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From chen...@apache.org
Subject svn commit: r1605564 - in /ctakes/trunk/ctakes-temporal/src: main/java/org/apache/ctakes/temporal/ae/ main/java/org/apache/ctakes/temporal/pipelines/ test/java/org/apach/ctakes/temporal/ae/
Date Wed, 25 Jun 2014 19:19:17 GMT
Author: chenpei
Date: Wed Jun 25 19:19:16 2014
New Revision: 1605564

URL: http://svn.apache.org/r1605564
Log:
CTAKES-297 - Updated the static methods to createAnnotatorDescription() to allow String for
modelPath instead of File.  File assumes physical local file, where as the String can also
handle InputStream where in this case- it can be read in from dependency jars.

Modified:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CRFTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -82,6 +82,33 @@ public class BackwardsTimeAnnotator exte
   }
 
   public static AnalysisEngineDescription createAnnotatorDescription(
+	      String modelPath) throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        BackwardsTimeAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
+  public static AnalysisEngineDescription createEnsembleDescription(String modelPath,
+	      String viewName) throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        BackwardsTimeAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        BackwardsTimeAnnotator.PARAM_TIMEX_VIEW,
+	        viewName,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
+  public static AnalysisEngineDescription createAnnotatorDescription(
       File modelDirectory) throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(
         BackwardsTimeAnnotator.class,
@@ -90,7 +117,11 @@ public class BackwardsTimeAnnotator exte
         GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
         new File(modelDirectory, "model.jar"));
   }
-
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
   public static AnalysisEngineDescription createEnsembleDescription(File modelDirectory,
       String viewName) throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CRFTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CRFTimeAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CRFTimeAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CRFTimeAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -72,6 +72,33 @@ public class CRFTimeAnnotator extends Te
 //        outputDirectory);
 //  }
 
+  public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+	      throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        CRFTimeAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
+  public static AnalysisEngineDescription createEnsembleDescription(String modelPath,
+	      String viewName) throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        CRFTimeAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        CRFTimeAnnotator.PARAM_TIMEX_VIEW,
+	        viewName,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
   public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
       throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(
@@ -82,6 +109,11 @@ public class CRFTimeAnnotator extends Te
         new File(modelDirectory, "model.jar"));
   }
 
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
   public static AnalysisEngineDescription createEnsembleDescription(File modelDirectory,
       String viewName) throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -94,6 +94,32 @@ TemporalEntityAnnotator_ImplBase {
         outputDirectory);
   }
 
+  public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+	      throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        ConstituencyBasedTimeAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
+  public static AnalysisEngineDescription createEnsembleDescription(String modelPath,
+	      String viewName) throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        ConstituencyBasedTimeAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        ConstituencyBasedTimeAnnotator.PARAM_TIMEX_VIEW,
+	        viewName,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
   public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
       throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(
@@ -104,6 +130,11 @@ TemporalEntityAnnotator_ImplBase {
         new File(modelDirectory, "model.jar"));
   }
 
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
   public static AnalysisEngineDescription createEnsembleDescription(File modelDirectory,
       String viewName) throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -58,7 +58,22 @@ public class ContextualModalityAnnotator
         DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
         outputDirectory);
   }
-
+  
+  public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+	      throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        ContextualModalityAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
   public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
       throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -73,6 +73,21 @@ public class DocTimeRelAnnotator extends
         outputDirectory);
   }
 
+  public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+	      throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        DocTimeRelAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
+  /**
+   * @deprecated use String path instead of File.
+   * ClearTK will automatically Resolve the String to an InputStream.
+   * This will allow resources to be read within from a jar as well as File.  
+   */
   public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
       throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -79,7 +79,22 @@ public class EventAdmissionTimeAnnotator
 				DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
 				outputDirectory);
 	}
+	
+	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+			throws ResourceInitializationException {
+		return AnalysisEngineFactory.createPrimitiveDescription(
+				EventAdmissionTimeAnnotator.class,
+				CleartkAnnotator.PARAM_IS_TRAINING,
+				false,
+				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+				modelPath);
+	}	
 
+	  /**
+	   * @deprecated use String path instead of File.
+	   * ClearTK will automatically Resolve the String to an InputStream.
+	   * This will allow resources to be read within from a jar as well as File.  
+	   */
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 			throws ResourceInitializationException {
 		return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -136,6 +136,16 @@ public class EventAnnotator extends Temp
         EventAnnotator.createFeatureSelectionURI(modelDirectory));
   }
 
+  public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+	      throws ResourceInitializationException {
+	    return AnalysisEngineFactory.createPrimitiveDescription(
+	        EventAnnotator.class,
+	        CleartkAnnotator.PARAM_IS_TRAINING,
+	        false,
+	        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+	        modelPath);
+	  }
+  
   public static AnalysisEngineDescription createAnnotatorDescription()
       throws ResourceInitializationException {
     return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -80,6 +80,20 @@ public class EventDischargeTimeAnnotator
 				outputDirectory);
 	}
 
+	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+			throws ResourceInitializationException {
+		return AnalysisEngineFactory.createPrimitiveDescription(
+				EventDischargeTimeAnnotator.class,
+				CleartkAnnotator.PARAM_IS_TRAINING,
+				false,
+				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+				modelPath);
+	}	
+	  /**
+	   * @deprecated use String path instead of File.
+	   * ClearTK will automatically Resolve the String to an InputStream.
+	   * This will allow resources to be read within from a jar as well as File.  
+	   */
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 			throws ResourceInitializationException {
 		return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -73,6 +73,21 @@ public class EventEventRelationAnnotator
 		            (float) probabilityOfKeepingANegativeExample);
 		      }
 	  
+	  public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+		      throws ResourceInitializationException {
+		    return AnalysisEngineFactory.createPrimitiveDescription(
+		        EventEventRelationAnnotator.class,
+		        CleartkAnnotator.PARAM_IS_TRAINING,
+		        false,
+		        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+		        modelPath);
+		  }
+	  
+	  /**
+	   * @deprecated use String path instead of File.
+	   * ClearTK will automatically Resolve the String to an InputStream.
+	   * This will allow resources to be read within from a jar as well as File.  
+	   */	  
 	  public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
 		    return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -77,6 +77,20 @@ public class EventTimeRelationAnnotator 
 				(float) probabilityOfKeepingANegativeExample);
 	}
 
+	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+			throws ResourceInitializationException {
+		return AnalysisEngineFactory.createPrimitiveDescription(
+				EventTimeRelationAnnotator.class,
+				CleartkAnnotator.PARAM_IS_TRAINING,
+				false,
+				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+				modelPath);
+	}
+	  /**
+	   * @deprecated use String path instead of File.
+	   * ClearTK will automatically Resolve the String to an InputStream.
+	   * This will allow resources to be read within from a jar as well as File.  
+	   */	 
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 			throws ResourceInitializationException {
 		return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -87,6 +87,21 @@ public class NEPredicateEventAnnotator e
 
 	}
 
+	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+		      throws ResourceInitializationException {
+		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    	NEPredicateEventAnnotator.class,
+		    	CleartkAnnotator.PARAM_IS_TRAINING,
+		        false,
+		        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+		        modelPath);
+	}
+	
+	  /**
+	   * @deprecated use String path instead of File.
+	   * ClearTK will automatically Resolve the String to an InputStream.
+	   * This will allow resources to be read within from a jar as well as File.  
+	   */	 
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
 		    return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
Wed Jun 25 19:19:16 2014
@@ -113,6 +113,21 @@ public class TimeAnnotator extends Tempo
 		        smoteNeighborNumber);
 	}
 
+	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
+			throws ResourceInitializationException {
+		return AnalysisEngineFactory.createPrimitiveDescription(
+				TimeAnnotator.class,
+				CleartkAnnotator.PARAM_IS_TRAINING,
+				false,
+				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+				modelPath);
+	}
+	
+	  /**
+	   * @deprecated use String path instead of File.
+	   * ClearTK will automatically Resolve the String to an InputStream.
+	   * This will allow resources to be read within from a jar as well as File.  
+	   */		
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 			throws ResourceInitializationException {
 		return AnalysisEngineFactory.createPrimitiveDescription(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
Wed Jun 25 19:19:16 2014
@@ -67,7 +67,7 @@ public class EventAndTimeExtractionPipel
 
 		AggregateBuilder aggregateBuilder = getPreprocessorAggregateBuilder();
 		aggregateBuilder.add(EventAnnotator.createAnnotatorDescription(new File(options.getEventModelDirectory())));
-		aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(new File(options.getTimeModelDirectory())));
+		aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(options.getTimeModelDirectory()
+ "model.jar"));
     AnalysisEngine xWriter = AnalysisEngineFactory.createPrimitive(
         XWriter.class,
         XWriter.PARAM_OUTPUT_DIRECTORY_NAME,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
Wed Jun 25 19:19:16 2014
@@ -79,10 +79,10 @@ public class FullTemporalExtractionPipel
 
     AggregateBuilder aggregateBuilder = getLightweightPreprocessorAggregateBuilder();
     aggregateBuilder.add(EventAnnotator.createAnnotatorDescription(new File(options.getEventModelDirectory())));
-    aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(new File(options.getTimeModelDirectory())));
+    aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(options.getTimeModelDirectory()
+ "/model.jar"));
     aggregateBuilder.add(EventTimeRelationAnnotator.createAnnotatorDescription(new File(options.getEventTimeRelationModelDirectory())));
     if(options.getEventEventRelationModelDirectory()!=null){
-      aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(new File(options.getEventEventRelationModelDirectory())));
+      aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(options.getEventEventRelationModelDirectory()
+ "/model.jar"));
     }
     AnalysisEngine xWriter = getXMIWriter(options.getOutputDirectory());
     

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
Wed Jun 25 19:19:16 2014
@@ -58,7 +58,7 @@ public class TimeExtractionPipeline exte
 				options.getInputDirectory());
 
 		AggregateBuilder aggregateBuilder = getPreprocessorAggregateBuilder();
-		aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(new File(options.getTimeModelDirectory())));
+		aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(options.getTimeModelDirectory()
+ "model.jar"));
 		
     AnalysisEngine xWriter = getXMIWriter(options.getOutputDirectory());
 	

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
Wed Jun 25 19:19:16 2014
@@ -52,45 +52,45 @@ public class BackwardsTimeAnnotatorTest 
 
 	// LOG4J logger based on class name
 	private Logger LOGGER = Logger.getLogger(getClass().getName());
-	
+
 	@Test
 	public void testPipeline() throws UIMAException, IOException {
-		
+
 		String note = "The patient is a 55-year-old man referred by Dr. Good for recently diagnosed
colorectal cancer.  "
 				+ "The patient was well till 6 months ago, when he started having a little blood with
stool.";
 		JCas jcas = JCasFactory.createJCas();
 		jcas.setDocumentText(note);
-  
-		//Get the default pipeline with umls dictionary lookup
-	    AggregateBuilder builder = new AggregateBuilder();
-	    builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
-	    builder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
-	    builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
-	    //Commented out the Dictionary lookup for the test
-	    //Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if needed
-	    //builder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
-	    builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
-		
-		//Add BackwardsTimeAnnotator
-	    builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-	            BackwardsTimeAnnotator.class,
-	            CleartkAnnotator.PARAM_IS_TRAINING,
-	            false,
-	            GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-	            "/org/apache/ctakes/temporal/ae/timeannotator/model.jar"));
-	    
-	    SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
-
-	    Collection<TimeMention> mentions = JCasUtil.select(jcas, TimeMention.class);
-
-	    ArrayList<String> temp = new ArrayList<>();
-	    for(TimeMention mention : mentions){
-	    	LOGGER.info("Event: " + mention.getCoveredText());
-	    	temp.add(mention.getCoveredText());
-	    }
-	    assertEquals(2, temp.size());	    
-	    assertTrue(temp.contains("recently"));
-	    assertTrue(temp.contains("6 months ago"));
+
+		// Get the default pipeline with umls dictionary lookup
+		AggregateBuilder builder = new AggregateBuilder();
+		builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
+		builder.add(AnalysisEngineFactory
+				.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+		builder.add(AnalysisEngineFactory
+				.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+		// Commented out the Dictionary lookup for the test
+		// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
+		// needed
+		// builder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
+		builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
+
+		// Add BackwardsTimeAnnotator
+		builder.add(BackwardsTimeAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/timeannotator/model.jar"));
+
+		SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
+
+		Collection<TimeMention> mentions = JCasUtil.select(jcas,
+				TimeMention.class);
+
+		ArrayList<String> temp = new ArrayList<>();
+		for (TimeMention mention : mentions) {
+			LOGGER.info("Event: " + mention.getCoveredText());
+			temp.add(mention.getCoveredText());
+		}
+		assertEquals(2, temp.size());
+		assertTrue(temp.contains("recently"));
+		assertTrue(temp.contains("6 months ago"));
 	}
 
 }

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
Wed Jun 25 19:19:16 2014
@@ -29,6 +29,7 @@ import org.apache.ctakes.clinicalpipelin
 import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.RemoveEnclosedLookupWindows;
 import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
 import org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator;
+import org.apache.ctakes.temporal.ae.ContextualModalityAnnotator;
 import org.apache.ctakes.temporal.ae.EventAnnotator;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -49,12 +50,9 @@ public class ContextualModalityAnnotator
 
 	// LOG4J logger based on class name
 	private Logger LOGGER = Logger.getLogger(getClass().getName());
-	
+
 	@Test
 	public void testPipeline() throws UIMAException, IOException {
-		
-		/** Not ready for prime time yet
-		 * Annotator Caused by: java.lang.IllegalArgumentException: Unrecognized BIO outcome: ACTUAL
 
 		String note = "The patient is a 55-year-old man referred by Dr. Good for recently diagnosed
colorectal cancer.  "
 				+ "The patient was well till 6 months ago, when he started having a little blood with
stool.";
@@ -75,22 +73,14 @@ public class ContextualModalityAnnotator
 		builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
 
 		// Add BackwardsTimeAnnotator
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-				BackwardsTimeAnnotator.class,
-				CleartkAnnotator.PARAM_IS_TRAINING, false,
-				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-				"/org/apache/ctakes/temporal/ae/timeannotator/model.jar"));
+		builder.add(BackwardsTimeAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/timeannotator/model.jar"));
 		// Add EventAnnotator
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-				EventAnnotator.class, CleartkAnnotator.PARAM_IS_TRAINING,
-				false, GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-				"/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
+		builder.add(EventAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
 		// Add Document Time Relative Annotator
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-				BackwardsTimeAnnotator.class,
-				CleartkAnnotator.PARAM_IS_TRAINING, false,
-				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-				"/org/apache/ctakes/temporal/ae/contextualmodality/model.jar"));
+		builder.add(ContextualModalityAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/contextualmodality/model.jar"));
 
 		SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
 
@@ -102,20 +92,20 @@ public class ContextualModalityAnnotator
 			String property = null;
 			if (entity.getEvent() != null
 					&& entity.getEvent().getProperties() != null
-					&& entity.getEvent().getProperties().getContextualModality() != null) {
+					&& entity.getEvent().getProperties()
+							.getContextualModality() != null) {
 
-				property = entity.getEvent().getProperties().getContextualModality();
+				property = entity.getEvent().getProperties()
+						.getContextualModality();
 				temp.add(entity.getCoveredText());
 			}
-			LOGGER.info("Entity: " + entity.getCoveredText() + "ContextualModality:"
-					+ property);
+			LOGGER.info("Entity: " + entity.getCoveredText()
+					+ "ContextualModality:" + property);
 		}
 		// assertEquals(2, temp.size());
 		// assertTrue(temp.contains("recently"));
 		// assertTrue(temp.contains("6 months ago"));
-		 
-		 
-	*/
+
 	}
-		
+
 }

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
Wed Jun 25 19:19:16 2014
@@ -29,6 +29,8 @@ import org.apache.ctakes.clinicalpipelin
 import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.RemoveEnclosedLookupWindows;
 import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
 import org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator;
+import org.apache.ctakes.temporal.ae.ClearTKDocTimeRelAnnotator;
+import org.apache.ctakes.temporal.ae.DocTimeRelAnnotator;
 import org.apache.ctakes.temporal.ae.EventAnnotator;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -72,22 +74,14 @@ public class DocTimeRelAnnotatorTest {
 		builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
 
 		// Add BackwardsTimeAnnotator
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-				BackwardsTimeAnnotator.class,
-				CleartkAnnotator.PARAM_IS_TRAINING, false,
-				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-				"/org/apache/ctakes/temporal/ae/timeannotator/model.jar"));
+		builder.add(BackwardsTimeAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/timeannotator/model.jar"));
 		// Add EventAnnotator
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-				EventAnnotator.class, CleartkAnnotator.PARAM_IS_TRAINING,
-				false, GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-				"/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
+		builder.add(EventAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
 		// Add Document Time Relative Annotator
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-				BackwardsTimeAnnotator.class,
-				CleartkAnnotator.PARAM_IS_TRAINING, false,
-				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-				"/org/apache/ctakes/temporal/ae/doctimerel/model.jar"));
+		builder.add(DocTimeRelAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/doctimerel/model.jar"));
 
 		SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
 

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java?rev=1605564&r1=1605563&r2=1605564&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java
Wed Jun 25 19:19:16 2014
@@ -50,48 +50,49 @@ public class EventAnnotatorTest {
 
 	// LOG4J logger based on class name
 	private Logger LOGGER = Logger.getLogger(getClass().getName());
-	
+
 	@Test
 	public void testPipeline() throws UIMAException, IOException {
-		
+
 		String note = "The patient is a 55-year-old man referred by Dr. Good for recently diagnosed
colorectal cancer.  "
 				+ "The patient was well till 6 months ago, when he started having a little blood with
stool.";
 		JCas jcas = JCasFactory.createJCas();
 		jcas.setDocumentText(note);
-  
-		//Get the default pipeline
-	    AggregateBuilder builder = new AggregateBuilder();
-	    builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
-	    builder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
-	    builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
-	    //Commented out the Dictionary lookup for the test
-	    //Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if needed
-	    //builder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
-	    builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
-		
-		//Add EventAnnotator
-	    builder.add(AnalysisEngineFactory.createPrimitiveDescription(
-	    		EventAnnotator.class,
-	            CleartkAnnotator.PARAM_IS_TRAINING,
-	            false,
-	            GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
-	            "/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
-	    
-	    SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
-
-	    Collection<EventMention> mentions = JCasUtil.select(jcas, EventMention.class);
-
-	    ArrayList<String> temp = new ArrayList<>();
-	    for(EventMention mention : mentions){
-	    	LOGGER.info("Event: " + mention.getCoveredText() + " Confidence:" + mention.getConfidence());
-	    	temp.add(mention.getCoveredText());
-	    }
-	   	assertEquals(6, temp.size());	    
-	    assertTrue(temp.contains("old"));
-	    assertTrue(temp.contains("referred"));	    
-	    assertTrue(temp.contains("cancer"));
-	    assertTrue(temp.contains("till"));
-	    assertTrue(temp.contains("blood"));
-	    assertTrue(temp.contains("stool"));
+
+		// Get the default pipeline
+		AggregateBuilder builder = new AggregateBuilder();
+		builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
+		builder.add(AnalysisEngineFactory
+				.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+		builder.add(AnalysisEngineFactory
+				.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+		// Commented out the Dictionary lookup for the test
+		// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
+		// needed
+		// builder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
+		builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
+
+		// Add EventAnnotator
+		builder.add(EventAnnotator
+				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
+
+		SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
+
+		Collection<EventMention> mentions = JCasUtil.select(jcas,
+				EventMention.class);
+
+		ArrayList<String> temp = new ArrayList<>();
+		for (EventMention mention : mentions) {
+			LOGGER.info("Event: " + mention.getCoveredText() + " Confidence:"
+					+ mention.getConfidence());
+			temp.add(mention.getCoveredText());
+		}
+		assertEquals(6, temp.size());
+		assertTrue(temp.contains("old"));
+		assertTrue(temp.contains("referred"));
+		assertTrue(temp.contains("cancer"));
+		assertTrue(temp.contains("till"));
+		assertTrue(temp.contains("blood"));
+		assertTrue(temp.contains("stool"));
 	}
 }



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