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From chen...@apache.org
Subject svn commit: r1491835 - in /ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup: ./ desc/analysis_engine/ src/main/java/org/apache/ctakes/dictionary/lookup/ae/
Date Tue, 11 Jun 2013 15:24:56 GMT
Author: chenpei
Date: Tue Jun 11 15:24:56 2013
New Revision: 1491835

URL: http://svn.apache.org/r1491835
Log:
CTAKES-207 - Reverting the dictionary lookup to r.1477364 (right before the EntityMention
type system changes for the jamia submission branch.

Modified:
    ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/.classpath
  (contents, props changed)
    ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
    ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/pom.xml
    ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java
    ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java

Modified: ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/.classpath
URL: http://svn.apache.org/viewvc/ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/.classpath?rev=1491835&r1=1491834&r2=1491835&view=diff
==============================================================================
--- ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/.classpath
(original)
+++ ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/.classpath
Tue Jun 11 15:24:56 2013
@@ -1,26 +1,26 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Propchange: ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/.classpath
            ('svn:eol-style' removed)

Modified: ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml?rev=1491835&r1=1491834&r2=1491835&view=diff
==============================================================================
--- ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
(original)
+++ ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
Tue Jun 11 15:24:56 2013
@@ -80,7 +80,7 @@
       <nameValuePair>
         <name>ctakes.umlsaddr</name>
         <value>
-          <string>https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser</string>
+          <string>https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser</string>
         </value>
       </nameValuePair>    
       <nameValuePair>

Modified: ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/pom.xml?rev=1491835&r1=1491834&r2=1491835&view=diff
==============================================================================
--- ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/pom.xml (original)
+++ ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/pom.xml Tue
Jun 11 15:24:56 2013
@@ -28,16 +28,16 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-		<dependencies>
-	     <dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dictionary-lookup-res</artifactId>
-		</dependency>		    
+	<dependencies>
 		<dependency>
 			<groupId>hsqldb</groupId>
 			<artifactId>hsqldb</artifactId>
 			<version>1.8.0.10</version>
-		</dependency>	
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dictionary-lookup-res</artifactId>
+		</dependency>			
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>

Modified: ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java?rev=1491835&r1=1491834&r2=1491835&view=diff
==============================================================================
--- ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java
(original)
+++ ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java
Tue Jun 11 15:24:56 2013
@@ -22,14 +22,9 @@ import org.apache.ctakes.dictionary.look
 import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
-import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
-import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.LabMention;
-import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
-import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
-import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
+import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
@@ -112,22 +107,11 @@ public class NamedEntityLookupConsumerIm
                codes.add( code );
             }
          }
-         
-         IdentifiedAnnotation neAnnot = new IdentifiedAnnotation(jcas);
-         if ( typeId == CONST.NE_TYPE_ID_DRUG ) {
-            neAnnot = new MedicationMention( jcas );
-         } else if ( typeId == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
-             neAnnot = new AnatomicalSiteMention( jcas );
-         } else if ( typeId == CONST.NE_TYPE_ID_DISORDER ) {
-             neAnnot = new DiseaseDisorderMention( jcas );
-         } else if ( typeId == CONST.NE_TYPE_ID_FINDING ) {
-             neAnnot = new SignSymptomMention( jcas );
-         } else if ( typeId == CONST.NE_TYPE_ID_LAB ) {
-             neAnnot = new LabMention( jcas );
-         } else if ( typeId == CONST.NE_TYPE_ID_PROCEDURE ) {
-             neAnnot = new ProcedureMention( jcas );
+         IdentifiedAnnotation neAnnot;
+         if ( typeId == CONST.NE_TYPE_ID_DRUG || typeId == CONST.NE_TYPE_ID_UNKNOWN ) {
+            neAnnot = new MedicationEventMention( jcas );
          } else {
-             neAnnot = new EntityMention( jcas );
+            neAnnot = new EntityMention( jcas );
          }
          final int neBegin = entry.getKey().__start;
          final int neEnd = entry.getKey().__end;

Modified: ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java?rev=1491835&r1=1491834&r2=1491835&view=diff
==============================================================================
--- ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java
(original)
+++ ctakes/branches/jamia-submission-relation-extractor/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java
Tue Jun 11 15:24:56 2013
@@ -23,14 +23,9 @@ import org.apache.ctakes.dictionary.look
 import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
-import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
-import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.LabMention;
-import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
-import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
-import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
+import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
@@ -255,19 +250,9 @@ public abstract class UmlsToSnomedConsum
                   IdentifiedAnnotation neAnnot;
                   final int conceptKey = conceptEntry.getKey();
                   if ( conceptKey == CONST.NE_TYPE_ID_DRUG ) {
-                     neAnnot = new MedicationMention( jcas );
-                  } else if ( conceptKey == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
-                      neAnnot = new AnatomicalSiteMention( jcas );
-                  } else if ( conceptKey == CONST.NE_TYPE_ID_DISORDER ) {
-                      neAnnot = new DiseaseDisorderMention( jcas );
-                  } else if ( conceptKey == CONST.NE_TYPE_ID_FINDING ) {
-                      neAnnot = new SignSymptomMention( jcas );
-                  } else if ( conceptKey == CONST.NE_TYPE_ID_LAB ) {
-                      neAnnot = new LabMention( jcas );
-                  } else if ( conceptKey == CONST.NE_TYPE_ID_PROCEDURE ) {
-                      neAnnot = new ProcedureMention( jcas );
+                     neAnnot = new MedicationEventMention( jcas );
                   } else {
-                      neAnnot = new EntityMention( jcas );
+                     neAnnot = new EntityMention( jcas );
                   }
                   neAnnot.setTypeID( conceptKey );
                   neAnnot.setBegin( neBegin );



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