Data and Widget Configuration
==========================================

The `webconfig-model.xml` file configures aspects of how data appears on the InterMine webapp.

This file allows for inheritance - a subclass will inherit from its parent class but only if that subclass has no configuration.  Configuration settings for the parent class do not overwrite settings for the subclass.

Field Configuration
----------------------

You can configure which fields are displayed on report and result pages for each class in your model.  

======================  ========================================================================  =========  ==============================
attribute name          purpose                                                                   required?  default
======================  ========================================================================  =========  ==============================
fieldExpr               field name                                                                yes        -
label                   human readable name                                                       no         generated automagically
showInInlineCollection  show field in inline collection (on report pages)                         no         true
showInSummary           add field to query when user clicks on 'Summary' button in  QueryBuilder  no         true
showInResults           show field in results table                                               no         true
outerInSummary          configure outer-joins when user clicks on 'Summary' in QueryBuilder       no         false
doNotTruncate           don't truncate display                                                    no         false
fieldExporter           specify class to export file field                                        no         -
sectionOnRight          show on the right side of the page                                        no         false
sectionTitle            if sectionOnRight="true", title for section on right                      no         -
openByDefault           if sectionOnRight="true", whether or not this section should be open      no         false
======================  ========================================================================  =========  ==============================

For example:

.. code-block:: guess

	  <class className="org.flymine.model.genomic.Protein">
 	    <fields>
 	      <fieldconfig fieldExpr="primaryIdentifier"/>
 	      <fieldconfig fieldExpr="primaryAccession"/>
 	      <fieldconfig fieldExpr="organism.name"/>
 	      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
 	    </fields>
 	    <bagdisplayers>
 	     < -- attribute links can now be displayed on protein list analysis pages -->
 	     <displayer src="attributeLinkDisplayer.tile"/>
 	    </bagdisplayers>
 	  </class>


Displaying Data on Report pages
--------------------------------------------

ReportDisplayers allow custom display of particular data types on report pages, typically to replace default tables with more appropriate presentation of data. 

.. code-block:: xml

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer"
                     jspName="model/cytoscapeNetworkDisplayer.jsp"
                     replacesFields="interactions"
                     placement="Interactions"


Export Configuration
----------------------

Users can export data from InterMine in comma or tab-delimited files.  InterMine also allows for the addition of custom exporters.  To add a custom exporter, create a Java class to format the data and add an entry to the web config file, for example:

.. code-block:: xml

  <tableExportConfig id="sequenceExporter" actionPath="/exportAction?type=sequenceExporter"
                     className="org.intermine.bio.web.export.SequenceHttpExporter"/>
  <tableExportConfig id="gff3Exporter" actionPath="/exportAction?type=gff3Exporter"
                     className="org.intermine.bio.web.export.GFF3HttpExporter"/>


Widget Configuration
----------------------

At the bottom of the config file are the configuration entries for widgets.  Please see [wiki:Widgets] for detailed information about how to configure widgets.

.. code-block:: xml

      <enrichmentwidgetdisplayer id="publication_enrichment"
                                 title="Publication Enrichment"
                                 description="Publications enriched for genes in this list."
                                 label="Publication"
                                 startClass="Gene"
                                 startClassDisplay="primaryIdentifier"
                                 enrich="publications.title"
                                 enrichIdentifier="publications.pubMedId"
                                 constraints="organism.name=[list],primaryIdentifier  = null"
                                 typeClass="org.intermine.model.bio.Gene"
                                 views="secondaryIdentifier, symbol, organism.name,
                                       publications.title, publications.firstAuthor,
                                       publications.journal, publications.year, publications.pubMedId"
                                 externalLink="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids="/>

.. index:: widgets, exporters, report displayers, webconfig-model.xml