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From seanfi...@apache.org
Subject svn commit: r1879557 - in /ctakes/trunk: ctakes-core/src/main/java/org/apache/ctakes/core/ae/ ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/ ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/ ctakes-dockhand/src/ma...
Date Mon, 06 Jul 2020 17:16:52 GMT
Author: seanfinan
Date: Mon Jul  6 17:16:52 2020
New Revision: 1879557

URL: http://svn.apache.org/viewvc?rev=1879557&view=rev
Log:
ListEntryNegator : add to the regex pattern
EssentialAnnotationUtil : add coreference methods that utilize assertion
Option : remove commented code
pom * : add snapshot repository reference
app , index : change label text to pretty, property to props

Modified:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
    ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Option.java
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/attribute_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/coreference_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/entity_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_coref_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_coreference_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_coref_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/token_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/coreference_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/entity_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_coref_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_coreference_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_coref_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_pom.xml
    ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/token_pom.xml
    ctakes/trunk/ctakes-tiny-rest/src/main/webapp/index.jsp
    ctakes/trunk/ctakes-tiny-rest/src/main/webapp/js/app.js

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
Mon Jul  6 17:16:52 2020
@@ -41,7 +41,7 @@ public class ListEntryNegator extends JC
 
    static private final Pattern NEGATIVE_PATTERN
          = Pattern
-         .compile( "(?:\\s?:\\s*)(?:NEGATIVE|(?:NO\\.?\\b)|NONE|(?:NOT (?:SEEN|PRESENT|INDICATED|FOUND|DISCOVERED)?)|DENIE[SD])",
+         .compile( "(?:\\s?:\\s*)(?:NEGATIVE|(?:NO\\.?\\b)|(?:N\\/A)|NONE|(?:NOT (?:APPLICABLE|INVOLVED|SEEN|PRESENT|INDICATED|FOUND|DISCOVERED)?)|DENIE[SD])",
                Pattern.CASE_INSENSITIVE );
 
    /**
@@ -53,7 +53,6 @@ public class ListEntryNegator extends JC
       LOGGER.info( "Adjusting attributes within Lists ..." );
       final Collection<List> lists = JCasUtil.select( jcas, List.class );
       lists.forEach( l -> processList( jcas, l ) );
-      LOGGER.info( "Finished Processing" );
    }
 
    static private void processList( final JCas jCas, final AnnotationFS list ) {

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
Mon Jul  6 17:16:52 2020
@@ -168,6 +168,63 @@ final public class EssentialAnnotationUt
       return corefMarkables;
    }
 
+   /**
+    * Sometimes there will be two overlapping annotations, 1 affirmed 1 negated.
+    * Use this for matching assertions in coreference chains.
+    *
+    * @param jCas ye olde ...
+    * @return a map of markables to indexed chain numbers
+    */
+   static public Map<IdentifiedAnnotation, Collection<Integer>> createAllMarkableAssertedCorefs(
final JCas jCas ) {
+      final Collection<CollectionTextRelation> corefs = JCasUtil.select( jCas, CollectionTextRelation.class
);
+      final Map<Markable, Collection<IdentifiedAnnotation>> markableAnnotations
+            = mapAllMarkableAnnotations( jCas, corefs );
+      return createAllMarkableAssertedCorefs( corefs, markableAnnotations );
+   }
+
+   /**
+    * @param corefs coreference chains
+    * @return a map of markables to indexed chain numbers
+    */
+   static public Map<IdentifiedAnnotation, Collection<Integer>> createAllMarkableAssertedCorefs(
+         final Collection<CollectionTextRelation> corefs,
+         final Map<Markable, Collection<IdentifiedAnnotation>> markableAnnotations
) {
+      if ( corefs == null || corefs.isEmpty() ) {
+         return Collections.emptyMap();
+      }
+
+      final List<List<IdentifiedAnnotation>> chains = new ArrayList<>();
+      for ( CollectionTextRelation coref : corefs ) {
+         final Map<String, List<IdentifiedAnnotation>> assertionMap = new HashMap<>();
+         final FSList chainHead = coref.getMembers();
+         final Collection<Markable> markables = FSCollectionFactory.create( chainHead,
Markable.class );
+         for ( Markable markable : markables ) {
+            for ( IdentifiedAnnotation annotation : markableAnnotations.get( markable ) )
{
+               final String assertion = getAssertion( annotation );
+               assertionMap.computeIfAbsent( assertion, a -> new ArrayList<>() ).add(
annotation );
+            }
+         }
+         for ( List<IdentifiedAnnotation> asserted : assertionMap.values() ) {
+            if ( asserted.size() > 1 ) {
+               asserted.sort( Comparator.comparingInt( Annotation::getBegin ) );
+               chains.add( asserted );
+            }
+         }
+      }
+      chains.sort( ( l1, l2 ) -> l1.get( 0 ).getBegin() - l2.get( 0 ).getBegin() );
+
+      final Map<IdentifiedAnnotation, Collection<Integer>> corefMarkables = new
HashMap<>();
+      int index = 1;
+      for ( Collection<IdentifiedAnnotation> chain : chains ) {
+         for ( IdentifiedAnnotation annotation : chain ) {
+            corefMarkables.computeIfAbsent( annotation, a -> new ArrayList<>() ).add(
index );
+         }
+         index++;
+      }
+      return corefMarkables;
+   }
+
+
    static private String getAssertion( final IdentifiedAnnotation annotation ) {
       final StringBuilder sb = new StringBuilder();
       if ( annotation.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT ) {
@@ -255,6 +312,97 @@ final public class EssentialAnnotationUt
    }
 
    /**
+    * This is a bit messy, but necessary.
+    *
+    * @param jCas   -
+    * @param corefs -
+    * @return map of markable to identified annotation
+    */
+   static public Map<Markable, Collection<IdentifiedAnnotation>> mapAllMarkableAnnotations(
+         final JCas jCas, final Collection<CollectionTextRelation> corefs ) {
+      if ( corefs == null || corefs.isEmpty() ) {
+         return Collections.emptyMap();
+      }
+      final Map<Markable, Collection<ConllDependencyNode>> markableNodes
+            = JCasUtil.indexCovered( jCas, Markable.class, ConllDependencyNode.class );
+      final Map<ConllDependencyNode, Collection<IdentifiedAnnotation>> nodeAnnotations
+            = JCasUtil.indexCovering( jCas, ConllDependencyNode.class, IdentifiedAnnotation.class
);
+      final Map<Markable, Collection<IdentifiedAnnotation>> annotationMap = new
HashMap<>();
+      for ( CollectionTextRelation coref : corefs ) {
+         final Collection<Markable> markables = JCasUtil.select( coref.getMembers(),
Markable.class );
+         for ( Markable markable : markables ) {
+            final Collection<ConllDependencyNode> nodes = markableNodes.get( markable
);
+            if ( nodes == null || nodes.isEmpty() ) {
+               LOGGER.warn( "No Dependency node for markable " + markable.getCoveredText()
);
+               continue;
+            }
+            final ConllDependencyNode headNode = getNominalHeadNode( new ArrayList<>(
nodes ) );
+            final Collection<IdentifiedAnnotation> headNodeAnnotations = nodeAnnotations.get(
headNode );
+            final Collection<IdentifiedAnnotation> essentialAnnotations
+                  = getEssentialAnnotations( headNodeAnnotations );
+            final Collection<IdentifiedAnnotation> nonEssentialAnnotations
+                  = getNonEssentialAnnotations( headNodeAnnotations,
+                  essentialAnnotations );
+
+//            IdentifiedAnnotation bestAnnotation = null;
+            final Collection<IdentifiedAnnotation> bestAnnotations = new ArrayList<>();
+            final Collection<IdentifiedAnnotation> overlapAnnotations = new ArrayList<>();
+            int bestLength = Integer.MAX_VALUE;
+            for ( IdentifiedAnnotation annotation : essentialAnnotations ) {
+               if ( !EventMention.class.equals( annotation.getClass() )
+                    && annotation.getBegin() == markable.getBegin()
+                    && annotation.getEnd() == markable.getEnd()
+                    && !bestAnnotations.contains( annotation ) ) {
+                  // Prefer an exact non-event match over the longest match
+                  bestAnnotations.add( annotation );
+               }
+               if ( ((annotation.getBegin() <= markable.getBegin() && markable.getEnd()
<= annotation.getEnd())
+                     || (markable.getBegin() <= annotation.getBegin() && annotation.getEnd()
<= markable.getEnd()))
+                    && annotation.getEnd() - annotation.getBegin() < bestLength
) {
+                  bestLength = annotation.getEnd() - annotation.getBegin();
+                  overlapAnnotations.add( annotation );
+               }
+            }
+            if ( bestAnnotations.isEmpty() && bestLength != Integer.MAX_VALUE ) {
+               for ( IdentifiedAnnotation annotation : overlapAnnotations ) {
+                  if ( annotation.getEnd() - annotation.getBegin() == bestLength ) {
+                     bestAnnotations.add( annotation );
+                  }
+               }
+            }
+
+            if ( !bestAnnotations.isEmpty() ) {
+               annotationMap.put( markable, bestAnnotations );
+               continue;
+            }
+            for ( IdentifiedAnnotation annotation : nonEssentialAnnotations ) {
+               if ( ((annotation.getBegin() <= markable.getBegin() && markable.getEnd()
<= annotation.getEnd())
+                     || (markable.getBegin() <= annotation.getBegin() && annotation.getEnd()
<= markable.getEnd()))
+                    && annotation.getEnd() - annotation.getBegin() < bestLength
) {
+                  bestLength = annotation.getEnd() - annotation.getBegin();
+                  overlapAnnotations.add( annotation );
+               }
+            }
+            if ( bestAnnotations.isEmpty() && bestLength != Integer.MAX_VALUE ) {
+               for ( IdentifiedAnnotation annotation : overlapAnnotations ) {
+                  if ( annotation.getEnd() - annotation.getBegin() == bestLength ) {
+                     bestAnnotations.add( annotation );
+                  }
+               }
+            }
+
+            if ( !bestAnnotations.isEmpty() ) {
+               annotationMap.put( markable, bestAnnotations );
+            } else {
+               annotationMap.put( markable, Collections.singletonList( markable ) );
+            }
+         }
+      }
+      return annotationMap;
+   }
+
+
+   /**
     * Finds the head node out of a few ConllDependencyNodes. Biased toward nouns.
     **/
    static public ConllDependencyNode getNominalHeadNode( final List<ConllDependencyNode>
nodes ) {

Modified: ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Option.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Option.java?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Option.java
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Option.java
Mon Jul  6 17:16:52 2020
@@ -30,22 +30,20 @@ public enum Option {
 
    PROSE_SENTENCE( "Prose Sentences",
          "Create Sentences when End of Line characters may not indicate sentence boundaries.",
-         "add SentenceDetectorAnnotatorBIO" //,
-//         "add EolSentenceFixer"
+         "add SentenceDetectorAnnotatorBIO classifierJarPath=/org/apache/ctakes/core/sentdetect/model.jar",
+         "add EolSentenceFixer",
+         "add MrsDrSentenceJoiner"
    ),
 
 
    PARAGRAPH( "Paragraphs",
          "Create Paragraphs based upon Whitespace.",
-         "add ParagraphAnnotator",
-         "add ParagraphSentenceFixer" ),
+         "add ParagraphAnnotator" ),
 
 
    LIST( "Lists",
          "Create Lists based upon formatted Sections.",
-         "add ListAnnotator",
-//         "add ListParagraphFixer",
-         "add ListSentenceFixer" ),
+         "add ListAnnotator" ),
 
 
    TOKEN( "Tokens",
@@ -60,7 +58,7 @@ public enum Option {
          "add Chunker",
          "addDescription adjuster.ChunkAdjuster NP,NP 1",
          "addDescription adjuster.ChunkAdjuster NP,PP,NP 2",
-         "// path to the xml file containing information for dictionary lookup configuration.",
+//         "// path to the xml file containing information for dictionary lookup configuration.",
 //         "cli LookupXml=l",
          "// umls credentials",
          "cli umlsUser=user",
@@ -155,11 +153,19 @@ public enum Option {
 
    // TODO make some sort of "enabled" list, so that a piper command is only added if previous
piper commands exist.
    public enum PiperLineRequirements {
-      LIST_PARAGRAPH_FIXER( "add ListParagraphFixer", "add ParagraphAnnotator", "add ListAnnotator"
),
-      SECTION_FILTER( "add SectionFilter", "add BsvRegexSectionizer" ),
-      SUBJECT_SECTION_FIXER( "add SubjectSectionFixer", "add BsvRegexSectionizer" ),
-      LIST_SENTENCE_FIXER( "add ListSentenceFixer", "add SentenceDetectorAnnotatorBIO", "add
ListAnnotator" ),
-      PARAGRAPH_SENTENCE_FIXER( "add ParagraphSentenceFixer", "add SentenceDetectorAnnotatorBIO",
"add ParagraphAnnotator" );
+      LIST_PARAGRAPH_FIXER( "add ListParagraphFixer",
+            "add ParagraphAnnotator",
+            "add ListAnnotator" ),
+      SECTION_FILTER( "add SectionFilter",
+            "add BsvRegexSectionizer" ),
+      SUBJECT_SECTION_FIXER( "add SubjectSectionFixer",
+            "add BsvRegexSectionizer" ),
+      LIST_SENTENCE_FIXER( "add ListSentenceFixer",
+            "add SentenceDetectorAnnotatorBIO classifierJarPath=/org/apache/ctakes/core/sentdetect/model.jar",
+            "add ListAnnotator" ),
+      PARAGRAPH_SENTENCE_FIXER( "add ParagraphSentenceFixer",
+            "add SentenceDetectorAnnotatorBIO classifierJarPath=/org/apache/ctakes/core/sentdetect/model.jar",
+            "add ParagraphAnnotator" );
 
       private final String _addable;
       private final String[] _requirements;

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/attribute_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/attribute_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/attribute_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/attribute_pom.xml
Mon Jul  6 17:16:52 2020
@@ -105,6 +105,20 @@
       </repository>
    </repositories>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
 
       <plugins>

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/coreference_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/coreference_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/coreference_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/coreference_pom.xml
Mon Jul  6 17:16:52 2020
@@ -119,6 +119,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/entity_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/entity_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/entity_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/entity_pom.xml
Mon Jul  6 17:16:52 2020
@@ -73,6 +73,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_coref_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_coref_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_coref_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_coref_pom.xml
Mon Jul  6 17:16:52 2020
@@ -121,6 +121,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_pom.xml
Mon Jul  6 17:16:52 2020
@@ -106,6 +106,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_coreference_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_coreference_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_coreference_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_coreference_pom.xml
Mon Jul  6 17:16:52 2020
@@ -112,6 +112,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_pom.xml
Mon Jul  6 17:16:52 2020
@@ -112,6 +112,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_coref_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_coref_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_coref_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_coref_pom.xml
Mon Jul  6 17:16:52 2020
@@ -116,6 +116,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_pom.xml
Mon Jul  6 17:16:52 2020
@@ -116,6 +116,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/token_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/token_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/token_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/token_pom.xml
Mon Jul  6 17:16:52 2020
@@ -62,6 +62,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/coreference_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/coreference_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/coreference_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/coreference_pom.xml
Mon Jul  6 17:16:52 2020
@@ -114,6 +114,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/entity_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/entity_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/entity_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/entity_pom.xml
Mon Jul  6 17:16:52 2020
@@ -67,6 +67,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_coref_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_coref_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_coref_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_coref_pom.xml
Mon Jul  6 17:16:52 2020
@@ -115,6 +115,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_pom.xml
Mon Jul  6 17:16:52 2020
@@ -99,6 +99,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_coreference_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_coreference_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_coreference_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_coreference_pom.xml
Mon Jul  6 17:16:52 2020
@@ -106,6 +106,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_pom.xml
Mon Jul  6 17:16:52 2020
@@ -107,6 +107,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_coref_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_coref_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_coref_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_coref_pom.xml
Mon Jul  6 17:16:52 2020
@@ -110,6 +110,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_pom.xml
Mon Jul  6 17:16:52 2020
@@ -110,6 +110,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/token_pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/token_pom.xml?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/token_pom.xml
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/token_pom.xml
Mon Jul  6 17:16:52 2020
@@ -56,6 +56,20 @@
 
    </dependencies>
 
+   <repositories>
+      <repository>
+         <id>apache.snapshots</id>
+         <name>Apache Development Snapshot Repository</name>
+         <url>https://repository.apache.org/content/groups/snapshots/</url>
+         <releases>
+            <enabled>false</enabled>
+         </releases>
+         <snapshots>
+            <enabled>true</enabled>
+         </snapshots>
+      </repository>
+   </repositories>
+
    <build>
       <plugins>
 

Modified: ctakes/trunk/ctakes-tiny-rest/src/main/webapp/index.jsp
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-tiny-rest/src/main/webapp/index.jsp?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-tiny-rest/src/main/webapp/index.jsp (original)
+++ ctakes/trunk/ctakes-tiny-rest/src/main/webapp/index.jsp Mon Jul  6 17:16:52 2020
@@ -16,8 +16,8 @@
       <br>
       <label>Process to: </label>
       <input type="button" class="button" value="FHIR" name="fhirjson" id="fhirjson"/>
-      <input type="button" class="button" value="Text" name="text" id="text"/>
-      <input type="button" class="button" value="Property" name="property" id="property"/>
+      <input type="button" class="button" value="Text" name="pretty" id="pretty"/>
+      <input type="button" class="button" value="Property" name="props" id="props"/>
       <input type="button" class="button" value="UMLS" name="umlsJson" id="umlsJson"/>
       <input type="button" class="button" value="CUI" name="cui" id="cui"/>
       <input type="button" class="button" value="XMI" name="xmi" id="xmi"/>

Modified: ctakes/trunk/ctakes-tiny-rest/src/main/webapp/js/app.js
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-tiny-rest/src/main/webapp/js/app.js?rev=1879557&r1=1879556&r2=1879557&view=diff
==============================================================================
--- ctakes/trunk/ctakes-tiny-rest/src/main/webapp/js/app.js (original)
+++ ctakes/trunk/ctakes-tiny-rest/src/main/webapp/js/app.js Mon Jul  6 17:16:52 2020
@@ -20,7 +20,7 @@ $(document).ready(function() {
              document.getElementById("resultText").innerHTML = "Error invoking REST call";
         }
     });
-     $('#text').click(function() {
+     $('#pretty').click(function() {
          document.getElementById("resultText").innerHTML = "Processing ...";
          try {
             $.ajax({
@@ -41,7 +41,7 @@ $(document).ready(function() {
              document.getElementById("resultText").innerHTML = "Error invoking REST call";
         }
     });
-     $('#property').click(function() {
+     $('#props').click(function() {
          document.getElementById("resultText").innerHTML = "Processing ...";
          try {
             $.ajax({



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