Hi Aminah, It is the plan to incorporate MartBuilder's features into MartConfigurator. However, at this time this is a low priority, MartConfigurator currently only supports very basic MartBuilder features, and it has not been properly tested. So it's not recommended to use MartConfigurator to transform source schema to BioMart schema yet.
Please feel free to let us know if you have any further questions. Thanks, Junjun On 11-07-27 3:51 AM, "Aminah Keliet" <[email protected]> wrote: >Hi, > >Yes, we use a chado schema postgres publicly available. >The current mart was built easily with martbuilder (martbuiler.sh). We >have chosen the feature table as main table without problems, and it >works well. > >I'll try to directly import existing marts with martconfigurator. I'll >keep you informed. > >Then, with this new release of Biomart (0.8 rc 6), we can't create new >mart from Chado schema, using the table feature as a main table? > > >Best regards, > > >Aminah, > > >Junjun Zhang 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.processParentDatasetTa >>ble(MartController.java:231) >> at >> >>org.biomart.configurator.controller.MartController.generateDatasetTable(M >>artController.java:369) >> at >> >>org.biomart.configurator.controller.MartController.generateDatasetTable(M >>artController.java:484) >> at >> >>org.biomart.configurator.controller.MartController.synchronise(MartContro >>ller.java:900) >> at >> >>org.biomart.configurator.controller.MartController.suggestMarts(MartContr >>oller.java:1375) >> at >> >>org.biomart.configurator.controller.MartController.requestCreateMartsFrom >>Source(MartController.java:1599) >> at >> >>org.biomart.configurator.controller.ObjectController.initMarts(ObjectCont >>roller.java:98) >> at >> >>org.biomart.configurator.view.component.container.SourceGroupPanel$1.cons >>truct(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.processParentDatasetTa >>ble(MartController.java:225) >> ... 9 more >> >> Do you have any idea ? >> Thanks >> >> _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
