Re: [Gusdev-gusdev] GBParser error

[Steve F. <sfi...@pc...>]

dear Jeetendra -

it looks like the genbank parser does force a new external database 
called taxon into the ExternalDatabase table, as it doesn't seem to have 
a facility to map 'taxon' to an alternative name for that db.

it looks like its failing because it may be having trouble with the 
sequence (db sequence, not bio sequence) which generates the next key.

did you send the complete error output?   I am not sure i understand why 
i am not seeing a primary key value in the insert statement.

steve


Jeetendra Soneja wrote:

>I am trying to upload a genbank flat file, and I am getting the error
>listed below.
>    When I looked at the source code of GbParser.pm, I figured out that
>the plugin is getting the database name as 'taxon' from the db_xref
>qualifier (e.g. db_xref='taxon:4932') and is trying to retrieve the
>external_database_id and external_database_release_id for the 'taxon'
>database. Now, even though I have an entry for 'Taxonomy' database in
>my Sres.ExternalDatabase table, it is unable to match that since it is
>looking for 'taxon' as the database name. Finally, it tries to insert
>new entry for 'taxon' database in the Sres.ExternalDatabase and
>Sres.ExternalDatabaseRelease tables, and the insert statement fails ..
>don't know why ?
>
>I would greatly appreciate if someone could help me on this.
>
>Thanks,
>Jeetendra.
>
>
>
>allNonNullsSet: db_ref_na_feature_id not set... = ''
>allNonNullsSet: external_database_id not set... = ''
>GUS::Model::SRes::ExternalDatabase->retrieveFromDB($doNotRetrieveAtts=,)
>Submitting GUS::Model::SRes::ExternalDatabase:
> Table: ExternalDatabase
>        lowercase_name: [taxon]
>        name: [taxon]
>
>HasChangedAttributes='0'
>Setting all foreign keys
>GUS::Model::SRes::ExternalDatabase->Submit: All foreign keys are
>set...proceeding
>allNonNullsSet: external_database_id not set... = ''
>Inserting:
>Table: ExternalDatabase
>        group_write: [1]
>        other_read: [1]
>        group_read: [1]
>        lowercase_name: [taxon]
>        name: [taxon]
>        user_read: [1]
>        row_user_id: [1]
>        modification_date: [SYSDATE]
>        other_write: [0]
>        row_alg_invocation_id: [171]
>        row_project_id: [1]
>        row_group_id: [1]
>        user_write: [1]
>DBD::Oracle::st execute failed: ORA-00001: unique constraint
>(SRES.PK_EXTERNALDATABASE) violated (DBD ERROR: OCIStmtExecute)$
>    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
>group_read, lowercase_name, name, user_read, row_user_id, $
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
>ParamValues: :p5='taxon', :p12='1', :p8='7', :p10='1$
>Wed Aug 18 17:44:50 2004        Genbank entries inserted= 0;  updated= 0;
>total #(inserted::updated::deleted)=16::::
>
>Wed Aug 18 17:44:50 2004        FAILURES        Unable to process 2
>entries. See gbparserFailures/
>Wed Aug 18 17:44:50 2004        RESULT  Genbank entries inserted= 0; 
>updated= 0;  failed= 2
>
>
>
>
>  
>