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From seanfi...@apache.org
Subject svn commit: r1876941 [1/3] - 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
Author: seanfinan
Date: Fri Apr 24 20:06:57 2020
New Revision: 1876941

URL: http://svn.apache.org/viewvc?rev=1876941&view=rev
Log:
Refactoring :
DocumentIDAnnotationUtil - renamed to DocIdUtil and moved to core.util.doc
WordTokenUtil - moved to core.util.annotation
DotLogger - moved to core.util.log
OntologyConceptUtil - moved to core.util.annotation
SourceMetadataUtil - moved to core.util.doc
EssentialAnnotationUtil - moved to core.util.annotation

ListParagraphFixer - Splits paragraphs by list entries
MrsDrSentenceJoiner - Removes Sentence breaks cause by Mrs. Mr. Dr. a.m. p.m.
IdentifiedAnnotationUtil - convenience methods for common identifiedAnnotation inquiries
CalendarUtil - Can create normalized calendar from text snippets, can create TimeMentions
SystemUtil - commented cmd output
ctakes-gui pom - removed ctakes-coreference dependency

Added:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CalendarUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
      - copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java
      - copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java
      - copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java
      - copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java
Removed:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/IdentifiedAnnotationUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java
Modified:
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
    ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
    ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java
    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/ae/SectionSegmentAnnotator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/SemanticGroup.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/note/NoteSpecs.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DateParser.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/EssentialAnnotationUtil.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java
    ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java
    ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
    ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
    ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java
    ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java
    ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
    ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java
    ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java
    ctakes/trunk/ctakes-gui/pom.xml
    ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java
    ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java
    ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java
    ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java
    ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java Fri Apr 24 20:06:57 2020
@@ -37,20 +37,9 @@ package org.apache.ctakes.assertion.cc;
  * under the License.
  */
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-
 import org.apache.ctakes.assertion.eval.AssertionEvaluation.Options;
 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.constants.CONST;
 import org.apache.ctakes.typesystem.type.relation.Relation;
 import org.apache.ctakes.typesystem.type.relation.RelationArgument;
@@ -64,7 +53,6 @@ import org.apache.uima.cas.impl.XCASSeri
 import org.apache.uima.cas.impl.XmiCasSerializer;
 import org.apache.uima.fit.component.JCasConsumer_ImplBase;
 import org.apache.uima.fit.descriptor.ConfigurationParameter;
-import org.apache.uima.fit.factory.initializable.InitializableFactory;
 import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.TOP;
@@ -72,6 +60,13 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.util.XMLSerializer;
 import org.xml.sax.SAXException;
 
+import java.io.*;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+
 /**
  * 
  * A simple CAS consumer that generates XCAS (XML representation of the CAS) files in the
@@ -178,7 +173,7 @@ public class JudgeAttributeInstances ext
 
 	@Override
 	public void process(JCas jCas) throws AnalysisEngineProcessException {
-		String sourceFileName = DocumentIDAnnotationUtil.getDocumentID(jCas);
+      String sourceFileName = DocIdUtil.getDocumentID( jCas );
 		System.out.println("==================\nFile: "+sourceFileName);
 		deletableMentions = new ArrayList<IdentifiedAnnotation>();
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java Fri Apr 24 20:06:57 2020
@@ -18,32 +18,30 @@
  */
 package org.apache.ctakes.assertion.cr;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.core.util.Mapper;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.jdom.Document;
 import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;
-import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 
-import org.apache.ctakes.typesystem.type.constants.CONST;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.EventMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.Mapper;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
 
 /**
  * Read named entity annotations from knowtator xml files into the CAS
@@ -83,8 +81,8 @@ public class GoldEntityAndAttributeReade
         initView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
       } catch (CASException e) {
         throw new AnalysisEngineProcessException(e);
-      } 
-			String goldFilePath = inputDirectory + DocumentIDAnnotationUtil.getDocumentID(jCas) + ".knowtator.xml";
+      }
+      String goldFilePath = inputDirectory + DocIdUtil.getDocumentID( jCas ) + ".knowtator.xml";
 			
       SAXBuilder builder = new SAXBuilder();
       Document document;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java Fri Apr 24 20:06:57 2020
@@ -18,45 +18,19 @@
  */
 package org.apache.ctakes.assertion.eval;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
+import com.google.common.base.Objects;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.common.collect.Sets;
 import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
 import org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator;
-import org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine;
+import org.apache.ctakes.assertion.medfacts.cleartk.*;
 import org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.FEATURE_CONFIG;
-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.PolarityFedaCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine;
 import org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus;
 import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.constants.CONST;
-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.syntax.*;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -73,11 +47,7 @@ import org.apache.uima.cas.Feature;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 import org.apache.uima.fit.component.NoOpAnnotator;
-import org.apache.uima.fit.factory.AggregateBuilder;
-import org.apache.uima.fit.factory.AnalysisEngineFactory;
-import org.apache.uima.fit.factory.CollectionReaderFactory;
-import org.apache.uima.fit.factory.ConfigurationParameterFactory;
-import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.factory.*;
 import org.apache.uima.fit.pipeline.JCasIterator;
 import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.fit.util.CasIOUtil;
@@ -103,10 +73,12 @@ import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 import org.kohsuke.args4j.spi.BooleanOptionHandler;
 
-import com.google.common.base.Objects;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
-import com.google.common.collect.Sets;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.*;
 
 public class AssertionEvaluation extends Evaluation_ImplBase<File, Map<String, AnnotationStatisticsCompact<String>>> {
   
@@ -916,7 +888,7 @@ public static void printScore(Map<String
 //      System.out.format("system entities: %d%nsystem events: %d%n%n", systemEntities.size(), systemEvents.size());
       
       if (evaluationOutputDirectory != null){
-          String sourceFileName = DocumentIDAnnotationUtil.getDocumentID(jCas);
+         String sourceFileName = DocIdUtil.getDocumentID( jCas );
           CasIOUtil.writeXmi(jCas, new File(evaluationOutputDirectory, sourceFileName + ".xmi"));
       }
       
@@ -1065,7 +1037,7 @@ private static void printErrors(JCas jCa
 		  Collection<IdentifiedAnnotation> goldEntitiesAndEvents,
 		  Collection<IdentifiedAnnotation> systemEntitiesAndEvents, String classifierType, Object trueCategory, Class<? extends Object> categoryClass) throws ResourceProcessException {
 
-	String documentId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+   String documentId = DocIdUtil.getDocumentID( jCas );
 	
 	  Map<HashableAnnotation, IdentifiedAnnotation> goldMap = Maps.newHashMap();
 	  for (IdentifiedAnnotation mention : goldEntitiesAndEvents) {
@@ -1142,7 +1114,7 @@ private static void printInstances(JCas
 		  File outputfile) 
 				  throws ResourceProcessException, IOException {
 
-	String documentId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+   String documentId = DocIdUtil.getDocumentID( jCas );
 	  Map<HashableAnnotation, IdentifiedAnnotation> goldMap = Maps.newHashMap();
 	  for (IdentifiedAnnotation mention : goldEntitiesAndEvents) {
 		  goldMap.put(new HashableAnnotation(mention), mention);

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java Fri Apr 24 20:06:57 2020
@@ -18,16 +18,9 @@
  */
 package org.apache.ctakes.assertion.eval;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.List;
-
 import org.apache.ctakes.assertion.util.AssertionConst;
 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.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -39,12 +32,6 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CollectionReader;
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
-import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.uima.resource.metadata.ResourceMetaData;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.apache.uima.util.CasCreationUtils;
 import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 import org.apache.uima.fit.component.NoOpAnnotator;
 import org.apache.uima.fit.component.ViewCreatorAnnotator;
@@ -53,10 +40,22 @@ import org.apache.uima.fit.factory.Analy
 import org.apache.uima.fit.factory.CollectionReaderFactory;
 import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
 import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.ResourceMetaData;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.apache.uima.util.CasCreationUtils;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
 
-import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
-import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.COREFERENCE_RELATION;
-import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.MARKABLE;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.DOCUMENT_ID;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION;
 
 /**
  * 
@@ -99,8 +98,8 @@ public class MergeGoldViewFromOneCasInto
 		
 		if (!goldViewDir.exists()) throw new AnalysisEngineProcessException(new RuntimeException("Directory with gold view annotations not found:" + dirWithGoldViews));
 		if (!goldViewDir.isDirectory()) throw new AnalysisEngineProcessException(new RuntimeException("What is supposed to be a directory with gold view annotations is not a directory:" + dirWithGoldViews));
-		
-		String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+
+      String docId = DocIdUtil.getDocumentID( jCas );
 		JCas correspondingCasThatHasGoldAnnotations = getCorrespondingCasThatHasGoldAnnotations(docId);
 		JCas viewWithPreexistingGoldAnnotations = null;
 		JCas newGoldView = null;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Fri Apr 24 20:06:57 2020
@@ -21,7 +21,7 @@ package org.apache.ctakes.assertion.medf
 import org.apache.commons.io.FilenameUtils;
 import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
 import org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
@@ -309,7 +309,7 @@ public abstract class AssertionCleartkAn
 
    @Override
    public void process( JCas jCas ) throws AnalysisEngineProcessException {
-      String documentId = DocumentIDAnnotationUtil.getDocumentID( jCas );
+      String documentId = DocIdUtil.getDocumentID( jCas );
       String domainId = "";
       String domainFeature = null;
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java Fri Apr 24 20:06:57 2020
@@ -26,7 +26,7 @@ import org.apache.ctakes.assertion.medfa
 import org.apache.ctakes.assertion.medfacts.cleartk.windowed.context.LastCoveredContext;
 import org.apache.ctakes.assertion.medfacts.cleartk.windowed.context.PrecedingContext;
 import org.apache.ctakes.assertion.medfacts.cleartk.windowed.context.feature.extractor.AbstractWindowedFeatureExtractor1;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
@@ -273,7 +273,7 @@ public abstract class WindowedAssertionC
 
    @Override
    public void process( JCas jCas ) throws AnalysisEngineProcessException {
-      String documentId = DocumentIDAnnotationUtil.getDocumentID( jCas );
+      String documentId = DocIdUtil.getDocumentID( jCas );
       String domainId = "";
       String domainFeature = null;
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java Fri Apr 24 20:06:57 2020
@@ -18,21 +18,13 @@
  */
 package org.apache.ctakes.assertion.pipelines;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
-
 import org.apache.ctakes.assertion.eval.XMIReader;
 import org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.ATTRIBUTE;
 import org.apache.ctakes.assertion.util.AssertionDepUtils;
 import org.apache.ctakes.assertion.util.AssertionTreeUtils;
 import org.apache.ctakes.assertion.util.SemanticClasses;
 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.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
@@ -51,6 +43,14 @@ import org.kohsuke.args4j.CmdLineExcepti
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
 public class GenerateDependencyRepresentation {
   public static class Options {
 
@@ -110,7 +110,7 @@ public class GenerateDependencyRepresent
   }
   
   public static void processDocument(JCas jcas) {
-    log.info("Processing document: " + DocumentIDAnnotationUtil.getDocumentID(jcas));
+     log.info( "Processing document: " + DocIdUtil.getDocumentID( jcas ) );
     Collection<Sentence> sents = JCasUtil.select(jcas, Sentence.class);
     Sentence lastSent=null;
     for(Sentence sent : sents){

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java Fri Apr 24 20:06:57 2020
@@ -18,19 +18,10 @@
  */
 package org.apache.ctakes.assertion.pipelines;
 
-import static org.apache.ctakes.assertion.util.AssertionTreeUtils.extractAboveLeftConceptTree;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
-
 import org.apache.ctakes.assertion.eval.XMIReader;
 import org.apache.ctakes.assertion.util.SemanticClasses;
 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.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
@@ -47,6 +38,15 @@ import org.kohsuke.args4j.CmdLineExcepti
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+import static org.apache.ctakes.assertion.util.AssertionTreeUtils.extractAboveLeftConceptTree;
+
 public class GenerateTreeRepresentation{
 
   enum ATTRIBUTE {NEG, UNC}
@@ -112,7 +112,7 @@ public class GenerateTreeRepresentation{
 	}
 
 	private static void processDocument(JCas jcas) {
-		log.info("Processing document: " + DocumentIDAnnotationUtil.getDocumentID(jcas));
+      log.info( "Processing document: " + DocIdUtil.getDocumentID( jcas ) );
 		Collection<IdentifiedAnnotation> mentions = JCasUtil.select(jcas, IdentifiedAnnotation.class);
 		for(IdentifiedAnnotation mention : mentions){
 		  if(mention instanceof EventMention || mention instanceof EntityMention){

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java Fri Apr 24 20:06:57 2020
@@ -19,11 +19,8 @@ package org.apache.ctakes.clinicalpipeli
  */
 
 
-import java.io.File;
-import java.util.Date;
-
 import org.apache.ctakes.assertion.util.AssertionConst;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.collection.CollectionReaderDescription;
 import org.apache.uima.fit.factory.AnalysisEngineFactory;
@@ -32,6 +29,9 @@ import org.apache.uima.fit.util.CasIOUti
 import org.apache.uima.jcas.JCas;
 import org.cleartk.util.cr.FilesCollectionReader;
 
+import java.io.File;
+import java.util.Date;
+
 /**
  * Run the plaintext clinical pipeline, using the dictionary of terms from UMLS.
  * Note you must have the UMLS password supplied in some way - see the 
@@ -63,7 +63,7 @@ public class ClinicalPipelineWithUmls {
 				"desc/analysis_engine/AggregatePlaintextUMLSProcessor");
 
 		for(JCas jCas : SimplePipeline.iteratePipeline(collectionReader, pipelineIncludingUmlsDictionaries)){
-			CasIOUtil.writeXmi(jCas, new File(AssertionConst.evalOutputDir, DocumentIDAnnotationUtil.getDocumentID(jCas) + ".xmi"));
+         CasIOUtil.writeXmi( jCas, new File( AssertionConst.evalOutputDir, DocIdUtil.getDocumentID( jCas ) + ".xmi" ) );
 		}
 		
 	    System.out.println("Done at " + new Date());

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.clinicalpipeline.ae;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.WordTokenUtil;
+import org.apache.ctakes.core.util.annotation.WordTokenUtil;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.clinicalpipeline.runtime;
 
 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.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
@@ -66,7 +66,7 @@ public abstract class BagOfAnnotationsGe
 		JCasIterator casIter = new JCasIterator(reader, ae);
 		while(casIter.hasNext()){
 			JCas jcas = casIter.next();
-			String docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
+         String docId = DocIdUtil.getDocumentID( jcas );
 			
 			// extract info from cas
 			processCas(jcas, outputDir + File.separator + docId);

Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java Fri Apr 24 20:06:57 2020
@@ -23,7 +23,7 @@ import opennlp.tools.parser.Parse;
 import opennlp.tools.parser.ParserModel;
 import opennlp.tools.parser.chunking.Parser;
 import org.apache.ctakes.constituency.parser.util.TreeUtils;
-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.TopTreebankNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
@@ -72,7 +72,7 @@ public class MaxentParserWrapper impleme
 	 */
 	@Override
    public void createAnnotations( final JCas jcas ) throws AnalysisEngineProcessException {
-      final String docId = DocumentIDAnnotationUtil.getDocumentID( jcas );
+      final String docId = DocIdUtil.getDocumentID( jcas );
       logger.info( "Started processing: " + docId );
       // iterate over sentences
 		Parse parse = null;

Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java Fri Apr 24 20:06:57 2020
@@ -22,7 +22,7 @@ import org.apache.ctakes.constituency.pa
 import org.apache.ctakes.constituency.parser.ParserWrapper;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java Fri Apr 24 20:06:57 2020
@@ -21,7 +21,7 @@ package org.apache.ctakes.core.ae;
 
 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.typesystem.type.textspan.Segment;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
@@ -137,7 +137,7 @@ public class CDASegmentAnnotator extends
   public void process(JCas jCas) throws AnalysisEngineProcessException {
 		String text = jCas.getDocumentText();
 		if (text == null) {
-			String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+         String docId = DocIdUtil.getDocumentID( jCas );
 			logger.info("text is null for docId=" + docId);
 		} else {
 			ArrayList<Segment> sorted_segments = new ArrayList<>();

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.core.ae;
 
 
 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.log4j.Logger;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -39,7 +39,7 @@ public class DocumentIdPrinterAnalysisEn
   @Override
   public void process(JCas jcas) throws AnalysisEngineProcessException
   {
-    String documentId = DocumentIDAnnotationUtil.getDocumentID(jcas);
+     String documentId = DocIdUtil.getDocumentID( jcas );
     String logMessage = String.format("##### current file document id: \"%s\"", documentId);
     logger.info(logMessage);
     System.out.println(logMessage);

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
 package org.apache.ctakes.core.ae;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.core.util.textspan.DefaultAspanComparator;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;

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=1876941&r1=1876940&r2=1876941&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 Fri Apr 24 20:06:57 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(?:S|D))",
+         .compile( "(?:\\s?:\\s*)(?:NEGATIVE|(?:NO\\.?\\b)|NONE|(?:NOT (?:SEEN|PRESENT|INDICATED|FOUND|DISCOVERED)?)|DENIE[SD])",
                Pattern.CASE_INSENSITIVE );
 
    /**

Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,96 @@
+package org.apache.ctakes.core.ae;
+
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.typesystem.type.textspan.List;
+import org.apache.ctakes.typesystem.type.textspan.Paragraph;
+import org.apache.log4j.Logger;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import java.util.*;
+import java.util.regex.Pattern;
+
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 9/28/2016
+ */
+@PipeBitInfo(
+      name = "List Paragraph Fixer",
+      description = "Re-annotates Paragraphs based upon existing Lists, preventing a Paragraph from spanning more than one List.",
+      dependencies = { PipeBitInfo.TypeProduct.LIST, PipeBitInfo.TypeProduct.SENTENCE }
+)
+final public class ListParagraphFixer extends JCasAnnotator_ImplBase {
+
+   static private final Logger LOGGER = Logger.getLogger( "ListSentenceFixer" );
+
+   static private final Pattern WHITESPACE = Pattern.compile( "\\s+" );
+
+   /**
+    * Where Sentence annotations and List entry annotation ends overlap, Sentences are abbreviated.
+    * For each List Entry with a boundary within a Sentence, a new Sentence is created
+    * {@inheritDoc}
+    */
+   @Override
+   public void process( final JCas jcas ) throws AnalysisEngineProcessException {
+      LOGGER.info( "Adjusting Sentences overlapping Lists ..." );
+      final Collection<List> lists = JCasUtil.select( jcas, List.class );
+      if ( lists == null || lists.isEmpty() ) {
+         LOGGER.info( "Finished Processing" );
+         return;
+      }
+      adjustListParagraphs( jcas );
+      LOGGER.info( "Finished Processing" );
+   }
+
+
+   static private void adjustListParagraphs( final JCas jCas ) {
+      final Collection<List> lists = JCasUtil.select( jCas, List.class );
+      final java.util.List<Paragraph> allParagraphs = new ArrayList<>( JCasUtil.select( jCas, Paragraph.class ) );
+      allParagraphs.sort( Comparator.comparingInt( Annotation::getBegin ) );
+      // gather map of paragraphs that cross boundaries of lists
+      final Map<Paragraph, Collection<Integer>> paragraphCrossBounds = new HashMap<>();
+      for ( List list : lists ) {
+         for ( Paragraph paragraph : allParagraphs ) {
+            if ( paragraph.getBegin() > list.getEnd() ) {
+               // past the list entry
+               break;
+            } else if ( paragraph.getEnd() < list.getBegin() ) {
+               // haven't reached the list entry
+               continue;
+            } else if ( paragraph.getBegin() >= list.getBegin() && paragraph.getEnd() <= list.getEnd() ) {
+               // within the list entry
+               continue;
+            }
+            // sentence overlaps but isn't contained
+            Collection<Integer> crossBounds = paragraphCrossBounds.get( paragraph );
+            if ( crossBounds == null ) {
+               crossBounds = new HashSet<>();
+               paragraphCrossBounds.put( paragraph, crossBounds );
+               crossBounds.add( paragraph.getBegin() );
+               crossBounds.add( paragraph.getEnd() );
+            }
+            crossBounds.add( Math.max( paragraph.getBegin(), list.getBegin() ) );
+            crossBounds.add( Math.min( paragraph.getEnd(), list.getEnd() ) );
+         }
+      }
+      for ( Map.Entry<Paragraph, Collection<Integer>> crossBounds : paragraphCrossBounds.entrySet() ) {
+         final java.util.List<Integer> sortedBounds = new ArrayList<>( crossBounds.getValue() );
+         Collections.sort( sortedBounds );
+         for ( int i = 0; i < sortedBounds.size() - 1; i++ ) {
+            final Paragraph paragraph = new Paragraph( jCas, sortedBounds.get( i ), sortedBounds.get( i + 1 ) );
+            if ( WHITESPACE.matcher( paragraph.getCoveredText() ).replaceAll( " " ).trim().length() > 0 ) {
+               paragraph.addToIndexes();
+            }
+         }
+         crossBounds.getKey().removeFromIndexes();
+         jCas.removeFsFromIndexes( crossBounds.getKey() );
+      }
+   }
+
+
+}

Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,93 @@
+package org.apache.ctakes.core.ae;
+
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.Collectors;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 4/15/2020
+ */
+@PipeBitInfo(
+      name = "MrsDrSentenceJoiner",
+      description = "Joins Sentences with person titles Mr. Mrs. Dr. that have been split by SentenceDetectorBIO.",
+      dependencies = PipeBitInfo.TypeProduct.SENTENCE,
+      role = PipeBitInfo.Role.SPECIAL
+)
+final public class MrsDrSentenceJoiner extends JCasAnnotator_ImplBase {
+
+   static private final Logger LOGGER = Logger.getLogger( "MrsDrSentenceJoiner" );
+
+   /**
+    * Joins Sentences with person titles Mr. Mrs. Dr. that have been split by SentenceDetectorBIO.
+    * Note : this does not take into account Sections or Paragraphs.
+    * {@inheritDoc}
+    */
+   @Override
+   public void process( final JCas jCas ) throws AnalysisEngineProcessException {
+      LOGGER.info( "Joining Sentences ending with person titles (Mr. Mrs. Dr.) ..." );
+      // Obtain a list of Sentences, sorted by character offset.
+      final List<Sentence> sentences
+            = JCasUtil.select( jCas, Sentence.class ).stream()
+                      .sorted( Comparator.comparingInt( Annotation::getBegin ) )
+                      .collect( Collectors.toList() );
+      // Account for (intentional?) EOL after person title.
+      final Collection<Integer> newlines = new HashSet<>();
+      final char[] chars = jCas.getDocumentText().toCharArray();
+      for ( int i = 0; i < chars.length; i++ ) {
+         if ( chars[ i ] == '\r' || chars[ i ] == '\n' ) {
+            newlines.add( i );
+         }
+      }
+      final int sentenceCount = sentences.size();
+      final Collection<Sentence> removalSentences = new HashSet<>();
+      boolean appendNextSentence = false;
+      int appendSentenceBegin = 0;
+      for ( int i = 0; i < sentenceCount; i++ ) {
+         final Sentence sentence = sentences.get( i );
+         final String text = sentence.getCoveredText();
+         if ( (text.endsWith( " Mr." ) || text.endsWith( " Mrs." ) || text.endsWith( " Dr." )
+               || text.endsWith( " a.m." ) || text.endsWith( " p.m." )
+               || text.equals( "Mr." ) || text.equals( "Mrs." ) || text.equals( "Dr." ))
+              && i < sentenceCount - 1
+              && !newlines.contains( sentence.getEnd() ) ) {
+            // Sentence ends with a person title AND is not the last sentence in the document.
+            if ( !appendNextSentence ) {
+               appendSentenceBegin = sentence.getBegin();
+            }
+            removalSentences.add( sentence );
+            appendNextSentence = true;
+            continue;
+         }
+         if ( appendNextSentence ) {
+            // Create a new sentence that spans this sentence plus the preceding sentence(s) ending with a title.
+            final Sentence newSentence = new Sentence( jCas, appendSentenceBegin, sentence.getEnd() );
+            newSentence.addToIndexes();
+            removalSentences.add( sentence );
+            appendNextSentence = false;
+         }
+      }
+      // Get rid of all of the original sentences that are now covered by new sentences.
+      removalSentences.forEach( Sentence::removeFromIndexes );
+      // Just in case, set sentence numbers.
+      final AtomicInteger index = new AtomicInteger( 0 );
+      JCasUtil.select( jCas, Sentence.class ).stream()
+              .sorted( Comparator.comparingInt( Annotation::getBegin ) )
+              .forEach( s -> s.setSentenceNumber( index.incrementAndGet() ) );
+   }
+
+
+}

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java Fri Apr 24 20:06:57 2020
@@ -22,8 +22,8 @@ import findstruct.Section;
 import findstruct.StructFinder;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.resource.FileResource;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.ctakes.core.util.DocumentSection;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
@@ -85,7 +85,7 @@ public class SectionSegmentAnnotator ext
 		String text = jCas.getDocumentText();
 
 		if (text == null) {
-			String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+         String docId = DocIdUtil.getDocumentID( jCas );
 			throw new AnalysisEngineProcessException("text is null for docId="
 					+ docId, null);
 		}

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.core.ae;
 
 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.textspan.Segment;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -61,7 +61,7 @@ public class SimpleSegmentAnnotator exte
 		segment.setBegin(0);
 		String text = jCas.getDocumentText();
 		if (text == null) {
-			String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+         String docId = DocIdUtil.getDocumentID( jCas );
 			throw new AnalysisEngineProcessException("text is null for docId="
 					+ docId, null);
 		}

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.core.ae;
 
 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.textspan.Segment;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
@@ -69,7 +69,7 @@ public class SimpleSegmentWithTagsAnnota
 		String text = jcas.getDocumentText();
 		if (text == null) {
 			System.out.println("text == null in Segmentannotator");
-			String docID = DocumentIDAnnotationUtil.getDocumentID(jcas);
+         String docID = DocIdUtil.getDocumentID( jcas );
 			System.out.println(" \t\tdocID=" + docID);
 		}
 		if (segmentId.compareTo("parseSectionTag") != 0) {

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.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.ctakes.typesystem.type.structured.DocumentIdPrefix;
 import org.apache.ctakes.typesystem.type.structured.DocumentPath;
 import org.apache.log4j.Logger;
@@ -68,7 +68,7 @@ abstract public class AbstractFileWriter
     */
    @Override
    public void process( final JCas jcas ) throws AnalysisEngineProcessException {
-      final String documentId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+      final String documentId = DocIdUtil.getDocumentIdForFile( jcas );
       final String outputDir = getOutputDirectory( jcas, getRootDirectory(), documentId );
       final String fileName = getSourceFileName( jcas, documentId );
       try {

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
 package org.apache.ctakes.core.cc;
 
 import org.apache.ctakes.core.resource.JdbcConnectionResource;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.typesystem.type.structured.SourceData;
 import org.apache.log4j.Logger;
 import org.apache.uima.cas.CAS;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.core.cc;
 
 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.log4j.Logger;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.impl.XCASSerializer;
@@ -73,10 +73,10 @@ public class CasConsumer extends CasCons
    private void processView( JCas view ) throws Exception {
       // String docText = view.getDocumentText();
 
-      String docName = DocumentIDAnnotationUtil.getDocumentID( view );
+      String docName = DocIdUtil.getDocumentID( view );
 
       File outputFile;
-      if ( docName == null || docName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+      if ( docName == null || docName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
          docName = "doc" + iv_procCount + ".xml";
       } else {
          docName = docName + ".xml";

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java Fri Apr 24 20:06:57 2020
@@ -1,8 +1,8 @@
 package org.apache.ctakes.core.cc;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-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.constants.CONST;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.log4j.Logger;
@@ -124,7 +124,7 @@ public class CuiCountFileWriter extends
     */
    public void process( final JCas jcas ) {
       LOGGER.info( "Starting processing" );
-      final String docId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+      final String docId = DocIdUtil.getDocumentIdForFile( jcas );
       File outputFile;
       if ( _outputDirPath == null || _outputDirPath.isEmpty() ) {
          outputFile = new File( docId + FILE_EXTENSION );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java Fri Apr 24 20:06:57 2020
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.cc;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.semantic.SemanticTui;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
 import org.apache.ctakes.core.util.RelationArgumentUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
 package org.apache.ctakes.core.cc;
 
 
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.core.cc;
 
 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.log4j.Logger;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -76,8 +76,8 @@ public class FilesInDirectoryCasConsumer
 
          String documentText = jcas.getDocumentText();
 
-         String documentID = DocumentIDAnnotationUtil.getDeepDocumentId( jcas );
-         if ( documentID == null || documentID.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+         String documentID = DocIdUtil.getDeepDocumentId( jcas );
+         if ( documentID == null || documentID.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
             documentID = "doc_" + new java.util.Date().getTime() + ".xml"; // use timestamp in name: doc_TIMESTAMP.xml
             LOGGER.warn( "Unable to find DocumentIDAnnotation, using " + documentID );
          }

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.core.cc;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.log4j.Logger;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,8 +19,8 @@
 package org.apache.ctakes.core.cc;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.WordTokenUtil;
+import org.apache.ctakes.core.util.annotation.WordTokenUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
@@ -83,7 +83,7 @@ public class NormalizedFilesInDirectoryC
                normalizedText.append( " " );
             }
          }
-         final String documentID = DocumentIDAnnotationUtil.getDocumentID( jcas );
+         final String documentID = DocIdUtil.getDocumentID( jcas );
          writeToFile( documentID, normalizedText.toString() );
       } catch ( CASException | IOException multE ) {
          throw new ResourceProcessException( multE );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java Fri Apr 24 20:06:57 2020
@@ -1,8 +1,8 @@
 package org.apache.ctakes.core.cc;
 
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.ctakes.core.util.JCasUtil;
+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.log4j.Logger;
@@ -99,7 +99,7 @@ public class SentenceTokensPrinter exten
          // JCasHashMap will throw this every once in a while.  Assume the sentences are done and move on
          LOGGER.warn( iobE.getMessage() );
       }
-      final String documentId = DocumentIDAnnotationUtil.getDocumentID( jcas );
+      final String documentId = DocIdUtil.getDocumentID( jcas );
       outputSentenceTokens( documentId, tokenizedSentences );
    }
 

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.cc;
 
 
 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.refsem.Entity;
 import org.apache.ctakes.typesystem.type.refsem.Event;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -119,7 +119,7 @@ public class TextSpanWriter extends CasC
     */
    public void process( final JCas jcas ) {
       LOGGER.info( "Starting processing" );
-      final String docId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+      final String docId = DocIdUtil.getDocumentIdForFile( jcas );
       File outputFile;
       if ( _outputDirPath == null || _outputDirPath.isEmpty() ) {
          outputFile = new File( docId + FILE_EXTENSION );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
 package org.apache.ctakes.core.cc;
 
 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.BaseToken;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -87,9 +87,9 @@ public class TokenOffsetsCasConsumer ext
 	        	BaseToken token = (BaseToken) tokenItr.next();
 	        	String offset = ""+token.getBegin()+"|"+token.getEnd();
 	        	offsets.add(offset);
-	        }	        	
+           }
 
-	        String documentID = DocumentIDAnnotationUtil.getDocumentID(jcas);
+         String documentID = DocIdUtil.getDocumentID( jcas );
 			writeToFile(documentID, offsets);
 			
 		}

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java Fri Apr 24 20:06:57 2020
@@ -38,7 +38,7 @@ package org.apache.ctakes.core.cc;
  */
 
 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.log4j.Logger;
 import org.apache.uima.UIMAFramework;
 import org.apache.uima.UimaContext;
@@ -125,11 +125,11 @@ public class XmiWriterCasConsumerCtakes
 			throw new AnalysisEngineProcessException( e1 );
 		}
 
-		String originalFileName = DocumentIDAnnotationUtil.getDocumentID( jcas );
+      String originalFileName = DocIdUtil.getDocumentID( jcas );
 		File outFile = null;
 		if ( originalFileName != null
-				&& !originalFileName.isEmpty()
-				&& !originalFileName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+           && !originalFileName.isEmpty()
+           && !originalFileName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
 			File inFile;
 			try {
 				String outFileName = null;
@@ -153,8 +153,8 @@ public class XmiWriterCasConsumerCtakes
 			File inFile;
 			String outFileName = null;
 			if ( originalFileName != null
-					&& !originalFileName.isEmpty()
-					&& !originalFileName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+              && !originalFileName.isEmpty()
+              && !originalFileName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
 				try {
 					if ( originalFileName.contains( "/" ) ) {
 						URI uri = UriUtils.quote( originalFileName );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java Fri Apr 24 20:06:57 2020
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.cc.Abstrac
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.semantic.SemanticGroup;
 import org.apache.ctakes.core.semantic.SemanticTui;
-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.core.util.textspan.DefaultTextSpan;
 import org.apache.ctakes.core.util.textspan.TextSpan;
 import org.apache.ctakes.typesystem.type.refsem.Event;
@@ -105,7 +105,7 @@ final public class HtmlTextWriter extend
       final File htmlFile = new File( outputDir, fileName + FILE_EXTENSION );
       LOGGER.info( "Writing HTML to " + htmlFile.getPath() + " ..." );
       try ( final BufferedWriter writer = new BufferedWriter( new FileWriter( htmlFile ) ) ) {
-         final String title = DocumentIDAnnotationUtil.getDocumentID( jCas );
+         final String title = DocIdUtil.getDocumentID( jCas );
          writer.write( startBody() );
          writer.write( getCssLink( CSS_FILENAME ) );
          writer.write( getJsLink( JS_FILENAME ) );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.cc.jdbc.i
 
 import org.apache.ctakes.core.cc.jdbc.field.*;
 import org.apache.ctakes.core.cc.jdbc.row.JdbcRow;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.structured.SourceData;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.cc.jdbc.t
 
 
 import org.apache.ctakes.core.cc.jdbc.row.JdbcRow;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.fit.util.JCasUtil;

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

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java Fri Apr 24 20:06:57 2020
@@ -4,8 +4,8 @@ package org.apache.ctakes.core.cc.pretty
 import org.apache.ctakes.core.cc.AbstractJCasFileWriter;
 import org.apache.ctakes.core.cc.pretty.SemanticGroup;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
-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.core.util.textspan.DefaultTextSpan;
 import org.apache.ctakes.core.util.textspan.TextSpan;
 import org.apache.ctakes.typesystem.type.refsem.Event;
@@ -105,7 +105,7 @@ final public class HtmlTextWriter extend
       final File htmlFile = new File( outputDir, fileName + FILE_EXTENSION );
       LOGGER.info( "Writing HTML to " + htmlFile.getPath() + " ..." );
       try ( final BufferedWriter writer = new BufferedWriter( new FileWriter( htmlFile ) ) ) {
-         final String title = DocumentIDAnnotationUtil.getDocumentID( jCas );
+         final String title = DocIdUtil.getDocumentID( jCas );
          writer.write( startBody() );
          writer.write( getCssLink( CSS_FILENAME ) );
          writer.write( getJsLink( JS_FILENAME ) );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java Fri Apr 24 20:06:57 2020
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.cc.pretty.
 import org.apache.ctakes.core.cc.pretty.cell.*;
 import org.apache.ctakes.core.cc.pretty.row.DefaultItemRow;
 import org.apache.ctakes.core.cc.pretty.row.ItemRow;
-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.core.util.textspan.DefaultTextSpan;
 import org.apache.ctakes.core.util.textspan.TextSpan;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
@@ -78,7 +78,7 @@ final public class PrettyTextWriter {
     */
    public void process( final JCas jcas ) {
       LOGGER.info( "Starting processing" );
-      final String docId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+      final String docId = DocIdUtil.getDocumentIdForFile( jcas );
       File outputFile;
       if ( _outputDirPath == null || _outputDirPath.isEmpty() ) {
          outputFile = new File( docId + FILE_EXTENSION );



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