I have downloaded 3.2.2 bin. In InteliJ IDE, I have added all JAR's from \lib, and trying to run /ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java.
For running the code, I right click on BagOfCUIsGenerator.java file and select run option. Here is the log --> Loading configuration. Loading feature templates. Loading lexica. Loading model: ........................................................................................ 20 May 2015 15:20:11 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 20 May 2015 15:20:11 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 20 May 2015 15:20:11 INFO ConstituencyParser - Initializing parser... 20 May 2015 15:20:16 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 20 May 2015 15:20:16 INFO StatusContextAnalyzer - initBoundaryData() called for ContextInitializer 20 May 2015 15:20:16 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 20 May 2015 15:20:16 INFO NegationContextAnalyzer - initBoundaryData() called for ContextInitializer Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine" failed. (Descriptor: file:/E:/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml) 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.produceResource(UIMAFramework.java:314) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineFromPath(AnalysisEngineFactory.java:773) at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:60) at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:54) at BagOfCUIsGenerator.<init>(BagOfCUIsGenerator.java:20) at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:54) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134) Caused by: org.apache.uima.resource.ResourceInitializationException at org.cleartk.ml.CleartkAnnotator.initialize(CleartkAnnotator.java:137) at org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.initialize(AssertionCleartkAnalysisEngine.java:192) at org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine.initialize(SubjectCleartkAnalysisEngine.java:44) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 24 more Caused by: java.io.FileNotFoundException: \org\apache\ctakes\assertion\models\subject\model.jar (The system cannot find the path specified) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(FileInputStream.java:146) at java.io.FileInputStream.<init>(FileInputStream.java:101) at org.cleartk.ml.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:69) at org.cleartk.ml.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35) at org.cleartk.ml.CleartkAnnotator.initialize(CleartkAnnotator.java:135) ... 27 more Process finished with exit code 1 On Wed, May 20, 2015 at 7:48 PM, Miller, Timothy < [email protected]> wrote: > What version are you using? Did you download src or bin? And what command > did you use to run it? > Thanks > Tim > > > On 05/20/2015 01:24 AM, Sangram Patil wrote: > > Hi, > > I pretty new to Java and cTakes !!! > > I am trying to run > /ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java, > but I am getting error - > org.apache.uima.resource.ResourceInitializationException: Initialization > of annotator class > "org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE" > failed. (Descriptor: > file:/E:/ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml > ) > > I have tried to run example in Intellij and Eclipse as well. I am > getting the same error. When I googled, the reason showed is classpath need > to be mentioned, that didn't solve the problem. > > Could you please provide me any direction and information. > > -- > > Sincerely, > Sangram Patil > > > > > > > -- ** Please include your practice ID in your correspondence.* Sincerely, Sangram Patil Team Lead-Core Dev Cell: +91 992 293 9497 figmd.com <http://www.figmd.com/> CONFIDENTIALITY NOTICE <http://www.figmd.com/terms/>
