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Posted to user@ctakes.apache.org by Prasanna Bala <ba...@gmail.com> on 2014/04/01 13:13:01 UTC
cTakes eclipse compile problem...
Hi,
I am having a problem compiling and running the developer version of cake
3.1.1-src. I actually import the ctakes src in the eclipse and built it
using maven and then compile it. I am able to run and compile for the first
time in eclipse. But when I closed the eclipse and restarted the eclipse
again, I run the eclipse for the developer version, I am getting the
following problem.
Can someone tell me why I am getting this error ?
java.io.FileNotFoundException:
org/apache/ctakes/dictionary/lookup/rxnorm_index
Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:80)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at
org.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineFromPath(AnalysisEngineFactory.java:147)
at
org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:42)
at
org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:36)
at
org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.<init>(BagOfCUIsGenerator.java:16)
at
org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:49)
Caused by: java.io.FileNotFoundException:
org/apache/ctakes/dictionary/lookup/rxnorm_index
at
org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:93)
at
org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:68)
at
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:58)
... 22 more
This happened repeatedly such that I have to delete the existing workspace
in eclipse and import the project again. I did this twice to run the
application.
Regards,
Prasanna
Re: cTakes eclipse compile problem...
Posted by Pei Chen <ch...@apache.org>.
Prasanna,
If this is running within Eclipse IDE, within the
ctakes-dictionary-lookup/pom.xml, there is a goal to automatically download
and unpack the resources from maven central for you.
the rx_norm folder/files should have been unpacked. If they are missing,
this process most likely did not complete successfully (it does take time
for the several hundred MB). You can try to manually invoke it again via
project>run-as>maven>compile or similar or from the command line mvn clean
compile and refresh your work space.
Perhaps, there may be a better place to place these files other than
target. Open to ideas..
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>unpack-dependencies</id>
<phase>process-resources</phase>
<goals>
<goal>unpack-dependencies</goal>
</goals>
<configuration>
<includeArtifactIds>ctakes-resources-umls2011ab</includeArtifactIds>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
On Tue, Apr 1, 2014 at 7:13 AM, Prasanna Bala
<ba...@gmail.com>wrote:
> Hi,
>
> I am having a problem compiling and running the developer version of cake
> 3.1.1-src. I actually import the ctakes src in the eclipse and built it
> using maven and then compile it. I am able to run and compile for the first
> time in eclipse. But when I closed the eclipse and restarted the eclipse
> again, I run the eclipse for the developer version, I am getting the
> following problem.
>
> Can someone tell me why I am getting this error ?
>
> java.io.FileNotFoundException:
> org/apache/ctakes/dictionary/lookup/rxnorm_index
>
>
> Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException
> at
> org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:80)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
> at
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
> at
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
> at
> org.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineFromPath(AnalysisEngineFactory.java:147)
> at
> org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:42)
> at
> org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:36)
> at
> org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.<init>(BagOfCUIsGenerator.java:16)
> at
> org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:49)
> Caused by: java.io.FileNotFoundException:
> org/apache/ctakes/dictionary/lookup/rxnorm_index
> at
> org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:93)
> at
> org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:68)
> at
> org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:58)
> ... 22 more
>
>
>
> This happened repeatedly such that I have to delete the existing workspace
> in eclipse and import the project again. I did this twice to run the
> application.
>
> Regards,
> Prasanna
>