ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From britt fitch <britt.fi...@wiredinformatics.com>
Subject Re: Initializing and using clinical pipleline from java
Date Wed, 03 Dec 2014 17:31:43 GMT
Hi Mansour, 

1.) Are you executing this from an IDE (i.e. Eclipse, etc..)
2.) Can you confirm what version of cTAKES you are running?
3.) Can you verify that you have the following in your .m2 directory: ~.m2/repository/org/cleartk/cleartk-ml-liblinear/2.0.0/cleartk-ml-liblinear-2.0.0.jar
?
4.) Can you describe how you are running this method? (i.e. from a class within a ctakes module
or a class from your own personal project)

Cheers, 

Britt


 	 	 	 
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com

On Dec 3, 2014, at 8:17 AM, Mansour Al Akeel <mansour.alakeel@gmail.com> wrote:

> Britt,
> 
> I didn't try the pom.xml you attached. However, I am using this code to initialize the
Engine, and getting another error:
> 
> 
> 
>     private static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException
>     {
> 
>     AggregateBuilder chunkAdjusterBuilder = new AggregateBuilder();
>     chunkAdjusterBuilder.add(ChunkAdjuster.createAnnotatorDescription(new String[] {
"NP", "NP" }, 1));
>     chunkAdjusterBuilder.add(ChunkAdjuster.createAnnotatorDescription(new String[] {
"NP", "PP", "NP" }, 2));
>     AnalysisEngineDescription chunkAdjusterAnnotator = chunkAdjusterBuilder.createAggregateDescription();
> 
>     URL lvgPropertiesURL = LvgCmdApiResourceImpl.class.getResource("/org/apache/ctakes/lvg/data/config/lvg.properties");
>     File propertiesFile = new File(lvgPropertiesURL.toString());
> 
>     AnalysisEngineDescription lvgAnalysisEngineDescription = AnalysisEngineFactory.createPrimitiveDescription(LvgAnnotator.class,
>         LvgAnnotator.PARAM_USE_CMD_CACHE, false, LvgAnnotator.PARAM_USE_LEMMA_CACHE,
false, LvgAnnotator.PARAM_USE_SEGMENTS, false,
>         LvgAnnotator.PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF, 20, LvgAnnotator.PARAM_LEMMA_FREQ_CUTOFF,
20,
>         LvgAnnotator.PARAM_POST_LEMMAS, false, LvgAnnotator.PARAM_LVGCMDAPI_RESRC_KEY,
>         ExternalResourceFactory.createExternalResourceDescription(LvgCmdApiResourceImpl.class,
propertiesFile));
> 
>     AggregateBuilder tokenizerPipeLine = new AggregateBuilder();
>     tokenizerPipeLine.add(SimpleSegmentAnnotator.createAnnotatorDescription());
>     tokenizerPipeLine.add(SentenceDetector.createAnnotatorDescription());
>     tokenizerPipeLine.add(TokenizerAnnotatorPTB.createAnnotatorDescription());
> //    tokenizerPipeLine.add(lvgAnalysisEngineDescription);
>     tokenizerPipeLine.add(ContextDependentTokenizerAnnotator.createAnnotatorDescription());
>     tokenizerPipeLine.add(POSTagger.createAnnotatorDescription());
>     tokenizerPipeLine.add(Chunker.createAnnotatorDescription());
>     tokenizerPipeLine.add(chunkAdjusterAnnotator);
> 
>     AggregateBuilder clinicalBuilder = new AggregateBuilder();
>     clinicalBuilder.add(tokenizerPipeLine.createAggregateDescription());
>     clinicalBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
>     clinicalBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
>     clinicalBuilder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
>     clinicalBuilder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
>     clinicalBuilder.add(MyPolarityCleartkAnalysisEngine.createAnnotatorDescription());
>     return clinicalBuilder.createAggregateDescription();
> 
>     }
> 
> 
> 
> Please note that I commentted out the LVG part. The error is: 
> 
> org.apache.uima.resource.ResourceInitializationException: Initialization of annotator
class "org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine" failed.
 (Descriptor: <unknown>)
>     at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:265)
>     at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
>     at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>     at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>     at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
>     at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
>     at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
>     at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:430)
>     at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:374)
>     at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:187)
>     at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>     at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>     at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
>     at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
>     ...
>     
> Caused by: java.lang.RuntimeException: ClassifierBuilder class read from manifest does
not exist
>     at org.cleartk.classifier.jar.JarClassifierBuilder.fromManifest(JarClassifierBuilder.java:107)
>     at org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:71)
>     at org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
>     at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:139)
>     at org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.initialize(AssertionCleartkAnalysisEngine.java:189)
>     at org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine.initialize(PolarityCleartkAnalysisEngine.java:53)
>     at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:263)
>     ... 37 more
> Caused by: java.lang.ClassNotFoundException: org.cleartk.classifier.liblinear.LIBLINEARStringOutcomeClassifierBuilder
>     at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>     at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>     at java.security.AccessController.doPrivileged(Native Method)
>     at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>     at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
>     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>     at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>     at java.lang.Class.forName0(Native Method)
>     at java.lang.Class.forName(Class.java:188)
>     at org.cleartk.classifier.jar.JarClassifierBuilder.fromManifest(JarClassifierBuilder.java:105)
>     ... 43 more
> 
> 
> 
> 
> Thank you.
> 


Mime
View raw message