forgot to cc scott
On Wed, Jul 27, 2011 at 1:55 PM, Arek Kasprzyk <[email protected]> wrote: > Junjun: > chado schema is publically available and i have done quite a bit of > work with it in the past. > The end result was that MBuilder could support 3NF transformation > quite well but this was not sufficient for chado. > Chado is a schema with a lot of recursive self-referencing based > around 'feature' table. This, of course, can still be transformed > using 3NF algorithm but the end result will not be as exiciting as one > would like to. I experimented with it a bit a few years ago and came > up with an alternative to 3NF algorihm which would work much better > with chado. However given that current MConfigurator has not even > acquired all the MBuilder features this seems to be a long way ahead. > It will be better if you concentrate on implementing basic features > for MConfigurator to get 3NF going properly first. This will give you > the basics for chado. Once this is sorted out I"ll be glad to help > with a proper algorithm for chado transformation > > > a > > > > On Tue, Jul 26, 2011 at 12:01 PM, Junjun Zhang <[email protected]> > wrote: >> Hi Aminah, >> >> Is that chado schema publicly available? It would be very helpful if we can >> test it out here. >> >> Also, I am just curious how your current mart is built. If you'd like to try >> 0.8 with the existing mart db, you can directly import it using >> martconfigurator. >> >> Best regards, >> >> Junjun >> Sent from my BBerry >> >> ----- Original Message ----- >> From: Aminah Keliet [mailto:[email protected]] >> Sent: Tuesday, July 26, 2011 10:34 AM >> To: [email protected] <[email protected]> >> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema >> >> Hi >> >> We are testing the new version of Biomart (0.8 rc 6) to replace our >> current install (v 0.7). We build mart on the GMOD-Chado schema using >> the feature table as main table for our marts. With the new version we >> get an error when we try to do the same thing. In the Add data source >> panel, we choose the feature table from the public schema, then we click >> add and we get : >> >> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings >> [Thread-104] INFO martconfigurator - Initialize source schema >> [Thread-104] INFO martconfigurator - Done synchronising >> [Thread-104] ERROR martconfigurator - duplicated relation >> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057] >> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in >> MartBuilder >> org.biomart.common.exceptions.BioMartError: >> org.biomart.common.exceptions.AssociationException: A relation between >> these two keys already exists. >> at >> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231) >> at >> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369) >> at >> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484) >> at >> org.biomart.configurator.controller.MartController.synchronise(MartController.java:900) >> at >> org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375) >> at >> org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599) >> at >> org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98) >> at >> org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85) >> at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128) >> at java.lang.Thread.run(Thread.java:619) >> Caused by: org.biomart.common.exceptions.AssociationException: A >> relation between these two keys already exists. >> at org.biomart.objects.objects.Relation.<init>(Relation.java:141) >> at >> org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17) >> at >> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225) >> ... 9 more >> >> Do you have any idea ? >> Thanks >> >> -- >> Aminah Olivia KELIET >> Ingenieur d'études en Bio-informatique >> >> Unité de recherche en Génomique-Info >> INRA Centre de Versailles >> Route de Saint Cyr >> 78026 Versailles Cedex >> >> email: [email protected] >> url:http://urgi.versailles.inra.fr >> tel: 01.30.83.37.74 >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
