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From britt fitch <britt.fi...@wiredinformatics.com>
Subject Re: Initializing and using clinical pipleline from java
Date Mon, 01 Dec 2014 16:07:26 GMT
Hi Mansour, 
One other option is you can use the attached pom.xml which essentially downloads and unpacks
the full LVG (~350MB) on your behalf.



Cheers,

Britt


 	 	 	 
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com

On Dec 1, 2014, at 11:02 AM, britt fitch <britt.fitch@wiredinformatics.com> wrote:

> 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 Fitch
> Wired Informatics
> 265 Franklin St Ste 1702
> Boston, MA 02110
> http://wiredinformatics.com
> Britt.Fitch@wiredinformatics.com
> 
> On Nov 29, 2014, at 10:54 AM, Mansour Al Akeel <mansour.alakeel@gmail.com> wrote:
> 
>> 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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