bio4j/angulillos-titan

use Titan with a lot of angulillos

Angulillos<Titan>

This is an implementation of the Angulillos API for the Titan graph database.

It is used in the Bio4j-Titan project, which implements the Bio4 graph model (defined using Angulillos) for the Titan backend.

angulillos-titan's Issues

Add indexes to graph schema

default key creation methods

For when we have a normal property so to say

Implement TypedVertexQuery

With TitanVertexQuery

Some code snippets:

<
  // source vertices
  S extends TypedVertex<S,ST,G,I,RV,RVT,RE,RET>,
  ST extends TypedVertex.Type<S,ST,G,I,RV,RVT,RE,RET>,
  // edge
  R extends TypedEdge<S,ST,G, R,RT,G,I,RV,RVT,RE,RET, N,NT,G>,
  RT extends TypedEdge.Type<S,ST,G, R,RT,G,I,RV,RVT,RE,RET, N,NT,G>,
  // the query
  Q extends VertexQueryIn<S,ST, R,RT, N,NT, Q, G,I,RV,RVT,RE,RET>,
>
Q queryIn();

<
  // edge
  R extends TypedEdge<N,NT,G, R,RT,G,I,RV,RVT,RE,RET, T,TT,G>,
  RT extends TypedEdge.Type<N,NT,G, R,RT,G,I,RV,RVT,RE,RET, T,TT,G>,
  // target vertices
  T extends TypedVertex<T,TT,G,I,RV,RVT,RE,RET>,
  TT extends TypedVertex.Type<T,TT,G,I,RV,RVT,RE,RET>,
  // the query
  Q extends VertexQueryOut<N,NT, R,RT, T,TT, Q, G,I,RV,RVT,RE,RET>,
>
Q queryOut();


public final class DefaultTitanVertexQuery<N,NT,E,ET,T,TT,G,I> extends VertexQueryOut<> {

  private final TitanVertexQuery raw;

  raw.buh()
}  

add orderBy support

Basic type creation tests

This is something that is easy to do without any data. I'm thinking about

• defining a test schema (maybe at the level of angulillos?)
• open an instance, create all the types and close gracefully

Once we have this we can move to things like type creation idempotence.

Improve the index management code

It is a bit funky right now. There's certainly room for improvement there. If someone wants to help, I'm all ears.

Rename to angulillos.titan

Exception related to this or angulillos library

Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: Permanent exception during backend operation
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.diskstorage.util.BackendOperation.execute(BackendOperation.java:65)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.diskstorage.BackendTransaction.executeRead(BackendTransaction.java:380)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.diskstorage.BackendTransaction.edgeStoreKeys(BackendTransaction.java:306)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.database.StandardTitanGraph.getVertexIDs(StandardTitanGraph.java:180)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.transaction.VertexIterable$1.<init>(VertexIterable.java:31)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.transaction.VertexIterable.iterator(VertexIterable.java:29)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.transaction.StandardTitanTx$5.execute(StandardTitanTx.java:925)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.transaction.StandardTitanTx$5.execute(StandardTitanTx.java:788)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.query.QueryProcessor$LimitAdjustingIterator.getNewIterator(QueryProcessor.java:231)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.query.LimitAdjustingIterator.hasNext(LimitAdjustingIterator.java:32)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.google.common.collect.Iterators$7.computeNext(Iterators.java:700)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.query.QueryProcessor$OuterIterator.nextInternal(QueryProcessor.java:75)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.query.QueryProcessor$OuterIterator.<init>(QueryProcessor.java:65)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.query.QueryProcessor.iterator(QueryProcessor.java:46)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.google.common.collect.Iterables$7.iterator(Iterables.java:613)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: java.lang.Iterable.spliterator(Iterable.java:101)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.angulillos.conversions.stream(conversions.java:10)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.angulillos.titan.TitanTypedVertexIndex$Default.query(TitanTypedVertexIndex.java:69)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.angulillos.TypedElementIndex$Unique.getElement(TypedElementIndex.java:39)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.angulillos.TypedVertexIndex$Unique.getVertex(TypedVertexIndex.java:41)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef.importUniprotUniRefFile(ImportUniprotUniRef.java:241)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef.importUniprotUniRef(ImportUniprotUniRef.java:75)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.titan.model.uniprot_uniref.programs.ImportUniprotUniRefTitan.execute(ImportUniprotUniRefTitan.java:44)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:11)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: Could not rollback after a failed commit
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.transaction.StandardTitanTx.commit(StandardTitanTx.java:1027)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.thinkaurelius.titan.graphdb.blueprints.TitanBlueprintsGraph.commit(TitanBlueprintsGraph.java:57)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.angulillos.titan.TitanUntypedGraph.commit(TitanUntypedGraph.java:20)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef.importUniprotUniRef(ImportUniprotUniRef.java:96)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.titan.model.uniprot_uniref.programs.ImportUniprotUniRefTitan.execute(ImportUniprotUniRefTitan.java:44)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.ohnosequences.util.ExecuteFromFile.main(ExecuteFromFile.java:66)
Nov 11, 2014 3:40:53 PM com.bio4j.model.uniprot_uniref.programs.ImportUniprotUniRef importUniprotUniRef
SEVERE: com.bio4j.titan.programs.ImportTitanDB.main(ImportTitanDB.java:11)

@eparejatobes Maybe it's actually a Titan exception?

update to Titan 0.5.2