Refactor project directory

Author: oshando

core/LICENSE renamed to swan-pipeline/LICENSE

@@ -49,4 +49,18 @@ public static Category getCategoryForCWE(String cweName) {
                 return c;
         return null;
     }
+
+    public static Category fromText(String text) {
+
+        for(Category cat: Category.values()){
+            if(cat.name().equalsIgnoreCase(text)){
+                return cat;
+            }
+        }
+
+        throw new IllegalArgumentException(String.format(
+                "There is no category with name '%s'",
+                text
+        ));
+    }
 }

core/src/main/java/de/fraunhofer/iem/swan/data/CWE.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/data/CWE.java

@@ -1,6 +1,6 @@
 package de.fraunhofer.iem.swan.data;
 
-import javafx.util.Pair;
+import org.apache.commons.lang3.tuple.Pair;
 import org.jdom2.Document;
 import org.jdom2.Element;
 import org.jdom2.Namespace;

core/src/main/java/de/fraunhofer/iem/swan/data/Category.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/data/Category.java

@@ -75,7 +75,6 @@ public void createInstances(Set<Method> trainingSet,
                 instances = addSwanDocInstances(instances,trainingSet, docFeatures, categories, instanceSet);
                 break;
         }
-
         //exportInstances(trainInstances, categories);
     }
 

core/src/main/java/de/fraunhofer/iem/swan/data/Constants.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/data/Constants.java

@@ -43,7 +43,7 @@ public static void main(String[] args) {
         //Export method and class doc comments
 
         Parser parser = new Parser();
-        parser.parse("/data-set-with-doc-comments.json");
+        parser.parse("/swan-dataset.json");
 
 //        for(Method method: parser.getMethods()){
 //            if(method.getJavadoc().getMethodComment().length()>0)

core/src/main/java/de/fraunhofer/iem/swan/data/Javadoc.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/data/Javadoc.java

@@ -4,7 +4,7 @@
 import de.fraunhofer.iem.swan.data.Constants;
 import de.fraunhofer.iem.swan.data.Method;
 import de.fraunhofer.iem.swan.data.XMLParser;
-import javafx.util.Pair;
+import org.apache.commons.lang3.tuple.Pair;
 import org.apache.commons.io.FileUtils;
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
@@ -256,13 +256,13 @@ public void writeResultsQwelXML(Set<Method> methods, String outputFile) {
 
             if (method.getCategoriesClassified().toString().contains(Constants.SOURCE)) {
                 sourcesList.append("/" + counter + " ");
-                methodList.put("m" + counter, new Pair(Constants.SOURCE, method.getTrimmedSignature()));
+                methodList.put("m" + counter,  Pair.of(Constants.SOURCE, method.getTrimmedSignature()));
                 counter++;
             }
 
             if (method.getCategoriesClassified().toString().contains(Constants.SINK)) {
                 sinksList.append("/" + counter + " ");
-                methodList.put("m" + counter, new Pair(Constants.SINK, method.getTrimmedSignature()));
+                methodList.put("m" + counter,  Pair.of(Constants.SINK, method.getTrimmedSignature()));
                 counter++;
             }
         }

core/src/main/java/de/fraunhofer/iem/swan/data/Method.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/data/Method.java

@@ -1,6 +1,7 @@
 package de.fraunhofer.iem.swan.io.doc;
 
-import com.sun.tools.javadoc.Main;
+//import com.sun.tools.javadoc.Main;
+//import jdk.javadoc.doclet.StandardDoclet;
 
 /**
  * @author Oshando Johnson on 03.06.20
@@ -45,7 +46,7 @@ public void runDoclet(String sourcePath, String packages, String outputPath) {
                 "-subpackages", packages
         };
         System.out.println();
-       Main.execute(docletParams);
+       //Main.execute(docletParams);
     }
 
     public void runDoclet(String sourcePath, String packages) {

core/src/main/java/de/fraunhofer/iem/swan/data/RelevantPart.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/data/RelevantPart.java

@@ -0,0 +1,169 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+  <xs:element name="ssldoclet" type="ssldocletType"/>
+  <xs:complexType name="ClassType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="final"/>
+        <xs:attribute type="xs:string" name="line"/>
+        <xs:attribute type="xs:string" name="serializable"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="InterfaceType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="final"/>
+        <xs:attribute type="xs:string" name="qualifiedType"/>
+        <xs:attribute type="xs:string" name="serializable"/>
+        <xs:attribute type="xs:string" name="type"/>
+        <xs:attribute type="xs:string" name="superclass"/>
+        <xs:attribute type="xs:string" name="superclassFullType"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="Interface_BlockType">
+    <xs:sequence>
+      <xs:element type="xs:string" name="Implements_Comment"/>
+      <xs:element type="InterfaceType" name="Interface"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="ExtendsType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="final"/>
+        <xs:attribute type="xs:string" name="qualifiedType"/>
+        <xs:attribute type="xs:string" name="serializable"/>
+        <xs:attribute type="xs:string" name="superclass"/>
+        <xs:attribute type="xs:string" name="superclassFullType"/>
+        <xs:attribute type="xs:string" name="type"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="Extends_BlockType">
+    <xs:sequence>
+      <xs:element type="xs:string" name="Extends_Comment"/>
+      <xs:element type="ExtendsType" name="Extends"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="Class_CommentType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="line"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="Class_Comment_BlockType">
+    <xs:sequence>
+      <xs:element type="Class_CommentType" name="Class_Comment"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="ConstructorType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="final"/>
+        <xs:attribute type="xs:string" name="interface"/>
+        <xs:attribute type="xs:string" name="line"/>
+        <xs:attribute type="xs:string" name="modifier"/>
+        <xs:attribute type="xs:string" name="signature"/>
+        <xs:attribute type="xs:string" name="static"/>
+        <xs:attribute type="xs:string" name="synchronized"/>
+        <xs:attribute type="xs:string" name="synthetic"/>
+        <xs:attribute type="xs:string" name="visibility"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="Constructor_CommentType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="line"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="Constructor_Comment_BlockType">
+    <xs:sequence>
+      <xs:element type="Constructor_CommentType" name="Constructor_Comment"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="Constructor_BlockType">
+    <xs:sequence>
+      <xs:element type="ConstructorType" name="Constructor"/>
+      <xs:element type="Constructor_Comment_BlockType" name="Constructor_Comment_Block"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="ConstructorsType">
+    <xs:sequence>
+      <xs:element type="Constructor_BlockType" name="Constructor_Block"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="MethodType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="abstract" use="optional"/>
+        <xs:attribute type="xs:string" name="final" use="optional"/>
+        <xs:attribute type="xs:string" name="interface" use="optional"/>
+        <xs:attribute type="xs:string" name="line" use="optional"/>
+        <xs:attribute type="xs:string" name="modifier" use="optional"/>
+        <xs:attribute type="xs:string" name="signature" use="optional"/>
+        <xs:attribute type="xs:string" name="static" use="optional"/>
+        <xs:attribute type="xs:string" name="synchronized" use="optional"/>
+        <xs:attribute type="xs:string" name="synthetic" use="optional"/>
+        <xs:attribute type="xs:string" name="visibility" use="optional"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="Method_CommentType">
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute type="xs:string" name="line" use="optional"/>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:complexType name="Method_Comment_BlockType">
+    <xs:sequence>
+      <xs:element type="Method_CommentType" name="Method_Comment"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="Return_BlockType">
+    <xs:sequence>
+      <xs:element type="xs:string" name="Return"/>
+      <xs:element type="xs:string" name="Return_Comment" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="Method_BlockType">
+    <xs:sequence>
+      <xs:element type="MethodType" name="Method"/>
+      <xs:element type="Method_Comment_BlockType" name="Method_Comment_Block"/>
+      <xs:element type="Return_BlockType" name="Return_Block"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="MethodsType">
+    <xs:sequence>
+      <xs:element type="Method_BlockType" name="Method_Block" maxOccurs="unbounded" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="Class_BlockType">
+    <xs:sequence>
+      <xs:element type="ClassType" name="Class"/>
+      <xs:element type="Interface_BlockType" name="Interface_Block"/>
+      <xs:element type="Extends_BlockType" name="Extends_Block"/>
+      <xs:element type="Class_Comment_BlockType" name="Class_Comment_Block"/>
+      <xs:element type="ConstructorsType" name="Constructors"/>
+      <xs:element type="MethodsType" name="Methods"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="Package_BlockType">
+    <xs:sequence>
+      <xs:element type="xs:string" name="Package"/>
+      <xs:element type="Class_BlockType" name="Class_Block"/>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="ssldocletType">
+    <xs:sequence>
+      <xs:element type="Package_BlockType" name="Package_Block"/>
+    </xs:sequence>
+    <xs:attribute type="xs:string" name="creation"/>
+    <xs:attribute type="xs:string" name="source"/>
+    <xs:attribute type="xs:string" name="version"/>
+  </xs:complexType>
+</xs:schema>

core/src/main/java/de/fraunhofer/iem/swan/data/XMLParser.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/data/XMLParser.java

@@ -2,6 +2,8 @@
 
 import de.fraunhofer.iem.swan.features.InstancesHandler;
 import de.fraunhofer.iem.swan.io.dataset.Writer;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import weka.classifiers.Classifier;
 import weka.classifiers.bayes.BayesNet;
 import weka.classifiers.bayes.NaiveBayes;
@@ -39,10 +41,9 @@ public enum EVAL_MODE {
     }
 
     private final int CROSS_EVALUATE_ITERATIONS = 10;
-    private final Writer writer;
+    private static final Logger logger = LoggerFactory.getLogger(Learner.class);
 
     public Learner(Writer writer) {
-        this.writer = writer;
 
     }
 
@@ -124,12 +125,12 @@ public void outputFMeasure(LinkedHashMap<String, HashMap<String, String>> fMeasu
         String value = fMeasure.keySet().toArray()[0].toString();
 
         for (Object srm : fMeasure.get(value).keySet()) {
-            System.out.println("---" + srm.toString() + "---");
+            logger.info("Classification complete for {}", srm.toString());
             for (String c : fMeasure.keySet()) {
 
-                String measures = fMeasure.get(c).get(srm.toString()).toString();
+                String measures = fMeasure.get(c).get(srm.toString());
                 measures = measures.replace(".", ",").substring(0, measures.lastIndexOf(";"));
-                System.out.println(measures);
+                logger.info("{} classification results using {}: {}", srm, c, measures);
             }
         }
     }

core/src/main/java/de/fraunhofer/iem/swan/features/InstancesHandler.java renamed to swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/InstancesHandler.java

@@ -101,15 +101,15 @@ public HashMap<String, String> evaluateDataset(InstancesHandler instancesHandler
                 //optimizedClassifier.fit(split.get(0));
 
 
-                String trainPath = "/Users/oshando/Projects/thesis/03-code/swan/swan_core/swan-out/mlplan/train-methods-dataset.arff";
+                String trainPath = "swan/swan_core/swan-out/mlplan/train-methods-dataset.arff";
                 ArffDatasetAdapter.serializeDataset(new File(trainPath), split.get(0));
                 ArffLoader trainLoader = new ArffLoader();
                 trainLoader.setFile(new File(trainPath));
                 Instances trainInstances = trainLoader.getDataSet();
                 trainInstances.setClassIndex(trainInstances.numAttributes() - 1);
 
 
-                String testPath = "/Users/oshando/Projects/thesis/03-code/swan/swan_core/swan-out/mlplan/test-methods-dataset.arff";
+                String testPath = "swan/swan_core/swan-out/mlplan/test-methods-dataset.arff";
                 ArffDatasetAdapter.serializeDataset(new File(testPath), split.get(1));
                 ArffLoader testLoader = new ArffLoader();
                 testLoader.setFile(new File(testPath));
@@ -154,7 +154,7 @@ public HashMap<String, String> evaluateDataset(InstancesHandler instancesHandler
 
     public void evaluateDataset(InstancesHandler instancesHandler, int k) {
 
-        //arffFilePath = "/Users/oshando/Projects/thesis/03-code/swan/swan_core/src/main/resources/waveform.arff";
+        //arffFilePath = "swan/swan_core/src/main/resources/waveform.arff";
         String arffFilePath = Util.exportInstancesToArff(instancesHandler.getInstances());
 
         String mClass = Util.getClassName(instancesHandler.getInstances());
@@ -188,7 +188,7 @@ public void evaluateDataset(InstancesHandler instancesHandler, int k) {
 
                     //   System.out.println(attribute.getName());
                 }
-                ArffDatasetAdapter.serializeDataset(new File("/Users/oshando/Projects/thesis/03-code/swan/swan_core/swan-out/mlplan/methods-dataset.arff"), split.get(1));
+                ArffDatasetAdapter.serializeDataset(new File("swan/swan_core/swan-out/mlplan/methods-dataset.arff"), split.get(1));
 
 
                 for (int x = 0; x < split.get(1).size(); x++) {
@@ -261,7 +261,7 @@ public Classifier getClassifier(ILabeledDataset<?> trainingSet) {
 
     public static void maihn(String[] args) {
 
-        String file = "/Users/oshando/Projects/thesis/03-code/swan/swan_core/src/main/resources/waveform.arff";
+        String file = "swan/swan_core/src/main/resources/waveform.arff";
 
         MLPlanExecutor mlPlan = new MLPlanExecutor();
         //  mlPlan.evaluateDataset(file, "sdfs");

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

@@ -1,7 +1,7 @@
 package de.fraunhofer.iem.swan.model;
 
 
-import de.fraunhofer.iem.swan.Main;
+import de.fraunhofer.iem.swan.SwanPipeline;
 import de.fraunhofer.iem.swan.features.InstancesHandler;
 import de.fraunhofer.iem.swan.util.Util;
 import weka.classifiers.Classifier;
@@ -123,7 +123,7 @@ public void evaluate(Classifier classifier, Instances trainInstances, Instances
 
             eval.evaluateModel(classifier, testInstances, abstractOutput);
 
-            System.out.println(eval.toClassDetailsString());
+            //System.out.println(eval.toClassDetailsString());
 
             String[] predictions = abstractOutput.getBuffer().toString().split("\n");
 
@@ -136,7 +136,7 @@ public void evaluate(Classifier classifier, Instances trainInstances, Instances
                         || entry[2].contains("auth")) {
 
                     String method = entry[5].replace("'", "");
-                    Main.predictions.get(Integer.toString(iteration)).add(method);
+                    SwanPipeline.predictions.get(Integer.toString(iteration)).add(method);
                 }
             }