[Biojava-l] Getting one feature of a organism

[Richard Holland]

That's very helpful - thanks.

I've also just committed some updates that might workaround the
problem. Could you try updating from the head of subversion and
compiling it locally (rather than downloading a precompiled version),
then retrying your original code?

cheers,
Richard

2008/6/19 Augusto Fernandes Vellozo <augustovmail-java at yahoo.com.br>:
> Hello.
>
> I've already discovered a workaround to this problem: after to execute the
> query I've just called feature.toString().
> I am not sure why this works, but I think that is because the method lazy to
> load the properties. With the call "toString()" the feature properties will
> be loaded.
>
> Thanks,
>
> Augusto
>
> 2008/6/19 Richard Holland <dicknetherlands at gmail.com>:
>>
>> Hello. You're the second person to hit this problem recently on this
>> list - it's a bug in BioJava that we need to fix. We'll let you know
>> how we get on.
>>
>> Richard.
>>
>> 2008/6/19 Augusto Fernandes Vellozo <augustovmail-java at yahoo.com.br>:
>> > Hi all
>> >
>> > I am new in BioJava and Hibernate. Sorry if the question is basic.
>> > I am trying to get one feature (gene) with this query:
>> >
>> >    public static SimpleRichFeature getGene(String geneName, NCBITaxon
>> > organism) {
>> >        Query query = session.createQuery("select f from Feature as f
>> > join
>> > f.parent as bioentry where "
>> >            + "f.name=:geneName and f.typeTerm=:geneTerm and
>> > bioentry.taxon=:taxonId ");
>> >        query.setString("geneName", geneName);
>> >        query.setParameter("taxonId", organism);
>> >        query.setParameter("geneTerm", TERM_GENE);
>> >        List features = query.list();
>> >        return (features.size() == 0) ?null :(SimpleRichFeature)
>> > features.get(0);
>> >    }
>> >
>> > I am getting the error:
>> >
>> > 35:55,061 ERROR AssertionFailure:22 - an assertion failure occured (this
>> > may
>> > indicate a bug in Hibernate, but is more likely due to unsafe use of the
>> > session)
>> > org.hibernate.AssertionFailure: collection [BioEntry.comments] was not
>> > processed by flush()
>> >    at
>> > org.hibernate.engine.CollectionEntry.postFlush(CollectionEntry.java:205)
>> >    at
>> >
>> > org.hibernate.event.def.AbstractFlushingEventListener.postFlush(AbstractFlushingEventListener.java:333)
>> >    at
>> >
>> > org.hibernate.event.def.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:42)
>> >    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 baobab.sequence.general.BioSql.getGene(BioSql.java:75)
>> >    at baobab.sequence.loads.LoadEstToKo.main(LoadEstToKo.java:120)
>> > Exception in thread "main" org.hibernate.AssertionFailure: collection
>> > [BioEntry.comments] was not processed by flush()
>> >    at
>> > org.hibernate.engine.CollectionEntry.postFlush(CollectionEntry.java:205)
>> >    at
>> >
>> > org.hibernate.event.def.AbstractFlushingEventListener.postFlush(AbstractFlushingEventListener.java:333)
>> >    at
>> >
>> > org.hibernate.event.def.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:42)
>> >    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 baobab.sequence.general.BioSql.getGene(BioSql.java:75)
>> >    at baobab.sequence.loads.LoadEstToKo.main(LoadEstToKo.java:120)
>> >
>> > Please, could one help me?
>> > What is my fault?
>> > How can i do this?
>> >
>> > Thanks a lot,
>> >
>> > Augusto
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>
>
>
> --
> Augusto F. Vellozo