Refactored code, fixed UpdateKnowledgeBase and FauxPropertiesUpdater.…

… Added tests.

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

@@ -39,13 +39,15 @@ public static VitroHomeDirectory find(ServletContext ctx) {
 	private final Path path;
 	private final String discoveryMessage;
     private Set<String> excludedHomeFiles = new HashSet<>(Arrays.asList("rdf"));
+    private String homeSourcePath;
 
 
 	public VitroHomeDirectory(ServletContext ctx, Path path,
 			String discoveryMessage) {
 		this.ctx = ctx;
 		this.path = path;
 		this.discoveryMessage = discoveryMessage;
+		setHomeSourcePath(ctx);
 	}
 
 	public ServletContext getCtx() {
@@ -60,6 +62,23 @@ public String getDiscoveryMessage() {
 		return discoveryMessage;
 	}
 
+    /**
+     * Get source home file directory path
+     * 
+     * @return source home files directory path
+     */
+    public String getSourcePath() {
+        return homeSourcePath;
+    }
+
+    private void setHomeSourcePath(ServletContext context) {
+        String location = "/WEB-INF/resources/home-files";
+        homeSourcePath = context.getRealPath(location);
+        if (homeSourcePath == null) {
+            throw new RuntimeException(String.format("Application home files not found in: %s", location));
+        }
+    }
+
 	/**
 	 * Find something that specifies the location of the Vitro home directory.
 	 * Look in the JDNI environment, the system properties, and the
@@ -221,75 +240,47 @@ public String toString() {
      * Populates home directory with home files, excluding the rdf directory
      */
     public void populate() {
-        File vhdDir = getPath().toFile();
+        File homeDestination = getPath().toFile();
 
-        if (!vhdDir.isDirectory() || vhdDir.list() == null) {
-            throw new RuntimeException("Application home dir is not a directory! " + vhdDir);
+        if (!homeDestination.isDirectory() || homeDestination.list() == null) {
+            throw new RuntimeException("Application home dir is not a directory! " + homeDestination);
         }
-
-        if (!vhdDir.canWrite()) {
-            throw new RuntimeException("Application home dir is not writable! " + vhdDir);
+        if (!homeDestination.canWrite()) {
+            throw new RuntimeException("Application home dir is not writable! " + homeDestination);
         }
         try {
-            copy(vhdDir);
+            copy(homeDestination);
         } catch(Exception e) {
-            log.error(e, e);
-            throw new RuntimeException("Failed to copy home files! " + vhdDir);
+            throw new RuntimeException("Failed to copy home files! " + homeDestination, e);
         }
-        log.info("Copied home files to " + vhdDir.toPath());
-
+        log.info("Copied home files to " + homeDestination.toPath());
     }
 
     /**
      * Create home directory
      */
-    private static void createHomeDirectory(Path vhdDir) {
+    private static void createHomeDirectory(Path homeDestination) {
         try {
-            vhdDir.toFile().mkdirs();
+            homeDestination.toFile().mkdirs();
         } catch (Exception e) {
-            log.error(e, e);
-            throw new RuntimeException("Failed to create home directory " + vhdDir);
+            throw new RuntimeException("Failed to create home directory " + homeDestination, e);
         }
     }
 
     /**
      * Copy file from home source to home destination
      */
     private void copy(File homeDestination) throws IOException {
-        File homeSrcPath = new File(getHomeSrcPath(ctx));
+        File homeSrcPath = new File(getSourcePath());
         File[] contents = homeSrcPath.listFiles();
         for (File child : contents) {
-            if (!isExcluded(child)) {
-                FileUtils.copyDirectory(child, homeDestination);
+            if (!excludedHomeFiles.contains(child.getName())) {
+                if (child.isDirectory()) {
+                    FileUtils.copyDirectoryToDirectory(child, homeDestination);
+                } else {
+                    FileUtils.copyFileToDirectory(child, homeDestination);
+                }
             }
         }
     }
-
-    /**
-     * Test if file name is excluded from copying
-     * 
-     * @return true if file should be excluded
-     */
-    private boolean isExcluded(File child) {
-        if (excludedHomeFiles.contains(child.getName())) {
-            return true;
-        }
-        return false;
-    }
-
-    /**
-     * Get source home file directory path
-     * 
-     * @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/migration/rel18/FauxPropertiesUpdater.java

@@ -78,8 +78,7 @@ private boolean isAlreadyUpdated() {
 	}
 
 	private boolean locateFile() {
-		String homePath = ApplicationUtils.instance().getHomeDirectory()
-				.getPath().toString();
+		String homePath = ApplicationUtils.instance().getHomeDirectory().getSourcePath();
 		propertyConfigPath = Paths.get(homePath, PATH_TO_PROPERTY_CONFIG);
 		if (Files.exists(propertyConfigPath)) {
 			return true;

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

@@ -32,8 +32,7 @@
 import org.apache.jena.query.Dataset;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
-
-import edu.cornell.mannlib.vitro.webapp.application.VitroHomeDirectory;
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 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;
@@ -121,7 +120,7 @@ public void contextInitialized(ServletContextEvent sce) {
 	private Set<Path> getFilegraphPaths(ServletContext ctx, String... strings) {
 		StartupStatus ss = StartupStatus.getBean(ctx);
 
-		String homeDirPath = VitroHomeDirectory.getHomeSrcPath(ctx);
+		String homeDirPath = ApplicationUtils.instance().getHomeDirectory().getSourcePath();
 		Path filegraphDir = Paths.get(homeDirPath, strings);
 
 		Set<Path> paths = new TreeSet<>();

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

@@ -31,8 +31,7 @@
 import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.rdf.model.Statement;
 import org.apache.jena.rdf.model.StmtIterator;
-
-import edu.cornell.mannlib.vitro.webapp.application.VitroHomeDirectory;
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 
 import javax.servlet.ServletContext;
 
@@ -221,7 +220,7 @@ else if (filename.endsWith("ttl"))
 	}
 
 	private static String locateHomeDirectory(ServletContext ctx) {
-		return VitroHomeDirectory.getHomeSrcPath(ctx);
+		return ApplicationUtils.instance().getHomeDirectory().getSourcePath();
 	}
 
 	/**

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

@@ -13,6 +13,7 @@
 import java.io.StringWriter;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -106,7 +107,7 @@ public void contextInitialized(ServletContextEvent sce) {
 			settings.setInferenceOntModelSelector(ModelAccess.on(ctx).getOntModelSelector(INFERENCES_ONLY));
 			settings.setUnionOntModelSelector(ModelAccess.on(ctx).getOntModelSelector());
 
-		    Path homeDir = ApplicationUtils.instance().getHomeDirectory().getPath();
+		    Path homeDir = Paths.get(ApplicationUtils.instance().getHomeDirectory().getSourcePath());
 			settings.setDisplayModel(ModelAccess.on(ctx).getOntModel(DISPLAY));
 			OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(oldTBoxModelDir()));
 			settings.setOldTBoxModel(oldTBoxModel);

api/src/test/java/edu/cornell/mannlib/vitro/webapp/application/VitroHomeDirectoryTest.java

@@ -0,0 +1,50 @@
+package edu.cornell.mannlib.vitro.webapp.application;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import stubs.javax.servlet.ServletContextStub;
+
+public class VitroHomeDirectoryTest {
+
+    private static final String FILE = "file";
+    private static final String CONFIG = "config";
+    private static final String RDF = "rdf";
+    @Rule
+    public TemporaryFolder src = new TemporaryFolder();
+    @Rule
+    public TemporaryFolder dst = new TemporaryFolder();
+
+    @Test
+    public void testGetHomeSrcPath() {
+        ServletContextStub sc = new ServletContextStub();
+        String expectedPath = "/opt/tomcat/webapp/app/WEB-INF/resources/home-files";
+        sc.setRealPath("/WEB-INF/resources/home-files", expectedPath);
+        VitroHomeDirectory vhd = new VitroHomeDirectory(sc, dst.getRoot().toPath(), "");
+        String realPath = vhd.getSourcePath();
+        assertEquals(expectedPath, realPath);
+    }
+
+    @Test
+    public void testPopulate() throws Exception {
+        ServletContextStub sc = new ServletContextStub();
+        src.newFolder(RDF);
+        src.newFile(FILE);
+        src.newFolder(CONFIG);
+        sc.setRealPath("/WEB-INF/resources/home-files", src.getRoot().getAbsolutePath());
+        VitroHomeDirectory vhd = new VitroHomeDirectory(sc, dst.getRoot().toPath(), "");
+        vhd.populate();
+        Set<String> files = new HashSet<String>(Arrays.asList(dst.getRoot().list()));
+        assertTrue(files.contains(CONFIG));
+        assertTrue(files.contains(FILE));
+        assertFalse(files.contains(RDF));
+    }
+}