[GUSDEV] Another GBParser error :-/

[<fab...@de...>]

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::GBPa=
rser
--file=3Dsequences.gb --gbRel=3D145.0 --db_rel_id=3D62" 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=3D1 ACC=3DNC_000521      =20
TOTAL_OBJECTS=3D17

ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name=
_class
=3D ? and  name =3D ?       2 rows returned!

ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name=
_class
=3D ? and  name =3D ?       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 constra=
int
"pk_externaldatabase" at
/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <GE=
N0>
line 26148.
Fri May  6 14:39:41 2005        Genbank entries inserted=3D 0;  updated=3D=
 0; total
#(inserted::updated::deleted)=3D19::::

Fri May  6 14:39:41 2005        FAILURES        Unable to process 2 entri=
es. See
gbparserFailures/
Fri May  6 14:39:41 2005        RESULT  Genbank entries inserted=3D 0;  u=
pdated=3D
0;  failed=3D 2





Our gbparserFailures/errors file has:

SQL ERROR!! involving

    INSERT INTO SRes.ExternalDatabase (  group_write, other_read, group_r=
ead,
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
      =20
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x8bd1=
cf0)','\x{a}
SQL ERROR!! involving\x{a} \x{a}    INSERT INTOSRes.ExternalDataba...') c=
alled
at /usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
      =20
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x8b=
d1cf0)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x94eed78)','ARRAY(0x94eedb=
4)','\x{a}
   INSERT INTO SRes.ExternalDatabase (  group_write, other_...') called a=
t
/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 689


We're sure that our --db_rel_id=3D62 as shown here:

gus=3D# select edbr.external_database_release_id=20
      from sres.externaldatabase edb, sres.externaldatabaserelease edbr
      where edb.external_database_id =3D edbr.external_database_id
      and edb.name =3D 'GenBank';

 external_database_release_id
------------------------------
                           62
(1 row)


Does anyone can help us to identify the trouble?

Thanks a lot.


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