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

[Hilmar Lapp]

Which rel. is the target Oracle DB?

What is the length of the sequence string causing trouble? If it is  
indeed longer than 4000 chars, does the problem disappear when you make  
the sequence shorter than 4000 chars? Which JDBC API call is used to  
set the sequence string in the biojava language binding? If it is  
indeed setString(), what happens if you change that to the streaming  
API?

	-hilmar

On Aug 9, 2004, at 10:08 AM, Michael Griffith wrote:

> 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(BioSQLSeq 
>>> ue
>>> 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(BioSQLSequ 
>>> en
>>> 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.ja 
>>> va
>>> :2047
>>> )
>>>      [java]     at
>>> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.jav 
>>> a:
>>> 1940)
>>>      [java]     at
>>> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStateme 
>>> nt
>>> .java
>>> :2709)
>>>      [java]     at
>>> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrepar 
>>> ed
>>> State
>>> ment.java:589)
>>>      [java]     at
>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Del 
>>> eg
>>> ating
>>> PreparedStatement.java:233)
>>>      [java]     at
>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Del 
>>> eg
>>> ating
>>> PreparedStatement.java:233)
>>>      [java]     at
>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeq 
>>> ue
>>> nceDB
>>> .java:455)
>>>      [java]     ... 2 more
>>>
>>> Any help would be greatly appreciated!
>>>
>>> Cheers!
>>>
>>> MG
>>>
>>>
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------