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Posted to commits@ctakes.apache.org by se...@apache.org on 2020/04/27 19:04:23 UTC
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...
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;