[Biojava-l] BioJava, BioSQL versions

[Gang Wu]

Dear All,

I am using the latest nightly built Biojava(biojava-20040608.jar) and BioSQL
v1.38 for MySQL. When I tried the following code:
=================================================================
    public static void main (String [] args) throws Exception {
       BioSQLSequenceDB bdb = new BioSQLSequenceDB(
            "com.mysql.jdbc.Driver",
            "jdbc:mysql://mysql_server_ip/biosqldb",
            "root",
            "password","biosqldb", true);
    }
=================================================================

I got the following exceptions:
============================================================================
=============
*** Importing a core ontology -- hope this is okay
*** Importing terms
Exception in thread "main" org.biojava.bio.BioException: Error accessing
ontologies
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:
238)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:
164)
        at biosql.MyTest.main(MyTest.java:13)
Caused by: java.sql.SQLException: Base table or view not found,  message
from server: "Table 'biosqldb.term_relationship_term' doesn't exist"
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1905)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1109)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1203)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:2090)
        at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1680)
        at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1527)
        at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating
PreparedStatement.java:233)
        at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating
PreparedStatement.java:233)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTriple(OntologySQL.java:616
)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:262)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:251)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.addCore(OntologySQL.java:218)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java:396)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL(OntologySQL.java:71
)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:
236)
        ... 2 more
============================================================================
================
I guess the message means it can find the MySQL driver and the database, but
the Java APIs does not match the BioSQL schema.
Does the "Table 'biosqldb.term_relationship_term' doesn't exist" mean I'm
using a wrong version of BioSQL? Anybody has any idea about it? Help is
needed and deeply  appreciated.

Gang


-----Original Message-----
From: mark.schreiber at group.novartis.com
[mailto:mark.schreiber at group.novartis.com]
Sent: Monday, June 07, 2004 9:27 PM
To: gwu at molbio.mgh.harvard.edu
Cc: biojava-l at open-bio.org; biojava-l-bounces at portal.open-bio.org
Subject: Re: [Biojava-l] BioJava, BioSQL versions


My understanding is that biojava 1.3.x is not compatable with the more
recent versions of biosql. To use the current biosql I reccommend getting
one of the nightly snapshots or the pre release version of biojava 1.4

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"Gang Wu" <gwu at molbio.mgh.harvard.edu>
Sent by: biojava-l-bounces at portal.open-bio.org
06/08/2004 02:26 AM
Please respond to gwu


        To:     <biojava-l at open-bio.org>
        cc:
        Subject:        [Biojava-l] BioJava, BioSQL versions



Can anybody tell me what versions of BioJava work with what versions of
BioSQL?

Thanks

Gang

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