[BioSQL-l] error with load_ontology

[Hilmar Lapp]

Song,

there should have been an error or warning that immediately preceded  
this errors. It is that one that's the root cause.

Also, are you using by any chance the BioSQL version for PostgreSQL  
that has the RULEs removed? If yes, then at this point you cannot use  
any Bioperl-db scripts (or code) with it, unless you install the rules  
before you run such a script (and presumably remove them again  
afterwards).

	-hilmar

On Aug 26, 2009, at 10:18 AM, Song Haili wrote:

> Hi All,
> I encountered an error message when using load_ontology.pl to load  
> gene ontology into biosql database. The command used is:
>
> perl load_ontology.pl --driver Pg --host pg-server --dbname dbname -- 
> dbuser dbsuer --dbpass dbpass --namespace "Gene Ontology" --format  
> obo /home/data/haili_biosql/GO/gene_ontology.1_2.obo --noobsolete.
>
> At the beginning,  data can be loaded with warnings, but late an  
> exception occurred and the loading was terminated. Waring and error  
> messages  shown below:
>
>  --------------------- WARNING ---------------------MSG: failed to  
> store term synonym (Bio::DB::BioSQL::TermAdaptor) with values (spHAS  
> RELATED EC:2.4.1.212) (FK 20447 to Bio::Ontology::OBOterm):ERROR:   
> current transaction is aborted, commands ignored until end of  
> transaction block--------------------------------------------------- 
> Could not store term GO:0050501, name 'hyaluronan synthase  
> activity':------------- EXCEPTION -------------MSG: error while  
> executing statement in  
> Bio::DB::BioSQL::DBLinkAdaptor::find_by_unique_key: ERROR:  current  
> transaction is aborted, commands ignored until end of transaction  
> blockSTACK  
> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /perl/ 
> lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: 
> 970STACK  
> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /perl/ 
> lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: 
> 873STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /perl/lib/ 
> site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195STACK  
> Bio::DB::BioSQL::TermAdaptor::store_children /perl/lib/site_perl/ 
> 5.10.0/Bio/DB/BioSQL/TermAdaptor.pm:306STACK  
> Bio::DB::BioSQL::BasePersistenceAdaptor::create /perl/lib/site_perl/ 
> 5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227STACK  
> Bio::DB::BioSQL::BasePersistenceAdaptor::store /perl/lib/site_perl/ 
> 5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264STACK  
> Bio::DB::Persistent::PersistentObject::store /perl/lib/site_perl/ 
> 5.10.0/Bio/DB/Persistent/PersistentObject.pm:284STACK (eval)  
> load_ontology.pl:812STACK main::persist_term load_ontology.pl: 
> 794STACK toplevel load_ontology.pl: 
> 617-------------------------------------
> Can you please help me to solve this problem out? Thank you very much.
> Best regards,
> song
>
>
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> BioSQL-l at lists.open-bio.org
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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