Sure, thanks Lincoln! Scott, can you please recommend any publicly available chado db dump so that we can load locally for testing BioMart data transformation?
Thanks, Junjun From: Lincoln Stein <[email protected]<mailto:[email protected]>> Date: Wed, 27 Jul 2011 08:25:44 -0400 To: jzhang <[email protected]<mailto:[email protected]>>, Scott Cain <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema 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]<mailto:[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]<mailto:[email protected]>] > Sent: Tuesday, July 26, 2011 10:34 AM > To: [email protected]<mailto:[email protected]> > <[email protected]<mailto:[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]<mailto:[email protected]> > url:http://urgi.versailles.inra.fr > tel: 01.30.83.37.74 > > _______________________________________________ > Users mailing list > [email protected]<mailto:[email protected]> > https://lists.biomart.org/mailman/listinfo/users > _______________________________________________ > Users mailing list > [email protected]<mailto:[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]<mailto:[email protected]>>
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