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From s..@apache.org
Subject svn commit: r1448717 - in /incubator/ctakes/trunk: ctakes-assertion/resources/launch/ ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/ ctakes-core/src/main/java/org/apache/ctakes/core/ae/ ctakes-core/src/main/java/org/apache/ctakes/core...
Date Thu, 21 Feb 2013 16:41:40 GMT
Author: swu
Date: Thu Feb 21 16:41:39 2013
New Revision: 1448717

URL: http://svn.apache.org/r1448717
Log:
updates for assertion: historyOf in sharpknowtatorxmlreader, some eval flag stuff, launches

Added:
    incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_crossvalidation.launch
    incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_test.launch
    incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_read_gold_and_preprocess.launch
Modified:
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
    incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
    incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java
    incubator/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml

Added: incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_crossvalidation.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_crossvalidation.launch?rev=1448717&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_crossvalidation.launch
(added)
+++ incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_crossvalidation.launch
Thu Feb 21 16:41:39 2013
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<stringAttribute key="bad_container_name" value="/ctakes-assertion/resour"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.debug.ui.ATTR_CAPTURE_IN_FILE" value="/tmp/assertion.log"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.ctakes.assertion.eval.AssertionEvaluation"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="--train-dir
sharp_data/train --models-dir sharp_data/model/eval.model --cross-validate 5"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-assertion"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx1600M"/>
+</launchConfiguration>

Added: incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_test.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_test.launch?rev=1448717&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_test.launch
(added)
+++ incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_test.launch
Thu Feb 21 16:41:39 2013
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<stringAttribute key="bad_container_name" value="/ctakes-assertion/resour"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.debug.ui.ATTR_CAPTURE_IN_FILE" value="/tmp/assertion.log"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.ctakes.assertion.eval.AssertionEvaluation"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="--train-dir
sharp_data/train --test-dir sharp_data/test --models-dir sharp_data/model/eval.model"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-assertion"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx1600M"/>
+</launchConfiguration>

Added: incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_read_gold_and_preprocess.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_read_gold_and_preprocess.launch?rev=1448717&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_read_gold_and_preprocess.launch
(added)
+++ incubator/ctakes/trunk/ctakes-assertion/resources/launch/ctakes_assertion_read_gold_and_preprocess.launch
Thu Feb 21 16:41:39 2013
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<stringAttribute key="bad_container_name" value="/ctakes-assertion/resour"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.debug.ui.ATTR_CAPTURE_IN_FILE" value="/tmp/assertion.log"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.ctakes.assertion.eval.AssertionEvaluation"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="--train-dir
sharp_data/train --test-dir sharp_data/test --dev-dir sharp_data/dev --models-dir sharp_data/model/eval.model
--preprocess-only &quot;/Users/m081914/work/data/sharp/Seed Corpus/Mayo/UMLS_CEM&quot;"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-assertion"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx1600M"/>
+</launchConfiguration>

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1448717&r1=1448716&r2=1448717&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
(original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
Thu Feb 21 16:41:39 2013
@@ -138,35 +138,35 @@ public class AssertionEvaluation extends
     public File evaluationOutputDirectory;
         
     @Option(
-            name = "--run-polarity",
-            usage = "specify whether polarity processing should be run (true or false). default:
true",
+            name = "--ignore-polarity",
+            usage = "specify whether polarity processing should be ignored (true or false).
default: false",
             required = false)
-    public boolean runPolarity = true;
+    public boolean ignorePolarity = false; // note that this is reversed from the "ignore"
statement
         
     @Option(
-            name = "--run-conditional",
-            usage = "specify whether conditional processing should be run (true or false).
default: true",
+            name = "--ignore-conditional",
+            usage = "specify whether conditional processing should be ignored (true or false).
default: false",
             required = false)
-    public boolean runConditional = true;
+    public boolean ignoreConditional = false;
         
     @Option(
-            name = "--run-uncertainty",
-            usage = "specify whether uncertainty processing should be run (true or false).
default: true",
+            name = "--ignore-uncertainty",
+            usage = "specify whether uncertainty processing should be ignored (true or false).
default: false",
             required = false)
-    public boolean runUncertainty = true;
+    public boolean ignoreUncertainty = false;
         
     @Option(
-            name = "--run-subject",
-            usage = "specify whether subject processing should be run (true or false). default:
true",
+            name = "--ignore-subject",
+            usage = "specify whether subject processing should be ignored (true or false).
default: false",
             required = false,
             handler=BooleanOptionHandler.class)
-    public boolean runSubject = true;
+    public boolean ignoreSubject = false;
         
     @Option(
-            name = "--run-generic",
-            usage = "specify whether generic processing should be run (true or false). default:
true",
+            name = "--ignore-generic",
+            usage = "specify whether generic processing should be ignored (true or false).
default: false",
             required = false)
-    public boolean runGeneric = true;
+    public boolean ignoreGeneric = false;
         
     @Option(
             name = "--cross-validation",
@@ -246,11 +246,11 @@ protected static Options options = new O
 
     //String [] annotationTypes = { "polarity", "conditional", "uncertainty", "subject",
"generic" };
     ArrayList<String> annotationTypes = new ArrayList<String>();
-    if (options.runPolarity) { annotationTypes.add("polarity"); }
-    if (options.runConditional) { annotationTypes.add("conditional"); }
-    if (options.runUncertainty) { annotationTypes.add("uncertainty"); }
-    if (options.runSubject) { annotationTypes.add("subject"); }
-    if (options.runGeneric) { annotationTypes.add("generic"); }
+    if (!options.ignorePolarity) { annotationTypes.add("polarity"); }
+    if (!options.ignoreConditional) { annotationTypes.add("conditional"); }
+    if (!options.ignoreUncertainty) { annotationTypes.add("uncertainty"); }
+    if (!options.ignoreSubject) { annotationTypes.add("subject"); }
+    if (!options.ignoreGeneric) { annotationTypes.add("generic"); }
     
     AssertionEvaluation evaluation = new AssertionEvaluation(
         modelsDir,
@@ -318,21 +318,21 @@ protected static Options options = new O
 	    "test dir: %s%n" + 
 	    "model dir: %s%n" +
 	    "cross-validation: %d%n" +
-	    "run polarity: %b%n" +
-	    "run conditional: %b%n" +
-	    "run uncertainty: %b%n" +
-	    "run subject: %b%n" +
-	    "run generic: %b%n" +
+	    "ignore polarity: %b%n" +
+	    "ignore conditional: %b%n" +
+	    "ignore uncertainty: %b%n" +
+	    "ignore subject: %b%n" +
+	    "ignore generic: %b%n" +
 	    "%n%n",
 	    options.trainDirectory.getAbsolutePath(),
 	    (options.testDirectory != null) ? options.testDirectory.getAbsolutePath() : "",
 	    options.modelsDirectory.getAbsolutePath(),
 	    options.crossValidationFolds,
-	    options.runPolarity,
-	    options.runConditional,
-	    options.runUncertainty,
-	    options.runSubject,
-	    options.runGeneric
+	    options.ignorePolarity,
+	    options.ignoreConditional,
+	    options.ignoreUncertainty,
+	    options.ignoreSubject,
+	    options.ignoreGeneric
 	    );
   }
 
@@ -446,7 +446,7 @@ public static void printScore(Map<String
         AnalysisEngineFactory.createAnalysisEngineDescription("org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator");
     builder.add(cuePhraseLookupAnnotator);
 
-    if (options.runPolarity)
+    if (!options.ignorePolarity)
     {
 	    AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 	    ConfigurationParameterFactory.addConfigurationParameters(
@@ -461,7 +461,7 @@ public static void printScore(Map<String
 	    builder.add(polarityAnnotator);
     }
 
-    if (options.runConditional)
+    if (!options.ignoreConditional)
     {
 	    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 	    ConfigurationParameterFactory.addConfigurationParameters(
@@ -476,7 +476,7 @@ public static void printScore(Map<String
 	    builder.add(conditionalAnnotator);
     }
 
-    if (options.runUncertainty)
+    if (!options.ignoreUncertainty)
     {
 	    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 	    ConfigurationParameterFactory.addConfigurationParameters(
@@ -491,7 +491,7 @@ public static void printScore(Map<String
 	    builder.add(uncertaintyAnnotator);
     }
 
-    if (options.runSubject)
+    if (!options.ignoreSubject)
     {
 	    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 	    ConfigurationParameterFactory.addConfigurationParameters(
@@ -506,7 +506,7 @@ public static void printScore(Map<String
 	    builder.add(subjectAnnotator);
     }
 
-    if (options.runGeneric)
+    if (!options.ignoreGeneric)
     {
 		AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
@@ -594,27 +594,27 @@ public static void printScore(Map<String
     AnnotationStatistics genericStats = new AnnotationStatistics();
     
     Map<String, AnnotationStatistics> map = new TreeMap<String, AnnotationStatistics>();

-    if (options.runPolarity)
+    if (!options.ignorePolarity)
     {
       map.put("polarity",  polarityStats);
     }
 
-    if (options.runConditional)
+    if (!options.ignoreConditional)
     {
       map.put("conditional",  conditionalStats);
     }
 
-    if (options.runUncertainty)
+    if (!options.ignoreUncertainty)
     {
       map.put("uncertainty",  uncertaintyStats);
     }
 
-    if (options.runSubject)
+    if (!options.ignoreSubject)
     {
       map.put("subject", subjectStats);
     }
 
-    if (options.runGeneric)
+    if (!options.ignoreGeneric)
     {
       map.put("generic", genericStats);
     }
@@ -644,35 +644,35 @@ public static void printScore(Map<String
       systemEntitiesAndEvents.addAll(systemEvents);
 //      System.out.format("system entities: %d%nsystem events: %d%n%n", systemEntities.size(),
systemEvents.size());
       
-      if (options.runPolarity)
+      if (!options.ignorePolarity)
       {
 	      polarityStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("polarity"));
       }
 
-      if (options.runConditional)
+      if (!options.ignoreConditional)
       {
 	      conditionalStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("conditional"));
       }
 
-      if (options.runUncertainty)
+      if (!options.ignoreUncertainty)
       {
 	      uncertaintyStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("uncertainty"));
       }
 
-      if (options.runSubject)
+      if (!options.ignoreSubject)
       {
 	      subjectStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("subject"));
       }
 
-      if (options.runGeneric)
+      if (!options.ignoreGeneric)
       {
 	      genericStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
 			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
@@ -746,7 +746,7 @@ private void addCleartkAttributeAnnotato
 	builder.add(mayoZonerAnnotator);
 
 	// RUN THE CLEARTK CLASSIFIERS
-	if (options.runPolarity)
+	if (!options.ignorePolarity)
 	{
 		AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
@@ -759,7 +759,7 @@ private void addCleartkAttributeAnnotato
 		builder.add(polarityAnnotator);
 	}
 
-	if (options.runConditional)
+	if (!options.ignoreConditional)
 	{
 		AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
@@ -772,7 +772,7 @@ private void addCleartkAttributeAnnotato
 		builder.add(conditionalAnnotator);
 	}
 
-	if (options.runUncertainty)
+	if (!options.ignoreUncertainty)
 	{
 		AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
@@ -785,7 +785,7 @@ private void addCleartkAttributeAnnotato
 		builder.add(uncertaintyAnnotator);
 	}
 
-	if (options.runSubject)
+	if (!options.ignoreSubject)
 	{
 		AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
@@ -798,7 +798,7 @@ private void addCleartkAttributeAnnotato
 		builder.add(subjectAnnotator);
 	}
 
-	if (options.runGeneric)
+	if (!options.ignoreGeneric)
 	{
 		AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class);
//,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java?rev=1448717&r1=1448716&r2=1448717&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
(original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
Thu Feb 21 16:41:39 2013
@@ -847,11 +847,13 @@ public class SHARPKnowtatorXMLReader ext
         String value = stringSlots.remove("historyOf_normalization");
         HistoryOfModifier modifier = new HistoryOfModifier(jCas, coveringSpan.begin, coveringSpan.end);
         if (null == value) {
-          modifier.setIndicated(false);
+          if (setDefaults) modifier.setHistoryOf(SHARPKnowtatorXMLDefaults.getHistoryOf());
         } else if ("historyOf_present".equals(value)) {
-          modifier.setIndicated(true);
+          modifier.setHistoryOf(CONST.NE_HISTORY_OF_PRESENT);
         } else if ("historyOf_absent".equals(value)) {
-          modifier.setIndicated(false);
+          modifier.setHistoryOf(CONST.NE_HISTORY_OF_ABSENT);
+        } else if (setDefaults) {
+          modifier.setHistoryOf(SHARPKnowtatorXMLDefaults.getHistoryOf());
         } else {
           LOGGER.error(String.format(
               "unrecognized history-of value \"%s\" on annotation with id \"%s\"",
@@ -1295,11 +1297,11 @@ public class SHARPKnowtatorXMLReader ext
       }
     });
     KnowtatorAnnotation historyOf = annotationSlots.remove("historyOf_CU");
+//    if (setDefaults && historyOf==null) { mention.setHistoryOf(SHARPKnowtatorXMLDefaults.getHistoryOf());
}
     delayedFeatures.add(new DelayedFeature(historyOf) {
       @Override
       protected void setValue(TOP value) {
-        HistoryOfModifier modifier = (HistoryOfModifier) value;
-        // TODO: where do we set the history of?
+        mention.setHistoryOf(((HistoryOfModifier) value).getHistoryOf());
       }
     });
     KnowtatorAnnotation negationIndicator = annotationSlots.remove("negation_indicator_CU");
@@ -1310,6 +1312,7 @@ public class SHARPKnowtatorXMLReader ext
       }
     });
     KnowtatorAnnotation subject = annotationSlots.remove("subject_CU");
+    if (setDefaults && subject==null) { mention.setSubject(SHARPKnowtatorXMLDefaults.getSubject());
}
     delayedFeatures.add(new DelayedFeature(subject) {
       @Override
       protected void setValue(TOP value) {

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java?rev=1448717&r1=1448716&r2=1448717&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java
(original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java
Thu Feb 21 16:41:39 2013
@@ -25,6 +25,10 @@ public class SHARPKnowtatorXMLDefaults {
 		return CONST.ATTR_SUBJECT_PATIENT;
 	}
 
+	public static int getHistoryOf() {
+		return CONST.NE_HISTORY_OF_ABSENT;
+	}
+
 //	public static String getSubject(Map<String, KnowtatorAnnotation> annotationSlots)
{
 //		if (annotationSlots.get("subject_CU")==null) {
 //			return CONST.ATTR_SUBJECT_PATIENT;

Modified: incubator/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml?rev=1448717&r1=1448716&r2=1448717&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
(original)
+++ incubator/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
Thu Feb 21 16:41:39 2013
@@ -1519,6 +1519,11 @@ More qualifying information on how the p
           <description/>
           <rangeTypeName>uima.cas.String</rangeTypeName>
         </featureDescription>
+        <featureDescription>
+          <name>historyOf</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
       </features>
     </typeDescription>
     <typeDescription>



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