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Posted to commits@ctakes.apache.org by ja...@apache.org on 2017/04/03 23:54:53 UTC
svn commit: r1790058 - in /ctakes/trunk: ctakes-assertion/
ctakes-assertion/lib/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/
ctakes-assertion/src/mai...
Author: james-masanz
Date: Mon Apr 3 23:54:52 2017
New Revision: 1790058
URL: http://svn.apache.org/viewvc?rev=1790058&view=rev
Log:
remove four 3rd-party jars (CTAKES-138) from Apache SVN. The code that uses those jars isn't part of the default pipeline and predates the similar ctakes machine learning assertion tool. For now replace classes from those jars with stubs so compile works. If those 3rd party jars get added to maven (See CTAKES-76) we can add them back as proper maven dependencies at that time.
Added:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverter.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptAnnotation.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptType.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java
Removed:
ctakes/trunk/ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar
ctakes/trunk/ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
ctakes/trunk/ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar
ctakes/trunk/ctakes-assertion/lib/med-facts-zoner-1.1.jar
Modified:
ctakes/trunk/ctakes-assertion/build.xml
ctakes/trunk/ctakes-assertion/pom.xml
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
ctakes/trunk/ctakes-clinical-pipeline/pom.xml
ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
ctakes/trunk/ctakes-ytex-uima/pom.xml
Modified: ctakes/trunk/ctakes-assertion/build.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/build.xml?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/build.xml (original)
+++ ctakes/trunk/ctakes-assertion/build.xml Mon Apr 3 23:54:52 2017
@@ -103,10 +103,6 @@
<pathelement location="../../../../.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.5.0/jackson-mapper-asl-1.5.0.jar"/>
<pathelement location="../../../../.m2/repository/org/scala-lang/scala-library/2.9.0/scala-library-2.9.0.jar"/>
<pathelement location="../../../../.m2/repository/org/scala-tools/sbinary/sbinary_2.9.0/0.4.0/sbinary_2.9.0-0.4.0.jar"/>
- <pathelement location="lib/med-facts-i2b2-1.2-SNAPSHOT.jar"/>
- <pathelement location="lib/med-facts-zoner-1.1.jar"/>
- <pathelement location="lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar"/>
- <pathelement location="lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar"/>
<pathelement location="../../../../../../ctakes-lvg"/>
<pathelement location="../../../../../../ctakes-lvg-res"/>
<pathelement location="../../../../.m2/repository/gov/nih/nlm/nls/lvg/lvg2010dist/0.0.1/lvg2010dist-0.0.1.jar"/>
Modified: ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/pom.xml?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion/pom.xml Mon Apr 3 23:54:52 2017
@@ -137,36 +137,6 @@
<version>0.4.0</version>
</dependency>
- <!-- Dependencies that still need to be uploaded to Maven Central; when
- done, the dependency versions should be moved into the parent pom -->
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-i2b2</artifactId>
- <version>1.2</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-zoner</artifactId>
- <version>1.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.core</groupId>
- <artifactId>jcarafe.core</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.ext</groupId>
- <artifactId>jcarafe.ext</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-lvg</artifactId>
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java Mon Apr 3 23:54:52 2017
@@ -42,16 +42,16 @@ import org.apache.uima.jcas.tcas.Annotat
import org.apache.uima.resource.ResourceAccessException;
import org.apache.uima.resource.ResourceInitializationException;
//import org.jfree.util.Log;
-import org.mitre.jcarafe.jarafe.JarafeMEDecoder;
-import org.mitre.medfacts.i2b2.annotation.PartOfSpeechTagger;
-import org.mitre.medfacts.i2b2.annotation.ScopeParser;
-import org.mitre.medfacts.i2b2.api.ApiConcept;
-import org.mitre.medfacts.i2b2.api.AssertionDecoderConfiguration;
-import org.mitre.medfacts.i2b2.api.SingleDocumentProcessor;
-import org.mitre.medfacts.i2b2.cli.BatchRunner;
-import org.mitre.medfacts.i2b2.util.StringHandling;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
-import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
+import org.apache.ctakes.assertion.stub.JarafeMEDecoder;
+import org.apache.ctakes.assertion.stub.PartOfSpeechTagger;
+import org.apache.ctakes.assertion.stub.ScopeParser;
+import org.apache.ctakes.assertion.stub.ApiConcept;
+import org.apache.ctakes.assertion.stub.AssertionDecoderConfiguration;
+import org.apache.ctakes.assertion.stub.SingleDocumentProcessor;
+import org.apache.ctakes.assertion.stub.BatchRunner;
+import org.apache.ctakes.assertion.stub.StringHandling;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverter;
+import org.apache.ctakes.assertion.stub.LineTokenToCharacterOffsetConverter;
import org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java Mon Apr 3 23:54:52 2017
@@ -14,13 +14,13 @@ 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.mitre.jcarafe.jarafe.JarafeMEDecoder;
-import org.mitre.medfacts.i2b2.annotation.PartOfSpeechTagger;
-import org.mitre.medfacts.i2b2.annotation.ScopeParser;
-import org.mitre.medfacts.i2b2.api.ApiConcept;
-import org.mitre.medfacts.i2b2.api.AssertionDecoderConfiguration;
-import org.mitre.medfacts.i2b2.cli.BatchRunner;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
+import org.apache.ctakes.assertion.stub.JarafeMEDecoder;
+import org.apache.ctakes.assertion.stub.PartOfSpeechTagger;
+import org.apache.ctakes.assertion.stub.ScopeParser;
+import org.apache.ctakes.assertion.stub.ApiConcept;
+import org.apache.ctakes.assertion.stub.AssertionDecoderConfiguration;
+import org.apache.ctakes.assertion.stub.BatchRunner;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverter;
import java.io.File;
import java.io.FileNotFoundException;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java Mon Apr 3 23:54:52 2017
@@ -39,15 +39,15 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceAccessException;
-import org.mitre.jcarafe.jarafe.JarafeMEDecoder;
-import org.mitre.medfacts.i2b2.annotation.ConceptType;
-import org.mitre.medfacts.i2b2.annotation.ScopeParser;
-import org.mitre.medfacts.i2b2.api.ApiConcept;
-import org.mitre.medfacts.i2b2.api.AssertionDecoderConfiguration;
-import org.mitre.medfacts.i2b2.api.SingleDocumentProcessor;
-import org.mitre.medfacts.i2b2.cli.BatchRunner;
-import org.mitre.medfacts.i2b2.util.StringHandling;
-import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
+import org.apache.ctakes.assertion.stub.JarafeMEDecoder;
+import org.apache.ctakes.assertion.stub.ConceptType;
+import org.apache.ctakes.assertion.stub.ScopeParser;
+import org.apache.ctakes.assertion.stub.ApiConcept;
+import org.apache.ctakes.assertion.stub.AssertionDecoderConfiguration;
+import org.apache.ctakes.assertion.stub.SingleDocumentProcessor;
+import org.apache.ctakes.assertion.stub.BatchRunner;
+import org.apache.ctakes.assertion.stub.StringHandling;
+import org.apache.ctakes.assertion.stub.LineTokenToCharacterOffsetConverter;
import org.apache.ctakes.assertion.medfacts.types.Assertion;
import org.apache.ctakes.assertion.medfacts.types.Concept;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java Mon Apr 3 23:54:52 2017
@@ -25,7 +25,7 @@ import org.apache.log4j.Logger;
import org.apache.uima.cas.FeatureStructure;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
-import org.mitre.medfacts.i2b2.annotation.ConceptType;
+import org.apache.ctakes.assertion.stub.ConceptType;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java Mon Apr 3 23:54:52 2017
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.assertion.medfacts;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverterDefaultImpl;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverter;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverterDefaultImpl;
import java.io.File;
import java.io.FileInputStream;
@@ -43,7 +43,7 @@ import org.apache.uima.util.InvalidXMLEx
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.tcas.Annotation;
-import org.mitre.medfacts.zoner.LineAndTokenPosition;
+import org.apache.ctakes.assertion.stub.LineAndTokenPosition;
import java.io.PrintWriter;
import java.io.IOException;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java Mon Apr 3 23:54:52 2017
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.assertion.medfacts;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverterDefaultImpl;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverter;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverterDefaultImpl;
import java.io.File;
import java.io.FileInputStream;
@@ -43,18 +43,19 @@ import org.apache.uima.jcas.cas.Sofa;
import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.apache.uima.util.InvalidXMLException;
import org.apache.uima.resource.ResourceInitializationException;
-import org.mitre.medfacts.i2b2.annotation.Annotation;
-import org.mitre.medfacts.i2b2.annotation.ConceptType;
+import org.apache.ctakes.assertion.stub.Annotation;
+import org.apache.ctakes.assertion.stub.AssertionAnnotation;
+import org.apache.ctakes.assertion.stub.ConceptType;
import org.apache.uima.cas.text.AnnotationIndex;
//import org.apache.uima.jcas.tcas.Annotation;
-import org.mitre.medfacts.zoner.LineAndTokenPosition;
+import org.apache.ctakes.assertion.stub.LineAndTokenPosition;
import java.io.PrintWriter;
import java.io.IOException;
-import org.mitre.medfacts.i2b2.api.SingleDocumentProcessor;
-import org.mitre.medfacts.i2b2.util.StringHandling;
-import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
-import org.mitre.medfacts.i2b2.processors.AssertionFileProcessor;
+import org.apache.ctakes.assertion.stub.SingleDocumentProcessor;
+import org.apache.ctakes.assertion.stub.StringHandling;
+import org.apache.ctakes.assertion.stub.LineTokenToCharacterOffsetConverter;
+import org.apache.ctakes.assertion.stub.AssertionFileProcessor;
import java.util.List;
import org.apache.ctakes.assertion.medfacts.types.Assertion;
@@ -64,13 +65,11 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
-import org.apache.uima.jcas.JCas;
import java.io.FileOutputStream;
import org.apache.uima.cas.impl.XmiCasSerializer;
import org.apache.uima.util.XMLSerializer;
-
/*
* Comments on using this class:
* This provides a utility to convert i2b2 format sentence and tokens to cTAKES Sentence and WordToken
@@ -198,7 +197,7 @@ public class Converti2b2AnnotationsToCTA
logger.info(" assertion: " + a.toString());
//Concept assertion = new Concept(jcas);
- org.mitre.medfacts.i2b2.annotation.AssertionAnnotation i2b2Assertion = (org.mitre.medfacts.i2b2.annotation.AssertionAnnotation)a;
+ AssertionAnnotation i2b2Assertion = (AssertionAnnotation)a;
ConceptType conceptType = i2b2Assertion.getConceptType();
IdentifiedAnnotation entityOrEventMention = null;
@@ -242,7 +241,7 @@ public class Converti2b2AnnotationsToCTA
private static void adjustAssertionAttributesByI2B2Convertion(
IdentifiedAnnotation entityOrEventMention,
- org.mitre.medfacts.i2b2.annotation.AssertionAnnotation i2b2Assertion)
+ AssertionAnnotation i2b2Assertion)
{
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java Mon Apr 3 23:54:52 2017
@@ -31,9 +31,9 @@ import org.apache.uima.cas.Type;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
-import org.mitre.medfacts.i2b2.api.ApiConcept;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
-import org.mitre.medfacts.zoner.LineAndTokenPosition;
+import org.apache.ctakes.assertion.stub.ApiConcept;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverter;
+import org.apache.ctakes.assertion.stub.LineAndTokenPosition;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java Mon Apr 3 23:54:52 2017
@@ -20,6 +20,8 @@ package org.apache.ctakes.assertion.medf
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
+
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import java.util.regex.Pattern;
@@ -37,11 +39,12 @@ import org.apache.uima.cas.TypeSystem;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
-import org.mitre.medfacts.i2b2.api.ApiConcept;
-import org.mitre.medfacts.i2b2.api.SingleDocumentProcessor;
-import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
-import org.mitre.medfacts.zoner.LineAndTokenPosition;
-import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
+import org.apache.ctakes.assertion.stub.ApiConcept;
+import org.apache.ctakes.assertion.stub.AssertionDecoderConfiguration;
+import org.apache.ctakes.assertion.stub.SingleDocumentProcessor;
+import org.apache.ctakes.assertion.stub.CharacterOffsetToLineTokenConverter;
+import org.apache.ctakes.assertion.stub.LineAndTokenPosition;
+import org.apache.ctakes.assertion.stub.LineTokenToCharacterOffsetConverter;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,15 @@
+package org.apache.ctakes.assertion.stub;
+
+public class Annotation {
+
+ public LineAndTokenPosition getEnd() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public LineAndTokenPosition getBegin() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,45 @@
+package org.apache.ctakes.assertion.stub;
+
+public class ApiConcept {
+
+ public void setText(String conceptText) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setBegin(int begin) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setEnd(int end) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setExternalId(int address) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setType(String conceptType) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public int getBegin() {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ public int getEnd() {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ public int getExternalId() {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,19 @@
+package org.apache.ctakes.assertion.stub;
+
+import org.apache.log4j.Logger;
+
+public class AssertionAnnotation extends ConceptAnnotation {
+
+ static private final Logger LOGGER = Logger.getLogger( "AssertionAnnotation" );
+
+ public ConceptType getConceptType() {
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+ return null;
+ }
+
+ public Object getAssertionValue() {
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+ return null;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,27 @@
+package org.apache.ctakes.assertion.stub;
+
+import java.util.Set;
+
+public class AssertionDecoderConfiguration {
+
+ public void setScopeParser(ScopeParser scopeParser) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setPosTagger(PartOfSpeechTagger posTagger) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setEnabledFeatureIdSet(Set<String> enabledFeatureIdSet) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setAssertionDecoder(JarafeMEDecoder assertionDecoder) {
+ // TODO Auto-generated method stub
+
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,17 @@
+package org.apache.ctakes.assertion.stub;
+
+import java.io.File;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+public class AssertionFileProcessor {
+
+ static private final Logger LOGGER = Logger.getLogger( "AssertionFileProcessor" );
+
+ public List<Annotation> processAnnotationFile(File assertionFile) {
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+ return null;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,17 @@
+package org.apache.ctakes.assertion.stub;
+
+import java.io.File;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+public class BatchRunner {
+
+ static private final Logger LOGGER = Logger.getLogger( "BatchRunner" );
+
+ public static Set<String> loadEnabledFeaturesFromFile(File enabledFeaturesFile) {
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+ return null;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverter.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverter.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverter.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,5 @@
+package org.apache.ctakes.assertion.stub;
+
+public interface CharacterOffsetToLineTokenConverter {
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,16 @@
+package org.apache.ctakes.assertion.stub;
+
+import org.apache.ctakes.assertion.stub.LineAndTokenPosition;
+
+public class CharacterOffsetToLineTokenConverterDefaultImpl {
+
+ public CharacterOffsetToLineTokenConverterDefaultImpl(String sofaString) {
+ // TODO Auto-generated constructor stub
+ }
+
+ public LineAndTokenPosition convert(int begin) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptAnnotation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptAnnotation.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptAnnotation.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptAnnotation.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,5 @@
+package org.apache.ctakes.assertion.stub;
+
+public class ConceptAnnotation extends Annotation{
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptType.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptType.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptType.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptType.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,9 @@
+package org.apache.ctakes.assertion.stub;
+
+public class ConceptType {
+
+ public static final ConceptType TREATMENT = null;
+ public static final ConceptType PROBLEM = null;
+ public static final ConceptType TEST = null;
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,16 @@
+package org.apache.ctakes.assertion.stub;
+
+import java.io.File;
+
+import org.apache.log4j.Logger;
+
+public class JarafeMEDecoder {
+
+ static private final Logger LOGGER = Logger.getLogger( "JarafeMEDecoder" );
+
+ public JarafeMEDecoder(File assertionModelFile) {
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,35 @@
+package org.apache.ctakes.assertion.stub;
+
+public class LineAndTokenPosition {
+
+ public void setTokenOffset(String string) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setLine(int lineNumber) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public String getTokenOffset() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public String getLine() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public void setLine(String line) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void setTokenOffset(int beginTokenWordNumber) {
+ // TODO Auto-generated method stub
+
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,28 @@
+package org.apache.ctakes.assertion.stub;
+
+public class LineTokenToCharacterOffsetConverter {
+
+ public class BeginAndEndCharacterOffsetPair {
+
+ public int getBegin() {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ public int getEnd() {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ }
+
+ public LineTokenToCharacterOffsetConverter(String contents) {
+ // TODO Auto-generated constructor stub
+ }
+
+ public LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair convert(LineAndTokenPosition sentEnd) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,9 @@
+package org.apache.ctakes.assertion.stub;
+
+public class PartOfSpeechTagger {
+
+ public PartOfSpeechTagger(String posModelFilePath) {
+ // TODO Auto-generated constructor stub
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,9 @@
+package org.apache.ctakes.assertion.stub;
+
+public class ScopeParser {
+
+ public ScopeParser(String scopeModelFilePath, String cueModelFilePath) {
+ // TODO Auto-generated constructor stub
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,80 @@
+package org.apache.ctakes.assertion.stub;
+
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl;
+import org.apache.log4j.Logger;
+
+public class SingleDocumentProcessor {
+ static private final Logger LOGGER = Logger.getLogger( "SingleDocumentProcessor" );
+
+ protected CharacterOffsetToLineTokenConverterCtakesImpl converter2;
+
+ protected String[][] arrayOfArrayOfTokens;
+
+ protected void preExecutionTest() {
+ // TODO Auto-generated method stub
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+
+ }
+
+ public Object addConcept(ApiConcept ac) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public void processSingleDocument() {
+ // TODO Auto-generated method stub
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+
+ }
+
+ public void setConverter2(CharacterOffsetToLineTokenConverter converter) {
+ // TODO Auto-generated method stub
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+
+ }
+
+
+ public void setAssertionDecoderConfiguration(AssertionDecoderConfiguration _assertionDecoderConfiguration) {
+ // TODO Auto-generated method stub
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+
+ }
+
+
+ public Map<Integer, String> getAssertionTypeMap() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+
+ public LineAndTokenPosition convertCharacterOffsetToLineToken(int characterOffset) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public List<LineAndTokenPosition> calculateBeginAndEndOfConcept(ApiConcept problem) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public void setContents(String contents) {
+ // TODO Auto-generated method stub
+
+ }
+
+
+ public void preprocess() {
+ // TODO Auto-generated method stub
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+
+ }
+
+ public String[][] getTokenArrays() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java?rev=1790058&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java Mon Apr 3 23:54:52 2017
@@ -0,0 +1,16 @@
+package org.apache.ctakes.assertion.stub;
+
+import java.io.File;
+
+import org.apache.log4j.Logger;
+
+public class StringHandling {
+ static private final Logger LOGGER = Logger.getLogger( "StringHandling" );
+
+ public static String readEntireContents(File file) {
+ // TODO Auto-generated method stub
+ LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
+ return null;
+ }
+
+}
Modified: ctakes/trunk/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/pom.xml?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/pom.xml (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/pom.xml Mon Apr 3 23:54:52 2017
@@ -126,36 +126,6 @@
</arguments>
</configuration>
<dependencies>
- <!-- System lib dependencies is causing a world of pain. Remove these
- when they're uploaded to Maven Central -->
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-i2b2</artifactId>
- <version>1.2</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-zoner</artifactId>
- <version>1.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-zoner-1.1.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.core</groupId>
- <artifactId>jcarafe.core</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.ext</groupId>
- <artifactId>jcarafe.ext</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
<dependency>
<groupId>gov.nih.nlm.nls.lvg</groupId>
<artifactId>lvgdist</artifactId>
@@ -201,36 +171,6 @@
</arguments>
</configuration>
<dependencies>
- <!-- System lib dependencies is causing a world of pain. Remove these
- when they're uploaded to Maven Central -->
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-i2b2</artifactId>
- <version>1.2</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-zoner</artifactId>
- <version>1.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-zoner-1.1.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.core</groupId>
- <artifactId>jcarafe.core</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.ext</groupId>
- <artifactId>jcarafe.ext</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
<dependency>
<groupId>gov.nih.nlm.nls.lvg</groupId>
<artifactId>lvgdist</artifactId>
Modified: ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (original)
+++ ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Mon Apr 3 23:54:52 2017
@@ -88,16 +88,6 @@
<fileSets>
<fileSet>
- <!-- Temporary workaround: Adding in the system scoped libraries. Remove
- these once they are in Maven Central -->
- <directory>../ctakes-assertion/lib</directory>
- <outputDirectory>lib</outputDirectory>
- <includes>
- <include>med-facts-i2b2-1.2-SNAPSHOT.jar</include>
- <include>med-facts-zoner-1.1.jar</include>
- <include>jcarafe-core_2.9.1-0.9.8.3.RC4.jar</include>
- <include>jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</include>
- </includes>
</fileSet>
<!-- The Type System needs to exist outside the lib/*.jar file. Otherwise it cannot be used with the CVD. -->
<fileSet>
Modified: ctakes/trunk/ctakes-ytex-uima/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/pom.xml?rev=1790058&r1=1790057&r2=1790058&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex-uima/pom.xml Mon Apr 3 23:54:52 2017
@@ -221,10 +221,6 @@
<additionalClasspathElement>${project.basedir}/../ctakes-smoking-status-res/src/main/resources</additionalClasspathElement>
<additionalClasspathElement>${project.basedir}/../ctakes-temporal-res/src/main/resources</additionalClasspathElement>
<additionalClasspathElement>${project.basedir}/../ctakes-ytex-res/src/main/resources</additionalClasspathElement>
- <additionalClasspathElement>${project.basedir}/../ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</additionalClasspathElement>
- <additionalClasspathElement>${project.basedir}/../ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</additionalClasspathElement>
- <additionalClasspathElement>${project.basedir}/../ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</additionalClasspathElement>
- <additionalClasspathElement>${project.basedir}/../ctakes-assertion/lib/med-facts-zoner-1.1.jar</additionalClasspathElement>
</additionalClasspathElements>
</configuration>
</execution>