Will, if i understand your question correctly, then the answer is no. What I mean by this is if you supply full URL in XML like the one i quoted for MSD, then the exturl param from settings.conf is ignored. However, if in your XML you supply a relative URL which is expected to begin with a forward slash (/) instead of (http), then the exturl param from the settings.conf is prepended to this. Yes, the to prepend or not check is based on forward slash. and unfortunately we only support one entry for exturl from settings.conf.
cheers syed On Fri, 2008-03-28 at 16:54 +0000, William Spooner wrote: > OK - So I assume that 'http://www.ebi.ac.uk' is substituted with > whatever is in 'exturl'? In which case I can work with this. Could you > confirm and I will add this to the job list. > > Will > > On 28 Mar 2008, at 16:26, Syed Haider wrote: > > fair enough. I thought you can add it like we do for MSD and Uniprot > > e.g exturl|http://www.ebi.ac.uk/msd-srv/atlas?id=%s > > > > added this on the requirements list for 0.8 release. > > > > cheers > > syed > > > > > > On Fri, 2008-03-28 at 16:18 +0000, William Spooner wrote: > >> Hi Syed, > >> > >> The URLs are internal (relative) to www.wormbase.org, or > >> dev.wormbase.org, or one of the wormbase mirrors depending on the > >> httpd. I set this on a per-server basis using exturl setting in > >> settings.conf. I cannot really hard-code the path due to mirroring > >> issues. > >> > >> Will > >> > >> > >> On 28 Mar 2008, at 16:08, Syed Haider wrote: > >>> > >>> Will, who runs Wormbase, is cc'ed would be able to comment. > >>> > >>> Will, you need to edit your XMLs and prepend servername for > >>> attributes > >>> with external URL links as this is expected to have www.wormbase.org > >>> instead of www.ensembl.org. > >>> > >>> > >>> > >>> > >>> On Fri, 2008-03-28 at 17:02 +0100, Isabelle Phan wrote: > >>>> wow that's real service! > >>>> > >>>> now the results look good: > >>>> > >>>> Anatomy Term ID Anatomy Term > >>>> WBbt:0003679 neuron > >>>> > >>>> however when I click on the link > >>>> > >>>> http://www.ensembl.org/db/ontology/anatomy?name=WBbt:0003679;class=Anatomy_term > >>>> > >>>> the page returns: > >>>> > >>>> 404 not found. > >>>> > >>>> ? > >>>> > >>>> > >>>> Isabelle > >>>> > >>>> Syed Haider wrote: > >>>>> Hi Isabelle, > >>>>> > >>>>> www.biomart.org has the patch now. thanks for your patience. > >>>>> > >>>>> cheers > >>>>> syed > >>>>> > >>>>> On Fri, 2008-03-28 at 11:32 -0400, Arek Kasprzyk wrote: > >>>>>> On 28-Mar-08, at 11:09 AM, Isabelle Phan wrote: > >>>>>> > >>>>>>> I have now found some queries that work great! > >>>>>>> However I will have a hard time explaining why some data seem to > >>>>>>> be > >>>>>>> missing from the results table.... > >>>>>>> > >>>>>>> MartView query: > >>>>>>> > >>>>>>> Dataset: MSD > >>>>>>> Filters: R < 2A, single crystal X-ray diffraction > >>>>>>> Attributes: Molecule name, Organism Name, PDB ID(s) > >>>>>>> > >>>>>>> combined with > >>>>>>> > >>>>>>> Dataset: Uniprot proteomes > >>>>>>> Filters: none > >>>>>>> Attributes: UniProt AC > >>>>>>> > >>>>>>> Filter for unique rows: selected > >>>>>>> View: 200 rows > >>>>>>> > >>>>>>> I am getting entries with no organism data, e.g.: > >>>>>>> CYCLOPHILIN 3 1e3b P52011 > >>>>>>> > >>>>>>> both the PDB and UniProt data seem to contain the correct > >>>>>>> organism > >>>>>>> (C.elegans) with the correct taxID. > >>>>>>> > >>>>>> Hi Isabelle, > >>>>>> > >>>>>>> Why is the query not returning the organism data? Is this a > >>>>>>> synchronization issue? > >>>>>>> > >>>>>> most likely, MSD as well as UNIPROT are just prototype data > >>>>>> sources so > >>>>>> not really kept up to date. > >>>>>> You would be probably better off using something which is > >>>>>> regularly > >>>>>> updated e.g. Ensembl > >>>>>> > >>>>>> a. > >>>>>> > >>>>>> PS. We are investigating the Wormbase issue that you reported. > >>>>>> we'll > >>>>>> get back to you on this shortly > >>>>>> thanks for spotting it > >>>>>> > >>>>>>> thanks for any hints you may provide! > >>>>>> > >>>>>> > >>>>>>> I. > >>>>>>> -- > >>>>>>> Isabelle Phan, D.Phil. > >>>>>>> Swiss Institute of Bioinformatics Tel: (+41 22) 379 51 > >>>>>>> 89 > >>>>>>> CMU - 1, rue Michel Servet Fax: (+41 22) 379 58 > >>>>>>> 58 > >>>>>>> CH - 1211 Geneva 4 Switzerland email: [EMAIL PROTECTED] > >>>> > >>>> > >>> -- > >>> ====================================== > >>> Syed Haider. > >>> EMBL-European Bioinformatics Institute > >>> Wellcome Trust Genome Campus, Hinxton, > >>> Cambridge CB10 1SD, UK. > >>> ====================================== > >> > >> --- > >> William Spooner > >> Visiting Scientist > >> [EMAIL PROTECTED] > >> > >> > > -- > > ====================================== > > Syed Haider. > > EMBL-European Bioinformatics Institute > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > ====================================== > > --- > William Spooner > Visiting Scientist > [EMAIL PROTECTED] > >
