Hi all,
I would like to query the features of a sequence with following code:
<code>
public class Test{
public static void main(String[] args) {
// load Hibernate config
SessionFactory sessionFactory = new
Configuration().configure().buildSessionFactory(); // open the
session
Session session = sessionFactory.openSession();
// connect it to BioJavaX
RichObjectFactory.connectToBioSQL(session);
Transaction tx = session.beginTransaction();
Query q1 = session.createQuery(
"from Feature as f " +
"inner join fetch f.noteSet as n " +
"where n.value=:val and f.typeTerm.name=:term");
q1.setString("val","TRNF");
q1.setString("term","gene");
List<SimpleRichFeature> li = q1.list();
System.out.println("Found:\t"+li.size());
for (Iterator<SimpleRichFeature> i = li.iterator(); i.hasNext(); ){
SimpleRichFeature f = i.next();
System.out.println("Term:\t"+f.getTypeTerm().getName());
System.out.println("Location:\t"+f.getLocation().getMin()+"\t"+f.getLocation().getMax());
System.out.println(f.getSequence().seqString());
Annotation a = f.getAnnotation();
for (Iterator keys = a.keys().iterator(); keys.hasNext(); ){
Object key = keys.next();
System.out.println(key+"\t"+a.getProperty(key));
}
}
tx.commit();
session.close();
}
}
</code>
When I try to print the SymbolList associated with the feature I receive
the following exception. I appreciate any hint because I do not know
what to do as it seems that the exception occurs somewhere within
BioJava code.
Exception in thread "main" org.hibernate.PropertyAccessException:
Exception occurred inside setter of
org.biojavax.bio.seq.SimpleRichFeature.locationSet
at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:65)
at
org.hibernate.tuple.entity.AbstractEntityTuplizer.setPropertyValues(AbstractEntityTuplizer.java:337)
at
org.hibernate.tuple.entity.PojoEntityTuplizer.setPropertyValues(PojoEntityTuplizer.java:200)
at
org.hibernate.persister.entity.AbstractEntityPersister.setPropertyValues(AbstractEntityPersister.java:3571)
at
org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:133)
at
org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:854)
at org.hibernate.loader.Loader.doQuery(Loader.java:729)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.loadCollection(Loader.java:1994)
at
org.hibernate.loader.collection.CollectionLoader.initialize(CollectionLoader.java:36)
at
org.hibernate.persister.collection.AbstractCollectionPersister.initialize(AbstractCollectionPersister.java:565)
at
org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:63)
at
org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1716)
at
org.hibernate.collection.AbstractPersistentCollection.forceInitialization(AbstractPersistentCollection.java:454)
at
org.hibernate.engine.StatefulPersistenceContext.initializeNonLazyCollections(StatefulPersistenceContext.java:844)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:241)
at org.hibernate.loader.Loader.loadEntity(Loader.java:1860)
at
org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48)
at
org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42)
at
org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3049)
at
org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:399)
at
org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:375)
at
org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:139)
at
org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:98)
at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878)
at org.hibernate.impl.SessionImpl.immediateLoad(SessionImpl.java:836)
at
org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:66)
at
org.hibernate.proxy.AbstractLazyInitializer.getImplementation(AbstractLazyInitializer.java:111)
at
org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.invoke(CGLIBLazyInitializer.java:150)
at
org.biojavax.bio.seq.ThinRichSequence$$EnhancerByCGLIB$$e3c3c7ff.seqString(<generated>)
at meinVersuch.TestAbfragen.main(TestAbfragen.java:59)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:42)
... 30 more
Caused by: java.lang.RuntimeException: Error while trying to call new
class org.biojavax.ontology.SimpleComparableOntology(class java.lang.String)
at
org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:166)
at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:105)
at
org.biojavax.RichObjectFactory.getDefaultOntology(RichObjectFactory.java:221)
at
org.biojavax.bio.seq.CompoundRichLocation.getJoinTerm(CompoundRichLocation.java:61)
at
org.biojavax.bio.seq.CompoundRichLocation.<init>(CompoundRichLocation.java:90)
at
org.biojavax.bio.seq.SimpleRichLocation.union(SimpleRichLocation.java:494)
at org.biojavax.bio.seq.RichLocation$Tools.merge(RichLocation.java:363)
at
org.biojavax.bio.seq.SimpleRichFeature.setLocationSet(SimpleRichFeature.java:181)
... 35 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at
org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:133)
... 42 more
Caused by: org.hibernate.HibernateException: A collection with
cascade="all-delete-orphan" was no longer referenced by the owning
entity instance: Feature.locationSet
at
org.hibernate.engine.Collections.processDereferencedCollection(Collections.java:96)
at
org.hibernate.engine.Collections.processUnreachableCollection(Collections.java:39)
at
org.hibernate.event.def.AbstractFlushingEventListener.flushCollections(AbstractFlushingEventListener.java:218)
at
org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:77)
at
org.hibernate.event.def.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:35)
at
org.hibernate.impl.SessionImpl.autoFlushIfRequired(SessionImpl.java:969)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1114)
at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
at
org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:811)
... 47 more
It would be very nice if someone can help me. I am grateful for any
hints. Thanks a lot.
Cheers,
Gabrielle
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