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

[<pi...@pc...>]

LoadTaxonomy was written to update taxon_id in child tables prior to deleting
the row in taxon_id so I suspect that something else is happening, for example
a group_write or group_id issue.

Debbie

Quoting Josef Jurek <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...
>
> voice: (773) 702-9559
> fax:   (773) 702-6648
>
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