Hi, a couple of queries regarding biomart 0.8.
I am looking at upgrading some existing biomart databases from 0.7 to 0.8 using
rc5
I tried connecting to the data sources by RDBMS – Relational Mart and this
worked fine for the first database but fails for the second with the following :
java.lang.NullPointerException
at
org.biomart.configurator.controller.ObjectController.createMartFromBC_db(ObjectController.java:239)
at
org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:152)
at
org.biomart.configurator.controller.ObjectController$1.construct(ObjectController.java:97)
at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
at java.lang.Thread.run(Thread.java:637)
The second database contains 2 datasets & the configurator goes on to create
the 2 datasets as data sources but it is not possible to create a config for
the second datasource so it looks like this is causing the problem. Is there a
way that I can isolate what this might be ?
If I ignore the existing config & build from scratch for the second data set,
the list of main tables is displayed & this will build a new config but does
not locate any of the associated dm tables.
Is there a way to build the dataset from scratch and automatically include the
dm tables in the config?
Thanks for your help
Ros Cutts
Barts Cancer Institute (QMUL)
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