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From Jay Urbain <jay.urb...@gmail.com>
Subject Re: ctakes uimafit analysis engine resource initialization errors
Date Tue, 01 Mar 2016 18:47:56 GMT
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 <chenpei@apache.org> 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
> <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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