Version: 4.0.0

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 automatically
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:

<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.

<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:

<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.

<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="/>