Hi, I am also new to cTakes and I would appretiate any help, since I want to begin using it programatically.
I am trying to run the ExampleAggregatePipeline. Everything works fine with the line: builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline()); However, it fails when I change it to: builder.add(ClinicalPipelineFactory.getDefaultPipeline()); 1. There is no "Failed to initilize. Invalid UMLS License” error (or at least, it is not visible) 2. ctakes.umlsuser and takes.umlspw are set in DictionaryLookupAnnotatorUMLS.xml 3. I am not using proxy and I am not behind a firewall 4. .../lookup/umls2011ab/umls does contain a data file 5. I am running the VM with the args: -Dctakes.umlsuser=MYUsername -Dctatkes.umlspw=ThePASSWORD 6. I can login to a https://uts-ws.nlm.nih.gov/home.html The error I get is similar to: http://t232398.apache-ctakes-development.apachetalk.us/question-about-cpe-descriptor-and-xml-file-t232398.html That is: Loading configuration. Loading feature templates. Loading lexica. Loading model: ........................................................................................ 17 May 2015 08:11:15 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 17 May 2015 08:11:19 INFO JdbcConnectionResourceImpl - Connection established to: jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls 17 May 2015 08:11:19 INFO JdbcConnectionResourceImpl - Connection established to: jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls 17 May 2015 08:11:19 INFO JdbcConnectionResourceImpl - Connection established to: jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/orange_book_hsqldb/umls 17 May 2015 08:11:19 INFO UmlsDictionaryLookupAnnotator - Parsing descriptor: /Users/damir/Documents/workspace/ctakes/ctakes-dictionary-lookup-res/target/classes/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml 17 May 2015 08:11:19 INFO FirstTokenPermLookupInitializerImpl - Exclusion tagset loaded: [pp, pdt, prp$, vbn, vbp, wdt, ls, vbz, dt, pos, md, wp, cc, cd, in, pp$, wrb, vb, prp, ex, vbd, vbg, to, wps, rp] 17 May 2015 08:11:19 INFO FirstTokenPermLookupInitializerImpl - Exclusion tagset loaded: [cc, pp, cd, pdt, vbn, vbp, in, pp$, wdt, wrb, ls, vb, vbz, dt, ex, pos, md, vbd, wp, vbg, to, wps, rp] 17 May 2015 08:11:19 INFO UmlsDictionaryLookupAnnotator - Using ctakes.umlsaddr: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser: null Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor: <unknown>) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) 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: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: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.produceResource(UIMAFramework.java:314) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:205) at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:226) at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259) at org.apache.ctakes.examples.pipelines.ExampleAggregatePipeline.main(ExampleAggregatePipeline.java:41) Caused by: org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:83) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 34 more Caused by: java.lang.NullPointerException at java.net.URLEncoder.encode(URLEncoder.java:204) at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:92) at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:74) ... 35 more ….. What am I doing wrong ???
