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
[email protected]
On Dec 3, 2014, at 8:17 AM, Mansour Al Akeel <[email protected]> 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.
>
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