I'm trying to run the AggregatePlaintextUMLSProcessor AE in Eclipse. - ctakes 3.2.3-SNAPSHOT
I'm getting ctakes uimafit analysis engine resource initialization errors. First, I have no compile errors, and I'm using the developer version of ctakes "out of the box," i.e., with know modifications except correcting maven dependency errors. I've been struggling resolving the following ResourceInitializationException: 3/1/16 5:31:44 AM - 18: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine" failed. (Descriptor: file:/Users/jayurbain/Dropbox/apache-ctakes-3.2.2/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml) org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine" failed. (Descriptor: file:/Users/jayurbain/Dropbox/apache-ctakes-3.2.2/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml) The failure is caused by: Caused by: java.lang.ClassNotFoundException: org.cleartk.ml.liblinear.LibLinearStringOutcomeClassifierBuilder at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:264) at org.cleartk.ml.jar.JarClassifierBuilder.fromManifest(JarClassifierBuilder.java:105) ... 61 more The code fails here: public class HistoryCleartkAnalysisEngine extends AssertionCleartkAnalysisEngine { boolean USE_DEFAULT_EXTRACTORS = false; @Override public void initialize(UimaContext context) throws ResourceInitializationException { super.initialize(context); // <--- fails here --- probabilityOfKeepingADefaultExample = 0.5; initialize_history_extractor(); initializeFeatureSelection(); } In the past, I've been able to fix these errors by fixing a missing dependency or by adding a specific version declaration to a dependency. Here's the declaration in AggregatePlaintextUMLSProcessor.xml: <delegateAnalysisEngine key="HistoryCleartkAnalysisEngine"> <import location="../../../ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml"/> The HistoryCleartkAnalysisEngine.xml is automatically generated by uimaFIT. I have the cleartk-ml-liblinear-2.0.0.jar in my .m2 repository. I have the following dependency in the ctakes-assert and the ctakes-clinical-pipeline pom.xml: <dependency> <groupId>org.cleartk</groupId> <artifactId>cleartk-ml</artifactId> <version>2.0.0</version> </dependency> Any guidance would be apprecaited. Thanks, Jay Urbain