cTakes - hsqldb connection problem
Hi, I have done following to get cTakes working. 1. Created java project 2. Created java class 3. Instanciated BagOfCUIsGenerator class with two arguments, input folder and output folder. 4. Added all required files in this java project. When I try to run application I am getting following error. I ran application in 'Debug' mode and I traced exception. I found out that exception is raised in JdbcConnectionResourceImpl.java file at line number 109, iv_conn is null. It seems that application is not properly connecting to hsqldb database. Error is as follows *Loading model:* *.* *Loading configuration.* *Loading feature templates.* *Loading lexica.* *Loading model:* ** *Loading model:* *.* *Exception in thread main org.apache.uima.resource.ResourceInitializationException* * at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)* * at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)* * at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)* * at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)* * 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:123)* * 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 org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.init(BagOfCUIsGenerator.java:34)* * at com.krixi.cTakesDemo.main(cTakesDemo.java:12)* * 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.sql.SQLException: File input/output error /org/apache/ctakes/dictionary/lookup/umls2011ab/umls.properties java.lang.NullPointerException* * at org.hsqldb.jdbc.Util.sqlException(Unknown Source)* * at org.hsqldb.jdbc.jdbcConnection.init(Unknown Source)* * at org.hsqldb.jdbcDriver.getConnection(Unknown Source)* * at org.hsqldb.jdbcDriver.connect(Unknown Source)* * at java.sql.DriverManager.getConnection(DriverManager.java:571)* * at java.sql.DriverManager.getConnection(DriverManager.java:215)* * at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109)* * ... 28 more* *Process finished with exit code 1* Please help me.
Apache cTAKES - ResourceInitializationException
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
