GettingStartedWebapp > Exercises

Day One

1. Build a template to find all publications for a protein (Protein --> Publications).
   • Try:
     • changing the sort order
     • adding another constraint, eg. chromosome location or GO term
2. Build a template to find all proteins for a specified protein domain. (Start with the protein class).
3. Make ProteinDomain.name autocomplete in template forms.
4. Make the templates you create viewable by all users of your webapp.
5. Add the templates to the front page.
6. Create a list and add it to front page.
7. Add the Protein.features collection to the "Summary" section of the Protein report page.

Day Two

If you weren't able to add KEGG pathways to your database, you can do the exercises with another data type, eg. GO or protein domains.

1. Add a KEGG pathway displayer to the gene report page.
   • add entry to Gene section of malariamine/webapp/resources/webapp/WEB-INF/webconfig-model.xml.

     <displayer src="/model/keggDisplayer.jsp"/>
     

   • create a JSP file:

     <%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
     
     <!-- malariamine/webapp/resources/webapp/model/keggDisplayer.jsp -->
     <c:if test="${!empty object.pathways}">
     <h3>Pathways</h3>
     
     <!-- loop through the pathways -->
     <c:forEach items="${object.pathways}" var="item">
     
          <!-- eg. http://www.genome.jp/kegg-bin/show_pathway?pfa00030+PF13_0143 -->
          <a href="http://www.genome.jp/kegg-bin/show_pathway?pfa${item.identifier}+${object.primaryIdentifier}">${item.identifier}</a><br/>
     
     </c:forEach>
     
     </c:if>
     <!-- keggDisplayer.jsp -->
     
     

2. Add a pathway table widget to the gene list analysis page by adding this to the widget section of malariamine/webapp/resources/webapp/WEB-INF/webconfig-model.xml:

   <bagtabledisplayer id="" 
       title=""
       pathStrings="" 
       description="" 
       typeClass="" 
       displayFields="identifier,name" 
       exportField="primaryIdentifier" 
       externalLink="http://www.genome.jp/dbget-bin/www_bget?pathway+pfa" 
       externalLinkLabel="KEGG" />
   

3. On the Pathway report page, create link to the KEGG page for that pathway.
   • Add an entry to web.properties
   • The imageName is KEGG_logo_mini.gif and the image is already in the correct location
4. Set Pathway.name field to autocomplete on the template form and in the QueryBuilder.
5. In the QueryBuilder, when you click on the SUMMARY button next to the Pathway class, nothing happens. Update the properties file so that Pathway.identifier and Pathway.name are added to the view list when you click on the SUMMARY button. (Hint: webconfig-model.xml)
6. When the Pathway.identifier and Pathway.name fields appear on the results page, the fields are not links. Make those fields links to their report page. (Hint: class_keys.properties)
7. Update the examples displayed in the search box in the top menu bar with an example gene identifier, list name and template keyword. (Hint: web.properties)
8. Update the example identifiers added by the "click to see an example" link on the list upload page. (Hint: web.properties)