Hi Berenice, Great, it finally worked for you.
To query mart through web services, you don't need to do any further configuration. The biomart server you just configured includes web services. To get some ideas of how to use biomart web services, please go to: http://www.biomart.org/martservice.html. For the examples showing on this page to retrieve Meta Data, you can substitute www.biomart.org<http://www.biomart.org> with your own host name to make it work in your mart services. You need to prepare a query XML file (one example is given as below), and then run a small script (an example code named webExample.pl is given under biomart-perl/scripts) to fire the query against a biomart web server, you need to change this line: my $path="http://www.biomart.org/biomart/martservice?";; to make it point to your biomart martservice. Hope this is useful. Please let us know if you have any other questions. Junjun Example query XML: <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE Query> <Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > <Dataset name = "hsapiens_gene_ensembl" interface = "default" > <Filter name = "chromosome_name" value = "1"/> <Filter name = "end" value = "10000000"/> <Filter name = "start" value = "1"/> <Attribute name = "ensembl_gene_id" /> <Attribute name = "ensembl_transcript_id" /> <Attribute name = "ensembl_peptide_id" /> <Attribute name = "canonical_transcript_stable_id" /> <Attribute name = "description" /> <Attribute name = "chromosome_name" /> <Attribute name = "start_position" /> <Attribute name = "end_position" /> </Dataset> </Query> ________________________________ From: [email protected] [mailto:[email protected]] Sent: Tuesday, February 24, 2009 11:55 AM To: Syed Haider Cc: Junjun Zhang; [email protected] Subject: Re: [mart-dev] Error Stating MartView 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 > > CropDesign N.V. > Technologiepark 3 > B-9052 Gent > Belgium > General Telephone: +32-9-241 50 80 > Fax: +32-9-241 50 89 > Confidentiality notice: The information contained in this e-mail is > confidential and may be the subject of legal professional privilege. It > is intended for the authorized use of the individual or entity > addressed. If the receiver or reader of this message is not the intended > recipient, you are hereby notified that any disclosure, copying, > distribution or use of the contents of this message is prohibited. If > this email is received in error, please accept our apologies, delete all > copies from your system, and notify us at [email protected]. > > > >
