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
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