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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: ctakes 3.2.2 AggregatePlaintextFastUMLSProcessor webproject integration
Date Mon, 16 May 2016 18:59:42 GMT
Hi Jan,
It looks like ou are basically trying to run the equivalent of:
ctakes-clinical-pipeline/desc/../analysis_engine/CuisOnlyPlaintextUMLSProcessor.xml

You could try swapping out the Aggregate... for that one and see what happens.

Sean

-----Original Message-----
From: Jan Zieher [mailto:JZieher@gmx.de] 
Sent: Monday, May 16, 2016 2:08 PM
To: dev@ctakes.apache.org
Subject: ctakes 3.2.2 AggregatePlaintextFastUMLSProcessor webproject integration

Hey,
I created a java webproject in netbeans 8.1 and integrated ctakes with the libs of the 3.2.2
binaries download, its desc and resource folder into the WEB-INF folder. I would like to run
the AggregatePlaintextFastUMLSProcessor AE. Through debugging the code below worked, if I
comment the following engines in the AE descriptor.

<node>HistoryCleartkAnalysisEngine</node>
<node>PolarityCleartkAnalysisEngine</node>
<node>SubjectCleartkAnalysisEngine</node>
<node>UncertaintyCleartkAnalysisEngine</node>

String s =  this.getServletContext().getRealPath("/WEB-INF/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml");
File aed = new File(s);
JCas jcas;
        
    try {
        pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createEngineDescriptionFromPath(s);
        AnalysisEngine ae = AnalysisEngineFactory.createEngine(pipelineIncludingUmlsDictionaries);
        jcas = JCasFactory.createJCas();
        jcas.setDocumentText("Fx of obesity but no fx of coronary artery diseases");
            
        SimplePipeline.runPipeline(jcas, ae);
            
        // Print out the IdentifiedAnnotation objects
                for (IdentifiedAnnotation entity : JCasUtil.select(jcas, IdentifiedAnnotation.class))
{
                    System.out.println("Entity: " + entity.getCoveredText()
+ " === Polarity: " + entity.getPolarity()+ "Class:"+ entity.getClass());
                        
                }
    } catch (UIMAException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    
If I uncomment the cleartk engines I get this class not found error, although the class exists
in the ctakes-assertion-3.2.2.jar.
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class
"org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine" failed.
(Descriptor: file:/C:/Users/..../Documents/NetBeansProjects/mta.parser/target/mta.parser-1.0-SNAPSHOT/WEB-INF/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml)

My first question is are these engines very necessary for the nlp results ? 

Could this class not found error also belong to path problems caused by the webcontent location
?

Has anyone a project or description how to set up such a webproject ? 

I would be very happy if someone could help me.

Best regards,
Jan
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