[Treebase-devel] failed TB unit test

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Hi, Rutger,

Right now, most of the failed unit test are fixed.
There are still 17 left, among those, these following 7 may related to
Mesquite or Nexus.
Will you be able to work on them?.

Youjun

-------------------------------------------------------------------------------
1. Test set: org.cipres.treebase.domain.matrix.MatrixTest
<<< FAILURE!
testGenerateNexusBlock(org.cipres.treebase.domain.matrix.MatrixTest)  Time
elapsed: 2.203 sec  <<< FAILURE!
junit.framework.AssertionFailedError
    at junit.framework.Assert.fail(Assert.java:47)
    at junit.framework.Assert.assertTrue(Assert.java:20)
    at junit.framework.Assert.assertTrue(Assert.java:27)
    at org.cipres.treebase.domain.matrix.MatrixTest.testGenerat

-------------------------------------------------------------------------------
2. Test set: org.cipres.treebase.service.matrix.RowSegmentServiceImplTest
<<< FAILURE!
testCreateRowSegments(org.cipres.treebase.service.matrix.RowSegmentServiceImplTest)
Time elapsed: 2.625 sec  <<< ERROR!
java.lang.NullPointerException
    at
org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:610)
    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.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
    at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
    at $Proxy81.addNexusFilesJDBC(Unknown Source)
    at
org.cipres.treebase.service.matrix.RowSegmentServiceImplTest.testCreateRowSegments(RowSegmentServiceImplTest.java:182)

-------------------------------------------------------------------------------
3. Test set: org.cipres.treebase.dao.tree.PhyloTreeDAOTest
<<< FAILURE!
testFindTreeBlocksByNexusFileName(org.cipres.treebase.dao.tree.PhyloTreeDAOTest)
Time elapsed: 0.203 sec  <<< ERROR!
org.springframework.dao.EmptyResultDataAccessException: Incorrect result
size: expected 1, actual 0
    at
org.springframework.dao.support.DataAccessUtils.requiredSingleResult(DataAccessUtils.java:71)
    at
org.springframework.jdbc.core.JdbcTemplate.queryForObject(JdbcTemplate.java:422)
    at
org.springframework.jdbc.core.JdbcTemplate.queryForObject(JdbcTemplate.java:426)
    at
org.cipres.treebase.dao.tree.PhyloTreeDAOTest.testFindTreeBlocksByNexusFileName(PhyloTreeDAOTest.java:536)

-------------------------------------------------------------------------------
4. Test set: org.cipres.treebase.service.nexus.NexusParserTest
<<< FAILURE!
testLoadPhyloDataSet(org.cipres.treebase.service.nexus.NexusParserTest)
Time elapsed: 0.125 sec  <<< ERROR!
java.lang.NullPointerException
    at
org.cipres.communication.Facilitator.registryIsColocated(Facilitator.java:190)
    at
org.cipres.communication.Facilitator.initializeORB(Facilitator.java:137)
    at org.cipres.communication.Facilitator.initialize(Facilitator.java:108)
    at
org.cipres.datatypes.PhyloDataset.initializeFromStringOrFile(PhyloDataset.java:170)
    at org.cipres.datatypes.PhyloDataset.initialize(PhyloDataset.java:208)
    at org.cipres.datatypes.PhyloDataset.<init>(PhyloDataset.java:117)
    at
org.cipres.treebase.service.nexus.NexusParserTest.testLoadPhyloDataSet(NexusParserTest.java:33)

-------------------------------------------------------------------------------
5. Test set: org.cipres.treebase.service.study.StudyServiceImplTest
<<< FAILURE!
testGenerateReconstructedNexusFile(org.cipres.treebase.service.study.StudyServiceImplTest)
Time elapsed: 0.079 sec  <<< ERROR!
java.lang.NullPointerException
    at
org.cipres.treebase.service.study.StudyServiceImplTest.testGenerateReconstructedNexusFile(StudyServiceImplTest.java:506)

-------------------------------------------------------------------------------
6. Test set: org.cipres.treebase.service.study.SubmissionServiceImplTest
<<< FAILURE!
testProcessNexusFile(org.cipres.treebase.service.study.SubmissionServiceImplTest)
Time elapsed: 0.61 sec  <<< ERROR!
java.lang.NullPointerException
    at
org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:610)
    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.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
    at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
    at $Proxy81.addNexusFilesJDBC(Unknown Source)
    at
org.cipres.treebase.service.study.SubmissionServiceImplTest.testProcessNexusFile(SubmissionServiceImplTest.java:226)

-------------------------------------------------------------------------------
7. Test set: org.cipres.treebase.domain.nexus.NexusMesquiteDataSetTest
<<< FAILURE!
testMesqutieFolderDir(org.cipres.treebase.domain.nexus.NexusMesquiteDataSetTest)
Time elapsed: 0.015 sec  <<< ERROR!
org.springframework.beans.factory.UnsatisfiedDependencyException: Error
creating bean with name
'org.cipres.treebase.domain.nexus.NexusMesquiteDataSetTest': Unsatisfied
dependency expressed through bean property 'fixture': There are 3 beans of
type [org.cipres.treebase.domain.nexus.NexusService] available for
autowiring by type: [nexusService, nexmlService, rdfaService]. There should
have been exactly 1 to be able to autowire property 'fixture' of bean
'org.cipres.treebase.domain.nexus.NexusMesquiteDataSetTest'. Consider using
autowiring by name instead.
    at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireByType(AbstractAutowireCapableBeanFactory.java:931)
    at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:829)
    at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireBeanProperties(AbstractAutowireCapableBeanFactory.java:274)
    at
org.springframework.test.AbstractDependencyInjectionSpringContextTests.injectDependencies(AbstractDependencyInjectionSpringContextTests.java:179)
    at
org.springframework.test.AbstractDependencyInjectionSpringContextTests.prepareTestInstance(AbstractDependencyInjectionSpringContextTests.java:158)
    at
org.springframework.test.AbstractSingleSpringContextTests.setUp(AbstractSingleSpringContextTests.java:88)
    at junit.framework.TestCase.runBare(TestCase.java:125)
    at
org.springframework.test.ConditionalTestCase.runBare(ConditionalTestCase.java:69)
    at junit.framework.TestResult$1.protect(TestResult.java:106)
    at junit.framework.TestResult.runProtected(TestResult.java:124)
    at junit.framework.TestResult.run(TestResult.java:109)
    at junit.framework.TestCase.run(TestCase.java:118)
    at junit.framework.TestSuite.runTest(TestSuite.java:208)
    at junit.framework.TestSuite.run(TestSuite.java:203)
    at sun.reflect.GeneratedMethodAccessor140.invoke(Unknown Source)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)
    at
org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:140)
    at
org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:127)
    at org.apache.maven.surefire.Surefire.run(Surefire.java:177)
    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.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:338)
    at
org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:997)