Hi Rosalind, In this case, it would require more thorough testing. Would it be possible to share your db schema with us so we can look into it here? If this is possible, please prepare a schema dump with no data. Also, from MartEditor, please do a 'Save All' and send me all the saved xml files.
You can send me the files directly (off the list). Thanks, Junjun On 11-03-16 9:39 AM, "Rosalind Cutts" <[email protected]> wrote: Hi, yes, the database is mysql with myisam engine. I tried importing the 0.7 mart via the registry file option and I get the same error. I also get an error if I try to use the url option to access the existing 0.7 web site. If I choose not to use an existing config, & pick the first level main table I only get filters & attributes created for the main table. Cheers Ros On 16/03/2011 12:29, "Junjun Zhang" <[email protected]> wrote: Hi Rosalind, What is the RDBMS you use? If is Mysql, is it myisam engine? Yes, if you choose not to use existing config, MC can import the source with all main and dm tables (you will need to choose the first level main when importing). There is another option to import exist 0.7 mart, that is to choose the Registry file option from the import source window, then pickup the 0.7 registry file. Hope this helps, let us know how it goes. Best, Junjun From: Rosalind Cutts [mailto:[email protected]] Sent: Wednesday, March 16, 2011 08:05 AM To: [email protected] <[email protected]> Subject: [BioMart Users] Using 0.8rc5 for existing biomart 0.7 databases. 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) This email may contain information that is privileged, confidential or otherwise protected from disclosure. It must not be used by, or its contents copied or disclosed to, persons other than the addressee. If you have received this email in error please notify the sender immediately and delete the email. This message has been scanned for viruses.
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