Hi Thomas, What happens if you launch the server and query it? If you do not materilize, the QueryCompiler will ignore the target schema and translate SQL against the source instead.
Could you try querying it to see if you are getting the results back? a On Wed, Oct 5, 2011 at 11:51 AM, Thomas TRIPLET <[email protected]>wrote: > Hi Arek, > > This is because my source schema is normalized. When added as a RDBMS data > source in BioMart, it is processed to build the target schema. The problem > is that the target schema that is generated is denormalized and unusable. > Here are 2 screenshots to illustrate the issue: > > - http://ttriplet.fg.concordia.ca/sourceDB.png > - http://ttriplet.fg.concordia.ca/targetDB.png > > I hope this clarifies my problem. > > 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 11:39 AM, Arek Kasprzyk <[email protected]>wrote: > >> 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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