[InterMine Dev] ensembl-compara in 1.1

Kalpana Karra kkarra at stanford.edu
Fri Oct 26 19:11:18 BST 2012


If I change type back to ensembl-compara, I still get the error..

ant clean build-db -Drelease=prod

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/ensembl/bin
		/Users/kkarra/Dev/intermine/bio/sources/ensembl

Total time: 15 seconds


On Oct 26, 2012, at 12:54 AM, Julie Sullivan wrote:

> You probably want to change type back to ensembl-compara.
> 
> The build will look for a source using the type (which will fail) then source name - which is successful.
> 
> On 25/10/12 17:24, Kalpana Karra wrote:
>> 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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