Hi Darren,
thanks for the fix, we will add it to the branch 0.7 soon.
Cheers
Syed
> Hi All,
>
> I think I've found a bit of a bug in the HTML formatting code for text.
>
> If someone has deliberately put some HTML in a field (in our case a
> pair of <sup> tags), the formatting code strips only portions of the
> offending tag(s) and leaves a bit left over.
>
> In our case it stripped the first < and the closing </sup>, but left
> sup> at the beginning of the text that was supposed to be superscripted.
>
> i.e. Art4<sup>tm1a(KOMP)Wtsi</sup> became Art4sup>tm1a(KOMP)Wtsi with
> some extra span tags to make the latter part superscript.
>
> I've had a look at the code and come up with a small fix that seems
> to work here so I thought i'd better let you guys know about it.
>
> Here's the diffs:
>
> Index: lib/BioMart/Formatter/HTML.pm
> ===================================================================
> RCS file: /cvsroot/biomart/biomart-perl/lib/BioMart/Formatter/HTML.pm,v
> retrieving revision 1.9
> diff -r1.9 HTML.pm
> 115,117c115,121
> < # superscripting for emma mart
> < $$row[$$attribute_positions[$i]] =~ s/\<(.*)\>/<span
> style="vertical-align:super;font-size:0.8em">$1<\/span>/;
> <
> ---
> > # catch html formatting...
> > if ( $$row[$$attribute_positions[$i]] =~ /\<.+\>.+\<\/.+
> \>/ ) {
> > # Do nothing - leave the original formatting
> > } else {
> > # superscripting for emma mart
> > $$row[$$attribute_positions[$i]] =~ s/\<(.*)\>/<span
> style="vertical-align:super;font-size:0.8em">$1<\/span>/;
> > }
>
> Index: lib/BioMart/Formatter/HTML_36.pm
> ===================================================================
> RCS file: /cvsroot/biomart/biomart-perl/lib/BioMart/Formatter/
> HTML_36.pm,v
> retrieving revision 1.5
> diff -r1.5 HTML_36.pm
> 256,259c256,263
> < # superscripting for emma mart
> < $$row[$$attribute_positions[$i]] =~ s/\<(.*)\>/<span
> style="vertical-align:super;font-size:0.8em">$1<\/span>/;
> <
> <
> ---
> > # catch html formatting...
> > if ( $$row[$$attribute_positions[$i]] =~ /\<.+\>.+\<\/.+
> \>/ ) {
> > # Do nothing - leave the original formatting
> > } else {
> > # superscripting for emma mart
> > $$row[$$attribute_positions[$i]] =~ s/\<(.*)\>/<span
> style="vertical-align:super;font-size:0.8em">$1<\/span>/;
> > }
>
> Hope this is useful!
>
> Cheers,
>
> Darren
>
> P.S. Cheers for making a great tool too!
>
>
>
> --
> 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.
>
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
