[Biojava-dev] MORE Oracle BioSQL & BioJava problems

[Michael Griffith]

Keith, 

Thanks for the reply.

Oracle Server is 9.2.0.4 running on Suse Linux
JDBC Client is 9.2.0.3 running on OSX
I've tried DBCP 1.1 and 1.2

According to what I've been able to trace to the source, autocommit is off.

I've never seen P6spy before -- so it will take some time to figure out how
it works. Once I have the SQL Statements, I'll post them to this thread.

Thanks for your suggestions -- any other help is greatly appreciated!

MG

On 8/9/04 12:21 PM, "Keith James" <kdj at sanger.ac.uk> wrote:

>>>>>> "Michael" == Michael Griffith <mg at base-pair.com> writes:
> 
> [...]
> 
>   Michael> The loop loads about 65 of the first 70 records, and
>   Michael> hangs on record #71, every time.  What is puzzling, is I
>   Michael> have never had any sort of these kinds of errors with any
>   Michael> other Java/Oracle application.
> 
>   Michael>  [java] org.biojava.bio.BioRuntimeException: Error adding
>   Michael> sequence: NM_019764 [java] at
>   Michael> 
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB
>   Michael> .java:498) [java] Trying to add: NM_021274 to the
>   Michael> database -- insert attemp #:71 [java] at
>   Michael> 
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB.
>   Michael> java:365) [java] at
>   Michael> com.gts.genebank.GeneralReader.main(GeneralReader.java:74)
>   Michael> [java] Caused by: java.sql.SQLException: No more data to
>   Michael> read from socket [java] at
>   Michael> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134)
> 
> Firstly, IANABU (I am not a BioSQL user), but here's some things to
> try anyway,
> 
> What version of Oracle and drivers? What DBCP version?
> 
> It looks like the BioSQL code is using streams for the sequence, so it
> shouldn't be a data size problem.
> 
> It looks like your connection may be getting closed too early. This
> could be a bad interaction with the the Oracle driver or it could be
> DBCP which in its 1.1 incarnation is quite flaky and prone to allowing
> shared connections. Is autocommit getting turned on accidentally?
> Anywhere a LOB gets populated it must be off in case multiple
> reads/writes are required (again this could be a symptom of a shared
> connection).
> 
> Try a more recent DBCP.
> 
> Use P6Spy (http://www.p6spy.com) to get the exact insert statements
> sent to the server and post them to the list.
> 
> Keith