Richard Holland wrote:
This happens in one of two situations:
1. Something else is modifying the database at the same time, e.g. if you are
running the same piece of code in parallel.
Ans: No, My program is the only thing which is working with the database
instance on which I am performing load operation and my program is
single thread based, i.e. it will create one richsequence and then
persist it to database and then move to next one.
2. The Hibernate session has become inconsistent with the database (possibly
due to partial or incomplete removal of cached objects because references to
them remain elsewhere).
Ans: I am not referencing cached objects any where else. The only
operation I do with rich sequence is to create one and then load it to
database and if it went successfully in to database, then forget about
it and create new, on failure clean everything and start with next
sequence. I don't know if RichSequenceFactory is doing something
internally as far as referencing is concerned. ?
In your code, you're doing a lot of session.clear() and session.flush() and
RichObjectFactory.clearLRUCache() calls - are these really necessary? Also your
code is creating the RichSequence objects outside of the transaction - this can
cause problems too.
The only reason for doing session.clear() and session.flush() and
clearLRUCache() was i don't need the richSequenceObject any time later
because my program sole purpose is load sequence into database from
genbank file. Also when I was trying to do this I found after loading
certain number of records to database if you don't clear session or
clear LRU cache things will get really slow and seems to be freezing.
http://www.biojava.org/pipermail/biojava-l/2008-May/006283.html
http://www.mail-archive.com/[email protected]/msg01379.html
As you suggested I tried creating richSequence object after starting a
transaction and its working for the records which are getting hibernate
exception, but I will only say its working once I test it on my complete
dataset which will take another 20 hours.
Thanks
Deepak Sheoran, BSc (Senior year)
North Dakota State University
There's some template code on Biojava.org which you can use as a shortcut to
what you're trying to do:
http://www.biojava.org/wiki/BioJava:BioJavaXDocs#BioEntryDB_and_RichSequenceDB_convenience_wrappers
cheers,
Richard
On 24 Jan 2010, at 21:20, Deepak Sheoran wrote:
org.hibernate.StaleStateException: Batch update returned unexpected row count
from update [1]; actual row count: 0; expected: 1
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
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