[InterMine Dev] Error when loading biogrid data into intermine

Julie Sullivan julie at flymine.org
Tue Mar 20 12:53:07 GMT 2012


We process PSI v. 2.5 files, can you try those?

	BIOGRID-ORGANISM-Homo_sapiens-3.1.86.psi25.xml
	BIOGRID-ORGANISM-Mus_musculus-3.1.86.psi25.xml

 > 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

You can use InterMine's IntAct parser.  To process IntAct files, do the same 
thing as you did with biogrid:

  1. download the intact files
  2. add intact to your project XML file

On 20/03/12 10:54, wang su wrote:
> 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
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



More information about the dev mailing list