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

[Daniel Asarnow]

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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