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

[Chris Fields]

Peter,

Unfortunately I'm unable to reproduce this using bioperl-live and  
bioperl-db (both from Subversion):

cjfields$ time perl load_seqdatabase.pl --dbname nano --namespace test  
--format genbank --dbpass ***** --dbuser foo NC_005213.gbk
Loading NC_005213.gbk ...

real	0m35.057s
user	0m26.480s
sys	0m4.456s

This problem is similar to one reported recently:

http://article.gmane.org/gmane.comp.lang.perl.bio.general/17360

I think the solution may have been making sure to install bioperl and  
bioperl-db from Subversion or (if you can't access it) the nightly  
builds.  Use 'sudo ./Build install --uninst 1' to remove old versions  
which may conflict.  The nightly build link:

http://bioperl.org/DIST/nightly_builds/

chris

On Aug 27, 2008, at 9:38 AM, Chris Fields wrote:

> 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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>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>

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