[BioSQL-l] error with load_ontology

Thu Aug 27 07:51:07 UTC 2009

Hi Hilmar,

I loaded the data again and found that the biological process GO terms were loaded, although with some warnings:
--------------------- WARNING ---------------------
MSG: DBLink exists in the dblink of _default
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: DBLink exists in the dblink of _default
---------------------------------------------------

But when starting to load molecular function GO terms, process terminated with the following warnings and error message.

        Done with biological_process.
Loading ontology molecular_function:
        ... terms

--------------------- WARNING ---------------------
MSG: failed to store term synonym (Bio::DB::BioSQL::TermAdaptor) with values (alternating UDP-alpha-N-acetyl-D-glucosamine:beta-D-glucuronosyl-(1->3)-nascent hyaluronan 4-N-acetyl-beta-D-glucosaminyltransferase and UDP-alpha-D-glucuronate:N-acetyl-beta-D-glucosaminyl-(1->4)-nascent hyaluronan 3-beta-D-glucuronosyltransferase activity EXACT EC:2.4.1.212) (FK 20401 to Bio::Ontology::OBOterm):
ERROR:  value too long for type character varying(255)
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: failed to store term synonym (Bio::DB::BioSQL::TermAdaptor) with values (HAS activity EXACT EC:2.4.1.212) (FK 20401 to Bio::Ontology::OBOterm):
ERROR:  current transaction is aborted, commands ignored until end of transaction block
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: failed to store term synonym (Bio::DB::BioSQL::TermAdaptor) with values (seHAS RELATED EC:2.4.1.212) (FK 20401 to Bio::Ontology::OBOterm):
ERROR:  current transaction is aborted, commands ignored until end of transaction block
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: failed to store term synonym (Bio::DB::BioSQL::TermAdaptor) with values (spHAS RELATED EC:2.4.1.212) (FK 20401 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 block
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:970
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195
STACK Bio::DB::BioSQL::TermAdaptor::store_children /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/TermAdaptor.pm:306
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
STACK Bio::DB::Persistent::PersistentObject::store /perl/lib/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284
STACK (eval) load_ontology.pl:812
STACK main::persist_term load_ontology.pl:794
STACK toplevel load_ontology.pl:617
-------------------------------------
 at load_ontology.pl line 824
        main::persist_term('-term', 'Bio::Ontology::OBOterm=HASH(0x96699d0)', '-db', 'Bio::DB::BioSQL::DBAdaptor=HASH(0xd90620)', '-termfactory', undef, '-throw', 'CODE(0x76ab60)', '-mergeobs', ...) called at load_ontology.pl line 617

I am using biosql-1.0.0 downloaded directly from http://www.biosql.org/wiki/Downloads without any changes. So I am not sure if the RULEs have been removed. By the way, before I met the above error, I was able to use the script load_seqdatabase.pl to load swissprot data with many warnings.

song

----- Original Message -----
From: Hilmar Lapp <hlapp at gmx.net>
Date: Wednesday, August 26, 2009 17:50
Subject: Re: [BioSQL-l] error with load_ontology
To: Song Haili <haili at mpiz-koeln.mpg.de>
Cc: biosql-l at lists.open-bio.org

> 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
> >
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biosql-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp 
> at gmx dot net :
> ===========================================================
> 
> 
>