[Biojava-dev] problems with biosql

[Matthew Pocock]

Hi,

We have been adding sequences (from embl files) into biosql (using the 
latest CVS biojava, and the latest CVS biosql schema) using the normal 
addSequence() method.

We have an exception loading data into biosql for just some sequences 
that I've tracked back to BioSQLSequenceDB.intern_ontology_term() and 
OntologySQL.termID() but this code is beyond me - It's not documented 
and I'm not sure what the contract for these methods is meant to be.

Thomas, did you write this? Any idea what is going wrong? In the mean 
time I will try to track down exactly what ontology term is causing the 
problems.

Matthew

org.biojava.bio.BioRuntimeException: Error adding BioSQL tables (rolled
back successfully)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequen
ceDB.java:464)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenc
eDB.java:315)
        at mbsample.EmblBase.main(EmblBase.java:68)
Caused by: java.sql.SQLException: Couldn't create term in legacy
ontology namespace
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioS
QLSequenceDB.java:903)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(B
ioSQLSequenceDB.java:857)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequen
ceDB.java:450)