[Bioperl-l] loading bioSQL schemas

[ulrik plate]

I seem to get all sort of different errormessages when I try to load with th 
efollowing command.
I'm new to the mazy world of biodatabases, so please how mercy on me if i 
seem to have completely lost it.

perl load_seqdatabase.pl --driver Pg --testonly -safe -dbuser ulrik -dbname 
dbname -namespace swissprot -format swiss /net/data/sprot/sprot.dat

The following is a small collection of the numerous exceptions and errors 
that I have cut pasted...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were 
("3SHD_NEUCR","","P07046","3-dehydroshikimate dehydratase (EC 4.2.1.-) (DHS 
dehydratase) (DHSase).","0","NEUCR") FKs (1,1011)
ERROR:  fktaxon_bioentry referential integrity violation - key referenced 
from bioentry not found in taxon
---------------------------------------------------
DBD::Pg::st execute failed: ERROR:  current transaction is aborted, queries 
ignored until end of transaction block at 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 892, 
<GEN0> line 29350.




-------------------- WARNING ---------------------
MSG: Could not store P23571:
------------- EXCEPTION  -------------
MSG: error while executing statement in 
Bio::DB::BioSQL::SeqFeatureAdaptor::find_by_unique_key: ERROR:  current 
transaction is aborted, queries ignored until end of transaction block
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:898
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:809
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:192
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:238
STACK Bio::DB::Persistent::PersistentObject::store 
/home/ulrik/bioperl-db/Bio/DB/Persistent/PersistentObject.pm:266
STACK Bio::DB::BioSQL::SeqAdaptor::store_children 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/SeqAdaptor.pm:246
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:203
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:238
STACK Bio::DB::Persistent::PersistentObject::store 
/home/ulrik/bioperl-db/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) load_seqdatabase.pl:424
STACK toplevel load_seqdatabase.pl:423




-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed, values 
were ("","12") FKs (423,26,4)
ERROR:  fkterm_seqfeature referential integrity violation - key referenced 
from seqfeature not found in term




-------------------- WARNING ---------------------
MSG: Could not store P30388:
------------- EXCEPTION  -------------
MSG: Invalid species name 'subsp. gorilla'
STACK Bio::Species::validate_species_name 
/home/ulrik/bioperl-live/Bio/Species.pm:322



MSG: Could not store Q07000:
------------- EXCEPTION  -------------
MSG: error while executing statement in 
Bio::DB::BioSQL::SeqFeatureAdaptor::find_by_unique_key: ERROR:  current 
transaction is aborted, queries ignored until end of transaction block
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:898
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:809
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:192
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:238
STACK Bio::DB::Persistent::PersistentObject::store 
/home/ulrik/bioperl-db/Bio/DB/Persistent/PersistentObject.pm:266
STACK Bio::DB::BioSQL::SeqAdaptor::store_children 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/SeqAdaptor.pm:246
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:203
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:238
STACK Bio::DB::Persistent::PersistentObject::store 
/home/ulrik/bioperl-db/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) load_seqdatabase.pl:424
STACK toplevel load_seqdatabase.pl:423

--------------------------------------

---------------------------------------------------
DBD::Pg::st execute failed: ERROR:  fkdbxref_dblink referential integrity 
violation - key referenced from bioentry_dbxref not found in dbxref at 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, 
<GEN0> line 18550.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted, queries 
ignored until end of transaction block at 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, 
<GEN0> line 18550.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted, queries 
ignored until end of transaction block at 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, 
<GEN0> line 18550.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted, queries 
ignored until end of transaction block at 
/home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.


Thanks
Ulrik

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