[Biojava-dev] MORE Oracle BioSQL & BioJava problems

[Keith James]

>>>>> "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

-- 

- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -