[BioSQL-l] Problem listing all species(final nodes) of Fungi -Web example

[alejandro]

Hi Peter,

Sorry about spam, I had a connection problem and I thought the messages
were not sent.

I'm using MySQL 14.14

mysql  Ver 14.14 Distrib 5.5.24, for debian-linux-gnu (x86_64) using
readline 6.2


BioSQL 1.0.1, just updated. The query I was running is the example provided
on the web:

 SELECT DISTINCT include.ncbi_taxon_id FROM taxon
    INNER JOIN taxon AS include ON
      (include.left_value BETWEEN taxon.left_value
        AND taxon.right_value)
 WHERE taxon.taxon_id IN
   (SELECT taxon_id FROM taxon_name
    WHERE name LIKE '%fungi%')

The query doesn't work neither when I use MySQL Workbench nor through mysql
console.


On Sun, Oct 7, 2012 at 1:01 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Fri, Oct 5, 2012 at 2:16 PM, alejandro <aebmad at gmail.com> wrote:
> > Hey hey,
> >
> > I have a problem trying to run the example provided in the web to list
> all
> > species of Fungi in the NCBI taxon table. The query it doesn't finish,
> not
> > even when instead of asking for all the children of 'Fungi' I ask for the
> > taxon offspring of 'allomyces macrogynus' which only have one descendent.
> > Do you have any idea what I'm doing wrong? I loaded the taxonomy from
> NCBI
> > with the script provided in the web.
> >
> > Best regards
> >
> > --
> > Alejandro Barrera
>
> Did you have trouble sending your email? It came three times:
> http://lists.open-bio.org/pipermail/biosql-l/2012-October/001829.html
> http://lists.open-bio.org/pipermail/biosql-l/2012-October/001830.html
> http://lists.open-bio.org/pipermail/biosql-l/2012-October/001831.html
>
> I assume you are trying an example on the BioSQL wiki:
> http://biosql.org/wiki/Schema_Overview
>
> Could you clarify a bit about what you are doing? e.g. Which
> database backend (MySQL?), which version of the BioSQL
> scheme (e.g. v1.0.2), how are you running the SQL queries, ...
>
> Peter
>



-- 
Alejandro Barrera
Visitor scientist
EMBL-EBI

EMBL Outstation - Hinxton <http://www.ebi.ac.uk/>,
European Bioinformatics Institute <http://www.ebi.ac.uk/>,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD
Alt. email:* abarrera at ebi.ac.uk*
Direct:* *+44 (0) 1223 492 578 (UK - Office hours)*  *
Cell: +44 (0) 77 424 72963 (UK) or +34 685 67 99 63 (SP)
Skype: aebmad