[InterMine Dev] ensembl-compara in 1.1

Kalpana Karra kkarra at stanford.edu
Thu Oct 25 16:54:55 BST 2012


Looks like ensembl-compara source is in places and causing problems?
bio/sources/ensembl-compara and bio/sources/ensembl/ensembl-compara

Which one should I delete?

Also, will the same config in project.xml work?
This is what I have..

<source name="ensembl-compara" type="ensembl-compara">
      <property name="src.data.dir" location="/Users/kkarra/share/intermine/data/yeast_orthologs/ensembl_compara"/>
      <property name="ensemblcompara.organisms" value="4932"/>
      <property name="ensemblcompara.homologues" value="9606 7227 6239 10090 10116 7955"/>
</source>


When I run ..
ant -v clean build-db -Drelease=prod

I get the following error..
BUILD FAILED
/Users/kkarra/Dev/intermine/imbuild/objectstore.xml:151: Error in project.xml: multiple directories found for source 'ensembl-compara'.  Each source type must be uniquely named within the 'source.location' directories specified. Found in: 
		/Users/kkarra/Dev/intermine/bio/sources
		/Users/kkarra/Dev/intermine/bio/sources/ensembl/bin
	at org.intermine.task.project.Project.validate(Project.java:181)
	at org.intermine.task.project.ProjectXmlBinding.unmarshall(ProjectXmlBinding.java:58)
	at org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:113)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	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:392)
	at org.apache.tools.ant.Target.performTasks(Target.java:413)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
	at org.apache.tools.ant.Main.runBuild(Main.java:811)
	at org.apache.tools.ant.Main.startAnt(Main.java:217)
	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

Total time: 18 seconds




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