[Bioperl-guts-l] [Bug 2572] New: get_dblinks in load_seqdatabase.pl is deprecated

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2572

           Summary: get_dblinks in load_seqdatabase.pl is deprecated
           Product: BioPerl
           Version: unspecified
          Platform: PC
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bioperl-db
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


When using load_seqdatabase.pl with current BioPerl to load a GenBank file into
BioSQL (using mysql), there are repeated deprecation warnings from get_dblinks

My copy of BioPerl was installed by gbrowse_netinstall.pl, while I fetched
load_seqdatabase.pl by hand 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

Steps to reproduce:

$ 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

Reported on the mailing list:
http://lists.open-bio.org/pipermail/biosql-l/2008-August/001332.html


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