I added the cleartk-ml-liblinear dependency you provided to ctakes-assertion/pom.xml. That did not work.
I then added the dependency to ctakes-clinical-pipeline/pom.xml and that did the trick. Many thanks. Jay On Tue, Mar 1, 2016 at 10:31 AM, Pei Chen <[email protected]> wrote: > Also, check that the liblinear dependency is in your pom.xml (it > should already be included in ctakes-assertion/pom.xml). > <dependency> > <groupId>org.cleartk</groupId> > <artifactId>cleartk-ml-liblinear</artifactId> > </dependency> > > On Tue, Mar 1, 2016 at 7:53 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 >
