[BioSQL-l] get_dblinks in load_seqdatabase.pl is deprecated

[Peter]

Hi,

In order to install GBrowse 1.69, I've updated my installation of
BioPerl (using gbrowse_netinstall.pl) and then by hand fetched the
latest BioPerl/BioSQL load_seqdatabase.pl from SVN,

http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-db/trunk/scripts/biosql/load_seqdatabase.pl

The new script seems to work, but prints out over a page of
deprecation warnings about get_dblinks (see below).  Should I file
this as a bug on bugzilla?

Do you think load_seqdatabase.pl be updated to work with the latest
BioPerl and still be backwards compatible with BioPerl 1.5.2?

Peter

$ mysql --user="gbrowse" --pass="biosql" test_biosql -e "truncate
table bioentry; truncate table seqfeature; truncate table
bioentry_dbxref; truncate table term; truncate table ontology;
truncate table reference; truncate table dbxref;"

$ time perl load_seqdatabase.pl --dbname test_biosql --namespace test
--format genbank --dbpass biosql --dbuser gbrowse
Nanoarchaeum_equitans/NC_005213.gbk
Loading Nanoarchaeum_equitans/NC_005213.gbk ...
Use of get_dblinks is deprecated.  Note that prior use
of this method could return either simple scalar values
or Bio::Annotation::DBLink instances; only
Bio::Annotation::DBLink is now supported.
 Use get_dbxrefs() instead
STACK Bio::Ontology::Term::get_dblinks
/Library/Perl/5.8.8/Bio/Ontology/Term.pm:437
STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD
/Library/Perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:552
STACK Bio::DB::BioSQL::TermAdaptor::store_children
/Library/Perl/5.8.8/Bio/DB/BioSQL/TermAdaptor.pm:280
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Library/Perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK Bio::DB::Persistent::PersistentObject::create
/Library/Perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:244
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Library/Perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/Library/Perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK Bio::DB::Persistent::PersistentObject::store
/Library/Perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK Bio::DB::BioSQL::SeqAdaptor::store_children
/Library/Perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:244
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Library/Perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/Library/Perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK Bio::DB::Persistent::PersistentObject::store
/Library/Perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK (eval) load_seqdatabase.pl:630
STACK toplevel load_seqdatabase.pl:612
[deprecation warning and stack repeated another six times]
real	0m15.479s
user	0m12.315s
sys	0m2.263s