On Thu, 2007-07-26 at 12:21 +0200, Matteo Floris wrote: > Thanks Syed > > I understand what you mean, but we are testing out tool, and > 1) if we talk to dicty directly we found a bug in the dicty XML > 2) if we talk to BioMart's server we cannot use it automatically > because the servervirtualSchemas are based on the dicty's server > parameters. > > The only solution we have is to ask to dictybase (and other servers, > I suppose) to update/debug their XML files. > But this is not a definitive solution, as you can imagine, if all > the servers with martservices are not automatically updated. > Cheers,
I believe you dont need to ask for any updates from anybody, just use what any server offers through the XML. Isnt it enough information for your client to run or does it carry out some kind matching if Biomart central server is in sink with some other XYZ server exposing the same mart? > > Matteo. > > > > > 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. > > ====================================== > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
