Cheers,
Britt
Britt FitchWired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
Hi Mansour, I am assuming you are trying to run this in a local development environment such as Eclipse IDE or similar? I had a closer look at ctakes-lvg-res/pom.xml, it looks like it tries to unpack a dummy lvg dictionary anyway. That probably isn't very useful for you; might as well just comment out the optional lvg component from your pipeline.
Cheers,
Britt
Britt FitchWired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
I solved this but got another error. I created the pipeline manually,
and used the File constuctory File(URL.toString()) instead of
File(URI):
private static AnalysisEngineDescription
createAnnotatorDescription() throws ResourceInitializationException
{
AggregateBuilder chunkAdjusterBuilder = new AggregateBuilder();
chunkAdjusterBuilder.add(ChunkAdjuster.createAnnotatorDescription(new
String[] { "NP", "NP" }, 1));
chunkAdjusterBuilder.add(ChunkAdjuster.createAnnotatorDescription(new
String[] { "NP", "PP", "NP" }, 2));
AnalysisEngineDescription chunkAdjusterAnnotator =
chunkAdjusterBuilder.createAggregateDescription();
URL lvgPropertiesURL =
LvgCmdApiResourceImpl.class.getResource("/org/apache/ctakes/lvg/data/config/lvg.properties");
File propertiesFile = new File(lvgPropertiesURL.toString());
AnalysisEngineDescription lvgAnalysisEngineDescription =
AnalysisEngineFactory.createPrimitiveDescription(LvgAnnotator.class,
LvgAnnotator.PARAM_USE_CMD_CACHE, false,
LvgAnnotator.PARAM_USE_LEMMA_CACHE, false,
LvgAnnotator.PARAM_USE_SEGMENTS, false,
LvgAnnotator.PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF, 20,
LvgAnnotator.PARAM_LEMMA_FREQ_CUTOFF, 20,
LvgAnnotator.PARAM_POST_LEMMAS, false,
LvgAnnotator.PARAM_LVGCMDAPI_RESRC_KEY,
ExternalResourceFactory.createExternalResourceDescription(LvgCmdApiResourceImpl.class,
propertiesFile));
AggregateBuilder tokenizerPipeLine = new AggregateBuilder();
tokenizerPipeLine.add(SimpleSegmentAnnotator.createAnnotatorDescription());
tokenizerPipeLine.add(SentenceDetector.createAnnotatorDescription());
tokenizerPipeLine.add(TokenizerAnnotatorPTB.createAnnotatorDescription());
tokenizerPipeLine.add(lvgAnalysisEngineDescription);
tokenizerPipeLine.add(ContextDependentTokenizerAnnotator.createAnnotatorDescription());
tokenizerPipeLine.add(POSTagger.createAnnotatorDescription());
tokenizerPipeLine.add(Chunker.createAnnotatorDescription());
tokenizerPipeLine.add(chunkAdjusterAnnotator);
AggregateBuilder clinicalBuilder = new AggregateBuilder();
clinicalBuilder.add(tokenizerPipeLine.createAggregateDescription());
clinicalBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
clinicalBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
clinicalBuilder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
clinicalBuilder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
clinicalBuilder.add(PolarityCleartkAnalysisEngine.createAnnotatorDescription());
return clinicalBuilder.createAggregateDescription();
}
The error is still in intializing the lvgAnalysisEngineDescription:
java.lang.NullPointerException
at gov.nih.nlm.nls.lvg.Lib.Configuration.SetConfiguration(Configuration.java:105)
at gov.nih.nlm.nls.lvg.Lib.Configuration.<init>(Configuration.java:34)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitConfigVars(LvgCmdApi.java:1506)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1428)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:86)
at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:89)
at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:620)
at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:456)
at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:193)
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:131)
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:279)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:430)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:374)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:187)
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:279)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:430)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:374)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:187)
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:279)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
....
On the console, I get this err message:
** Configuration Error:
/home/mansour/workspace/test/diagnosis/jar:file:/home/mansour/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file:
'/home/mansour/workspace/test/diagnosis/jar:file:/home/mansour/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
I am not sure why it's adding the
"/home/mansour/workspace/test/diagnosis/" to the URL
"jar:file:/home/mansour/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties"!
Any advice ?
Thank you.
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pom.xml