1) Your version of Apache Part of redhat 4.0 installation: enterprise 2.0.52-25
2) The version of ModPerl that is installed as part of Apache mod_per-1.99_16-4 3) The commandline you use to start Apache (and hence start MartView) (root) /etc/init.d/httpd restart (me) ~/.html/biomart/biomart-perl >cgi-bin/martview.cgi Regards, Etai On 2/8/07, Richard Holland <[EMAIL PROTECTED]> wrote:
I'm really not sure what is going on here. That particular error gets thrown when the MartView (Web.pm) module does not get passed a reference to a registry file from the Apache process that starts it. That might happen if the Apache config was incorrect, or your installation of Apache/ModPerl is somehow broken. Could you double-check the following for me? 1) Your version of Apache 2) The version of ModPerl that is installed as part of Apache 3) The commandline you use to start Apache (and hence start MartView) Could you also slightly edit your registry XML file then re-run the configure process. I need you to change the MartDBLocation tag, find the bit that says default="" and change it to default="1" . This is the only other thing I can think of - that the registry may not get created at all because none of the locations in it are configured to be the default location. Let us know how you get on. cheers, Richard On Thu, February 8, 2007 9:55 am, Etai Jacob wrote: > Hi, > > I have installed biomart and did the following before executing martview: > > 1) Define your mart in MartBuilder > 2) Use MartBuilder to generate SQL that will create the mart out of your > source data. Run that SQL. > 3) Connect to the created mart using MartEditor and configure the > attributes and filters you want (the Naive option will do this for you > with sensible defaults) > 4) Export the config from MartEditor so that it is saved in your mart > 5) Create a registry XML file that describes how to find your newly > configured mart > 6) Run bin/configure.pl using the registry XML and --clean > 7) Start up MartView > > as described in [[mart-dev] martview problems, Jennifer Siepen] > > The registry.xml file: > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE MartRegistry> > <MartRegistry> > <virtualSchema name="default" visible="1" default="1"> > <MartDBLocation > name = "DGV" > displayName = "DGV" > databaseType = "mysql" > host = "dell7" > port = "3306" > database = "DGV" > schema = "DGV" > user = "****" > password = "****" > visible = "1" > default = "" > includeDatasets = "" > /> > </virtualSchema> > </MartRegistry> > > I keep getting the error (web): > > ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method > "settingsParams" on an undefined value at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 116. > > If you repeatedly get directed to this error page, there may be a > problem with your current session parameters. To clear your session > and start with a clean slate, please click the button below. > > Stacktrace: > Exception::Class::Base::new > /home/etai/.html/biomart/biomart-perl/cgi-bin/martview.cgi:80 > > Running the martview from command line results with the same error. > I followed each step as described in ([mart-dev] martview problems, > Jennifer Siepen) but I am still getting the same error. > > Any suggestions are happily welcome. > > Thanks, > Etai > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK
