Blackbox

.classpath

@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="src" path="CTD/src"/>
+	<classpathentry kind="src" path="data/F19_Project_3_2/task1/[email protected]_social-network_p32-task1_20191013053247"/>
+	<classpathentry kind="src" path="data/F19_Project_3_2/task2/[email protected]_social-network_p32-task2_20191013053354"/>
+	<classpathentry kind="src" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013050650"/>
+	<classpathentry kind="src" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013051101"/>
+	<classpathentry kind="src" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013051714"/>
+	<classpathentry kind="src" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013051925"/>
+	<classpathentry kind="src" path="HintEvaluation/src"/>
+	<classpathentry kind="src" path="HintServer/src"/>
+	<classpathentry kind="src" path="iSnap/src"/>
+	<classpathentry kind="src" path="JavaParser/src"/>
+	<classpathentry kind="src" path="QualityScore/src"/>
+	<classpathentry kind="src" path="SnapParser/src"/>
+	<classpathentry kind="src" path="Templater/src"/>
+	<classpathentry kind="lib" path="CTD/RTED_v1.1.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013184035/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013184306/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013185737/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task4/[email protected]_social-network_p32-task4_20191013190657/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task5/[email protected]_social-network_p32-task5_20191013193400/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task5/[email protected]_social-network_p32-task5_20191013193529/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task5/[email protected]_social-network_p32-task5_20191013193622/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="data/F19_Project_3_2/task5/[email protected]_social-network_p32-task5_20191013193716/target/undertow-server-1.0-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="HintEvaluation/apted.jar"/>
+	<classpathentry kind="lib" path="HintEvaluation/FITObjectGraphAPI-3.0.1.jar"/>
+	<classpathentry kind="lib" path="HintEvaluation/FITObjectGraphs-3.0.1.jar"/>
+	<classpathentry kind="lib" path="HintEvaluation/FITValidators-2.0.0.jar"/>
+	<classpathentry kind="output" path="CTD/target/classes"/>
+</classpath>

.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Clustering</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

CTD/.classpath

@@ -6,17 +6,18 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry exported="true" kind="lib" path="RTED_v1.1.jar"/>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
 		</attributes>
 	</classpathentry>
-	<classpathentry exported="true" kind="lib" path="RTED_v1.1.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

CTD/src/edu/isnap/hint/HintConfig.java

@@ -11,6 +11,9 @@ public abstract class HintConfig implements Serializable {
 
 	/** If true, uses new version of SourceCheck with more global alignment */
 	public boolean sourceCheckV2 = false;
+
+	/** If true, uses reference solutions to get high-level hints */
+	public boolean useAnnotation = true;
 
 	/**
 	 * Should return true if the hint generator can expect traces to keep consistent node IDs

CTD/src/edu/isnap/hint/HintData.java

@@ -1,6 +1,7 @@
 package edu.isnap.hint;
 
 import java.util.ArrayList;
+import java.util.LinkedHashMap;
 import java.util.List;
 
 import edu.isnap.ctd.hint.CTDHintGenerator;
@@ -17,7 +18,15 @@ public class HintData {
 	public final double minGrade;
 	public final HintConfig config;
 	private final List<IDataModel> dataModels;
+	private LinkedHashMap<Integer, Node> referenceSolutions;
 
+	/**
+	 * @param assignment the name of java file used in this assignment. Omit ".java".
+	 * @param config
+	 * @param minGrade
+	 * @param consumer
+	 * @param additionalConsumers
+	 */
 	public HintData(String assignment, HintConfig config, double minGrade,
 			IDataConsumer consumer, IDataConsumer... additionalConsumers) {
 		this.assignment = assignment;
@@ -29,6 +38,7 @@ public HintData(String assignment, HintConfig config, double minGrade,
 		for (IDataConsumer con : additionalConsumers) {
 			addDataModels(con.getRequiredData(this));
 		}
+		referenceSolutions = new LinkedHashMap<>();
 	}
 
 	private void addDataModels(IDataModel[] models) {
@@ -73,4 +83,12 @@ public CTDHintGenerator hintGenerator() {
 	public HintHighlighter hintHighlighter() {
 		return new HintHighlighter(this);
 	}
+
+	public LinkedHashMap<Integer, Node> getReferenceSolutions() {
+		return referenceSolutions;
+	}
+
+	public Node addReferenceSoltion(int clusterID, Node solution) {
+		return referenceSolutions.put(clusterID, solution);
+	}
 }

CTD/src/edu/isnap/hint/util/Alignment.java

@@ -25,6 +25,14 @@ public static double normAlignCost(String[] sequenceA, String[] sequenceB, int i
 	}
 
 	// Credit: http://introcs.cs.princeton.edu/java/96optimization/Diff.java.html
+	/**
+	 * @param sequenceA
+	 * @param sequenceB
+	 * @param insCost
+	 * @param delCost
+	 * @param subCost
+	 * @return Levenshtein distance between "sequenceA" and "sequenceB"??
+	 */
 	public static int alignCost(String[] sequenceA, String[] sequenceB, int insCost, int delCost,
 			int subCost) {
 		int[][] opt = createAlignmentMatrix(sequenceA, sequenceB, insCost, delCost, subCost, false);
@@ -300,7 +308,7 @@ private static int correspondingIndexBefore(List<int[]> pairs, List<String> sequ
 		return closestA;
 	}
 
-	private static int[][] createAlignmentMatrix(String[] sequenceA, String[] sequenceB,
+	public static int[][] createAlignmentMatrix(String[] sequenceA, String[] sequenceB,
 			int insCost, int delCost, int subCost, boolean flipInvalid) {
 		// The penalties to apply
 		int matchCost = 0;
@@ -397,7 +405,7 @@ public static int[] reorderIndices(String[] from, String[] to, int[] toOrderGrou
 		return toIndices;
 	}
 
-	public static int getProgress(String[] from, String[] to, int orderReward, int unorderReward) {
+	public static double getProgress(String[] from, String[] to, int orderReward, int unorderReward) {
 		return (int) Math.round(getProgress(from, to, orderReward, unorderReward, 0));
 	}
 
@@ -417,14 +425,19 @@ public static double getProgress(String[] from, String[] to, int[] toOrderGroups
 	private static double getProgress(String[] from, String[] to, int[] toOrderGroups,
 			int orderReward, int unorderReward, double skipCost, int[] toIndices) {
 		// TODO: This can and should be much more efficient
+		// toList[k] = "\0" if the k-th node in c(b_{rj}) is in c(a_{ri})
 		List<String> toList = new LinkedList<>(Arrays.asList(to));
 
+		// If indices[k] = l, k-th node in c(a_{ri}) is l-th node in c(b_{rj})
+		// If indices[k] = -1, k-th node in c(a_{ri}) is not in c(b_{rj})
 		int[] indices = new int[from.length];
 		for (int i = 0; i < from.length; i++) {
 			String item = from[i];
 			int index = toList.indexOf(item);
-			if (index >= 0) {
-				toList.set(index, "\0");
+			if (index >= 0) { // i-th node in c(a_{ri}) is in c(b_{rj})
+//				if (orderReward == 1 && unorderReward == 1) {
+					toList.set(index, "\0"); // prevents multiple matches
+//				}
 				indices[i] = index;
 			} else {
 				indices[i] = -1;
@@ -437,7 +450,7 @@ private static double getProgress(String[] from, String[] to, int[] toOrderGroup
 		int lastIndex = -1;
 		int maxIndex = -1;
 		for (Integer index : indices) {
-			if (index < 0) continue;
+			if (index < 0) continue; // don't change reward if k-th node in c(a_{ri}) is not in c(b_{rj})
 			int adjIndex = index;
 			int group;
 //			System.out.println(index);
@@ -487,7 +500,7 @@ private static double getProgress(String[] from, String[] to, int[] toOrderGroup
 	 * including duplicates
 	 */
 	public static int getMissingNodeCount(String[] from, String[] to) {
-		return to.length - getProgress(to, from, 1, 1);
+		return to.length - (int) getProgress(to, from, 1, 1);
 	}
 
 	public static void main(String[] args) {

CTD/src/edu/isnap/node/Node.java

@@ -37,6 +37,8 @@ public abstract class Node extends StringHashable implements INode {
 	public final String value;
 	public final Node parent;
 	public final List<Node> children = new ArrayList<>();
+	private String studentID;
+	private String submissionTime;
 
 	public transient Object tag;
 	public final transient List<Canonicalization> canonicalizations = new ArrayList<>();
@@ -501,6 +503,10 @@ public String prettyPrintWithIDs() {
 		return prettyPrint(false, new HashMap<Node, String>());
 	}
 
+	/**
+	 * @return a list of strings of types obtained by depth-first iteration of
+	 * the AST rooted at this node
+	 */
 	public String[] depthFirstIteration() {
 		String[] array = new String[treeSize()];
 		depthFirstIteration(array, 0);
@@ -683,6 +689,11 @@ public static Node fromASTNode(ASTNode astNode, Node parent, NodeConstructor con
 		Node node = constructor.constructNode(parent, type, astNode.value, astNode.id);
 		node.readFromASTNode(astNode);
 		node.tag = astNode;
+		if (astNode.annotation != null) {
+			node.writableAnnotations();
+			TextHint hint = new TextHint(astNode.annotation, 1);
+			node.addTextHint(hint);			
+		}
 		for (ASTNode child : astNode.children()) {
 			node.children.add(fromASTNode(child, node, constructor));
 		}
@@ -697,4 +708,20 @@ protected void readFromASTNode(ASTNode node) {
 	public String toString() {
 		return prettyPrint(true);
 	}
+
+	public String getStudentID() {
+		return studentID;
+	}
+
+	public void setStudentID(String studentID) {
+		this.studentID = studentID;
+	}
+
+	public String getSubmissionTime() {
+		return submissionTime;
+	}
+
+	public void setSubmissionTime(String submissionTime) {
+		this.submissionTime = submissionTime;
+	}
 }

CTD/src/edu/isnap/node/TextualNode.java

@@ -1,15 +1,16 @@
 package edu.isnap.node;
 
-import java.util.Optional;
 
-import org.json.JSONObject;
 
+import java.util.Optional;
+import org.json.JSONObject;
 import edu.isnap.node.ASTNode.SourceLocation;
 import edu.isnap.sourcecheck.NodeAlignment.Mapping;
 
 public abstract class TextualNode extends Node {
 
 	public Optional<Boolean> correct = Optional.empty();
+	public Optional<Integer> cluster = Optional.empty();
 	private String source;
 
 	// TODO: Protect
@@ -49,7 +50,7 @@ public String getSource() {
 		String rootSource = ((TextualNode) root()).source;
 		if (startSourceLocation == null && endSourceLocation == null) return null;
 		return rootSource.substring(
-				toIndex(rootSource, startSourceLocation),
+				toIndex(rootSource, startSourceLocation) - 1,
 				toIndex(rootSource, endSourceLocation));
 	}
 
@@ -104,12 +105,27 @@ public SourceLocation getLocationOfChildIndex(int index) {
 		return null;
 	}
 
-	public static TextualNode fromJSON(JSONObject jsonAST, String source,
-			NodeConstructor constructor) {
+	public static TextualNode fromJSON(JSONObject jsonAST, String source, NodeConstructor constructor) {
 		ASTSnapshot astNode = ASTSnapshot.parse(jsonAST, source);
 		TextualNode node = (TextualNode) fromASTNode(astNode, constructor);
 		node.source = source;
 		node.correct = Optional.of(astNode.isCorrect);
 		return node;
 	}
+
+	/**
+	 * Overloaded method to get clusterID
+	 * @param jsonAST
+	 * @param id
+	 * @param source
+	 * @param constructor
+	 * @return
+	 */
+	public static TextualNode fromJSON(JSONObject jsonAST,String id, String source, NodeConstructor constructor) {
+		ASTSnapshot astNode = ASTSnapshot.parse(jsonAST, id, source);
+		TextualNode node = (TextualNode) fromASTNode(astNode, constructor);
+		node.source = source;
+		node.correct = Optional.of(astNode.isCorrect);
+		return node;
+	}
 }

CTD/src/edu/isnap/sourcecheck/ConsensusHintHighlighter.java

@@ -38,7 +38,7 @@ public List<EditHint> highlightConsensus(Node node) {
 		double consensusThreshold = 0.6;
 
 		List<Mapping> matches = NodeAlignment.findBestMatches(
-				node, solutions, getDistanceMeasure(config), config, nMatches);
+				node, getSolutions(), getDistanceMeasure(config), config, nMatches);
 
 		final int n = matches.size();
 		final int thresh = (int) Math.ceil(n * consensusThreshold);