treebase-devel

[Treebase-devel] a error in unit test related to mesquite

[youjun g. <you...@ya...>]

Hi, Rutger,

This unit test error may related to mesquite, please have a look on it.

Youjun


-------------------------------------------------------------------------------
Test set: org.cipres.treebase.service.matrix.RowSegmentServiceImplTest
-------------------------------------------------------------------------------
Tests run: 2, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 8.641 sec
<<< FAILURE!
testCreateRowSegments(org.cipres.treebase.service.matrix.RowSegmentServiceImplTest)
Time elapsed: 8.594 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)

Re: [Treebase-devel] a error in unit test related to mesquite

[Rutger V. <rut...@gm...>]

Hi Youjun,

is this still happening? Last time I saw that NPE was when mesquite
wasn't working.

Rutger

On Tue, Dec 22, 2009 at 7:11 PM, youjun guo <you...@ya...> wrote:
> Hi, Rutger,
>
> This unit test error may related to mesquite, please have a look on it.
>
> Youjun
>
>
> -------------------------------------------------------------------------------
> Test set: org.cipres.treebase.service.matrix.RowSegmentServiceImplTest
> -------------------------------------------------------------------------------
> Tests run: 2, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 8.641 sec
> <<< FAILURE!
> testCreateRowSegments(org.cipres.treebase.service.matrix.RowSegmentServiceImplTest)
> Time elapsed: 8.594 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)
>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] a error in unit test related to mesquite

[youjun g. <you...@ya...>]

Rutger,

It seems to me that there are more than I estimated test fails and test
errors (null point) related to mesquite and nexus i/o (about 10 of them). I
expect most of them may disappear once the mesquite is fully function.

Right now, our database server is not working, I am not be able to give you
the most updated test result. I will send them to you once they are
available. I think they may also helpful for your mesquite setting up.

Youjun

On Mon, Jan 4, 2010 at 7:39 AM, Rutger Vos <rut...@gm...> wrote:

> Hi Youjun,
>
> is this still happening? Last time I saw that NPE was when mesquite
> wasn't working.
>
> Rutger
>
> On Tue, Dec 22, 2009 at 7:11 PM, youjun guo <you...@ya...> wrote:
> > Hi, Rutger,
> >
> > This unit test error may related to mesquite, please have a look on it.
> >
> > Youjun
> >
> >
> >
> -------------------------------------------------------------------------------
> > Test set: org.cipres.treebase.service.matrix.RowSegmentServiceImplTest
> >
> -------------------------------------------------------------------------------
> > Tests run: 2, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 8.641 sec
> > <<< FAILURE!
> >
> testCreateRowSegments(org.cipres.treebase.service.matrix.RowSegmentServiceImplTest)
> > Time elapsed: 8.594 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)
> >
> >
>
>
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>