Copy resources directly without zip

Instead of using zip files, use the source files in the
resources directory. This allows to track differences
easily over git as zip files cannot be compared
between commits easily.

src/main/java/widoco/Configuration.java

@@ -134,7 +134,7 @@ public Configuration() {
 			// create a temporal folder with all LODE resources
 			tmpFolder = new File("tmp" + new Date().getTime());
 			tmpFolder.mkdir();
-			WidocoUtils.unZipIt(Constants.LODE_RESOURCES, tmpFolder.getName());
+			WidocoUtils.copyResourceDir(Constants.LODE_PATH, tmpFolder);
 		} catch (Exception ex) {
 			logger.error("Error while creating the temporal file for storing the intermediate Widoco files.");
 		}

src/main/java/widoco/Constants.java

@@ -1241,9 +1241,9 @@ public static String getProvenanceRDF(Configuration c) {
 		return provrdf;
 	}
 
-	public static final String LODE_RESOURCES = "/lode.zip";
-	public static final String OOPS_RESOURCES = "/oops.zip";
-	public static final String WEBVOWL_RESOURCES = "/webvowl_1.1.7_patched.zip";
+	public static final String LODE_PATH = "lode";
+	public static final String OOPS_PATH = "oops";
+	public static final String WEBVOWL_PATH = "webvowl_1.1.7_patched";
 
 	public static final String CONFIG_PATH = "config" + File.separator + "config.properties";
 

src/main/java/widoco/CreateOOPSEvalInThread.java

@@ -94,7 +94,7 @@ public void run() {
                             if (!evalFolder.exists())
                                     evalFolder.mkdir();
                             evalResourcesFolder.mkdir();
-                            WidocoUtils.unZipIt(Constants.OOPS_RESOURCES, evalResourcesFolder.getAbsolutePath());
+                            WidocoUtils.copyResourceDir(Constants.OOPS_PATH, evalResourcesFolder);
                             //eval = new OOPSevaluation("", content);
                             eval = new OOPSevaluation(content);
                             evaluation = eval.printEvaluation();

src/main/java/widoco/CreateResources.java

@@ -137,7 +137,7 @@ public static void generateDocumentation(String outFolder, Configuration c, File
 		}
 	}
 
-	public static void generateSkeleton(String folderOut, Configuration c, Properties l) {
+	public static void generateSkeleton(String folderOut, Configuration c, Properties l) throws IOException {
 		// c.setTitle("Skeleton title");
 		c.setIncludeDiagram(false);
 		c.setPublishProvenance(false);
@@ -426,7 +426,7 @@ public static void saveDocument(String path, String textToWrite, Configuration c
 
 	}
 
-	private static void createFolderStructure(String s, Configuration c, Properties lang) {
+	private static void createFolderStructure(String s, Configuration c, Properties lang) throws IOException {
 		File f = new File(s);
                 if(!c.isIncludeAllSectionsInOneDocument()){
                     File sections = new File(s + File.separator + "sections");
@@ -484,7 +484,7 @@ private static void createFolderStructure(String s, Configuration c, Properties
 		if (c.isCreateWebVowlVisualization()) {
 			File webvowl = new File(s + File.separator + "webvowl");
 			webvowl.mkdir();
-			WidocoUtils.unZipIt(Constants.WEBVOWL_RESOURCES, webvowl.getAbsolutePath());
+			WidocoUtils.copyResourceDir(Constants.WEBVOWL_PATH, webvowl);
 		}
 	}
 

src/main/java/widoco/WidocoUtils.java

@@ -23,6 +23,8 @@
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.net.HttpURLConnection;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Paths;
@@ -32,6 +34,7 @@
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.apache.commons.io.FileUtils;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.io.FileDocumentSource;
 import org.semanticweb.owlapi.model.*;
@@ -44,7 +47,7 @@
 public class WidocoUtils {
 
 	private static final Logger logger = LoggerFactory.getLogger(WidocoUtils.class);
-
+	public static final char JAR_SEPARATOR = '/';
 	/**
 	 * Method that will download the ontology to document with Widoco.
 	 * 
@@ -198,6 +201,89 @@ public static void copyResourceFolder(String[] resources, String savePath) throw
 		}
 	}
 
+	public static void copyResourceDir(String resourceFolder, File destinationFolder) throws IOException {
+		// Determine if running from JAR or as source
+		logger.info("copyResourceFolder from "+resourceFolder+" to "+ destinationFolder);
+		URL resourceUrl = WidocoUtils.class.getClassLoader().getResource(resourceFolder);
+		if (!destinationFolder.exists())
+			destinationFolder.mkdirs();
+		if (resourceUrl == null || !resourceUrl.getProtocol().equals("file")) {
+			// Running from JAR, use getResourceAsStream
+			copyDirFromJar(resourceFolder, destinationFolder);
+
+		} else {
+			// Running from source, use Files.copy
+			copyDirFromSrc(resourceFolder, destinationFolder);
+		}
+
+	}
+	// inspired from
+	// https://github.com/TriggerReactor/TriggerReactor/blob/7e71958b27231032c04d09795122dfc1d80c51b1/core/src/main/java/io/github/wysohn/triggerreactor/tools/JarUtil.java
+	public static void copyDirFromJar(String folderName, File destFolder) throws IOException {
+
+		byte[] buffer = new byte[1024];
+		File fullPath = null;
+		String path = WidocoUtils.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+		try {
+			if (!path.startsWith("file"))
+				path = "file://" + path;
+
+			fullPath = new File(new URI(path));
+		} catch (URISyntaxException e) {
+			logger.error("URI syntax error");
+		}
+		ZipInputStream zis = new ZipInputStream(new FileInputStream(fullPath));
+
+		ZipEntry entry;
+		while ((entry = zis.getNextEntry()) != null) {
+			if (!entry.getName().startsWith(folderName + JAR_SEPARATOR))
+				continue;
+
+			String fileName = entry.getName();
+
+			// Remove the folderName from the fileName
+			fileName = fileName.substring((folderName + JAR_SEPARATOR).length());
+
+			File file = new File(destFolder + File.separator + fileName);
+
+			if (fileName.isEmpty() || fileName.charAt(fileName.length() - 1) == JAR_SEPARATOR) {
+				// Skip empty or directory entries
+				continue;
+			}
+
+			if (!file.getParentFile().exists())
+				file.getParentFile().mkdirs();
+
+			if (!file.exists())
+				file.createNewFile();
+			FileOutputStream fos = new FileOutputStream(file);
+
+			int len;
+			while ((len = zis.read(buffer)) > 0) {
+				fos.write(buffer, 0, len);
+			}
+			fos.close();
+		}
+		zis.closeEntry();
+		zis.close();
+	}
+
+	private static void copyDirFromSrc(String resourceFolder, File destinationFolder) throws IOException {
+		URL resource = WidocoUtils.class.getClassLoader().getResource(resourceFolder);
+
+		if (resource == null) {
+			throw new IllegalArgumentException("Resource not found: " + resourceFolder);
+		}
+		try {
+			File sourceFolder = new File(resource.toURI());
+			// Copy only the contents of the source folder to the destination folder
+			FileUtils.copyDirectory(sourceFolder, destinationFolder);
+		} catch (URISyntaxException e) {
+			throw new IOException("Error copying resources to the temp folder: " + e.getMessage(), e);
+		} catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
 	/**
 	 * Method used to copy the local files: styles, images, etc.
 	 *