span_from_question stage name invalid?

[Emily Greenfest-Allen]

Hi all-

I am getting the following error when I try to join two gene queries in
a strategy using co-location:

353702 [ERROR] org.gusdb.wdk.controller.action.WizardAction:122 - -
[19/Oct/2011:07:02:00 -0400] org.gusdb.wdk.model.WdkUserException: The
stage name [span_from_question] is invalid.

I traced this through the java and see that the error is thrown from
WDK/Controller/src/java/org/gusdb/wdk/controller/wizard/Wizard.java;
line 160 in the queryStage function because the value of "stage" (Stage
stage = stageMap.get(stageName);) is null.

I'm thinking I might have failed to define something in my model -- any
ideas? The question GenesBySpanLogic and underlying query are defined
in spanQuestions.xml.

Thanks,
-Emily

[Cristina Aurrecoechea]

Emily: so you do not get to see the colocation popup, right?

[Jerric Gao]

Hi Emily,

You need this file: ApiCommonWebsite/Model/lib/wdk/wizard/apicomm-wizard.xml

Put it into your project's similar place. And then it should work.

Jerric

[Emily Greenfest-Allen]

Jerric-

I've done that, but on looking at the contents of apicomm-wizard.xml,
but for the record I see that it references the following java files,
which I will also have to bring into our project. I'll let you know if
I run into any issues.

org.apidb.apicommon.controller.wizard.SpanFromQuestionStageHandler
org.apidb.apicommon.controller.wizard.SpanFromStrategyStageHandler
org.apidb.apicommon.controller.wizard.ProcessSpanStageHandler
org.apidb.apicommon.controller.wizard.SpanFromReviseStageHandler

Also I see that after the sections dealing with SpanLogic in
apicomm-wizard.xml there are the following for the ortholog transform:

<!-- show the transform question page -->
<stage name="show_ortholog"
display="Select parameters for Transform"

handlerClass="org.apidb.apicommon.controller.wizard.ShowOrthologStageHandler">
<description>Go to transform question page.</description>
<result type="view">/wdkCustomization/jsp/wizard/ortholog.jsp</result>
</stage>

<!-- process the question. the question could be any question other than
a boolean operation. -->
<stage name="process_ortholog"
display="Process Normal or Transform Question">
<description>Process a normal question (the first question) or a
transform.</description>
<result type="action">/processStep.do</result>
</stage>

We, of course, don't need this, but I did want to implement transforms
between a couple of our record types. Will we need something
equivalent? Or are Orthologs a special case?

Thanks,

Emily