Re: [GUSDEV] Another GBParser error :-/

[Thomas O. <ot...@fi...>]

Hi,

I think that you inserted twice the taxonomie... so it gives back two 
result. You will have to delete one... take the modification_date in the 
where select.

Cheers,
Thomas
fab...@de... wrote:

>Hello all,
>
>our GBParser initial error was solved (Thanks Jeetendra, Thomas and Pablo)...
>now we have another one. Running the plugin "ga GUS::Common::Plugin::GBParser
>--file=sequences.gb --gbRel=145.0 --db_rel_id=62" we're getting the following
>messages:
>
>...
>RUN     1037631..1047290
>RUN     1047319..1050482
>RUN     1052519..1054589
>RUN     1059492..1060087
>VLD     CBIL::Bio::GenBank::Features    1
>VLD     CBIL::Bio::GenBank::Origin      1
>Fri May  6 14:38:56 2005        STATUS  N=1 ACC=NC_000521       
>TOTAL_OBJECTS=17
>
>ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name_class
>= ? and  name = ?       2 rows returned!
>
>ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name_class
>= ? and  name = ?       2 rows returned!
>Fri May  6 14:39:40 2005        INVALID QUALIFIER       GUS::Model::DoTS::Source
>       ::      mol_type        ::      genomic DNA
>
>DBD::Pg::st execute failed: ERROR:  duplicate key violates unique constraint
>"pk_externaldatabase" at
>/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <GEN0>
>line 26148.
>Fri May  6 14:39:41 2005        Genbank entries inserted= 0;  updated= 0; total
>#(inserted::updated::deleted)=19::::
>
>Fri May  6 14:39:41 2005        FAILURES        Unable to process 2 entries. See
>gbparserFailures/
>Fri May  6 14:39:41 2005        RESULT  Genbank entries inserted= 0;  updated=
>0;  failed= 2
>
>
>
>
>
>Our gbparserFailures/errors file has:
>
>SQL ERROR!! involving
>
>    INSERT INTO SRes.ExternalDatabase (  group_write, other_read, group_read,
>lowercase_name, name, user_read, row_user_id, external_database_id,
>modification_date, other_write, row_alg_invocation_id, row_project_id,
>row_group_id, user_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
> Values: 1, 1, 1, geneid, GeneID, 1, 1, 8, 0, 62, 1, 1, 1 at
>/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 187
>       
>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8bd1cf0)','\x{a}
>SQL ERROR!! involving\x{a} \x{a}    INSERT INTOSRes.ExternalDataba...') called
>at /usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
>       
>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8bd1cf0)','GUS::ObjRelP::DbiDbHandle::st=HASH(0x94eed78)','ARRAY(0x94eedb4)','\x{a}
>   INSERT INTO SRes.ExternalDatabase (  group_write, other_...') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 689
>
>
>We're sure that our --db_rel_id=62 as shown here:
>
>gus=# select edbr.external_database_release_id 
>      from sres.externaldatabase edb, sres.externaldatabaserelease edbr
>      where edb.external_database_id = edbr.external_database_id
>      and edb.name = 'GenBank';
>
> external_database_release_id
>------------------------------
>                           62
>(1 row)
>
>
>Does anyone can help us to identify the trouble?
>
>Thanks a lot.
>
>
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