Hi Syed I have now added all fields that should be omitted from the interface into an attribute collection called 'dont_display'. I set hideDisplay for this collection to '1' and then tried 'true'. Neither work, so I now see all the fields I'd like to hide in one place on the interface :-P Anything else I can try? If I use hidden 'true' will this be a big issue? I don't quite understand the implication for putting 'hidden'. In the documentation its says "it will be ignored by the BioMart APIs which is useful for turning off an attribute or filter that you do not want to reappear next time you update the configuration against the database" does it really affect my biomart, then? Thanks, Jenny
-----Original Message----- From: Syed Haider [mailto:[email protected]] Sent: 29 April 2009 16:41 To: Mead, Jennifer Cc: Junjun Zhang Subject: Re: [mart-dev] Federating queries - thanks, and hideDisplay issues Hi Jennifer, Unfortunately, its seems incosistent, rather broken :) Please set hideDisplay of everthing upstream -> (AttributeCollection, AttribtueGroup, AttributePage for that attribute), all will disappear. I presume thats not what you want. The best is to declare an attributePage, group, collection (hideDisplay of all these set to true) and organise all those attributes (with hideDisplay set to true) which you want to hide from interface under the said tree. Best, Syed Mead, Jennifer wrote: > Thanks Syed and Junjun, > I will look into this for federating my queries asap, and get back to you on > how it goes. Before I get cracking though, a little thing is bugging me. > When I set hideDisplay to 'true' for my attributes, they don't disappear from > my martview interface. I have tried exporting it, running the 'blah blah > --clean' command, clicked the 'new' button and have restarted apache but > nothing seems to get rid of them. The weird thing is it works for hiding > filters? Am I going mad? > Thanks > Jenny > > > -----Original Message----- > From: Syed Haider [mailto:[email protected]] > Sent: 29 April 2009 15:12 > To: Mead, Jennifer > Cc: [email protected] > Subject: Re: [mart-dev] Federating queries > > Hi Jennifer, > > ---------- > MARTEDITOR > ---------- > you need to declare importable/exportable pairs (see docs for details). > Exportable is an attribute which one dataset returns to the linkable > dataset having an importable (which is a filter) having *same* name. > > please connect to ensembl using the credentials and see possible > exportables/importables you can use to link up. > > to connect, you need credentials shown here: > http://www.ebi.ac.uk/~syed/MartEditor_ensembl.png > > --------- > MartView > --------- > to make ensembl available as second dataset, you need to add it to your > registry file and then reconfigure (perl bin/configure.pl.....) and > restart apache. > > you need to add the following to your registry for ensembl: > > <MartURLLocation database="ensembl_mart_53" default="1" > displayName="ENSEMBL 53 GENES (SANGER UK)" host="www.biomart.org" > includeDatasets="" martUser="" name="ensembl" > path="/biomart/martservice" port="80" serverVirtualSchema="default" > visible="1" /> > > <MartURLLocation database="genomic_features_mart_53" default="0" > displayName="ENSEMBL 53 GENOMIC FEATURES (SANGER UK)" > host="www.biomart.org" includeDatasets="" martUser="" > name="genomic_features" path="/biomart/martservice" port="80" > serverVirtualSchema="default" visible="0" /> > > <MartURLLocation database="ontology_mart_53" default="0" > displayName="ENSEMBL 53 ONTOLOGY (SANGER UK)" host="www.biomart.org" > includeDatasets="" martUser="" name="ontology" > path="/biomart/martservice" port="80" serverVirtualSchema="default" > visible="0" /> > > <MartURLLocation database="sequence_mart_53" default="0" > displayName="ENSEMBL 53 SEQUENCE (SANGER UK)" host="www.biomart.org" > includeDatasets="" martUser="" name="sequence" > path="/biomart/martservice" port="80" serverVirtualSchema="default" > visible="0" /> > > > Hope this helps, > Syed > > > Mead, Jennifer wrote: >> Hi guys, >> >> I would like to perform queries using Martview for my own mart AND >> Ensembl database(s) at the same time. Basically, in my mart DB I have >> stored Ensembl gene ids for each entry, but I have not stored the >> protein names/descriptions. Instead I was hoping to perform federated >> queries, whereby I could use the Ensembl gene id in my mart to link to >> Ensembl at EBI to retrieve the descriptions on the fly. This way I hope >> to keep my database protein info up-to-date and save space in my local >> mart. Where can I find information regarding the implementation of >> federated queries using martbuilder/marteditor/martview? Would it >> perhaps be possible for a live example of this to be put on the FAQs >> page at www.biomart.org <http://www.biomart.org>? One little >> complication is that my gene ids are not just human - but they are all >> from species for which Ensembl has an existing build. >> >> Thanks very much, >> >> Jenny >> >> >> >> >> >> >>
