martview.cgi is not designed for direct access. You must always reference it via the Apache configured location, which by default is http://yourhost:yourport/biomart/martview . If you don't reference it in that manner then it will never pick up the settings that were created during configure.pl.
cheers, Richard On Thu, February 8, 2007 10:57 am, Etai Jacob wrote: > ---------- Forwarded message ---------- > From: Etai Jacob <[EMAIL PROTECTED]> > Date: Feb 8, 2007 12:52 PM > Subject: Re: [mart-dev] Problems with executing martview > To: Syed Haider <[EMAIL PROTECTED]> > > > this is the output when running configure.pl: > perl bin/configure.pl --clean -r conf/DGV_registry.xml > > Do you want to install in API only mode [y/n] [n]: n > > Checking prerequisites ...[Looks good] > Use of uninitialized value in string ne at > /home/etai/.html/biomart/biomart-perl/bin/configureBioMart.pl line 83. > Use of uninitialized value in regexp compilation at > /home/etai/.html/biomart/biomart-perl/bin/configureBioMart.pl line 85. > > rm /home/etai/.html/biomart/biomart-perl/conf/templates/default/*.ttc > > DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n > Checking several common Apache locations...done. > > Select either one of the detected httpd paths on the list, OR enter > the path you wish to use: > /usr/sbin/httpd > [1]: > Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl > configuration > > Enter the server host OR default [dell5.compugen.co.il]: > > Enter the server port OR default [5555]: > > Enter proxy OR default : > > Enter the required script location OR default [biomart]: > Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC > Libdir /home/etai/.html/biomart/biomart-perl/lib is not in @INC, adding to > @INC > > > Optional setting for martUser in MartDBLocation location:DGV not > defined - setting to default values > > > > [NEW CONFIGURATION] .... WITH MEMORY [default] > default ... DGV ...................... 001/001 ... variation > ................................. (RDBMS) dell7:3306 > .................... OK > Setting possible links between datasets > ....(scanning) 100% > ....(linking) 100% > ....(sorting) 100% > ....(clustering) 1/1 - 0 remain > ....(resolving) 100% > Building templates for visible datasets > .... 100% > Compiling templates for visible datasets > .... 100% > > > > this is the output when I am running the martview from the commandline: > > cgi-bin/martview.cgi > Subroutine BioMart::Web::Zlib::adler32 redefined at > /opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65. > at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20 > Subroutine BioMart::Web::Zlib::crc32 redefined at > /opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65. > at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20 > Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at > /opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65. > at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20 > Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at > /opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65. > at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20 > Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at > /opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65. > at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20 > Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at > /opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65. > at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20 > Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at > /opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65. > at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20 > 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. > > Stacktrace: > Exception::Class::Base::new cgi-bin/martview.cgi:80 > Content-Type: text/html; charset=ISO-8859-1 > > <br/><br/><br/> > > YOUR SITE HEADER HERE > > <br/><br/><br/><br/> > > <div id="mart_containerpanel"> > > <p> > 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.<br > /> > </p> > <p> > 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. > </p> > <form name="mainform" action="martview" method="post" > enctype="multipart/form-data"> > <input type="submit" name="newsession" value="New Session" /> > </form> > > <p> > Stacktrace:<br /> Exception::Class::Base::new cgi-bin/martview.cgi:80<br > /> > </p> > > </div> <!-- martpanel closes --> > > <!-- : footer.tt,v 1.2 2006/11/23 15:59:13 syed Exp --> > > <!-- > <br><br> > >       <font ="" size="1" >YOUR SITE FOOTER HERE</font> > > <br> > --> > > Thanks! > > > On 2/8/07, Syed Haider <[EMAIL PROTECTED]> wrote: >> On Thu, 2007-02-08 at 11:55 +0200, Etai Jacob wrote: >> >> Hi Etai >> >> > 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 >> >> Looks as if your registry is not getting configured properly. Could be >> due to incorrect xmls representing your marts (I am not talking about >> registry.xml file). Could you please have a look at the on-screen >> messages while you are configuring your martview and see if there is >> somehting wrong there. Might help us understanding your problem in a >> better way. >> >> Kind regards >> Syed >> >> >> > 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 >> -- >> ====================================== >> Syed Haider. >> EMBL-European Bioinformatics Institute >> Wellcome Trust Genome Campus, Hinxton, >> Cambridge CB10 1SD, UK. >> ====================================== >> >> > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK
