That didn't to it. But _thanks_!
Jay On Tue, Mar 1, 2016 at 6:53 AM, Miller, Timothy < [email protected]> wrote: > 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 >
