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

[Michael Heuer]

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
>>
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