Britt, Thank you again for your time. On Wed, Dec 3, 2014 at 12:31 PM, britt fitch < [email protected]> wrote:
> Hi Mansour, > > 1.) Are you executing this from an IDE (i.e. Eclipse, etc..) > Yes, I am running this from eclipse IDE and through JUNIT. > 2.) Can you confirm what version of cTAKES you are running? > cTAKES 3.2.0 > 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 > ? > No, it does not exist in the local repo. 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) > > Currently, this is only a junit method that I run it through eclipse, and debug it. Once it works, I will need to move it to its own class that will be initialized by spring. > 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. > > >
