[Bigdata-developers] NPE ....

[Jeremy C. <jj...@gm...>]

I got an NPE trying to materialize a transitive closure.

The vocab I am using is quite a big one.
I believe this code worked on a different instance running same blazegraph version 1.5.3

I will retry …
any interpretation. Strong desire not to have to start over, I have a lot of data in the journal (approx 1B triples)


Jeremy



2016-01-29 20:05:29,340 [ERROR] syapse.sparql.endpoint: Query did not complete (after 22.6046221256 seconds):
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix s: </bdm/api/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bds: <http://www.bigdata.com/rdf/search#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix syapse: </graph/syapse#>


    INSERT {
      GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
        ?subNew <https://swedish.syapse.com/graph/syapse#broader> ?superNew .
      }
    }
    
    WHERE
    {
        { 
         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
        
} UNION {

         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
         }
    }
    
java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: org.openrdf.query.UpdateExecutionException: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.rdf.sail.webapp.BigdataServlet.submitApiTask(BigdataServlet.java:281)
	at com.bigdata.rdf.sail.webapp.QueryServlet.doSparqlUpdate(QueryServlet.java:448)
	at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:233)
	at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:248)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:769)
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577)
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1125)
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1059)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:110)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
	at org.eclipse.jetty.server.Server.handle(Server.java:497)
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:311)
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:248)
	at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:610)
	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:539)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: org.openrdf.query.UpdateExecutionException: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.rdf.sail.webapp.QueryServlet$SparqlUpdateTask.call(QueryServlet.java:552)
	at com.bigdata.rdf.sail.webapp.QueryServlet$SparqlUpdateTask.call(QueryServlet.java:460)
	at com.bigdata.rdf.task.ApiTaskForIndexManager.call(ApiTaskForIndexManager.java:68)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	... 1 more
Caused by: org.openrdf.query.UpdateExecutionException: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.rdf.sparql.ast.eval.ASTEvalHelper.executeUpdate(ASTEvalHelper.java:1099)
	at com.bigdata.rdf.sail.BigdataSailUpdate.execute2(BigdataSailUpdate.java:152)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$UpdateTask.doQuery(BigdataRDFContext.java:1964)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.innerCall(BigdataRDFContext.java:1567)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1532)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:704)
	... 4 more
Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
	at com.bigdata.rdf.sparql.ast.eval.ASTConstructIterator.hasNext(ASTConstructIterator.java:621)
	at info.aduna.iteration.IterationWrapper.hasNext(IterationWrapper.java:68)
	at com.bigdata.rdf.sparql.ast.eval.AST2BOpUpdate.convertDeleteInsert(AST2BOpUpdate.java:1015)
	at com.bigdata.rdf.sparql.ast.eval.AST2BOpUpdate.convertUpdateSwitch(AST2BOpUpdate.java:435)
	at com.bigdata.rdf.sparql.ast.eval.AST2BOpUpdate.convertUpdate(AST2BOpUpdate.java:288)
	at com.bigdata.rdf.sparql.ast.eval.ASTEvalHelper.executeUpdate(ASTEvalHelper.java:1091)
	... 9 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
	at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
	at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
	at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
	... 15 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
	... 20 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
	at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
	at com.bigdata.striterator.ChunkedWrappedIterator.close(ChunkedWrappedIterator.java:180)
	at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:297)
	at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
	... 4 more
Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
	at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1514)
	at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
	at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
	... 8 more
Caused by: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1337)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:896)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:791)
	... 3 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1317)
	... 8 more
Caused by: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.bop.join.PipelineJoin$JoinTask.call(PipelineJoin.java:643)
	at com.bigdata.bop.join.PipelineJoin$JoinTask.call(PipelineJoin.java:343)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1316)
	... 8 more
Caused by: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.bop.join.PipelineJoin$JoinTask$BindingSetConsumerTask.call(PipelineJoin.java:988)
	at com.bigdata.bop.join.PipelineJoin$JoinTask.consumeSource(PipelineJoin.java:700)
	at com.bigdata.bop.join.PipelineJoin$JoinTask.call(PipelineJoin.java:584)
	... 12 more
Caused by: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.btree.Leaf.getKeys(Leaf.java:180)
	at com.bigdata.btree.Leaf.indexOf(Leaf.java:873)
	at com.bigdata.btree.Node.indexOf(Node.java:988)
	at com.bigdata.btree.Node.indexOf(Node.java:988)
	at com.bigdata.btree.Node.indexOf(Node.java:988)
	at com.bigdata.btree.AbstractBTree.rangeCount(AbstractBTree.java:2636)
	at com.bigdata.btree.UnisolatedReadWriteIndex.rangeCount(UnisolatedReadWriteIndex.java:442)
	at com.bigdata.relation.accesspath.AccessPath.historicalRangeCount(AccessPath.java:1418)
	at com.bigdata.relation.accesspath.AccessPath.rangeCount(AccessPath.java:1386)
	at com.bigdata.bop.join.PipelineJoin$JoinTask$AccessPathTask.call(PipelineJoin.java:1620)
	at com.bigdata.bop.join.PipelineJoin$JoinTask$BindingSetConsumerTask.executeTasks(PipelineJoin.java:1353)
	at com.bigdata.bop.join.PipelineJoin$JoinTask$BindingSetConsumerTask.call(PipelineJoin.java:977)
	... 14 more

Query: base <https://swedish.syapse.com/>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix s: </bdm/api/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bds: <http://www.bigdata.com/rdf/search#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix syapse: </graph/syapse#>


    INSERT {
      GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
        ?subNew <https://swedish.syapse.com/graph/syapse#broader> ?superNew .
      }
    }
    
    WHERE
    {
        { 
         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
        
} UNION {

         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
         }
    }
    
2016-01-29 20:05:29,558 [ERROR] syapse.apps.vocab.service: Error during load of vocab from file '/tmp/rxnorm-nlmSsZbQ5-20160128194506'; cleaning up by removing graph 'rxnorm-nlm'
Traceback (most recent call last):
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/apps/vocab/service.py", line 200, in load_from_service
    load_from_file(local_file)
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/apps/vocab/service.py", line 148, in load_from_file
    infer_properties_for_graph(graph_name)
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/sem/named_graphs/loader.py", line 122, in infer_properties_for_graph
    STANDARD_PREFIX_MAP.shrink(row.target))
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/sem/named_graphs/inferences.py", line 198, in materialize_inferences
    timeouts=settings.SPARQL_VERY_LONG_TIMEOUTS)
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/sparql/endpoint.py", line 432, in raw_update
    prefixed_update, sparql_endpoint=sparql_endpoint)
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/sparql/endpoint.py", line 213, in __call__
    result = self.call(*args, **kwargs)
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/sparql/endpoint.py", line 319, in call
    result = super(CallRawUpdate, self).call(*args, **kwargs)
  File "/home/ubuntu/webapps/syapse/src/syapse/python/syapse/sparql/endpoint.py", line 307, in call
    rst = method(query, default_graph=named_graphs, named_graph=named_graphs)
  File "/home/ubuntu/webapps/syapse/src/pymantic/pymantic/sparql.py", line 210, in update
    return _Update(self, sparql, **kwargs).execute()
  File "/home/ubuntu/webapps/syapse/src/pymantic/pymantic/sparql.py", line 95, in execute
    (response.headers, response.content, self.sparql))
SPARQLQueryException: {'transfer-encoding': 'chunked', 'content-type': 'text/plain', 'server': 'Jetty(9.2.3.v20140905)'}: SPARQL-UPDATE: updateStr=base <https://swedish.syapse.com/>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix s: </bdm/api/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bds: <http://www.bigdata.com/rdf/search#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix syapse: </graph/syapse#>


    INSERT {
      GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
        ?subNew <https://swedish.syapse.com/graph/syapse#broader> ?superNew .
      }
    }
    
    WHERE
    {
        { 
         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
        
} UNION {

         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
         }
    }
    
java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: org.openrdf.query.UpdateExecutionException: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.rdf.sail.webapp.BigdataServlet.submitApiTask(BigdataServlet.java:281)
	at com.bigdata.rdf.sail.webapp.QueryServlet.doSparqlUpdate(QueryServlet.java:448)
	at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:233)
	at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:248)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:769)
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577)
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1125)
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1059)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:110)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
	at org.eclipse.jetty.server.Server.handle(Server.java:497)
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:311)
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:248)
	at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:610)
	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:539)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: org.openrdf.query.UpdateExecutionException: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.rdf.sail.webapp.QueryServlet$SparqlUpdateTask.call(QueryServlet.java:552)
	at com.bigdata.rdf.sail.webapp.QueryServlet$SparqlUpdateTask.call(QueryServlet.java:460)
	at com.bigdata.rdf.task.ApiTaskForIndexManager.call(ApiTaskForIndexManager.java:68)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	... 1 more
Caused by: org.openrdf.query.UpdateExecutionException: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.rdf.sparql.ast.eval.ASTEvalHelper.executeUpdate(ASTEvalHelper.java:1099)
	at com.bigdata.rdf.sail.BigdataSailUpdate.execute2(BigdataSailUpdate.java:152)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$UpdateTask.doQuery(BigdataRDFContext.java:1964)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.innerCall(BigdataRDFContext.java:1567)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1532)
	at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:704)
	... 4 more
Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
	at com.bigdata.rdf.sparql.ast.eval.ASTConstructIterator.hasNext(ASTConstructIterator.java:621)
	at info.aduna.iteration.IterationWrapper.hasNext(IterationWrapper.java:68)
	at com.bigdata.rdf.sparql.ast.eval.AST2BOpUpdate.convertDeleteInsert(AST2BOpUpdate.java:1015)
	at com.bigdata.rdf.sparql.ast.eval.AST2BOpUpdate.convertUpdateSwitch(AST2BOpUpdate.java:435)
	at com.bigdata.rdf.sparql.ast.eval.AST2BOpUpdate.convertUpdate(AST2BOpUpdate.java:288)
	at com.bigdata.rdf.sparql.ast.eval.ASTEvalHelper.executeUpdate(ASTEvalHelper.java:1091)
	... 9 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
	at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
	at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
	at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
	... 15 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
	... 20 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
	at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
	at com.bigdata.striterator.ChunkedWrappedIterator.close(ChunkedWrappedIterator.java:180)
	at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:297)
	at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
	... 4 more
Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
	at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1514)
	at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
	at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
	... 8 more
Caused by: java.lang.Exception: task=ChunkTask{query=1c9bcb20-b416-4e5a-b2cf-2a062936e4f9,bopId=29,partitionId=-1,sinkId=1,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1337)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:896)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:791)
	... 3 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1317)
	... 8 more
Caused by: java.lang.RuntimeException: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.bop.join.PipelineJoin$JoinTask.call(PipelineJoin.java:643)
	at com.bigdata.bop.join.PipelineJoin$JoinTask.call(PipelineJoin.java:343)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
	at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1316)
	... 8 more
Caused by: java.lang.RuntimeException: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.bop.join.PipelineJoin$JoinTask$BindingSetConsumerTask.call(PipelineJoin.java:988)
	at com.bigdata.bop.join.PipelineJoin$JoinTask.consumeSource(PipelineJoin.java:700)
	at com.bigdata.bop.join.PipelineJoin$JoinTask.call(PipelineJoin.java:584)
	... 12 more
Caused by: java.lang.NullPointerException: leaf=com.bigdata.btree.Leaf@c08fb46#-1396626998477973526(deleted){ isDirty=false, isDeleted=true, addr=-1396626998477973526, parent=N/A, isRoot=false, data=NA}
	at com.bigdata.btree.Leaf.getKeys(Leaf.java:180)
	at com.bigdata.btree.Leaf.indexOf(Leaf.java:873)
	at com.bigdata.btree.Node.indexOf(Node.java:988)
	at com.bigdata.btree.Node.indexOf(Node.java:988)
	at com.bigdata.btree.Node.indexOf(Node.java:988)
	at com.bigdata.btree.AbstractBTree.rangeCount(AbstractBTree.java:2636)
	at com.bigdata.btree.UnisolatedReadWriteIndex.rangeCount(UnisolatedReadWriteIndex.java:442)
	at com.bigdata.relation.accesspath.AccessPath.historicalRangeCount(AccessPath.java:1418)
	at com.bigdata.relation.accesspath.AccessPath.rangeCount(AccessPath.java:1386)
	at com.bigdata.bop.join.PipelineJoin$JoinTask$AccessPathTask.call(PipelineJoin.java:1620)
	at com.bigdata.bop.join.PipelineJoin$JoinTask$BindingSetConsumerTask.executeTasks(PipelineJoin.java:1353)
	at com.bigdata.bop.join.PipelineJoin$JoinTask$BindingSetConsumerTask.call(PipelineJoin.java:977)
	... 14 more

Query: base <https://swedish.syapse.com/>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix s: </bdm/api/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bds: <http://www.bigdata.com/rdf/search#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix syapse: </graph/syapse#>


    INSERT {
      GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
        ?subNew <https://swedish.syapse.com/graph/syapse#broader> ?superNew .
      }
    }
    
    WHERE
    {
        { 
         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
        
} UNION {

         GRAPH <https://swedish.syapse.com/graph/vocabulary/nlm/rxnorm#> {
             ?superNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         }
         ?subNew skos:broader * ?superNew .
         ?subNew rdf:type <http://www.w3.org/2004/02/skos/core#Concept> .
         hint:Prior hint:runLast true .
         }
    }