Guide to Customising your Web Application

• Guide to Customising Blue Genes
• Home page
  • Boxes Customization
  • Popular Templates Customization
  • Featured Lists
  • RSS/Blog Feed
• Report page
  • Report Page
  • Report Displayers
  • Report Displayers Examples
  • Webapp Tables CSS & HTML
  • Report Widgets
• Lists
  • Lists page
  • List upload
  • List upgrade
  • List analysis
  • List Widgets
• Template Queries
  • Dropdowns
  • Auto-completion
  • Optional constraints
  • Templates page
• Query Results
  • export
  • column headers
  • links
  • weird brackets
  • The initial Page Size
  • Icons
  • The initial state of Sub-Tables
  • Cell Formatters
  • Branding
• QueryBuilder
  • Select a Data Type to Begin a Query
  • query builder
  • Hiding fields
• Keyword Search
  • Config file
  • Search Results
  • Search Index
  • Lucene
• General Layout
  • Parts
  • Changing look and feel, the theme
• Region Search
  • Configuration
  • Region Search V2
  • Adding the strand specific search option
• Customise Web Application
  • Database and Web application
  • Text and messages
  • Features
  • Data and Widget Configuration
  • Class keys
  • Setting Javascript Options
• Data Categories
  • Aspects.xml
  • Configuration
  • Data page/tab
• Help
  • Top Links
  • Take a tour link
  • Contextual help, the ? on each page
  • Data definitions
• Linking in to your mine
  • Link directly to query results
  • Link to List Analysis page
  • Query builder
  • Report page
  • Link into Mine with Orthologues
  • Convert any identifiers to Genes
  • More examples
• Third party tools
  • Cytoscape network viewer
  • EsyN
  • Galaxy
  • GBrowse
  • Heatmap
  • JBrowse
• Monitoring Site Usage
  • Google Analytics
  • InterMine User Tracking
  • Search engines
• Website Admin
  • Templates
  • Tagging
• User Accounts
  • Userprofile
  • Open ID
• Performance
  • Setting up your own Content Delivery Network
• Diagnostic
  • Restart Tomcat
  • Verify MINE.properties file
  • Verify Tomcat config
  • Force recompile
  • Re-release webapp
• Building Javadoc
  • Package-specific Javadoc
  • Intermine Javadoc
  • Using Travis to auto-deploy Javadoc to GitHub Pages
• Customising the default queries in your io-docs application

Overwrite any JSP

When the webapp is compiled, the order of projects is:

1. intermine/webapp
2. bio/webapp <– overwrites files in intermine/webapp
3. MINE_NAME/webapp <– overwrites files in intermine/webapp and bio/webapp

You can overwrite any JSP in the intermine or bio/webapp projects by having a JSP of the same name in your mine’s webapp directory. The danger of this is that you will have to upgrade these JSPs manually.