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From Pei Chen <chen...@apache.org>
Subject Re: ctakes uimafit analysis engine resource initialization errors
Date Tue, 01 Mar 2016 16:31:12 GMT
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
<Timothy.Miller@childrens.harvard.edu> 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 <jay.urbain@gmail.com>
> Sent: Tuesday, March 1, 2016 7:21 AM
> To: dev@ctakes.apache.org
> 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

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