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From chen...@apache.org
Subject svn commit: r1388196 [2/12] - in /incubator/ctakes/trunk: ctakes-chunker/desc/ ctakes-chunker/src/main/java/edu/mayo/bmi/uima/adjuster/ ctakes-chunker/src/main/java/edu/mayo/bmi/uima/chunker/ ctakes-chunker/test/data/output/ ctakes-chunker/test/desc/ c...
Date Thu, 20 Sep 2012 20:25:58 GMT
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
Thu Sep 20 20:25:49 2012
@@ -135,13 +135,13 @@ and requires an UMLS license.  Please up
       <description>For subiterator</description>
       <version>1.0</version>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
       </priorityList>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
       </priorityList>
     </typePriorities>
     <fsIndexCollection/>
@@ -149,48 +149,48 @@ and requires an UMLS license.  Please up
       <capability>
         <inputs/>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NewlineToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.WordToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.VP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.UmlsConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.UCP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SymbolToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspanSegment</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SBAR</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RomanNumeralAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RangeAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PunctuationToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Property</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Properties</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.PersonTitleAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PRT</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.OntologyConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NumToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.MeasurementAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NewlineToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.VP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.UCP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SymbolToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspanSegment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SBAR</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RangeAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PunctuationToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Property</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Properties</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PRT</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.OntologyConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NumToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation</type>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Lemma</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.LST</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.INTJ</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.FractionAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.structured.DocumentID</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Lemma</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.LST</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.INTJ</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.structured.DocumentID</type>
           <type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.DateAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopySrcAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopyDestAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.ContractionToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.ContextAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Chunk</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.CONJP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.DateAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.ContractionToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.ContextAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Chunk</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.CONJP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
           <type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
           <type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADVP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADJP</type>
       
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADVP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADJP</type>
       
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml
Thu Sep 20 20:25:49 2012
@@ -47,10 +47,10 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NP</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NP</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml
Thu Sep 20 20:25:49 2012
@@ -98,13 +98,13 @@ selector=A or B or BOTH</description>
 <nameValuePair>
 <name>A_ObjectClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>B_ObjectClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml
Thu Sep 20 20:25:49 2012
@@ -55,13 +55,13 @@
 <nameValuePair>
 <name>srcObjClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.NP</string>
+<string>org.apache.ctakes.typesystem.type.syntax.NP</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>destObjClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -79,12 +79,12 @@
 </imports>
 <types>
 <typeDescription>
-<name>edu.mayo.bmi.uima.core.type.CopySrcAnnotation</name>
+<name>org.apache.ctakes.typesystem.type.CopySrcAnnotation</name>
 <description>Used for testing CopyAnnotator.</description>
 <supertypeName>uima.tcas.Annotation</supertypeName>
 </typeDescription>
 <typeDescription>
-<name>edu.mayo.bmi.uima.core.type.CopyDestAnnotation</name>
+<name>org.apache.ctakes.typesystem.type.CopyDestAnnotation</name>
 <description>Used for testing CopyAnnotator.</description>
 <supertypeName>uima.tcas.Annotation</supertypeName>
 </typeDescription>
@@ -93,10 +93,10 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NP</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NP</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NegationAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NegationAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NegationAnnotator.xml
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/NegationAnnotator.xml
Thu Sep 20 20:25:49 2012
@@ -110,19 +110,19 @@
 <nameValuePair>
 <name>WindowAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>FocusAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -141,8 +141,8 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml
Thu Sep 20 20:25:49 2012
@@ -62,7 +62,7 @@
       <capability>
         <inputs/>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml
Thu Sep 20 20:25:49 2012
@@ -48,7 +48,7 @@
 <capability>
 <inputs/>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java
Thu Sep 20 20:25:49 2012
@@ -32,13 +32,13 @@ import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.TOP;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.type.refsem.OntologyConcept;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.type.util.Pair;
-import edu.mayo.bmi.uima.core.type.util.Pairs;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.util.Pair;
+import org.apache.ctakes.typesystem.type.util.Pairs;
 
 /**
  * UIMA annotator that prepares the CAS for output - performs



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