Hi,
It's works. :))
Then, the idea is to query the mart using webservice. I suppose that I
have to configure correctly the registryURLLocation, right?
Could you indicate me if I fill well the information. What I need to
indicate in name?
name = "????"
host = "adress of the machine where is running my apache"
port = "port of my apache"
path = ""
includeMarts = "the datasets that will be accessible".
Should I first run configure.pl on martDBLocation and after with
registryURLLocation?
Thanks a lot.
Bérénice
Syed Haider <[email protected]>
24/02/2009 16:05
To
[email protected]
cc
Junjun Zhang <[email protected]>, "[email protected]"
<[email protected]>
Subject
Re: [mart-dev] Error Stating MartView
Hi Berenice,
the user with which you have started apache does not have write
permissions. Please add apache user directive in conf/httpd.conf and see
if it works,
Good Luck!
Syed
[email protected] wrote:
>
> Hi Junjun,
>
> I tried to start martview. But I have well the first page but when I
> click on start marview session, I obtain this error :
>
> ERROR: caught BioMart::Exception: non-BioMart die(): mkdir
> /home/cropdesign/biomart/biomart-perl/conf/sessions: Permission denied
> at
> /usr/local/share/perl/5.10.0/CGI/Session/Driver/db_file.pm line 32
>
> 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 New button below.
>
> Stacktrace:
> Exception::Class::Base::new
> /home/cropdesign/biomart/biomart-perl/cgi-bin/martview:101
>
>
ModPerl::ROOT::ModPerl::Registry::home_cropdesign_biomart_biomart_2dperl_cgi_2dbin_martview::handler
>
> /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
> (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
> ModPerl::RegistryCooker::run
> /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
> ModPerl::RegistryCooker::default_handler
> /usr/lib/perl5/ModPerl/Registry.pm:31
> ModPerl::Registry::handler -e:0
> (eval) -e:0
>
> When I tried to use the registryURLPointer file that you indicate, I
> obtain :
> Problem with the web server: 500 Can't connect to
> www.biomart.org:80 (Bas hostname 'www.biomart.org')
>
> Best regards,
> Berénice
>
>
>
>
>
>
> *Junjun Zhang <[email protected]>*
> Sent by: [email protected]
>
> 24/02/2009 06:18
>
>
> To
> "[email protected]"
<[email protected]>
> cc
> "[email protected]" <[email protected]>
> Subject
> RE: [mart-dev] Error Stating MartView
>
>
>
>
>
>
>
>
> Hi Berenice,
>
> Glad that you have solved the problem with missing DBD module. With the
> message you sent to us below, it seemed configure.pl had run
> successfully with martDBLocation.xml registry file. I am wondering after
> the configuration if you've even tried starting apache server and
> checking the martview from your web browser. If you did try, how was it?
>
> As for the registryURLPointer.xml file, it is intended for other people
> to use to include your datamart as part of their mart federation (of
> course you must expose your mart to them first). For your self-made
> mart, martDBLocation.xml is the only choice to bring your datamart
> online. registryURLPointer.xml (as you showed below) will NOT work, just
> as the name suggested, it's a pointer pointing to a running BioMart
> server instance (which has to be configured using martDBLocation in the
> first place), in other words, registryURLPointer can not be used to
> configure a first-hand (ie, self-made) datamart.
>
> If you really want to try out a registryURLPointer file, try this one:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
> <RegistryURLPointer
> name = "central_server"
> host = "www.biomart.org"
> port = "80"
> path = ""
> includeMarts = "ensembl,sequence"
> />
> </MartRegistry>
>
> This will work, because there is a running biomart server
> (www.biomart.org) which will provide you services including full
> configuration of the marts you are going to include in your mart
federation.
>
> Hope this helps a bit.
>
> Junjun
>
>
>
>
>
--------------------------------------------------------------------------------
> From: [email protected] [mailto:[email protected]] On
> Behalf Of [email protected]
> Sent: Monday, February 23, 2009 9:06 AM
> To: Syed Haider
> Cc: [email protected]; [email protected]; Syed Haider
> Subject: Re: [mart-dev] Error Stating MartView
>
>
>
> Hi,
>
> I corrected the error of connection. In fact there was a missing perl
> library DBD.
>
> Now, When, I launch the command perl bin/configure.pl -r
> conf/martDBLocation.xml --clean
> The trace is :
> Connection parameters of [Testsysbio] [ OK ]
> [NEW CONFIGURATION] .... WITH MEMORY [default]
> default ... Testsysbio ............... 001/001 ... AraGene
> ................................... (RDBMS) XXXXXXXXXXXXX: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
> [1/1] Attribute Panel of Dataset.. :AraGene
> [1/1] Filter Panel of Dataset..... :AraGene
>
> But when I lauch the command perl bin/configure.pl -r
> conf/registryURLPointer.xml
> I have reconfigure a little the registryURLPointer.xml
> </MartRegistry>
> This is my RegistryDBPointer.xml, I added here my own mart.
> <?xml version="1.0" encoding="UTF-8" ?>
> <!DOCTYPE MartRegistry (View Source for full doctype...)>
> <MartRegistry>
> <RegistryDBPointer name="Testsysbio" host="XXXXXX" port="3306"
> user="XXXXX" password="XXXXXX" database="Testsysbio" schema="
> Testsysbio" databaseType="mysql" includeMarts="AraGene" />
> </MartRegistry>
> there is still an error.
> Checking prerequisites ...[Looks good]
>
> rm
> /home/cropdesign/biomart/biomart-perl/conf/templates/default/*.ttc
> APACHE: /usr/sbin/apache2
> HOST: localhost
> PORT: 80
> PROXY:
> LOCATION: /home/cropdesign/biomart/biomart-perl
> APXS/2:
> You can change the above configuration by editing
> "biomart-perl/conf/settings.conf"
> Got usable Apache in /usr/sbin/apache2, probing for version &
> ModPerl configuration
> Have Apache DSO-support and ModPerl library file present,
> configuring ModPerl in httpd.conf.
> Libdir /home/cropdesign/biomart/biomart-perl/lib is not in @INC,
> adding to @INC
> Cached Registry Unavailable...
> Running Complete Clean...
> ERROR something wrong with your registry:
> syntax error at line 1, column 0, byte 0 at
> /usr/lib/perl5/XML/Parser.pm line 187
>
> Do you have an idea on my error?
>
> Best regards,
> Thanks,
>
> Bérénice
>
>
> Berenice Wulbrecht
> Phone: +32 9 242 9172, E-Mail: [email protected]
> Postal Address: CropDesign N.V., - - CD2, 9052 Gent (Zwijnaarde),
Belgium
>
> CropDesign N.V. - A BASF Plant Science Company
>
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