner
testGetTestCommand
testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.LimitTester
@Test
testLimitExceeded
testLoadLimits
@BeforeClass
@BeforeMethod
setup runner
@AfterMethod
@AfterClass
compbio.engine.local.LocalRunnerTester
@Test
testCancelLocally engine
testMultipleCancelLocally engine
testCancelCompletedTaskLocally engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.Tmhmm2Tester
@Test
testBuildCommand cluster runner
testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleParametersTester
@Test
testConstrainedParametersMaxValues runner
testConstrainedParametersRandomValues runner
testConstrainedParametersMinValues runner
testArguments runner
testOptions runner
testDefaultParameters runner
testParameters runner
testPresets runner
testConfiguration
@BeforeClass
@BeforeMethod
setup runner
@AfterMethod
@AfterClass
compbio.data.sequence.FastaSequenceGeneratorTester
@Test
testProteinSequenceGeneration
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.ClusterSessionTester
@Test
testTaskList engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.FastaReaderTester
@Test
test
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.FastaSequenceTester
@Test
testGetFormattedFasta
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.SequenceUtilTester
@Test
testReadIUPredForGlobDomain
testDeepCleanSequence
testReadIUPredForShortAndLongDisorder
testCleanProteinSequence
testReadWriteFasta
testReadAAConResults
testReadGlobPlotResults
testReadDisemblResults
loadJronnFile
testisNonAmbNucleotideSequence
testisProteinSequence
testCleanSequence
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.TcoffeeParametersTester
@Test
testConstrainedParametersMaxValues runner non_windows
testConstrainedParametersRandomValues runner non_windows
testConstrainedParametersMinValues runner non_windows
testArguments runner non_windows
testOptions runner non_windows
testDefaultParameters runner non_windows
testParameters runner non_windows
testPresets runner non_windows
testConfiguration
@BeforeClass
@BeforeMethod
setup runner non_windows
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.UtilTester
@Test
testParser
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ClustalWTester
@Test
testRunOnCluster cluster runner
testAddParameters
testPersistance runner
testOptionsLocally runner
readStatisticsClusterExecution cluster runner
testRunWithMatrix runner
testConfigurationLoading runner
readStatistics runner
testRunLocally runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.conf.DirectoryManagerTester
@Test
testGetDirectory
testNanoTime
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.PresetTester
@Test
testPresetWithMuptiOptions
marshallPreset
validatePresets
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.OptionMarshallerTester
@Test
testUnMarshalling
testMarshalling
@BeforeClass
@BeforeMethod
setup
@AfterMethod
@AfterClass
compbio.runner.msa.ClustalWParametersTester
@Test
testConstrainedParametersMaxValues runner
testConstrainedParametersRandomValues runner
testConstrainedParametersMinValues runner
testArguments runner
testOptions runner
testDefaultParameters runner
testParameters runner
testPresets runner
testConfiguration
@BeforeClass
@BeforeMethod
setup runner
@AfterMethod
@AfterClass
compbio.engine.conf.RunnerConfigMarshallerTester
@Test
testValidationOnMarshalling
testUnMarshalling
testValidation
testSchemaFromCodeGeneration
testMarshalling
@BeforeClass
@BeforeMethod
setup
@AfterMethod
@AfterClass
diff --git a/website/tests/Ant suite/groups.html b/website/tests/Ant suite/groups.html new file mode 100644 index 0000000..73208cf --- /dev/null +++ b/website/tests/Ant suite/groups.html @@ -0,0 +1,6 @@ +

Class name	Method name	Groups
compbio.engine.client.CommandBuilderTester
@Test
	testOptionsToCommand
	testSpaceDelimiterExecutable
	testCommandBuilding
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.NetNglycTester
@Test
	testBuildCommand	cluster runner
	testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.EngineConfiguratorTester
@Test
	testGetAsyncEngine
	testGetSyncEngine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.disorder.GlobPlotTester
@Test
	testRunOnCluster	cluster runner
	testPersistance	runner
	testRunOnClusterAsync	cluster runner
	testConfigurationLoading	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
	init
@AfterMethod
@AfterClass
compbio.stat.collector.ExecutionStatCollectorTester
@Test
	testHasCompleted
	testHasTimedOut
	testCollectStat
	testUpdateStatTester
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.local.AsyncLocalRunnerTester
@Test
	testCancelLocally	engine
	testMultipleCancelLocally	engine
	testAsyncCancelOperation	engine
	testAsyncRetrievOperation	engine
	testSubmitLocally	engine
	testCancelCompletedTaskLocally	engine
	testGetStatus	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MafftTester
@Test
	testExecute	runner non_windows
	testRunOnClusterAsyncCheckStatusShortPoolingTime	cluster runner non_windows
	testPersistance	runner non_windows
	testClusterExecute	cluster runner non_windows
	testSetInputTester	runner non_windows
	testConfigurationLoading	runner
	readStatistics	runner non_windows
	testRunOnClusterAsyncCheckStatusLongPoolingTime	cluster runner non_windows
@BeforeClass
@BeforeMethod
	init	cluster runner non_windows
@AfterMethod
@AfterClass
compbio.data.sequence.ClustalAlignmentUtilTester
@Test
	testReadClustalFile
	testReadClustalFileLongNames
	testReadClustalFileShortNames
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.disorder.IUPredTester
@Test
	testRunOnCluster	cluster runner
	testReadResults	runner
	testPersistance	runner
	testRunOnClusterAsync	cluster runner
	testSetParameter	runner
	testConfigurationLoading	runner
	testRunLocally	runner
	testRunLocallyWithParams	runner
@BeforeClass
@BeforeMethod
	init
@AfterMethod
@AfterClass
compbio.engine.client.PathValidatorTester
@Test
	testIsAbsolutePath
	testGetClassPath
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.stat.collector.StatDBTester
@Test
	testReadOneMonthData
	testVerifyJobsCount
	testReadYearData
	testGetEarliestRecord
@BeforeClass
	init
@BeforeMethod
@AfterMethod
@AfterClass
compbio.stat.servlet.util.StatCollectionTester
@Test
	testGetStats
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester
@Test
	testSubmit	engine cluster
	testCancel	engine cluster
	testGetJobStatus	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester
@Test
	testSubmit	engine cluster
	testCancel	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.conservation.AAConTester
@Test
	testRunOnCluster	runner
	testRunLocallyWithPreset	runner
	testPersistance	runner
	testRunOnClusterAsync	cluster runner
	testRunLocallyOnTwoCpu	runner
	testConfigurationLoading	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
	init
@AfterMethod
@AfterClass
compbio.runner._impl.RPSBlastTester
@Test
	testBuildCommand	cluster runner
	testGetTestCommand
	testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.PulledFileCacheTester
@Test
	test
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.disorder.DisemblTester
@Test
	testRunOnCluster	cluster runner
	testPersistance	runner
	testRunOnClusterAsync	cluster runner
	testConfigurationLoading	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
	init
@AfterMethod
@AfterClass
compbio.runner._impl.MclTester
@Test
	testBuildCommand	cluster runner
	testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.dundee._QueueTester
@Test
	testQueue
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.LoadBalancerTester
@Test
	testLoadBalance
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ProbconsParametersTester
@Test
	testConstrainedParametersMaxValues	runner non_windows
	testConstrainedParametersRandomValues	runner non_windows
	testConstrainedParametersMinValues	runner non_windows
	testArguments	runner non_windows
	testOptions	runner non_windows
	testDefaultParameters	runner non_windows
	testParameters	runner non_windows
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner non_windows
@AfterMethod
@AfterClass
compbio.metadata.RunnerConfigTester
@Test
	testValidateUpperBoundaryConstrainCheck
	testOptionSetInvalidValue
	testValidateBoundaryConstrainCheck
	testValidateValueConstrain
	testCreateParameterWithValidValueConstrain
	testValidateLowerBoundaryConstrainCheck
	testOptionNoDefaultValidate
	testCreateParameter
	testOptionToCommand
	testParameterToCommand
	testCreateNumParameterWithoutValidValue
	testValidate
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
compbio.runner.disorder.JronnTester
@Test
	testRunOnCluster	cluster runner
	testPersistance	runner
	testRunOnClusterAsync	cluster runner
	testRunLocallyOnTwoCpu	runner
	testConfigurationLoading	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
	init
@AfterMethod
@AfterClass
compbio.runner.msa.MafftParametersTester
@Test
	testConstrainedParametersMaxValues	runner non_windows
	testConstrainedParametersRandomValues	runner non_windows
	testConstrainedParametersMinValues	runner non_windows
	testArguments	runner non_windows
	testOptions	runner non_windows
	testDefaultParameters	runner non_windows
	testParameters	runner non_windows
	testPresets	runner non_windows
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner non_windows
@AfterMethod
@AfterClass
compbio.runner._impl.RonnTester
@Test
	testBuildCommand	cluster runner
	testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ProbconsTester
@Test
	testExecute	runner non_windows
	testPersistance	runner non_windows
	testClusterExecute	cluster runner non_windows
	testSetInputTester	runner non_windows
	testConfigurationLoading	runner
	readStatistics	runner non_windows
@BeforeClass
@BeforeMethod
	init	cluster runner non_windows
@AfterMethod
@AfterClass
compbio.engine.conf.PropertyHelperManagerTester
@Test
	testClusterEngineConf	cluster
	validateClustalConfiguration
	validateTcoffeeConfiguration
	validateMuscleConfiguration
	validateMafftConfiguration
@BeforeClass
	testLoadResources
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.OptionCombinatorTester
@Test
	testgetAllParameters
	testgetAllOptions
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
compbio.engine.FilePullerTester
@Test
	testGet
	testCache	engine
	testGetDelay	engine
	testPull	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleTester
@Test
	testRunOnCluster	cluster runner
	testPersistance	runner
	testRunOnClusterAsync	cluster runner
	testConfigurationLoading	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
	init
@AfterMethod
@AfterClass
compbio.runner.msa.TcoffeeTester
@Test
	testExecute	runner non_windows
	testPersistance	cluster runner non_windows
	testNcore	runner non_windows
	testClusterExecute	cluster runner non_windows
	testConfigurationLoading	runner
	readStatistics	runner non_windows
@BeforeClass
@BeforeMethod
	init	cluster runner non_windows
@AfterMethod
@AfterClass
compbio.runner._impl.OBTester
@Test
	testBuildCommand	cluster runner
	testGetTestCommand
	testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.LimitTester
@Test
	testLimitExceeded
	testLoadLimits
@BeforeClass
@BeforeMethod
	setup	runner
@AfterMethod
@AfterClass
compbio.engine.local.LocalRunnerTester
@Test
	testCancelLocally	engine
	testMultipleCancelLocally	engine
	testCancelCompletedTaskLocally	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.Tmhmm2Tester
@Test
	testBuildCommand	cluster runner
	testGetTestCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleParametersTester
@Test
	testConstrainedParametersMaxValues	runner
	testConstrainedParametersRandomValues	runner
	testConstrainedParametersMinValues	runner
	testArguments	runner
	testOptions	runner
	testDefaultParameters	runner
	testParameters	runner
	testPresets	runner
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner
@AfterMethod
@AfterClass
compbio.data.sequence.FastaSequenceGeneratorTester
@Test
	testProteinSequenceGeneration
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.ClusterSessionTester
@Test
	testTaskList	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.FastaReaderTester
@Test
	test
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.FastaSequenceTester
@Test
	testGetFormattedFasta
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.SequenceUtilTester
@Test
	testReadIUPredForGlobDomain
	testDeepCleanSequence
	testReadIUPredForShortAndLongDisorder
	testCleanProteinSequence
	testReadWriteFasta
	testReadAAConResults
	testReadGlobPlotResults
	testReadDisemblResults
	loadJronnFile
	testisNonAmbNucleotideSequence
	testisProteinSequence
	testCleanSequence
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.TcoffeeParametersTester
@Test
	testConstrainedParametersMaxValues	runner non_windows
	testConstrainedParametersRandomValues	runner non_windows
	testConstrainedParametersMinValues	runner non_windows
	testArguments	runner non_windows
	testOptions	runner non_windows
	testDefaultParameters	runner non_windows
	testParameters	runner non_windows
	testPresets	runner non_windows
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner non_windows
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.UtilTester
@Test
	testParser
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ClustalWTester
@Test
	testRunOnCluster	cluster runner
	testAddParameters
	testPersistance	runner
	testOptionsLocally	runner
	readStatisticsClusterExecution	cluster runner
	testRunWithMatrix	runner
	testConfigurationLoading	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.conf.DirectoryManagerTester
@Test
	testGetDirectory
	testNanoTime
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.PresetTester
@Test
	testPresetWithMuptiOptions
	marshallPreset
	validatePresets
@BeforeClass

Groups used for this test run

+ + + + +

Group name	Methods
cluster	compbio.runner.disorder.DisemblTester.testRunOnClusterAsync() compbio.runner.msa.TcoffeeTester.testPersistance() compbio.runner.conservation.AAConTester.testRunOnClusterAsync() compbio.runner.msa.ProbconsTester.testClusterExecute() compbio.runner.disorder.GlobPlotTester.testRunOnClusterAsync() compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution() compbio.runner.disorder.IUPredTester.testRunOnCluster() compbio.runner.disorder.JronnTester.testRunOnCluster() compbio.runner.msa.ClustalWTester.testRunOnCluster() compbio.runner.disorder.GlobPlotTester.testRunOnCluster() compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList() compbio.runner.msa.MuscleTester.testRunOnCluster() compbio.runner.disorder.IUPredTester.testRunOnClusterAsync() compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel() compbio.runner.msa.MafftTester.testClusterExecute() compbio.runner.disorder.DisemblTester.testRunOnCluster() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit() compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf() compbio.runner.msa.TcoffeeTester.testClusterExecute() compbio.runner.disorder.JronnTester.testRunOnClusterAsync()
engine	compbio.engine.local.AsyncLocalRunnerTester.testGetStatus() compbio.engine.local.LocalRunnerTester.testCancelLocally() compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally() compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally() compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally() compbio.engine.FilePullerTester.testCache() compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation() compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation() compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally() compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus() compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally() compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel() compbio.engine.FilePullerTester.testGetDelay() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit() compbio.engine.FilePullerTester.testPull()
non_windows	compbio.runner.msa.MafftTester.readStatistics() compbio.runner.msa.MafftParametersTester.testParameters() compbio.runner.msa.MafftParametersTester.testDefaultParameters() compbio.runner.msa.TcoffeeTester.testExecute() compbio.runner.msa.MafftParametersTester.testPresets() compbio.runner.msa.MafftTester.testSetInputTester() compbio.runner.msa.ProbconsParametersTester.testArguments() compbio.runner.msa.TcoffeeTester.readStatistics() compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.MafftTester.testExecute() compbio.runner.msa.ProbconsTester.readStatistics() compbio.runner.msa.TcoffeeParametersTester.testArguments() compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime() compbio.runner.msa.TcoffeeTester.testNcore() compbio.runner.msa.MafftParametersTester.testOptions() compbio.runner.msa.ProbconsTester.testSetInputTester() compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.ProbconsTester.testExecute() compbio.runner.msa.TcoffeeParametersTester.testParameters() compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters() compbio.runner.msa.TcoffeeTester.testPersistance() compbio.runner.msa.ProbconsParametersTester.testOptions() compbio.runner.msa.ProbconsTester.testClusterExecute() compbio.runner.msa.TcoffeeParametersTester.testPresets() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.MafftTester.testPersistance() compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MafftParametersTester.testArguments() compbio.runner.msa.TcoffeeParametersTester.testOptions() compbio.runner.msa.ProbconsParametersTester.testDefaultParameters() compbio.runner.msa.ProbconsParametersTester.testParameters() compbio.runner.msa.MafftTester.testClusterExecute() compbio.runner.msa.ProbconsTester.testPersistance() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.TcoffeeTester.testClusterExecute()
runner	compbio.runner.conservation.AAConTester.testRunLocallyWithPreset() compbio.runner.disorder.DisemblTester.testRunOnClusterAsync() compbio.runner.msa.MafftParametersTester.testParameters() compbio.runner.conservation.AAConTester.testPersistance() compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues() compbio.runner.disorder.JronnTester.testRunLocally() compbio.runner.msa.ProbconsParametersTester.testArguments() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.MafftTester.testExecute() compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues() compbio.runner.disorder.IUPredTester.testRunOnClusterAsync() compbio.runner.msa.ClustalWTester.testRunWithMatrix() compbio.runner.msa.ProbconsTester.testConfigurationLoading() compbio.runner.msa.TcoffeeParametersTester.testParameters() compbio.runner.disorder.JronnTester.testConfigurationLoading() compbio.runner.disorder.GlobPlotTester.testPersistance() compbio.runner.disorder.JronnTester.testRunOnCluster() compbio.runner.disorder.DisemblTester.readStatistics() compbio.runner.msa.MafftTester.testPersistance() compbio.runner.msa.MuscleParametersTester.testParameters() compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.ClustalWTester.testOptionsLocally() compbio.runner.msa.MafftTester.testClusterExecute() compbio.runner.msa.TcoffeeTester.testConfigurationLoading() compbio.runner.msa.ClustalWParametersTester.testParameters() compbio.runner.disorder.IUPredTester.testRunOnCluster() compbio.runner.msa.TcoffeeTester.readStatistics() compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues() compbio.runner.disorder.IUPredTester.testConfigurationLoading() compbio.runner.msa.ProbconsTester.readStatistics() compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime() compbio.runner.msa.MafftParametersTester.testOptions() compbio.runner.disorder.JronnTester.readStatistics() compbio.runner.disorder.DisemblTester.testRunOnCluster() compbio.runner.msa.ProbconsTester.testSetInputTester() compbio.runner.msa.ClustalWTester.testPersistance() compbio.runner.disorder.DisemblTester.testConfigurationLoading() compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution() compbio.runner.msa.MuscleTester.testPersistance() compbio.runner.disorder.IUPredTester.testRunLocally() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.ClustalWParametersTester.testOptions() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.TcoffeeParametersTester.testOptions() compbio.runner.disorder.JronnTester.testRunLocallyOnTwoCpu() compbio.runner.msa.ProbconsParametersTester.testDefaultParameters() compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues() compbio.runner.disorder.IUPredTester.testRunLocallyWithParams() compbio.runner.disorder.DisemblTester.testRunLocally() compbio.runner.msa.MuscleParametersTester.testOptions() compbio.runner.disorder.JronnTester.testRunOnClusterAsync() compbio.runner.msa.ClustalWTester.testConfigurationLoading() compbio.runner.disorder.DisemblTester.testPersistance() compbio.runner.msa.MafftTester.readStatistics() compbio.runner.msa.MafftParametersTester.testDefaultParameters() compbio.runner.conservation.AAConTester.testRunOnClusterAsync() compbio.runner.msa.MafftTester.testSetInputTester() compbio.runner.conservation.AAConTester.testRunLocallyOnTwoCpu() compbio.runner.msa.ClustalWTester.testRunOnCluster() compbio.runner.disorder.GlobPlotTester.readStatistics() compbio.runner.disorder.IUPredTester.testPersistance() compbio.runner.msa.TcoffeeTester.testNcore() compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MuscleTester.testRunLocally() compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters() compbio.runner.msa.ClustalWTester.testRunLocally() compbio.runner.msa.ProbconsParametersTester.testOptions() compbio.runner.disorder.GlobPlotTester.testRunOnClusterAsync() compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MuscleParametersTester.testDefaultParameters() compbio.runner.conservation.AAConTester.readStatistics() compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MuscleTester.testRunOnCluster() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.ClustalWParametersTester.testDefaultParameters() compbio.runner.msa.MuscleTester.testConfigurationLoading() compbio.runner.disorder.IUPredTester.testReadResults() compbio.runner.msa.MafftParametersTester.testPresets() compbio.runner.msa.TcoffeeTester.testExecute() compbio.runner.msa.MuscleTester.readStatistics() compbio.runner.msa.ClustalWParametersTester.testArguments() compbio.runner.msa.TcoffeeParametersTester.testArguments() compbio.runner.conservation.AAConTester.testRunOnCluster() compbio.runner.msa.MuscleParametersTester.testArguments() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.ProbconsTester.testExecute() compbio.runner.disorder.GlobPlotTester.testRunLocally() compbio.runner.conservation.AAConTester.testConfigurationLoading() compbio.runner.msa.TcoffeeTester.testPersistance() compbio.runner.msa.ProbconsTester.testClusterExecute() compbio.runner.msa.TcoffeeParametersTester.testPresets() compbio.runner.msa.MuscleParametersTester.testPresets() compbio.runner.disorder.IUPredTester.testSetParameter() compbio.runner.msa.MafftParametersTester.testArguments() compbio.runner.disorder.GlobPlotTester.testRunOnCluster() compbio.runner.msa.MafftTester.testConfigurationLoading() compbio.runner.msa.ClustalWTester.readStatistics() compbio.runner.msa.ProbconsParametersTester.testParameters() compbio.runner.msa.ProbconsTester.testPersistance() compbio.runner.msa.ClustalWParametersTester.testPresets() compbio.runner.disorder.GlobPlotTester.testConfigurationLoading() compbio.runner.conservation.AAConTester.testRunLocally() compbio.runner.msa.TcoffeeTester.testClusterExecute() compbio.runner.disorder.JronnTester.testPersistance()

diff --git a/website/tests/Ant suite/index.html b/website/tests/Ant suite/index.html new file mode 100644 index 0000000..7c18f73 --- /dev/null +++ b/website/tests/Ant suite/index.html @@ -0,0 +1,6 @@ +Results for Ant suite + + + + + diff --git a/website/tests/Ant suite/main.html b/website/tests/Ant suite/main.html new file mode 100644 index 0000000..0198e44 --- /dev/null +++ b/website/tests/Ant suite/main.html @@ -0,0 +1,2 @@ +Results for Ant suite +Select a result on the left-hand pane. diff --git a/website/tests/Ant suite/methods-alphabetical.html b/website/tests/Ant suite/methods-alphabetical.html new file mode 100644 index 0000000..fa1d655 --- /dev/null +++ b/website/tests/Ant suite/methods-alphabetical.html @@ -0,0 +1,696 @@ +

Methods run, sorted chronologically

>> means before, << means after

Ant suite

(Hover the method name to see the test class name)

Methods that were not run

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +

compbio.ws.client.WSTesterTester.testAllWindowsWS

compbio.ws.server.RegistryWSTester.testTestService

compbio.runner._impl.RPSBlastTester.testBuildCommand

compbio.stat.collector.ExecutionStatCollectorTester.testHasTimedOut

compbio.ws.server.RegistryWSTester.testTestAllServices

compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce

compbio.runner.msa.ClustalWTester.testAddParameters

compbio.runner._impl.MclTester.testBuildCommand

compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusShortPoolingTime

compbio.stat.collector.StatDBTester.testGetEarliestRecord

compbio.ws.server.RegistryWSTester.testIsOperating

compbio.ws.server.RegistryWSTester.testGetSupportedServices

compbio.ws.client.TestAAConWS.testAnalize

compbio.ws.client.WSTesterTester.testAllWS

compbio.runner._impl.OBTester.testBuildCommand

compbio.stat.collector.StatDBTester.testReadYearData

compbio.runner.msa.MuscleTester.testRunOnClusterAsync

compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes

compbio.runner._impl.Tmhmm2Tester.testBuildCommand

compbio.ws.server.RegistryWSTester.testGetLastTestedOn

compbio.ws.client.TestAAConWS.testCustomAnalize

compbio.engine.conf.DirectoryManagerTester.testNanoTime

compbio.ws.client.TestAAConWS.testPresetAnalize

compbio.ws.server.RegistryWSTester.testGetLastTested

compbio.runner._impl.NetNglycTester.testBuildCommand

compbio.runner._impl.RonnTester.testBuildCommand

compbio.stat.collector.StatDBTester.testReadOneMonthData

\ No newline at end of file diff --git a/website/tests/Ant suite/methods.html b/website/tests/Ant suite/methods.html new file mode 100644 index 0000000..b7e84ad --- /dev/null +++ b/website/tests/Ant suite/methods.html @@ -0,0 +1,696 @@ +

Methods run, sorted chronologically

>> means before, << means after

Ant suite

(Hover the method name to see the test class name)

Reporter output

\ No newline at end of file diff --git a/website/tests/Ant suite/testng-failed.xml b/website/tests/Ant suite/testng-failed.xml new file mode 100644 index 0000000..e3d6ed0 --- /dev/null +++ b/website/tests/Ant suite/testng-failed.xml @@ -0,0 +1,131 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/tests/Ant suite/testng.xml.html b/website/tests/Ant suite/testng.xml.html new file mode 100644 index 0000000..fedf3bc --- /dev/null +++ b/website/tests/Ant suite/testng.xml.html @@ -0,0 +1 @@ +testng.xml for Ant suite<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"> <suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Ant suite" junit="false" annotations="JDK" data-provider-thread-count="10"> <test name="Ant test" junit="false"> <groups> <run> <exclude name="performance"/> <exclude name="webservices"/> </run> </groups> <classes> <class name="compbio.data._structure.JnetAnnotation$AType"/> <class name="compbio.data._structure.JnetAnnotation"/> <class name="compbio.data._structure.JpredAnnotation"/> <class name="compbio.data._structure.JpredResult"/> <class name="compbio.data.msa.JABAService"/> <class name="compbio.data.msa.JManagement"/> <class name="compbio.data.msa.Metadata"/> <class name="compbio.data.msa.MsaWS"/> <class name="compbio.data.msa.RegistryWS"/> <class name="compbio.data.msa.SequenceAnnotation"/> <class name="compbio.data.msa.jaxws.Align"/> <class name="compbio.data.msa.jaxws.AlignResponse"/> <class name="compbio.data.msa.jaxws.Analize"/> <class name="compbio.data.msa.jaxws.AnalizeResponse"/> <class name="compbio.data.msa.jaxws.CancelJob"/> <class name="compbio.data.msa.jaxws.CancelJobResponse"/> <class name="compbio.data.msa.jaxws.CustomAlign"/> <class name="compbio.data.msa.jaxws.CustomAlignResponse"/> <class name="compbio.data.msa.jaxws.CustomAnalize"/> <class name="compbio.data.msa.jaxws.CustomAnalizeResponse"/> <class name="compbio.data.msa.jaxws.GetAnnotation"/> <class name="compbio.data.msa.jaxws.GetAnnotationResponse"/> <class name="compbio.data.msa.jaxws.GetConservation"/> <class name="compbio.data.msa.jaxws.GetConservationResponse"/> <class name="compbio.data.msa.jaxws.GetJobStatus"/> <class name="compbio.data.msa.jaxws.GetJobStatusResponse"/> <class name="compbio.data.msa.jaxws.GetLastTested"/> <class name="compbio.data.msa.jaxws.GetLastTestedOn"/> <class name="compbio.data.msa.jaxws.GetLastTestedOnResponse"/> <class name="compbio.data.msa.jaxws.GetLastTestedResponse"/> <class name="compbio.data.msa.jaxws.GetLimit"/> <class name="compbio.data.msa.jaxws.GetLimitResponse"/> <class name="compbio.data.msa.jaxws.GetLimits"/> <class name="compbio.data.msa.jaxws.GetLimitsResponse"/> <class name="compbio.data.msa.jaxws.GetPresets"/> <class name="compbio.data.msa.jaxws.GetPresetsResponse"/> <class name="compbio.data.msa.jaxws.GetResult"/> <class name="compbio.data.msa.jaxws.GetResultResponse"/> <class name="compbio.data.msa.jaxws.GetRunnerOptions"/> <class name="compbio.data.msa.jaxws.GetRunnerOptionsResponse"/> <class name="compbio.data.msa.jaxws.GetSupportedServices"/> <class name="compbio.data.msa.jaxws.GetSupportedServicesResponse"/> <class name="compbio.data.msa.jaxws.IsOperating"/> <class name="compbio.data.msa.jaxws.IsOperatingResponse"/> <class name="compbio.data.msa.jaxws.JobSubmissionExceptionBean"/> <class name="compbio.data.msa.jaxws.LimitExceededExceptionBean"/> <class name="compbio.data.msa.jaxws.PresetAlign"/> <class name="compbio.data.msa.jaxws.PresetAlignResponse"/> <class name="compbio.data.msa.jaxws.PresetAnalize"/> <class name="compbio.data.msa.jaxws.PresetAnalizeResponse"/> <class name="compbio.data.msa.jaxws.PullExecStatistics"/> <class name="compbio.data.msa.jaxws.PullExecStatisticsResponse"/> <class name="compbio.data.msa.jaxws.ResultNotAvailableExceptionBean"/> <class name="compbio.data.msa.jaxws.TestAllServices"/> <class name="compbio.data.msa.jaxws.TestAllServicesResponse"/> <class name="compbio.data.msa.jaxws.TestService"/> <class name="compbio.data.msa.jaxws.TestServiceResponse"/> <class name="compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean"/> <class name="compbio.data.msa.jaxws.WrongParameterExceptionBean"/> <class name="compbio.data.sequence.Alignment"/> <class name="compbio.data.sequence.AlignmentMetadata"/> <class name="compbio.data.sequence.ClustalAlignmentUtil"/> <class name="compbio.data.sequence.ClustalAlignmentUtilTester"/> <class name="compbio.data.sequence.ConservationMethod"/> <class name="compbio.data.sequence.DisemblResult"/> <class name="compbio.data.sequence.DisorderMethod"/> <class name="compbio.data.sequence.FastaGeneratorManager"/> <class name="compbio.data.sequence.FastaReader$1"/> <class name="compbio.data.sequence.FastaReader"/> <class name="compbio.data.sequence.FastaReaderTester"/> <class name="compbio.data.sequence.FastaSequence"/> <class name="compbio.data.sequence.FastaSequenceGenerator$1"/> <class name="compbio.data.sequence.FastaSequenceGenerator$DNAAlphabet"/> <class name="compbio.data.sequence.FastaSequenceGenerator$Letters"/> <class name="compbio.data.sequence.FastaSequenceGenerator$ProteinAlphabet"/> <class name="compbio.data.sequence.FastaSequenceGenerator$SeqType"/> <class name="compbio.data.sequence.FastaSequenceGenerator"/> <class name="compbio.data.sequence.FastaSequenceGeneratorTester"/> <class name="compbio.data.sequence.FastaSequenceTester"/> <class name="compbio.data.sequence.GlobProtResult"/> <class name="compbio.data.sequence.IUPredResult"/> <class name="compbio.data.sequence.Program"/> <class name="compbio.data.sequence.Range"/> <class name="compbio.data.sequence.SMERFSConstraints"/> <class name="compbio.data.sequence.Score"/> <class name="compbio.data.sequence.ScoreManager$ScoreHolder"/> <class name="compbio.data.sequence.ScoreManager"/> <class name="compbio.data.sequence.SequenceUtil"/> <class name="compbio.data.sequence.SequenceUtilTester$Trial"/> <class name="compbio.data.sequence.SequenceUtilTester"/> <class name="compbio.data.sequence.UnknownFileFormatException"/> <class name="compbio.engine.AsyncExecutor"/> <class name="compbio.engine.Cleaner"/> <class name="compbio.engine.ClusterJobId"/> <class name="compbio.engine.Configurator"/> <class name="compbio.engine.EngineConfiguratorTester"/> <class name="compbio.engine.FilePuller"/> <class name="compbio.engine.FilePullerTester"/> <class name="compbio.engine.Job"/> <class name="compbio.engine.LoadBalancer"/> <class name="compbio.engine.LoadBalancerTester"/> <class name="compbio.engine.ProgressGetter"/> <class name="compbio.engine.PulledFileCache"/> <class name="compbio.engine.PulledFileCacheTester"/> <class name="compbio.engine.SubmissionManager"/> <class name="compbio.engine.SyncExecutor"/> <class name="compbio.engine.client.CommandBuilder$Parameter"/> <class name="compbio.engine.client.CommandBuilder"/> <class name="compbio.engine.client.CommandBuilderTester"/> <class name="compbio.engine.client.ConfExecutable"/> <class name="compbio.engine.client.ConfiguredExecutable"/> <class name="compbio.engine.client.EnvVariableProcessor"/> <class name="compbio.engine.client.Executable$ExecProvider"/> <class name="compbio.engine.client.Executable"/> <class name="compbio.engine.client.PathValidator"/> <class name="compbio.engine.client.PathValidatorTester"/> <class name="compbio.engine.client.PipedExecutable"/> <class name="compbio.engine.client.RunConfiguration"/> <class name="compbio.engine.client.SkeletalExecutable"/> <class name="compbio.engine.client.Util"/> <class name="compbio.engine.cluster.drmaa.AsyncJobRunner"/> <class name="compbio.engine.cluster.drmaa.ClusterSession$1"/> <class name="compbio.engine.cluster.drmaa.ClusterSession"/> <class name="compbio.engine.cluster.drmaa.ClusterSessionTester"/> <class name="compbio.engine.cluster.drmaa.ClusterUtil"/> <class name="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/> <class name="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/> <class name="compbio.engine.cluster.drmaa.JobRunner"/> <class name="compbio.engine.cluster.drmaa.StatisticManager"/> <class name="compbio.engine.cluster.drmaa.UtilTester"/> <class name="compbio.engine.cluster.drmaa._DrmaaExample"/> <class name="compbio.engine.cluster.drmaa._JobStatus"/> <class name="compbio.engine.cluster.dundee._Queue$1"/> <class name="compbio.engine.cluster.dundee._Queue"/> <class name="compbio.engine.cluster.dundee._QueueConstraints"/> <class name="compbio.engine.cluster.dundee._QueueTester"/> <class name="compbio.engine.conf.DirectoryManager"/> <class name="compbio.engine.conf.DirectoryManagerTester"/> <class name="compbio.engine.conf.PropertyHelperManager"/> <class name="compbio.engine.conf.PropertyHelperManagerTester"/> <class name="compbio.engine.conf.RunnerConfigMarshaller$MySchemaOutputResolver"/> <class name="compbio.engine.conf.RunnerConfigMarshaller"/> <class name="compbio.engine.conf.RunnerConfigMarshallerTester"/> <class name="compbio.engine.conf._Key"/> <class name="compbio.engine.local.AsyncLocalRunner"/> <class name="compbio.engine.local.AsyncLocalRunnerTester"/> <class name="compbio.engine.local.EngineResourcesLeakTester"/> <class name="compbio.engine.local.ExecutableWrapper$1"/> <class name="compbio.engine.local.ExecutableWrapper"/> <class name="compbio.engine.local.LocalEngineUtil"/> <class name="compbio.engine.local.LocalExecutorService$1"/> <class name="compbio.engine.local.LocalExecutorService"/> <class name="compbio.engine.local.LocalRunner"/> <class name="compbio.engine.local.LocalRunnerTester"/> <class name="compbio.engine.local.StreamGobbler$OutputType"/> <class name="compbio.engine.local.StreamGobbler"/> <class name="compbio.engine.local._TrackingExecutor$1"/> <class name="compbio.engine.local._TrackingExecutor$2"/> <class name="compbio.engine.local._TrackingExecutor"/> <class name="compbio.metadata.AllTestSuit"/> <class name="compbio.metadata.Argument"/> <class name="compbio.metadata.ChunkHolder"/> <class name="compbio.metadata.JobExecutionException"/> <class name="compbio.metadata.JobStatus"/> <class name="compbio.metadata.JobSubmissionException"/> <class name="compbio.metadata.Limit"/> <class name="compbio.metadata.LimitExceededException"/> <class name="compbio.metadata.LimitsManager"/> <class name="compbio.metadata.Option"/> <class name="compbio.metadata.OptionCombinatorTester"/> <class name="compbio.metadata.OptionMarshallerTester"/> <class name="compbio.metadata.Parameter"/> <class name="compbio.metadata.Preset"/> <class name="compbio.metadata.PresetManager"/> <class name="compbio.metadata.PresetTester"/> <class name="compbio.metadata.ResultNotAvailableException"/> <class name="compbio.metadata.RunnerConfig"/> <class name="compbio.metadata.RunnerConfigTester"/> <class name="compbio.metadata.UnsupportedRuntimeException"/> <class name="compbio.metadata.ValueConstrain$1"/> <class name="compbio.metadata.ValueConstrain$Type"/> <class name="compbio.metadata.ValueConstrain"/> <class name="compbio.metadata.WrongParameterException"/> <class name="compbio.pipeline._jpred.BlastBlastComparator"/> <class name="compbio.pipeline._jpred.BlastHmmerComparator"/> <class name="compbio.pipeline._jpred.BlastParser"/> <class name="compbio.pipeline._jpred.Hit$EvalueComporator"/> <class name="compbio.pipeline._jpred.Hit$NumberComporator"/> <class name="compbio.pipeline._jpred.Hit"/> <class name="compbio.pipeline._jpred.JackHmmerHitParser"/> <class name="compbio.pipeline._jpred.Jpred4"/> <class name="compbio.pipeline._jpred.PScore"/> <class name="compbio.pipeline._jpred.Pairwise"/> <class name="compbio.runner.OptionCombinator"/> <class name="compbio.runner.Util"/> <class name="compbio.runner._NativeSpecHelper"/> <class name="compbio.runner._SkeletalCommandBuilder"/> <class name="compbio.runner._impl.BlastAll$blastType"/> <class name="compbio.runner._impl.BlastAll$dataBase"/> <class name="compbio.runner._impl.BlastAll"/> <class name="compbio.runner._impl.BlastParameters"/> <class name="compbio.runner._impl.Environment"/> <class name="compbio.runner._impl.Mcl"/> <class name="compbio.runner._impl.MclTester"/> <class name="compbio.runner._impl.NetNglyc"/> <class name="compbio.runner._impl.NetNglycTester"/> <class name="compbio.runner._impl.OB"/> <class name="compbio.runner._impl.OBTester"/> <class name="compbio.runner._impl.PSIBlast$blastType"/> <class name="compbio.runner._impl.PSIBlast$dataBase"/> <class name="compbio.runner._impl.PSIBlast"/> <class name="compbio.runner._impl.RPSBlast$DB"/> <class name="compbio.runner._impl.RPSBlast"/> <class name="compbio.runner._impl.RPSBlastTester"/> <class name="compbio.runner._impl.Ronn"/> <class name="compbio.runner._impl.RonnTester"/> <class name="compbio.runner._impl.Runners"/> <class name="compbio.runner._impl.Tmhmm2"/> <class name="compbio.runner._impl.Tmhmm2Tester"/> <class name="compbio.runner._jpred._Jpred"/> <class name="compbio.runner.conservation.AACon"/> <class name="compbio.runner.conservation.AAConTester"/> <class name="compbio.runner.disorder.Disembl"/> <class name="compbio.runner.disorder.DisemblTester"/> <class name="compbio.runner.disorder.GlobPlot"/> <class name="compbio.runner.disorder.GlobPlotTester"/> <class name="compbio.runner.disorder.IUPred"/> <class name="compbio.runner.disorder.IUPredTester"/> <class name="compbio.runner.disorder.Jronn"/> <class name="compbio.runner.disorder.JronnTester"/> <class name="compbio.runner.msa.ClustalW"/> <class name="compbio.runner.msa.ClustalWParametersTester"/> <class name="compbio.runner.msa.ClustalWTester"/> <class name="compbio.runner.msa.LimitTester"/> <class name="compbio.runner.msa.Mafft"/> <class name="compbio.runner.msa.MafftParametersTester"/> <class name="compbio.runner.msa.MafftTester"/> <class name="compbio.runner.msa.Muscle"/> <class name="compbio.runner.msa.MuscleParametersTester"/> <class name="compbio.runner.msa.MuscleTester"/> <class name="compbio.runner.msa.Probcons"/> <class name="compbio.runner.msa.ProbconsParametersTester"/> <class name="compbio.runner.msa.ProbconsTester"/> <class name="compbio.runner.msa.Tcoffee"/> <class name="compbio.runner.msa.TcoffeeParametersTester"/> <class name="compbio.runner.msa.TcoffeeTester"/> <class name="compbio.runner.psiblast.PsiBlast"/> <class name="compbio.stat.collector.ExecutionStatCollector$1"/> <class name="compbio.stat.collector.ExecutionStatCollector$JobDirectory"/> <class name="compbio.stat.collector.ExecutionStatCollector"/> <class name="compbio.stat.collector.ExecutionStatCollectorTester"/> <class name="compbio.stat.collector.JobStat$1"/> <class name="compbio.stat.collector.JobStat$2"/> <class name="compbio.stat.collector.JobStat$3"/> <class name="compbio.stat.collector.JobStat"/> <class name="compbio.stat.collector.StatDB"/> <class name="compbio.stat.collector.StatDBTester"/> <class name="compbio.stat.collector.StatProcessor"/> <class name="compbio.stat.servlet.AnnualStat"/> <class name="compbio.stat.servlet.DisplayStat"/> <class name="compbio.stat.servlet.Joblist"/> <class name="compbio.stat.servlet.StatisticCollector"/> <class name="compbio.stat.servlet.util.StatCollection$Stattype"/> <class name="compbio.stat.servlet.util.StatCollection"/> <class name="compbio.stat.servlet.util.StatCollectionTester"/> <class name="compbio.stat.servlet.util.Totals"/> <class name="compbio.ws.client.AAConClient"/> <class name="compbio.ws.client.AAConWSClientExample"/> <class name="compbio.ws.client.CmdHelper"/> <class name="compbio.ws.client.Constraints"/> <class name="compbio.ws.client.IOHelper"/> <class name="compbio.ws.client.Jws2Client"/> <class name="compbio.ws.client.MetadataHelper"/> <class name="compbio.ws.client.Services$1"/> <class name="compbio.ws.client.Services"/> <class name="compbio.ws.client.TestAAConWS"/> <class name="compbio.ws.client.WSTester"/> <class name="compbio.ws.client.WSTesterTester"/> <class name="compbio.ws.server.AAConWS"/> <class name="compbio.ws.server.ClustalWS"/> <class name="compbio.ws.server.DisemblWS"/> <class name="compbio.ws.server.GenericMetadataService"/> <class name="compbio.ws.server.GlobPlotWS"/> <class name="compbio.ws.server.IUPredWS"/> <class name="compbio.ws.server.JronnWS"/> <class name="compbio.ws.server.MafftWS"/> <class name="compbio.ws.server.MuscleWS"/> <class name="compbio.ws.server.ProbconsWS"/> <class name="compbio.ws.server.RegistryWS"/> <class name="compbio.ws.server.RegistryWSTester"/> <class name="compbio.ws.server.SequenceAnnotationService"/> <class name="compbio.ws.server.ShutdownEngines"/> <class name="compbio.ws.server.SimpleWSPublisher"/> <class name="compbio.ws.server.TcoffeeWS"/> <class name="compbio.ws.server.WSUtil"/> <class name="compbio.ws.server._MsaService"/> <class name="compbio.ws.server._WSLogger"/> </classes> </test> </suite> \ No newline at end of file diff --git a/website/tests/Ant suite/toc.html b/website/tests/Ant suite/toc.html new file mode 100644 index 0000000..f379739 --- /dev/null +++ b/website/tests/Ant suite/toc.html @@ -0,0 +1,30 @@ + + +Results for Ant suite + + + + +

Results for
Ant suite

+ + + + + + + + + + +

1 test	50 classes	205 methods: + chronological + alphabetical + not run (27)
4 groups	reporter output	testng.xml

+ +

Ant test (216/0/0)

+ Results +

+ \ No newline at end of file diff --git a/website/tests/emailable-report.html b/website/tests/emailable-report.html new file mode 100644 index 0000000..97fda3c --- /dev/null +++ b/website/tests/emailable-report.html @@ -0,0 +1,738 @@ + + + +TestNG: Unit Test + + + + + + +

Test	Methods Passed	Scenarios Passed	# skipped	# failed	Total Time	Included Groups	Excluded Groups
Ant test	205	216	0	0	453.9 seconds		webservices performance

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Class	Method	# of Scenarios	Time (Msecs)
Ant test — passed
compbio.data.sequence.ClustalAlignmentUtilTester	testReadClustalFile	1	12
	testReadClustalFileLongNames	1	19
	testReadClustalFileShortNames	1	14
compbio.data.sequence.FastaReaderTester	test	1	18
compbio.data.sequence.FastaSequenceGeneratorTester	testProteinSequenceGeneration	1	7
compbio.data.sequence.FastaSequenceTester	testGetFormattedFasta	1	0
compbio.data.sequence.SequenceUtilTester	loadJronnFile	1	27
	testCleanProteinSequence	1	1
	testCleanSequence	1	0
	testDeepCleanSequence	1	0
	testReadAAConResults	1	269
	testReadDisemblResults	1	125
	testReadGlobPlotResults	1	104
	testReadIUPredForGlobDomain	1	6
	testReadIUPredForShortAndLongDisorder	1	36
	testReadWriteFasta	1	8
	testisNonAmbNucleotideSequence	1	1
	testisProteinSequence	1	0
compbio.engine.EngineConfiguratorTester	testGetAsyncEngine	1	12
compbio.engine.EngineConfiguratorTester	testGetSyncEngine	1	1
compbio.engine.FilePullerTester	testCache (engine)	1	6008
	testGet	1	2
	testGetDelay (engine)	1	0
	testPull (engine)	1	14
compbio.engine.LoadBalancerTester	testLoadBalance	1	57
compbio.engine.PulledFileCacheTester	test	1	5011
compbio.engine.client.CommandBuilderTester	testCommandBuilding	1	1
	testOptionsToCommand	1	40
	testSpaceDelimiterExecutable	1	0
compbio.engine.client.PathValidatorTester	testGetClassPath	1	1
compbio.engine.client.PathValidatorTester	testIsAbsolutePath	1	0
compbio.engine.cluster.drmaa.ClusterSessionTester	testTaskList (engine, cluster)	1	3953
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester	testCancel (engine, cluster)	1	1257
	testGetJobStatus (engine, cluster)	1	4765
	testSubmit (engine, cluster)	1	3976
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester	testCancel (engine, cluster)	1	1538
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester	testSubmit (engine, cluster)	1	3508
compbio.engine.cluster.drmaa.UtilTester	testParser	1	1
compbio.engine.cluster.dundee._QueueTester	testQueue	1	0
compbio.engine.conf.DirectoryManagerTester	testGetDirectory	4	105
compbio.engine.conf.PropertyHelperManagerTester	testClusterEngineConf (cluster)	1	1
	validateClustalConfiguration	1	0
	validateMafftConfiguration	1	2
	validateMuscleConfiguration	1	0
	validateTcoffeeConfiguration	1	0
compbio.engine.conf.RunnerConfigMarshallerTester	testMarshalling	1	4
	testSchemaFromCodeGeneration	1	130
	testUnMarshalling	1	17
	testValidation	1	82
	testValidationOnMarshalling	1	10
compbio.engine.local.AsyncLocalRunnerTester	testAsyncCancelOperation (engine)	1	17
	testAsyncRetrievOperation (engine)	1	124
	testCancelCompletedTaskLocally (engine)	1	3017
	testCancelLocally (engine)	1	13
	testGetStatus (engine)	5	38622
	testMultipleCancelLocally (engine)	1	54
	testSubmitLocally (engine)	5	229
compbio.engine.local.LocalRunnerTester	testCancelCompletedTaskLocally (engine)	1	49
	testCancelLocally (engine)	1	17
	testMultipleCancelLocally (engine)	1	44
compbio.metadata.OptionCombinatorTester	testgetAllOptions	1	1
compbio.metadata.OptionCombinatorTester	testgetAllParameters	1	3
compbio.metadata.OptionMarshallerTester	testMarshalling	1	33
compbio.metadata.OptionMarshallerTester	testUnMarshalling	1	65
compbio.metadata.PresetTester	marshallPreset	1	14
	testPresetWithMuptiOptions	1	1
	validatePresets	1	1
compbio.metadata.RunnerConfigTester	testCreateNumParameterWithoutValidValue	1	0
	testCreateParameter	1	0
	testCreateParameterWithValidValueConstrain	1	0
	testOptionNoDefaultValidate	1	0
	testOptionSetInvalidValue	1	0
	testOptionToCommand	1	0
	testParameterToCommand	1	0
	testValidate	1	0
	testValidateBoundaryConstrainCheck	1	0
	testValidateLowerBoundaryConstrainCheck	1	0
	testValidateUpperBoundaryConstrainCheck	1	1
	testValidateValueConstrain	1	0
compbio.runner._impl.MclTester	testGetTestCommand	1	0
compbio.runner._impl.NetNglycTester	testGetTestCommand	1	1
compbio.runner._impl.OBTester	testGetTestArgsCommand	1	0
compbio.runner._impl.OBTester	testGetTestCommand	1	0
compbio.runner._impl.RPSBlastTester	testGetTestArgsCommand	1	0
compbio.runner._impl.RPSBlastTester	testGetTestCommand	1	0
compbio.runner._impl.RonnTester	testGetTestCommand	1	0
compbio.runner._impl.Tmhmm2Tester	testGetTestCommand	1	0
compbio.runner.conservation.AAConTester	readStatistics (runner)	1	1493
	testConfigurationLoading (runner)	1	113
	testPersistance (runner)	1	775
	testRunLocally (runner)	1	827
	testRunLocallyOnTwoCpu (runner)	1	289
	testRunLocallyWithPreset (runner)	1	653
	testRunOnCluster (runner)	1	3640
	testRunOnClusterAsync (cluster, runner)	1	5018
compbio.runner.disorder.DisemblTester	readStatistics (runner)	1	0
	testConfigurationLoading (runner)	1	44
	testPersistance (runner)	1	1297
	testRunLocally (runner)	1	579
	testRunOnCluster (cluster, runner)	1	2047
	testRunOnClusterAsync (cluster, runner)	1	6011
compbio.runner.disorder.GlobPlotTester	readStatistics (runner)	1	0
	testConfigurationLoading (runner)	1	43
	testPersistance (runner)	1	980
	testRunLocally (runner)	1	454
	testRunOnCluster (cluster, runner)	1	2503
	testRunOnClusterAsync (cluster, runner)	1	6021
compbio.runner.disorder.IUPredTester	testConfigurationLoading (runner)	1	69
	testPersistance (runner)	1	308
	testReadResults (runner)	1	25
	testRunLocally (runner)	1	196
	testRunLocallyWithParams (runner)	1	71
	testRunOnCluster (cluster, runner)	1	3308
	testRunOnClusterAsync (cluster, runner)	1	6025
	testSetParameter (runner)	1	0
compbio.runner.disorder.JronnTester	readStatistics (runner)	1	18639
	testConfigurationLoading (runner)	1	45
	testPersistance (runner)	1	18613
	testRunLocally (runner)	1	18541
	testRunLocallyOnTwoCpu (runner)	1	7131
	testRunOnCluster (cluster, runner)	1	13058
	testRunOnClusterAsync (cluster, runner)	1	11022
compbio.runner.msa.ClustalWParametersTester	testArguments (runner)	1	1649
	testConfiguration	1	1
	testConstrainedParametersMaxValues (runner)	1	678
	testConstrainedParametersMinValues (runner)	1	682
	testConstrainedParametersRandomValues (runner)	1	672
	testDefaultParameters (runner)	1	129
	testOptions (runner)	1	396
	testParameters (runner)	1	1074
	testPresets (runner)	1	129
compbio.runner.msa.ClustalWTester	readStatistics (runner)	1	518
	readStatisticsClusterExecution (cluster, runner)	1	1640
	testConfigurationLoading (runner)	1	46
	testOptionsLocally (runner)	1	429
	testPersistance (runner)	1	303
	testRunLocally (runner)	1	132
	testRunOnCluster (cluster, runner)	1	5003
	testRunWithMatrix (runner)	1	130
compbio.runner.msa.LimitTester	testLimitExceeded	1	14
compbio.runner.msa.LimitTester	testLoadLimits	1	0
compbio.runner.msa.MafftParametersTester	testArguments (runner, non_windows)	1	3027
	testConfiguration	1	0
	testConstrainedParametersMaxValues (runner, non_windows)	1	1461
	testConstrainedParametersMinValues (runner, non_windows)	1	886
	testConstrainedParametersRandomValues (runner, non_windows)	1	3530
	testDefaultParameters (runner, non_windows)	1	4507
	testOptions (runner, non_windows)	1	971
	testParameters (runner, non_windows)	1	1179
	testPresets (runner, non_windows)	1	965
compbio.runner.msa.MafftTester	readStatistics (runner, non_windows)	1	516
	testClusterExecute (cluster, runner, non_windows)	1	1264
	testConfigurationLoading (runner)	1	62
	testExecute (runner, non_windows)	1	162
	testPersistance (runner, non_windows)	1	305
	testRunOnClusterAsyncCheckStatusLongPoolingTime (cluster, runner, non_windows)	1	5535
	testSetInputTester (runner, non_windows)	1	0
compbio.runner.msa.MuscleParametersTester	testArguments (runner)	1	4387
	testConfiguration	1	1
	testConstrainedParametersMaxValues (runner)	1	1977
	testConstrainedParametersMinValues (runner)	1	1112
	testConstrainedParametersRandomValues (runner)	1	2749
	testDefaultParameters (runner)	1	100
	testOptions (runner)	1	1360
	testParameters (runner)	1	1919
	testPresets (runner)	1	242
compbio.runner.msa.MuscleTester	readStatistics (runner)	1	520
	testConfigurationLoading (runner)	1	43
	testPersistance (runner)	1	233
	testRunLocally (runner)	1	100
	testRunOnCluster (cluster, runner)	1	3867
compbio.runner.msa.ProbconsParametersTester	testArguments (runner, non_windows)	1	1819
	testConfiguration	1	0
	testConstrainedParametersMaxValues (runner, non_windows)	1	37102
	testConstrainedParametersMinValues (runner, non_windows)	1	768
	testConstrainedParametersRandomValues (runner, non_windows)	1	70319
	testDefaultParameters (runner, non_windows)	1	4845
	testOptions (runner, non_windows)	1	443
	testParameters (runner, non_windows)	1	1344
compbio.runner.msa.ProbconsTester	readStatistics (runner, non_windows)	1	455
	testClusterExecute (cluster, runner, non_windows)	1	2710
	testConfigurationLoading (runner)	1	89
	testExecute (runner, non_windows)	1	455
	testPersistance (runner, non_windows)	1	527
	testSetInputTester (runner, non_windows)	1	0
compbio.runner.msa.TcoffeeParametersTester	testArguments (runner, non_windows)	1	4098
	testConfiguration	1	0
	testConstrainedParametersMaxValues (runner, non_windows)	1	4319
	testConstrainedParametersMinValues (runner, non_windows)	1	2887
	testConstrainedParametersRandomValues (runner, non_windows)	1	8762
	testDefaultParameters (runner, non_windows)	1	3850
	testOptions (runner, non_windows)	1	377
	testParameters (runner, non_windows)	1	3800
	testPresets (runner, non_windows)	1	214
compbio.runner.msa.TcoffeeTester	readStatistics (runner, non_windows)	1	516
	testClusterExecute (cluster, runner, non_windows)	1	5084
	testConfigurationLoading (runner)	1	39
	testExecute (runner, non_windows)	1	364
	testNcore (runner, non_windows)	1	0
	testPersistance (cluster, runner, non_windows)	1	769
compbio.stat.collector.ExecutionStatCollectorTester	testCollectStat	1	271
	testHasCompleted	1	1
	testUpdateStatTester	1	35012
compbio.stat.collector.StatDBTester	testVerifyJobsCount	1	412
compbio.stat.servlet.util.StatCollectionTester "Ant test"	testGetStats	1	22

Time	Delta (ms)	Test configuration	Class configuration	Method configuration	Test method	Thread
11/06/23 10:34:54	0	>>init				main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:22	88022			>>init		main@1225898256
11/06/23 10:36:31	97012			>>init		main@1225898256
11/06/23 10:36:31	97012			>>init		main@1225898256
11/06/23 10:36:31	97012			>>init		main@1225898256
11/06/23 10:36:31	97012			>>init		main@1225898256
11/06/23 10:36:31	97012			>>init		main@1225898256
11/06/23 10:36:31	97012			>>init		main@1225898256
11/06/23 10:36:41	107005			>>init		main@1225898256
11/06/23 10:36:41	107005			>>init		main@1225898256
11/06/23 10:36:41	107005			>>init		main@1225898256
11/06/23 10:36:41	107005			>>init		main@1225898256
11/06/23 10:36:41	107005			>>init		main@1225898256
11/06/23 10:36:41	107005			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:36:57	123031			>>init		main@1225898256
11/06/23 10:38:13	199064			>>init		main@1225898256
11/06/23 10:38:13	199064			>>init		main@1225898256
11/06/23 10:38:13	199064			>>init		main@1225898256
11/06/23 10:38:13	199064			>>init		main@1225898256
11/06/23 10:38:13	199064			>>init		main@1225898256
11/06/23 10:38:13	199064			>>init		main@1225898256
11/06/23 10:38:13	199064			>>init		main@1225898256
11/06/23 10:38:57	243086			>>init		main@1225898256
11/06/23 10:38:57	243086			>>init		main@1225898256
11/06/23 10:38:57	243086			>>init		main@1225898256
11/06/23 10:38:57	243086			>>init		main@1225898256
11/06/23 10:38:57	243086			>>init		main@1225898256
11/06/23 10:38:57	243086			>>init		main@1225898256
11/06/23 10:38:57	243086			>>init		main@1225898256
11/06/23 10:39:12	258166			>>init		main@1225898256
11/06/23 10:39:12	258166			>>init		main@1225898256
11/06/23 10:39:12	258166			>>init		main@1225898256
11/06/23 10:39:12	258166			>>init		main@1225898256
11/06/23 10:39:12	258166			>>init		main@1225898256
11/06/23 10:41:17	383100			>>init		main@1225898256
11/06/23 10:41:17	383100			>>init		main@1225898256
11/06/23 10:41:17	383100			>>init		main@1225898256
11/06/23 10:41:17	383100			>>init		main@1225898256
11/06/23 10:41:17	383100			>>init		main@1225898256
11/06/23 10:41:17	383100			>>init		main@1225898256
11/06/23 10:41:51	417418			>>init		main@1225898256
11/06/23 10:41:51	417418			>>init		main@1225898256
11/06/23 10:41:51	417418			>>init		main@1225898256
11/06/23 10:41:51	417418			>>init		main@1225898256
11/06/23 10:41:51	417418			>>init		main@1225898256
11/06/23 10:41:51	417418			>>init		main@1225898256
11/06/23 10:42:27	453471		>>init			main@1225898256
11/06/23 10:35:06	12349				loadJronnFile	main@1225898256
11/06/23 10:34:54	295	>>loadPresets				main@1225898256
11/06/23 10:36:14	80044				marshallPreset	main@1225898256
11/06/23 10:36:14	80227				readStatistics	main@1225898256
11/06/23 10:36:27	93041				readStatistics	main@1225898256
11/06/23 10:36:37	103023				readStatistics	main@1225898256
11/06/23 10:36:57	123032				readStatistics	main@1225898256
11/06/23 10:38:31	217039				readStatistics	main@1225898256
11/06/23 10:38:49	235241				readStatistics	main@1225898256
11/06/23 10:39:11	257268				readStatistics	main@1225898256
11/06/23 10:41:12	378863				readStatistics	main@1225898256
11/06/23 10:41:45	411411				readStatistics	main@1225898256
11/06/23 10:38:24	210396				readStatisticsClusterExecution	main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:06	12097			>>setup		main@1225898256
11/06/23 10:35:31	37457			>>setup		main@1225898256
11/06/23 10:35:31	37457			>>setup		main@1225898256
11/06/23 10:35:31	37457			>>setup		main@1225898256
11/06/23 10:35:31	37457			>>setup		main@1225898256
11/06/23 10:35:31	37457			>>setup		main@1225898256
11/06/23 10:36:13	79841			>>setup		main@1225898256
11/06/23 10:36:13	79841			>>setup		main@1225898256
11/06/23 10:36:14	79979			>>setup		main@1225898256
11/06/23 10:36:14	79979			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:36:14	80211			>>setup		main@1225898256
11/06/23 10:38:32	218328			>>setup		main@1225898256
11/06/23 10:38:32	218328			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:38:48	234240			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:39:11	256990			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:11	377497			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:41:45	411196			>>setup		main@1225898256
11/06/23 10:35:06	12322				test	main@1225898256
11/06/23 10:35:07	13000				test	main@1225898256
11/06/23 10:35:00	6456				testArguments	main@1225898256
11/06/23 10:38:32	218385				testArguments	main@1225898256
11/06/23 10:38:57	243135				testArguments	main@1225898256
11/06/23 10:39:16	262069				testArguments	main@1225898256
11/06/23 10:41:17	383101				testArguments	main@1225898256
11/06/23 10:35:31	37481				testAsyncCancelOperation	main@1225898256
11/06/23 10:35:31	37498				testAsyncRetrievOperation	main@1225898256
11/06/23 10:34:54	396				testCache	main@1225898256
11/06/23 10:35:16	22007				testCancel	main@1225898256
11/06/23 10:35:26	32005				testCancel	main@1225898256
11/06/23 10:35:31	37623				testCancelCompletedTaskLocally	main@1225898256
11/06/23 10:36:13	79596				testCancelCompletedTaskLocally	main@1225898256
11/06/23 10:35:34	40640				testCancelLocally	main@1225898256
11/06/23 10:36:13	79645				testCancelLocally	main@1225898256
11/06/23 10:35:06	12376				testCleanProteinSequence	main@1225898256
11/06/23 10:35:06	12377				testCleanSequence	main@1225898256
11/06/23 10:35:31	37164				testClusterEngineConf	main@1225898256
11/06/23 10:38:49	235757				testClusterExecute	main@1225898256
11/06/23 10:41:13	379318				testClusterExecute	main@1225898256
11/06/23 10:41:46	411928				testClusterExecute	main@1225898256
11/06/23 10:41:52	418187				testCollectStat	main@1225898256
11/06/23 10:35:12	18011				testCommandBuilding	main@1225898256
11/06/23 10:35:02	8158				testConfiguration	main@1225898256
11/06/23 10:38:35	221480				testConfiguration	main@1225898256
11/06/23 10:39:01	247559				testConfiguration	main@1225898256
11/06/23 10:39:17	263910				testConfiguration	main@1225898256
11/06/23 10:41:21	387200				testConfiguration	main@1225898256
11/06/23 10:36:15	81721				testConfigurationLoading	main@1225898256
11/06/23 10:36:27	93041				testConfigurationLoading	main@1225898256
11/06/23 10:36:37	103024				testConfigurationLoading	main@1225898256
11/06/23 10:36:47	113026				testConfigurationLoading	main@1225898256
11/06/23 10:37:15	141672				testConfigurationLoading	main@1225898256
11/06/23 10:38:24	210218				testConfigurationLoading	main@1225898256
11/06/23 10:38:51	237021				testConfigurationLoading	main@1225898256
11/06/23 10:39:11	257788				testConfigurationLoading	main@1225898256
11/06/23 10:41:16	382028				testConfigurationLoading	main@1225898256
11/06/23 10:41:51	417013				testConfigurationLoading	main@1225898256
11/06/23 10:35:02	8215				testConstrainedParametersMaxValues	main@1225898256
11/06/23 10:38:35	221517				testConstrainedParametersMaxValues	main@1225898256
11/06/23 10:39:01	247594				testConstrainedParametersMaxValues	main@1225898256
11/06/23 10:39:18	263931				testConstrainedParametersMaxValues	main@1225898256
11/06/23 10:41:21	387200				testConstrainedParametersMaxValues	main@1225898256
11/06/23 10:35:03	8944				testConstrainedParametersMinValues	main@1225898256
11/06/23 10:38:37	223016				testConstrainedParametersMinValues	main@1225898256
11/06/23 10:39:03	249607				testConstrainedParametersMinValues	main@1225898256
11/06/23 10:39:55	301055				testConstrainedParametersMinValues	main@1225898256
11/06/23 10:41:25	391520				testConstrainedParametersMinValues	main@1225898256
11/06/23 10:35:03	9682				testConstrainedParametersRandomValues	main@1225898256
11/06/23 10:38:38	223939				testConstrainedParametersRandomValues	main@1225898256
11/06/23 10:39:04	250755				testConstrainedParametersRandomValues	main@1225898256
11/06/23 10:39:55	301846				testConstrainedParametersRandomValues	main@1225898256
11/06/23 10:41:28	394407				testConstrainedParametersRandomValues	main@1225898256
11/06/23 10:36:14	80074				testCreateNumParameterWithoutValidValue	main@1225898256
11/06/23 10:36:14	80088				testCreateParameter	main@1225898256
11/06/23 10:36:14	80102				testCreateParameterWithValidValueConstrain	main@1225898256
11/06/23 10:35:06	12377				testDeepCleanSequence	main@1225898256
11/06/23 10:35:04	10402				testDefaultParameters	main@1225898256
11/06/23 10:38:41	227506				testDefaultParameters	main@1225898256
11/06/23 10:39:07	253539				testDefaultParameters	main@1225898256
11/06/23 10:41:06	372187				testDefaultParameters	main@1225898256
11/06/23 10:41:37	403169				testDefaultParameters	main@1225898256
11/06/23 10:38:51	237083				testExecute	main@1225898256
11/06/23 10:41:16	382117				testExecute	main@1225898256
11/06/23 10:41:51	417052				testExecute	main@1225898256
11/06/23 10:35:07	12941				testGet	main@1225898256
11/06/23 10:35:07	12928				testGetAsyncEngine	main@1225898256
11/06/23 10:35:12	18052				testGetClassPath	main@1225898256
11/06/23 10:35:07	12941				testGetDelay	main@1225898256
11/06/23 10:35:31	37055				testGetDirectory	pool-4-thread-1@518626575
11/06/23 10:35:31	37058				testGetDirectory	pool-4-thread-4@648070975
11/06/23 10:35:31	37062				testGetDirectory	pool-4-thread-2@2142675396
11/06/23 10:35:31	37063				testGetDirectory	pool-4-thread-3@854581883
11/06/23 10:35:06	12349				testGetFormattedFasta	main@1225898256
11/06/23 10:35:17	23264				testGetJobStatus	main@1225898256
11/06/23 10:42:27	453894				testGetStats	main@1225898256
11/06/23 10:35:34	40668				testGetStatus	pool-5-thread-1@1771952507
11/06/23 10:35:34	40669				testGetStatus	pool-5-thread-4@999692932
11/06/23 10:35:34	40670				testGetStatus	pool-5-thread-2@2104442583
11/06/23 10:35:34	40670				testGetStatus	pool-5-thread-3@2080187854
11/06/23 10:35:54	59992				testGetStatus	pool-5-thread-2@2104442583
11/06/23 10:35:07	12940				testGetSyncEngine	main@1225898256
11/06/23 10:36:14	80225				testGetTestArgsCommand	main@1225898256
11/06/23 10:36:14	80225				testGetTestArgsCommand	main@1225898256
11/06/23 10:36:14	80224				testGetTestCommand	main@1225898256
11/06/23 10:36:14	80224				testGetTestCommand	main@1225898256
11/06/23 10:36:14	80225				testGetTestCommand	main@1225898256
11/06/23 10:36:14	80225				testGetTestCommand	main@1225898256
11/06/23 10:36:14	80226				testGetTestCommand	main@1225898256
11/06/23 10:36:14	80226				testGetTestCommand	main@1225898256
11/06/23 10:41:52	418458				testHasCompleted	main@1225898256
11/06/23 10:35:12	18052				testIsAbsolutePath	main@1225898256
11/06/23 10:38:32	218313				testLimitExceeded	main@1225898256
11/06/23 10:35:07	12943				testLoadBalance	main@1225898256
11/06/23 10:38:32	218346				testLoadLimits	main@1225898256
11/06/23 10:35:31	37164		>>testLoadResources			main@1225898256
11/06/23 10:35:31	37182				testMarshalling	main@1225898256
11/06/23 10:36:14	79945				testMarshalling	main@1225898256
11/06/23 10:36:13	79293				testMultipleCancelLocally	main@1225898256
11/06/23 10:36:13	79662				testMultipleCancelLocally	main@1225898256
11/06/23 10:41:51	417417				testNcore	main@1225898256
11/06/23 10:36:14	80116				testOptionNoDefaultValidate	main@1225898256
11/06/23 10:36:14	80130				testOptionSetInvalidValue	main@1225898256
11/06/23 10:36:14	80143				testOptionToCommand	main@1225898256
11/06/23 10:35:04	10579				testOptions	main@1225898256
11/06/23 10:38:46	232048				testOptions	main@1225898256
11/06/23 10:39:07	253675				testOptions	main@1225898256
11/06/23 10:41:11	377053				testOptions	main@1225898256
11/06/23 10:41:41	407019				testOptions	main@1225898256
11/06/23 10:38:31	217557				testOptionsLocally	main@1225898256
11/06/23 10:35:12	18012				testOptionsToCommand	main@1225898256
11/06/23 10:36:14	80157				testParameterToCommand	main@1225898256
11/06/23 10:35:05	11023				testParameters	main@1225898256
11/06/23 10:38:47	233060				testParameters	main@1225898256
11/06/23 10:39:09	255070				testParameters	main@1225898256
11/06/23 10:41:11	377519				testParameters	main@1225898256
11/06/23 10:41:41	407396				testParameters	main@1225898256
11/06/23 10:35:31	37051				testParser	main@1225898256
11/06/23 10:36:15	81834				testPersistance	main@1225898256
11/06/23 10:36:27	93086				testPersistance	main@1225898256
11/06/23 10:36:37	103067				testPersistance	main@1225898256
11/06/23 10:36:47	113096				testPersistance	main@1225898256
11/06/23 10:37:15	141718				testPersistance	main@1225898256
11/06/23 10:38:32	217987				testPersistance	main@1225898256
11/06/23 10:38:51	237245				testPersistance	main@1225898256
11/06/23 10:39:11	257832				testPersistance	main@1225898256
11/06/23 10:41:16	382573				testPersistance	main@1225898256
11/06/23 10:41:51	417418				testPersistance	main@1225898256
11/06/23 10:36:14	80058				testPresetWithMuptiOptions	main@1225898256
11/06/23 10:35:06	12147				testPresets	main@1225898256
11/06/23 10:38:48	234276				testPresets	main@1225898256
11/06/23 10:39:11	257026				testPresets	main@1225898256
11/06/23 10:41:45	411196				testPresets	main@1225898256
11/06/23 10:35:06	12341				testProteinSequenceGeneration	main@1225898256
11/06/23 10:34:54	377				testPull	main@1225898256
11/06/23 10:35:31	37052				testQueue	main@1225898256
11/06/23 10:35:06	12377				testReadAAConResults	main@1225898256
11/06/23 10:35:06	12277				testReadClustalFile	main@1225898256
11/06/23 10:35:06	12289				testReadClustalFileLongNames	main@1225898256
11/06/23 10:35:06	12308				testReadClustalFileShortNames	main@1225898256
11/06/23 10:35:06	12646				testReadDisemblResults	main@1225898256
11/06/23 10:35:06	12772				testReadGlobPlotResults	main@1225898256
11/06/23 10:35:06	12876				testReadIUPredForGlobDomain	main@1225898256
11/06/23 10:35:06	12883				testReadIUPredForShortAndLongDisorder	main@1225898256
11/06/23 10:36:47	113404				testReadResults	main@1225898256
11/06/23 10:35:06	12919				testReadWriteFasta	main@1225898256
11/06/23 10:36:16	82610				testRunLocally	main@1225898256
11/06/23 10:36:28	94384				testRunLocally	main@1225898256
11/06/23 10:36:38	104047				testRunLocally	main@1225898256
11/06/23 10:36:47	113429				testRunLocally	main@1225898256
11/06/23 10:37:34	160332				testRunLocally	main@1225898256
11/06/23 10:38:24	210264				testRunLocally	main@1225898256
11/06/23 10:39:12	258066				testRunLocally	main@1225898256
11/06/23 10:36:17	83438				testRunLocallyOnTwoCpu	main@1225898256
11/06/23 10:37:52	178874				testRunLocallyOnTwoCpu	main@1225898256
11/06/23 10:36:47	113626				testRunLocallyWithParams	main@1225898256
11/06/23 10:36:17	83728				testRunLocallyWithPreset	main@1225898256
11/06/23 10:36:18	84382				testRunOnCluster	main@1225898256
11/06/23 10:36:29	94964				testRunOnCluster	main@1225898256
11/06/23 10:36:38	104501				testRunOnCluster	main@1225898256
11/06/23 10:36:47	113698				testRunOnCluster	main@1225898256
11/06/23 10:38:00	186006				testRunOnCluster	main@1225898256
11/06/23 10:38:26	212036				testRunOnCluster	main@1225898256
11/06/23 10:39:12	258166				testRunOnCluster	main@1225898256
11/06/23 10:36:22	88022				testRunOnClusterAsync	main@1225898256
11/06/23 10:36:31	97012				testRunOnClusterAsync	main@1225898256
11/06/23 10:36:41	107005				testRunOnClusterAsync	main@1225898256
11/06/23 10:36:51	117006				testRunOnClusterAsync	main@1225898256
11/06/23 10:38:13	199065				testRunOnClusterAsync	main@1225898256
11/06/23 10:38:51	237551				testRunOnClusterAsyncCheckStatusLongPoolingTime	main@1225898256
11/06/23 10:38:24	210088				testRunWithMatrix	main@1225898256
11/06/23 10:35:31	37200				testSchemaFromCodeGeneration	main@1225898256
11/06/23 10:38:57	243086				testSetInputTester	main@1225898256
11/06/23 10:41:17	383101				testSetInputTester	main@1225898256
11/06/23 10:36:57	123031				testSetParameter	main@1225898256
11/06/23 10:35:12	18052				testSpaceDelimiterExecutable	main@1225898256
11/06/23 10:35:22	28029				testSubmit	main@1225898256
11/06/23 10:35:27	33543				testSubmit	main@1225898256
11/06/23 10:36:13	79366				testSubmitLocally	pool-6-thread-1@786838719
11/06/23 10:36:13	79367				testSubmitLocally	pool-6-thread-4@583745848
11/06/23 10:36:13	79367				testSubmitLocally	pool-6-thread-3@1005978672
11/06/23 10:36:13	79368				testSubmitLocally	pool-6-thread-2@344787473
11/06/23 10:36:13	79490				testSubmitLocally	pool-6-thread-3@1005978672
11/06/23 10:35:12	18053				testTaskList	main@1225898256
11/06/23 10:35:31	37344				testUnMarshalling	main@1225898256
11/06/23 10:36:14	79979				testUnMarshalling	main@1225898256
11/06/23 10:41:52	418459				testUpdateStatTester	main@1225898256
11/06/23 10:36:14	80170				testValidate	main@1225898256
11/06/23 10:36:14	80184				testValidateBoundaryConstrainCheck	main@1225898256
11/06/23 10:36:14	80197				testValidateLowerBoundaryConstrainCheck	main@1225898256
11/06/23 10:36:14	80210				testValidateUpperBoundaryConstrainCheck	main@1225898256
11/06/23 10:36:14	80224				testValidateValueConstrain	main@1225898256
11/06/23 10:35:31	37375				testValidation	main@1225898256
11/06/23 10:35:31	37471				testValidationOnMarshalling	main@1225898256
11/06/23 10:42:27	453482				testVerifyJobsCount	main@1225898256
11/06/23 10:36:13	79840				testgetAllOptions	main@1225898256
11/06/23 10:36:14	79942				testgetAllParameters	main@1225898256
11/06/23 10:35:07	12927				testisNonAmbNucleotideSequence	main@1225898256
11/06/23 10:35:07	12928				testisProteinSequence	main@1225898256
11/06/23 10:35:31	37165				validateClustalConfiguration	main@1225898256
11/06/23 10:35:31	37165				validateMafftConfiguration	main@1225898256
11/06/23 10:35:31	37167				validateMuscleConfiguration	main@1225898256
11/06/23 10:36:14	80059				validatePresets	main@1225898256
11/06/23 10:35:31	37167				validateTcoffeeConfiguration	main@1225898256

Tests passed/Failed/Skipped:	1/0/0
Started on:	Tue Jun 21 17:36:46 BST 2011
Total time:	1 seconds (1625 ms)
Included groups:
Excluded groups:

PASSED TESTS
Test method	Exception	Time (seconds)	Instance
test Test class: compbio.data.sequence.FastaReaderTester		1	compbio.data.sequence.FastaReaderTester@a6d51e

Tests passed/Failed/Skipped:	12/0/0
Started on:	Thu Jun 16 14:51:10 BST 2011
Total time:	1 seconds (1469 ms)
Included groups:
Excluded groups:

Tests passed/Failed/Skipped:	3/0/0
Started on:	Wed Jun 15 13:47:01 BST 2011
Total time:	0 seconds (546 ms)
Included groups:
Excluded groups:

Tests passed/Failed/Skipped:	8/0/0
Started on:	Wed Jun 22 18:24:39 BST 2011
Total time:	16 seconds (16124 ms)
Included groups:
Excluded groups:

Tests passed/Failed/Skipped:	6/0/0
Started on:	Thu Feb 10 11:47:14 GMT 2011
Total time:	12 seconds (12747 ms)
Included groups:
Excluded groups:

Tests passed/Failed/Skipped:	7/0/0
Started on:	Thu Feb 10 11:51:51 GMT 2011
Total time:	87 seconds (87343 ms)
Included groups:
Excluded groups:

Tests passed/Failed/Skipped:	9/0/0
Started on:	Tue Jun 21 12:17:21 BST 2011
Total time:	13 seconds (13899 ms)
Included groups:
Excluded groups:

Tests passed/Failed/Skipped:	4/0/0
Started on:	Thu Jun 23 10:10:22 BST 2011
Total time:	1 seconds (1446 ms)
Included groups:
Excluded groups:

Time	Delta (ms)	Method configuration	Test method	Thread
11/06/23 10:12:02	0	>>init		main@225912260
11/06/23 10:12:02	0	>>init		main@225912260
11/06/23 10:12:02	0	>>init		main@225912260
11/06/23 10:12:02	0	>>init		main@225912260
11/06/23 10:12:02	0	>>init		main@225912260
11/06/23 10:12:02	0	>>init		main@225912260
11/06/23 10:11:53	-8750		readStatistics	main@225912260
11/06/23 10:11:53	-8749		testConfigurationLoading	main@225912260
11/06/23 10:11:53	-8701		testPersistance	main@225912260
11/06/23 10:11:54	-7713		testRunLocally	main@225912260
11/06/23 10:11:54	-7156		testRunOnCluster	main@225912260
11/06/23 10:12:02	0		testRunOnClusterAsync	main@225912260

1 test	1 class	6 methods: + chronological + alphabetical + not run (0)
2 groups	reporter output	testng.xml

Ant test

Groups used for this test run

Methods run, sorted chronologically

>> means before, << means after

Methods that were not run

Methods run, sorted chronologically

>> means before, << means after

Reporter output

Results forAnt suite

Ant test

compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFile

compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames

compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames

compbio.data.sequence.FastaReaderTester:test

compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration

compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta

compbio.data.sequence.SequenceUtilTester:loadJronnFile

compbio.data.sequence.SequenceUtilTester:testCleanProteinSequence

compbio.data.sequence.SequenceUtilTester:testCleanSequence

compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence

compbio.data.sequence.SequenceUtilTester:testReadAAConResults

compbio.data.sequence.SequenceUtilTester:testReadDisemblResults

compbio.data.sequence.SequenceUtilTester:testReadGlobPlotResults

compbio.data.sequence.SequenceUtilTester:testReadIUPredForGlobDomain

compbio.data.sequence.SequenceUtilTester:testReadIUPredForShortAndLongDisorder

compbio.data.sequence.SequenceUtilTester:testReadWriteFasta

compbio.data.sequence.SequenceUtilTester:testisNonAmbNucleotideSequence

compbio.data.sequence.SequenceUtilTester:testisProteinSequence

compbio.engine.EngineConfiguratorTester:testGetAsyncEngine

compbio.engine.EngineConfiguratorTester:testGetSyncEngine

compbio.engine.FilePullerTester:testCache

compbio.engine.FilePullerTester:testGet

compbio.engine.FilePullerTester:testGetDelay

compbio.engine.FilePullerTester:testPull

compbio.engine.LoadBalancerTester:testLoadBalance

compbio.engine.PulledFileCacheTester:test

compbio.engine.client.CommandBuilderTester:testCommandBuilding

compbio.engine.client.CommandBuilderTester:testOptionsToCommand

compbio.engine.client.CommandBuilderTester:testSpaceDelimiterExecutable

compbio.engine.client.PathValidatorTester:testGetClassPath

compbio.engine.client.PathValidatorTester:testIsAbsolutePath

compbio.engine.cluster.drmaa.ClusterSessionTester:testTaskList

compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testCancel

compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus

compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testSubmit

compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testCancel

compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testSubmit

compbio.engine.cluster.drmaa.UtilTester:testParser

compbio.engine.cluster.dundee._QueueTester:testQueue

compbio.engine.conf.DirectoryManagerTester:testGetDirectory

compbio.engine.conf.PropertyHelperManagerTester:testClusterEngineConf

compbio.engine.conf.PropertyHelperManagerTester:validateClustalConfiguration

compbio.engine.conf.PropertyHelperManagerTester:validateMafftConfiguration

compbio.engine.conf.PropertyHelperManagerTester:validateMuscleConfiguration

compbio.engine.conf.PropertyHelperManagerTester:validateTcoffeeConfiguration

compbio.engine.conf.RunnerConfigMarshallerTester:testMarshalling

compbio.engine.conf.RunnerConfigMarshallerTester:testSchemaFromCodeGeneration

compbio.engine.conf.RunnerConfigMarshallerTester:testUnMarshalling

compbio.engine.conf.RunnerConfigMarshallerTester:testValidation

compbio.engine.conf.RunnerConfigMarshallerTester:testValidationOnMarshalling

compbio.engine.local.AsyncLocalRunnerTester:testAsyncCancelOperation

compbio.engine.local.AsyncLocalRunnerTester:testAsyncRetrievOperation

compbio.engine.local.AsyncLocalRunnerTester:testCancelCompletedTaskLocally

compbio.engine.local.AsyncLocalRunnerTester:testCancelLocally

compbio.engine.local.AsyncLocalRunnerTester:testGetStatus

compbio.engine.local.AsyncLocalRunnerTester:testMultipleCancelLocally

compbio.engine.local.AsyncLocalRunnerTester:testSubmitLocally

compbio.engine.local.LocalRunnerTester:testCancelCompletedTaskLocally

compbio.engine.local.LocalRunnerTester:testCancelLocally

compbio.engine.local.LocalRunnerTester:testMultipleCancelLocally

compbio.metadata.OptionCombinatorTester:testgetAllOptions

compbio.metadata.OptionCombinatorTester:testgetAllParameters

compbio.metadata.OptionMarshallerTester:testMarshalling

compbio.metadata.OptionMarshallerTester:testUnMarshalling

compbio.metadata.PresetTester:marshallPreset

compbio.metadata.PresetTester:testPresetWithMuptiOptions

compbio.metadata.PresetTester:validatePresets

compbio.metadata.RunnerConfigTester:testCreateNumParameterWithoutValidValue

compbio.metadata.RunnerConfigTester:testCreateParameter

compbio.metadata.RunnerConfigTester:testCreateParameterWithValidValueConstrain

Results for
Ant suite