ctakes-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From seanfi...@apache.org
Subject svn commit: r1876941 [3/3] - in /ctakes/trunk: ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/ ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/ ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/ ctakes-asserti...
Date Fri, 24 Apr 2020 20:06:58 GMT
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,188 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ * <p>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p>
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.core.util.doc;
+
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
+import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
+import org.apache.log4j.Logger;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.cas.CASRuntimeException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+
+import java.util.Collection;
+import java.util.Objects;
+import java.util.regex.Pattern;
+
+/**
+ * Utility class for fetching document id
+ */
+final public class DocIdUtil {
+
+   // Added for CTAKES-365
+   static public final String NO_DOCUMENT_ID = "UnknownDocument";
+   static public final String NO_DOCUMENT_ID_PREFIX = "UnknownDocumentPrefix";
+
+   static private final Logger LOGGER = Logger.getLogger( "DocumentIDAnnotationUtil" );
+
+   static private final Pattern FILE_FIX_PATTERN = Pattern.compile( "[^A-Za-z0-9\\.]" );
+
+   static private long _noDocIdIndex = 1;
+
+   // Utility classes should be final and have only a private constructor
+   private DocIdUtil() {
+   }
+
+   /**
+    * Check the jcas for a document id.  Unlike {@link #getDeepDocumentId(JCas)},
+    * this method does not progress into deeper jcas layers/views.
+    *
+    * @param jcas ye olde ...
+    * @return the document id contained in the type "DocumentID" or {@link #NO_DOCUMENT_ID}
+    */
+   public static String getDocumentID( final JCas jcas ) {
+      if ( jcas == null ) {
+         // could throw an IllegalArgumentException,
+         // but a caller might be providing a null view, so a graceful handling is better
+         LOGGER.debug( "NULL CAS" );
+         return NO_DOCUMENT_ID;
+      }
+      final Collection<DocumentID> idSet = JCasUtil.select( jcas, DocumentID.class );
+      final DocumentID id = idSet.stream().filter( Objects::nonNull ).findAny().orElse( null );
+      if ( id == null ) {
+         return createDocumentId( jcas );
+      }
+      try {
+         return id.getDocumentID();
+      } catch ( CASRuntimeException casRTE ) {
+         final String newId = NO_DOCUMENT_ID + _noDocIdIndex;
+         _noDocIdIndex++;
+         LOGGER.warn( "document Id Annotation does not have the id feature set, setting to " + newId, casRTE );
+         id.setDocumentID( newId );
+         return newId;
+      }
+   }
+
+
+   /**
+    * Gets the document Id by progressing through 3 layers until an Id is found: starting JCas, Initial View, Plaintext View
+    *
+    * @param startingJcas initial JCas to start the checking
+    * @return Document Id from the starting JCas, the Initial View, the Plaintext View, or {@link #NO_DOCUMENT_ID}
+    */
+   static public String getDeepDocumentId( final JCas startingJcas ) {
+      String documentID = getDocumentID( startingJcas );
+      if ( documentID == null || documentID.equals( NO_DOCUMENT_ID ) ) {
+         LOGGER.debug( "Checking document Id for initial view" );
+         try {
+            final JCas viewJcas = startingJcas.getView( "_InitialView" );
+            documentID = getDocumentID( viewJcas );
+         } catch ( CASException | CASRuntimeException casE ) {
+            LOGGER.warn( casE.getMessage() );
+            documentID = NO_DOCUMENT_ID;
+         }
+         if ( documentID == null || documentID.equals( NO_DOCUMENT_ID ) ) {
+            LOGGER.debug( "Checking document Id for plaintext view" );
+            try {
+               final JCas viewJcas = startingJcas.getView( "plaintext" );
+               documentID = getDocumentID( viewJcas );
+            } catch ( CASException | CASRuntimeException casE ) {
+               LOGGER.warn( casE.getMessage() );
+               documentID = NO_DOCUMENT_ID;
+            }
+            if ( documentID == null || documentID.equals( NO_DOCUMENT_ID ) ) {
+               LOGGER.warn( "Unable to find DocumentIDAnnotation" );
+               return createDocumentId( startingJcas );
+            }
+         }
+      }
+      return documentID;
+   }
+
+   /**
+    * Create a unique id for the document that can be used for an output filename or url.
+    * Will be the source document file name if possible,
+    * otherwise the first 10 characters of the text plus text hashcode,
+    * or "Unknown_" and the current millis if there is no text.
+    * Non-alphanumeric characters are replaced with '_'.
+    *
+    * @param jcas -
+    * @return an ok document id
+    */
+   static public String getDocumentIdForFile( final JCas jcas ) {
+      String docId = getDeepDocumentId( jcas );
+      if ( docId == null || docId.isEmpty() ) {
+         String casDocText = jcas.getDocumentText();
+         if ( casDocText != null ) {
+            casDocText = casDocText.trim();
+            if ( !casDocText.isEmpty() ) {
+               docId = casDocText.substring( 0, Math.min( casDocText.length(), 10 ) ) + "_" + casDocText.hashCode();
+            }
+         }
+      }
+      if ( docId == null || docId.isEmpty() ) {
+         docId = "Unknown_" + System.currentTimeMillis();
+      }
+      return FILE_FIX_PATTERN.matcher( docId ).replaceAll( "_" );
+   }
+
+   /**
+    * @param jCas -
+    * @return {@link #NO_DOCUMENT_ID} plus an index based upon the number of documents without IDs fetched with this class.
+    * This may lead to documents having ids indexed out of order with respect to the order in which they were run.
+    */
+   static private String createDocumentId( final JCas jCas ) {
+      final String newId = NO_DOCUMENT_ID + _noDocIdIndex;
+      _noDocIdIndex++;
+      LOGGER.debug( "Creating document ID " + newId );
+      final DocumentID documentIDAnnotation = new DocumentID( jCas );
+      documentIDAnnotation.setDocumentID( newId );
+      documentIDAnnotation.addToIndexes();
+      return newId;
+   }
+
+   /**
+    * Check the jcas for a document id prefix.  Unlike {@link #getDeepDocumentId(JCas)},
+    * this method does not progress into deeper jcas layers/views.
+    *
+    * @param jcas ye olde ...
+    * @return the document id prefix contained in the type "DocumentIdPrefix" or {@link #NO_DOCUMENT_ID}
+    */
+   public static String getDocumentIdPrefix( final JCas jcas ) {
+      if ( jcas == null ) {
+         // could throw an IllegalArgumentException,
+         // but a caller might be providing a null view, so a graceful handling is better
+         LOGGER.debug( "NULL CAS" );
+         return NO_DOCUMENT_ID_PREFIX;
+      }
+      final Collection<DocumentIdPrefix> prefices = JCasUtil.select( jcas, DocumentIdPrefix.class );
+      final DocumentIdPrefix prefix = prefices.stream().filter( Objects::nonNull ).findAny().orElse( null );
+      if ( prefix == null ) {
+         LOGGER.debug( "No document id prefix information for " + getDocumentID( jcas ) );
+         return NO_DOCUMENT_ID_PREFIX;
+      }
+      try {
+         return prefix.getDocumentIdPrefix();
+      } catch ( CASRuntimeException casRTE ) {
+         LOGGER.debug( "No document id prefix information for " + getDocumentID( jcas ) );
+         return NO_DOCUMENT_ID_PREFIX;
+      }
+   }
+
+}

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java (from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java&r1=1876940&r2=1876941&rev=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java Fri Apr 24 20:06:57 2020
@@ -1,4 +1,4 @@
-package org.apache.ctakes.core.util;
+package org.apache.ctakes.core.util.doc;
 
 import org.apache.ctakes.typesystem.type.structured.Metadata;
 import org.apache.ctakes.typesystem.type.structured.SourceData;
@@ -40,7 +40,7 @@ final public class SourceMetadataUtil {
             return patientId;
          }
       }
-      final String docPrefix = DocumentIDAnnotationUtil.getDocumentIdPrefix( jcas );
+      final String docPrefix = DocIdUtil.getDocumentIdPrefix( jcas );
       if ( docPrefix != null && !docPrefix.isEmpty() ) {
          return docPrefix;
       }

Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,60 @@
+package org.apache.ctakes.core.util.log;
+
+import java.io.Closeable;
+import java.io.IOException;
+import java.util.TimerTask;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.TimeUnit;
+
+/**
+ * Dot Logger Usable in try as resource blocks.  Logs a dot every 0.5 seconds until a process completes.
+ *
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 3/18/2016
+ */
+final public class DotLogger implements Closeable {
+
+   static private final org.apache.log4j.Logger DOT_LOGGER = org.apache.log4j.Logger.getLogger( "ProgressAppender" );
+   static private final org.apache.log4j.Logger EOL_LOGGER = org.apache.log4j.Logger.getLogger( "ProgressDone" );
+
+   private final ExecutorService _timer;
+
+   /**
+    * Starts the Dot Logging
+    */
+   public DotLogger() {
+      _timer = Executors.newScheduledThreadPool( 1 );
+      ((ScheduledExecutorService)_timer).scheduleAtFixedRate(
+            new DotPlotter(), 500, 500, TimeUnit.MILLISECONDS );
+   }
+
+   /**
+    * {@inheritDoc}
+    */
+   @Override
+   public void close() throws IOException {
+      _timer.shutdownNow();
+      EOL_LOGGER.info( "" );
+   }
+
+   private class DotPlotter extends TimerTask {
+      private int _count = 0;
+
+      @Override
+      public void run() {
+         DOT_LOGGER.info( "." );
+         _count++;
+         if ( _count % 60 == 0 ) {
+            if ( _count % 120 == 0 ) {
+               EOL_LOGGER.info( " " + (_count / 2) );
+            } else {
+               DOT_LOGGER.info( " " + (_count / 2) + " " );
+            }
+         }
+      }
+   }
+
+}

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java (from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java&r1=1876940&r2=1876941&rev=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java Fri Apr 24 20:06:57 2020
@@ -1,4 +1,4 @@
-package org.apache.ctakes.core.util;
+package org.apache.ctakes.core.util.log;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.pipeline.ProgressManager;

Modified: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java (original)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java Fri Apr 24 20:06:57 2020
@@ -1,5 +1,6 @@
 package org.apache.ctakes.core.util;
 
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java Fri Apr 24 20:06:57 2020
@@ -1,15 +1,11 @@
 package org.apache.ctakes.coreference.ae;
 
-import java.io.*;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-
+import com.google.common.collect.HashMultiset;
+import com.google.common.collect.Multiset;
 import org.apache.ctakes.constituency.parser.util.TreeUtils;
 import org.apache.ctakes.core.config.ConfigParameterConstants;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
 import org.apache.ctakes.typesystem.type.relation.RelationArgument;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -31,8 +27,14 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.apache.uima.resource.ResourceInitializationException;
 import org.cleartk.util.ViewUriUtil;
 
-import com.google.common.collect.HashMultiset;
-import com.google.common.collect.Multiset;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
 
 @PipeBitInfo(
       name = "Coreference Score Writer",
@@ -105,7 +107,7 @@ public class CoreferenceChainScoringOutp
     try{
       filename = new File(ViewUriUtil.getURI(jCas));
     }catch(Exception e){
-      filename = new File(DocumentIDAnnotationUtil.getDocumentID(jCas));
+       filename = new File( DocIdUtil.getDocumentID( jCas ) );
     }
 
     JCas chainsCas = null;

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java Fri Apr 24 20:06:57 2020
@@ -3,8 +3,8 @@ package org.apache.ctakes.coreference.ae
 import org.apache.ctakes.core.ae.NamedEngine;
 import org.apache.ctakes.core.patient.PatientViewUtil;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
 import org.apache.ctakes.core.util.ListFactory;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.ctakes.coreference.ae.features.cluster.*;
 import org.apache.ctakes.coreference.ae.pairing.cluster.*;
 import org.apache.ctakes.coreference.util.ClusterMentionFetcher;

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java Fri Apr 24 20:06:57 2020
@@ -18,30 +18,11 @@
  */
 package org.apache.ctakes.coreference.ae;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
+import libsvm.svm_node;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.coreference.type.BooleanLabeledFS;
-import org.apache.ctakes.coreference.type.DemMarkable;
-import org.apache.ctakes.coreference.type.Markable;
-import org.apache.ctakes.coreference.type.MarkablePairSet;
-import org.apache.ctakes.coreference.type.NEMarkable;
-import org.apache.ctakes.coreference.type.PronounMarkable;
-import org.apache.ctakes.coreference.util.AbstractClassifier;
-import org.apache.ctakes.coreference.util.CorefConsts;
-import org.apache.ctakes.coreference.util.FSIteratorToList;
-import org.apache.ctakes.coreference.util.FeatureVector;
-import org.apache.ctakes.coreference.util.MarkableTreeUtils;
-import org.apache.ctakes.coreference.util.SvmVectorCreator;
-import org.apache.ctakes.coreference.util.SyntaxAttributeCalculator;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.coreference.type.*;
+import org.apache.ctakes.coreference.util.*;
 import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
 import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
 import org.apache.ctakes.typesystem.type.relation.RelationArgument;
@@ -59,7 +40,8 @@ import org.apache.uima.jcas.cas.NonEmpty
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import libsvm.svm_node;
+import java.io.File;
+import java.util.*;
 
 @PipeBitInfo(
 		name = "SVM Chain Creator (MiPACQ)",
@@ -146,7 +128,7 @@ public class MipacqSvmChainCreator exten
 		LinkedList<Annotation> lm = FSIteratorToList.convert(
 				jcas.getJFSIndexRepository().getAnnotationIndex(Markable.type).iterator());
 		Map<Markable, NonEmptyFSList> collectionRas = new HashMap<>();
-		String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);
+      String docName = DocIdUtil.getDocumentID( jcas );
 		logger.info("Classifying coreference in document: " + docName);
 //		ArrayList<CollectionTextRelation> chains = new ArrayList<CollectionTextRelation>();
 		int chainId = 0;

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java Fri Apr 24 20:06:57 2020
@@ -6,7 +6,7 @@ import org.apache.ctakes.core.patient.Pa
 import org.apache.ctakes.core.patient.PatientNoteStore;
 import org.apache.ctakes.core.patient.PatientViewUtil;
 import org.apache.ctakes.core.util.ListFactory;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.coreference.eval.EvaluationOfEventCoreference;
 import org.apache.ctakes.coreference.util.ThymeCasOrderer;
 import org.apache.ctakes.temporal.eval.Evaluation_ImplBase;
@@ -46,8 +46,6 @@ import java.net.MalformedURLException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.*;
-import java.util.stream.Collectors;
-import java.util.stream.IntStream;
 
 /**
  * Created by tmill on 2/22/18.

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java Fri Apr 24 20:06:57 2020
@@ -1,12 +1,6 @@
 package org.apache.ctakes.coreference.ae.features;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;
 import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
@@ -22,6 +16,8 @@ import org.apache.uima.jcas.cas.FSArray;
 import org.cleartk.ml.Feature;
 import org.cleartk.util.ViewUriUtil;
 
+import java.util.*;
+
 public class UMLSFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
 
   String docId = null;
@@ -140,9 +136,11 @@ public class UMLSFeatureExtractor implem
 
 	public static String getDocId(JCas jcas) {
 	  String docId = null;
-	  
-	  docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
-	  if(docId != DocumentIDAnnotationUtil.NO_DOCUMENT_ID) return docId;
+
+      docId = DocIdUtil.getDocumentID( jcas );
+      if ( docId != DocIdUtil.NO_DOCUMENT_ID ) {
+         return docId;
+      }
 	  
 	  try{
 	    if(jcas.getView(ViewUriUtil.URI) != null){

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java Fri Apr 24 20:06:57 2020
@@ -18,34 +18,14 @@
  */
 package org.apache.ctakes.coreference.cc;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.Scanner;
-
 import libsvm.svm_node;
-
 import org.apache.ctakes.constituency.parser.treekernel.TreeExtractor;
 import org.apache.ctakes.constituency.parser.util.TreeUtils;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.coreference.type.BooleanLabeledFS;
-import org.apache.ctakes.coreference.type.DemMarkable;
-import org.apache.ctakes.coreference.type.Markable;
-import org.apache.ctakes.coreference.type.MarkablePairSet;
-import org.apache.ctakes.coreference.type.NEMarkable;
-import org.apache.ctakes.coreference.util.CorefConsts;
-import org.apache.ctakes.coreference.util.FSIteratorToList;
-import org.apache.ctakes.coreference.util.GoldStandardLabeler;
-import org.apache.ctakes.coreference.util.MarkableTreeUtils;
-import org.apache.ctakes.coreference.util.PairAttributeCalculator;
-import org.apache.ctakes.coreference.util.SvmVectorCreator;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.coreference.type.*;
+import org.apache.ctakes.coreference.util.*;
 import org.apache.ctakes.relationextractor.eval.XMIReader;
 import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 import org.apache.ctakes.utils.tree.SimpleTree;
@@ -56,15 +36,19 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.FSIterator;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.apache.uima.fit.factory.AnalysisEngineFactory;
-import org.apache.uima.fit.factory.CollectionReaderFactory;
-import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
-import org.apache.uima.fit.pipeline.SimplePipeline;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.Scanner;
 
 @PipeBitInfo(
 		name = "ODIE Vector File Writer",
@@ -211,7 +195,7 @@ public class ODIEVectorFileWriter extend
 //			return;
 //		}
 
-		String docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
+      String docId = DocIdUtil.getDocumentID( jcas );
 		docId = docId.substring(docId.lastIndexOf('/')+1, docId.length());
 //		Hashtable<Integer, Integer> sysId2AlignId = new Hashtable<Integer, Integer>();
 //		Hashtable<Integer, Integer> goldId2AlignId = new Hashtable<Integer, Integer>();

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.coreference.cc;
 
 import org.apache.ctakes.core.config.ConfigParameterConstants;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.uima.UIMAException;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -122,8 +122,8 @@ public class PreprocessAndWriteXmi {
             // FIXME - not using this right now, just use default jcas
 //				JCas goldView = jCas.getView(RelationExtractorEvaluation.GOLD_VIEW_NAME);
             JCas goldView = jCas;
-            String documentID = DocumentIDAnnotationUtil.getDocumentID( goldView );
-            if ( documentID == null || documentID.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+            String documentID = DocIdUtil.getDocumentID( goldView );
+            if ( documentID == null || documentID.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
                throw new IllegalArgumentException( "No documentID for CAS:\n" + jCas );
             }
             File outFile = new File( this.outputDirectory, documentID + ".xmi" );

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java Fri Apr 24 20:06:57 2020
@@ -16,7 +16,7 @@ import org.apache.ctakes.core.patient.Pa
 import org.apache.ctakes.core.patient.PatientViewUtil;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.coreference.ae.*;
 import org.apache.ctakes.coreference.factory.CoreferenceAnnotatorFactory;
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;
@@ -26,7 +26,10 @@ import org.apache.ctakes.temporal.ae.Doc
 import org.apache.ctakes.temporal.ae.EventAnnotator;
 import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
 import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase;
-import org.apache.ctakes.typesystem.type.relation.*;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
+import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
+import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -508,8 +511,8 @@ public class EvaluationOfEventCoreferenc
     static Logger logger = Logger.getLogger(DocumentIDPrinter.class);
     @Override
     public void process(JCas jCas) throws AnalysisEngineProcessException {
-      String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
-      if(docId.startsWith(DocumentIDAnnotationUtil.NO_DOCUMENT_ID)){
+       String docId = DocIdUtil.getDocumentID( jCas );
+       if ( docId.startsWith( DocIdUtil.NO_DOCUMENT_ID ) ) {
         docId = new File(ViewUriUtil.getURI(jCas)).getName();
       }
       logger.info(String.format("Processing %s\n", docId));

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java Fri Apr 24 20:06:57 2020
@@ -43,7 +43,7 @@ package org.apache.ctakes.dependency.par
 
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.log4j.Logger;
@@ -100,10 +100,10 @@ public class DependencyNodeWriter extend
    private void processView( JCas jCas ) throws Exception {
       // String docText = view.getDocumentText();
 
-      String docName = DocumentIDAnnotationUtil.getDocumentID( jCas );
+      String docName = DocIdUtil.getDocumentID( jCas );
 
       File outputFile;
-      if ( docName == null || docName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+      if ( docName == null || docName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
          docName = "doc" + iv_procCount + "." + iv_outputFormat.toLowerCase();
       } else {
          docName = docName + "." + iv_outputFormat.toLowerCase();

Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.dictionary.lookup2.util;
 
 import org.apache.ctakes.core.ae.UmlsEnvironmentConfiguration;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.ctakes.utils.env.EnvironmentVariable;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;

Modified: ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java (original)
+++ ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java Fri Apr 24 20:06:57 2020
@@ -151,17 +151,17 @@ final public class SystemUtil {
       processBuilder.command( "cmd.exe", "/c", command.replace( '/', '\\' ) );
       final Process process = processBuilder.start();
 
-      final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
-      String line;
-      while ( (line = reader.readLine()) != null ) {
-         System.out.println( line );
-      }
-
-      final BufferedReader errors = new BufferedReader( new InputStreamReader( process.getErrorStream() ) );
-      String error;
-      while ( (error = errors.readLine()) != null ) {
-         System.err.println( error );
-      }
+//      final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
+//      String line;
+//      while ( (line = reader.readLine()) != null ) {
+//         System.out.println( line );
+//      }
+//
+//      final BufferedReader errors = new BufferedReader( new InputStreamReader( process.getErrorStream() ) );
+//      String error;
+//      while ( (error = errors.readLine()) != null ) {
+//         System.err.println( error );
+//      }
 
       int exitCode = process.waitFor();
 //      System.out.println( "\nCMD Exited with error code : " + exitCode );
@@ -177,12 +177,12 @@ final public class SystemUtil {
       processBuilder.command( "bash", "-c", command );
       final Process process = processBuilder.start();
 
-      final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
-
-      String line;
-      while ( (line = reader.readLine()) != null ) {
-         System.out.println( line );
-      }
+//      final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
+//
+//      String line;
+//      while ( (line = reader.readLine()) != null ) {
+//         System.out.println( line );
+//      }
 
       int exitCode = process.waitFor();
 //      System.out.println( "\nBASH Exited with error code : " + exitCode );

Modified: ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java (original)
+++ ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java Fri Apr 24 20:06:57 2020
@@ -18,99 +18,26 @@
  */
 package org.apache.ctakes.drugner.ae;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
 import org.apache.ctakes.core.ae.TokenizerAnnotator;
-import org.apache.ctakes.core.fsm.adapters.ContractionTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.DecimalTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.NewlineTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.PunctuationTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.SymbolTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.WordTokenAdapter;
+import org.apache.ctakes.core.fsm.adapters.*;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DateParser;
+import org.apache.ctakes.core.util.CalendarUtil;
 import org.apache.ctakes.core.util.FSUtil;
 import org.apache.ctakes.core.util.JCasUtil;
 import org.apache.ctakes.core.util.ParamUtil;
 import org.apache.ctakes.drugner.DrugMention;
 import org.apache.ctakes.drugner.elements.DrugChangeStatusElement;
-import org.apache.ctakes.drugner.fsm.machines.elements.DecimalStrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FormFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM;
+import org.apache.ctakes.drugner.fsm.machines.elements.*;
 import org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM;
 import org.apache.ctakes.drugner.fsm.machines.util.SuffixStrengthFSM;
-import org.apache.ctakes.drugner.fsm.output.elements.BaseTokenImpl;
-import org.apache.ctakes.drugner.fsm.output.elements.DosageToken;
-import org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken;
-import org.apache.ctakes.drugner.fsm.output.elements.DurationToken;
-import org.apache.ctakes.drugner.fsm.output.elements.FormToken;
-import org.apache.ctakes.drugner.fsm.output.elements.FrequencyToken;
-import org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken;
-import org.apache.ctakes.drugner.fsm.output.elements.RouteToken;
-import org.apache.ctakes.drugner.fsm.output.elements.StrengthToken;
-import org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitCombinedToken;
-import org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitToken;
+import org.apache.ctakes.drugner.fsm.output.elements.*;
 import org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator;
 import org.apache.ctakes.drugner.fsm.output.util.SuffixStrengthToken;
-import org.apache.ctakes.drugner.type.ChunkAnnotation;
-import org.apache.ctakes.drugner.type.DecimalStrengthAnnotation;
-import org.apache.ctakes.drugner.type.DosagesAnnotation;
-import org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation;
-import org.apache.ctakes.drugner.type.DrugMentionAnnotation;
-import org.apache.ctakes.drugner.type.DurationAnnotation;
-import org.apache.ctakes.drugner.type.FormAnnotation;
-import org.apache.ctakes.drugner.type.FractionStrengthAnnotation;
-import org.apache.ctakes.drugner.type.FrequencyAnnotation;
-import org.apache.ctakes.drugner.type.FrequencyUnitAnnotation;
-import org.apache.ctakes.drugner.type.RangeStrengthAnnotation;
-import org.apache.ctakes.drugner.type.RouteAnnotation;
-import org.apache.ctakes.drugner.type.StrengthAnnotation;
-import org.apache.ctakes.drugner.type.StrengthUnitAnnotation;
-import org.apache.ctakes.drugner.type.SubSectionAnnotation;
-import org.apache.ctakes.drugner.type.SuffixStrengthAnnotation;
+import org.apache.ctakes.drugner.type.*;
 import org.apache.ctakes.typesystem.type.constants.CONST;
-import org.apache.ctakes.typesystem.type.refsem.Date;
-import org.apache.ctakes.typesystem.type.refsem.MedicationDosage;
-import org.apache.ctakes.typesystem.type.refsem.MedicationDuration;
-import org.apache.ctakes.typesystem.type.refsem.MedicationForm;
-import org.apache.ctakes.typesystem.type.refsem.MedicationFrequency;
-import org.apache.ctakes.typesystem.type.refsem.MedicationRoute;
-import org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange;
-import org.apache.ctakes.typesystem.type.refsem.MedicationStrength;
-import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
-import org.apache.ctakes.typesystem.type.syntax.BaseToken;
-import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
-import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
-import org.apache.ctakes.typesystem.type.syntax.NumToken;
-import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
-import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
-import org.apache.ctakes.typesystem.type.syntax.WordToken;
-import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
-import org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier;
-import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.ctakes.typesystem.type.refsem.*;
+import org.apache.ctakes.typesystem.type.syntax.*;
+import org.apache.ctakes.typesystem.type.textsem.*;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.log4j.Logger;
@@ -123,9 +50,10 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.apache.uima.resource.ResourceAccessException;
 import org.apache.uima.resource.ResourceInitializationException;
 
+import java.util.*;
+
 
 /**
  * Finds tokens based on context. There are two major groupings or ranges that
@@ -404,13 +332,15 @@ public class DrugMentionAnnotator extend
 			medicationMention.setMedicationStrength(modifier);
 		}
 
-		if (fromAnnotation.getStartDate()!=null) {
-			Date d = DateParser.parse(jcas, fromAnnotation.getStartDate());
-			TimeMention timeMention = new TimeMention(jcas);
-			timeMention.setDate(d);
-			timeMention.setTimeClass(CONST.TIME_CLASS_DATE);
+      if ( fromAnnotation.getStartDate() != null ) {
+//			Date d = DateParser.parse(jcas, fromAnnotation.getStartDate());
+//			TimeMention timeMention = new TimeMention(jcas);
+//			timeMention.setDate(d);
+//			timeMention.setTimeClass(CONST.TIME_CLASS_DATE);
 			// if (d!=null) d.addToIndexes(); // don't need to be able to get these directly from the AnnotationIndex
-			if (d!=null) medicationMention.setStartDate(timeMention);
+//			if (d!=null) medicationMention.setStartDate(timeMention);
+         final TimeMention timeMention = CalendarUtil.createTimeMention( jcas, fromAnnotation.getStartDate() );
+         medicationMention.setStartDate( timeMention );
 		}
 		// Add fix CTAKES-129 Populate the Drug NER named entity confidence attribute 
 		if (fromAnnotation.getConfidence() != 0.0 ) {

Modified: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper (original)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper Fri Apr 24 20:06:57 2020
@@ -1,34 +1,48 @@
+//set InputFileName=C:/Spiffy/ctakes_data/alon_geva/temp/temp.txt
+//reader LinesFromFileCollectionReader
 
 // Advanced Tokenization: Regex sectionization, BIO Sentence Detector (lumper), Paragraphs, Lists
-load FullTokenizerPipeline
+//load FullTokenizerPipeline
 // OR use the standard tokenizer pipeline:
 //load DefaultTokenizerPipeline
 
+add BsvRegexSectionizer SectionsBsv=org/apache/ctakes/core/sections/NaaccrXmlSections.bsv
+
+add SectionFilter ValidSectionList=org/apache/ctakes/core/sections/NaaccrXmlSections.bsv
+
+add SentenceDetector
+add TokenizerAnnotatorPTB
+
 // Always need these ...
-add ContextDependentTokenizerAnnotator
+//add ContextDependentTokenizerAnnotator
 add POSTagger
 
 // Chunkers
-load ChunkerSubPipe
+//load ChunkerSubPipe
 
 // Default fast dictionary lookup
-set minimumSpan=2
+//set minimumSpan=2
 load DictionarySubPipe
 
 // Cleartk Entity Attributes (negation, uncertainty, etc.)
-load AttributeCleartkSubPipe
+//load AttributeCleartkSubPipe
+
+//package org.apache.ctakes.examples.ae
+//add BodySideFinder
 
 // Entity Relations (degree/severity, anatomical location)
-load RelationSubPipe
+//load RelationSubPipe
 
 // Temporal (event, time, dtr, tlink)
-load TemporalSubPipe
+//load TemporalSubPipe
 
 // Coreferences (e.g. patient = he)
-load CorefSubPipe
+//load CorefSubPipe
 
 // Html output
 add pretty.html.HtmlTextWriter
 
 // XMI output
 //writeXmis
+
+//add SentenceFirstCuiWriter

Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java Fri Apr 24 20:06:57 2020
@@ -18,21 +18,14 @@
  */
 package org.apache.ctakes.examples.pipeline;
 
-import java.io.IOException;
-
-import org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine;
+import org.apache.ctakes.assertion.medfacts.cleartk.*;
 import org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator;
 import org.apache.ctakes.core.ae.SentenceDetector;
 import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
 import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
 import org.apache.ctakes.core.config.ConfigParameterConstants;
 import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
 import org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator;
 import org.apache.ctakes.lvg.ae.ThreadSafeLvg;
@@ -53,6 +46,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.ProcessTrace;
 
+import java.io.IOException;
+
 public class MultiThreadedPipeline {
 
   public static final int NUM_THREADS = 3;
@@ -152,7 +147,7 @@ public class MultiThreadedPipeline {
     public void entityProcessComplete(CAS aCas, EntityProcessStatus aStatus) {
       try {
         JCas jcas = aCas.getJCas();
-        String docId = DocumentIDAnnotationUtil.getDeepDocumentId(jcas);
+         String docId = DocIdUtil.getDeepDocumentId( jcas );
         System.out.println("Doc id for entity process complete: " + docId);
         System.out.println("Found " + JCasUtil.select(jcas, IdentifiedAnnotation.class).size() + " medical terms.");
         // The following was a bit verbose, but here's how you'd print out the text of each discovered entity span:

Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
 package org.apache.ctakes.fhir.cc;
 
 
-import org.apache.ctakes.core.util.EssentialAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.EssentialAnnotationUtil;
 import org.apache.ctakes.fhir.element.FhirElementFactory;
 import org.apache.ctakes.fhir.resource.*;
 import org.apache.ctakes.fhir.util.FhirNoteSpecs;

Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java Fri Apr 24 20:06:57 2020
@@ -3,8 +3,8 @@ package org.apache.ctakes.fhir.element;
 
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import org.apache.ctakes.core.semantic.SemanticGroup;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.refsem.Event;
 import org.apache.ctakes.typesystem.type.refsem.EventProperties;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
@@ -161,7 +161,7 @@ final public class FhirElementFactory {
     * @return fhir id containing name and code.
     */
    static public String createId( final JCas jCas, final String name, final String code ) {
-      return DocumentIDAnnotationUtil.getDocumentID( jCas ) + DIVIDER_CHAR + name + DIVIDER_CHAR + code;
+      return DocIdUtil.getDocumentID( jCas ) + DIVIDER_CHAR + name + DIVIDER_CHAR + code;
    }
 
 //   Identifiers are 0 .. 1 , so unnecessary

Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java Fri Apr 24 20:06:57 2020
@@ -1,8 +1,8 @@
 package org.apache.ctakes.fhir.resource;
 
 import org.apache.ctakes.core.semantic.SemanticGroup;
-import org.apache.ctakes.core.util.EssentialAnnotationUtil;
-import org.apache.ctakes.core.util.IdentifiedAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.EssentialAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.IdentifiedAnnotationUtil;
 import org.apache.ctakes.fhir.element.FhirElementFactory;
 import org.apache.ctakes.fhir.util.FhirNoteSpecs;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;

Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.fhir.util;
 
 
 import org.apache.ctakes.core.note.NoteSpecs;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.fhir.element.FhirElementFactory;
 import org.apache.ctakes.typesystem.type.structured.SourceData;
 import org.apache.log4j.Logger;

Modified: ctakes/trunk/ctakes-gui/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/pom.xml?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/pom.xml (original)
+++ ctakes/trunk/ctakes-gui/pom.xml Fri Apr 24 20:06:57 2020
@@ -18,10 +18,6 @@
          <groupId>org.apache.ctakes</groupId>
          <artifactId>ctakes-gui-res</artifactId>
       </dependency>
-      <!--      <dependency>-->
-      <!--         <groupId>org.apache.ctakes</groupId>-->
-      <!--          <artifactId>ctakes-coreference</artifactId>-->
-      <!--      </dependency>-->
        <dependency>
            <groupId>org.apache.ctakes</groupId>
            <artifactId>ctakes-core</artifactId>

Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java Fri Apr 24 20:06:57 2020
@@ -5,7 +5,7 @@ import io.github.lukehutch.fastclasspath
 import io.github.lukehutch.fastclasspathscanner.ScanInterruptedException;
 import io.github.lukehutch.fastclasspathscanner.matchprocessor.SubclassMatchProcessor;
 import io.github.lukehutch.fastclasspathscanner.scanner.ScanResult;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.log4j.Logger;
 import org.apache.uima.analysis_component.Annotator_ImplBase;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java Fri Apr 24 20:06:57 2020
@@ -25,7 +25,7 @@ import com.google.common.collect.Orderin
 import com.lexicalscope.jewel.cli.Option;
 import org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.uima.UIMAFramework;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -183,7 +183,7 @@ public class SHARPXMI {
          for ( Iterator<JCas> casIter = new JCasIterator( reader, builder.createAggregate() ); casIter.hasNext(); ) {
             JCas jCas = casIter.next();
             JCas goldView = jCas.getView( GOLD_VIEW_NAME );
-            String documentID = DocumentIDAnnotationUtil.getDocumentID( goldView );
+            String documentID = DocIdUtil.getDocumentID( goldView );
             if ( documentID == null ){//|| documentID.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
                throw new IllegalArgumentException( "No documentID for CAS:\n" + jCas );
             }

Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java Fri Apr 24 20:06:57 2020
@@ -18,18 +18,11 @@
  */
 package org.apache.ctakes.sideeffect.ae;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
+import org.apache.ctakes.core.util.FSUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.sideeffect.type.PSESentence;
+import org.apache.ctakes.sideeffect.type.PSESentenceFeature;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -38,11 +31,11 @@ import org.apache.uima.jcas.JFSIndexRepo
 import org.apache.uima.jcas.cas.StringArray;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.FSUtil;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.sideeffect.type.PSESentence;
-import org.apache.ctakes.sideeffect.type.PSESentenceFeature;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.*;
 
 /**
  * Extract SE sentence (from PSESentence) features and add them to
@@ -76,7 +69,7 @@ public class SESentenceFeatureAnnotator
 
 	public void process(JCas jcas)
 			throws AnalysisEngineProcessException {
-		String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);
+      String docName = DocIdUtil.getDocumentID( jcas );
 		System.out.println("---" + docName + "---");
 
 		// add features to cas

Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java Fri Apr 24 20:06:57 2020
@@ -18,17 +18,16 @@
  */
 package org.apache.ctakes.sideeffect.ae;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.core.util.FSUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.drugner.type.SubSectionAnnotation;
+import org.apache.ctakes.sideeffect.type.SESentence;
+import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
+import org.apache.ctakes.sideeffect.util.PatternMatch;
+import org.apache.ctakes.sideeffect.util.SEUtil;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -36,16 +35,10 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import org.apache.ctakes.core.resource.FileResource;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.FSUtil;
-import org.apache.ctakes.sideeffect.util.PatternMatch;
-import org.apache.ctakes.sideeffect.util.SEUtil;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.ctakes.drugner.type.SubSectionAnnotation;
-import org.apache.ctakes.sideeffect.type.SESentence;
-import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.util.*;
 
 /**
  * Rule-based side effect extraction. 
@@ -157,8 +150,8 @@ public class SideEffectAnnotator extends
 	{
 		List<PotentialSideEffect> potentialSideEffectLst;
 		List<SideEffect> sideEffectLst;
-		
-        String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);        
+
+      String docName = DocIdUtil.getDocumentID( jcas );
         System.out.println("---"+docName+" processed---");
         
         //remove duplicated named entities

Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -18,13 +18,8 @@
  */
 package org.apache.ctakes.sideeffect.cc;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Iterator;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
 import org.apache.ctakes.sideeffect.util.SEUtil;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -34,7 +29,11 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
 
-import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Iterator;
 
 public class SideEffectCasConsumer extends CasConsumer_ImplBase {
 	public static final String PARAM_OUTPUT_FILE = "OutputFile";
@@ -73,10 +72,10 @@ public class SideEffectCasConsumer exten
 			if(jcas == null){
 				jcas = cas.getJCas(); 
 			}
-			
-			JFSIndexRepository indexes = jcas.getJFSIndexRepository();			
-			
-	        String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);        
+
+         JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+
+         String docName = DocIdUtil.getDocumentID( jcas );
 
 	        Iterator seIter = indexes.getAnnotationIndex(SideEffectAnnotation.type).iterator();
 	        while(seIter.hasNext()) {

Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -18,13 +18,8 @@
  */
 package org.apache.ctakes.sideeffect.cc;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Iterator;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.sideeffect.type.SESentence;
 import org.apache.ctakes.sideeffect.util.SEUtil;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -34,7 +29,11 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
 
-import org.apache.ctakes.sideeffect.type.SESentence;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Iterator;
 
 public class SideEffectSentenceCasConsumer extends CasConsumer_ImplBase {
 	public static final String PARAM_OUTPUT_FILE = "OutputFile";
@@ -65,9 +64,9 @@ public class SideEffectSentenceCasConsum
 		try {
 			JCas jcas;
 			jcas = SEUtil.getJCasViewWithDefault(cas, "plaintext");
-			JFSIndexRepository indexes = jcas.getJFSIndexRepository();			
-			
-	        String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);        
+         JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+
+         String docName = DocIdUtil.getDocumentID( jcas );
 
 	        Iterator ssIter = indexes.getAnnotationIndex(SESentence.type).iterator();
 	        while(ssIter.hasNext()) {

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=1876941&r1=1876940&r2=1876941&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 Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.temporal.ae;
 
 import com.google.common.collect.Lists;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.ctakes.temporal.ae.feature.ParseSpanFeatureExtractor;
 import org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
 package org.apache.ctakes.temporal.ae;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.temporal.utils.CalendarUtil;
 import org.apache.ctakes.typesystem.type.structured.SourceData;
 import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;

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=1876941&r1=1876940&r2=1876941&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 Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.temporal.ae;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.ctakes.temporal.ae.feature.*;
 import org.apache.ctakes.temporal.utils.SoftMaxUtil;
 import org.apache.ctakes.typesystem.type.refsem.Event;

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=1876941&r1=1876940&r2=1876941&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 Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.temporal.ae;
 
 import com.google.common.collect.Lists;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
 import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
 import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;

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=1876941&r1=1876940&r2=1876941&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 Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.temporal.ae;
 
 import com.google.common.collect.Lists;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
 import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
 import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java Fri Apr 24 20:06:57 2020
@@ -2,8 +2,8 @@ package org.apache.ctakes.temporal.ae;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
 import org.apache.ctakes.core.util.Pair;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.temporal.utils.CalendarUtil;
 import org.apache.ctakes.typesystem.type.refsem.Date;
 import org.apache.ctakes.typesystem.type.syntax.Chunk;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.temporal.ae;
 
 
 import com.google.common.collect.Lists;
-import org.apache.ctakes.core.util.WordTokenUtil;
+import org.apache.ctakes.core.util.annotation.WordTokenUtil;
 import org.apache.ctakes.typesystem.type.relation.RelationArgument;
 import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java Fri Apr 24 20:06:57 2020
@@ -18,28 +18,22 @@
  */
 package org.apache.ctakes.temporal.ae.feature;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-//import java.util.logging.Logger;
-import java.util.Set;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
-import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.cleartk.ml.Feature;
 import org.cleartk.ml.feature.extractor.CleartkExtractorException;
 import org.cleartk.ml.feature.extractor.FeatureExtractor1;
-import org.cleartk.util.ViewUriUtil;
+
+import java.util.*;
+
+//import java.util.logging.Logger;
 
 public class EventPropertyExtractor implements FeatureExtractor1<Annotation> {
 
@@ -87,7 +81,7 @@ public class EventPropertyExtractor impl
 		//get Document ID:
 		String fname;
 		try {
-			String docID = DocumentIDAnnotationUtil.getDocumentID(view);//ViewUriUtil.getURI(view).toString();
+         String docID = DocIdUtil.getDocumentID( view );//ViewUriUtil.getURI(view).toString();
 			
 			int begin = docID.lastIndexOf("_");
 			fname = docID.substring(begin+1);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java Fri Apr 24 20:06:57 2020
@@ -18,26 +18,24 @@
  */
 package org.apache.ctakes.temporal.ae.feature;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Multimap;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
 import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
-import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.cleartk.ml.Feature;
 import org.cleartk.util.ViewUriUtil;
-import org.apache.uima.fit.util.JCasUtil;
 
-import com.google.common.collect.HashMultimap;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Multimap;
+import java.util.ArrayList;
+import java.util.List;
 /**
  * Given a pair of arguments, if any one of them is an event, get the related event-sectiontime as features 
  * @author CH151862
@@ -58,7 +56,7 @@ RelationFeaturesExtractor<IdentifiedAnno
 		try{
 			docId = ViewUriUtil.getURI(jCas).toString();// get docID
 		}catch(Exception e){
-			docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+         docId = DocIdUtil.getDocumentID( jCas );
 		}
 		if(!docId.equals(cachedDocID)){
 			// rebuild cache

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java Fri Apr 24 20:06:57 2020
@@ -18,13 +18,8 @@
  */
 package org.apache.ctakes.temporal.ae.feature;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
 import org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
@@ -36,21 +31,14 @@ import org.apache.uima.fit.util.JCasUtil
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.cleartk.ml.Feature;
-import org.cleartk.ml.feature.extractor.CleartkExtractor;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Bag;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Covered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Following;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding;
-import org.cleartk.ml.feature.extractor.CombinedExtractor1;
-import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
-import org.cleartk.ml.feature.extractor.DistanceExtractor;
-import org.cleartk.ml.feature.extractor.FeatureExtractor1;
-import org.cleartk.ml.feature.extractor.NamingExtractor1;
+import org.cleartk.ml.feature.extractor.*;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.*;
 import org.cleartk.util.ViewUriUtil;
 
-import com.google.common.collect.Multimap;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
 
 /**
  * for every UMLS entities covering the annotation, extracted related token features
@@ -114,7 +102,7 @@ public class MultiTokenFeaturesExtractor
 		try{
 			docId = ViewUriUtil.getURI(jCas).toString();// get docID
 		}catch(Exception e){
-			docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+         docId = DocIdUtil.getDocumentID( jCas );
 		}
 		if(!docId.equals(cachedDocID)){
 			// rebuild event-event map

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java Fri Apr 24 20:06:57 2020
@@ -1,24 +1,8 @@
 package org.apache.ctakes.temporal.nn.ae;
 
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
+import com.google.common.collect.Lists;
 import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
 import org.apache.ctakes.temporal.nn.ae.EventTimeTokenBasedAnnotator.OutputMode;
 import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
@@ -39,7 +23,9 @@ import org.cleartk.ml.Feature;
 import org.cleartk.ml.Instance;
 import org.cleartk.util.ViewUriUtil;
 
-import com.google.common.collect.Lists;
+import java.io.*;
+import java.util.*;
+import java.util.Map.Entry;
 /**
  * a joint annotator for annotating both event-time and event-event relations using neural models.
  * @author chenlin

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java Fri Apr 24 20:06:57 2020
@@ -26,6 +26,7 @@ import static java.util.Calendar.*;
  * @author SPF , chip-nlp
  * @version %I%
  * @since 1/8/2019
+ * @deprecated use CalendarUtil in core.util
  */
 final public class CalendarUtil {
 



Mime
View raw message