Hi Erik, Is it possible for you to send me (off the list)the database schema? It would be very helpful if I can test it out here. Thanks, Junjun Sent from my BBerry
----- Original Message ----- From: Erik Dassi [mailto:[email protected]] Sent: Thursday, July 21, 2011 03:23 AM To: Junjun Zhang Cc: [email protected] <[email protected]> Subject: Re: [BioMart Users] MartEditor error Dear Junjun, I have tried to do what you suggested but nothing changed, I am still getting the same error ("Problems with exporting requested dataset. Check that dataset id is unique, you have write permissions and the meta_configuration tables are in the required format.") when doing Export. thanks, Erik Junjun Zhang ha scritto: > Dear Erik, > > Can you please try the following? I hope this could help sort things > out or at least narrow down the problem. > > * in you newly created database, only keep tables that are > generated by MartBuilder, remove all other tables including the > ones start with ‘meta_’ > * in MartEditor, connect to the database, do ‘naïve’, then do > ‘export’ right away (ie, after naïve, do not do anything else) > > > Hope this way, ‘export’ would succeed. > > Let us know how that goes. > > Cheers, > Junjun > > > > On 11-07-20 9:42 AM, "Erik Dassi" <[email protected]> wrote: > > Hi, > I am in the process of building and configuring a Mart from a > pre-existing database. > I was able to create the datasets by means of MartBuilder, correctly > executing SQL with MartRunner and I can now see all the tables it has > created in my schema filled with data. > I was then approaching the Mart configuration with MartEditor: I can > connect to the Mart without any problem, I choose the Naive > option, for > one of the datasets and everything seems ok (it passes the validation > through the Validate menu), but when I click on "Export" to save the > configuration in the db I am presented with the following error > message: > > Problems with exporting requested dataset. Check that dataset > id is > unique, you have write permissions and the meta_configuration > tables are > in the required format. > > In the console window I can read the following messages: > > SELECT dataset_id_key FROM UTRMart.meta_conf__dataset__main where > dataset='UTR' > and type='TableSet' and display_name='UTR' > STORING XML: UTR UTR > select count(*) from UTRMart.meta_conf__dataset__main where > dataset_id_key = ? > select count(*) from UTRMart.meta_conf__dataset__main where > dataset_id_key = ? > org.ensembl.mart.lib.config.ConfigurationException: Caught > SQLException > updating > xml for default, UTR: Incorrect arguments to mysqld_stmt_execute > at > org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.storeCompresse > dXML(DatabaseDatasetConfigUtils.java:3026) > at > org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.storeDatasetCo > nfiguration(DatabaseDatasetConfigUtils.java:948) > at > org.ensembl.mart.editor.DatasetConfigTree.export(DatasetConfigTree.ja > va:1559) > at > org.ensembl.mart.editor.DatasetConfigTreeWidget.exportTemplate(Datase > tConfigTreeWidget.java:478) > at > org.ensembl.mart.editor.MartEditor.exportTemplate(MartEditor.java:111 > 5) > at > org.ensembl.mart.editor.MartEditor$MenuActionListener.actionPerformed > (MartEditor.java:654) > at javax.swing.AbstractButton.fireActionPerformed(Unknown > Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown > Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown > Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at javax.swing.AbstractButton.doClick(Unknown Source) > at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown > Source) > at > javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown > Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at > java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at > java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown > Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Window.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown > Source) > at > java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown > Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > > > I have checked permissions for the db user and they are ok. > Any guess on what may be happening ? > > Thank you very much, > Erik Dassi > > -- > Erik Dassi > PhD Student > Laboratory of Translational Genomics > CIBIO - Center for Integrative Biology > Via delle Regole, 101 > 38123 MATTARELLO (TN) > Italy > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > -- Erik Dassi PhD Student Laboratory of Translational Genomics CIBIO - Center for Integrative Biology Via delle Regole, 101 38123 MATTARELLO (TN) Italy _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
