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Posted to commits@ctakes.apache.org by st...@apache.org on 2012/10/24 18:37:45 UTC
svn commit: r1401767 - in
/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal:
ae/ ae/feature/ eval/
Author: stevenbethard
Date: Wed Oct 24 16:37:44 2012
New Revision: 1401767
URL: http://svn.apache.org/viewvc?rev=1401767&view=rev
Log:
Fixes new warnings in ctakes-temporal revealed by new warnings settings
Modified:
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/AnnotationCopier.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java?rev=1401767&r1=1401766&r2=1401767&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java Wed Oct 24 16:37:44 2012
@@ -40,7 +40,8 @@ import org.cleartk.classifier.feature.ex
import org.cleartk.classifier.feature.extractor.simple.CoveredTextExtractor;
import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.JarClassifierFactory;
+import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
+import org.cleartk.classifier.jar.GenericJarClassifierFactory;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.util.JCasUtil;
@@ -55,7 +56,7 @@ public class DocTimeRelAnnotator extends
true,
DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
dataWriterClass,
- DefaultDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
+ DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
outputDirectory);
}
@@ -65,7 +66,7 @@ public class DocTimeRelAnnotator extends
DocTimeRelAnnotator.class,
CleartkAnnotator.PARAM_IS_TRAINING,
false,
- JarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+ GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
new File(modelDirectory, "model.jar"));
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java?rev=1401767&r1=1401766&r2=1401767&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java Wed Oct 24 16:37:44 2012
@@ -53,7 +53,8 @@ import org.cleartk.classifier.feature.ex
import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.JarClassifierFactory;
+import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
+import org.cleartk.classifier.jar.GenericJarClassifierFactory;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.util.JCasUtil;
@@ -75,7 +76,7 @@ public class EventAnnotator extends Clea
true,
DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
dataWriterClass,
- DefaultDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
+ DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
outputDirectory);
}
@@ -85,7 +86,7 @@ public class EventAnnotator extends Clea
EventAnnotator.class,
CleartkAnnotator.PARAM_IS_TRAINING,
false,
- JarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+ GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
new File(modelDirectory, "model.jar"));
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java?rev=1401767&r1=1401766&r2=1401767&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java Wed Oct 24 16:37:44 2012
@@ -45,7 +45,8 @@ import org.cleartk.classifier.feature.ex
import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.JarClassifierFactory;
+import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
+import org.cleartk.classifier.jar.GenericJarClassifierFactory;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.util.JCasUtil;
@@ -60,7 +61,7 @@ public class TimeAnnotator extends Clear
true,
DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
dataWriterClass,
- DefaultDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
+ DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
outputDirectory);
}
@@ -70,7 +71,7 @@ public class TimeAnnotator extends Clear
TimeAnnotator.class,
CleartkAnnotator.PARAM_IS_TRAINING,
false,
- JarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+ GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
new File(modelDirectory, "model.jar"));
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java?rev=1401767&r1=1401766&r2=1401767&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java Wed Oct 24 16:37:44 2012
@@ -64,8 +64,8 @@ public class CoveredTextToValuesExtracto
}
ArrayList<Feature> features = new ArrayList<Feature>();
for (int i = 0; i < values.length; ++i) {
- String name = Feature.createName(this.name, String.valueOf(i));
- features.add(new Feature(name, values[i]));
+ String featureName = Feature.createName(this.name, String.valueOf(i));
+ features.add(new Feature(featureName, values[i]));
}
return features;
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/AnnotationCopier.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/AnnotationCopier.java?rev=1401767&r1=1401766&r2=1401767&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/AnnotationCopier.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/AnnotationCopier.java Wed Oct 24 16:37:44 2012
@@ -65,22 +65,22 @@ public class AnnotationCopier extends JC
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
- JCas sourceView, targetView;
+ JCas sourceJCas, targetJCas;
try {
- sourceView = jCas.getView(this.sourceView);
- targetView = jCas.getView(this.targetView);
+ sourceJCas = jCas.getView(this.sourceView);
+ targetJCas = jCas.getView(this.targetView);
} catch (CASException e) {
throw new AnalysisEngineProcessException(e);
}
- CasCopier copier = new CasCopier(sourceView.getCas(), targetView.getCas());
- for (TOP annotation : JCasUtil.select(sourceView, this.annotationClass)) {
+ CasCopier copier = new CasCopier(sourceJCas.getCas(), targetJCas.getCas());
+ for (TOP annotation : JCasUtil.select(sourceJCas, this.annotationClass)) {
TOP copy = (TOP) copier.copyFs(annotation);
// CasCopier does not change sofa of annotation; without the code below, you get the error:
// the Annotation "..." is over view "GoldView" and cannot be added to indexes associated
// with the different view "_InitialView".
Feature sofaFeature = copy.getType().getFeatureByBaseName(CAS.FEATURE_BASE_NAME_SOFA);
if (sofaFeature != null) {
- copy.setFeatureValue(sofaFeature, targetView.getSofa());
+ copy.setFeatureValue(sofaFeature, targetJCas.getSofa());
}
copy.addToIndexes();
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1401767&r1=1401766&r2=1401767&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java Wed Oct 24 16:37:44 2012
@@ -70,7 +70,7 @@ public abstract class Evaluation_ImplBas
public enum AnnotatorType {
PART_OF_SPEECH_TAGS, UMLS_NAMED_ENTITIES, LEXICAL_VARIANTS, DEPENDENCIES, SEMANTIC_ROLES
- };
+ }
protected final String GOLD_VIEW_NAME = "GoldView";
@@ -112,9 +112,9 @@ public abstract class Evaluation_ImplBas
}
@Override
- protected CollectionReader getCollectionReader(List<Integer> patientSets) throws Exception {
+ protected CollectionReader getCollectionReader(List<Integer> selectedPatientSets) throws Exception {
List<File> files = new ArrayList<File>();
- for (Integer set : patientSets) {
+ for (Integer set : selectedPatientSets) {
File setTextDirectory = new File(this.rawTextDirectory, "doc" + set);
for (File file : setTextDirectory.listFiles()) {
files.add(file);
@@ -137,7 +137,7 @@ public abstract class Evaluation_ImplBas
private static enum PipelineType {
TRAIN, TEST
- };
+ }
private AnalysisEngineDescription getPreprocessorDescription(PipelineType pipelineType)
throws Exception {