[Biojava-dev] problems with biosql

[Matthew Pocock]

And here's another stack-trace we get after getting the SQLException to use initCause() - it's a monster trace :) Apparently, part of the code things that a term needs adding to the database, but another part thinks it already exists. At least that's the best I can figure from the undocumented code & exceptions that don't say very much. Sorry - long day.

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.FeaturesSQL.persistProperty(FeaturesSQL.ja
va:1016)
        at
org.biojava.bio.seq.db.biosql.FeaturesSQL.persistFeature(FeaturesSQL.jav
a:880)
        at
org.biojava.bio.seq.db.biosql.FeaturesSQL.persistFeatures(FeaturesSQL.ja
va:739)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequen
ceDB.java:434)
        ... 2 more
Caused by: org.biojava.bio.BioRuntimeException: Error removing from
BioSQL tables (rolled back successfully)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:4
49)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java:58
)
        at
org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(Ont
ologySQL.java:416)
        at
org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java:3
02)
        at org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:312)
        at
org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:321)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioS
QLSequenceDB.java:899)
        ... 6 more
Caused by: java.sql.SQLException: ERROR:  current transaction is
aborted, queries ignored until end of transaction block

        at
org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:131)
        at
org.postgresql.jdbc1.AbstractJdbc1Connection.ExecSQL(AbstractJdbc1Connec
tion.java:505)
        at
org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Stateme
nt.java:320)
        at
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Stateme
nt.java:48)
        at
org.postgresql.jdbc1.AbstractJdbc1Statement.executeUpdate(AbstractJdbc1S
tatement.java:197)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:4
64)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:4
37)
        ... 12 more