Hi Mansour, it looks like you are lacking required mvn dependencies. 1.) are you able to cd to the ctakes directory and execute ‘mvn clean package’ from the command line?
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
[email protected]
On Dec 4, 2014, at 10:01 AM, Mansour Al Akeel <[email protected]> wrote:
> 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.
>>
>
>
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