2018-02-06 18:40 GMT+01:00 Andy Seaborne <[email protected]>:
> An oddity:
>
> The only way I can see to set with a null binding (and not get a warning)
> is on the path where the dataset is not a TDB one, but with a graph in a
> general dataset.
>
> Is that the setup here?
>
The TDB is created and opened always by the same application , by
TDBFactory.createDataset(Paths.get(database_location).toString())
I forgot to say that sometimes during the tuning of my app. , there were
uncaught exception that caused end() being called without commit or
rollback .
> (that said, tracing down and eliminating all other possible routes back
> isn't simple so I might have missed another route)
>
> Andy
>
>
> On 06/02/18 14:24, Andy Seaborne wrote:
>
>> Can you dump the database?
>>
>>
>> On 06/02/18 10:32, Jean-Marc Vanel wrote:
>>
>>> Hi
>>>
>>> I consistently get a NullPointerException from this query on my test TDB
>>> on laptop.
>>>
>>> SELECT DISTINCT ?thing
>>> WHERE {
>>> graph ?thing {
>>> [] ?p ?O .
>>> }
>>> } LIMIT 200
>>>
>>> Looking into code : BindingBase.java line 203 , it appears that a
>>> binding's
>>> node is null for one SELECT result.
>>>
>>
>> In which case there is a binding and the value (Node) is null.
>>
>> We can put in null checks to catch it earlier (that would be a good idea
>> anyway) but still not at the point where the problem starts because there
>> isn't one such point - it depends on cache flush order.
>>
>> This binding stands for a named graph.
>>>
>>
>> Just a though - do your named graph have URI names? or are any blank
>> nodes?
>>
>> So the database is probably broken. Of course, this is a work and test
>>> database whose content has no value, but I try to understand and prevent
>>> this to happen on production database.
>>> Is a there a bug somewhere ?
>>>
>>
>> Yes :-) Where? now that is the question!
>>
>> What is the likely cause ? During tests and debugs, transactions may have
>>> not been rolled back , application was killed, etc .
>>> How could the database be repaired in such cases ? By doing a tdbdump and
>>> recreate the TDB ?
>>>
>>
>> Non-transactional TDB needs to explicitly flush modification to disk
>> (TDB.sync). Now due to caching something are being written all the time
>> but not competently and consistently.
>>
>> If an index gets to disk, with new Nodes (not already used) nodes, then
>> the NodeTable also needs to be written. If it is not, a later lookup of
>> the NodeId can't find the node -> null.
>>
>> If it is transactional, and is always used transactionally, the problem
>> does not arise.
>>
>> You might try TDB2 - it does not allow non-transactional use.
>>
>> In the future, it might get an "autocommit" feature ... but then users@
>> will get questions about why it is so slow. Full SQL compatibility!
>>
>> Andy
>>
>>
>>> Running on Jena 3.6.0 and Ubuntu 2017.10 and java version "1.8.0_121" .
>>>
>>> java.lang.NullPointerException
>>> at
>>> org.apache.jena.sparql.engine.binding.BindingBase.hashCode(BindingBase.java:203)
>>>
>>> at
>>> org.apache.jena.sparql.engine.binding.BindingBase.hashCode(BindingBase.java:183)
>>>
>>> at java.util.HashMap.hash(HashMap.java:338)
>>> at java.util.HashMap.containsKey(HashMap.java:595)
>>> at java.util.HashSet.contains(HashSet.java:203)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIterDistinct.get
>>> InputNextUnseen(QueryIterDistinct.java:106)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIterDistinct.has
>>> NextBinding(QueryIterDistinct.java:70)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.has
>>> Next(QueryIteratorBase.java:114)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIterSlice.hasNex
>>> tBinding(QueryIterSlice.java:76)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.has
>>> Next(QueryIteratorBase.java:114)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.
>>> hasNextBinding(QueryIteratorWrapper.java:39)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.has
>>> Next(QueryIteratorBase.java:114)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.
>>> hasNextBinding(QueryIteratorWrapper.java:39)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.has
>>> Next(QueryIteratorBase.java:114)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.
>>> hasNextBinding(QueryIteratorWrapper.java:39)
>>> at
>>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.has
>>> Next(QueryIteratorBase.java:114)
>>> at
>>> org.apache.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:74)
>>>
>>> * at
>>> org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNex
>>> t(ResultSetCheckCondition.java:55)*
>>> at
>>> scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42)
>>>
>>> at scala.collection.Iterator$class.toStream(Iterator.scala:1320)
>>> at scala.collection.AbstractIterator.toStream(Iterator.scala:1334)
>>> at
>>> scala.collection.Iterator$$anonfun$toStream$1.apply(Iterator.scala:1320)
>>> at
>>> scala.collection.Iterator$$anonfun$toStream$1.apply(Iterator.scala:1320)
>>> at scala.collection.immutable.Stream$Cons.tail(Stream.scala:1233)
>>> at scala.collection.immutable.Stream$Cons.tail(Stream.scala:1223)
>>> at
>>> scala.collection.immutable.Stream$$anonfun$map$1.apply(Stream.scala:418)
>>> at
>>> scala.collection.immutable.Stream$$anonfun$map$1.apply(Stream.scala:418)
>>> at scala.collection.immutable.Stream$Cons.tail(Stream.scala:1233)
>>> at scala.collection.immutable.Stream$Cons.tail(Stream.scala:1223)
>>> at scala.collection.generic.Growable$class.loop$1(Growable.
>>> scala:54)
>>> at
>>> scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:57)
>>> at
>>> scala.collection.mutable.ListBuffer.$plus$plus$eq(ListBuffer.scala:183)
>>> at
>>> scala.collection.mutable.ListBuffer.$plus$plus$eq(ListBuffer.scala:45)
>>> at scala.collection.TraversableLike$class.to(TraversableLike.
>>> scala:590)
>>> at scala.collection.AbstractTraversable.to(Traversable.scala:104)
>>> at
>>> deductions.runtime.sparql_cache.SPARQLHelpers$$anonfun$sparq
>>> lSelectQueryVariablesNT$1.apply(SPARQLHelpers.scala:426)
>>>
>>>
>>>
>>>
--
Jean-Marc Vanel
http://www.semantic-forms.cc:9111/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me#subject
<http://www.semantic-forms.cc:9111/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me>
Déductions SARL - Consulting, services, training,
Rule-based programming, Semantic Web
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
