[Biojava-l] Problem Inserting Genbank File

[Richard Holland]

Hello. I have a sneaking suspicion I know what is wrong, but I can't
tell for sure without seeing your full source code. Could you post that?
It'd certainly help a lot in trying to find the exact cause of the
problem.

cheers,
Richard

On Tue, 2006-08-01 at 07:50 +1000, Michael Joss wrote:
> Hi all,
>         I am pretty new to this whole BioJava/BioJavaX thing. I thought
> I would start with something reasonably basic. At least what I thought
> would be. I wanted to open a Genbank file and save it into a BioSQL DB.
> I have got the BioSQL Database all running and BioJava and BioJavaX seem
> to be working ok ( I might have messed up some stuff along the way but
> it does appear to be working). I can open the file and can convert it to
> fasta etc .. all the code was found in various examples. When I use
> session.saveOrUpdate:
> 
>             BufferedReader br = new BufferedReader(new
> FileReader("C:/CODE/AY928791.GBANK"));
> // a namespace to override that in the file
>             Namespace ns = RichObjectFactory.getDefaultNamespace();
> // we are reading DNA sequences
>             RichSequenceIterator seqs =
> RichSequence.IOTools.readGenbankDNA(br,ns);
>             while (seqs.hasNext()) {
>                   RichSequence rs = seqs.nextRichSequence();
>                   session.saveOrUpdate("Sequence",rs);
>             }  
> 
> I get an error saying it can't insert a taxon, the taxon and taxon_name
> tables seem to be populated correctly and I am not sure how to work out
> why its attempting to insert a taxon that is already there? I just don't
> know enough about .. well anything.. but hibernate in particular. Any
> ideas? 
> If you need anything else please let me know? The file is simply a
> single genbank record with locus the same name as the file. I tried a
> few others and got the same result. I am using the latest CVS of
> BioJavaX and BioJava 1.4 and Hibernate 3.1.
> 
> Cheers 
> 
> Joss
> 
> 6860 [main] DEBUG org.hibernate.engine.Cascade  - processing cascade
> ACTION_SAVE_UPDATE for: Sequence
> 6860 [main] DEBUG org.hibernate.engine.CascadingAction  - cascading to
> saveOrUpdate: Taxon
> 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener  -
> transient instance of: Taxon
> 6860 [main] DEBUG
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener  - saving
> transient instance
> 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener  -
> saving [Taxon#<null>]
> 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener  -
> executing insertions
> 6860 [main] DEBUG org.hibernate.event.def.WrapVisitor  - Wrapped
> collection in role: Taxon.nameSet
> 6875 [main] DEBUG org.hibernate.persister.entity.AbstractEntityPersister
>  - Inserting entity: Taxon (native id)
> 6875 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - about to open
> PreparedStatement (open PreparedStatements: 0, globally: 0)
> 6875 [main] DEBUG org.hibernate.SQL  - insert into taxon (ncbi_taxon_id,
> node_rank, genetic_code, mito_genetic_code, left_value, right_value,
> parent_taxon_id) values (?, ?, ?, ?, ?, ?, ?)
> 6875 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - preparing
> statement
> 6891 [main] DEBUG org.hibernate.persister.entity.AbstractEntityPersister
>  - Dehydrating entity: [Taxon#<null>]
> 6891 [main] DEBUG org.hibernate.type.IntegerType  - binding '36865' to
> parameter: 1
> 6891 [main] DEBUG org.hibernate.type.StringType  - binding null to
> parameter: 2
> 6891 [main] DEBUG org.hibernate.type.IntegerType  - binding null to
> parameter: 3
> 6891 [main] DEBUG org.hibernate.type.IntegerType  - binding null to
> parameter: 4
> 6891 [main] DEBUG org.hibernate.type.IntegerType  - binding null to
> parameter: 5
> 6891 [main] DEBUG org.hibernate.type.IntegerType  - binding null to
> parameter: 6
> 6891 [main] DEBUG org.hibernate.type.IntegerType  - binding null to
> parameter: 7
> 6953 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - about to close
> PreparedStatement (open PreparedStatements: 1, globally: 1)
> 6953 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - closing
> statement
> 6953 [main] DEBUG org.hibernate.util.JDBCExceptionReporter  - could not
> insert: [Taxon] [insert into taxon (ncbi_taxon_id, node_rank,
> genetic_code, mito_genetic_code, left_value, right_value,
> parent_taxon_id) values (?, ?, ?, ?, ?, ?, ?)]
> java.sql.SQLException: Duplicate entry '36865' for key 2
> 
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416