[InterMine Dev] ensembl-compara in 1.1

Julie Sullivan julie at flymine.org
Fri Oct 26 08:54:37 BST 2012


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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