Debugging chado export

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

Debugging chado export

Marc Höppner-3
Hi,

sorry for the mail flood… I have another short question about chado exports. Specifically, is there a way to debug the export somehow? I found an option in hibernate.xml, but couldn’t quite figure out where that would be written to.

While exporting to chado works in principle, I noticed that it starts failing when I load an entire annotation to the user curation track. IN my test setup, I have one scaffold and corresponding maker models loaded. Adding those models manually works fine (have only tried it with a couple), but using the perl script from the WebApollo distribution apparently causes some kind of problem. I am guessing one or several models violate some rules (?). Would be good to see the reason for the failing export to Chado.

Cheers,

Marc
Reply | Threaded
Open this post in threaded view
|

Re: Debugging chado export

nathandunn

> On Oct 23, 2014, at 4:48 AM, Marc Höppner <[hidden email]> wrote:
>
> Hi,
>
> sorry for the mail flood… I have another short question about chado exports. Specifically, is there a way to debug the export somehow? I found an option in hibernate.xml, but couldn’t quite figure out where that would be written to.

Are you seeing anything in the tomcat / jetty log-file?

> While exporting to chado works in principle, I noticed that it starts failing when I load an entire annotation to the user curation track. IN my test setup, I have one scaffold and corresponding maker models loaded. Adding those models manually works fine (have only tried it with a couple), but using the perl script from the WebApollo distribution apparently causes some kind of problem. I am guessing one or several models violate some rules (?). Would be good to see the reason for the failing export to Chado.

That’s possible.   Both tomcat and postgres should be dumping out log-files.     You can probably turn show_sql=“true” in hibernate.xml, as well and watch the tomcat log files on export.  

<!-- Echo all executed SQL to stdout -->
<property name="show_sql">false</property>
<property name="format_sql">true</property>


Nathan