Hi Siddhartha This is fixed and in cvs now. You may 'cvs update' and reconfigure with switch 'clean'.
Thanks for spotting. Cheers Syed On Wed, 2007-06-20 at 06:36 -0400, Siddhartha Basu wrote: > 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. > > ====================================== > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
