Hi All, Thanks for bringing me into the conversation; please let me know if there is anything I can do to help.
Scott On Wed, Jul 27, 2011 at 8:25 AM, Lincoln Stein <[email protected]> wrote: > > 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]> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
