Apache Jena TDB error for generated RDF database

[abargnesi]

An RDF query for concepts in the Entrez Gene concept scheme will result in a TDB error:

org.apache.jena.tdb.base.file.FileException: ObjectFileStorage.read[nodes](185300)[filesize=169662695][file.size()=169662695]: Impossibly large object : 779055205 bytes > filesize-(loc+SizeOfInt)=169477391
    at org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:348)
    at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78)
    at org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186)
    at org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111)
    at org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70)
    at org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128)
    at org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82)
    at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:54)
    at org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
    at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:54)
    at org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122)
    at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121)
    at org.apache.jena.sparql.core.VarExprList.get(VarExprList.java:77)
    at org.apache.jena.sparql.engine.iterator.QueryIterGroup.copyProject(QueryIterGroup.java:193)
    at org.apache.jena.sparql.engine.iterator.QueryIterGroup.genKey(QueryIterGroup.java:183)
    at org.apache.jena.sparql.engine.iterator.QueryIterGroup.access$000(QueryIterGroup.java:43)
...

This has something to do with an incomplete node table during the write of this RDF dataset. See SO post.

Adding TDB.sync(dataset) after writes should allow the TDB on disk to reflect the RDF data in memory.