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Move features to new package
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89 files changed

+613
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swan_core/src/main/java/de/fraunhofer/iem/swan/model/InstancesHandler.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/InstancesHandler.java

Lines changed: 45 additions & 77 deletions
Original file line numberDiff line numberDiff line change
@@ -1,24 +1,16 @@
1-
package de.fraunhofer.iem.swan.model;
1+
package de.fraunhofer.iem.swan.features;
22

33
import de.fraunhofer.iem.swan.data.Category;
44
import de.fraunhofer.iem.swan.data.Method;
5-
import de.fraunhofer.iem.swan.doc.features.DocFeatureHandler;
6-
import de.fraunhofer.iem.swan.doc.features.automatic.DocCommentVector;
7-
import de.fraunhofer.iem.swan.doc.features.manual.IDocFeature;
8-
import de.fraunhofer.iem.swan.doc.nlp.AnnotatedMethod;
9-
import de.fraunhofer.iem.swan.doc.nlp.CoreNLPExecutor;
10-
import de.fraunhofer.iem.swan.doc.nlp.NLPUtils;
11-
import de.fraunhofer.iem.swan.features.type.IFeature;
12-
import de.fraunhofer.iem.swan.util.SwanConfig;
13-
import org.nd4j.linalg.cpu.nativecpu.NDArray;
5+
import de.fraunhofer.iem.swan.features.doc.DocFeatureHandler;
6+
import de.fraunhofer.iem.swan.features.doc.manual.IDocFeature;
7+
import de.fraunhofer.iem.swan.features.doc.nlp.AnnotatedMethod;
8+
import de.fraunhofer.iem.swan.features.code.type.IFeature;
149
import weka.core.Attribute;
1510
import weka.core.DenseInstance;
1611
import weka.core.Instance;
1712
import weka.core.Instances;
18-
import weka.core.converters.ArffSaver;
1913

20-
import java.io.File;
21-
import java.io.IOException;
2214
import java.util.*;
2315

2416
/**
@@ -36,20 +28,18 @@ public class InstancesHandler {
3628
public enum INSTANCE_SET {
3729
SWAN,
3830
SWAN_SWANDOC_MANUAL,
39-
SWAN_SWANDOC_AUTOMATIC,
31+
SWAN_SWANDOC_WORD_EMBEDDING,
4032
SWANDOC_MANUAL,
41-
SWANDOC_AUTOMATIC
33+
SWANDOC_WORD_EMBEDDING
4234
}
4335

4436
private ArrayList<Attribute> attributes;
4537
private Map<IFeature, Attribute> swanFeatureAttribs;
46-
private Set<Class<? extends IDocFeature>> swanDocFeatureSet;
4738
private HashMap<String, Integer> instanceMap;
48-
private HashMap<String, Method> methodMap;
39+
private Instances instances;
4940

5041
public InstancesHandler() {
5142
this.instanceMap = new HashMap<>();
52-
this.methodMap = new HashMap<>();
5343
}
5444

5545
/**
@@ -59,39 +49,34 @@ public InstancesHandler() {
5949
* @param instanceSet
6050
* @return
6151
*/
62-
public Instances createInstances(Set<Method> trainingSet,
52+
public void createInstances(Set<Method> trainingSet,
6353
Map<Category, Set<IFeature>> features, DocFeatureHandler docFeatures, Set<Category> categories,
6454
INSTANCE_SET instanceSet) {
6555

66-
for (Method method : trainingSet) {
67-
methodMap.put(method.getSignature(), method);
68-
}
69-
7056
//Initialize instances
7157
initializeInstances(features, docFeatures, categories, trainingSet, null, instanceSet);
7258

7359
// Set attributes to the train instances.
74-
Instances trainInstances = new Instances("training-methods", attributes, 0);
75-
trainInstances.setClass(trainInstances.attribute("class"));
60+
instances = new Instances("training-methods", attributes, 0);
61+
instances.setClass(instances.attribute("class"));
7662

7763
//Populate SWAN feature attributes
7864
switch (instanceSet) {
7965
case SWAN:
80-
trainInstances = addSwanInstances(trainInstances, trainingSet, categories);
66+
instances = addSwanInstances(instances, trainingSet, categories);
8167
break;
8268
case SWANDOC_MANUAL:
83-
case SWANDOC_AUTOMATIC:
84-
trainInstances = addSwanDocInstances(trainInstances, docFeatures, categories, instanceSet);
69+
case SWANDOC_WORD_EMBEDDING:
70+
instances = addSwanDocInstances(instances, trainingSet, docFeatures, categories, instanceSet);
8571
break;
8672
case SWAN_SWANDOC_MANUAL:
87-
case SWAN_SWANDOC_AUTOMATIC:
88-
trainInstances = addSwanInstances(trainInstances, trainingSet, categories);
89-
trainInstances = addSwanDocInstances(trainInstances, docFeatures, categories, instanceSet);
73+
case SWAN_SWANDOC_WORD_EMBEDDING:
74+
instances = addSwanInstances(instances, trainingSet, categories);
75+
instances = addSwanDocInstances(instances,trainingSet, docFeatures, categories, instanceSet);
9076
break;
9177
}
9278

93-
exportInstances(trainInstances, categories);
94-
return trainInstances;
79+
//exportInstances(trainInstances, categories);
9580
}
9681

9782

@@ -116,30 +101,27 @@ public void initializeInstances(Map<Category, Set<IFeature>> features, DocFeatur
116101
initializeSwanFeatures(features, categories);
117102
break;
118103
case SWAN_SWANDOC_MANUAL:
119-
case SWAN_SWANDOC_AUTOMATIC:
104+
case SWAN_SWANDOC_WORD_EMBEDDING:
120105
initializeSwanFeatures(features, categories);
121106
initializeSwanDocFeatures(docFeatures, instanceSet);
122107
break;
123108
case SWANDOC_MANUAL:
124-
case SWANDOC_AUTOMATIC:
109+
case SWANDOC_WORD_EMBEDDING:
125110
initializeSwanDocFeatures(docFeatures, instanceSet);
126111
break;
127112
}
128113

129114
// Add method signatures as id attribute
130115
ArrayList<String> methodStrings = new ArrayList<>();
131116

117+
// System.out.println("TOTAL SET...."+trainingSet.size());
132118
int c = 0;
133119
for (Method am : trainingSet) {
134-
methodStrings.add(am.getSignature().replace(",", "+"));
120+
methodStrings.add(am.getArffSafeSignature());
121+
//System.out.println("ini: "+am.getArffSafeSignature());
135122
c++;
136123
}
137124

138-
if (testSet != null)
139-
for (Method am : testSet) {
140-
methodStrings.add(am.getSignature());
141-
}
142-
143125
Attribute idAttr = new Attribute("id", methodStrings);
144126
attributes.add(idAttr);
145127

@@ -203,8 +185,8 @@ public void initializeSwanDocFeatures(DocFeatureHandler features, INSTANCE_SET i
203185
attributes.add(attribute);
204186
}
205187
break;
206-
case SWAN_SWANDOC_AUTOMATIC:
207-
case SWANDOC_AUTOMATIC:
188+
case SWAN_SWANDOC_WORD_EMBEDDING:
189+
case SWANDOC_WORD_EMBEDDING:
208190

209191
for (String feature : features.getAutomaticFeatureSet()) {
210192
Attribute attribute = new Attribute(feature);
@@ -269,11 +251,11 @@ public Instances addSwanInstances(Instances trainInstances, Set<Method> training
269251
}
270252

271253
//Set id attribute
272-
inst.setValue(trainInstances.attribute("id"), am.getSignature().replace(",", "+"));
254+
inst.setValue(trainInstances.attribute("id"), am.getArffSafeSignature());
273255
c++;
274256

275257
trainInstances.add(inst);
276-
instanceMap.put(am.getSignature(), instanceIndex++);
258+
instanceMap.put(am.getArffSafeSignature(), instanceIndex++);
277259
}
278260
return trainInstances;
279261
}
@@ -286,25 +268,30 @@ public Instances addSwanInstances(Instances trainInstances, Set<Method> training
286268
* @param categories set of categories
287269
* @return Instances containing data from SWAN-DOC
288270
*/
289-
public Instances addSwanDocInstances(Instances trainInstances, DocFeatureHandler docFeatures, Set<Category> categories, INSTANCE_SET instanceSet) {
271+
public Instances addSwanDocInstances(Instances trainInstances, Set<Method> trainingSet, DocFeatureHandler docFeatures, Set<Category> categories, INSTANCE_SET instanceSet) {
290272

291-
for (Method method : docFeatures.getMethodSet()) {
273+
// System.out.println("TOTAL DOCS...."+docFeatures.getMethodSet().size());
274+
for (Method method : trainingSet) {
292275

276+
// System.out.println("Value not found: "+method.getArffSafeSignature());
293277
Instance inst;
278+
boolean isNewInstance = false;
294279

295280
//If instance exists already, update it. Otherwise create a new instance
296-
if (instanceMap.containsKey(method.getSignature())) {
281+
if (instanceMap.containsKey(method.getArffSafeSignature())) {
297282

298-
inst = trainInstances.instance(instanceMap.get(method.getSignature()));
283+
inst = trainInstances.instance(instanceMap.get(method.getArffSafeSignature()));
299284
// System.out.println("Instance for: "+ inst.attribute());
300285
// trainInstances.delete(instanceMap.get(method.getMethod().getSignature()));
301286
} else {
302287
inst = new DenseInstance(attributes.size());
303288
inst.setDataset(trainInstances);
289+
isNewInstance = true;
304290
}
305291

306-
//System.out.println(method.getMethod().getSignature());
307-
inst.setValue(trainInstances.attribute("id"), method.getSignature().replace(",", "+"));
292+
// System.out.println("Value really not found: "+method.getArffSafeSignature());
293+
inst.setValue(trainInstances.attribute("id"), method.getArffSafeSignature());
294+
308295
Category categoryClassified = null;
309296

310297
for (Category category : method.getCategoriesTrained()) {
@@ -329,11 +316,9 @@ public Instances addSwanDocInstances(Instances trainInstances, DocFeatureHandler
329316
case SWAN_SWANDOC_MANUAL:
330317
for (Class<? extends IDocFeature> feature : docFeatures.getManualFeatureSet()) {
331318

332-
IDocFeature javadocFeature;
333-
334319
try {
335320

336-
javadocFeature = feature.newInstance();
321+
IDocFeature javadocFeature = feature.newInstance();
337322
AnnotatedMethod annotatedMethod = docFeatures.getManualFeatureData().get(method.getSignature());
338323
//System.out.println("Adding: "+trainInstances.attribute(feature.getSimpleName())+" "+ javadocFeature.evaluate(method).getTotalValue());
339324
inst.setValue(trainInstances.attribute(feature.getSimpleName()), javadocFeature.evaluate(annotatedMethod).getTotalValue());
@@ -342,39 +327,22 @@ public Instances addSwanDocInstances(Instances trainInstances, DocFeatureHandler
342327
}
343328
}
344329
break;
345-
case SWANDOC_AUTOMATIC:
346-
case SWAN_SWANDOC_AUTOMATIC:
330+
case SWANDOC_WORD_EMBEDDING:
331+
case SWAN_SWANDOC_WORD_EMBEDDING:
347332
HashMap<String, Double> vectorValues = docFeatures.getAutomaticFeatureData().get(method.getSignature());
348333

349334
for (String key : vectorValues.keySet()) {
350335
inst.setValue(trainInstances.attribute(key), vectorValues.get(key));
351336
}
352337
break;
353338
}
354-
trainInstances.add(inst);
339+
if (isNewInstance)
340+
trainInstances.add(inst);
355341
}
356342
return trainInstances;
357343
}
358344

359-
public void exportInstances(Instances trainInstances, Set<Category> categories) {
360-
SwanConfig swanConfig = new SwanConfig();
361-
Properties config = swanConfig.getConfig();
362-
363-
if (Boolean.parseBoolean(config.getProperty("output_train_arff_data"))) {
364-
// Save arff data.
365-
ArffSaver saver = new ArffSaver();
366-
saver.setInstances(trainInstances);
367-
List<Category> fileNameList = new ArrayList<>(categories);
368-
Collections.sort(fileNameList);
369-
String fileName = fileNameList.toString();
370-
fileName = fileName.substring(1, fileName.length() - 1);
371-
fileName = fileName.replace(", ", "_");
372-
try {
373-
saver.setFile(new File("/Users/oshando/Projects/thesis/03-code/swan/swan_core/swan-out/weka/" + "Train_" + fileName + ".arff"));
374-
saver.writeBatch();
375-
} catch (IOException e) {
376-
e.printStackTrace();
377-
}
378-
}
345+
public Instances getInstances() {
346+
return instances;
379347
}
380348
}

swan_core/src/main/java/de/fraunhofer/iem/swan/features/FeatureHandler.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/FeatureHandler.java

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,15 @@
1-
package de.fraunhofer.iem.swan.features;
1+
package de.fraunhofer.iem.swan.features.code;
22

33
import java.util.Arrays;
44
import java.util.HashMap;
55
import java.util.HashSet;
66
import java.util.Map;
77
import java.util.Set;
88

9-
import de.fraunhofer.iem.swan.Main;
109
import de.fraunhofer.iem.swan.data.Category;
11-
import de.fraunhofer.iem.swan.features.type.*;
12-
import de.fraunhofer.iem.swan.features.type.MethodClassModifierFeature.ClassModifier;
13-
import de.fraunhofer.iem.swan.features.type.MethodModifierFeature.Modifier;
10+
import de.fraunhofer.iem.swan.features.code.type.*;
11+
import de.fraunhofer.iem.swan.features.code.type.MethodClassModifierFeature.ClassModifier;
12+
import de.fraunhofer.iem.swan.features.code.type.MethodModifierFeature.Modifier;
1413
import org.slf4j.Logger;
1514
import org.slf4j.LoggerFactory;
1615

swan_core/src/main/java/de/fraunhofer/iem/swan/soot/InitializeSoot.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/soot/InitializeSoot.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.soot;
1+
package de.fraunhofer.iem.swan.features.code.soot;
22

33
import soot.Scene;
44
import soot.options.Options;

swan_core/src/main/java/de/fraunhofer/iem/swan/io/Loader.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/soot/Loader.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.io;
1+
package de.fraunhofer.iem.swan.features.code.soot;
22

33
import java.util.ArrayList;
44
import java.util.HashSet;
@@ -7,7 +7,7 @@
77

88
import de.fraunhofer.iem.swan.data.Category;
99
import de.fraunhofer.iem.swan.data.Method;
10-
import de.fraunhofer.iem.swan.features.type.AbstractSootFeature;
10+
import de.fraunhofer.iem.swan.features.code.type.AbstractSootFeature;
1111
import de.fraunhofer.iem.swan.util.Util;
1212
import soot.Scene;
1313
import soot.SootClass;

swan_core/src/main/java/de/fraunhofer/iem/swan/features/type/AbstractSootFeature.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/type/AbstractSootFeature.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.features.type;
1+
package de.fraunhofer.iem.swan.features.code.type;
22

33
import java.util.HashMap;
44
import java.util.List;

swan_core/src/main/java/de/fraunhofer/iem/swan/features/type/BaseNameOfClassPackageName.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/type/BaseNameOfClassPackageName.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.features.type;
1+
package de.fraunhofer.iem.swan.features.code.type;
22

33
import de.fraunhofer.iem.swan.data.Method;
44

swan_core/src/main/java/de/fraunhofer/iem/swan/features/type/IFeature.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/type/IFeature.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.features.type;
1+
package de.fraunhofer.iem.swan.features.code.type;
22

33
import de.fraunhofer.iem.swan.data.Method;
44

swan_core/src/main/java/de/fraunhofer/iem/swan/features/type/IsImplicitMethod.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/type/IsImplicitMethod.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.features.type;
1+
package de.fraunhofer.iem.swan.features.code.type;
22

33
import de.fraunhofer.iem.swan.data.Method;
44

swan_core/src/main/java/de/fraunhofer/iem/swan/features/type/IsThreadRunFeature.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/type/IsThreadRunFeature.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.features.type;
1+
package de.fraunhofer.iem.swan.features.code.type;
22

33
import de.fraunhofer.iem.swan.data.Method;
44
import soot.SootMethod;

swan_core/src/main/java/de/fraunhofer/iem/swan/features/type/MethodAnonymousClassFeature.java renamed to core/src/main/java/de/fraunhofer/iem/swan/features/code/type/MethodAnonymousClassFeature.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package de.fraunhofer.iem.swan.features.type;
1+
package de.fraunhofer.iem.swan.features.code.type;
22

33
import java.util.regex.Pattern;
44

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