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.processParentDatasetTable(MartController.java:231)
at
org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
at
org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
at
org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
at
org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
at
org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
at
org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
at
org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(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.processParentDatasetTable(MartController.java:225)
... 9 more
Do you have any idea ?
Thanks
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