InterMine Project Description File Format

What this file governs

The Project XML File Format

• properties
  • target.model
    • the name of the model created and used by this project
  • common.os.prefix
    • used by the integration system to choose which database properties to use
  • intermine.properties.file
    • the name of the file in the home directory which contains properties such as database name, user names and passwords.
    • These properties override the contents of default.intermine.properties.file.
  • default.intermine.properties.file
    • the location of the default properties for this mine
• sources
  • The sources element gives a list of sources to integrate along with any properties specific to those sources.
  • Properties within the <source> tag are used only when processing the given source and will override any properties in the source's project.properties file.

See: BioSources

• Post processing
  • These are tasks that run after the data loading is completed.
  • They are used to set calculate/set fields that are difficult to do when data loading or that require multiple sources to be loaded.

See: PostProcessing

A short example

<project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="flymine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>
    <source name="wormbase-identifiers" type="wormbase-identifiers">
      <property name="src.data.dir" location="/shared/data/wormbase/current"/>
    </source>
  </sources>
  <post-processing>
    <post-process name="make-spanning-locations"/>
    <post-process name="create-chromosome-locations-and-lengths"/>
    <post-process name="create-overlap-relations-flymine" dump="true"/>
    <post-process name="do-sources"/>
  </post-processing>
</project>

For a more complete example, see flymine/project.xml which covers all the projects currently available in the model.

See also: RunningABuild