From: pvtroshin Date: Thu, 23 Jun 2011 09:46:17 +0000 (+0000) Subject: Remove old test from web site to replace with most recent X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=550d715f5af9271247b20363d1212e7e0279f9ee;p=jabaws.git Remove old test from web site to replace with most recent git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4312 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/website/tests/Ant suite/Ant test.html b/website/tests/Ant suite/Ant test.html deleted file mode 100644 index 98af8e8..0000000 --- a/website/tests/Ant suite/Ant test.html +++ /dev/null @@ -1,1621 +0,0 @@ - - -TestNG: Ant test - - - - - - - - -

Ant test

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Tests passed/Failed/Skipped:	165/0/0
Started on:	Wed Feb 17 15:34:08 GMT 2010
Total time:	524 seconds (524407 ms)
Included groups:
Excluded groups:	performance

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

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PASSED TESTS
Test method Instance Time (seconds) Exception
marshallPreset
Test class:Ant test compbio.metadata.PresetTester@50009f0d 0
readStatistics
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 1
readStatistics
Test class:Ant test compbio.runner.msa.MafftTester@259a8416 0
readStatistics
Test class:Ant test compbio.runner.msa.MuscleTester@37b994de 0
readStatistics
Test class:Ant test compbio.runner.msa.ProbconsTester@5a57e787 0
readStatistics
Test class:Ant test compbio.runner.msa.TcoffeeTester@7df1bd98 0
readStatisticsClusterExecution
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 8
test
Test class:Ant test compbio.engine.PulledFileCacheTester@1164b9b6 5
testArguments
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 3
testArguments
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 6
testArguments
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 7
testArguments
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 2
testArguments
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 8
testAsyncCancelOperation
Test class:Ant test compbio.engine.local.AsyncLocalRunnerTester@7461f533 0
testAsyncRetrievOperation
Test class:Ant test compbio.engine.local.AsyncLocalRunnerTester@7461f533 0
testCache
Test class:Ant test compbio.engine.FilePullerTester@5fa80aea 6
testCancel
Test class:Ant test compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18 1
compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found! - at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79) - at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37) - at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206) - at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109) -Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found! - at compbio.runner.Util.readClustalFile(Util.java:126) - at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76) - ... 25 more -... Removed 22 stack frames
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compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found! - at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79) - at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37) - at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206) - at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109) - 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/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found! - at compbio.runner.Util.readClustalFile(Util.java:126) - at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76) - ... 25 more -
testCancel
Test class:Ant test compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93 1
testCancelCompletedTaskLocally
Test class:Ant test compbio.engine.local.AsyncLocalRunnerTester@7461f533 3
testCancelCompletedTaskLocally
Test class:Ant test compbio.engine.local.LocalRunnerTester@4b2922f6 0
java.util.concurrent.CancellationException - at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) - at java.util.concurrent.FutureTask.get(FutureTask.java:83) - at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) - at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) - at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139) -... Removed 22 stack frames
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java.util.concurrent.CancellationException - at java.util.concurrent.FutureTask$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@7461f533 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@4b2922f6 0
java.util.concurrent.CancellationException - at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) - at java.util.concurrent.FutureTask.get(FutureTask.java:83) - at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) - at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) - at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66) -... Removed 22 stack frames
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java.util.concurrent.CancellationException - at java.util.concurrent.FutureTask$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) -
testCleanSequence
Test class:Ant test compbio.data.sequence.SequenceUtilTester@ad72200 0
testClusterEngineConf
Test class:Ant test compbio.engine.conf.PropertyHelperManagerTester@307bd0d 0
testClusterExecute
Test class:Ant test compbio.runner.msa.MafftTester@259a8416 11
testClusterExecute
Test class:Ant test compbio.runner.msa.ProbconsTester@5a57e787 19
testClusterExecute
Test class:Ant test compbio.runner.msa.TcoffeeTester@7df1bd98 5
testCommandBuilding
Test class:Ant test compbio.engine.client.CommandBuilderTester@6bdc64a5 0
testConfiguration
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 0
testConfiguration
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 0
testConfiguration
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 0
testConfiguration
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 0
testConfiguration
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 0
testConfigurationLoading
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 0
testConfigurationLoading
Test class:Ant test compbio.runner.msa.MafftTester@259a8416 0
testConfigurationLoading
Test class:Ant test compbio.runner.msa.MuscleTester@37b994de 0
testConfigurationLoading
Test class:Ant test compbio.runner.msa.ProbconsTester@5a57e787 0
testConfigurationLoading
Test class:Ant test compbio.runner.msa.TcoffeeTester@7df1bd98 0
testConstrainedParametersMaxValues
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 1
testConstrainedParametersMaxValues
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 3
testConstrainedParametersMaxValues
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 1
testConstrainedParametersMaxValues
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 38
testConstrainedParametersMaxValues
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 11
testConstrainedParametersMinValues
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 1
testConstrainedParametersMinValues
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 1
testConstrainedParametersMinValues
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 0
testConstrainedParametersMinValues
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 0
testConstrainedParametersMinValues
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 5
testConstrainedParametersRandomValues
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 3
testConstrainedParametersRandomValues
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 7
testConstrainedParametersRandomValues
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 7
testConstrainedParametersRandomValues
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 61
testConstrainedParametersRandomValues
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 21
testCreateNumParameterWithoutValidValue
Test class:Ant test compbio.metadata.RunnerConfigTester@58ca3783 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@58ca3783 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
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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@58ca3783 0
testDeepCleanSequence
Test class:Ant test compbio.data.sequence.SequenceUtilTester@ad72200 0
testDefaultParameters
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 0
testDefaultParameters
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 20
testDefaultParameters
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 0
testDefaultParameters
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 14
testDefaultParameters
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 10
testExecute
Test class:Ant test compbio.runner.msa.MafftTester@259a8416 0
testExecute
Test class:Ant test compbio.runner.msa.ProbconsTester@5a57e787 0
testExecute
Test class:Ant test compbio.runner.msa.TcoffeeTester@7df1bd98 0
testGet
Test class:Ant test compbio.engine.FilePullerTester@5fa80aea 0
testGetAsyncEngine
Test class:Ant test compbio.engine.EngineConfiguratorTester@31f9338f 0
testGetClassPath
Test class:Ant test compbio.engine.client.PathValidatorTester@5253c3f5 0
testGetDelay
Test class:Ant test compbio.engine.FilePullerTester@5fa80aea 0
testGetDirectory compbio.engine.conf.DirectoryManagerTester@1c1474ea 0
testGetDirectory compbio.engine.conf.DirectoryManagerTester@1c1474ea 0
testGetDirectory compbio.engine.conf.DirectoryManagerTester@1c1474ea 0
testGetDirectory compbio.engine.conf.DirectoryManagerTester@1c1474ea 0
testGetFormattedFasta
Test class:Ant test compbio.data.sequence.FastaSequenceTester@ec0a9f9 0
testGetJobStatus
Test class:Ant test compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18 20
testGetStatus compbio.engine.local.AsyncLocalRunnerTester@7461f533 20
testGetStatus compbio.engine.local.AsyncLocalRunnerTester@7461f533 20
testGetStatus compbio.engine.local.AsyncLocalRunnerTester@7461f533 21
testGetStatus compbio.engine.local.AsyncLocalRunnerTester@7461f533 40
testGetStatus compbio.engine.local.AsyncLocalRunnerTester@7461f533 20
testGetSyncEngine
Test class:Ant test compbio.engine.EngineConfiguratorTester@31f9338f 0
testGetTestArgsCommand
Test class:Ant test compbio.runner._impl.OBTester@327124af 0
testGetTestArgsCommand
Test class:Ant test compbio.runner._impl.RPSBlastTester@221f7708 0
testGetTestCommand
Test class:Ant test compbio.runner._impl.MclTester@4402a6ff 0
testGetTestCommand
Test class:Ant test compbio.runner._impl.NetNglycTester@a21d23b 0
testGetTestCommand
Test class:Ant test compbio.runner._impl.OBTester@327124af 0
testGetTestCommand
Test class:Ant test compbio.runner._impl.RPSBlastTester@221f7708 0
testGetTestCommand
Test class:Ant test compbio.runner._impl.RonnTester@3fbfbfb8 0
testGetTestCommand
Test class:Ant test compbio.runner._impl.Tmhmm2Tester@45c3e9ba 0
testIsAbsolutePath
Test class:Ant test compbio.engine.client.PathValidatorTester@5253c3f5 0
testLoadLimits
Test class:Ant test compbio.runner.msa.LimitTester@1b0c6cfc 0
testMarshalling
Test class:Ant test compbio.engine.conf.RunnerConfigMarshallerTester@710ca208 0
testMarshalling
Test class:Ant test compbio.metadata.OptionMarshallerTester@372c9557 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:328) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) - at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) - at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) - at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140) -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:124) - at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102) - at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697) - at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65) - at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168) - at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325) - ... 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:328) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) - at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) - at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) - at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140) - 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:124) - at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102) - at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697) - at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65) - at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168) - at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325) - ... 26 more -
testMultipleCancelLocally
Test class:Ant test compbio.engine.local.AsyncLocalRunnerTester@7461f533 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@4b2922f6 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@7df1bd98 0
testOptionNoDefaultValidate
Test class:Ant test compbio.metadata.RunnerConfigTester@58ca3783 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@58ca3783 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@58ca3783 0
testOptions
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 2
testOptions
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 4
testOptions
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 2
testOptions
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 0
testOptions
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 0
testOptionsLocally
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 1
testOptionsToCommand
Test class:Ant test compbio.engine.client.CommandBuilderTester@6bdc64a5 0
testParameterToCommand
Test class:Ant test compbio.metadata.RunnerConfigTester@58ca3783 0
testParameters
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 2
testParameters
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 2
testParameters
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 4
testParameters
Test class:Ant test compbio.runner.msa.ProbconsParametersTester@78dc9766 1
testParameters
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 12
testParser
Test class:Ant test compbio.engine.cluster.drmaa.UtilTester@22e90943 0
testPersistance
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 0
testPersistance
Test class:Ant test compbio.runner.msa.MafftTester@259a8416 1
testPersistance
Test class:Ant test compbio.runner.msa.MuscleTester@37b994de 0
testPersistance
Test class:Ant test compbio.runner.msa.ProbconsTester@5a57e787 0
testPersistance
Test class:Ant test compbio.runner.msa.TcoffeeTester@7df1bd98 1
testPresets
Test class:Ant test compbio.runner.msa.ClustalWParametersTester@132803ba 0
testPresets
Test class:Ant test compbio.runner.msa.MafftParametersTester@4cc72243 2
testPresets
Test class:Ant test compbio.runner.msa.MuscleParametersTester@4355d3a3 0
testPresets
Test class:Ant test compbio.runner.msa.TcoffeeParametersTester@41217e67 1
testProteinSequenceGeneration
Test class:Ant test compbio.data.sequence.FastaSequenceGeneratorTester@163b4b1e 0
testPull
Test class:Ant test compbio.engine.FilePullerTester@5fa80aea 0
testQueue
Test class:Ant test compbio.engine.cluster.dundee._QueueTester@715f1f9c 0
testReadClustalFile
Test class:Ant test compbio.data.sequence.ClustalAlignmentUtilTester@38c52200 0
testReadClustalFileLongNames
Test class:Ant test compbio.data.sequence.ClustalAlignmentUtilTester@38c52200 0
testReadClustalFileShortNames
Test class:Ant test compbio.data.sequence.ClustalAlignmentUtilTester@38c52200 0
testReadWriteFasta
Test class:Ant test compbio.data.sequence.SequenceUtilTester@ad72200 0
testRunLocally
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 0
testRunLocally
Test class:Ant test compbio.runner.msa.MuscleTester@37b994de 0
testRunOnCluster
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 15
testRunOnCluster
Test class:Ant test compbio.runner.msa.MuscleTester@37b994de 8
testRunOnClusterAsyncCheckStatusLongPoolingTime
Test class:Ant test compbio.runner.msa.MafftTester@259a8416 21
testRunWithMatrix
Test class:Ant test compbio.runner.msa.ClustalWTester@4125d61e 0
testSchemaFromCodeGeneration
Test class:Ant test compbio.engine.conf.RunnerConfigMarshallerTester@710ca208 0
testSetInputTester
Test class:Ant test compbio.runner.msa.MafftTester@259a8416 0
testSetInputTester
Test class:Ant test compbio.runner.msa.ProbconsTester@5a57e787 0
testSpaceDelimiterExecutable
Test class:Ant test compbio.engine.client.CommandBuilderTester@6bdc64a5 0
testSubmit
Test class:Ant test compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18 18
testSubmit
Test class:Ant test compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93 17
testSubmitLocally compbio.engine.local.AsyncLocalRunnerTester@7461f533 0
testSubmitLocally compbio.engine.local.AsyncLocalRunnerTester@7461f533 0
testSubmitLocally compbio.engine.local.AsyncLocalRunnerTester@7461f533 0
testSubmitLocally compbio.engine.local.AsyncLocalRunnerTester@7461f533 0
testSubmitLocally compbio.engine.local.AsyncLocalRunnerTester@7461f533 0
testTaskList
Test class:Ant test compbio.engine.cluster.drmaa.ClusterSessionTester@7966340c 8
testUnMarshalling
Test class:Ant test compbio.engine.conf.RunnerConfigMarshallerTester@710ca208 0
testUnMarshalling
Test class:Ant test compbio.metadata.OptionMarshallerTester@372c9557 0
testValidate
Test class:Ant test compbio.metadata.RunnerConfigTester@58ca3783 0
testValidateBoundaryConstrainCheck
Test class:Ant test compbio.metadata.RunnerConfigTester@58ca3783 0
testValidateLowerBoundaryConstrainCheck
Test class:Ant test compbio.metadata.RunnerConfigTester@58ca3783 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@58ca3783 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@58ca3783 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@710ca208 0
testValidationOnMarshalling
Test class:Ant test compbio.engine.conf.RunnerConfigMarshallerTester@710ca208 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:328) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) - at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) - at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) - at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258) -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:124) - at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102) - at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697) - at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65) - at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168) - at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325) - ... 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:328) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) - at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) - at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) - at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258) - 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:124) - at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102) - at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697) - at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65) - at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168) - at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592) - at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320) - at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493) - at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325) - ... 26 more -
testgetAllOptions
Test class:Ant test compbio.metadata.OptionCombinatorTester@79b66b06 0
testgetAllParameters
Test class:Ant test compbio.metadata.OptionCombinatorTester@79b66b06 0
testisNonAmbNucleotideSequence
Test class:Ant test compbio.data.sequence.SequenceUtilTester@ad72200 0
testisProteinSequence
Test class:Ant test compbio.data.sequence.SequenceUtilTester@ad72200 0
validateClustalConfiguration
Test class:Ant test compbio.engine.conf.PropertyHelperManagerTester@307bd0d 0
validateMafftConfiguration
Test class:Ant test compbio.engine.conf.PropertyHelperManagerTester@307bd0d 0
validateMuscleConfiguration
Test class:Ant test compbio.engine.conf.PropertyHelperManagerTester@307bd0d 0
validatePresets
Test class:Ant test compbio.metadata.PresetTester@50009f0d 0
validateTcoffeeConfiguration
Test class:Ant test compbio.engine.conf.PropertyHelperManagerTester@307bd0d 0

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Class name Method name Groups
compbio.engine.client.CommandBuilderTester
@Test
testOptionsToCommand
testSpaceDelimiterExecutable
testCommandBuilding
@BeforeClass
@BeforeMethod
@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._impl.NetNglycTester
@Test
testGetTestCommand
testBuildCommand cluster runner
@BeforeClass
@BeforeMethod
@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.engine.EngineConfiguratorTester
@Test
testGetAsyncEngine
testGetSyncEngine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.RonnTester
@Test
testGetTestCommand
testBuildCommand cluster runner
@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.engine.FilePullerTester
@Test
testGet
testCache engine
testGetDelay engine
testPull engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.OptionCombinatorTester
@Test
testgetAllParameters
testgetAllOptions
@BeforeClass
@BeforeMethod
setup
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleTester
@Test
testRunOnCluster cluster runner
testRunOnClusterAsync cluster runner
testPersistance 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.msa.LimitTester
@Test
testLoadLimits
@BeforeClass
@BeforeMethod
setup runner
@AfterMethod
@AfterClass
compbio.runner._impl.OBTester
@Test
testGetTestCommand
testBuildCommand cluster runner
testGetTestArgsCommand
@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.engine.local.LocalRunnerTester
@Test
testCancelLocally engine
testMultipleCancelLocally engine
testCancelCompletedTaskLocally engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.Tmhmm2Tester
@Test
testGetTestCommand
testBuildCommand cluster runner
@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.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.FastaSequenceTester
@Test
testGetFormattedFasta
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.client.PathValidatorTester
@Test
testIsAbsolutePath
testGetClassPath
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.SequenceUtilTester
@Test
testDeepCleanSequence
testReadWriteFasta
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.runner.msa.ClustalWTester
@Test
testRunOnCluster cluster runner
testPersistance runner
testAddParameters
testOptionsLocally runner
readStatisticsClusterExecution cluster runner
testConfigurationLoading runner
testRunWithMatrix runner
readStatistics runner
testRunLocally runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.UtilTester
@Test
testParser
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.conf.DirectoryManagerTester
@Test
testGetDirectory
testNanoTime
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester
@Test
testSubmit engine cluster
testCancel engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester
@Test
testSubmit engine cluster
testCancel engine cluster
testGetJobStatus engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.PresetTester
@Test
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.runner._impl.RPSBlastTester
@Test
testGetTestCommand
testBuildCommand cluster runner
testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.PulledFileCacheTester
@Test
test
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.MclTester
@Test
testGetTestCommand
testBuildCommand cluster runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.dundee._QueueTester
@Test
testQueue
@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.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 deleted file mode 100644 index de93281..0000000 --- a/website/tests/Ant suite/groups.html +++ /dev/null @@ -1,6 +0,0 @@ -

Class name	Method name	Groups
compbio.engine.client.CommandBuilderTester
@Test
	testOptionsToCommand
	testSpaceDelimiterExecutable
	testCommandBuilding
@BeforeClass
@BeforeMethod
@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._impl.NetNglycTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@BeforeClass
@BeforeMethod
@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.engine.EngineConfiguratorTester
@Test
	testGetAsyncEngine
	testGetSyncEngine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.RonnTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@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.engine.FilePullerTester
@Test
	testGet
	testCache	engine
	testGetDelay	engine
	testPull	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.OptionCombinatorTester
@Test
	testgetAllParameters
	testgetAllOptions
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleTester
@Test
	testRunOnCluster	cluster runner
	testRunOnClusterAsync	cluster runner
	testPersistance	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.msa.LimitTester
@Test
	testLoadLimits
@BeforeClass
@BeforeMethod
	setup	runner
@AfterMethod
@AfterClass
compbio.runner._impl.OBTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
	testGetTestArgsCommand
@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.engine.local.LocalRunnerTester
@Test
	testCancelLocally	engine
	testMultipleCancelLocally	engine
	testCancelCompletedTaskLocally	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.Tmhmm2Tester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@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.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.FastaSequenceTester
@Test
	testGetFormattedFasta
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.client.PathValidatorTester
@Test
	testIsAbsolutePath
	testGetClassPath
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.SequenceUtilTester
@Test
	testDeepCleanSequence
	testReadWriteFasta
	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.runner.msa.ClustalWTester
@Test
	testRunOnCluster	cluster runner
	testPersistance	runner
	testAddParameters
	testOptionsLocally	runner
	readStatisticsClusterExecution	cluster runner
	testConfigurationLoading	runner
	testRunWithMatrix	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.UtilTester
@Test
	testParser
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.conf.DirectoryManagerTester
@Test
	testGetDirectory
	testNanoTime
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester
@Test
	testSubmit	engine cluster
	testCancel	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester
@Test
	testSubmit	engine cluster
	testCancel	engine cluster
	testGetJobStatus	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.PresetTester
@Test
	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.runner._impl.RPSBlastTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
	testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.PulledFileCacheTester
@Test
	test
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.MclTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.dundee._QueueTester
@Test
	testQueue
@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.engine.conf.RunnerConfigMarshallerTester
@Test
	testValidationOnMarshalling
	testUnMarshalling
	testValidation
	testSchemaFromCodeGeneration
	testMarshalling
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass

Groups used for this test run

- - - - -

Group name	Methods
cluster	compbio.runner.msa.TcoffeeTester.testPersistance() compbio.runner.msa.ProbconsTester.testClusterExecute() compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution() compbio.runner.msa.ClustalWTester.testRunOnCluster() compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList() compbio.runner.msa.MuscleTester.testRunOnCluster() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus() compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel() compbio.runner.msa.MafftTester.testClusterExecute() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit() compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf() compbio.runner.msa.TcoffeeTester.testClusterExecute()
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.DrmaaAsyncClusterEngineTester.testCancel() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel() compbio.engine.FilePullerTester.testGetDelay() compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit() compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.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.msa.ClustalWTester.testConfigurationLoading() compbio.runner.msa.MafftTester.readStatistics() compbio.runner.msa.MafftParametersTester.testParameters() compbio.runner.msa.MafftParametersTester.testDefaultParameters() compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.MafftTester.testSetInputTester() compbio.runner.msa.ProbconsParametersTester.testArguments() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.ClustalWTester.testRunOnCluster() compbio.runner.msa.MafftTester.testExecute() compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.TcoffeeTester.testNcore() compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MuscleTester.testRunLocally() compbio.runner.msa.TcoffeeParametersTester.testParameters() compbio.runner.msa.ProbconsTester.testConfigurationLoading() compbio.runner.msa.ClustalWTester.testRunWithMatrix() compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters() compbio.runner.msa.ClustalWTester.testRunLocally() compbio.runner.msa.ProbconsParametersTester.testOptions() compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MafftTester.testPersistance() compbio.runner.msa.MuscleParametersTester.testParameters() compbio.runner.msa.MuscleParametersTester.testDefaultParameters() compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MuscleTester.testRunOnCluster() compbio.runner.msa.ClustalWTester.testOptionsLocally() compbio.runner.msa.MafftTester.testClusterExecute() compbio.runner.msa.TcoffeeTester.testConfigurationLoading() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.ClustalWParametersTester.testParameters() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.ClustalWParametersTester.testDefaultParameters() compbio.runner.msa.MuscleTester.testConfigurationLoading() compbio.runner.msa.TcoffeeTester.testExecute() compbio.runner.msa.MafftParametersTester.testPresets() compbio.runner.msa.TcoffeeTester.readStatistics() compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.MuscleTester.readStatistics() compbio.runner.msa.ClustalWParametersTester.testArguments() compbio.runner.msa.ProbconsTester.readStatistics() compbio.runner.msa.TcoffeeParametersTester.testArguments() compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime() compbio.runner.msa.MafftParametersTester.testOptions() compbio.runner.msa.ProbconsTester.testSetInputTester() compbio.runner.msa.MuscleParametersTester.testArguments() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues() compbio.runner.msa.ClustalWTester.testPersistance() compbio.runner.msa.ProbconsTester.testExecute() compbio.runner.msa.TcoffeeTester.testPersistance() compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.ProbconsTester.testClusterExecute() compbio.runner.msa.TcoffeeParametersTester.testPresets() compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution() compbio.runner.msa.MuscleTester.testPersistance() compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.ClustalWParametersTester.testOptions() compbio.runner.msa.MuscleParametersTester.testPresets() compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues() compbio.runner.msa.MafftParametersTester.testArguments() compbio.runner.msa.MafftTester.testConfigurationLoading() compbio.runner.msa.TcoffeeParametersTester.testOptions() compbio.runner.msa.ClustalWTester.readStatistics() compbio.runner.msa.ProbconsParametersTester.testDefaultParameters() compbio.runner.msa.ProbconsParametersTester.testParameters() compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues() compbio.runner.msa.ProbconsTester.testPersistance() compbio.runner.msa.ClustalWParametersTester.testPresets() compbio.runner.msa.MuscleParametersTester.testOptions() compbio.runner.msa.TcoffeeTester.testClusterExecute()

diff --git a/website/tests/Ant suite/index.html b/website/tests/Ant suite/index.html deleted file mode 100644 index 7c18f73..0000000 --- a/website/tests/Ant suite/index.html +++ /dev/null @@ -1,6 +0,0 @@ -Results for Ant suite - - - - - diff --git a/website/tests/Ant suite/main.html b/website/tests/Ant suite/main.html deleted file mode 100644 index 0198e44..0000000 --- a/website/tests/Ant suite/main.html +++ /dev/null @@ -1,2 +0,0 @@ -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 deleted file mode 100644 index 7cfdc6e..0000000 --- a/website/tests/Ant suite/methods-alphabetical.html +++ /dev/null @@ -1,520 +0,0 @@ -

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.runner._impl.RPSBlastTester.testBuildCommand

compbio.runner._impl.OBTester.testBuildCommand

compbio.runner.msa.MuscleTester.testRunOnClusterAsync

compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce

compbio.runner.msa.ClustalWTester.testAddParameters

compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes

compbio.runner._impl.MclTester.testBuildCommand

compbio.runner._impl.DisEMBLTester.testBuildCommand

compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusShortPoolingTime

compbio.runner._impl.Tmhmm2Tester.testBuildCommand

compbio.engine.conf.DirectoryManagerTester.testNanoTime

compbio.runner._impl.NetNglycTester.testBuildCommand

compbio.runner._impl.RonnTester.testBuildCommand

\ No newline at end of file diff --git a/website/tests/Ant suite/methods.html b/website/tests/Ant suite/methods.html deleted file mode 100644 index 78a4826..0000000 --- a/website/tests/Ant suite/methods.html +++ /dev/null @@ -1,520 +0,0 @@ -

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 deleted file mode 100644 index 2a331c9..0000000 --- a/website/tests/Ant suite/testng-failed.xml +++ /dev/null @@ -1,99 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/website/tests/Ant suite/testng.xml.html b/website/tests/Ant suite/testng.xml.html deleted file mode 100644 index 40f9b9a..0000000 --- a/website/tests/Ant suite/testng.xml.html +++ /dev/null @@ -1 +0,0 @@ -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"/> </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.MsaWS"/> <class name="compbio.data.msa.jaxws.Align"/> <class name="compbio.data.msa.jaxws.AlignResponse"/> <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.GetJobStatus"/> <class name="compbio.data.msa.jaxws.GetJobStatusResponse"/> <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.GetProgress"/> <class name="compbio.data.msa.jaxws.GetProgressResponse"/> <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.JobExecutionExceptionBean"/> <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.PullExecStatistics"/> <class name="compbio.data.msa.jaxws.PullExecStatisticsResponse"/> <class name="compbio.data.msa.jaxws.PullFile"/> <class name="compbio.data.msa.jaxws.PullFileResponse"/> <class name="compbio.data.msa.jaxws.ResultNotAvailableExceptionBean"/> <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.FastaGeneratorManager"/> <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$SeqType"/> <class name="compbio.data.sequence.FastaSequenceGenerator"/> <class name="compbio.data.sequence.FastaSequenceGeneratorTester"/> <class name="compbio.data.sequence.FastaSequenceTester"/> <class name="compbio.data.sequence.Program"/> <class name="compbio.data.sequence.SequenceUtil"/> <class name="compbio.data.sequence.SequenceUtilTester"/> <class name="compbio.data.sequence.UnknownFileFormatException"/> <class name="compbio.engine.AsyncExecutor"/> <class name="compbio.engine.Cleaner"/> <class name="compbio.engine.ClusterJobId"/> <class name="compbio.engine.Configurator"/> <class name="compbio.engine.EngineConfiguratorTester"/> <class name="compbio.engine.FilePuller"/> <class name="compbio.engine.FilePullerTester"/> <class name="compbio.engine.Job"/> <class name="compbio.engine.LoadBalancer"/> <class name="compbio.engine.ProgressGetter"/> <class name="compbio.engine.PulledFileCache"/> <class name="compbio.engine.PulledFileCacheTester"/> <class name="compbio.engine.SubmissionManager"/> <class name="compbio.engine.SyncExecutor"/> <class name="compbio.engine.client.ClusterNativeSpecExecutable"/> <class name="compbio.engine.client.CommandBuilder$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.BlastParser$Psiseq"/> <class name="compbio.pipeline._jpred.BlastParser"/> <class name="compbio.pipeline._jpred.Jpred4"/> <class name="compbio.pipeline._jpred.PScore"/> <class name="compbio.pipeline._jpred.Pairwise"/> <class name="compbio.runner.OptionCombinator"/> <class name="compbio.runner.Util"/> <class name="compbio.runner._NativeSpecHelper"/> <class name="compbio.runner._SkeletalCommandBuilder"/> <class name="compbio.runner._impl.BlastAll$blastType"/> <class name="compbio.runner._impl.BlastAll$dataBase"/> <class name="compbio.runner._impl.BlastAll"/> <class name="compbio.runner._impl.BlastParameters"/> <class name="compbio.runner._impl.DisEMBLTester"/> <class name="compbio.runner._impl.Disembl"/> <class name="compbio.runner._impl.Environment"/> <class name="compbio.runner._impl.Mcl"/> <class name="compbio.runner._impl.MclTester"/> <class name="compbio.runner._impl.NetNglyc"/> <class name="compbio.runner._impl.NetNglycTester"/> <class name="compbio.runner._impl.OB"/> <class name="compbio.runner._impl.OBTester"/> <class name="compbio.runner._impl.PSIBlast$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.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.ws.client.Jws2Client$Services"/> <class name="compbio.ws.client.Jws2Client"/> <class name="compbio.ws.client.WSTester"/> <class name="compbio.ws.server.ClustalWS"/> <class name="compbio.ws.server.MafftWS"/> <class name="compbio.ws.server.MuscleWS"/> <class name="compbio.ws.server.ProbconsWS"/> <class name="compbio.ws.server.SimpleWSPublisher"/> <class name="compbio.ws.server.TcoffeeWS"/> <class name="compbio.ws.server.WSUtil"/> </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 deleted file mode 100644 index bfce6b9..0000000 --- a/website/tests/Ant suite/toc.html +++ /dev/null @@ -1,30 +0,0 @@ - - -Results for Ant suite - - - - -

Results for
Ant suite

- - - - - - - - - - -

1 test	40 classes	154 methods: - chronological - alphabetical - not run (13)
4 groups	reporter output	testng.xml

- -

Ant test (165/0/0)

- Results -

- \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/Ant test(failed).html b/website/tests/Failed suite [Ant suite]/Ant test(failed).html deleted file mode 100644 index 77319bf..0000000 --- a/website/tests/Failed suite [Ant suite]/Ant test(failed).html +++ /dev/null @@ -1,84 +0,0 @@ - - -TestNG: Ant test(failed) - - - - - - - - -

Ant test(failed)

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	1/0/0
Started on:	Mon Feb 08 18:30:13 GMT 2010
Total time:	1 seconds (1098 ms)
Included groups:
Excluded groups:	performance

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

- - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
readStatistics
Test class:Ant test(failed) compbio.runner.msa.ProbconsTester@60cbf9bd 0

- - \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/Ant test(failed).properties b/website/tests/Failed suite [Ant suite]/Ant test(failed).properties deleted file mode 100644 index 840adb8..0000000 --- a/website/tests/Failed suite [Ant suite]/Ant test(failed).properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult Ant test(failed)] \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/Ant test(failed).xml b/website/tests/Failed suite [Ant suite]/Ant test(failed).xml deleted file mode 100644 index a488254..0000000 --- a/website/tests/Failed suite [Ant suite]/Ant test(failed).xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/website/tests/Failed suite [Ant suite]/classes.html b/website/tests/Failed suite [Ant suite]/classes.html deleted file mode 100644 index 08936eb..0000000 --- a/website/tests/Failed suite [Ant suite]/classes.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Class name Method name Groups
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
diff --git a/website/tests/Failed suite [Ant suite]/groups.html b/website/tests/Failed suite [Ant suite]/groups.html deleted file mode 100644 index 1fc18ba..0000000 --- a/website/tests/Failed suite [Ant suite]/groups.html +++ /dev/null @@ -1,4 +0,0 @@ -

Class name	Method name	Groups
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

Groups used for this test run

- - -

Group name	Methods
non_windows	compbio.runner.msa.ProbconsTester.readStatistics()
runner	compbio.runner.msa.ProbconsTester.readStatistics()

diff --git a/website/tests/Failed suite [Ant suite]/index.html b/website/tests/Failed suite [Ant suite]/index.html deleted file mode 100644 index 7746c5f..0000000 --- a/website/tests/Failed suite [Ant suite]/index.html +++ /dev/null @@ -1,6 +0,0 @@ -Results for Failed suite [Ant suite] - - - - - diff --git a/website/tests/Failed suite [Ant suite]/main.html b/website/tests/Failed suite [Ant suite]/main.html deleted file mode 100644 index 62581b7..0000000 --- a/website/tests/Failed suite [Ant suite]/main.html +++ /dev/null @@ -1,2 +0,0 @@ -Results for Failed suite [Ant suite] -Select a result on the left-hand pane. diff --git a/website/tests/Failed suite [Ant suite]/methods-alphabetical.html b/website/tests/Failed suite [Ant suite]/methods-alphabetical.html deleted file mode 100644 index a133bb8..0000000 --- a/website/tests/Failed suite [Ant suite]/methods-alphabetical.html +++ /dev/null @@ -1,12 +0,0 @@ -

Methods run, sorted chronologically

>> means before, << means after

Failed suite [Ant suite]

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

- - - - - - - - - - -
Time Delta (ms) Suite
configuration Test
configuration Class
configuration Groups
configuration Method
configuration Test
method Thread Instances
10/02/08 18:30:13 0 >>init main@1369543768
10/02/08 18:30:14 525 >>init main@1369543768
10/02/08 18:30:14 452 >>loadPresets main@1369543768
10/02/08 18:30:14 526 readStatistics main@1369543768
diff --git a/website/tests/Failed suite [Ant suite]/methods-not-run.html b/website/tests/Failed suite [Ant suite]/methods-not-run.html deleted file mode 100644 index 909d7cb..0000000 --- a/website/tests/Failed suite [Ant suite]/methods-not-run.html +++ /dev/null @@ -1,105 +0,0 @@ -

Methods that were not run

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compbio.metadata.OptionCombinatorTester.testgetAllParameters

compbio.runner.msa.MafftParametersTester.testParameters

compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues

compbio.runner.msa.ProbconsParametersTester.testArguments

compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues

compbio.runner.msa.MafftTester.testExecute

compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration

compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusShortPoolingTime

compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues

compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue

compbio.metadata.OptionMarshallerTester.testMarshalling

compbio.engine.FilePullerTester.testGetDelay

compbio.runner.msa.TcoffeeParametersTester.testParameters

compbio.runner.msa.ProbconsTester.testConfigurationLoading

compbio.engine.conf.RunnerConfigMarshallerTester.testValidation

compbio.runner.msa.MuscleParametersTester.testParameters

compbio.runner.msa.MafftTester.testPersistance

compbio.metadata.RunnerConfigTester.testParameterToCommand

compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate

compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues

compbio.runner.msa.MafftTester.testClusterExecute

compbio.runner.msa.TcoffeeTester.testConfigurationLoading

compbio.runner.msa.ClustalWParametersTester.testParameters

compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration

compbio.runner.msa.LimitTester.testLoadLimits

compbio.metadata.PresetTester.marshallPreset

compbio.runner.msa.TcoffeeTester.readStatistics

compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration

compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues

compbio.metadata.RunnerConfigTester.testValidateValueConstrain

compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime

compbio.runner.msa.MafftParametersTester.testOptions

compbio.runner.msa.ProbconsTester.testSetInputTester

compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling

compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues

compbio.runner.msa.MuscleTester.testPersistance

compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue

compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues

compbio.runner.msa.ClustalWParametersTester.testOptions

compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues

compbio.runner.msa.TcoffeeParametersTester.testOptions

compbio.runner.msa.ProbconsParametersTester.testConfiguration

compbio.runner.msa.ProbconsParametersTester.testDefaultParameters

compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration

compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues

compbio.runner.msa.MuscleParametersTester.testOptions

compbio.metadata.RunnerConfigTester.testOptionToCommand

compbio.runner.msa.MafftTester.readStatistics

compbio.runner.msa.MafftParametersTester.testDefaultParameters

compbio.runner.msa.MafftParametersTester.testConfiguration

compbio.runner.msa.MafftTester.testSetInputTester

compbio.metadata.RunnerConfigTester.testCreateParameter

compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling

compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling

compbio.runner.msa.TcoffeeTester.testNcore

compbio.metadata.OptionCombinatorTester.testgetAllOptions

compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues

compbio.engine.FilePullerTester.testPull

compbio.runner.msa.MuscleTester.testRunLocally

compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters

compbio.runner.msa.TcoffeeParametersTester.testConfiguration

compbio.runner.msa.ProbconsParametersTester.testOptions

compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues

compbio.runner.msa.MuscleParametersTester.testDefaultParameters

compbio.runner.msa.MuscleParametersTester.testConfiguration

compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues

compbio.runner.msa.MuscleTester.testRunOnCluster

compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck

compbio.runner.msa.ClustalWParametersTester.testConfiguration

compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues

compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues

compbio.runner.msa.ClustalWParametersTester.testDefaultParameters

compbio.runner.msa.MuscleTester.testConfigurationLoading

compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf

compbio.runner.msa.MafftParametersTester.testPresets

compbio.runner.msa.TcoffeeTester.testExecute

compbio.metadata.RunnerConfigTester.testValidate

compbio.metadata.PresetTester.validatePresets

compbio.engine.FilePullerTester.testCache

compbio.runner.msa.MuscleTester.readStatistics

compbio.runner.msa.ClustalWParametersTester.testArguments

compbio.metadata.OptionMarshallerTester.testUnMarshalling

compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain

compbio.runner.msa.TcoffeeParametersTester.testArguments

compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration

compbio.runner.msa.MuscleParametersTester.testArguments

compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues

compbio.runner.msa.ProbconsTester.testExecute

compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck

compbio.runner.msa.TcoffeeTester.testPersistance

compbio.engine.conf.PropertyHelperManagerTester.testLocalEngineConf

compbio.runner.msa.ProbconsTester.testClusterExecute

compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck

compbio.runner.msa.TcoffeeParametersTester.testPresets

compbio.runner.msa.MuscleTester.testRunOnClusterAsync

compbio.runner.msa.MuscleParametersTester.testPresets

compbio.runner.msa.MafftParametersTester.testArguments

compbio.runner.msa.MafftTester.testConfigurationLoading

compbio.runner.msa.ProbconsParametersTester.testParameters

compbio.engine.FilePullerTester.testGet

compbio.runner.msa.ProbconsTester.testPersistance

compbio.runner.msa.ClustalWParametersTester.testPresets

compbio.runner.msa.TcoffeeTester.testClusterExecute

\ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/methods.html b/website/tests/Failed suite [Ant suite]/methods.html deleted file mode 100644 index 632a9da..0000000 --- a/website/tests/Failed suite [Ant suite]/methods.html +++ /dev/null @@ -1,12 +0,0 @@ -

Methods run, sorted chronologically

>> means before, << means after

Failed suite [Ant suite]

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

- - - - - - - - - - -
Time Delta (ms) Suite
configuration Test
configuration Class
configuration Groups
configuration Method
configuration Test
method Thread Instances
10/02/08 18:30:13 0 >>init main@1369543768
10/02/08 18:30:14 452 >>loadPresets main@1369543768
10/02/08 18:30:14 525 >>init main@1369543768
10/02/08 18:30:14 526 readStatistics main@1369543768
diff --git a/website/tests/Failed suite [Ant suite]/reporter-output.html b/website/tests/Failed suite [Ant suite]/reporter-output.html deleted file mode 100644 index 063bc2e..0000000 --- a/website/tests/Failed suite [Ant suite]/reporter-output.html +++ /dev/null @@ -1 +0,0 @@ -

Reporter output

\ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/testng-failed.xml b/website/tests/Failed suite [Ant suite]/testng-failed.xml deleted file mode 100644 index 624888d..0000000 --- a/website/tests/Failed suite [Ant suite]/testng-failed.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - diff --git a/website/tests/Failed suite [Ant suite]/testng.xml.html b/website/tests/Failed suite [Ant suite]/testng.xml.html deleted file mode 100644 index 0a8a7ad..0000000 --- a/website/tests/Failed suite [Ant suite]/testng.xml.html +++ /dev/null @@ -1 +0,0 @@ -testng.xml for Failed suite [Ant suite]<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"> <suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Failed suite [Ant suite]" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10"> <test name="Ant test(failed)" junit="false" annotations="JDK"> <groups> <run> <exclude name="performance"/> </run> </groups> <classes> <class name="compbio.runner.msa.MuscleTester"> <methods> <include name="init"/> </methods> </class> <class name="compbio.runner.msa.LimitTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.runner.msa.ClustalWParametersTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.runner.msa.TcoffeeParametersTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.metadata.OptionMarshallerTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.metadata.PresetTester"> <methods> <include name="loadPresets"/> </methods> </class> <class name="compbio.runner.msa.MafftTester"> <methods> <include name="init"/> </methods> </class> <class name="compbio.runner.msa.ProbconsTester"> <methods> <include name="readStatistics"/> <include name="init"/> </methods> </class> <class name="compbio.runner.msa.MuscleParametersTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.engine.conf.PropertyHelperManagerTester"> <methods> <include name="testLoadResources"/> </methods> </class> <class name="compbio.metadata.RunnerConfigTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.runner.msa.MafftParametersTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.metadata.OptionCombinatorTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.runner.msa.ProbconsParametersTester"> <methods> <include name="setup"/> </methods> </class> <class name="compbio.runner.msa.TcoffeeTester"> <methods> <include name="init"/> </methods> </class> <class name="compbio.engine.FilePullerTester"> <methods> <include name="init"/> </methods> </class> <class name="compbio.engine.conf.RunnerConfigMarshallerTester"> <methods> <include name="setup"/> </methods> </class> </classes> </test> </suite> \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/toc.html b/website/tests/Failed suite [Ant suite]/toc.html deleted file mode 100644 index ad058ee..0000000 --- a/website/tests/Failed suite [Ant suite]/toc.html +++ /dev/null @@ -1,30 +0,0 @@ - - -Results for Failed suite [Ant suite] - - - - -

Results for
Failed suite [Ant suite]

- - - - - - - - - - -

1 test	1 class	1 method: - chronological - alphabetical - not run (103)
2 groups	reporter output	testng.xml

- -

Ant test(failed) (1/0/0)

- Results -

- \ No newline at end of file diff --git a/website/tests/JWS2/classes.html b/website/tests/JWS2/classes.html deleted file mode 100644 index 52eb8da..0000000 --- a/website/tests/JWS2/classes.html +++ /dev/null @@ -1,34 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Class name	Method name	Groups
compbio.engine.local.EngineResourcesLeakTester
@Test
	loadEngineRetrieveResultsManyTimes	engine
	loadEngineRetrieveResultsOnce	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass

diff --git a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.html b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.html deleted file mode 100644 index 2b3cebd..0000000 --- a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.html +++ /dev/null @@ -1,153 +0,0 @@ - - -TestNG: compbio.engine.local.EngineResourcesLeakTester - - - - - - - - -

compbio.engine.local.EngineResourcesLeakTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	0/2/0
Started on:	Wed Jan 27 15:33:57 GMT 2010
Total time:	1 seconds (1330 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - - - - - - -
FAILED TESTS
Test method Instance Time (seconds) Exception
loadEngineRetrieveResultsManyTimes
Test class:compbio.engine.local.EngineResourcesLeakTester compbio.engine.local.EngineResourcesLeakTester@444cee32 1
java.lang.AssertionError: expected:<true> but was:<false> - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45) -... Removed 27 stack frames
Click to show all stack frames -
java.lang.AssertionError: expected:<true> but was:<false> - at org.testng.Assert.fail(Assert.java:86) - at org.testng.Assert.failNotEquals(Assert.java:440) - at org.testng.Assert.assertTrue(Assert.java:34) - at org.testng.Assert.assertNotNull(Assert.java:354) - at org.testng.Assert.assertNotNull(Assert.java:344) - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45) - 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) -
loadEngineRetrieveResultsOnce
Test class:compbio.engine.local.EngineResourcesLeakTester compbio.engine.local.EngineResourcesLeakTester@444cee32 0
java.lang.AssertionError: expected:<true> but was:<false> - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113) -... Removed 27 stack frames
Click to show all stack frames -
java.lang.AssertionError: expected:<true> but was:<false> - at org.testng.Assert.fail(Assert.java:86) - at org.testng.Assert.failNotEquals(Assert.java:440) - at org.testng.Assert.assertTrue(Assert.java:34) - at org.testng.Assert.assertNotNull(Assert.java:354) - at org.testng.Assert.assertNotNull(Assert.java:344) - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113) - 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) -

- - \ No newline at end of file diff --git a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.properties b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.properties deleted file mode 100644 index 221a183..0000000 --- a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.engine.local.EngineResourcesLeakTester] \ No newline at end of file diff --git a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.xml b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.xml deleted file mode 100644 index 34e2af7..0000000 --- a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - - but was: - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45) -... Removed 27 stack frames]]> - - - - - but was: - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113) -... Removed 27 stack frames]]> - - - diff --git a/website/tests/JWS2/groups.html b/website/tests/JWS2/groups.html deleted file mode 100644 index 16b0e43..0000000 --- a/website/tests/JWS2/groups.html +++ /dev/null @@ -1,3 +0,0 @@ -

Groups used for this test run

- -

Group name	Methods
engine	compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce() compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes()

diff --git a/website/tests/JWS2/index.html b/website/tests/JWS2/index.html deleted file mode 100644 index bc45584..0000000 --- a/website/tests/JWS2/index.html +++ /dev/null @@ -1,6 +0,0 @@ -Results for JWS2 - - - - - diff --git a/website/tests/JWS2/main.html b/website/tests/JWS2/main.html deleted file mode 100644 index 9acc40e..0000000 --- a/website/tests/JWS2/main.html +++ /dev/null @@ -1,2 +0,0 @@ -Results for JWS2 -Select a result on the left-hand pane. diff --git a/website/tests/JWS2/methods-alphabetical.html b/website/tests/JWS2/methods-alphabetical.html deleted file mode 100644 index 9249041..0000000 --- a/website/tests/JWS2/methods-alphabetical.html +++ /dev/null @@ -1,8 +0,0 @@ -

Methods run, sorted chronologically

>> means before, << means after

JWS2

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

- - - - - - -
Time Delta (ms) Suite
configuration Test
configuration Class
configuration Groups
configuration Method
configuration Test
method Thread Instances
10/01/27 15:33:57 0 loadEngineRetrieveResultsManyTimes main@1663273938
10/01/27 15:33:58 1249 loadEngineRetrieveResultsOnce main@1663273938
diff --git a/website/tests/JWS2/methods-not-run.html b/website/tests/JWS2/methods-not-run.html deleted file mode 100644 index 54b14cb..0000000 --- a/website/tests/JWS2/methods-not-run.html +++ /dev/null @@ -1,2 +0,0 @@ -

Methods that were not run

\ No newline at end of file diff --git a/website/tests/JWS2/methods.html b/website/tests/JWS2/methods.html deleted file mode 100644 index 9249041..0000000 --- a/website/tests/JWS2/methods.html +++ /dev/null @@ -1,8 +0,0 @@ -

Methods run, sorted chronologically

>> means before, << means after

JWS2

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

- - - - - - -
Time Delta (ms) Suite
configuration Test
configuration Class
configuration Groups
configuration Method
configuration Test
method Thread Instances
10/01/27 15:33:57 0 loadEngineRetrieveResultsManyTimes main@1663273938
10/01/27 15:33:58 1249 loadEngineRetrieveResultsOnce main@1663273938
diff --git a/website/tests/JWS2/reporter-output.html b/website/tests/JWS2/reporter-output.html deleted file mode 100644 index 063bc2e..0000000 --- a/website/tests/JWS2/reporter-output.html +++ /dev/null @@ -1 +0,0 @@ -

Reporter output

\ No newline at end of file diff --git a/website/tests/JWS2/testng-failed.xml b/website/tests/JWS2/testng-failed.xml deleted file mode 100644 index 58cda06..0000000 --- a/website/tests/JWS2/testng-failed.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - diff --git a/website/tests/JWS2/testng.xml.html b/website/tests/JWS2/testng.xml.html deleted file mode 100644 index 3d0e061..0000000 --- a/website/tests/JWS2/testng.xml.html +++ /dev/null @@ -1 +0,0 @@ -testng.xml for JWS2<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"> <suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="JWS2" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10"> <test verbose="2" name="compbio.engine.local.EngineResourcesLeakTester" junit="false" annotations="JDK"> <classes> <class name="compbio.engine.local.EngineResourcesLeakTester"/> </classes> </test> </suite> \ No newline at end of file diff --git a/website/tests/JWS2/toc.html b/website/tests/JWS2/toc.html deleted file mode 100644 index 94b16d1..0000000 --- a/website/tests/JWS2/toc.html +++ /dev/null @@ -1,30 +0,0 @@ - - -Results for JWS2 - - - - -

Results for
JWS2

- - - - - - - - - - -

1 test	1 class	2 methods: - chronological - alphabetical - not run (0)
1 group	reporter output	testng.xml

- -

compbio.engine.local.EngineResourcesLeakTester (0/2/0)

- Results -

- \ No newline at end of file diff --git a/website/tests/clustengine/classes.html b/website/tests/clustengine/classes.html deleted file mode 100644 index ca7c305..0000000 --- a/website/tests/clustengine/classes.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Class name	Method name	Groups
compbio.engine.conf.PropertyHelperManagerTester
@Test
	testClusterEngineConf	cluster
	validateClustalConfiguration
	validateTcoffeeConfiguration
	validateMuscleConfiguration
	validateMafftConfiguration
@BeforeClass
	testLoadResources
@BeforeMethod
@AfterMethod
@AfterClass

diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.html b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.html deleted file mode 100644 index 5e1694d..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.html +++ /dev/null @@ -1,84 +0,0 @@ - - -TestNG: compbio.engine.cluster.drmaa.ClusterSessionTester - - - - - - - - -

compbio.engine.cluster.drmaa.ClusterSessionTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	1/0/0
Started on:	Mon Dec 21 16:10:22 GMT 2009
Total time:	13 seconds (13917 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
testTaskList
Test class:compbio.engine.cluster.drmaa.ClusterSessionTester compbio.engine.cluster.drmaa.ClusterSessionTester@2321ab80 13

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.properties b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.properties deleted file mode 100644 index cdc5679..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.engine.cluster.drmaa.ClusterSessionTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.xml b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.xml deleted file mode 100644 index b238c95..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.html b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.html deleted file mode 100644 index 30abc5d..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.html +++ /dev/null @@ -1,129 +0,0 @@ - - -TestNG: compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester - - - - - - - - -

compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	3/0/0
Started on:	Mon Dec 21 16:16:04 GMT 2009
Total time:	31 seconds (31283 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
testCancel
Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e369 0
compbio.engine.ResultNotAvailableException: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/ClustalW#556313082813930709 with file name TO1381.clustal.cluster.out is not found! - at compbio.data.sequence.ClustalAlignmentUtil.readClustalFile(ClustalAlignmentUtil.java:258) - at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:54) - at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:15) - at compbio.runner.ConfExecutable.getResults(ConfExecutable.java:158) - at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:94) -... Removed 22 stack frames
Click to show all stack frames -
compbio.engine.ResultNotAvailableException: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/ClustalW#556313082813930709 with file name TO1381.clustal.cluster.out is not found! - at compbio.data.sequence.ClustalAlignmentUtil.readClustalFile(ClustalAlignmentUtil.java:258) - at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:54) - at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:15) - at compbio.runner.ConfExecutable.getResults(ConfExecutable.java:158) - at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:94) - 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) -
testGetJobStatus
Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e369 11
testSubmit
Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e369 18

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.properties b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.properties deleted file mode 100644 index c90302d..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.xml b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.xml deleted file mode 100644 index 8e5131c..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.xml +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.html b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.html deleted file mode 100644 index d48dd63..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.html +++ /dev/null @@ -1,84 +0,0 @@ - - -TestNG: compbio.engine.cluster.drmaa.DrmaaClusterEngineTester - - - - - - - - -

compbio.engine.cluster.drmaa.DrmaaClusterEngineTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	1/0/0
Started on:	Mon Dec 21 13:38:22 GMT 2009
Total time:	4 seconds (4831 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
testSubmit
Test class:compbio.engine.cluster.drmaa.DrmaaClusterEngineTester compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@13b8f864 4

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.properties b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.properties deleted file mode 100644 index 4b7bcd4..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.engine.cluster.drmaa.DrmaaClusterEngineTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.xml b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.xml deleted file mode 100644 index 1b02fe9..0000000 --- a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.html b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.html deleted file mode 100644 index 316b0a9..0000000 --- a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.html +++ /dev/null @@ -1,109 +0,0 @@ - - -TestNG: compbio.engine.conf.DirectoryManagerTester - - - - - - - - -

compbio.engine.conf.DirectoryManagerTester

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Tests passed/Failed/Skipped:	6/0/0
Started on:	Thu Jan 07 16:48:50 GMT 2010
Total time:	0 seconds (209 ms)
Included groups:
Excluded groups:

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

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PASSED TESTS
Test method Instance Time (seconds) Exception
testGetDirectory compbio.engine.conf.DirectoryManagerTester@2ca6d51e 0
testGetDirectory compbio.engine.conf.DirectoryManagerTester@2ca6d51e 0
testGetDirectory compbio.engine.conf.DirectoryManagerTester@2ca6d51e 0
testGetDirectory compbio.engine.conf.DirectoryManagerTester@2ca6d51e 0
testLongDirName
Test class:compbio.engine.conf.DirectoryManagerTester compbio.engine.conf.DirectoryManagerTester@2ca6d51e 0
testNanoTime
Test class:compbio.engine.conf.DirectoryManagerTester compbio.engine.conf.DirectoryManagerTester@2ca6d51e 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.properties b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.properties deleted file mode 100644 index 9df1de2..0000000 --- a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.engine.conf.DirectoryManagerTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.xml b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.xml deleted file mode 100644 index d20c2da..0000000 --- a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.html b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.html deleted file mode 100644 index 3b0cffc..0000000 --- a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.html +++ /dev/null @@ -1,104 +0,0 @@ - - -TestNG: compbio.engine.conf.PropertyHelperManagerTester - - - - - - - - -

compbio.engine.conf.PropertyHelperManagerTester

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Tests passed/Failed/Skipped:	5/0/0
Started on:	Wed Feb 17 15:33:15 GMT 2010
Total time:	0 seconds (723 ms)
Included groups:
Excluded groups:

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

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PASSED TESTS
Test method Instance Time (seconds) Exception
testClusterEngineConf
Test class:compbio.engine.conf.PropertyHelperManagerTester compbio.engine.conf.PropertyHelperManagerTester@4e99353f 0
validateClustalConfiguration
Test class:compbio.engine.conf.PropertyHelperManagerTester compbio.engine.conf.PropertyHelperManagerTester@4e99353f 0
validateMafftConfiguration
Test class:compbio.engine.conf.PropertyHelperManagerTester compbio.engine.conf.PropertyHelperManagerTester@4e99353f 0
validateMuscleConfiguration
Test class:compbio.engine.conf.PropertyHelperManagerTester compbio.engine.conf.PropertyHelperManagerTester@4e99353f 0
validateTcoffeeConfiguration
Test class:compbio.engine.conf.PropertyHelperManagerTester compbio.engine.conf.PropertyHelperManagerTester@4e99353f 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.properties b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.properties deleted file mode 100644 index 3272d4d..0000000 --- a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.engine.conf.PropertyHelperManagerTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.xml b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.xml deleted file mode 100644 index eedcc52..0000000 --- a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - - - - - - diff --git a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.html b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.html deleted file mode 100644 index 61ec4fe..0000000 --- a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.html +++ /dev/null @@ -1,119 +0,0 @@ - - -TestNG: compbio.engine.local.EngineResourcesLeakTester - - - - - - - - -

compbio.engine.local.EngineResourcesLeakTester

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Tests passed/Failed/Skipped:	0/1/0
Started on:	Tue Jan 26 17:00:52 GMT 2010
Total time:	0 seconds (782 ms)
Included groups:
Excluded groups:

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

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FAILED TESTS
Test method Instance Time (seconds) Exception
loadEngine
Test class:compbio.engine.local.EngineResourcesLeakTester compbio.engine.local.EngineResourcesLeakTester@116471f 0
java.lang.IllegalArgumentException: Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist! - at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) - at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75) - at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist! - at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) - at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75) - at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28) - 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:644) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:546) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:700) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1002) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:137) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:121) - at org.testng.TestRunner.runWorkers(TestRunner.java:908) - at org.testng.TestRunner.privateRun(TestRunner.java:617) - at org.testng.TestRunner.run(TestRunner.java:498) - at org.testng.SuiteRunner.runTest(SuiteRunner.java:329) - at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324) - at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296) - at org.testng.SuiteRunner.run(SuiteRunner.java:201) - at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915) - at org.testng.TestNG.runSuitesLocally(TestNG.java:879) - at org.testng.TestNG.run(TestNG.java:787) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127) -

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.properties b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.properties deleted file mode 100644 index 221a183..0000000 --- a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.engine.local.EngineResourcesLeakTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.xml b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.xml deleted file mode 100644 index 4bc270f..0000000 --- a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - (ExecutableWrapper.java:87) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) - at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75) - at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28) -... Removed 22 stack frames]]> - - - diff --git a/website/tests/clustengine/compbio.metadata.PresetTester.html b/website/tests/clustengine/compbio.metadata.PresetTester.html deleted file mode 100644 index 6ff65b4..0000000 --- a/website/tests/clustengine/compbio.metadata.PresetTester.html +++ /dev/null @@ -1,127 +0,0 @@ - - -TestNG: compbio.metadata.PresetTester - - - - - - - - -

compbio.metadata.PresetTester

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Tests passed/Failed/Skipped:	0/0/2
Started on:	Mon Jan 25 15:45:52 GMT 2010
Total time:	0 seconds (110 ms)
Included groups:
Excluded groups:

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

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FAILED CONFIGURATIONS
Test method Instance Time (seconds) Exception
loadPresets
Test class:compbio.metadata.PresetTester null 0
java.lang.AssertionError: null - at compbio.metadata.PresetTester.loadPresets(PresetTester.java:85) -... Removed 20 stack frames
Click to show all stack frames -
java.lang.AssertionError: null - at org.testng.Assert.fail(Assert.java:87) - at compbio.metadata.PresetTester.loadPresets(PresetTester.java:85) - 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:644) - at org.testng.internal.Invoker.invokeConfigurationMethod(Invoker.java:443) - at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:160) - at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:90) - at org.testng.TestRunner.beforeRun(TestRunner.java:522) - at org.testng.TestRunner.run(TestRunner.java:490) - at org.testng.SuiteRunner.runTest(SuiteRunner.java:329) - at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324) - at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296) - at org.testng.SuiteRunner.run(SuiteRunner.java:201) - at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915) - at org.testng.TestNG.runSuitesLocally(TestNG.java:879) - at org.testng.TestNG.run(TestNG.java:787) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127) -

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SKIPPED TESTS
Test method Instance Time (seconds) Exception
marshallPreset
Test class:compbio.metadata.PresetTester compbio.metadata.PresetTester@1171b26 0
validatePresets
Test class:compbio.metadata.PresetTester compbio.metadata.PresetTester@1171b26 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.metadata.PresetTester.properties b/website/tests/clustengine/compbio.metadata.PresetTester.properties deleted file mode 100644 index 604ca3e..0000000 --- a/website/tests/clustengine/compbio.metadata.PresetTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.metadata.PresetTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.metadata.PresetTester.xml b/website/tests/clustengine/compbio.metadata.PresetTester.xml deleted file mode 100644 index a425b4d..0000000 --- a/website/tests/clustengine/compbio.metadata.PresetTester.xml +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - - - - - - - - - diff --git a/website/tests/clustengine/compbio.runner.CommandBuilderTester.html b/website/tests/clustengine/compbio.runner.CommandBuilderTester.html deleted file mode 100644 index 794bf77..0000000 --- a/website/tests/clustengine/compbio.runner.CommandBuilderTester.html +++ /dev/null @@ -1,84 +0,0 @@ - - -TestNG: compbio.runner.CommandBuilderTester - - - - - - - - -

compbio.runner.CommandBuilderTester

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Tests passed/Failed/Skipped:	1/0/0
Started on:	Thu Jan 14 14:12:38 GMT 2010
Total time:	0 seconds (32 ms)
Included groups:
Excluded groups:

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

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PASSED TESTS
Test method Instance Time (seconds) Exception
testCommandBuilding
Test class:compbio.runner.CommandBuilderTester compbio.runner.CommandBuilderTester@34a1fc 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.CommandBuilderTester.properties b/website/tests/clustengine/compbio.runner.CommandBuilderTester.properties deleted file mode 100644 index b4c9fb5..0000000 --- a/website/tests/clustengine/compbio.runner.CommandBuilderTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.CommandBuilderTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.CommandBuilderTester.xml b/website/tests/clustengine/compbio.runner.CommandBuilderTester.xml deleted file mode 100644 index cb26c89..0000000 --- a/website/tests/clustengine/compbio.runner.CommandBuilderTester.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.html b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.html deleted file mode 100644 index 1b2d8f5..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.html +++ /dev/null @@ -1,406 +0,0 @@ - - -TestNG: compbio.runner.clustal.ClustalWParametersTester - - - - - - - - -

compbio.runner.clustal.ClustalWParametersTester

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Tests passed/Failed/Skipped:	0/8/0
Started on:	Mon Dec 21 18:09:47 GMT 2009
Total time:	2 seconds (2219 ms)
Included groups:
Excluded groups:

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

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FAILED TESTS
Test method Time (seconds) Exception
testArguments 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137) - 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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -
testConstrainedParametersMaxValues 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151) - 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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -
testConstrainedParametersMinValues 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144) - 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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -
testConstrainedParametersRandomValues 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164) - 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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -
testDefaultParameters 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -
testOptions 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122) - 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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -
testParameters 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129) - 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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -
testPresets 0
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist! - at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231) - 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:607) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:517) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110) - 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:877) - at org.testng.TestNG.runSuitesLocally(TestNG.java:842) - at org.testng.TestNG.run(TestNG.java:751) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124) -

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.properties b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.properties deleted file mode 100644 index 89fb9a5..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.clustal.ClustalWParametersTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.xml b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.xml deleted file mode 100644 index 9b22c51..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.xml +++ /dev/null @@ -1,96 +0,0 @@ - - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231) -... Removed 22 stack frames]]> - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137) -... Removed 22 stack frames]]> - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129) -... Removed 22 stack frames]]> - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105) -... Removed 22 stack frames]]> - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) - at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122) -... Removed 22 stack frames]]> - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144) -... Removed 22 stack frames]]> - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151) -... Removed 22 stack frames]]> - - - - - (ExecutableWrapper.java:57) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) - at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) - at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164) -... Removed 22 stack frames]]> - - - diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.html b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.html deleted file mode 100644 index 225516c..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.html +++ /dev/null @@ -1,84 +0,0 @@ - - -TestNG: compbio.runner.clustal.ClustalWTester - - - - - - - - -

compbio.runner.clustal.ClustalWTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	1/0/0
Started on:	Fri Jan 15 16:55:36 GMT 2010
Total time:	0 seconds (285 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
testRunWithMatrix
Test class:compbio.runner.clustal.ClustalWTester compbio.runner.clustal.ClustalWTester@3d860038 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.properties b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.properties deleted file mode 100644 index 41b902e..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.clustal.ClustalWTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.xml b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.xml deleted file mode 100644 index 28e3f4a..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/website/tests/clustengine/compbio.runner.clustal.LimitTester.html b/website/tests/clustengine/compbio.runner.clustal.LimitTester.html deleted file mode 100644 index ecf2617..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.LimitTester.html +++ /dev/null @@ -1,83 +0,0 @@ - - -TestNG: compbio.runner.clustal.LimitTester - - - - - - - - -

compbio.runner.clustal.LimitTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	1/0/0
Started on:	Mon Dec 21 17:22:34 GMT 2009
Total time:	0 seconds (719 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - -
PASSED TESTS
Test method Time (seconds) Exception
testLoadLimits 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.LimitTester.properties b/website/tests/clustengine/compbio.runner.clustal.LimitTester.properties deleted file mode 100644 index 5bece15..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.LimitTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.clustal.LimitTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.LimitTester.xml b/website/tests/clustengine/compbio.runner.clustal.LimitTester.xml deleted file mode 100644 index 1d5674a..0000000 --- a/website/tests/clustengine/compbio.runner.clustal.LimitTester.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/website/tests/clustengine/compbio.runner.mafft.MafftTester.html b/website/tests/clustengine/compbio.runner.mafft.MafftTester.html deleted file mode 100644 index 364217f..0000000 --- a/website/tests/clustengine/compbio.runner.mafft.MafftTester.html +++ /dev/null @@ -1,84 +0,0 @@ - - -TestNG: compbio.runner.mafft.MafftTester - - - - - - - - -

compbio.runner.mafft.MafftTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	1/0/0
Started on:	Mon Jan 25 17:07:55 GMT 2010
Total time:	0 seconds (682 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
testExecute
Test class:compbio.runner.mafft.MafftTester compbio.runner.mafft.MafftTester@13b8f864 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.mafft.MafftTester.properties b/website/tests/clustengine/compbio.runner.mafft.MafftTester.properties deleted file mode 100644 index b36a025..0000000 --- a/website/tests/clustengine/compbio.runner.mafft.MafftTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.mafft.MafftTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.mafft.MafftTester.xml b/website/tests/clustengine/compbio.runner.mafft.MafftTester.xml deleted file mode 100644 index 4b8fe84..0000000 --- a/website/tests/clustengine/compbio.runner.mafft.MafftTester.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.html b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.html deleted file mode 100644 index 3a62862..0000000 --- a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.html +++ /dev/null @@ -1,117 +0,0 @@ - - -TestNG: compbio.runner.muscle.MuscleTester - - - - - - - - -

compbio.runner.muscle.MuscleTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	0/1/0
Started on:	Mon Jan 25 17:08:34 GMT 2010
Total time:	6 seconds (6782 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - -
FAILED TESTS
Test method Instance Time (seconds) Exception
testRunLocally
Test class:compbio.runner.muscle.MuscleTester compbio.runner.muscle.MuscleTester@18020cc 1
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist! - at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) - at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173) -... Removed 22 stack frames
Click to show all stack frames -
java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist! - at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93) - at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) - at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173) - 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:644) - at org.testng.internal.Invoker.invokeMethod(Invoker.java:546) - at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:700) - at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1002) - at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:137) - at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:121) - at org.testng.TestRunner.runWorkers(TestRunner.java:908) - at org.testng.TestRunner.privateRun(TestRunner.java:617) - at org.testng.TestRunner.run(TestRunner.java:498) - at org.testng.SuiteRunner.runTest(SuiteRunner.java:329) - at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324) - at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296) - at org.testng.SuiteRunner.run(SuiteRunner.java:201) - at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915) - at org.testng.TestNG.runSuitesLocally(TestNG.java:879) - at org.testng.TestNG.run(TestNG.java:787) - at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75) - at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127) -

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.properties b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.properties deleted file mode 100644 index 87d54e7..0000000 --- a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.muscle.MuscleTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.xml b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.xml deleted file mode 100644 index bbcd8d6..0000000 --- a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.xml +++ /dev/null @@ -1,14 +0,0 @@ - - - - - - (ExecutableWrapper.java:87) - at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) - at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173) -... Removed 22 stack frames]]> - - - diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.html b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.html deleted file mode 100644 index e93ca5d..0000000 --- a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.html +++ /dev/null @@ -1,114 +0,0 @@ - - -TestNG: compbio.runner.probcons.ProbconsParametersTester - - - - - - - - -

compbio.runner.probcons.ProbconsParametersTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	7/0/0
Started on:	Mon Jan 11 16:11:14 GMT 2010
Total time:	140 seconds (140484 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
testArguments
Test class:compbio.runner.probcons.ProbconsParametersTester compbio.runner.probcons.ProbconsParametersTester@6513cf0 1
testConstrainedParametersMaxValues
Test class:compbio.runner.probcons.ProbconsParametersTester compbio.runner.probcons.ProbconsParametersTester@6513cf0 37
testConstrainedParametersMinValues
Test class:compbio.runner.probcons.ProbconsParametersTester compbio.runner.probcons.ProbconsParametersTester@6513cf0 0
testConstrainedParametersRandomValues
Test class:compbio.runner.probcons.ProbconsParametersTester compbio.runner.probcons.ProbconsParametersTester@6513cf0 74
testDefaultParameters
Test class:compbio.runner.probcons.ProbconsParametersTester compbio.runner.probcons.ProbconsParametersTester@6513cf0 24
testOptions
Test class:compbio.runner.probcons.ProbconsParametersTester compbio.runner.probcons.ProbconsParametersTester@6513cf0 0
testParameters
Test class:compbio.runner.probcons.ProbconsParametersTester compbio.runner.probcons.ProbconsParametersTester@6513cf0 1

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.properties b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.properties deleted file mode 100644 index a9fa110..0000000 --- a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.probcons.ProbconsParametersTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.xml b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.xml deleted file mode 100644 index 96f8857..0000000 --- a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - - - - diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.html b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.html deleted file mode 100644 index b824aff..0000000 --- a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.html +++ /dev/null @@ -1,112 +0,0 @@ - - -TestNG: compbio.runner.probcons.ProbconsTester - - - - - - - - -

compbio.runner.probcons.ProbconsTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	0/1/0
Started on:	Fri Jan 15 17:16:57 GMT 2010
Total time:	0 seconds (549 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - -
FAILED TESTS
Test method Instance Time (seconds) Exception
testExecute
Test class:compbio.runner.probcons.ProbconsTester compbio.runner.probcons.ProbconsTester@5cbfe9d 0
java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found! - at compbio.runner.probcons.ProbconsTester.testExecute(ProbconsTester.java:99) -... Removed 23 stack frames
Click to show all stack frames -
java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found! - at org.testng.Assert.fail(Assert.java:86) - at compbio.runner.probcons.ProbconsTester.testExecute(ProbconsTester.java:99) - 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) -

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.properties b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.properties deleted file mode 100644 index 6110b4f..0000000 --- a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.probcons.ProbconsTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.xml b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.xml deleted file mode 100644 index 5822b7c..0000000 --- a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - - diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.html b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.html deleted file mode 100644 index 18d211c..0000000 --- a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.html +++ /dev/null @@ -1,119 +0,0 @@ - - -TestNG: compbio.runner.tcoffee.TcoffeeParametersTester - - - - - - - - -

compbio.runner.tcoffee.TcoffeeParametersTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	8/0/0
Started on:	Fri Jan 15 12:35:10 GMT 2010
Total time:	69 seconds (69406 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
PASSED TESTS
Test method Instance Time (seconds) Exception
testArguments
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 5
testConstrainedParametersMaxValues
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 8
testConstrainedParametersMinValues
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 4
testConstrainedParametersRandomValues
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 17
testDefaultParameters
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 21
testOptions
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 1
testParameters
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 9
testPresets
Test class:compbio.runner.tcoffee.TcoffeeParametersTester compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7 0

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.properties b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.properties deleted file mode 100644 index f22ffc3..0000000 --- a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.tcoffee.TcoffeeParametersTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.xml b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.xml deleted file mode 100644 index 882a0d1..0000000 --- a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.html b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.html deleted file mode 100644 index fae5fe0..0000000 --- a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.html +++ /dev/null @@ -1,112 +0,0 @@ - - -TestNG: compbio.runner.tcoffee.TcoffeeTester - - - - - - - - -

compbio.runner.tcoffee.TcoffeeTester

- - - - - - - - - - - -

Tests passed/Failed/Skipped:	0/1/0
Started on:	Fri Jan 15 17:10:30 GMT 2010
Total time:	1 seconds (1723 ms)
Included groups:
Excluded groups:

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

- - - - - - - - - - - - -
FAILED TESTS
Test method Instance Time (seconds) Exception
testExecute
Test class:compbio.runner.tcoffee.TcoffeeTester compbio.runner.tcoffee.TcoffeeTester@13b8f864 1
java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found! - at compbio.runner.tcoffee.TcoffeeTester.testExecute(TcoffeeTester.java:92) -... Removed 23 stack frames
Click to show all stack frames -
java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found! - at org.testng.Assert.fail(Assert.java:86) - at compbio.runner.tcoffee.TcoffeeTester.testExecute(TcoffeeTester.java:92) - 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) -

- - \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.properties b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.properties deleted file mode 100644 index b30cf76..0000000 --- a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.properties +++ /dev/null @@ -1 +0,0 @@ -[SuiteResult compbio.runner.tcoffee.TcoffeeTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.xml b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.xml deleted file mode 100644 index 573ffeb..0000000 --- a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - - diff --git a/website/tests/clustengine/groups.html b/website/tests/clustengine/groups.html deleted file mode 100644 index 1910670..0000000 --- a/website/tests/clustengine/groups.html +++ /dev/null @@ -1,3 +0,0 @@ -

Groups used for this test run

- -

Group name	Methods
cluster	compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()

diff --git a/website/tests/clustengine/index.html b/website/tests/clustengine/index.html deleted file mode 100644 index 4b5a4d2..0000000 --- a/website/tests/clustengine/index.html +++ /dev/null @@ -1,6 +0,0 @@ -Results for clustengine - - - - - diff --git a/website/tests/clustengine/main.html b/website/tests/clustengine/main.html deleted file mode 100644 index 280992c..0000000 --- a/website/tests/clustengine/main.html +++ /dev/null @@ -1,2 +0,0 @@ -Results for clustengine -Select a result on the left-hand pane. diff --git a/website/tests/clustengine/methods-alphabetical.html b/website/tests/clustengine/methods-alphabetical.html deleted file mode 100644 index a993f34..0000000 --- a/website/tests/clustengine/methods-alphabetical.html +++ /dev/null @@ -1,16 +0,0 @@ -

Methods run, sorted chronologically

>> means before, << means after

clustengine

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

- - - - - - - - - - - - - - -
Time Delta (ms) Suite
configuration Test
configuration Class
configuration Groups
configuration Method
configuration Test
method Thread Instances
10/02/17 15:33:16 0 testClusterEngineConf main@1421571929
10/02/17 15:33:15 -606 >>testLoadResources main@1421571929
10/02/17 15:33:16 13 validateClustalConfiguration main@1421571929
10/02/17 15:33:16 68 validateMafftConfiguration main@1421571929
10/02/17 15:33:16 80 validateMuscleConfiguration main@1421571929
10/02/17 15:33:16 92 validateTcoffeeConfiguration main@1421571929
diff --git a/website/tests/clustengine/methods-not-run.html b/website/tests/clustengine/methods-not-run.html deleted file mode 100644 index 54b14cb..0000000 --- a/website/tests/clustengine/methods-not-run.html +++ /dev/null @@ -1,2 +0,0 @@ -

Methods that were not run

\ No newline at end of file diff --git a/website/tests/clustengine/methods.html b/website/tests/clustengine/methods.html deleted file mode 100644 index e499aaf..0000000 --- a/website/tests/clustengine/methods.html +++ /dev/null @@ -1,16 +0,0 @@ -

Methods run, sorted chronologically

>> means before, << means after

clustengine

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

- - - - - - - - - - - - - - -
Time Delta (ms) Suite
configuration Test
configuration Class
configuration Groups
configuration Method
configuration Test
method Thread Instances
10/02/17 15:33:15 0 >>testLoadResources main@1421571929
10/02/17 15:33:16 606 testClusterEngineConf main@1421571929
10/02/17 15:33:16 619 validateClustalConfiguration main@1421571929
10/02/17 15:33:16 674 validateMafftConfiguration main@1421571929
10/02/17 15:33:16 686 validateMuscleConfiguration main@1421571929
10/02/17 15:33:16 698 validateTcoffeeConfiguration main@1421571929
diff --git a/website/tests/clustengine/reporter-output.html b/website/tests/clustengine/reporter-output.html deleted file mode 100644 index 063bc2e..0000000 --- a/website/tests/clustengine/reporter-output.html +++ /dev/null @@ -1 +0,0 @@ -

Reporter output

\ No newline at end of file diff --git a/website/tests/clustengine/testng-failed.xml b/website/tests/clustengine/testng-failed.xml deleted file mode 100644 index b9ea5c6..0000000 --- a/website/tests/clustengine/testng-failed.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - diff --git a/website/tests/clustengine/testng.xml.html b/website/tests/clustengine/testng.xml.html deleted file mode 100644 index dec3522..0000000 --- a/website/tests/clustengine/testng.xml.html +++ /dev/null @@ -1 +0,0 @@ -testng.xml for clustengine<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"> <suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="clustengine" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10"> <test verbose="2" name="compbio.engine.conf.PropertyHelperManagerTester" junit="false" annotations="JDK"> <classes> <class name="compbio.engine.conf.PropertyHelperManagerTester"/> </classes> </test> </suite> \ No newline at end of file diff --git a/website/tests/clustengine/toc.html b/website/tests/clustengine/toc.html deleted file mode 100644 index 0c29c08..0000000 --- a/website/tests/clustengine/toc.html +++ /dev/null @@ -1,30 +0,0 @@ - - -Results for clustengine - - - - -

Results for
clustengine

- - - - - - - - - - -

1 test	1 class	5 methods: - chronological - alphabetical - not run (0)
1 group	reporter output	testng.xml

- -

compbio.engine.conf.PropertyHelperManagerTester (5/0/0)

- Results -

- \ No newline at end of file diff --git a/website/tests/emailable-report.html b/website/tests/emailable-report.html deleted file mode 100644 index 25d37af..0000000 --- a/website/tests/emailable-report.html +++ /dev/null @@ -1,626 +0,0 @@ - - - -TestNG: Unit Test - - - - - - -

Test	Methods Passed	Scenarios Passed	# skipped	# failed	Total Time	Included Groups	Excluded Groups
Ant test	154	165	0	0	524.4 seconds		performance

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Class	Method	# of Scenarios	Time (Msecs)
Ant test — passed
compbio.data.sequence.ClustalAlignmentUtilTester	testReadClustalFile	1	22
	testReadClustalFileLongNames	1	52
	testReadClustalFileShortNames	1	54
compbio.data.sequence.FastaSequenceGeneratorTester	testProteinSequenceGeneration	1	8
compbio.data.sequence.FastaSequenceTester	testGetFormattedFasta	1	0
compbio.data.sequence.SequenceUtilTester	testCleanSequence	1	0
	testDeepCleanSequence	1	0
	testReadWriteFasta	1	16
	testisNonAmbNucleotideSequence	1	0
	testisProteinSequence	1	0
compbio.engine.EngineConfiguratorTester	testGetAsyncEngine	1	296
compbio.engine.EngineConfiguratorTester	testGetSyncEngine	1	0
compbio.engine.FilePullerTester	testCache (engine)	1	6006
	testGet	1	46
	testGetDelay (engine)	1	0
	testPull (engine)	1	450
compbio.engine.PulledFileCacheTester	test	1	5187
compbio.engine.client.CommandBuilderTester	testCommandBuilding	1	1
	testOptionsToCommand	1	567
	testSpaceDelimiterExecutable	1	0
compbio.engine.client.PathValidatorTester	testGetClassPath	1	234
compbio.engine.client.PathValidatorTester	testIsAbsolutePath	1	0
compbio.engine.cluster.drmaa.ClusterSessionTester	testTaskList (engine, cluster)	1	8964
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester	testCancel (engine, cluster)	1	1273
	testGetJobStatus (engine, cluster)	1	20778
	testSubmit (engine, cluster)	1	18714
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester	testCancel (engine, cluster)	1	1587
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester	testSubmit (engine, cluster)	1	17835
compbio.engine.cluster.drmaa.UtilTester	testParser	1	0
compbio.engine.cluster.dundee._QueueTester	testQueue	1	0
compbio.engine.conf.DirectoryManagerTester	testGetDirectory	4	111
compbio.engine.conf.PropertyHelperManagerTester	testClusterEngineConf (cluster)	1	104
	validateClustalConfiguration	1	43
	validateMafftConfiguration	1	1
	validateMuscleConfiguration	1	4
	validateTcoffeeConfiguration	1	4
compbio.engine.conf.RunnerConfigMarshallerTester	testMarshalling	1	20
	testSchemaFromCodeGeneration	1	504
	testUnMarshalling	1	580
	testValidation	1	636
	testValidationOnMarshalling	1	11
compbio.engine.local.AsyncLocalRunnerTester	testAsyncCancelOperation (engine)	1	48
	testAsyncRetrievOperation (engine)	1	560
	testCancelCompletedTaskLocally (engine)	1	3053
	testCancelLocally (engine)	1	27
	testGetStatus (engine)	5	41735
	testMultipleCancelLocally (engine)	1	267
	testSubmitLocally (engine)	5	634
compbio.engine.local.LocalRunnerTester	testCancelCompletedTaskLocally (engine)	1	336
	testCancelLocally (engine)	1	20
	testMultipleCancelLocally (engine)	1	58
compbio.metadata.OptionCombinatorTester	testgetAllOptions	1	1
compbio.metadata.OptionCombinatorTester	testgetAllParameters	1	3
compbio.metadata.OptionMarshallerTester	testMarshalling	1	58
compbio.metadata.OptionMarshallerTester	testUnMarshalling	1	386
compbio.metadata.PresetTester	marshallPreset	1	899
compbio.metadata.PresetTester	validatePresets	1	1
compbio.metadata.RunnerConfigTester	testCreateNumParameterWithoutValidValue	1	1
	testCreateParameter	1	0
	testCreateParameterWithValidValueConstrain	1	0
	testOptionNoDefaultValidate	1	0
	testOptionSetInvalidValue	1	1
	testOptionToCommand	1	0
	testParameterToCommand	1	0
	testValidate	1	0
	testValidateBoundaryConstrainCheck	1	1
	testValidateLowerBoundaryConstrainCheck	1	0
	testValidateUpperBoundaryConstrainCheck	1	0
	testValidateValueConstrain	1	0
compbio.runner._impl.MclTester	testGetTestCommand	1	1
compbio.runner._impl.NetNglycTester	testGetTestCommand	1	0
compbio.runner._impl.OBTester	testGetTestArgsCommand	1	0
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.msa.ClustalWParametersTester	testArguments (runner)	1	3518
	testConfiguration	1	1
	testConstrainedParametersMaxValues (runner)	1	1835
	testConstrainedParametersMinValues (runner)	1	1232
	testConstrainedParametersRandomValues (runner)	1	3105
	testDefaultParameters (runner)	1	502
	testOptions (runner)	1	2109
	testParameters (runner)	1	2680
	testPresets (runner)	1	177
compbio.runner.msa.ClustalWTester	readStatistics (runner)	1	1178
	readStatisticsClusterExecution (cluster, runner)	1	8121
	testConfigurationLoading (runner)	1	688
	testOptionsLocally (runner)	1	1932
	testPersistance (runner)	1	431
	testRunLocally (runner)	1	171
	testRunOnCluster (cluster, runner)	1	15937
	testRunWithMatrix (runner)	1	824
compbio.runner.msa.LimitTester	testLoadLimits	1	0
compbio.runner.msa.MafftParametersTester	testArguments (runner, non_windows)	1	6103
	testConfiguration	1	1
	testConstrainedParametersMaxValues (runner, non_windows)	1	3235
	testConstrainedParametersMinValues (runner, non_windows)	1	1326
	testConstrainedParametersRandomValues (runner, non_windows)	1	7672
	testDefaultParameters (runner, non_windows)	1	20463
	testOptions (runner, non_windows)	1	4449
	testParameters (runner, non_windows)	1	2422
	testPresets (runner, non_windows)	1	2136
compbio.runner.msa.MafftTester	readStatistics (runner, non_windows)	1	639
	testClusterExecute (cluster, runner, non_windows)	1	11340
	testConfigurationLoading (runner)	1	435
	testExecute (runner, non_windows)	1	428
	testPersistance (runner, non_windows)	1	1033
	testRunOnClusterAsyncCheckStatusLongPoolingTime (cluster, runner, non_windows)	1	21418
	testSetInputTester (runner, non_windows)	1	0
compbio.runner.msa.MuscleParametersTester	testArguments (runner)	1	7798
	testConfiguration	1	0
	testConstrainedParametersMaxValues (runner)	1	1534
	testConstrainedParametersMinValues (runner)	1	845
	testConstrainedParametersRandomValues (runner)	1	7603
	testDefaultParameters (runner)	1	622
	testOptions (runner)	1	2481
	testParameters (runner)	1	4773
	testPresets (runner)	1	856
compbio.runner.msa.MuscleTester	readStatistics (runner)	1	932
	testConfigurationLoading (runner)	1	313
	testPersistance (runner)	1	241
	testRunLocally (runner)	1	101
	testRunOnCluster (cluster, runner)	1	8142
compbio.runner.msa.ProbconsParametersTester	testArguments (runner, non_windows)	1	2874
	testConfiguration	1	1
	testConstrainedParametersMaxValues (runner, non_windows)	1	38416
	testConstrainedParametersMinValues (runner, non_windows)	1	768
	testConstrainedParametersRandomValues (runner, non_windows)	1	61881
	testDefaultParameters (runner, non_windows)	1	14704
	testOptions (runner, non_windows)	1	433
	testParameters (runner, non_windows)	1	1321
compbio.runner.msa.ProbconsTester	readStatistics (runner, non_windows)	1	441
	testClusterExecute (cluster, runner, non_windows)	1	19326
	testConfigurationLoading (runner)	1	107
	testExecute (runner, non_windows)	1	436
	testPersistance (runner, non_windows)	1	509
	testSetInputTester (runner, non_windows)	1	0
compbio.runner.msa.TcoffeeParametersTester	testArguments (runner, non_windows)	1	8765
	testConfiguration	1	0
	testConstrainedParametersMaxValues (runner, non_windows)	1	11166
	testConstrainedParametersMinValues (runner, non_windows)	1	5507
	testConstrainedParametersRandomValues (runner, non_windows)	1	21942
	testDefaultParameters (runner, non_windows)	1	10988
	testOptions (runner, non_windows)	1	891
	testParameters (runner, non_windows)	1	12717
	testPresets (runner, non_windows)	1	1094
compbio.runner.msa.TcoffeeTester "Ant test"	readStatistics (runner, non_windows)	1	876
	testClusterExecute (cluster, runner, non_windows)	1	5526
	testConfigurationLoading (runner)	1	99
	testExecute (runner, non_windows)	1	868
	testNcore (runner, non_windows)	1	1
	testPersistance (cluster, runner, non_windows)	1	1771

Time	Delta (ms)	Test configuration	Class configuration	Method configuration	Test method	Thread
10/02/17 15:34:08	0	>>init				main@277466206
10/02/17 15:38:32	264017			>>init		main@277466206
10/02/17 15:38:32	264017			>>init		main@277466206
10/02/17 15:38:32	264017			>>init		main@277466206
10/02/17 15:38:32	264017			>>init		main@277466206
10/02/17 15:38:32	264017			>>init		main@277466206
10/02/17 15:38:32	264017			>>init		main@277466206
10/02/17 15:38:32	264017			>>init		main@277466206
10/02/17 15:39:01	292556			>>init		main@277466206
10/02/17 15:39:01	292556			>>init		main@277466206
10/02/17 15:39:01	292556			>>init		main@277466206
10/02/17 15:39:01	292556			>>init		main@277466206
10/02/17 15:39:01	292556			>>init		main@277466206
10/02/17 15:41:30	442181			>>init		main@277466206
10/02/17 15:41:30	442181			>>init		main@277466206
10/02/17 15:41:30	442181			>>init		main@277466206
10/02/17 15:41:30	442181			>>init		main@277466206
10/02/17 15:41:30	442181			>>init		main@277466206
10/02/17 15:41:30	442181			>>init		main@277466206
10/02/17 15:42:51	522627			>>init		main@277466206
10/02/17 15:42:51	522627			>>init		main@277466206
10/02/17 15:42:51	522627			>>init		main@277466206
10/02/17 15:42:51	522627			>>init		main@277466206
10/02/17 15:42:51	522627			>>init		main@277466206
10/02/17 15:42:51	522627			>>init		main@277466206
10/02/17 15:34:10	1737	>>loadPresets				main@277466206
10/02/17 15:36:38	149837				marshallPreset	main@277466206
10/02/17 15:36:39	151131				readStatistics	main@277466206
10/02/17 15:37:57	228724				readStatistics	main@277466206
10/02/17 15:38:59	290965				readStatistics	main@277466206
10/02/17 15:41:09	421361				readStatistics	main@277466206
10/02/17 15:42:43	515257				readStatistics	main@277466206
10/02/17 15:36:40	152310				readStatisticsClusterExecution	main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:34:32	24054			>>setup		main@277466206
10/02/17 15:35:50	102092			>>setup		main@277466206
10/02/17 15:35:50	102092			>>setup		main@277466206
10/02/17 15:35:50	102092			>>setup		main@277466206
10/02/17 15:35:50	102092			>>setup		main@277466206
10/02/17 15:35:50	102092			>>setup		main@277466206
10/02/17 15:36:37	149279			>>setup		main@277466206
10/02/17 15:36:37	149279			>>setup		main@277466206
10/02/17 15:36:38	149451			>>setup		main@277466206
10/02/17 15:36:38	149451			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:36:39	151114			>>setup		main@277466206
10/02/17 15:37:09	180414			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:37:55	226540			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:38:58	290061			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:41:08	420008			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:42:42	514162			>>setup		main@277466206
10/02/17 15:34:33	24806				test	main@277466206
10/02/17 15:34:17	8754				testArguments	main@277466206
10/02/17 15:37:09	180523				testArguments	main@277466206
10/02/17 15:38:32	264102				testArguments	main@277466206
10/02/17 15:39:09	300748				testArguments	main@277466206
10/02/17 15:41:30	442182				testArguments	main@277466206
10/02/17 15:35:50	102119				testAsyncCancelOperation	main@277466206
10/02/17 15:35:50	102168				testAsyncRetrievOperation	main@277466206
10/02/17 15:34:11	2379				testCache	main@277466206
10/02/17 15:34:48	39760				testCancel	main@277466206
10/02/17 15:35:29	80525				testCancel	main@277466206
10/02/17 15:35:51	102728				testCancelCompletedTaskLocally	main@277466206
10/02/17 15:36:37	148461				testCancelCompletedTaskLocally	main@277466206
10/02/17 15:35:54	105781				testCancelLocally	main@277466206
10/02/17 15:36:37	148798				testCancelLocally	main@277466206
10/02/17 15:34:33	24445				testCleanSequence	main@277466206
10/02/17 15:35:48	100065				testClusterEngineConf	main@277466206
10/02/17 15:37:57	229363				testClusterExecute	main@277466206
10/02/17 15:41:10	421803				testClusterExecute	main@277466206
10/02/17 15:42:44	516133				testClusterExecute	main@277466206
10/02/17 15:34:38	29993				testCommandBuilding	main@277466206
10/02/17 15:34:20	12305				testConfiguration	main@277466206
10/02/17 15:37:15	186680				testConfiguration	main@277466206
10/02/17 15:38:40	271944				testConfiguration	main@277466206
10/02/17 15:39:12	303651				testConfiguration	main@277466206
10/02/17 15:41:39	450947				testConfiguration	main@277466206
10/02/17 15:36:49	160431				testConfigurationLoading	main@277466206
10/02/17 15:38:09	240703				testConfigurationLoading	main@277466206
10/02/17 15:39:00	291898				testConfigurationLoading	main@277466206
10/02/17 15:41:29	441129				testConfigurationLoading	main@277466206
10/02/17 15:42:50	521659				testConfigurationLoading	main@277466206
10/02/17 15:34:20	12333				testConstrainedParametersMaxValues	main@277466206
10/02/17 15:37:15	186725				testConstrainedParametersMaxValues	main@277466206
10/02/17 15:38:40	271986				testConstrainedParametersMaxValues	main@277466206
10/02/17 15:39:12	303681				testConstrainedParametersMaxValues	main@277466206
10/02/17 15:41:39	450948				testConstrainedParametersMaxValues	main@277466206
10/02/17 15:34:22	14199				testConstrainedParametersMinValues	main@277466206
10/02/17 15:37:18	190008				testConstrainedParametersMinValues	main@277466206
10/02/17 15:38:42	273564				testConstrainedParametersMinValues	main@277466206
10/02/17 15:39:50	342135				testConstrainedParametersMinValues	main@277466206
10/02/17 15:41:50	462115				testConstrainedParametersMinValues	main@277466206
10/02/17 15:34:24	15492				testConstrainedParametersRandomValues	main@277466206
10/02/17 15:37:20	191380				testConstrainedParametersRandomValues	main@277466206
10/02/17 15:38:43	274453				testConstrainedParametersRandomValues	main@277466206
10/02/17 15:39:51	342932				testConstrainedParametersRandomValues	main@277466206
10/02/17 15:41:56	467622				testConstrainedParametersRandomValues	main@277466206
10/02/17 15:36:39	150771				testCreateNumParameterWithoutValidValue	main@277466206
10/02/17 15:36:39	150787				testCreateParameter	main@277466206
10/02/17 15:36:39	150802				testCreateParameterWithValidValueConstrain	main@277466206
10/02/17 15:34:33	24446				testDeepCleanSequence	main@277466206
10/02/17 15:34:27	18651				testDefaultParameters	main@277466206
10/02/17 15:37:27	199100				testDefaultParameters	main@277466206
10/02/17 15:38:50	282098				testDefaultParameters	main@277466206
10/02/17 15:40:53	404843				testDefaultParameters	main@277466206
10/02/17 15:42:18	489565				testDefaultParameters	main@277466206
10/02/17 15:38:09	241138				testExecute	main@277466206
10/02/17 15:41:29	441236				testExecute	main@277466206
10/02/17 15:42:50	521758				testExecute	main@277466206
10/02/17 15:34:33	24760				testGet	main@277466206
10/02/17 15:34:33	24462				testGetAsyncEngine	main@277466206
10/02/17 15:34:39	30561				testGetClassPath	main@277466206
10/02/17 15:34:33	24760				testGetDelay	main@277466206
10/02/17 15:35:48	99951				testGetDirectory	pool-4-thread-1@98491205
10/02/17 15:35:48	99957				testGetDirectory	pool-4-thread-2@1476184699
10/02/17 15:35:48	99959				testGetDirectory	pool-4-thread-3@819697057
10/02/17 15:35:48	99959				testGetDirectory	pool-4-thread-4@709342045
10/02/17 15:34:33	24445				testGetFormattedFasta	main@277466206
10/02/17 15:34:49	41033				testGetJobStatus	main@277466206
10/02/17 15:35:54	105819				testGetStatus	pool-5-thread-1@764103883
10/02/17 15:35:54	105819				testGetStatus	pool-5-thread-2@341752521
10/02/17 15:35:54	105823				testGetStatus	pool-5-thread-4@409692872
10/02/17 15:35:54	105823				testGetStatus	pool-5-thread-3@1513312339
10/02/17 15:36:15	126691				testGetStatus	pool-5-thread-2@341752521
10/02/17 15:34:33	24759				testGetSyncEngine	main@277466206
10/02/17 15:36:39	151130				testGetTestArgsCommand	main@277466206
10/02/17 15:36:39	151130				testGetTestArgsCommand	main@277466206
10/02/17 15:36:39	151129				testGetTestCommand	main@277466206
10/02/17 15:36:39	151130				testGetTestCommand	main@277466206
10/02/17 15:36:39	151130				testGetTestCommand	main@277466206
10/02/17 15:36:39	151131				testGetTestCommand	main@277466206
10/02/17 15:36:39	151131				testGetTestCommand	main@277466206
10/02/17 15:36:39	151131				testGetTestCommand	main@277466206
10/02/17 15:34:39	30795				testIsAbsolutePath	main@277466206
10/02/17 15:37:09	180475				testLoadLimits	main@277466206
10/02/17 15:35:48	100064		>>testLoadResources			main@277466206
10/02/17 15:35:48	100251				testMarshalling	main@277466206
10/02/17 15:36:38	149393				testMarshalling	main@277466206
10/02/17 15:36:36	147556				testMultipleCancelLocally	main@277466206
10/02/17 15:36:37	148818				testMultipleCancelLocally	main@277466206
10/02/17 15:42:51	522626				testNcore	main@277466206
10/02/17 15:36:39	150817				testOptionNoDefaultValidate	main@277466206
10/02/17 15:36:39	150832				testOptionSetInvalidValue	main@277466206
10/02/17 15:36:39	150848				testOptionToCommand	main@277466206
10/02/17 15:34:27	19210				testOptions	main@277466206
10/02/17 15:37:48	219617				testOptions	main@277466206
10/02/17 15:38:51	282763				testOptions	main@277466206
10/02/17 15:41:08	419575				testOptions	main@277466206
10/02/17 15:42:29	500553				testOptions	main@277466206
10/02/17 15:36:49	161119				testOptionsLocally	main@277466206
10/02/17 15:34:38	29994				testOptionsToCommand	main@277466206
10/02/17 15:36:39	150863				testParameterToCommand	main@277466206
10/02/17 15:34:30	21374				testParameters	main@277466206
10/02/17 15:37:52	224118				testParameters	main@277466206
10/02/17 15:38:53	285288				testParameters	main@277466206
10/02/17 15:41:08	420039				testParameters	main@277466206
10/02/17 15:42:30	501445				testParameters	main@277466206
10/02/17 15:35:48	99948				testParser	main@277466206
10/02/17 15:36:51	163051				testPersistance	main@277466206
10/02/17 15:38:10	241567				testPersistance	main@277466206
10/02/17 15:39:00	292212				testPersistance	main@277466206
10/02/17 15:41:30	441672				testPersistance	main@277466206
10/02/17 15:42:51	522627				testPersistance	main@277466206
10/02/17 15:34:32	24131				testPresets	main@277466206
10/02/17 15:37:55	226587				testPresets	main@277466206
10/02/17 15:38:58	290109				testPresets	main@277466206
10/02/17 15:42:42	514162				testPresets	main@277466206
10/02/17 15:34:33	24437				testProteinSequenceGeneration	main@277466206
10/02/17 15:34:10	1923				testPull	main@277466206
10/02/17 15:35:48	99948				testQueue	main@277466206
10/02/17 15:34:32	24308				testReadClustalFile	main@277466206
10/02/17 15:34:32	24330				testReadClustalFileLongNames	main@277466206
10/02/17 15:34:33	24382				testReadClustalFileShortNames	main@277466206
10/02/17 15:34:33	24446				testReadWriteFasta	main@277466206
10/02/17 15:36:52	163482				testRunLocally	main@277466206
10/02/17 15:39:01	292454				testRunLocally	main@277466206
10/02/17 15:36:52	163653				testRunOnCluster	main@277466206
10/02/17 15:39:01	292556				testRunOnCluster	main@277466206
10/02/17 15:38:11	242600				testRunOnClusterAsyncCheckStatusLongPoolingTime	main@277466206
10/02/17 15:37:08	179590				testRunWithMatrix	main@277466206
10/02/17 15:35:48	100287				testSchemaFromCodeGeneration	main@277466206
10/02/17 15:38:32	264017				testSetInputTester	main@277466206
10/02/17 15:41:30	442181				testSetInputTester	main@277466206
10/02/17 15:34:39	30561				testSpaceDelimiterExecutable	main@277466206
10/02/17 15:35:10	61811				testSubmit	main@277466206
10/02/17 15:35:30	82112				testSubmit	main@277466206
10/02/17 15:36:36	147825				testSubmitLocally	pool-6-thread-1@97575625
10/02/17 15:36:36	147826				testSubmitLocally	pool-6-thread-2@598639019
10/02/17 15:36:36	147826				testSubmitLocally	pool-6-thread-3@772581038
10/02/17 15:36:36	147828				testSubmitLocally	pool-6-thread-4@1330799835
10/02/17 15:36:36	147951				testSubmitLocally	pool-6-thread-3@772581038
10/02/17 15:34:39	30795				testTaskList	main@277466206
10/02/17 15:35:49	100858				testUnMarshalling	main@277466206
10/02/17 15:36:38	149451				testUnMarshalling	main@277466206
10/02/17 15:36:39	150878				testValidate	main@277466206
10/02/17 15:36:39	151082				testValidateBoundaryConstrainCheck	main@277466206
10/02/17 15:36:39	151098				testValidateLowerBoundaryConstrainCheck	main@277466206
10/02/17 15:36:39	151114				testValidateUpperBoundaryConstrainCheck	main@277466206
10/02/17 15:36:39	151129				testValidateValueConstrain	main@277466206
10/02/17 15:35:50	101456				testValidation	main@277466206
10/02/17 15:35:50	102108				testValidationOnMarshalling	main@277466206
10/02/17 15:36:37	149278				testgetAllOptions	main@277466206
10/02/17 15:36:38	149390				testgetAllParameters	main@277466206
10/02/17 15:34:33	24462				testisNonAmbNucleotideSequence	main@277466206
10/02/17 15:34:33	24462				testisProteinSequence	main@277466206
10/02/17 15:35:48	100169				validateClustalConfiguration	main@277466206
10/02/17 15:35:48	100212				validateMafftConfiguration	main@277466206
10/02/17 15:35:48	100214				validateMuscleConfiguration	main@277466206
10/02/17 15:36:39	150736				validatePresets	main@277466206
10/02/17 15:35:48	100218				validateTcoffeeConfiguration	main@277466206

PASSED TESTS
Test method	Instance	Time (seconds)	Exception
readStatistics Test class:Ant test(failed)	compbio.runner.msa.ProbconsTester@60cbf9bd	0

Time	Delta (ms)	Test configuration	Method configuration	Test method	Thread
10/02/08 18:30:13	0	>>init			main@1369543768
10/02/08 18:30:14	525		>>init		main@1369543768
10/02/08 18:30:14	452	>>loadPresets			main@1369543768
10/02/08 18:30:14	526			readStatistics	main@1369543768

FAILED TESTS
Test method	Instance	Time (seconds)	Exception
loadEngineRetrieveResultsManyTimes Test class:compbio.engine.local.EngineResourcesLeakTester	compbio.engine.local.EngineResourcesLeakTester@444cee32	1	java.lang.AssertionError: expected:<true> but was:<false> - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45) -... Removed 27 stack frames Click to show all stack frames - java.lang.AssertionError: expected:<true> but was:<false> - at org.testng.Assert.fail(Assert.java:86) - at org.testng.Assert.failNotEquals(Assert.java:440) - at org.testng.Assert.assertTrue(Assert.java:34) - at org.testng.Assert.assertNotNull(Assert.java:354) - at org.testng.Assert.assertNotNull(Assert.java:344) - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45) - 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) -
loadEngineRetrieveResultsOnce Test class:compbio.engine.local.EngineResourcesLeakTester	compbio.engine.local.EngineResourcesLeakTester@444cee32	0	java.lang.AssertionError: expected:<true> but was:<false> - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113) -... Removed 27 stack frames Click to show all stack frames - java.lang.AssertionError: expected:<true> but was:<false> - at org.testng.Assert.fail(Assert.java:86) - at org.testng.Assert.failNotEquals(Assert.java:440) - at org.testng.Assert.assertTrue(Assert.java:34) - at org.testng.Assert.assertNotNull(Assert.java:354) - at org.testng.Assert.assertNotNull(Assert.java:344) - at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113) - 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) -

Time	Delta (ms)	Suite configuration	Test configuration	Class configuration	Groups configuration	Method configuration	Test method	Thread	Instances
10/01/27 15:33:57	0						loadEngineRetrieveResultsManyTimes	main@1663273938
10/01/27 15:33:58	1249						loadEngineRetrieveResultsOnce	main@1663273938

SKIPPED TESTS
Test method	Instance	Time (seconds)	Exception
marshallPreset Test class:compbio.metadata.PresetTester	compbio.metadata.PresetTester@1171b26	0
validatePresets Test class:compbio.metadata.PresetTester	compbio.metadata.PresetTester@1171b26	0

Time	Delta (ms)	Class configuration	Test method	Thread
10/02/17 15:33:16	0		testClusterEngineConf	main@1421571929
10/02/17 15:33:15	-606	>>testLoadResources		main@1421571929
10/02/17 15:33:16	13		validateClustalConfiguration	main@1421571929
10/02/17 15:33:16	68		validateMafftConfiguration	main@1421571929
10/02/17 15:33:16	80		validateMuscleConfiguration	main@1421571929
10/02/17 15:33:16	92		validateTcoffeeConfiguration	main@1421571929

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(failed)

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 forFailed suite [Ant suite]

compbio.engine.local.EngineResourcesLeakTester

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 forJWS2

compbio.engine.cluster.drmaa.ClusterSessionTester

compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester

compbio.engine.cluster.drmaa.DrmaaClusterEngineTester

compbio.engine.conf.DirectoryManagerTester

compbio.engine.conf.PropertyHelperManagerTester

compbio.engine.local.EngineResourcesLeakTester

compbio.metadata.PresetTester

compbio.runner.CommandBuilderTester

compbio.runner.clustal.ClustalWParametersTester

compbio.runner.clustal.ClustalWTester

compbio.runner.clustal.LimitTester

compbio.runner.mafft.MafftTester

compbio.runner.muscle.MuscleTester

compbio.runner.probcons.ProbconsParametersTester

compbio.runner.probcons.ProbconsTester

compbio.runner.tcoffee.TcoffeeParametersTester

compbio.runner.tcoffee.TcoffeeTester

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 forclustengine

Ant test

compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFile

compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames

compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames

compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration

compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta

compbio.data.sequence.SequenceUtilTester:testCleanSequence

compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence

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.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

Results for
Ant suite

Results for
Failed suite [Ant suite]

Results for
JWS2

Results for
clustengine