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Posted to commits@ctakes.apache.org by al...@apache.org on 2017/11/20 00:58:52 UTC
svn commit: r1815766 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/
Author: alexz
Date: Mon Nov 20 00:58:52 2017
New Revision: 1815766
URL: http://svn.apache.org/viewvc?rev=1815766&view=rev
Log:
CTAKES-465: Fix deprecation for createAnnotatorDescription
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventCRFRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventDeepPheRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventHybridModelsRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventCRFRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventCRFRelations.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventCRFRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventCRFRelations.java Mon Nov 20 00:58:52 2017
@@ -59,6 +59,7 @@ import org.cleartk.util.ViewUriUtil;
import java.io.File;
import java.net.URI;
+import java.nio.file.Paths;
import java.util.*;
//import org.apache.ctakes.temporal.ae.EventTimeSyntacticAnnotator;
@@ -322,8 +323,12 @@ EvaluationOfTemporalRelations_ImplBase{
GOLD_VIEW_NAME);
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
- aggregateBuilder.add(EventEventCRFRelationAnnotator.createAnnotatorDescription(new File(directory,"event-event")));
-
+ aggregateBuilder.add(
+ EventEventCRFRelationAnnotator.createAnnotatorDescription(
+ Paths.get(directory.getAbsolutePath(), "event-event").toAbsolutePath().toString()
+ )
+ );
+
//count how many system predicted relations, their arguments are close to each other, without any other event in between
// aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CountCloseRelation.class));
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventDeepPheRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventDeepPheRelations.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventDeepPheRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventDeepPheRelations.java Mon Nov 20 00:58:52 2017
@@ -59,6 +59,7 @@ import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.net.URI;
+import java.nio.file.Paths;
import java.util.*;
//import org.apache.ctakes.temporal.ae.EventTimeSyntacticAnnotator;
@@ -291,7 +292,11 @@ EvaluationOfTemporalRelations_ImplBase{
GOLD_VIEW_NAME);
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
- aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(new File(directory,"event-event")));
+ aggregateBuilder.add(
+ EventEventRelationAnnotator.createAnnotatorDescription(
+ Paths.get(directory.getAbsolutePath(), "event-event").toAbsolutePath().toString()
+ )
+ );
//count how many system predicted relations, their arguments are close to each other, without any other event in between
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CountCloseRelation.class));
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventHybridModelsRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventHybridModelsRelations.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventHybridModelsRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventHybridModelsRelations.java Mon Nov 20 00:58:52 2017
@@ -61,6 +61,7 @@ import org.cleartk.util.ViewUriUtil;
import java.io.File;
import java.net.URI;
+import java.nio.file.Paths;
import java.util.*;
//import org.apache.ctakes.temporal.ae.EventTimeSyntacticAnnotator;
@@ -353,8 +354,16 @@ EvaluationOfTemporalRelations_ImplBase{
GOLD_VIEW_NAME);
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
- aggregateBuilder.add(EventEventCRFRelationAnnotator.createAnnotatorDescription(new File(directory,"event-event-crf")));
- aggregateBuilder.add(EventEventRelationSeedBasedAnnotator.createAnnotatorDescription(new File(directory,"event-event-svm")));
+ aggregateBuilder.add(
+ EventEventCRFRelationAnnotator.createAnnotatorDescription(
+ Paths.get(directory.getAbsolutePath(), "event-event-crf").toAbsolutePath().toString()
+ )
+ );
+ aggregateBuilder.add(
+ EventEventRelationSeedBasedAnnotator.createAnnotatorDescription(
+ Paths.get(directory.getAbsolutePath(),"event-event-svm").toAbsolutePath().toString()
+ )
+ );
if(this.i2b2Output != null){
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteAnaforaXML.class, WriteAnaforaXML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java Mon Nov 20 00:58:52 2017
@@ -137,7 +137,8 @@ EvaluationOfTemporalRelations_ImplBase {
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
aggregateBuilder.add(
- EventEventRelationAnnotator.createAnnotatorDescription(directory));
+ EventEventRelationAnnotator.createAnnotatorDescription(directory.getAbsolutePath())
+ );
Function<BinaryTextRelation, ?> getSpan = new Function<BinaryTextRelation, HashableArguments>() {
public HashableArguments apply(BinaryTextRelation relation) {
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java Mon Nov 20 00:58:52 2017
@@ -64,6 +64,7 @@ import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.net.URI;
+import java.nio.file.Paths;
import java.util.*;
//import org.apache.ctakes.temporal.ae.EventTimeSyntacticAnnotator;
@@ -416,8 +417,13 @@ EvaluationOfTemporalRelations_ImplBase{
// aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveNonUMLSEvents.class));
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
- aggregateBuilder.add(this.baseline ? RecallBaselineEventTimeRelationAnnotator.createAnnotatorDescription(directory) :
- EventEventRelationAnnotator.createAnnotatorDescription(new File(directory,"event-event")));
+ aggregateBuilder.add(
+ this.baseline ?
+ RecallBaselineEventTimeRelationAnnotator.createAnnotatorDescription(directory) :
+ EventEventRelationAnnotator.createAnnotatorDescription(
+ Paths.get(directory.getAbsolutePath(),"event-event").toAbsolutePath().toString()
+ )
+ );
//count how many system predicted relations, their arguments are close to each other, without any other event in between
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CountCloseRelation.class));
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java Mon Nov 20 00:58:52 2017
@@ -74,7 +74,7 @@ public class EvaluationOfNEPredicateEven
throws ResourceInitializationException {
// not training a model - just using the NEs and predicates
// return AnalysisEngineFactory.createEngineDescription(NoOpAnnotator.class);
- return NEPredicateEventAnnotator.createAnnotatorDescription(directory);
+ return NEPredicateEventAnnotator.createAnnotatorDescription(directory.getAbsolutePath());
}
@Override
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java Mon Nov 20 00:58:52 2017
@@ -61,6 +61,7 @@ import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.net.URI;
+import java.nio.file.Paths;
import java.util.*;
//import java.util.HashSet;
@@ -354,7 +355,11 @@ EvaluationOfTemporalRelations_ImplBase{
GOLD_VIEW_NAME);
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
- aggregateBuilder.add(EventTimeRelationAnnotator.createAnnotatorDescription(new File(directory,"event-time")));
+ aggregateBuilder.add(
+ EventTimeRelationAnnotator.createAnnotatorDescription(
+ Paths.get(directory.getAbsolutePath(),"event-time").toAbsolutePath().toString()
+ )
+ );
if(this.i2b2Output != null){
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java?rev=1815766&r1=1815765&r2=1815766&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java Mon Nov 20 00:58:52 2017
@@ -287,7 +287,7 @@ public class EvaluationOfTimeSpans exten
if(MetaTimeAnnotator.class.isAssignableFrom(this.annotatorClass)){
return MetaTimeAnnotator.getAnnotatorDescription(directory);
}else if("org.apache.ctakes.temporal.ae.TimeAnnotator".equals(this.annotatorClass.getName() )){
- return TimeAnnotator.createAnnotatorDescription(this.getModelDirectory(directory));
+ return TimeAnnotator.createAnnotatorDescription(this.getModelDirectory(directory).getAbsolutePath());
}
return AnalysisEngineFactory.createEngineDescription(
this.annotatorClass,