Hi Well you haven't shown a minimal complete code sample so we can't tell if you "use transaction perfectly". Even if you are using transactions correctly now the corruption may have happened at some point in the past when you weren't doing so (or if you've had this database around for several years from a time before TDB supported transactions)
The fact that the error only happens some of the time means it is an intermittent error. That it happens when you don't include a LIMIT is down the fact that without a LIMIT your queries are more likely to touch the entire database and therefore more likely to try and read the corrupted portion of the database. The solution is to rebuild a fresh database from the original source data, there is no way to repair the corruption Rob On 01/09/2014 02:53, "Wang Dongsheng" <[email protected]> wrote: >Hi Vesse, > >Thank you for your answer and sorry to reply so late due to a long time >absent. > >But I think I use transaction perfectly for each functions. > >And the error does not happen intermittently, it must happen when I do not >put a "limit" keyword. > >I don't know whether the two " Impossibly large object" errors mean the >same one, and I still could not find out the solutions. :( > > > >On Thu, Aug 21, 2014 at 12:49 PM, Rob Vesse <[email protected]> wrote: > >> Please see the TDB FAQs, more specifically "What is the Impossibly Large >> Object exception?" >> >> >>https://jena.apache.org/documentation/tdb/faqs.html#impossibly-large-obje >>ct >> >> Rob >> >> On 20/08/2014 18:25, "Wang Dongsheng" <[email protected]> wrote: >> >> >Hi, all >> > >> >If I put a "limit 200" at the end of the query it works, but If I do >>not >> >set a limit keyword the error happened as the following. >> > >> >-----------error code location---------------- >> > >> >ResultSet rs = qExec.execSelect(); >> >while(rs.hasNext()){ // here is error of >> >(DiseaseTDBConnection.java:745) >> > ..... >> >} >> >--------------------------- >> > >> >com.hp.hpl.jena.tdb.base.file.FileException: >> >>>ObjectFileStorage.read[nodes.dat](47756900)[filesize=295558078][file.siz >>>e( >> >)=295558078]: >> >Impossibly large object : 1630433138 bytes > >> >filesize-(loc+SizeOfInt)=247801174 >> > >> >>com.hp.hpl.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStor >> >age.java:346) >> > com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeFromTable(NodeTable >> >Native.java:178) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeT >> >ableNative.java:103) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableN >> >ative.java:74) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTa >> >bleCache.java:103) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCa >> >che.java:74) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTable >> >Wrapper.java:55) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableI >> >nline.java:67) >> > >> >>com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTable >> >Wrapper.java:55) >> > com.hp.hpl.jena.tdb.lib.TupleLib.quad(TupleLib.java:159) >> > com.hp.hpl.jena.tdb.lib.TupleLib.quad(TupleLib.java:153) >> > com.hp.hpl.jena.tdb.lib.TupleLib.access$100(TupleLib.java:45) >> > com.hp.hpl.jena.tdb.lib.TupleLib$4.convert(TupleLib.java:87) >> > com.hp.hpl.jena.tdb.lib.TupleLib$4.convert(TupleLib.java:83) >> > org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:299) >> > >> >>com.hp.hpl.jena.tdb.store.GraphTDBBase$ProjectQuadsToTriples.next(GraphTD >> >BBase.java:199) >> > >> >>com.hp.hpl.jena.tdb.store.GraphTDBBase$ProjectQuadsToTriples.next(GraphTD >> >BBase.java:187) >> > >> >>com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:9 >> >4) >> > >> >>org.apache.jena.atlas.iterator.IteratorConcat.next(IteratorConcat.java:81 >> >) >> > org.apache.jena.atlas.iterator.Iter$3.hasNext(Iter.java:184) >> > >> >>com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.jav >> >a:90) >> > >> >>com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.jav >> >a:90) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMappe >> >r.hasNextBinding(QueryIterTriplePattern.java:151) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBindin >> >g(QueryIterRepeatApply.java:81) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage >> >(QueryIterRepeatApply.java:108) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBindin >> >g(QueryIterRepeatApply.java:67) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage >> >(QueryIterRepeatApply.java:108) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBindin >> >g(QueryIterRepeatApply.java:67) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage >> >(QueryIterRepeatApply.java:108) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBindin >> >g(QueryIterRepeatApply.java:67) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage >> >(QueryIterRepeatApply.java:108) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBindin >> >g(QueryIterRepeatApply.java:67) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage >> >(QueryIterRepeatApply.java:108) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBindin >> >g(QueryIterRepeatApply.java:67) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage >> >(QueryIterRepeatApply.java:108) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBindin >> >g(QueryIterRepeatApply.java:67) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterBlockTriples.hasNextBindi >> >ng(QueryIterBlockTriples.java:64) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>org.apache.jena.atlas.data.AbstractDataBag.addAll(AbstractDataBag.java:74 >> >) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterSort$SortedBindingIterato >> >r.initializeIterator(QueryIterSort.java:89) >> > >> >>org.apache.jena.atlas.iterator.IteratorDelayedInitialization.init(Iterato >> >rDelayedInitialization.java:40) >> > >> >>org.apache.jena.atlas.iterator.IteratorDelayedInitialization.hasNext(Iter >> >atorDelayedInitialization.java:50) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterPlainWrapper.hasNextBindi >> >ng(QueryIterPlainWrapper.java:54) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIterConvert.hasNextBinding(Qu >> >eryIterConvert.java:59) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBindin >> >g(QueryIteratorWrapper.java:40) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBindin >> >g(QueryIteratorWrapper.java:40) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBindin >> >g(QueryIteratorWrapper.java:40) >> > >> >>com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIte >> >ratorBase.java:112) >> > >> >>com.hp.hpl.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.jav >> >a:75) >> > >> >>com.wds.util.DiseaseTDBConnection.htmlQuery(DiseaseTDBConnection.java:745 >> >) >> > >>com.wds.servlet.relateness.ListReg2Dis.service(ListReg2Dis.java:86) >> > javax.servlet.http.HttpServlet.service(HttpServlet.java:728) >> > >> > >> >Thanks in advance if anyone can give some advise.. >> >> >> >> >>
