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

[Chris Fields]

Go ahead and file a bug for tracking.  I'll see if I can track this  
down; I'm wondering if there is something within bioperl-db/bioperl- 
live still using get_dblinks, though it's called through AUTOLOAD.

chris

On Aug 27, 2008, at 8:51 AM, Peter wrote:

> 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
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign