[InterMine Dev] malariamine tutorial error

Julie Sullivan julie at flymine.org
Tue Oct 18 09:02:27 BST 2011


 > dataDir is not a directory:uniprot

That meants the build is looking for the UniProt files in the directory 
`uniprot` but can't find them.

Check the UniProt entry in your project XML file is correct:

	<property name="src.data.dir" location="/data/uniprot"/>

And then make sure you have the UniProt files in that directory.


On 18/10/11 01:53, Quang Trinh wrote:
> Hi,
>    I am going through the malariamine tutorial and get this error
> message on step 7.1 ( ant -Dsource=uniprot-malaria -v ):
>
>
> BUILD FAILED
> /u/qtrinh/intermine/intermine_0_98/imbuild/integrate.xml:54: The
> following error occurred while executing this line:
> /u/qtrinh/intermine/intermine_0_98/bio/sources/uniprot/build.xml:24:
> dataDir is not a directory:uniprot
> 	at org.apache.tools.ant.ProjectHelper.addLocationToBuildException(ProjectHelper.java:541)
> 	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:419)
> 	at org.intermine.task.Integrate.performAction(Integrate.java:223)
> 	at org.intermine.task.Integrate.performAction(Integrate.java:135)
> 	at org.intermine.task.Integrate.execute(Integrate.java:127)
> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 	at sun.reflect.GeneratedMethodAccessor2.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:105)
> 	at org.apache.tools.ant.Task.perform(Task.java:348)
> 	at org.apache.tools.ant.Target.execute(Target.java:357)
> 	at org.apache.tools.ant.Target.performTasks(Target.java:385)
> 	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
> 	at org.apache.tools.ant.Project.executeTarget(Project.java:1298)
> 	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> 	at org.apache.tools.ant.Project.executeTargets(Project.java:1181)
> 	at org.apache.tools.ant.Main.runBuild(Main.java:698)
> 	at org.apache.tools.ant.Main.startAnt(Main.java:199)
> 	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> 	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
> Caused by: /u/qtrinh/intermine/intermine_0_98/bio/sources/uniprot/build.xml:24:
> dataDir is not a directory:uniprot
> 	at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:63)
> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 	at sun.reflect.GeneratedMethodAccessor2.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:105)
> 	at org.apache.tools.ant.Task.perform(Task.java:348)
> 	at org.apache.tools.ant.Target.execute(Target.java:357)
> 	at org.apache.tools.ant.Target.performTasks(Target.java:385)
> 	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
> 	at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> 	at org.apache.tools.ant.Project.executeTargets(Project.java:1181)
> 	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
> 	... 19 more
> --- Nested Exception ---
> /u/qtrinh/intermine/intermine_0_98/bio/sources/uniprot/build.xml:24:
> dataDir is not a directory:uniprot
> 	at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:63)
> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 	at sun.reflect.GeneratedMethodAccessor2.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:105)
> 	at org.apache.tools.ant.Task.perform(Task.java:348)
> 	at org.apache.tools.ant.Target.execute(Target.java:357)
> 	at org.apache.tools.ant.Target.performTasks(Target.java:385)
> 	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
> 	at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> 	at org.apache.tools.ant.Project.executeTargets(Project.java:1181)
> 	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
> 	at org.intermine.task.Integrate.performAction(Integrate.java:223)
> 	at org.intermine.task.Integrate.performAction(Integrate.java:135)
> 	at org.intermine.task.Integrate.execute(Integrate.java:127)
> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 	at sun.reflect.GeneratedMethodAccessor2.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:105)
> 	at org.apache.tools.ant.Task.perform(Task.java:348)
> 	at org.apache.tools.ant.Target.execute(Target.java:357)
> 	at org.apache.tools.ant.Target.performTasks(Target.java:385)
> 	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
> 	at org.apache.tools.ant.Project.executeTarget(Project.java:1298)
> 	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> 	at org.apache.tools.ant.Project.executeTargets(Project.java:1181)
> 	at org.apache.tools.ant.Main.runBuild(Main.java:698)
> 	at org.apache.tools.ant.Main.startAnt(Main.java:199)
> 	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> 	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
>
>    Could someone tell me how to get around this error message?
>
> Thanks,
>
> Q
>
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