[BioMart Users] v0.8 rc4 feedback

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[BioMart Users] v0.8 rc4 feedback

Peter Stevenson
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         | [hidden email]
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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Re: [BioMart Users] v0.8 rc4 feedback

Syed Haider
Hi Peter,

The default property on attributes and filters will get enabled for
sure. And so would be the documentation on properties editable by
deployers.

Many thanks for bringing this forward.

Syed

On 09/02/2011 16:45, Peter Stevenson wrote:

> 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.
>
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