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
