[InterMine Dev] ensembl-compara in 1.1

julie at flymine.org julie at flymine.org
Thu Oct 25 17:10:39 BST 2012


We moved ensembl-compara to a subdirectory:

https://github.com/intermine/intermine/tree/master/bio/sources/ensembl

But that's not being reflected in your checkout for some reason. Can you
manually remove "bio/sources/ensembl-compara" for now?

I'll research how to fix this in git.

> 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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