Hi, It is working: The problem was that we used a general purpose httpd which didn't fit. We configured a special httpd with the configurations needed to biomart and used the exact path you specified (alias) and that's all.
I appreciate your fast responses, Etai On 2/8/07, Richard Holland <[EMAIL PROTECTED]> wrote:
That's not the path you configured with configure.pl. Going by the output from configure.pl that you have previously sent us, the URL you should be using is: http://dell5.compugen.co.il:5555/biomart/martview Also, the command you should be using to start/stop MartView is not /etc/init.d/httpd restart (unless you have altered that script to use MartView instead of the default settings). The command should be: /usr/sbin/httpd -d /home/etai/.html/biomart/biomart-perl I also noticed that you have installed biomart inside your .html folder. It does not need to be in there, and would be safer installed elsewhere. (Everything inside .html is visible to everyone who can see your Apache instance, including all your config files with passwords etc.). cheers, Richard On Thu, February 8, 2007 11:39 am, Etai Jacob wrote: > I did it and I still get the same error. > http://dell5/cgi-bin/martview > Thanks, > Etai > > On 2/8/07, Richard Holland <[EMAIL PROTECTED]> wrote: >> >> 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 >> >> > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK
