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bio4j / bio4j-titan

Titan-specific bio4j implementation
https://github.com/bio4j/bio4j
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Index not found with unique index query #53

Closed eparejatobes closed 9 years ago

eparejatobes commented 9 years ago

We get

Could not find a suitable index to answer graph query and graph scans are disabled: [(com.bio4j.model.uniprot.UniprotGraph.FeatureTypeType.name = compositionally biased region AND label = com.bio4j.model.uniprot.UniprotGraph.FeatureTypeType)]:VERTEX

It could be something about spaces and the like.

eparejatobes commented 9 years ago

Most likely this is about a missing commit in the UniProt graph constructor, I'm publishing this.

pablopareja commented 9 years ago

We have a new exception now:

Reading conf file...
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: Exception retrieving protein Q6GZV8
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: null
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.angulillos.titan.TitanUntypedGraph.addVertex(TitanUntypedGraph.java:32)
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.angulillos.titan.TitanUntypedGraph.addVertex(TitanUntypedGraph.java:14)
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.angulillos.TypedGraph.addVertex(TypedGraph.java:32)
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.model.uniprot.programs.ImportUniprot.importProteinCitations(ImportUniprot.java:1926)
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.model.uniprot.programs.ImportUniprot.importUniprot(ImportUniprot.java:464)
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.execute(ImportUniprotTitan.java:58)
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
Dec 09, 2014 3:45:20 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:8)
Dec 09, 2014 3:45:20 PM com.ohnosequences.util.ExecuteFromFile main
SEVERE: null
java.lang.IllegalArgumentException: The property key is already indexed with the same index name and incompatible characteristics
        at com.bio4j.angulillos.titan.TitanTypedVertexIndex$DefaultUnique.<init>(TitanTypedVertexIndex.java:205)
        at com.bio4j.titan.model.uniprot.TitanUniprotGraph.initIndices(TitanUniprotGraph.java:1059)
        at com.bio4j.titan.model.uniprot.TitanUniprotGraph.<init>(TitanUniprotGraph.java:460)
        at com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.config(ImportUniprotTitan.java:49)
        at com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.config(ImportUniprotTitan.java:37)
        at com.bio4j.model.uniprot.programs.ImportUniprot.importUniprot(ImportUniprot.java:151)
        at com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.execute(ImportUniprotTitan.java:58)
        at com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
        at com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:8)
pablopareja commented 9 years ago

Are VertexLabelMaker instances doing the same thing under the hood as creating indices?

eparejatobes commented 9 years ago

@pablopareja what do you mean?

pablopareja commented 9 years ago

I'm still getting this:

Reading conf file...
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: Exception retrieving protein Q6GZV8
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: null
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.angulillos.titan.TitanUntypedGraph.addVertex(TitanUntypedGraph.java:32)
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.angulillos.titan.TitanUntypedGraph.addVertex(TitanUntypedGraph.java:14)
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.angulillos.TypedGraph.addVertex(TypedGraph.java:32)
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.model.uniprot.programs.ImportUniprot.importProteinCitations(ImportUniprot.java:1926)
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.model.uniprot.programs.ImportUniprot.importUniprot(ImportUniprot.java:464)
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.execute(ImportUniprotTitan.java:58)
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
Dec 09, 2014 4:22:40 PM com.bio4j.model.uniprot.programs.ImportUniprot importUniprot
SEVERE: com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:8)
Dec 09, 2014 4:22:40 PM com.ohnosequences.util.ExecuteFromFile main
SEVERE: null
java.lang.IllegalArgumentException: The property key is already indexed with the same index name and incompatible characteristics
        at com.bio4j.angulillos.titan.TitanTypedVertexIndex$DefaultUnique.<init>(TitanTypedVertexIndex.java:205)
        at com.bio4j.titan.model.uniprot.TitanUniprotGraph.initIndices(TitanUniprotGraph.java:1060)
        at com.bio4j.titan.model.uniprot.TitanUniprotGraph.<init>(TitanUniprotGraph.java:461)
        at com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.config(ImportUniprotTitan.java:49)
        at com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.config(ImportUniprotTitan.java:37)
        at com.bio4j.model.uniprot.programs.ImportUniprot.importUniprot(ImportUniprot.java:151)
        at com.bio4j.titan.model.uniprot.programs.ImportUniprotTitan.execute(ImportUniprotTitan.java:58)
        at com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
        at com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:8)
eparejatobes commented 9 years ago

It looks like that last part was about types without any label at the Titan level.

eparejatobes commented 9 years ago

after bio4j/angulillos-titan#11 this is solved, closing