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bio4j / bio4j-titan

Titan-specific bio4j implementation
https://github.com/bio4j/bio4j
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Problem importing UniProtGo with the last version #60

Closed pablopareja closed 9 years ago

pablopareja commented 9 years ago

This is the exception:


SEVERE: null
java.lang.NullPointerException
        at com.bio4j.model.uniprot_go.UniProtGoGraph$GoAnnotationType.<init>(UniProtGoGraph.java:79)
        at com.bio4j.titan.model.uniprot_go.TitanUniProtGoGraph.initTypes(TitanUniProtGoGraph.java:58)
        at com.bio4j.titan.model.uniprot_go.TitanUniProtGoGraph.<init>(TitanUniProtGoGraph.java:37)
        at com.bio4j.titan.model.uniprot_go.programs.ImportUniProtGoTitan.config(ImportUniProtGoTitan.java:46)
        at com.bio4j.titan.model.uniprot_go.programs.ImportUniProtGoTitan.config(ImportUniProtGoTitan.java:39)
        at com.bio4j.model.uniprot_go.programs.ImportUniProtGo.importUniProtGo(ImportUniProtGo.java:57)
        at com.bio4j.titan.model.uniprot_go.programs.ImportUniProtGoTitan.execute(ImportUniProtGoTitan.java:55)
        at com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
        at com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:8)

@eparejatobes could you give me a hand figuring out a way to fix it?

eparejatobes commented 9 years ago

hey @pablopareja you need to create the level-0 graphs first in a separate statement. Could be only that, but maybe there's something else.

pablopareja commented 9 years ago

OK, I'm already working on that, let's see what happens...

pablopareja commented 9 years ago

I still get the same exception...


SEVERE: null
java.lang.NullPointerException
        at com.bio4j.model.uniprot_go.UniProtGoGraph$GoAnnotationType.<init>(UniProtGoGraph.java:79)
        at com.bio4j.titan.model.uniprot_go.TitanUniProtGoGraph.initTypes(TitanUniProtGoGraph.java:58)
        at com.bio4j.titan.model.uniprot_go.TitanUniProtGoGraph.<init>(TitanUniProtGoGraph.java:37)
        at com.bio4j.titan.model.uniprot_go.programs.ImportUniProtGoTitan.config(ImportUniProtGoTitan.java:49)
        at com.bio4j.titan.model.uniprot_go.programs.ImportUniProtGoTitan.config(ImportUniProtGoTitan.java:39)
        at com.bio4j.model.uniprot_go.programs.ImportUniProtGo.importUniProtGo(ImportUniProtGo.java:57)
        at com.bio4j.titan.model.uniprot_go.programs.ImportUniProtGoTitan.execute(ImportUniProtGoTitan.java:58)
        at com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
        at com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:8)

any ideas?

eparejatobes commented 9 years ago

@pablopareja this should be reproducible inside a test with empty graphs were we only create the types. Let's write that first.

pablopareja commented 9 years ago

OK :wink:

pablopareja commented 9 years ago

Should I create the Scala test like those for GO and Enzyme modules?

eparejatobes commented 9 years ago

as you please

eparejatobes commented 9 years ago

@pablopareja this branch?

pablopareja commented 9 years ago

@eparejatobes This branch is the most up-to-date one and includes all the last fixes I implemented for the few issues that we got lately. If I manage to finally import UniRef 100 with this (and even if we don't ), we could merge this into master since it holds the current reference code for the Titan implementation.