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From Mansour Al Akeel <mansour.alak...@gmail.com>
Subject Re: Initializing and using clinical pipleline from java
Date Sat, 29 Nov 2014 15:54:56 GMT
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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