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
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