Hi,
I have been trying out biomart v0.8 rc4 and have some issues to feedback.
I tried to import my 3 current (v0.7) data sources as relational marts
in MartConfigurator using the existing config.
The simplest one (a single table) imported OK. However the "default"
property of the attributes is not set where it had been in v0.7, and
MartConfigurator does not allow that property to be edited. (BTW is
there going to be any documentation on what the properties mean in the
configuration tool?). Otherwise this mart deploys OK.
The second data source fails to import at all -
WARN [AWT-EventQueue-0] (Log.java:187) - Exception occurred in MartBuilder
java.lang.NullPointerException
at
org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:168)
at
org.biomart.configurator.controller.ObjectController$1.construct(ObjectController.java:88)
at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
at java.lang.Thread.run(Thread.java:662)
The third source partially imports but I get many messages like this example:-
ERROR [Thread-88] (Log.java:197) - Can't create attribute, because
table WET_REPORTER_TB__dm not found; trying TB__WET_REPORTER_TB__dm
...and similar messages for several tables. The actual table name for
this example is in fact GENE_TB__WET_REPORTER_TB__dm.
Other error messages during import like:-
[Thread-88] ERROR martconfigurator - Exportable warning:
experiment_exportable not added
[Thread-88] ERROR martconfigurator - Importable warning:
experiment_exportable not added
I assume that this is because importables/exportables are replaced by
pointer attributes and filters in this release?
Regards,
Peter.
--
Peter Stevenson | [email protected]
EMAP Computer Support | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
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