Version: 5.0.0

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

For example:

  <class className="org.intermine.model.bio.Gene">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="length"/>
      <fieldconfig fieldExpr="chromosomeLocation" showInResults="false" />
      <fieldconfig fieldExpr="chromosome.primaryIdentifier" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.start" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.end" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="organism.shortName" />
    </field

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="/>