Hi, I want to parse clinical documents using Apache cTAKES. I have a set of clinical documents as plain texts. For this, I am using BagOfCUIsGenerator.java and cTAKES jars. I configured this in IntelliJ IDEA as a java project.
When I try to run, I am getting exception and error as follows. Output: *log4j:WARN No appenders could be found for logger (org.springframework.validation.DataBinder).* *log4j:WARN Please initialize the log4j system properly.* *log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig <http://logging.apache.org/log4j/1.2/faq.html#noconfig> for more info.* *Loading configuration.* *Loading feature templates.* *Loading lexica.* *Loading model:* *........................................................................................* *Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine" failed. (Descriptor: file:/D:/Dev/Savy/java_projects/cTakes/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:251)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:155)* * 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:21)* * at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:61)* * 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: java.lang.NullPointerException* * at java.io.Reader.<init>(Reader.java:78)* * at java.io.InputStreamReader.<init>(InputStreamReader.java:72)* * at java.util.Scanner.<init>(Scanner.java:608)* * at org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor.<init>(ContextWordWindowExtractor.java:55)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize_history_extractor(HistoryCleartkAnalysisEngine.java:58)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize(HistoryCleartkAnalysisEngine.java:49)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:249)* * ... 24 more* *Process finished with exit code 1* Please help. Thanks Pankaj Shinde
