[InterMine Dev] Error when loading biogrid data into intermine

wang su wangsu0623 at gmail.com
Tue Mar 20 10:54:16 GMT 2012


Hi all,

I downloaded Biogrid Interact data from http://thebiogrid.org/download.php, I want to load  BIOGRID-ORGANISM-Homo_sapiens-3.1.86.psi.xml and BIOGRID-ORGANISM-Mus_musculus-3.1.86.psi.xml into my database built by InterMine.

I add the 

   <source name="biogrid" type="biogrid">
      <property name="src.data.dir" location="/mnt/Storage/home/wangs/dev/pathmine/data/Biogrid/"/>
      <property name="src.data.dir.includes" value="*.psi.xml"/>
    </source>

 in the project.xml, then add the
# human
9606.symbol = shortLabel

# mouse
10090.symbol = shortLabel
in dev/bio/sources/biogrid/main/resources/biogrid_config.properties

in order to display it, I added

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

in /dev/pathmine/webapp/resources/webapp/WEB-INF/webconfig-model.xml

but when I run the ant -v -Dsource=all

it said 

-set-custom-file-includes:
Skipped because property 'src.data.dir.includes' set.

-set-custom-file-excludes:

-retrieve-tgt-from-custom-file:
[integrate] Processing file: /mnt/Storage/home/wangs/dev/pathmine/data/Biogrid/Homo_sapiens.psi.xml
     [null] Exiting /mnt/Storage/home/wangs/dev/bio/sources/biogrid/build.xml.

BUILD FAILED
/mnt/Storage/home/wangs/dev/imbuild/integrate.xml:54: The following error occurred while executing this line:
/mnt/Storage/home/wangs/dev/imbuild/source.xml:145: java.lang.NullPointerException
	at org.intermine.bio.dataconversion.BioGridConverter.process(BioGridConverter.java:112)
	at org.intermine.task.FileConverterTask.execute(FileConverterTask.java:118)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:348)
	at org.apache.tools.ant.Target.execute(Target.java:390)
	at org.apache.tools.ant.Target.performTasks(Target.java:411)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
	at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
	at org.intermine.task.Integrate.performAction(Integrate.java:223)
	at org.intermine.task.Integrate.performAction(Integrate.java:135)
	at org.intermine.task.Integrate.execute(Integrate.java:127)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:348)
	at org.apache.tools.ant.Target.execute(Target.java:390)
	at org.apache.tools.ant.Target.performTasks(Target.java:411)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
	at org.apache.tools.ant.Main.runBuild(Main.java:801)
	at org.apache.tools.ant.Main.startAnt(Main.java:218)
	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

Can you help me to solve this error.

In addition, if I want to load the intAct data into it, do I need to build a source named intact like http://intermine.org/wiki/BioSources


Thanks very much!

Best wishes!
Su


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