Hi Matteo you are right, but as you can see in our registry entry for dicty, there exist ( redirect = "1" ), which means that the servervirtualSchema is not the name of our (biomart) server's vritualschema but dicty's server virtualschema. As dicty is a MartURLLocation in our registry so we encourage users/clients to talk to dicty directly rather going through a long/indirect route via biomart server.
hope this helps. Cheers syed On Thu, 2007-07-26 at 11:54 +0200, Matteo Floris wrote: > Ok, > > but let me know if this should be your URL of the XML for dicty/gene > dataset: > > http://www.biomart.org/biomart/martservice? > type=configuration&dataset=gene&virtualschema=dictyMart > > (this url string is based on your biomart registry, but is not valid). > > it seems that the virtualschema should be default, not dictyMart. > > > M. > > > > Hi Matteo > > Probably the version of XML we ave configured with had this > > information > > while the same info is missing from Dicty's own mart as well. You amy > > write to them and ask about the difference. They should be able to > > suggest the correct reason. > > > > Cheers > > syed > > > > > > On Thu, 2007-07-26 at 09:31 +0200, Matteo Floris wrote: > >> Hi Syed, > >> > >> > >> sorry but it doesn't work... > >> > >> > >> if you look at the > >> XML http://www.dictybase.org:80/biomart/martservice? > >> type=configuration&dataset=gene&virtualschema=dictyMart > >> > >> > >> there a some attributes without description.... > >> an example: if you look at the dictybase/gene dataset from the > >> bioMart > >> website, you can see a description "Flank (Tran. Coding Region)" that > >> is not present > >> in http://www.dictybase.org:80/biomart/martservice? > >> type=configuration&dataset=gene&virtualschema=dictyMart ... > >> > >> > >> Did you check this file also? > >> > >> > >> Thanks, > >> > >> > >> Matteo. > >> > >> > >> > >> > >> > >> Il giorno 25/lug/07, alle ore 21:58, Syed Haider ha scritto: > >> > >>> Hi Matteo, > >>> this is fixed now, you may check live server to see if your client > >>> works > >>> with dictyBase. > >>> > >>> > >>> Cheers > >>> syed > >>> > >>> > >>> > >>> > >>>> Thanks Syed for your kind reply, > >>>> > >>>> > >>>> I'm going to try the test server. > >>>> I'll inform you about the results. > >>>> > >>>> > >>>> Cheers, > >>>> > >>>> > >>>> Matteo. > >>>> > >>>> > >>>> > >>>> > >>>>> Hi Matteo > >>>>> apologies, the dicty update couldnt make it last evening. > >>>>> > >>>>> > >>>>> I would suggest to test this dicty case on test server which is > >>>>> running > >>>>> on > >>>>> test.biomart.org/biomart/martview and you will have the changes > >>>>> available there. Central server will hopefully reflect these > >>>>> changes as > >>>>> well very soon. As soon as I do it, i will let you know. > >>>>> > >>>>> > >>>>> thanks for your patience. > >>>>> Syed > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On Tue, 2007-07-24 at 11:43 +0200, Matteo Floris wrote: > >>>>>> Thanks Syed for you help. > >>>>>> > >>>>>> > >>>>>> Cheers, > >>>>>> > >>>>>> > >>>>>> Matteo. > >>>>>> > >>>>>> > >>>>>> Il giorno 24/lug/07, alle ore 11:38, Syed Haider ha scritto: > >>>>>> > >>>>>> > >>>>>>> Hi Matteo > >>>>>>> It happens to be absent in our central registry. I will add > >>>>>>> it and > >>>>>>> updated server will be available from tomorrow. > >>>>>>> > >>>>>>> > >>>>>>> thanks for your patience. > >>>>>>> > >>>>>>> > >>>>>>> Cheers > >>>>>>> syed > >>>>>>> > >>>>>>> > >>>>>>> On Tue, 2007-07-24 at 11:21 +0200, Matteo Floris wrote: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Dear developers, > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> from the > >>>>>>>> registry > >>>>>>>> http://www.biomart.org/biomart/martservice?type=registry > >>>>>>>> the path of the dictybase schema should > >>>>>>>> be http://www.dictybase.org:80/?type=datasets&mart=dicty > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> <MartURLLocation default="0" displayName="DICTYBASE > >>>>>>>> (NORTHWESTERN)" > >>>>>>>> host="www.dictybase.org" includeDatasets="" martUser="" > >>>>>>>> name="dicty" > >>>>>>>> path="" port="80" redirect="1" > >>>>>>>> serverVirtualSchema="dictyMart" > >>>>>>>> visible="1" /> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> but the correct url is this: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> http://www.dictybase.org:80/biomart/martservice? > >>>>>>>> type=datasets&mart=dicty > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> We don't understand if this is a bug or we wave to > >>>>>>>> complete the url > >>>>>>>> with "biomart/martservice". > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Can you help me? > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks in advance, > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Matteo Floris. > >>>>>>> -- > >>>>>>> ====================================== > >>>>>>> Syed Haider. > >>>>>>> EMBL-European Bioinformatics Institute > >>>>>>> Wellcome Trust Genome Campus, Hinxton, > >>>>>>> Cambridge CB10 1SD, UK. > >>>>>>> ====================================== > >>>>>>> > >>>>>>> > >>>>> -- > >>>>> ====================================== > >>>>> Syed Haider. > >>>>> EMBL-European Bioinformatics Institute > >>>>> Wellcome Trust Genome Campus, Hinxton, > >>>>> Cambridge CB10 1SD, UK. > >>>>> ====================================== > >>>>> > >>>>> > >>>> > >>>> > >>> > >>> > >>> > >>> > >>> ====================================== > >>> Syed Haider. > >>> EMBL-European Bioinformatics Institute > >>> Wellcome Trust Genome Campus, Hinxton, > >>> Cambridge CB10 1SD, UK. > >>> ====================================== > >>> > >>> > >> > > -- > > ====================================== > > Syed Haider. > > EMBL-European Bioinformatics Institute > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > ====================================== > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
