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From britt fitch <britt.fi...@wiredinformatics.com>
Subject Re: Initializing and using clinical pipleline from java
Date Thu, 04 Dec 2014 15:32:40 GMT
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
Britt.Fitch@wiredinformatics.com

On Dec 4, 2014, at 10:01 AM, Mansour Al Akeel <mansour.alakeel@gmail.com> wrote:

> 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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