Re: [GUSDEV] Out of Memory while loading Taxonomy data

[<ju...@cs...>]

"Kumar, Sanjeev" <San...@ng...> writes:
>
> But I am getting a new type of error message, provided below. Can some
> one pl. help me in understanding/resolving the error message.
>
>
> GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D
> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54)
> DBD::Oracle::db do failed: ORA-02292: integrity constraint
> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD ERROR:OCIStmtExecute)
>  [for Statement "DELETE FROM
> SRes.Taxon WHERE  taxon_id =3D 525455
> "] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 119, <MERGED> line 5476.
> [...]

I ran into this very same error as well.  What is happening
is that LoadTaxon is attempting to delete obsolete
taxonomy entries _however_ some of these taxonomy
entries are still referenced by the TAXON_ID field
of DoTS.NASequence.

What LoadTaxon _should_ _do_ is update all places
in DoTS.NASequence/DoTS.AASequence (and possibly
other tables) so that obsolete taxonomy entries
are replace in the tables that reference
them _before_ LoadTaxon tries to delete them
from SRes.Taxon.

My jury-rig (and I do mean jury-rig) was
to run a perl script on merged.dmp to
convert each data line to a SQL line which
might look like:

  update DoTS.ExternalAASequence set taxon_id = 255892 where taxon_id = 256194;

thus, updating the taxon_id fields.

When it comes to updating Taxonomy information
LoadTaxon does not appear to be very robust.

Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

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