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

[Michael Heuer]

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