[Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems

[Michael Griffith]

Hilmar, 

Thanks for the reply.

Just to make sure I had the latest and greatest JDBC driver, I downloaded
9.2.0.3 from Oracle's web site.  I got the same exact error, in the same
exact order.

I am still puzzled as to what is going on.

MG


On 8/9/04 11:25 AM, "Hilmar Lapp" <hlapp at gnf.org> wrote:

> This smells like a problem with one of the LOB columns, which is
> Anncomment.Comment_Text and Biosequence.Seq, and the stack trace looks
> like it's the Seq column (which holds the sequence).
> 
> LOB columns in Oracle need to be streamed if they are over 4000 chars
> (otherwise the server can do the conversion). I believe the more recent
> versions of the Oracle JDBC driver do that transparently behind the
> scenes if you call {set,get}String() on a column that in reality is a
> LOB.
> 
> Are you by any chance trying to communicate with a 9i+ database using
> an 8i driver?
> 
> -hilmar
> 
> On Monday, August 9, 2004, at 09:03  AM, Michael Griffith wrote:
> 
>> Hi,
>> 
>> I have been trying to get the latest BioSQL (Oracle) and BioJava to
>> play
>> nicely -- and I feel that I am close, but I am still getting errors.
>> I am
>> trying to read a GenBank file to the Oracle BioSQL schema with the
>> following
>> code:
>> 
>> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass
>> biodatabase, create);
>> 
>>     SequenceIterator iter =
>>             (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha,
>> br);
>>    int counter= 0;
>> 
>>     while (iter.hasNext()) {
>> 
>>         Sequence seq = iter.nextSequence();
>> 
>>         try {
>>             db.addSequence(seq);
>>         }
>>         catch (Exception e) {
>>             e.printStackTrace();
>>         }
>>         ...
>>     }
>> 
>> This code works perfectly well with the mySQL version of the bio-sql
>> schema,
>> however with the oracle version, I get the following SQLException
>> stack.
>> 
>> The loop loads about 65 of the first 70 records, and hangs on record
>> #71,
>> every time.  What is puzzling, is I have never had any sort of these
>> kinds
>> of errors with any other Java/Oracle application.
>> 
>>  [java] org.biojava.bio.BioRuntimeException: Error adding sequence:
>> NM_019764
>>      [java]     at
>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque
>> nceDB
>> .java:498)
>>      [java] Trying to add: NM_021274 to the database -- insert attemp
>> #:71
>>      [java]     at
>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequen
>> ceDB.
>> java:365)
>>      [java]     at
>> com.gts.genebank.GeneralReader.main(GeneralReader.java:74)
>>      [java] Caused by: java.sql.SQLException: No more data to read from
>> socket
>>      [java]     at
>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134)
>>      [java]     at
>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179)
>>      [java]     at
>> oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160)
>>      [java]     at
>> oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963)
>>      [java]     at
>> oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893)
>>      [java]     at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369)
>>      [java]     at
>> oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891)
>>      [java]     at
>> oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java:1093)
>>      [java]     at
>> oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement.java
>> :2047
>> )
>>      [java]     at
>> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.java:
>> 1940)
>>      [java]     at
>> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement
>> .java
>> :2709)
>>      [java]     at
>> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrepared
>> State
>> ment.java:589)
>>      [java]     at
>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg
>> ating
>> PreparedStatement.java:233)
>>      [java]     at
>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg
>> ating
>> PreparedStatement.java:233)
>>      [java]     at
>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque
>> nceDB
>> .java:455)
>>      [java]     ... 2 more
>> 
>> Any help would be greatly appreciated!
>> 
>> Cheers!
>> 
>> MG
>> 
>>