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From seanfi...@apache.org
Subject svn commit: r1877091 - in /ctakes/trunk: ctakes-core/src/main/java/org/apache/ctakes/core/cc/ ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/ ctakes-core/src/main/java/org/apache/ctakes/core/cr/ ctakes-core/src/main/java/org/apache/ctakes/cor...
Date Mon, 27 Apr 2020 19:04:23 GMT
Author: seanfinan
Date: Mon Apr 27 19:04:22 2020
New Revision: 1877091

URL: http://svn.apache.org/viewvc?rev=1877091&view=rev
Log:
Refactoring :
SemanticGroup - moved to core.utl.annotation
SemanticTui - moved to core.util.annotation
JCasBuilder - moved to core.util.doc
NoteSpecs - moved to core.util.doc
TextBySectionBuilder - moved to core.util.doc
TextBySentenceBuilder - moved to core.util.doc

Dockhand:
LocalInstallBuilder - prompt user to start pfs gui
MavenHelper - log out and err to pom directory logs/
Output - refactor FinishedLogger to be in util.log.
DialogUtil - add prompt user to start pfs gui dialog
SystemUtil - add out and err logging to external command processing

Added:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticGroup.java
      - copied, changed from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticTui.java
      - copied, changed from r1877090, 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/doc/JCasBuilder.java
      - copied, changed from r1877090, 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/util/doc/NoteSpecs.java
      - copied, changed from r1877090, 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/util/doc/TextBySectionBuilder.java
      - copied, changed from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySectionBuilder.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySentenceBuilder.java
      - copied, changed from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySentenceBuilder.java
Removed:
    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/cr/TextBySectionBuilder.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySentenceBuilder.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/note/
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java
Modified:
    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/html/HtmlTextWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/SemanticMarkup.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/util/Mapper.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java
    ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/DefaultConcept.java
    ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
    ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/SemanticUtil.java
    ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
    ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/MavenHelper.java
    ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/output/Output.java
    ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/DialogUtil.java
    ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.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/resource/IdentifiedAnnotationParser.java
    ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java

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=1877091&r1=1877090&r2=1877091&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
Mon Apr 27 19:04:22 2020
@@ -2,9 +2,9 @@ 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.RelationArgumentUtil;
 import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.SemanticTui;
 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/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=1877091&r1=1877090&r2=1877091&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
Mon Apr 27 19:04:22 2020
@@ -3,9 +3,9 @@ package org.apache.ctakes.core.cc.html;
 
 import org.apache.ctakes.core.cc.AbstractJCasFileWriter;
 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.annotation.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
+import org.apache.ctakes.core.util.annotation.SemanticTui;
 import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.core.util.textspan.DefaultTextSpan;
 import org.apache.ctakes.core.util.textspan.TextSpan;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/SemanticMarkup.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/SemanticMarkup.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/SemanticMarkup.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/SemanticMarkup.java
Mon Apr 27 19:04:22 2020
@@ -1,8 +1,8 @@
 package org.apache.ctakes.core.cc.html;
 
-import org.apache.ctakes.core.semantic.SemanticGroup;
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
 
-import static org.apache.ctakes.core.semantic.SemanticGroup.*;
+import static org.apache.ctakes.core.util.annotation.SemanticGroup.*;
 
 
 public enum SemanticMarkup {

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
Mon Apr 27 19:04:22 2020
@@ -1,11 +1,12 @@
 package org.apache.ctakes.core.cr;
 
 import org.apache.ctakes.core.config.ConfigParameterConstants;
-import org.apache.ctakes.core.note.NoteSpecs;
 import org.apache.ctakes.core.patient.PatientNoteStore;
 import org.apache.ctakes.core.pipeline.ProgressManager;
 import org.apache.ctakes.core.resource.FileLocator;
 import org.apache.ctakes.core.util.NumberedSuffixComparator;
+import org.apache.ctakes.core.util.doc.JCasBuilder;
+import org.apache.ctakes.core.util.doc.NoteSpecs;
 import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java Mon Apr
27 19:04:22 2020
@@ -26,14 +26,14 @@ import org.apache.ctakes.typesystem.type
  * automatically is passed, "unknown relation" id is returned.
  *  
  * @author dmitriy dligach
- * @deprecated use org.apache.ctakes.core.semantic.SemanticGroup.  e.g. SemanticGroup.getBestGroup(
annotation ).getCode();
+ * @deprecated use org.apache.ctakes.core.util.annotation.SemanticGroup.  e.g. SemanticGroup.getBestGroup(
annotation ).getCode();
  */
 @Deprecated
 public class Mapper {
 
 	/**
 	 * Map entity type to its integer id.
-    * @deprecated use org.apache.ctakes.core.semantic.SemanticGroup.  SemanticGroup.getGroup(
name ).getCode();
+    * @deprecated use org.apache.ctakes.core.util.annotation.SemanticGroup.  SemanticGroup.getGroup(
name ).getCode();
 	 */
    @Deprecated
    public static int getEntityTypeId( String entityType ) {
@@ -48,7 +48,7 @@ public class Mapper {
 	
 	/**
 	 * Map modifier type to its integer id.
-    * @deprecated use org.apache.ctakes.core.semantic.SemanticGroup.  SemanticGroup.getGroup(
name ).getCode();
+    * @deprecated use org.apache.ctakes.core.util.annotation.SemanticGroup.  SemanticGroup.getGroup(
name ).getCode();
 	 */
    @Deprecated
    public static int getModifierTypeId( String modifierType ) {

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java
Mon Apr 27 19:04:22 2020
@@ -1,8 +1,6 @@
 package org.apache.ctakes.core.util.annotation;
 
 
-import org.apache.ctakes.core.semantic.SemanticGroup;
-import org.apache.ctakes.core.semantic.SemanticTui;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticGroup.java
(from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticGroup.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticGroup.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java&r1=1877090&r2=1877091&rev=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticGroup.java
Mon Apr 27 19:04:22 2020
@@ -1,4 +1,4 @@
-package org.apache.ctakes.core.semantic;
+package org.apache.ctakes.core.util.annotation;
 
 import org.apache.ctakes.typesystem.type.textsem.*;
 import org.apache.uima.jcas.JCas;

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticTui.java
(from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticTui.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticTui.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java&r1=1877090&r2=1877091&rev=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticTui.java
Mon Apr 27 19:04:22 2020
@@ -1,6 +1,5 @@
-package org.apache.ctakes.core.semantic;
+package org.apache.ctakes.core.util.annotation;
 
-import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -12,7 +11,7 @@ import java.util.Collections;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
-import static org.apache.ctakes.core.semantic.SemanticGroup.*;
+import static org.apache.ctakes.core.util.annotation.SemanticGroup.*;
 
 public enum SemanticTui {
    T116( 116, "Amino Acid, Peptide, or Protein", DRUG ),

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/JCasBuilder.java
(from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/JCasBuilder.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/JCasBuilder.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java&r1=1877090&r2=1877091&rev=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/JCasBuilder.java
Mon Apr 27 19:04:22 2020
@@ -1,9 +1,6 @@
-package org.apache.ctakes.core.cr;
+package org.apache.ctakes.core.util.doc;
 
 
-import org.apache.ctakes.core.note.NoteSpecs;
-import org.apache.ctakes.core.util.doc.DocIdUtil;
-import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.typesystem.type.structured.*;
 import org.apache.uima.UIMAException;
 import org.apache.uima.fit.factory.JCasFactory;

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java
(from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/note/NoteSpecs.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/note/NoteSpecs.java&r1=1877090&r2=1877091&rev=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/note/NoteSpecs.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java
Mon Apr 27 19:04:22 2020
@@ -1,8 +1,6 @@
-package org.apache.ctakes.core.note;
+package org.apache.ctakes.core.util.doc;
 
 
-import org.apache.ctakes.core.util.doc.DocIdUtil;
-import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.typesystem.type.structured.SourceData;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.log4j.Logger;

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySectionBuilder.java
(from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySectionBuilder.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySectionBuilder.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySectionBuilder.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySectionBuilder.java&r1=1877090&r2=1877091&rev=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySectionBuilder.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySectionBuilder.java
Mon Apr 27 19:04:22 2020
@@ -1,4 +1,4 @@
-package org.apache.ctakes.core.cr;
+package org.apache.ctakes.core.util.doc;
 
 
 import org.apache.ctakes.typesystem.type.textspan.Segment;

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySentenceBuilder.java
(from r1877090, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySentenceBuilder.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySentenceBuilder.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySentenceBuilder.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySentenceBuilder.java&r1=1877090&r2=1877091&rev=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextBySentenceBuilder.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySentenceBuilder.java
Mon Apr 27 19:04:22 2020
@@ -1,4 +1,4 @@
-package org.apache.ctakes.core.cr;
+package org.apache.ctakes.core.util.doc;
 
 
 import org.apache.ctakes.typesystem.type.textspan.Segment;

Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/DefaultConcept.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/DefaultConcept.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/DefaultConcept.java
(original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/DefaultConcept.java
Mon Apr 27 19:04:22 2020
@@ -1,7 +1,7 @@
 package org.apache.ctakes.dictionary.lookup2.concept;
 
-import org.apache.ctakes.core.semantic.SemanticGroup;
-import org.apache.ctakes.core.semantic.SemanticTui;
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
+import org.apache.ctakes.core.util.annotation.SemanticTui;
 import org.apache.ctakes.core.util.collection.CollectionMap;
 import org.apache.ctakes.core.util.collection.HashSetMap;
 import org.apache.ctakes.core.util.collection.ImmutableCollectionMap;

Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
(original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
Mon Apr 27 19:04:22 2020
@@ -19,8 +19,8 @@
 package org.apache.ctakes.dictionary.lookup2.consumer;
 
 import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.semantic.SemanticGroup;
-import org.apache.ctakes.core.semantic.SemanticTui;
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
+import org.apache.ctakes.core.util.annotation.SemanticTui;
 import org.apache.ctakes.core.util.collection.CollectionMap;
 import org.apache.ctakes.core.util.collection.HashSetMap;
 import org.apache.ctakes.dictionary.lookup2.concept.Concept;

Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/SemanticUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/SemanticUtil.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/SemanticUtil.java
(original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/SemanticUtil.java
Mon Apr 27 19:04:22 2020
@@ -18,7 +18,7 @@
  */
 package org.apache.ctakes.dictionary.lookup2.util;
 
-import org.apache.ctakes.core.semantic.SemanticTui;
+import org.apache.ctakes.core.util.annotation.SemanticTui;
 
 /**
  *

Modified: ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
Mon Apr 27 19:04:22 2020
@@ -61,9 +61,9 @@ final public class LocalInstallBuilder i
       if ( finished ) {
          DialogUtil.showInstalledDialog( INSTALL_TYPE, installPath );
       }
-
-      startGui( "Running Apache cTAKES ...<BR>   RunPiperGui", installPath + "/" +
INSTALL_DIRNAME );
-
+      if ( DialogUtil.showStartGui() ) {
+         startGui( "Running Apache cTAKES ...<BR>   RunPiperGui", installPath + "/"
+ INSTALL_DIRNAME );
+      }
    }
 
    static private boolean cleanup( final String installPath ) {
@@ -117,8 +117,12 @@ final public class LocalInstallBuilder i
 
    public boolean startGui( final String title, final String installDirectory ) {
       try {
+         new File( installDirectory + "/logs" ).mkdirs();
          final SystemUtil.CommandRunner runner
-               = new SystemUtil.CommandRunner( installDirectory, "RunPiperGui" );
+               = new SystemUtil.CommandRunner( installDirectory,
+               installDirectory + "/logs/RunOutput.txt",
+               installDirectory + "/logs/RunError.txt",
+               "RunPiperGui" );
          return RunnerUtil.runWithProgress( title, runner );
       } catch ( Exception e ) {
          DialogUtil.showError( e.getMessage() );

Modified: ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/MavenHelper.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/MavenHelper.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/MavenHelper.java
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/MavenHelper.java
Mon Apr 27 19:04:22 2020
@@ -128,8 +128,12 @@ public enum MavenHelper {
 
    public boolean packagePom( final String title, final String pomDirectory ) {
       try {
+         new File( pomDirectory + "/logs" ).mkdirs();
          final CommandRunner packager
-               = new CommandRunner( pomDirectory, getMavenDir().getAbsolutePath() + "/mvn
clean package" );
+               = new CommandRunner( pomDirectory,
+               pomDirectory + "/logs/MavenOutput.txt",
+               pomDirectory + "/logs/MavenError.txt",
+               getMavenDir().getAbsolutePath() + "/mvn clean package" );
          return RunnerUtil.runWithProgress( title, packager );
       } catch ( Exception e ) {
          DialogUtil.showError( e.getMessage() );

Modified: ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/output/Output.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/output/Output.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/output/Output.java
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/output/Output.java
Mon Apr 27 19:04:22 2020
@@ -31,7 +31,7 @@ public enum Output {
          "add CuiLookupLister SubDirectory=CUI" ),
    FINISHED( "Run Summary",
          "Summary Information Log after run completion.",
-         "addLast util.FinishedLogger" );
+         "addLast util.log.FinishedLogger" );
 
    private final String _name;
    private final String _description;

Modified: ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/DialogUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/DialogUtil.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/DialogUtil.java
(original)
+++ ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/DialogUtil.java
Mon Apr 27 19:04:22 2020
@@ -121,6 +121,16 @@ final public class DialogUtil {
       showMessageDialog( name + " Installation Cancelled." );
    }
 
+   static public boolean showStartGui() {
+      final Component rootPane = SwingUtilities.getRoot( DisablerPane.getInstance() );
+      final int start = JOptionPane.showConfirmDialog( rootPane,
+            "Start cTAKES Piper File Submitter GUI?",
+            "Start cTAKES",
+            JOptionPane.YES_NO_OPTION,
+            JOptionPane.QUESTION_MESSAGE );
+      return start == JOptionPane.YES_OPTION;
+   }
+
    static public void showMessageDialog( final String message ) {
       final Component rootPane = SwingUtilities.getRoot( DisablerPane.getInstance() );
       JOptionPane.showMessageDialog( rootPane, message );

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=1877091&r1=1877090&r2=1877091&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
Mon Apr 27 19:04:22 2020
@@ -130,78 +130,73 @@ final public class SystemUtil {
    }
 
 
-   static private boolean runLocally( final String directory, final String command )
+   static private boolean runLocally( final String directory,
+                                      final String outLog,
+                                      final String errLog,
+                                      final String command )
          throws IOException, InterruptedException {
       final String os = System.getProperty( "os.name" );
       if ( os.toLowerCase().contains( "windows" ) ) {
-         return runOnWindows( directory, command );
+         return runOnWindows( directory, outLog, errLog, command );
       } else {
-         return runOnLinux( directory, command );
+         return runOnLinux( directory, outLog, errLog, command );
       }
    }
 
-   static private boolean runOnWindows( final String directory, final String command )
+   static private boolean runOnWindows( final String directory,
+                                        final String outLog,
+                                        final String errLog,
+                                        final String command )
          throws IOException, InterruptedException {
-      final ProcessBuilder processBuilder = new ProcessBuilder();
-      processBuilder.directory( new File( directory ) );
+      final ProcessBuilder processBuilder = new ProcessBuilder()
+            .directory( new File( directory ) )
+            .command( "cmd.exe", "/c", command.replace( '/', '\\' ) )
+            .redirectOutput( new File( outLog ) )
+            .redirectError( new File( errLog ) );
       final Map<String, String> env = processBuilder.environment();
       if ( !env.containsKey( "JAVA_HOME" ) ) {
          env.put( "JAVA_HOME", System.getProperty( "java.home" ) );
       }
-      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 );
-//      }
-
       int exitCode = process.waitFor();
-//      System.out.println( "\nCMD Exited with error code : " + exitCode );
-
       return true;
    }
 
 
-   static private boolean runOnLinux( final String directory, final String command )
+   static private boolean runOnLinux( final String directory,
+                                      final String outLog,
+                                      final String errLog,
+                                      final String command )
          throws IOException, InterruptedException {
-      final ProcessBuilder processBuilder = new ProcessBuilder();
-      processBuilder.directory( new File( directory ) );
-      processBuilder.command( "bash", "-c", command );
+      final ProcessBuilder processBuilder = new ProcessBuilder()
+            .directory( new File( directory ) )
+            .command( "bash", "-c", command )
+            .redirectOutput( new File( outLog ) )
+            .redirectError( new File( errLog ) );
       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 );
-//      }
-
       int exitCode = process.waitFor();
-//      System.out.println( "\nBASH Exited with error code : " + exitCode );
-
       return true;
    }
 
 
    static public class CommandRunner implements Callable<Boolean> {
       private final String _dir;
+      private final String _outLog;
+      private final String _errLog;
       private final String _command;
 
-      public CommandRunner( final String directory, final String command ) {
+      public CommandRunner( final String directory,
+                            final String outLog,
+                            final String errLog,
+                            final String command ) {
          _dir = directory;
+         _outLog = outLog;
+         _errLog = errLog;
          _command = command;
       }
 
       public Boolean call() throws IOException, InterruptedException {
-         return runLocally( _dir, _command );
+         return runLocally( _dir, _outLog, _errLog, _command );
       }
    }
 

Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
(original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
Mon Apr 27 19:04:22 2020
@@ -1,9 +1,9 @@
 package org.apache.ctakes.examples.ae;
 
 import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
-import org.apache.ctakes.core.cr.TextBySentenceBuilder;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.pipeline.PipelineBuilder;
+import org.apache.ctakes.core.util.doc.TextBySentenceBuilder;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;

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=1877091&r1=1877090&r2=1877091&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
Mon Apr 27 19:04:22 2020
@@ -2,8 +2,8 @@ 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.annotation.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
 import org.apache.ctakes.core.util.doc.DocIdUtil;
 import org.apache.ctakes.typesystem.type.refsem.Event;
 import org.apache.ctakes.typesystem.type.refsem.EventProperties;

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=1877091&r1=1877090&r2=1877091&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
Mon Apr 27 19:04:22 2020
@@ -1,8 +1,8 @@
 package org.apache.ctakes.fhir.resource;
 
-import org.apache.ctakes.core.semantic.SemanticGroup;
 import org.apache.ctakes.core.util.annotation.EssentialAnnotationUtil;
 import org.apache.ctakes.core.util.annotation.IdentifiedAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
 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/resource/IdentifiedAnnotationParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java?rev=1877091&r1=1877090&r2=1877091&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java
(original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java
Mon Apr 27 19:04:22 2020
@@ -1,6 +1,6 @@
 package org.apache.ctakes.fhir.resource;
 
-import org.apache.ctakes.core.semantic.SemanticGroup;
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
 import org.apache.ctakes.fhir.element.FhirElementParser;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.Event;

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=1877091&r1=1877090&r2=1877091&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
Mon Apr 27 19:04:22 2020
@@ -1,7 +1,7 @@
 package org.apache.ctakes.fhir.util;
 
 
-import org.apache.ctakes.core.note.NoteSpecs;
+import org.apache.ctakes.core.util.doc.NoteSpecs;
 import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.fhir.element.FhirElementFactory;
 import org.apache.ctakes.typesystem.type.structured.SourceData;



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