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Re: [Gusdev-gusdev] GBParser error
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From: Jeetendra S. <so...@vb...> - 2004-08-19 04:08:44
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Dear Steve,
Thank you for your reply. You were right, I accidently pasted incomplete
error message.
As you and Pablo suggested, I took a look at the sequence value for
the ExternalDatabase table, and it was set to '1'. I altered the
sequence and set its value to the number of records in
ExternalDatabase table. It's working fine now.
Some thoughts on how this problem might have occured. As suggested in
the GUS documentation, I populated the Sres.ExternalDatabase and
Sres.ExternalDatabaseRelease tables using the SubmitRow plugin. I
suppose that SubmitRow doesn't use the sequence value associated with
these tables, and hence they retain their initial value (equal to 1).
This can cause conflict as it did in my case. Is that correct ?
Also, it would be nice if we could link the 'db_xref="taxon:xxxx"'
qualifier of Genbank file to Sres.Taxon and Sres.TaxonName tables.
Regards,
Jeetendra.
> 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
>>
>>
>>
>>
>>
>>
>
>
>
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--
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu
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