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From Mansour Al Akeel <mansour.alak...@gmail.com>
Subject Re: Initializing and using clinical pipleline from java
Date Thu, 04 Dec 2014 15:01:02 GMT
Britt,
Thank you again for your time.

On Wed, Dec 3, 2014 at 12:31 PM, britt fitch <
britt.fitch@wiredinformatics.com> 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
> 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.
>
>
>

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