[BioSQL-l] Problems with load_seqdatabase and genbank files

[Hilmar Lapp]

> -----Original Message-----
> From: albert vilella [mailto:vilella at bio.ub.es] 
> Sent: Tuesday, June 10, 2003 10:03 AM
> To: biosql-l at open-bio.org
> Subject: [BioSQL-l] Problems with load_seqdatabase and genbank files
> 
> 
> Hello everybody,
> 
> I am trying to populate a database(biosql) with a little 
> GenBank sequence file using load_seqdatabase.pl (redhat linux).
> 
> I seems to be parsing the file correctly, but when it starts 
> to store the entries, it fails with the following error:
> 
> Loading /data/database/10014.gbk ...
> DBD::mysql::st execute failed: Table 'biosql.term' doesn't 

If you did instantiate the latest version of biosql then this message
should not occur. It is a clear indication that you are trying to run
off of an old schema version. If you type the following in the mysql
shell, what do you see?

	mysql> show tables like 'term%'; # should show 5 tables
	mysql> describe term;            # should show the table's
columns
	mysql> describe ontology_term;   # should raise an error

It also seems you did not configure MySQL to enable the InnoDB table
handler. Check the INSTALL document for how to do this. If you issue in
mysql

	mysql> show variables like 'have_innodb';

You should get 1 row and 'YES' in the right column if you have
successfully enabled InnoDB.

	-hilmar

> exist at 
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
> line 903, <GEN0> line 599.
> DBD::mysql::db rollback failed: Warning:  Some 
> non-transactional changed tables couldn't be rolled back at 
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm 
> line 1649, <GEN0> line 599. Could not store NC_001321:
> ------------- EXCEPTION  -------------
> MSG: error while executing statement in
> Bio::DB::BioSQL::SimpleValueAdaptor::find_by_unique_key: 
> Table 'biosql.term' doesn't exist STACK 
> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:909
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:820
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:182
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:249
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:266
> STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/AnnotationCollect
> ionAdaptor.pm:218
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:214
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:249
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:266
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/SeqAdaptor.pm:226
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:214
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:249
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:266
> STACK (eval) ./load_seqdatabase.pl:437
> STACK toplevel ./load_seqdatabase.pl:421
>  
> --------------------------------------
> 
> I cvs'ed the last version of bioperl-db and biosql-schema, so 
> I'm using the latest version. Is the version that I should be using?
> 
> Any hint about what might be the problem?
> 
> Thanks in advance,
> 
> Albert
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org http://open-bio.org/mailman/listinfo/biosql-l
>