Struggling with the GO term enrichment widget

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Struggling with the GO term enrichment widget

joe carlson
Hello,

I’ve been struggling with the GO term enrichment widget for a couple of days now. There must be a simple thing that I’m missing since I think I’m close, but cannot get the widget to appear on the bagDetails page.

I have data in the Gene and GoAnnotation tables. And everything is linked properly. The GO terms appear on the Gene page if I look at one gene at a time.

And I can make a web service call with wget to /service/list/enrichment?list=<mylist>&token=… and this returns a proper JSON string with lots of GO terms that I expect to see. When I run tomcat through the debugger I can set breakpoints in the java routines for the enrichment widgets and they all look good.

But when I access the bagDetails page, I only see an empty box for the GO enrichment (and chromosome location) widgets. See the attached screenshot. I’ve put enough alert and prints into widget.jsp and widgetScript.jsp to know that these are getting loaded. But as far as I can tell, the request initiated by the jQuery script in widgetScript.jsp is not hitting my tomcat.: I never hit a breakpoint in the enrichment widget java classes, nor do I see anything in the log files indicating a request.

Is there a simple configuration parameter that I need to check to make sure these requests are going to the right place? Can you suggest something to look at for a clearer diagnosis?

Thanks,

Joe
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Re: Struggling with the GO term enrichment widget

joe carlson
I forgot my silly screenshot





On Apr 30, 2014, at 5:42 PM, Joe Carlson <[hidden email]> wrote:

Hello,

I’ve been struggling with the GO term enrichment widget for a couple of days now. There must be a simple thing that I’m missing since I think I’m close, but cannot get the widget to appear on the bagDetails page.

I have data in the Gene and GoAnnotation tables. And everything is linked properly. The GO terms appear on the Gene page if I look at one gene at a time.

And I can make a web service call with wget to /service/list/enrichment?list=<mylist>&token=… and this returns a proper JSON string with lots of GO terms that I expect to see. When I run tomcat through the debugger I can set breakpoints in the java routines for the enrichment widgets and they all look good.

But when I access the bagDetails page, I only see an empty box for the GO enrichment (and chromosome location) widgets. See the attached screenshot. I’ve put enough alert and prints into widget.jsp and widgetScript.jsp to know that these are getting loaded. But as far as I can tell, the request initiated by the jQuery script in widgetScript.jsp is not hitting my tomcat.: I never hit a breakpoint in the enrichment widget java classes, nor do I see anything in the log files indicating a request.

Is there a simple configuration parameter that I need to check to make sure these requests are going to the right place? Can you suggest something to look at for a clearer diagnosis?

Thanks,

Joe


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Re: Struggling with the GO term enrichment widget

vkrishna
Hi Joe,

In our ThaleMine instance (for the Arabidopsis thaliana genome data), we have the GO Enrichment widget turned on and here is what we see for a list of genes I just created (I used the query builder to return all Genes whose briefDescription CONTAINS “kinase” and saved the result to the list and then visited the list page). Here is what I see:


In order to enable this widget, we added the following configuration to our webconfig-model.xml file. You can cross-check your configuration against ours to see if you may be missing something.
Our instance is accessible here: https://apps.araport.org/thalemine.

Hope this helps!

Thank you.
Vivek

On Apr 30, 2014, at 8:43 PM, Joe Carlson <[hidden email]> wrote:

I forgot my silly screenshot


<Screen Shot 2014-04-30 at 4.56.19 PM.png>


On Apr 30, 2014, at 5:42 PM, Joe Carlson <[hidden email]> wrote:

Hello,

I’ve been struggling with the GO term enrichment widget for a couple of days now. There must be a simple thing that I’m missing since I think I’m close, but cannot get the widget to appear on the bagDetails page.

I have data in the Gene and GoAnnotation tables. And everything is linked properly. The GO terms appear on the Gene page if I look at one gene at a time.

And I can make a web service call with wget to /service/list/enrichment?list=<mylist>&token=… and this returns a proper JSON string with lots of GO terms that I expect to see. When I run tomcat through the debugger I can set breakpoints in the java routines for the enrichment widgets and they all look good.

But when I access the bagDetails page, I only see an empty box for the GO enrichment (and chromosome location) widgets. See the attached screenshot. I’ve put enough alert and prints into widget.jsp and widgetScript.jsp to know that these are getting loaded. But as far as I can tell, the request initiated by the jQuery script in widgetScript.jsp is not hitting my tomcat.: I never hit a breakpoint in the enrichment widget java classes, nor do I see anything in the log files indicating a request.

Is there a simple configuration parameter that I need to check to make sure these requests are going to the right place? Can you suggest something to look at for a clearer diagnosis?

Thanks,

Joe

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Re: Struggling with the GO term enrichment widget

joe carlson
Hi Vivek,

Thanks for the reply.

I checked my webconfig file and the only big difference I saw was the correctionCoefficent class. (I haven’t merged with the mail source tree in a while; otherwise what have have is straight from 1.1 on github) But that wasn’t the problem. Still blank. The fact that I can make the web service call directly makes me think this config setup is not the problem. 

I’ll poke at it some more to see if I can get it. By the way, we should talk about putting one another on the friendly mine list to have a group of the plant mines.

Thanks,

joe

 
On Apr 30, 2014, at 6:11 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Joe,

In our ThaleMine instance (for the Arabidopsis thaliana genome data), we have the GO Enrichment widget turned on and here is what we see for a list of genes I just created (I used the query builder to return all Genes whose briefDescription CONTAINS “kinase” and saved the result to the list and then visited the list page). Here is what I see:

<PastedGraphic-2.png>

In order to enable this widget, we added the following configuration to our webconfig-model.xml file. You can cross-check your configuration against ours to see if you may be missing something.
Our instance is accessible here: https://apps.araport.org/thalemine.

Hope this helps!

Thank you.
Vivek

On Apr 30, 2014, at 8:43 PM, Joe Carlson <[hidden email]> wrote:

I forgot my silly screenshot


<Screen Shot 2014-04-30 at 4.56.19 PM.png>


On Apr 30, 2014, at 5:42 PM, Joe Carlson <[hidden email]> wrote:

Hello,

I’ve been struggling with the GO term enrichment widget for a couple of days now. There must be a simple thing that I’m missing since I think I’m close, but cannot get the widget to appear on the bagDetails page.

I have data in the Gene and GoAnnotation tables. And everything is linked properly. The GO terms appear on the Gene page if I look at one gene at a time.

And I can make a web service call with wget to /service/list/enrichment?list=<mylist>&token=… and this returns a proper JSON string with lots of GO terms that I expect to see. When I run tomcat through the debugger I can set breakpoints in the java routines for the enrichment widgets and they all look good.

But when I access the bagDetails page, I only see an empty box for the GO enrichment (and chromosome location) widgets. See the attached screenshot. I’ve put enough alert and prints into widget.jsp and widgetScript.jsp to know that these are getting loaded. But as far as I can tell, the request initiated by the jQuery script in widgetScript.jsp is not hitting my tomcat.: I never hit a breakpoint in the enrichment widget java classes, nor do I see anything in the log files indicating a request.

Is there a simple configuration parameter that I need to check to make sure these requests are going to the right place? Can you suggest something to look at for a clearer diagnosis?

Thanks,

Joe

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Re: Struggling with the GO term enrichment widget

joe carlson
In reply to this post by joe carlson
After further work, I think I found that  my problem is that I’ve messed up some links to my jQuery installation. That would certainly explain why the web service was never getting called.

Sorry for any confusion I may have caused.

Joe

On Apr 30, 2014, at 5:43 PM, Joe Carlson <[hidden email]> wrote:

I forgot my silly screenshot


<Screen Shot 2014-04-30 at 4.56.19 PM.png>


On Apr 30, 2014, at 5:42 PM, Joe Carlson <[hidden email]> wrote:

Hello,

I’ve been struggling with the GO term enrichment widget for a couple of days now. There must be a simple thing that I’m missing since I think I’m close, but cannot get the widget to appear on the bagDetails page.

I have data in the Gene and GoAnnotation tables. And everything is linked properly. The GO terms appear on the Gene page if I look at one gene at a time.

And I can make a web service call with wget to /service/list/enrichment?list=<mylist>&token=… and this returns a proper JSON string with lots of GO terms that I expect to see. When I run tomcat through the debugger I can set breakpoints in the java routines for the enrichment widgets and they all look good.

But when I access the bagDetails page, I only see an empty box for the GO enrichment (and chromosome location) widgets. See the attached screenshot. I’ve put enough alert and prints into widget.jsp and widgetScript.jsp to know that these are getting loaded. But as far as I can tell, the request initiated by the jQuery script in widgetScript.jsp is not hitting my tomcat.: I never hit a breakpoint in the enrichment widget java classes, nor do I see anything in the log files indicating a request.

Is there a simple configuration parameter that I need to check to make sure these requests are going to the right place? Can you suggest something to look at for a clearer diagnosis?

Thanks,

Joe



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