[Biojava-dev] Fwd: CathDomainTest.test:19 » NullPointer

[Michael Heuer]

Yes, I'll look into it further.

   michael

On Mon, Oct 13, 2014 at 12:37 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Michael,
> Are you able to access these files through your web browser?
>
> http://release.cathdb.info/v3.5.0/CathDomall
> http://release.cathdb.info/v3.5.0/CathDomainList.v3.5.0
>
> If so we should probably dig deeper. (You might also double check your
> temp directory is writable from the test process).
>
> -da
>
> On Mon, Oct 13, 2014 at 8:00 AM, Michael Heuer <heuermh at gmail.com> wrote:
>> Hello Daniel,
>>
>> Thanks for the reply.  I'm still seeing the same error this week; just
>> chalk it up to network issues I guess?
>>
>>    michael
>>
>>
>> On Fri, Oct 10, 2014 at 12:53 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
>>> Sorry, forgot to CC the list.
>>>
>>> Michael,
>>> I was able to run this test successfully. Have you tried just
>>> re-running it? When we wrote the CATH modules we found the CATH
>>> download server could be a little flaky (we ended up skipping their
>>> larger files because of frequent lost connections).
>>>
>>> If the PDB_DIR and PDB_CACHE_DIR variables aren't set, the system temp
>>> directory is used. In that case, the test will also fail if it can't
>>> download the CATH files (e.g. no space, wrong permissions on temp
>>> directory).
>>>
>>> Best,
>>> -da
>>>
>>> On Fri, Oct 10, 2014 at 9:43 AM, Michael Heuer <heuermh at gmail.com> wrote:
>>>> Hello,
>>>>
>>>> I'm getting a consistent unit test failure in the integration test module
>>>>
>>>> $ mvn clean install
>>>> ...
>>>> Running org.biojava.structure.test.cath.CathDomainTest
>>>> java.lang.ArrayIndexOutOfBoundsException: 9
>>>>     at org.biojava.bio.structure.cath.CathInstallation.parseCathListFileLine(CathInstallation.java:516)
>>>>     at org.biojava.bio.structure.cath.CathInstallation.parseCathDomainList(CathInstallation.java:356)
>>>>     at org.biojava.bio.structure.cath.CathInstallation.parseCathDomainList(CathInstallation.java:348)
>>>>     at org.biojava.bio.structure.cath.CathInstallation.ensureDomainListInstalled(CathInstallation.java:739)
>>>>     at org.biojava.bio.structure.cath.CathInstallation.ensureDomallInstalled(CathInstallation.java:795)
>>>>     at org.biojava.bio.structure.cath.CathInstallation.getDomainByCathId(CathInstallation.java:305)
>>>>     at org.biojava.structure.test.cath.CathDomainTest.test(CathDomainTest.java:18)
>>>>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>>     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>>>>     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>>     at java.lang.reflect.Method.invoke(Method.java:606)
>>>>     at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
>>>>     at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
>>>>     at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
>>>>     at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
>>>>     at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
>>>>     at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
>>>>     at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
>>>>     at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
>>>>     at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
>>>>     at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
>>>>     at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
>>>>     at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
>>>>     at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
>>>>     at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:264)
>>>>     at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:153)
>>>>     at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:124)
>>>>     at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:200)
>>>>     at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:153)
>>>>     at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:103)
>>>> Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.264
>>>> sec <<< FAILURE! - in org.biojava.structure.test.cath.CathDomainTest
>>>> test(org.biojava.structure.test.cath.CathDomainTest)  Time elapsed:
>>>> 1.209 sec  <<< ERROR!
>>>> java.lang.NullPointerException: null
>>>>     at org.biojava.bio.structure.cath.CathDomain.getResidueRanges(CathDomain.java:433)
>>>>     at org.biojava.bio.structure.cath.CathDomain.getIdentifier(CathDomain.java:426)
>>>>     at org.biojava.structure.test.cath.CathDomainTest.test(CathDomainTest.java:19)
>>>> ...
>>>> Tests in error:
>>>>   CathDomainTest.test:19 » NullPointer
>>>>
>>>> Tests run: 113, Failures: 0, Errors: 1, Skipped: 0
>>>>
>>>>
>>>> I'm not sure why this doesn't show up in Travis CI.  Is it necessary
>>>> to set the PDB_DIR and PDB_CACHE_DIR environment variables?
>>>>
>>>>    michael
>>>>
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at mailman.open-bio.org
>>>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev