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

[Daniel Asarnow]

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
>>>
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>>
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