[InterMine Dev] malariamine tutorial error

Quang Trinh quang.trinh at gmail.com
Tue Oct 18 14:30:14 BST 2011


  THanks, it works now ( I had an extra character in my path ).

On Tue, Oct 18, 2011 at 4:02 AM, Julie Sullivan <julie at flymine.org> wrote:
>> 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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>>
>
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