Re: [GeneX-dev] Extra Species in the Database

[<ja...@op...>]

"Harry J. Mangalam" <hj...@nc...> writes:

> On 9 Mar 2001, Jason E. Stewart wrote:
> 
> > I'm not sure what you mean by 'that they don't work'. The annoyance
> > that I'm aware of just has to do with the list being very long. So
> > when there's a select list, you have to scroll forever. 
> 
> I meant that there's no experiments that match them so a user could be
> clicking and getting the 'Sorry, no experiments matched your query' response
> for a long time.  We don;t have to remvoe all of them but we should remove
> those that we'll not support for a long time (like purple wombat, red kanga,
> blue shark, variagated plover, etc).

Hey what's wrong with plovers? I think they're cute...

I see. I forgot the query page also used the. There's a better way of
doing that for the Query Page. We should only be displaying Species
for which there exist Experiments in the DB that have SequenceFeatures
of that species. 

There is in fact a utility function in the DB fetch_es_species() that
does the necessary JOIN and returns the (single) species object for
each Experiment in the DB.

So instead of this code (from query-intro.pl.in):

my $species_names_sql = create_select_sql($dbh,COLUMNS=>['spc_pk',
							 'common_names'], 
					  FROM=>['Species']);
my @species_names;
if ($array_ref = $dbh->selectall_arrayref($species_names_sql)) {
  foreach (@{$array_ref}) {
    push(@species_names,$_);
  }
} else {
  die "Couldn't get Species names";
}

we want:
my @species_names;
foreach (@exp_set_names) {
  my $spc_obj = fetch_es_species($_->[0]);
  push(@species_names,[$spc_obj->spc_pk,$spc_obj->primary_scientific_name]);
}

I've just checked this code into CVS.

jas.


> > > What's the effort in removing the unsupported Species names in the
> > > Db for now and adding them back only when there's SF support for
> > > them?  Or (he said, demonstrating his lack of attention to the SF
> > > area) are they required for client-side-loading of SF data?
> > 
> > Before anyone can add an array-layout into the DB the species for all
> > their USF must first exist in the DB. 
> 
> OK - so we should keep things like Arab. thaliana, mouse, but remove some of
> the more exotic species.
> 
> 
> What say ye, others?
> 
> hjm
> 
> 
> > I have no problem removing species without SF, and especially those
> > that we never will, like Red Kangaroo. They were put there to help the
> > CT folks test out the organism table.
> > 
> > jas.
> > 
> > 
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> 
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