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
CropDesign N.V.
Technologiepark 3
B-9052 Gent
Belgium
General Telephone: +32-9-241 50 80
Fax: +32-9-241 50 89
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