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. | _______________________________________________ Users mailing list [hidden email] https://lists.biomart.org/mailman/listinfo/users |
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. > Users mailing list [hidden email] https://lists.biomart.org/mailman/listinfo/users |
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