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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: ctakes uimafit analysis engine resource initialization errors
Date Tue, 01 Mar 2016 12:53:28 GMT
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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