[InterMine Dev] ensembl-compara in 1.1

Julie Sullivan julie at flymine.org
Tue Oct 30 10:42:46 GMT 2012


Sorry Kalpana,

Can you remove this directory:

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

I think we have git set up to ignore all /bin directories so that directory 
wasn't removed properly.

Try again?

On 26/10/12 19:11, Kalpana Karra wrote:
> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> dev at intermine.org
>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>>
>>>>>
>>>
>>>
>
>



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