[InterMine Dev] ensembl-compara in 1.1

Kalpana Karra kkarra at stanford.edu
Thu Oct 25 17:24:53 BST 2012


Yes, removed that directory and changed type to reflect sub-directory..
   
<source name="ensembl-compara" type="ensembl/ensembl-compara">


On Oct 25, 2012, at 9:10 AM, julie at flymine.org wrote:

> 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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>> 
>> 




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