[BioSQL-l] errors (?) with store()

[Marc Logghe]

Hi,
We have noticed something strange when edited persistence objects are stored into biosql. The flow looked like this. A multiple genbank file was loaded into biosql using the load_seqdatabase.pl script. Afterwards, bioeintries were fetched from the database (persistent seq objects) a new feature was added and the seq object was put back using store(). During that process we get loads of errors like these:
DBD::Oracle::st execute failed: ORA-00001: unique constraint (BIOSQL.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD ERROR: OCIStmtExecute) [for statement ``INSERT INTO bioentry_qualifier_value (ent_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)'' with params: :p4=1, :p1='2136287', :p2='1909583', :p3=undef]) at /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 418, <> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint (BIOSQL.XPKBIOENTRY_REF_ASSOC) violated (DBD ERROR: OCIStmtExecute) [for statement ``INSERT INTO bioentry_reference (ent_oid, ref_oid, end_pos, start_pos, rank) VALUES (?, ?, ?, ?, ?)'' with params: :p4='1', :p5=1, :p1='2136287', :p2='1910107', :p3='161']) at /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 418, <> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint (BIOSQL.XPKSEQFEATURE_QUALIFIER_ASSOC) violated (DBD ERROR: OCIStmtExecute) [for statement ``INSERT INTO seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)'' with params: :p4=1, :p1='2136291', :p2=1910113, :p3='W09C5.6a']) at /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 418, <> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint (BIOSQL.XPKSEQFEATURE_QUALIFIER_ASSOC) violated (DBD ERROR: OCIStmtExecute) [for statement ``INSERT INTO seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)'' with params: :p4=2, :p1='2136291', :p2=1910113, :p3='W09C5.6b']) at /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 418, <> line 1.
However, the resulting record, when dumped in genbank, looks fine.
Not 100% sure though, but we have the impression these kind of errors do not occur when we work with entries which were added from an Bio::Seq::RichSeq object created from scratch, e.g. not via a genbank record.
Does this make sense ?
Regards,
Marc

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Marc Logghe, Ph.D.
Senior Scientist
Scientific Computing Group
deVGen
Technologiepark 9
9052 Zwijnaarde
Belgium
tel: +32 (0) 9 324 24 88
fax: +32 (0) 9 324 24 25
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