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

[<jl...@vb...>]

What I did to update taxonomy is to use SQL commnds. Assume you only have
taxon_id on DoTS.Sequence table.
1. Backup your old taxon_id
SQL>CREATE TABLE DoTS.NASequenceTaxonID AS
select a.na_sequence_id, a.taxon_id, b.ncbi_tax_id from dots.nasequence a,
sres.taxon b where a.taxon_id=b.taxon_id;

2. Delete taxon_id on DoTS.Sequence table
SQL>update dots.nasequence set taxon_id = null;

3. Delete taxonomy data
SQL>delete from sres.taxonname;
SQL>delete from sres.taxon;

4.Run plugin to load new taxonomy data

5.Restore taxon_id on DoTS.Sequence table
SQL>update dots.nasequence s set taxon_id=(select b.taxon_id from
dots.nasequencetaxonid a, sres.taxon b
where a.ncbi_tax_id=b.ncbi_tax_id and a.na_sequence_id=s.na_sequence_id);


On Wed, July 12, 2006 1:31 pm, Josef Jurek wrote:
>

> "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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> fax:   (773) 702-6648
>
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