Hi Junjun, I'm bringing Scott Cain into this conversation as he supports the Chado schema for GMOD.
Lincoln On Tuesday, July 26, 2011, 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 > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <[email protected]>
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