Re: Greek characters

Hi Jonathan,

apologies for the delay, i guess i missed some emails on this. Did the 
trick James proposed, browser charset settings worked ???

I remember, you mentioned for the XML query in shell, the characters 
were printed just fine.

thanks
Syed

Moore, Jonathan wrote:
> Hi James and Syed,
> 
> Any advance on the character set issue?
> 
> Dr. Jonathan Moore
> Senior Research Fellow in Bioinformatics
> --
> Warwick Systems Biology Centre
> Coventry House
> University of Warwick
> Coventry CV4 7AL
> U.K.
> +44 (0)24 761 50332
> http://www.warwick.ac.uk/go/jaymoore
> 
> 
> 
> -----Original Message-----
> From: James Smith [mailto:js5 <at> sanger.ac.uk]
> Sent: Tue 4/21/2009 2:30 PM
> To: Syed Haider
> Cc: Moore, Jonathan; mart-dev <at> ebi.ac.uk
> Subject: Re: [mart-dev] Greek characters
> 
> Syed Haider wrote:
>  > Hello Jonathan,
>  >
>  >
>  > Before we embark on characterset fix, could you please do a little
>  > test for us:
>  >
>  > copy  the XML equivalent of your query from MartView XML button. Paste
>  > it into biomart-perl/scripts/Query.xml
>  >
>  > edit biomart-perl/scripts/webExample.pl to point to your biomart server
>  >
>  > now run:
>  >
>  > perl webExample.pl Query.xml
>  > from the shell and see what you get - alpha or I+- :)
>  >
>  > thanks
>  > Syed
>  >
>  >
>  > Moore, Jonathan wrote:
>  >> Hello,
>  >>
>  >> Sorry if this has been addressed but I couldn't find a reference in
>  >> the list archive.
>  >>
>  >> We have a number of columns containing suggested gene names for our
>  >> organism which contain greek letters (alpha, beta, etc) as part of
>  >> the names.  These are stored OK in the mart MySQL database, as I've
>  >> verified at the command line using mysql and SELECT...  However,
>  >> martview is not showing them up correctly, for instance the alpha
>  >> character (?) is showing up as α (capital I hat plus/minus).
>  >> Now I understand a little of the basics of character sets, so I know
>  >> it is an ongoing bane, but is there a way to configure e.g. MySQL to
>  >> propagate this data correctly from back to front-end?
>  >>
> This looks like an encoding error biomart/martview is defaulting to
> output in ISO-8859-1(or whatever your default charset is) the data is
> stored in UTF-8, try in your browser forcing the character encoding...
> (Firefox View -> Character encoding -> UTF-8) and see if you get the
> right output...
> 
> James
>  >> (Regardless of whether this is a great idea, in terms of gene
>  >> nomenclature!)
>  >>
>  >> Dr. Jay Moore
>  >> Senior Research Fellow in Bioinformatics
>  >> --
>  >> Warwick Systems Biology Centre
>  >> Coventry House
>  >> University of Warwick
>  >> Coventry CV4 7AL
>  >> U.K.
>  >> +44 (0)24 761 50332
>  >> http://www2.warwick.ac.uk/fac/sci/systemsbiology/
>  >>
> 
> 
> 
> --
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