On Wed, 20 Jun 2007, Syed Haider wrote:
> Hi Siddhartha
> run the example as
> perl scripts/apiExample.pl instead. Hope this would work.
>
> Regards
> Syed
Hi,
Thanks. Yes that runs the script properly, however it really does not solve the
problem i was refering in my earlier post. My questions are
How can i run any one of my program written based on biomart perl-api
i) Not from a fixed location that is top of a conf folder.
ii) without resorting to having 'mart_0_5_0_6.xsl' in a predefined
place such as inside the conf folder.
iii) The doc for 0.6 clearly says that use of perl-api only
requires presence of registry file whose location is configurable. So,
why and where the presence of 'mart_0_5_0_6.xsl' is coming from, what am
i missing here.
I ask that because all of my program based on 0.5 used to run just by
giving the location of the registry file, there was no requirement of
xsl file in a hardcoded location.
Thanks again.
-siddhartha
>
>
>
> > Hi,
> >
> > I have just upgraded to 0.6 biomart perl-api and while trying to test
> > the 'apiExample.pl' in the scripts folder it is throwing out the
> > following error (using the apiExampleRegistry.xml) .......
> >
> > default ... ensembl .................. 003/018 ...
> > hsapiens_gene_ensembl..................... (WEB) www.biomart.org:80
> > ............ ->
> > upgrading to 0.6 ... Content-type:text/html
> >
> > <html><body>XML error cannot read data or file, see log file
> >
> > -----------------------
> >
> > also getting identical error with the 'registryURLPointer.xml' file
> > The output of log file ......
> >
> > ERROR:
> > XML error in file
> > "/home/basu/Work/biomart-perl/scripts/conf/mart_0_5_0_6.xsl":
> > Couldn't open
> > /home/basu/Work/biomart-perl/scripts/conf/mart_0_5_0_6.xsl:
> > No such file or directory at /home/basu/My_perl/BioMart/Web/CGIXSLT.pm
> > line 221
> >
> > DATE: Tue Jun 19 18:18:29 2007
> > REMOTE_ADDR:
> > PARAMETERS PASSED:
> > source="temp.xml"
> > style="/home/basu/Work/biomart-perl/scripts/conf/mart_0_5_0_6.xsl"
> >
> >
> > -------------------------
> >
> > I am running the program inside the 'scripts' folder and it seems to be
> > looking for 'mart_0_5_0_6.xsl' file which is expected to be under a 'conf'
> > folder relative from where the program is run. As i understand,
> > biomart-perl api only requires the 'registry' file whose location is
> > configurable. The example and rest of my scripts were running fine with
> > previous version(0.5), so any idea how to get them running with the
> > current one (0.6).
> >
> >
> > -siddhartha
> >
>
>
> ======================================
> Syed Haider.
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus, Hinxton,
> Cambridge CB10 1SD, UK.
> ======================================
>
