Re: [Gusdev-gusdev] Re: LoadTaxon.pm

[Jonathan C. <cra...@pc...>]

Hi Chetna-

> That is because without --commit option the table TaxonName is empty and
> thats why the loading stops. Oracle checks that is the specified row 

That's not quite true (or at least it shouldn't be); without the --commit
option the plugins will still do all of the same inserts that they would
do with the --commit option.  By default these inserts are all performed
in a single transaction and until that transaction is either rolled back
or committed, it is true that *other* transactions won't be able to see the
new rows in TaxonName (or Taxon, actually, since the reference in question
was TaxonName.taxon_id.)  However, the plugin itself *should* be able to see
the new rows in Taxon/TaxonName, so long as it doesn't roll the transaction
back and start a new one.  The crucial thing to realize is that a table can
appear to be empty in one transaction/session, but not empty in another.
So even though the Taxon table might not contain any rows that have
been committed, it could still contain rows that are visible to the plugin
itself (and that could be used to establish a foreign key constraint from
TaxonName.)  The crucial question (I think) is whether the plugin is doing
a commit or rollback between the time it inserts the Taxon rows and the time
it inserts the TaxonName rows.  I don't think I've looked at this code but
it should be easy to figure out why it's getting a null taxon_id and it should
be possible to get it to work in no-commit mode.

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115