[BioMart Users] Bug when materializing marts

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

[BioMart Users] Bug when materializing marts

Thomas TRIPLET
Hello,

I noticed a bug in MartConfigurator. I've added a data source from a Postgres database schema. However, when I try to materialize the view, I get an error due to case sensitivity. From the log, it appears that the SQL generator does not encapsulate the table names with quotes and thus does not support table names with caps.  Is there a way this could be fixed?

Also, is materialization strictly necessary to run BioMart with sources from an external database schema? The psql database schema runs on the same machine as BioMart. I've added the data source as mentioned in the documentation, then started the the server. On the web page, I do get the list of data sources, with appropriate fields. However, it looks like there's is no data at all as any query return "no result". It worked fine though with the example from the documentation, so I was wondering if extra steps are needed for custom data sources (sorry for my ignorance, I'm just starting with BioMart, and I'll probably have a few questions in the next few weeks)

Thanks a lot for any input
Thomas

--
Thomas Triplet, Ph.D.
http://www.thomastriplet.net

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] Bug when materializing marts

Arek Kasprzyk
Hi Thomas,
materialization is no longer necessary in 0.8, You can interact with the source schema through a 'virtual dataset'. The compiler will compile SQL against the source. Just create a dataset, launch the server and query it.

As for the materilize bugs Junjun will be able to help you more

a


On Fri, Sep 30, 2011 at 4:59 PM, Thomas TRIPLET <[hidden email]> wrote:
Hello,

I noticed a bug in MartConfigurator. I've added a data source from a Postgres database schema. However, when I try to materialize the view, I get an error due to case sensitivity. From the log, it appears that the SQL generator does not encapsulate the table names with quotes and thus does not support table names with caps.  Is there a way this could be fixed?

Also, is materialization strictly necessary to run BioMart with sources from an external database schema? The psql database schema runs on the same machine as BioMart. I've added the data source as mentioned in the documentation, then started the the server. On the web page, I do get the list of data sources, with appropriate fields. However, it looks like there's is no data at all as any query return "no result". It worked fine though with the example from the documentation, so I was wondering if extra steps are needed for custom data sources (sorry for my ignorance, I'm just starting with BioMart, and I'll probably have a few questions in the next few weeks)

Thanks a lot for any input
Thomas

--
Thomas Triplet, Ph.D.
http://www.thomastriplet.net

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



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