[Biojava-dev] BioJava + Oracle BioSQL

[Michael Griffith]

Hi, 

I am able to get the latest BioJava 1.4 release to work with the BioSQL
schema on MySQL, but I am having problems with setting up the oracle
version.  

I have downloaded and installed the BS-create-Biosql-API2.sql file posted a
week ago by Hilmar Lapp.  Hilmar also informed me that there was a table
missing -- which I believe is the term_relationship_term table.  This table
was also missing from the mySQL schema.

I've recreated the DB with this table, and the new improved API/views.
However when I am trying to load a Genebank record into the database, I get
the following exception stack:

[java] org.biojava.bio.BioRuntimeException: Error adding sequence: AA000001
(rolled back successfully)
[java]     at 
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB
.java:498)
{java]     at 
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB.
java:365)
[java]     at com.gts.genebank.GeneralReader.main(GeneralReader.java:74)
[java] Caused by: java.sql.SQLException: ORA-02290: check constraint
(BIOSQL_APP.ALPHABET4) violated
[java]     at 
oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134)
     [java]     at oracle.jdbc.ttc7.TTIoer.processError(TTIoer.java:289)

My code is simply doing the following:

SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass,
biodatabase, create);

    SequenceIterator iter =
        (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, br);
    
    while (iter.hasNext()) {
        Sequence seq = iter.nextSequence();
        try {
            db.addSequence(seq);
         } catch (Exception e) {
                    e.printStackTrace();
         }
    }


This code works successfully against the mySQL version of the current biosql
schema.  Although there was a problem with the term.name field and case
sensitivity in that version as well. In order to get that to work, the field
had to be marked as binary.  I am wondering if I am running into a similar
problem here? 

Any help would be greatly appreciated!

Cheers!

Michael Griffith