Hi Thomas, you lost me here. Why would you want to use the same schema for source and target? Could you elaborate on this please?
a On Wed, Oct 5, 2011 at 11:24 AM, Thomas TRIPLET <[email protected]>wrote: > Syed, > Thanks for your reply. Sorry I wasn't clear enough, I am trying to use the > data source as it is, not materializing it as a mart. But when I add the > data source as a Postgres RDBMS, MartConfigurator *automatically* uses the > source schema to build the target schema. Is it possible to disable this > feature and force MartConfigurator to use the same schema for the target > database as for the source database? > Thanks > Thomas > > > -- > Thomas Triplet, Ph.D. > http://www.thomastriplet.net > > Centre for Structural and Functional Genomics > Concordia University > 7141 West Sherbrooke St > Montreal QC H4B 1R6 > > > > > > On Wed, Oct 5, 2011 at 9:07 AM, Syed Haider <[email protected]> wrote: > >> >> Thomas, >> >> Converting your source database into a mart is not mandatory, its only >> recommended for performance reasons. Try using the source schema & create a >> dataset straight out of your source database (without materialising to mart) >> and the subsequent querying and web interfaces should work just fine (at >> least in theory). >> >> W.r.t your second question, Martconfigurator is not able to read GFF or >> other text file formats. The input to Martconfigurator should either be an >> existing biomart webserver end point or a database. >> >> HTH, >> Syed >> >> >> >> On 04/10/2011 22:03, Thomas TRIPLET wrote: >> >>> Hello, >>> >>> I'm trying to build a mart (v0.8rc6) from a normalized (3NF) PostgreSQL >>> database. So far, it looks really great, except for one issue I have. When I >>> look at the source database schema (using MartConfigurator), it is just >>> fine, so the database seems properly imported. However, the corresponding >>> target database really messes things up as it tries to merge everything >>> together. Here is a simple example to illustrate the problem: >>> >>> [cid:ii_132d0b1d058ca382] [cid:ii_132d0b234e4777ae] >>> >>> >>> >>> The target database is clearly problematic, and not usable as such. Is >>> there a way to force BioMart to keep the source schema untouched, or at >>> least, control how it is processed ? ALl relations in the source database >>> are defined as [1:M] so I'm not sure what's wrong here. >>> >>> Also, it is my understanding that a database must exist in the form of a >>> database in order to be imported (whether it is actually accessed using >>> RDBMS/URL/registry), or can it also be defined as raw datafiles (e.g GFF >>> files) along with a parser. Could you please confirm this? >>> >>> Thanks a lot for your help. >>> >>> Thomas >>> >>> -- >>> Thomas Triplet, Ph.D. >>> http://www.thomastriplet.net >>> >>> Centre for Structural and Functional Genomics >>> Concordia University >>> 7141 West Sherbrooke St >>> Montreal QC H4B 1R6 >>> >>> >>> >>> >>> > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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