Updated home directory on startup, fixed rdf file loading

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/ApplicationSetup.java

@@ -45,6 +45,8 @@ public void contextInitialized(ServletContextEvent sce) {
 			this.vitroHomeDir = VitroHomeDirectory.find(ctx);
 			ss.info(this, vitroHomeDir.getDiscoveryMessage());
 
+			this.vitroHomeDir.populate();
+
 			locateApplicationConfigFile();
 			loadApplicationConfigFile();
 			createConfigurationBeanLoader();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/VitroHomeDirectory.java

@@ -4,16 +4,22 @@
 
 import static edu.cornell.mannlib.vitro.webapp.application.BuildProperties.WEBAPP_PATH_BUILD_PROPERTIES;
 
+import java.io.File;
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import javax.naming.InitialContext;
 import javax.servlet.ServletContext;
 
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -32,6 +38,8 @@ public static VitroHomeDirectory find(ServletContext ctx) {
 	private final ServletContext ctx;
 	private final Path path;
 	private final String discoveryMessage;
+    private Set<String> excludedHomeFiles = new HashSet<>(Arrays.asList("rdf"));
+
 
 	public VitroHomeDirectory(ServletContext ctx, Path path,
 			String discoveryMessage) {
@@ -210,4 +218,59 @@ public String toString() {
 		}
 	}
 
+    /**
+     * Populates home directory with home files, excluding the rdf directory
+     */
+    public void populate() {
+        File vhdDir = getPath().toFile();
+
+        if (!vhdDir.isDirectory() || vhdDir.list() == null) {
+            throw new RuntimeException("Application home dir is not a directory! " + vhdDir);
+        }
+
+        if (!vhdDir.canWrite()) {
+            throw new RuntimeException("Application home dir is not writable! " + vhdDir);
+        }
+        try {
+            copy(vhdDir);
+        } catch(Exception e) {
+            log.error(e, e);
+            throw new RuntimeException("Failed to copy home files! " + vhdDir);
+        }
+        log.info("Copied home files to " + vhdDir.toPath());
+
+    }
+
+    private void copy(File homeDestination) throws IOException {
+        File homeSrcPath = new File(getHomeSrcPath(ctx));
+        File[] contents = homeSrcPath.listFiles();
+        for (File child : contents) {
+            if (!isExcluded(child)) {
+                FileUtils.copyDirectory(child, homeDestination);
+            }
+        }
+    }
+
+    private boolean isExcluded(File child) {
+        if (excludedHomeFiles.contains(child.getName())) {
+            return true;
+        }
+        return false;
+    }
+
+    /**
+     * Get source home files.
+     * 
+     * @return source home files directory path
+     */
+    public static String getHomeSrcPath(ServletContext context) {
+        String location = "/WEB-INF/resources/home-files";
+        String realPath = context.getRealPath(location);
+        if (realPath == null) {
+            log.error("Application home files not found in: " + location);
+            throw new RuntimeException("Application home files not found in: " + location);
+        }
+        return realPath;
+    }
+
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java

@@ -33,7 +33,7 @@
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 
-import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
+import edu.cornell.mannlib.vitro.webapp.application.VitroHomeDirectory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
@@ -121,8 +121,8 @@ public void contextInitialized(ServletContextEvent sce) {
 	private Set<Path> getFilegraphPaths(ServletContext ctx, String... strings) {
 		StartupStatus ss = StartupStatus.getBean(ctx);
 
-		String homeDirProperty = ApplicationUtils.instance().getHomeDirectory().getPath().toString();
-		Path filegraphDir = Paths.get(homeDirProperty, strings);
+		String homeDirPath = VitroHomeDirectory.getHomeSrcPath(ctx);
+		Path filegraphDir = Paths.get(homeDirPath, strings);
 
 		Set<Path> paths = new TreeSet<>();
 		if (Files.isDirectory(filegraphDir)) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFFilesLoader.java

@@ -32,7 +32,7 @@
 import org.apache.jena.rdf.model.Statement;
 import org.apache.jena.rdf.model.StmtIterator;
 
-import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
+import edu.cornell.mannlib.vitro.webapp.application.VitroHomeDirectory;
 
 import javax.servlet.ServletContext;
 
@@ -81,7 +81,7 @@ public boolean accept(Path p) throws IOException {
 	public static void loadFirstTimeFiles(ServletContext ctx, String modelPath, Model model,
 			boolean firstTime) {
 		if (firstTime) {
-			String home = locateHomeDirectory();
+			String home = locateHomeDirectory(ctx);
 
 			// Load common files
 			Set<Path> paths = getPaths(home, RDF, modelPath, FIRST_TIME);
@@ -113,7 +113,7 @@ public static void loadFirstTimeFiles(ServletContext ctx, String modelPath, Mode
 	public static void loadEveryTimeFiles(ServletContext ctx, String modelPath, OntModel model) {
 		OntModel everytimeModel = ModelFactory
 				.createOntologyModel(OntModelSpec.OWL_MEM);
-		String home = locateHomeDirectory();
+		String home = locateHomeDirectory(ctx);
 
 		// Load common files
 		Set<Path> paths = getPaths(home, RDF, modelPath, EVERY_TIME);
@@ -220,9 +220,8 @@ else if (filename.endsWith("ttl"))
 			return DEFAULT_RDF_FORMAT;
 	}
 
-	private static String locateHomeDirectory() {
-		return ApplicationUtils.instance().getHomeDirectory().getPath()
-				.toString();
+	private static String locateHomeDirectory(ServletContext ctx) {
+		return VitroHomeDirectory.getHomeSrcPath(ctx);
 	}
 
 	/**