[Biojava-dev] biojavax stress test

[Richard HOLLAND]

Hi all.

Mark noticed some time ago that getMembers() didn't work, for exactly
the reason you state below - it cannot be guaranteed to return the
correct answer. So we removed it - the current biojava-live does not
have it and its gone from the javadocs too.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: mark.schreiber at novartis.com 
> [mailto:mark.schreiber at novartis.com] 
> Sent: Monday, January 16, 2006 10:32 AM
> To: Michael Heuer
> Cc: biojava-dev at biojava.org; Richard HOLLAND
> Subject: Re: [Biojava-dev] biojavax stress test
> 
> 
> >Finally, if I create the RichStreamReader with a null 
> Namespace, letting
> >the sequence files provide the namespace, I can retrieve the 
> persisted
> >Namespace and BioEntries using hibernate queries, but the 
> BioEntries are
> >not associated with the Namespace via the getMembers() 
> method as in the
> >biojavax docs.
> >
> >e.g.
> >
> >Query query = session.createQuery("from Namespace");
> >List namespaces = query.list();
> >for (Iterator i = namespaces.iterator(); i.hasNext(); )
> >{
> >  Namespace namespace = (Namespace) i.next();
> >  System.out.println("Namespace: " + namespace.getName());
> >
> > for (Iterator j = namespace.getMembers().iterator(); j.hasNext(); )
> >  {
> >    BioEntry bioEntry = (BioEntry) j.next();
> >    System.out.println("   BioEntry: " + bioEntry.getName());
> >  }
> >}
> >
> >returns
> >
> >Namespace: MyNamespace
> >
> >
> >whereas
> >
> >Query query = session.createQuery("from BioEntry");
> >List bioEntries = query.list();
> >for (Iterator i = bioEntries.iterator(); i.hasNext(); )
> >{
> >  BioEntry bioEntry = (BioEntry) i.next();
> >  System.out.println("BioEntry: " + bioEntry.getName() +
> >                     "  Namespace: " + bioEntry.getNamespace());
> >}
> >
> >returns
> >
> >BioEntry: 12345  Namespace: MyNamespace
> >BioEntry: 23456  Namespace: MyNamespace
> >...
> >
> >   michael
> >
> 
> Seems odd, it looks like Hibernate is not loading the contents of the 
> Namespaces on demand. Richard, is this some sort of lazy 
> loading issue?
> 
> - Mark
> 
> 
>