Re: Greek characters

Hi Jonathan,

this is fixed now.

The solution was to set the CGI header to UTF-8 rather its default which 
is ISO-8859-1.

please cvs update your code (biomart-perl-0_7) and all should be fine.

Cheers
Syed

Moore, Jonathan wrote:
> Hi Syed,
> 
> Sorry I didn't cc you with my replies to James.  Please see below:
> 
> Hi James,

Thanks for the suggestion.  I've tried this in Safari and 
> Firefox now, and both give identical results either using the default 
> character set or forcing UTF-8: the alpha character is returned as 
> capital I hat plus/minus in all cases.
> 
> 

In command line, using SELECT through mysql or using Syed's suggestion 
> of scripts/webExample.pl both return an alpha character correctly.


> 
> I also tried pasting the gene name with the alpha character in as a 
> filter.  In this case, the alpha character shows up correctly in the 
> filter panel in the left window of martview, but no records are returned.


> 
> Further to using the gene name with the alpha character as a filter, I 
> though you might be interested in how it looks in the XML query.
> 
> 

In the previous case (returning a value from the database containing 
> the alpha character) it was displayed in martview as capital-I-hat 
> plus-minus (two characters). 

In the case of using the alpha character 
> as a filter and looking at the resulting XML query, it shows as 
> capital-A-tilde capital-Z-accent capital-A-hat plus-minus (4 characters).


> 
> 
> 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: Syed Haider [mailto:syed <at> ebi.ac.uk]
> Sent: Sat 5/2/2009 11:04 AM
> To: Moore, Jonathan
> Cc: James Smith; mart-dev <at> ebi.ac.uk
> Subject: Re: [mart-dev] 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/
>  >  >>
>  >
>  >
>  >
>  > --
>  >  The Wellcome Trust Sanger Institute is operated by Genome Research
>  >  Limited, a charity registered in England with number 1021457 and a
>  >  company registered in England with number 2742969, whose registered
>  >  office is 215 Euston Road, London, NW1 2BE.
>  >
>