Report Displayers

Note Report Displayers Examples

Report displayers allow custom display of particular data types on report pages (only), typically to replace default tables with more appropriate presentation of data.

Widgets:

1. Use a simple framework to add a JSP for display and optionally Java code to run queries, hold caches, etc.
2. Are assigned to the summary section at the top of the page or a particular data category
3. Can replace fields from the report page to override default display of attributes or collections
4. Are configured in the webconfig-model.xml file in your Mine

This page describes how to configure your Mine to include widgets for common data types and how to create your own custom widget.

Configuring displayers

Configuration is placed in a <reportdisplayers> section of webconfig-model.xml:

<reportdisplayers>

<reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"

jspName="model/geneOntologyDisplayer.jsp"

replacesFields="goAnnotation,ontologyAnnotations"

placement="Function"

types="Gene"/>

</reportdisplayers>

javaClass

an optional Java class to run before display, typically, this performs database queries or creates data structures used by the JSP. The class should extend ReportDisplayer and implement a display() method.

jspName

the JSP file used to display output

replacesFields

a comma separated list of fields that should not appear on the report page when the displayer is used

showImmediately

set to true to display the displayer immediately as the page loads, without waiting (false by default)

placement

the section on the report page the displayer should appear in, can be 'summary' or a valid data category name.

types

a comma separated list of class names for this displayer can be used

parameters

this is a JSON string used to pass arbitrary parameters to particular displayers, you can make use of this for detailed configuration of any displayers you write. For example, the HomologueDisplayer.java is passed a list of data sets to displayer homologues from: parameters="{'dataSets': ['TreeFam data set', 'KEGG orthologues data set']}".

Useful displayers

There are several displayers for common data types that may be useful in many Mines. To enable these, just copy the configuration from FlyMine's webconfig-model.xml.

For examples of the common displayers and configuration details please see Report Displayers Examples.

Creating a new Displayer

If you've loaded some new data into your Mine or have some great ideas about presenting data from the common data loaders, you can create a new displayer. Here are brief instructions, take a look at the many examples for more details.

1. Create a Java class [1] in your mine, e.g. /displayers that inherits from org.intermine.web.displayer.ReportDisplayer.

2. Implement

   public void display(HttpServletRequest request, ReportObject reportObject)

   to perform any queries or processing required and put results on the

   request.

3. Create a JSP file in webapp/src/main/webapp/model to display the results.

4. Add configuration to

   webapp/src/main/webapp/WEB-INF/webconfig-model.xml to set up the javaClass and jspName created above and set the types for which the displayer should appear and the summary or a data category (aspect) as the placement for the displayer. Optionally set any fields in the report page that should be hidden when this displayer is used.

Troubleshooting

As we use AJAX to load the displayers to speed up the initial load of a Report page, JavaScript calls to when a document is ready are executed immediately the page has finished loading already. Specifically when using GoogleCharts API, one needs to amend the initial loading code with a callback like so:

google.load("visualization", "1", {"packages": ["corechart"], "callback": drawFlyAtlasChart});

[1] ReportDisplayer makes available a variable called im which is the InterMineAPI which provides access to config and query execution classes.