[Biojava-l] Getting one feature of a organism

[Richard Holland]

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
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