new parser for xml file in mybatis

core/src/main/java/mrmathami/cia/java/project/JavaProject.java

@@ -22,7 +22,10 @@
 import mrmathami.cia.java.JavaCiaException;
 import mrmathami.cia.java.tree.dependency.JavaDependencyWeightTable;
 import mrmathami.utils.Pair;
+import org.xml.sax.SAXException;
 
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
@@ -52,7 +55,7 @@ public interface JavaProject {
 	@Nonnull
 	JavaProjectSnapshot createSnapshot(@Nonnull String snapshotName,
 			@Nonnull Map<String, Pair<Path, List<Path>>> javaSources, @Nonnull List<Path> classPaths,
-			@Nonnull JavaDependencyWeightTable dependencyWeightTable, boolean enableRecovery) throws JavaCiaException;
+			@Nonnull JavaDependencyWeightTable dependencyWeightTable, boolean enableRecovery, Path configurationPath) throws JavaCiaException, ParserConfigurationException, SAXException, IOException;
 
 	/**
 	 * @param comparisonName comparison name

core/src/main/java/mrmathami/cia/java/tree/node/JavaXMLNode.java

@@ -22,6 +22,7 @@ default JavaXMLNode asXMLNode() {
 		return this;
 	}
 
+
 	@Nonnull
 	String getTextContent();
 

jdt/pom.xml

@@ -135,6 +135,31 @@
 					</execution>
 				</executions>
 			</plugin>
+
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<version>3.2.0</version>
+				<configuration>
+					<archive>
+						<manifest>
+							<mainClass>mrmathami.cia.java.jdt.Run</mainClass>
+						</manifest>
+					</archive>
+					<descriptorRefs>
+						<descriptorRef>jar-with-dependencies</descriptorRef>
+					</descriptorRefs>
+				</configuration>
+				<executions>
+					<execution>
+						<id>make-assembly</id>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 	</build>
 

jdt/src/main/java/mrmathami/cia/java/jdt/ProjectBuilders.java

@@ -28,7 +28,10 @@
 import mrmathami.cia.java.project.JavaProjectSnapshotComparison;
 import mrmathami.cia.java.tree.dependency.JavaDependencyWeightTable;
 import mrmathami.utils.Pair;
+import org.xml.sax.SAXException;
 
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
@@ -46,8 +49,8 @@ public static JavaProject createProject(@Nonnull String name) {
 	@Nonnull
 	public static JavaProjectSnapshot createProjectSnapshot(@Nonnull String snapshotName,
 			@Nonnull Map<String, Pair<Path, List<Path>>> javaSources, @Nonnull List<Path> classPaths,
-			@Nonnull JavaDependencyWeightTable dependencyWeightTable, boolean enableRecovery) throws JavaCiaException {
-		return JavaSnapshotBuilder.build(snapshotName, javaSources, classPaths, dependencyWeightTable, enableRecovery);
+			@Nonnull JavaDependencyWeightTable dependencyWeightTable, boolean enableRecovery, Path configurationPath) throws JavaCiaException, ParserConfigurationException, SAXException, IOException {
+		return JavaSnapshotBuilder.build(snapshotName, javaSources, classPaths, dependencyWeightTable, enableRecovery, configurationPath);
 	}
 
 	@Nonnull

jdt/src/main/java/mrmathami/cia/java/jdt/Run.java

@@ -0,0 +1,78 @@
+package mrmathami.cia.java.jdt;
+
+import mrmathami.cia.java.JavaCiaException;
+import mrmathami.cia.java.project.JavaProjectSnapshot;
+import mrmathami.cia.java.tree.dependency.JavaDependency;
+import mrmathami.cia.java.tree.dependency.JavaDependencyWeightTable;
+import mrmathami.utils.Pair;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+public class Run {
+	public static final JavaDependencyWeightTable DEPENDENCY_WEIGHT_TABLE = JavaDependencyWeightTable.of(Map.of(
+			JavaDependency.USE, 1.0,
+			JavaDependency.MEMBER, 1.0,
+			JavaDependency.INHERITANCE, 4.0,
+			JavaDependency.INVOCATION, 4.0,
+			JavaDependency.OVERRIDE, 1.0
+	));
+	//private static final Path configurationPath = Path.of("D:\\project\\MyBatis Collection\\mybatis-XML\\mybatis-example-1\\resources\\SqlMapConfig.xml");
+	private static Path configurationPath = null;
+
+	public static void main(String[] args) throws JavaCiaException, IOException, ParserConfigurationException, SAXException {
+		Path corePath = null;
+		String output = "";
+		if (args.length < 3) {
+			configurationPath = Path.of("");
+			corePath = Path.of(args[0]);
+			output = args[1];
+		} else if (args.length == 3) {
+			configurationPath = Path.of(args[0]);
+			corePath = Path.of(args[1]);
+			output = args[2];
+		}
+		final List<Path> coreFiles = getFileList(new ArrayList<>(), corePath);
+		final Map<String, Pair<Path, List<Path>>> javaSources = Map.of(
+				"core", Pair.immutableOf(corePath, coreFiles)
+		);
+		final List<Path> classPaths = List.of(
+				//List classPaths in here
+		);
+
+
+		long timeStart = System.nanoTime();
+		final JavaProjectSnapshot projectSnapshot = ProjectBuilders.createProjectSnapshot("before",
+				javaSources, classPaths, DEPENDENCY_WEIGHT_TABLE, true, configurationPath);
+		long timeParseA = System.nanoTime();
+
+		final String jsonA = projectSnapshot.getRootNode().toJson();
+
+		Files.write(Path.of(output + "output.txt"), jsonA.getBytes(StandardCharsets.UTF_8));
+
+		System.out.printf("Parse A time: %s\n", (timeParseA - timeStart) / 1000000.0);
+	}
+
+	private static List<Path> getFileList(List<Path> fileList, Path dir) {
+		try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir)) {
+			for (Path path : stream) {
+				if (path.toFile().isDirectory()) {
+					getFileList(fileList, path);
+				} else {
+					fileList.add(path);
+				}
+			}
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		return fileList;
+	}
+}

jdt/src/main/java/mrmathami/cia/java/jdt/gephi/Printer.java

@@ -0,0 +1,133 @@
+package mrmathami.cia.java.jdt.gephi;
+
+import mrmathami.cia.java.jdt.gephi.model.EdgeGephi;
+import mrmathami.cia.java.jdt.gephi.model.NodeGephi;
+import mrmathami.cia.java.project.JavaNodeWeightTable;
+import mrmathami.cia.java.project.JavaProject;
+import mrmathami.cia.java.project.JavaProjectSnapshot;
+import mrmathami.cia.java.project.JavaProjectSnapshotComparison;
+import mrmathami.cia.java.tree.node.JavaNode;
+import mrmathami.utils.Pair;
+import org.w3c.dom.Node;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public class Printer {
+	public String writeGephi(JavaProjectSnapshot projectSnapshot) {
+		List<? extends JavaNode> nodeList = projectSnapshot.getRootNode().getAllNodes();
+		HashMap<JavaNode, Set<? extends JavaNode>> dependencyToMap = new HashMap<>();
+		for (JavaNode node : nodeList) {
+			Set<? extends JavaNode> dependencyToNodes = node.getDependencyToNodes();
+			dependencyToMap.put(node, dependencyToNodes);
+		}
+		List<NodeGephi> nodeGephiList = new ArrayList<>();
+		List<EdgeGephi> edgeGephiList = new ArrayList<>();
+		int count = 0;
+		for (Map.Entry<JavaNode, Set<? extends JavaNode>> entry : dependencyToMap.entrySet()) {
+			NodeGephi nodeGephi = new NodeGephi(entry.getKey().getId(), entry.getKey().getNodeName(), NodeGephi.Type.UNCHANGE);
+			nodeGephiList.add(nodeGephi);
+			Set<? extends JavaNode> value = entry.getValue();
+			for (JavaNode javaNode : value) {
+				EdgeGephi edgeGephi = new EdgeGephi(count, entry.getKey().getId(), javaNode.getId());
+				count++;
+				edgeGephiList.add(edgeGephi);
+			}
+		}
+
+		final String open = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
+				"<gexf xmlns=\"http://www.gexf.net/1.3\" version=\"1.3\" xmlns:viz=\"http://www.gexf.net/1.3/viz\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd\">" +
+				"\n<graph defaultedgetype=\"directed\" mode=\"static\">\n";
+
+		String listNode = writeListNodes(nodeGephiList);
+		String listEdge = writeListEdges(edgeGephiList);
+
+		return open + listNode + listEdge + "\n</graph>\n" + "</gexf>";
+	}
+	public String writeGephiComparison(JavaProjectSnapshotComparison comparison) {
+		final Set<JavaNode> addedNodes = comparison.getAddedNodes();
+		final Set<Pair<JavaNode, JavaNode>> changedNodes = comparison.getChangedNodes();
+		final Set<JavaNode> removedNodes = comparison.getRemovedNodes();
+		final Set<Pair<JavaNode, JavaNode>> unchangedNodes = comparison.getUnchangedNodes();
+
+		HashMap<JavaNode, Set<? extends JavaNode>> dependencyToMap = new HashMap<>();
+		final List<? extends JavaNode> allNodes = comparison.getCurrentSnapshot().getRootNode().getAllNodes();
+		final JavaNodeWeightTable nodeImpactTable = comparison.getNodeImpactTable();
+
+		for (JavaNode node : allNodes) {
+			final Set<? extends JavaNode> dependencyToNodes = node.getDependencyToNodes();
+			dependencyToMap.put(node, dependencyToNodes);
+		}
+		List<NodeGephi> nodeGephiList = new ArrayList<>();
+		List<EdgeGephi> edgeGephiList = new ArrayList<>();
+		int count = 0;
+		for (Map.Entry<JavaNode, Set<? extends JavaNode>> entry : dependencyToMap.entrySet()) {
+			NodeGephi nodeGephi = null;
+			if (addedNodes.contains(entry.getKey())) {
+				nodeGephi = new NodeGephi(entry.getKey().getId(), entry.getKey().getNodeName() + " weight: " + nodeImpactTable.getWeight(entry.getKey()), NodeGephi.Type.ADD);
+			}
+
+			for (Pair<JavaNode, JavaNode> pair : changedNodes) {
+				final JavaNode pairB = pair.getB();
+				if (entry.getKey() == pairB) {
+					nodeGephi = new NodeGephi(pairB.getId(), pairB.getNodeName() + " weight: " + nodeImpactTable.getWeight(pairB), NodeGephi.Type.CHANGE);
+				}
+			}
+			for (Pair<JavaNode, JavaNode> pair : unchangedNodes) {
+				final JavaNode pairB = pair.getB();
+				if (entry.getKey() == pairB) {
+					nodeGephi = new NodeGephi(pairB.getId(), pairB.getNodeName() + " weight: " + nodeImpactTable.getWeight(pairB), NodeGephi.Type.UNCHANGE);
+				}
+			}
+			nodeGephiList.add(nodeGephi);
+			final Set<? extends JavaNode> value = entry.getValue();
+			for (JavaNode javaNode : value) {
+				EdgeGephi edgeGephi = new EdgeGephi(count, entry.getKey().getId(), javaNode.getId());
+				count++;
+				edgeGephiList.add(edgeGephi);
+			}
+		}
+
+		for (JavaNode node : removedNodes) {
+			NodeGephi nodeGephi = new NodeGephi(node.getId() + nodeGephiList.size(), node.getNodeName(), NodeGephi.Type.DELETE);
+			final Set<? extends JavaNode> dependencyToNodes = node.getDependencyToNodes();
+			for (JavaNode javaNode : dependencyToNodes) {
+				EdgeGephi edgeGephi = new EdgeGephi(count, node.getId() + nodeGephiList.size(), javaNode.getId());
+				count++;
+				edgeGephiList.add(edgeGephi);
+			}
+			nodeGephiList.add(nodeGephi);
+		}
+
+		final String open = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
+				"<gexf xmlns=\"http://www.gexf.net/1.3\" version=\"1.3\" xmlns:viz=\"http://www.gexf.net/1.3/viz\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd\">" +
+				"\n<graph defaultedgetype=\"directed\" mode=\"static\">\n";
+
+		String listNode = writeListNodes(nodeGephiList);
+		String listEdge = writeListEdges(edgeGephiList);
+
+		return open + listNode + listEdge + "\n</graph>\n" + "</gexf>";
+	}
+
+	public String writeListNodes(List<NodeGephi> nodeGephiList) {
+		StringBuilder result = new StringBuilder("\t<nodes>");
+		for (NodeGephi node : nodeGephiList) {
+			result.append("\n\t\t").append(node.toString());
+		}
+		result.append("\n\t</nodes>");
+		return result.toString();
+	}
+
+	public String writeListEdges(List<EdgeGephi> edgeGephiList) {
+		StringBuilder result = new StringBuilder("\n\t<edges>");
+		for (EdgeGephi node : edgeGephiList) {
+			result.append("\n\t\t").append(node.toString());
+		}
+		result.append("\n\t</edges>");
+		return result.toString();
+	}
+
+}

jdt/src/main/java/mrmathami/cia/java/jdt/gephi/model/EdgeGephi.java

@@ -0,0 +1,24 @@
+package mrmathami.cia.java.jdt.gephi.model;
+
+public class EdgeGephi {
+	private int id;
+	private int source;
+	private int target;
+
+	public EdgeGephi(int id, int source, int target) {
+		this.id = id;
+		this.source = source;
+		this.target = target;
+	}
+
+	@Override
+	public String toString() {
+		return "<edge " +
+				"id='" + id + '\'' +
+				" source='" + source + '\'' +
+				" target='" + target + '\'' +
+				">" +
+				"\n\t\t\t" + "<viz:color r=\"102\" g=\"102\" b=\"102\"></viz:color>" +
+				"\n\t\t</edge>";
+	}
+}

jdt/src/main/java/mrmathami/cia/java/jdt/gephi/model/NodeGephi.java

@@ -0,0 +1,50 @@
+package mrmathami.cia.java.jdt.gephi.model;
+
+public class NodeGephi {
+	public enum Type {
+		UNCHANGE(115, 115, 115),//charcoal blue
+		DELETE(255, 0, 0),//red
+		CHANGE(255, 255, 0),//yellow
+		ADD(0, 255, 153);//light green
+
+		private final int r;
+		private final int g;
+		private final int b;
+
+		Type(int r, int g, int b) {
+			this.r = r;
+			this.g = g;
+			this.b = b;
+		}
+	}
+
+	private final int id;
+	private final String label;
+	private final String size = "<viz:size value='8.0'></viz:size>";
+	private final Type type;
+
+	public NodeGephi(int id, String label, Type type) {
+		this.id = id;
+		this.label = label;
+		this.type = type;
+	}
+
+	@Override
+	public String toString() {
+		return "<node " +
+				"id='" + id + '\'' +
+				" label='" + label + '\'' +
+				'>' +
+				"\n\t\t\t" + size +
+				toStringType(type) +
+				"\n\t\t</node>";
+	}
+
+	private String toStringType(Type type) {
+		return "\n\t\t\t<viz:color" +
+				" r='" + type.r + '\'' +
+				" g='" + type.g + '\'' +
+				" b='" + type.b + '\'' +
+				"></viz:color>";
+	}
+}

jdt/src/main/java/mrmathami/cia/java/jdt/project/Project.java

@@ -27,7 +27,10 @@
 import mrmathami.cia.java.project.JavaProjectSnapshotComparison;
 import mrmathami.cia.java.tree.dependency.JavaDependencyWeightTable;
 import mrmathami.utils.Pair;
+import org.xml.sax.SAXException;
 
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
 import java.io.Serializable;
 import java.nio.file.Path;
 import java.util.Collections;
@@ -82,9 +85,9 @@ public List<ProjectSnapshotComparison> getSnapshotComparisons() {
 	@Override
 	public JavaProjectSnapshot createSnapshot(@Nonnull String snapshotName,
 			@Nonnull Map<String, Pair<Path, List<Path>>> javaSources, @Nonnull List<Path> classPaths,
-			@Nonnull JavaDependencyWeightTable dependencyWeightTable, boolean enableRecovery) throws JavaCiaException {
+			@Nonnull JavaDependencyWeightTable dependencyWeightTable, boolean enableRecovery, Path configurationPath) throws JavaCiaException, ParserConfigurationException, SAXException, IOException {
 		final ProjectSnapshot snapshot = JavaSnapshotBuilder.build(
-				snapshotName, javaSources, classPaths, dependencyWeightTable, enableRecovery);
+				snapshotName, javaSources, classPaths, dependencyWeightTable, enableRecovery, configurationPath);
 		snapshots.add(snapshot);
 		return snapshot;
 	}