Hi Jay, I've never seen that one before -- sounds like you're looking in the right place. The first thing I would try is to manually delete the cleartk-ml-liblinear folder in your .m2 directory and then do a mvn project update (from eclipse) or mvn clean compile (from cmd line) in case there was an issue with the downloaded jar. But that is kind of grasping at straws -- hopefully someone else will have some other things to try.
Tim ________________________________________ From: Jay Urbain <[email protected]> Sent: Tuesday, March 1, 2016 7:21 AM To: [email protected] Subject: ctakes uimafit analysis engine resource initialization errors 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
