VIVO-906 Assemble application at runtime.

Create an object to represent VitroHomeDirectory
Instantiate TripleSources, FileStorage, etc, based on the config file.

webapp/build.xml

@@ -269,6 +269,12 @@
 				<include name="example.developer.properties" />
 			</fileset>
 		</copy>
+		<mkdir dir="${vitrohome.image.dir}/config" />
+		<copy todir="${vitrohome.image.dir}/config" >
+			<fileset dir="${appbase.dir}/config" >
+				<include name="applicationSetup.n3" />
+			</fileset>
+		</copy>
 		<copy todir="${vitrohome.image.dir}" >
 			<fileset dir="${appbase.dir}" >
 				<include name="rdf/**/*" />

webapp/src/edu/cornell/mannlib/vitro/webapp/application/ApplicationImpl.java

@@ -2,21 +2,28 @@
 
 package edu.cornell.mannlib.vitro.webapp.application;
 
+import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService.CONFIGURATION;
+
 import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
-import edu.cornell.mannlib.vitro.webapp.filestorage.impl.FileStorageImplWrapper;
-import edu.cornell.mannlib.vitro.webapp.imageprocessor.jai.JaiImageProcessor;
+import com.hp.hpl.jena.ontology.OntDocumentManager;
+
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.modules.Application;
 import edu.cornell.mannlib.vitro.webapp.modules.ComponentStartupStatus;
 import edu.cornell.mannlib.vitro.webapp.modules.fileStorage.FileStorage;
 import edu.cornell.mannlib.vitro.webapp.modules.imageProcessor.ImageProcessor;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine;
-import edu.cornell.mannlib.vitro.webapp.searchengine.InstrumentedSearchEngineWrapper;
-import edu.cornell.mannlib.vitro.webapp.searchengine.solr.SolrSearchEngine;
+import edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ConfigurationTripleSource;
+import edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ContentTripleSource;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
+import edu.cornell.mannlib.vitro.webapp.triplesource.impl.BasicCombinedTripleSource;
 import edu.cornell.mannlib.vitro.webapp.startup.ComponentStartupStatusImpl;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.Property;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.Validation;
 
 /**
  * The basic implementation of the Application interface.
@@ -26,12 +33,16 @@ public class ApplicationImpl implements Application {
 	// The instance
 	// ----------------------------------------------------------------------
 
-	private final ServletContext ctx;
+	private ServletContext ctx;
+	private VitroHomeDirectory homeDirectory;
+
 	private SearchEngine searchEngine;
 	private ImageProcessor imageProcessor;
 	private FileStorage fileStorage;
+	private ContentTripleSource contentTripleSource;
+	private ConfigurationTripleSource configurationTripleSource;
 
-	public ApplicationImpl(ServletContext ctx) {
+	public void setServletContext(ServletContext ctx) {
 		this.ctx = ctx;
 	}
 
@@ -40,13 +51,29 @@ public class ApplicationImpl implements Application {
 		return ctx;
 	}
 
+	@Override
+	public VitroHomeDirectory getHomeDirectory() {
+		return homeDirectory;
+	}
+
+	public void setHomeDirectory(VitroHomeDirectory homeDirectory) {
+		this.homeDirectory = homeDirectory;
+	}
+
 	@Override
 	public SearchEngine getSearchEngine() {
 		return searchEngine;
 	}
 
-	public void setSearchEngine(SearchEngine searchEngine) {
-		this.searchEngine = searchEngine;
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasSearchEngine")
+	public void setSearchEngine(SearchEngine se) {
+		if (searchEngine == null) {
+			searchEngine = se;
+		} else {
+			throw new IllegalStateException(
+					"Configuration includes multiple SearchEngine instancess: "
+							+ searchEngine + ", and " + se);
+		}
 	}
 
 	@Override
@@ -54,8 +81,15 @@ public class ApplicationImpl implements Application {
 		return imageProcessor;
 	}
 
-	public void setImageProcessor(ImageProcessor imageProcessor) {
-		this.imageProcessor = imageProcessor;
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasImageProcessor")
+	public void setImageProcessor(ImageProcessor ip) {
+		if (imageProcessor == null) {
+			imageProcessor = ip;
+		} else {
+			throw new IllegalStateException(
+					"Configuration includes multiple ImageProcessor instancess: "
+							+ imageProcessor + ", and " + ip);
+		}
 	}
 
 	@Override
@@ -63,57 +97,151 @@ public class ApplicationImpl implements Application {
 		return fileStorage;
 	}
 
-	public void setFileStorage(FileStorage fileStorage) {
-		this.fileStorage = fileStorage;
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasFileStorage")
+	public void setFileStorage(FileStorage fs) {
+		if (fileStorage == null) {
+			fileStorage = fs;
+		} else {
+			throw new IllegalStateException(
+					"Configuration includes multiple FileStorage intances: "
+							+ fileStorage + ", and " + fs);
+		}
+	}
+
+	@Override
+	public ContentTripleSource getContentTripleSource() {
+		return contentTripleSource;
+	}
+
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasContentTripleSource")
+	public void setContentTripleSource(ContentTripleSource source) {
+		if (contentTripleSource == null) {
+			contentTripleSource = source;
+		} else {
+			throw new IllegalStateException(
+					"Configuration includes multiple intances of ContentTripleSource: "
+							+ contentTripleSource + ", and " + source);
+		}
+	}
+
+	@Override
+	public ConfigurationTripleSource getConfigurationTripleSource() {
+		return configurationTripleSource;
+	}
+
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasConfigurationTripleSource")
+	public void setConfigurationTripleSource(ConfigurationTripleSource source) {
+		if (configurationTripleSource == null) {
+			configurationTripleSource = source;
+		} else {
+			throw new IllegalStateException(
+					"Configuration includes multiple intances of ConfigurationTripleSource: "
+							+ configurationTripleSource + ", and " + source);
+		}
+	}
+
+	@Validation
+	public void validate() throws Exception {
+		if (searchEngine == null) {
+			throw new IllegalStateException(
+					"Configuration did not include a SearchEngine.");
+		}
+		if (imageProcessor == null) {
+			throw new IllegalStateException(
+					"Configuration did not include an ImageProcessor.");
+		}
+		if (fileStorage == null) {
+			throw new IllegalStateException(
+					"Configuration did not include a FileStorage.");
+		}
+		if (contentTripleSource == null) {
+			throw new IllegalStateException(
+					"Configuration did not include a ContentTripleSource.");
+		}
+		if (configurationTripleSource == null) {
+			throw new IllegalStateException(
+					"Configuration did not include a ConfigurationTripleSource.");
+		}
+	}
+
+	@Override
+	public void shutdown() {
+		getFileStorage().shutdown(this);
+		getImageProcessor().shutdown(this);
+		getSearchEngine().shutdown(this);
 	}
 
 	// ----------------------------------------------------------------------
-	// The Setup class.
+	// Setup the major components.
+	//
+	// This must happen after the ConfigurationProperties and some other stuff.
 	// ----------------------------------------------------------------------
 
-	public static class Setup implements ServletContextListener {
-		private ApplicationImpl application;
-
+	public static class ComponentsSetup implements ServletContextListener {
 		@Override
 		public void contextInitialized(ServletContextEvent sce) {
 			ServletContext ctx = sce.getServletContext();
+			Application app = ApplicationUtils.instance();
 			StartupStatus ss = StartupStatus.getBean(ctx);
+			ComponentStartupStatus css = new ComponentStartupStatusImpl(this,
+					ss);
 
-			try {
-				application = new ApplicationImpl(ctx);
+			SearchEngine searchEngine = app.getSearchEngine();
+			searchEngine.startup(app, css);
+			ss.info(this, "Started the SearchEngine: " + searchEngine);
 
-				ComponentStartupStatus css = new ComponentStartupStatusImpl(
-						this, ss);
+			ImageProcessor imageProcessor = app.getImageProcessor();
+			imageProcessor.startup(app, css);
+			ss.info(this, "Started the ImageProcessor: " + imageProcessor);
 
-				SearchEngine searchEngine = new InstrumentedSearchEngineWrapper(
-						new SolrSearchEngine());
-				searchEngine.startup(application, css);
-				application.setSearchEngine(searchEngine);
-				ss.info(this, "Started the searchEngine: " + searchEngine);
+			FileStorage fileStorage = app.getFileStorage();
+			fileStorage.startup(app, css);
+			ss.info(this, "Started the FileStorage system: " + fileStorage);
 
-				ImageProcessor imageProcessor = new JaiImageProcessor();
-				imageProcessor.startup(application, css);
-				application.setImageProcessor(imageProcessor);
-				ss.info(this, "Started the ImageProcessor: " + searchEngine);
+			ContentTripleSource contentTripleSource = app
+					.getContentTripleSource();
+			contentTripleSource.startup(app, css);
+			ss.info(this, "Started the ContentTripleSource: "
+					+ contentTripleSource);
 
-				FileStorage fileStorage = new FileStorageImplWrapper();
-				fileStorage.startup(application, css);
-				application.setFileStorage(fileStorage);
-				ss.info(this, "Started the FileStorage system: " + searchEngine);
+			ConfigurationTripleSource configurationTripleSource = app
+					.getConfigurationTripleSource();
+			configurationTripleSource.startup(app, css);
+			ss.info(this, "Started the ConfigurationTripleSource: "
+					+ configurationTripleSource);
 
-				ApplicationUtils.setInstance(application);
-				ss.info(this, "Appliation is configured.");
-			} catch (Exception e) {
-				ss.fatal(this, "Failed to initialize the Application.", e);
+			configureJena();
+			prepareCombinedTripleSource(app, ctx);
 		}
+
+		private void configureJena() {
+			// we do not want to fetch imports when we wrap Models in OntModels
+			OntDocumentManager.getInstance().setProcessImports(false);
+		}
+
+		private void prepareCombinedTripleSource(Application app,
+				ServletContext ctx) {
+			ContentTripleSource contentSource = app.getContentTripleSource();
+			ConfigurationTripleSource configurationSource = app
+					.getConfigurationTripleSource();
+			BasicCombinedTripleSource source = new BasicCombinedTripleSource(
+					contentSource, configurationSource);
+
+			RDFServiceUtils.setRDFServiceFactory(ctx,
+					contentSource.getRDFServiceFactory());
+			RDFServiceUtils.setRDFServiceFactory(ctx,
+					configurationSource.getRDFServiceFactory(), CONFIGURATION);
+
+			ModelAccess.setCombinedTripleSource(source);
 		}
 
 		@Override
 		public void contextDestroyed(ServletContextEvent sce) {
-			application.getFileStorage().shutdown(application);
-			application.getImageProcessor().shutdown(application);
-			application.getSearchEngine().shutdown(application);
+			Application app = ApplicationUtils.instance();
+			app.getSearchEngine().shutdown(app);
+			app.getImageProcessor().shutdown(app);
+			app.getFileStorage().shutdown(app);
+		}
 	}
 
 }
-}

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

@@ -0,0 +1,115 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.application;
+
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Set;
+
+import javax.servlet.ServletContext;
+import javax.servlet.ServletContextEvent;
+import javax.servlet.ServletContextListener;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
+import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.ConfigurationBeanLoader;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.ConfigurationBeanLoaderException;
+import edu.cornell.mannlib.vitro.webapp.utils.jena.criticalsection.LockableModel;
+
+/**
+ * Read the application setup file and create the components it describes.
+ */
+public class ApplicationSetup implements ServletContextListener {
+	private static final String APPLICATION_SETUP_PATH = "config/applicationSetup.n3";
+
+	private ServletContext ctx;
+	private StartupStatus ss;
+
+	private ApplicationImpl app;
+
+	private VitroHomeDirectory vitroHomeDir;
+
+	private Path configFile;
+	private LockableModel configModel;
+	private ConfigurationBeanLoader loader;
+
+	@Override
+	public void contextInitialized(ServletContextEvent sce) {
+		try {
+			this.ctx = sce.getServletContext();
+			this.ss = StartupStatus.getBean(ctx);
+
+			this.vitroHomeDir = VitroHomeDirectory.find(ctx);
+			ss.info(this, vitroHomeDir.getDiscoveryMessage());
+
+			locateApplicationConfigFile();
+			loadApplicationConfigFile();
+			createConfigurationBeanLoader();
+			instantiateTheApplication();
+
+			app.setServletContext(this.ctx);
+			app.setHomeDirectory(this.vitroHomeDir);
+
+			ApplicationUtils.setInstance(app);
+			ss.info(this, "Application is configured.");
+		} catch (Exception e) {
+			ss.fatal(this, "Failed to initialize the Application.", e);
+		}
+	}
+
+	private void locateApplicationConfigFile() {
+		Path path = this.vitroHomeDir.getPath().resolve(APPLICATION_SETUP_PATH);
+		if (!Files.exists(path)) {
+			throw new IllegalStateException("'" + path + "' does not exist.");
+		}
+		if (!Files.isReadable(path)) {
+			throw new IllegalStateException("Can't read '" + path + "'");
+		}
+		this.configFile = path;
+	}
+
+	private void loadApplicationConfigFile() {
+		try (InputStream in = Files.newInputStream(this.configFile)) {
+			Model m = ModelFactory.createDefaultModel();
+			m.read(in, null, "N3");
+			this.configModel = new LockableModel(m);
+		} catch (Exception e) {
+			throw new RuntimeException("Failed to read '" + this.configFile
+					+ "'", e);
+		}
+	}
+
+	private void createConfigurationBeanLoader() {
+		this.loader = new ConfigurationBeanLoader(configModel);
+	}
+
+	private void instantiateTheApplication() {
+		try {
+			Set<ApplicationImpl> apps = loader.loadAll(ApplicationImpl.class);
+			if (apps.isEmpty()) {
+				throw new IllegalStateException("'" + this.configFile
+						+ "' does not define an instance of "
+						+ ApplicationImpl.class.getName());
+			} else if (apps.size() > 1) {
+				throw new IllegalStateException("'" + this.configFile
+						+ "' defines " + apps.size() + " instances of "
+						+ ApplicationImpl.class.getName());
+			} else {
+				this.app = apps.iterator().next();
+			}
+		} catch (ConfigurationBeanLoaderException e) {
+			throw new IllegalStateException("Failed to setup the application",
+					e);
+		}
+	}
+
+	@Override
+	public void contextDestroyed(ServletContextEvent sce) {
+		if (app != null) {
+			app.shutdown();
+		}
+	}
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/application/ApplicationUtils.java

@@ -29,5 +29,4 @@ public class ApplicationUtils {
 	static void setInstance(Application application) {
 		instance = application;
 	}
-
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/application/BuildProperties.java

@@ -0,0 +1,54 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.application;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.servlet.ServletContext;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+/**
+ * Obtains and provides the contents of the build.properties file.
+ */
+public class BuildProperties {
+	private static final Log log = LogFactory.getLog(BuildProperties.class);
+
+	/** Path to the file of build properties baked into the webapp. */
+	public static final String WEBAPP_PATH_BUILD_PROPERTIES = "/WEB-INF/resources/build.properties";
+
+	private final Map<String, String> propertyMap;
+
+	public BuildProperties(ServletContext ctx) {
+		Map<String, String> map = new HashMap<>();
+
+		try (InputStream stream = ctx
+				.getResourceAsStream(WEBAPP_PATH_BUILD_PROPERTIES)) {
+			if (stream == null) {
+				log.debug("Didn't find a resource at '"
+						+ WEBAPP_PATH_BUILD_PROPERTIES + "'.");
+			} else {
+				Properties props = new Properties();
+				props.load(stream);
+				for (String key : props.stringPropertyNames()) {
+					map.put(key, props.getProperty(key));
+				}
+			}
+		} catch (IOException e) {
+			throw new RuntimeException("Failed to load from '"
+					+ WEBAPP_PATH_BUILD_PROPERTIES + "'.", e);
+		}
+		propertyMap = Collections.unmodifiableMap(map);
+	}
+
+	public Map<String, String> getMap() {
+		return this.propertyMap;
+	}
+
+}

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

@@ -0,0 +1,213 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.application;
+
+import static edu.cornell.mannlib.vitro.webapp.application.BuildProperties.WEBAPP_PATH_BUILD_PROPERTIES;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import javax.naming.InitialContext;
+import javax.servlet.ServletContext;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+/**
+ * Encapsulates some of the info relating to the Vitro home directory.
+ */
+public class VitroHomeDirectory {
+	private static final Log log = LogFactory.getLog(VitroHomeDirectory.class);
+	
+	public static VitroHomeDirectory find(ServletContext ctx) {
+		HomeDirectoryFinder finder = new HomeDirectoryFinder(ctx);
+		return new VitroHomeDirectory(ctx, finder.getPath(),
+				finder.getMessage());
+	}
+
+	private final ServletContext ctx;
+	private final Path path;
+	private final String discoveryMessage;
+
+	public VitroHomeDirectory(ServletContext ctx, Path path,
+			String discoveryMessage) {
+		this.ctx = ctx;
+		this.path = path;
+		this.discoveryMessage = discoveryMessage;
+	}
+
+	public ServletContext getCtx() {
+		return ctx;
+	}
+
+	public Path getPath() {
+		return path;
+	}
+
+	public String getDiscoveryMessage() {
+		return discoveryMessage;
+	}
+	
+	/**
+	 * Find something that specifies the location of the Vitro home directory.
+	 * Look in the JDNI environment, the system properties, and the
+	 * build.properties file.
+	 * 
+	 * If we don't find it, fail. If we find it more than once, use the first
+	 * one (with a warning). If it is not an existing, readable directory, fail.
+	 */
+	private static class HomeDirectoryFinder {
+		/** JNDI path that defines the Vitro home directory */
+		private static final String VHD_JNDI_PATH = "java:comp/env/vitro/home";
+
+		/** System property that defines the Vitro home directory */
+		private static final String VHD_SYSTEM_PROPERTY = "vitro.home";
+
+		/** build.properties property that defines the Vitro home directory */
+		private static final String VHD_BUILD_PROPERTY = "vitro.home";
+
+		private final ServletContext ctx;
+		private final List<Found> foundLocations = new ArrayList<>();
+
+		public HomeDirectoryFinder(ServletContext ctx) {
+			this.ctx = ctx;
+
+			getVhdFromJndi();
+			getVhdFromSystemProperties();
+			getVhdFromBuildProperties();
+			confirmExactlyOneResult();
+			confirmValidDirectory();
+		}
+
+		public String getMessage() {
+			return foundLocations.get(0).getMessage();
+		}
+
+		public Path getPath() {
+			return foundLocations.get(0).getPath();
+		}
+		
+		public void getVhdFromJndi() {
+			try {
+				String vhdPath = (String) new InitialContext()
+						.lookup(VHD_JNDI_PATH);
+				if (vhdPath == null) {
+					log.debug("Didn't find a JNDI value at '" + VHD_JNDI_PATH
+							+ "'.");
+				} else {
+					log.debug("'" + VHD_JNDI_PATH + "' as specified by JNDI: "
+							+ vhdPath);
+					String message = String.format(
+							"JNDI environment '%s' was set to '%s'",
+							VHD_JNDI_PATH, vhdPath);
+					foundLocations.add(new Found(Paths.get(vhdPath), message));
+				}
+			} catch (Exception e) {
+				log.debug("JNDI lookup failed. " + e);
+			}
+		}
+
+		private void getVhdFromSystemProperties() {
+			String vhdPath = System.getProperty(VHD_SYSTEM_PROPERTY);
+			if (vhdPath == null) {
+				log.debug("Didn't find a system property value at '"
+						+ VHD_SYSTEM_PROPERTY + "'.");
+			} else {
+				log.debug("'" + VHD_SYSTEM_PROPERTY
+						+ "' as specified by system property: " + vhdPath);
+				String message = String.format(
+						"System property '%s' was set to '%s'",
+						VHD_SYSTEM_PROPERTY, vhdPath);
+				foundLocations.add(new Found(Paths.get(vhdPath), message));
+			}
+		}
+
+		private void getVhdFromBuildProperties() {
+			try {
+				Map<String, String> buildProps = new BuildProperties(ctx)
+						.getMap();
+				String vhdPath = buildProps.get(VHD_BUILD_PROPERTY);
+				if (vhdPath == null) {
+					log.debug("build properties doesn't contain a value for '"
+							+ VHD_BUILD_PROPERTY + "'.");
+				} else {
+					log.debug("'" + VHD_BUILD_PROPERTY
+							+ "' as specified by build.properties: " + vhdPath);
+					String message = String.format(
+							"In resource '%s', '%s' was set to '%s'.",
+							WEBAPP_PATH_BUILD_PROPERTIES, VHD_BUILD_PROPERTY,
+							vhdPath);
+					foundLocations.add(new Found(Paths.get(vhdPath), message));
+				}
+			} catch (Exception e) {
+				log.warn("Reading build properties failed. " + e);
+			}
+		}
+
+		private void confirmExactlyOneResult() {
+			if (foundLocations.isEmpty()) {
+				String message = String.format("Can't find a value "
+						+ "for the Vitro home directory. "
+						+ "Looked in JNDI environment at '%s'. "
+						+ "Looked for a system property named '%s'. "
+						+ "Looked in 'WEB-INF/resources/build.properties' "
+						+ "for '%s'.", VHD_JNDI_PATH, VHD_SYSTEM_PROPERTY,
+						VHD_BUILD_PROPERTY);
+				throw new IllegalStateException(message);
+			} else if (foundLocations.size() > 1) {
+				String message = String.format("Found multiple values for the "
+						+ "Vitro home directory: " + foundLocations);
+				log.warn(message);
+			}
+		}
+
+		private void confirmValidDirectory() {
+			Path vhd = getPath();
+			if (!Files.exists(vhd)) {
+				throw new IllegalStateException("Vitro home directory '" + vhd
+						+ "' does not exist.");
+			}
+			if (!Files.isDirectory(vhd)) {
+				throw new IllegalStateException("Vitro home directory '" + vhd
+						+ "' is not a directory.");
+			}
+			if (!Files.isReadable(vhd)) {
+				throw new IllegalStateException(
+						"Cannot read Vitro home directory '" + vhd + "'.");
+			}
+			if (!Files.isWritable(vhd)) {
+				throw new IllegalStateException(
+						"Can't write to Vitro home directory: '" + vhd + "'.");
+			}
+		}
+
+		/** We found it: where and how. */
+		private static class Found {
+			private final Path path;
+			private final String message;
+
+			public Found(Path path, String message) {
+				this.path = path;
+				this.message = message;
+			}
+
+			public Path getPath() {
+				return path;
+			}
+
+			public String getMessage() {
+				return message;
+			}
+
+			@Override
+			public String toString() {
+				return "Found[path=" + path + ", message=" + message + "]";
+			}
+		}
+	}
+
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/config/ConfigurationPropertiesSetup.java

@@ -7,12 +7,8 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.HashMap;
-import java.util.LinkedHashMap;
 import java.util.Map;
-import java.util.Properties;
 
-import javax.naming.InitialContext;
-import javax.naming.NamingException;
 import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
@@ -20,6 +16,8 @@ import javax.servlet.ServletContextListener;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
+import edu.cornell.mannlib.vitro.webapp.application.BuildProperties;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
@@ -48,23 +46,11 @@ public class ConfigurationPropertiesSetup implements ServletContextListener {
 	private static final Log log = LogFactory
 			.getLog(ConfigurationPropertiesSetup.class);
 
-	/** JNDI path that defines the Vitro home directory */
-	private static final String VHD_JNDI_PATH = "java:comp/env/vitro/home";
-
-	/** System property that defines the Vitro home directory */
-	private static final String VHD_SYSTEM_PROPERTY = "vitro.home";
-
-	/** build.properties property that defines the Vitro home directory */
-	private static final String VHD_BUILD_PROPERTY = "vitro.home";
-
-	/** Configuration property to store the Vitro home directory */
-	private static final String VHD_CONFIGURATION_PROPERTY = "vitro.home";
-
 	/** Name of the file that contains runtime properties. */
 	private static final String FILE_RUNTIME_PROPERTIES = "runtime.properties";
 
-	/** Path to the file of build properties baked into the webapp. */
-	private static final String PATH_BUILD_PROPERTIES = "/WEB-INF/resources/build.properties";
+	/** Configuration property to store the Vitro home directory */
+	private static final String VHD_CONFIGURATION_PROPERTY = "vitro.home";
 
 	@Override
 	public void contextInitialized(ServletContextEvent sce) {
@@ -74,7 +60,8 @@ public class ConfigurationPropertiesSetup implements ServletContextListener {
 		try {
 			InputStream stream = null;
 			try {
-				File vitroHomeDir = locateVitroHomeDirectory(ctx, ss);
+				File vitroHomeDir = ApplicationUtils.instance()
+						.getHomeDirectory().getPath().toFile();
 
 				File runtimePropertiesFile = locateRuntimePropertiesFile(
 						vitroHomeDir, ss);
@@ -84,7 +71,7 @@ public class ConfigurationPropertiesSetup implements ServletContextListener {
 						VHD_CONFIGURATION_PROPERTY, vitroHomeDir);
 
 				ConfigurationPropertiesImpl bean = new ConfigurationPropertiesImpl(
-						stream, preempts, getBuildProperties(ctx));
+						stream, preempts, new BuildProperties(ctx).getMap());
 
 				ConfigurationProperties.setBean(ctx, bean);
 				ss.info(this, "Loaded " + bean.getPropertyMap().size()
@@ -103,141 +90,6 @@ public class ConfigurationPropertiesSetup implements ServletContextListener {
 		}
 	}
 
-	/**
-	 * Look in the JDNI environment, the system properties, and the
-	 * build.properties file.
-	 * 
-	 * If we don't find it, fail. If we find it more than once, warn and use the
-	 * first one.
-	 * 
-	 * Confirm that it is an existing, readable directory.
-	 */
-	private File locateVitroHomeDirectory(ServletContext ctx, StartupStatus ss) {
-		Map<String, String> whereWasIt = new LinkedHashMap<String, String>();
-		getVhdFromJndi(whereWasIt);
-		getVhdFromSystemProperties(whereWasIt);
-		getVhdFromBuildProperties(ctx, whereWasIt);
-
-		if (whereWasIt.isEmpty()) {
-			String message = String.format("Can't find a value "
-					+ "for the Vitro home directory. "
-					+ "Looked in JNDI environment at '%s'. "
-					+ "Looked for a system property named '%s'. "
-					+ "Looked in 'WEB-INF/resources/build.properties' "
-					+ "for '%s'.", VHD_JNDI_PATH, VHD_SYSTEM_PROPERTY,
-					VHD_BUILD_PROPERTY);
-			throw new IllegalStateException(message);
-		} else if (whereWasIt.size() > 1) {
-			String message = String.format("Found multiple values for the "
-					+ "Vitro home directory: " + whereWasIt.keySet());
-			ss.warning(this, message);
-		}
-		String message = whereWasIt.keySet().iterator().next();
-		String vhdPath = whereWasIt.values().iterator().next();
-
-		ss.info(this, message);
-
-		File vhd = new File(vhdPath);
-		if (!vhd.exists()) {
-			throw new IllegalStateException("Vitro home directory '" + vhdPath
-					+ "' does not exist.");
-		}
-		if (!vhd.isDirectory()) {
-			throw new IllegalStateException("Vitro home directory '" + vhdPath
-					+ "' is not a directory.");
-		}
-		if (!vhd.canRead()) {
-			throw new IllegalStateException("Vitro home directory '" + vhdPath
-					+ "' cannot be read.");
-		}
-		if (!vhd.canWrite()) {
-			throw new IllegalStateException(
-					"Can't write to Vitro home directory: '" + vhdPath + "'.");
-		}
-
-		return vhd;
-	}
-
-	private void getVhdFromJndi(Map<String, String> whereWasIt) {
-		try {
-			String vhdPath = (String) new InitialContext()
-					.lookup(VHD_JNDI_PATH);
-
-			if (vhdPath == null) {
-				log.debug("Didn't find a JNDI value at '" + VHD_JNDI_PATH
-						+ "'.");
-				return;
-			}
-
-			log.debug("'" + VHD_JNDI_PATH + "' as specified by JNDI: "
-					+ vhdPath);
-			String message = String.format(
-					"JNDI environment '%s' was set to '%s'", VHD_JNDI_PATH,
-					vhdPath);
-			whereWasIt.put(message, vhdPath);
-		} catch (NamingException e) {
-			log.debug("JNDI lookup failed. " + e);
-		}
-	}
-
-	private void getVhdFromSystemProperties(Map<String, String> whereWasIt) {
-		String vhdPath = System.getProperty(VHD_SYSTEM_PROPERTY);
-
-		if (vhdPath == null) {
-			log.debug("Didn't find a system property value at '"
-					+ VHD_SYSTEM_PROPERTY + "'.");
-			return;
-		}
-
-		log.debug("'" + VHD_SYSTEM_PROPERTY
-				+ "' as specified by system property: " + vhdPath);
-		String message = String.format("System property '%s' was set to '%s'",
-				VHD_SYSTEM_PROPERTY, vhdPath);
-		whereWasIt.put(message, vhdPath);
-	}
-
-	private void getVhdFromBuildProperties(ServletContext ctx,
-			Map<String, String> whereWasIt) {
-		Map<String, String> buildProps = getBuildProperties(ctx);
-		String vhdPath = buildProps.get(VHD_BUILD_PROPERTY);
-		if (vhdPath == null) {
-			log.debug("'" + PATH_BUILD_PROPERTIES
-					+ "' didn't contain a value for '" + VHD_BUILD_PROPERTY
-					+ "'.");
-			return;
-		}
-
-		log.debug("'" + VHD_BUILD_PROPERTY
-				+ "' as specified by build.properties: " + vhdPath);
-		String message = String.format(
-				"In resource '%s', '%s' was set to '%s'.",
-				PATH_BUILD_PROPERTIES, VHD_BUILD_PROPERTY, vhdPath);
-		whereWasIt.put(message, vhdPath);
-	}
-
-	private Map<String, String> getBuildProperties(ServletContext ctx) {
-		Map<String, String> map = new HashMap<>();
-
-		try (InputStream stream = ctx
-				.getResourceAsStream(PATH_BUILD_PROPERTIES)) {
-			if (stream == null) {
-				log.debug("Didn't find a resource at '" + PATH_BUILD_PROPERTIES
-						+ "'.");
-			} else {
-
-				Properties props = new Properties();
-				props.load(stream);
-				for (String key : props.stringPropertyNames()) {
-					map.put(key, props.getProperty(key));
-				}
-			}
-		} catch (IOException e) {
-			throw new SetupException("Failed to load from '"
-					+ PATH_BUILD_PROPERTIES + "'.", e);
-		}
-		return map;
-	}
-
 	private File locateRuntimePropertiesFile(File vitroHomeDir, StartupStatus ss) {
 		File rpf = new File(vitroHomeDir, FILE_RUNTIME_PROPERTIES);
 
@@ -270,13 +122,4 @@ public class ConfigurationPropertiesSetup implements ServletContextListener {
 		// No need to remove the bean. It's only a map of strings, and if we
 		// restart the app, it will be replaced.
 	}
-
-	/**
-	 * Indicates a problem setting up. Abandon ship.
-	 */
-	private static class SetupException extends RuntimeException {
-		public SetupException(String message, Throwable cause) {
-			super(message, cause);
-		}
-	}
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/config/ConfigurationPropertiesSmokeTests.java

@@ -25,7 +25,6 @@ public class ConfigurationPropertiesSmokeTests implements
 	private static final Log log = LogFactory
 			.getLog(ConfigurationPropertiesSmokeTests.class);
 
-	private static final String PROPERTY_HOME_DIRECTORY = "vitro.home";
 	private static final String PROPERTY_DEFAULT_NAMESPACE = "Vitro.defaultNamespace";
 	private static final String PROPERTY_LANGUAGE_BUILD = "languages.addToBuild";
 	private static final String PROPERTY_LANGUAGE_SELECTABLE = "languages.selectableLocales";
@@ -38,47 +37,10 @@ public class ConfigurationPropertiesSmokeTests implements
 		ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
 		StartupStatus ss = StartupStatus.getBean(ctx);
 
-		checkHomeDirectory(ctx, props, ss);
 		checkDefaultNamespace(ctx, props, ss);
 		checkLanguages(props, ss);
 	}
 
-	/**
-	 * Confirm that: a home directory has been specified; it exists; it is a
-	 * directory; it is readable and writable.
-	 */
-	private void checkHomeDirectory(ServletContext ctx,
-			ConfigurationProperties props, StartupStatus ss) {
-		String homeDirectoryPath = props.getProperty(PROPERTY_HOME_DIRECTORY);
-		if (homeDirectoryPath == null || homeDirectoryPath.isEmpty()) {
-			ss.fatal(this, "Can't find a value for the home directory: '"
-					+ PROPERTY_HOME_DIRECTORY + "'");
-			return;
-		}
-
-		File homeDirectory = new File(homeDirectoryPath);
-		if (!homeDirectory.exists()) {
-			ss.fatal(this, PROPERTY_HOME_DIRECTORY + " '" + homeDirectoryPath
-					+ "' does not exist.");
-			return;
-		}
-		if (!homeDirectory.isDirectory()) {
-			ss.fatal(this, PROPERTY_HOME_DIRECTORY + " '" + homeDirectoryPath
-					+ "' is not a directory.");
-			return;
-		}
-
-		if (!homeDirectory.canRead()) {
-			ss.fatal(this, PROPERTY_HOME_DIRECTORY + " '" + homeDirectoryPath
-					+ "' cannot be read.");
-		}
-		if (!homeDirectory.canWrite()) {
-			ss.fatal(this, PROPERTY_HOME_DIRECTORY + " '" + homeDirectoryPath
-					+ "' cannot be written to.");
-		}
-	}
-
-	
 	/**
 	 * Confirm that the default namespace is specified and a syntactically valid
 	 * URI. It should also end with "/individual/".

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ContactMailController.java

@@ -25,8 +25,8 @@ import javax.servlet.http.HttpServletRequest;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
-import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.TemplateProcessingHelper.TemplateProcessingException;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
@@ -50,7 +50,6 @@ public class ContactMailController extends FreemarkerHttpServlet {
     private final static String TEMPLATE_ERROR = "contactForm-error.ftl";
     private final static String TEMPLATE_FORM = "contactForm-form.ftl";
     
-	private static final String PROPERTY_VITRO_HOME_DIR = "vitro.home";
 	private static final String EMAIL_JOURNAL_FILE_DIR = "emailJournal";
 	private static final String EMAIL_JOURNAL_FILE_NAME = "contactFormEmails.html";
     
@@ -116,7 +115,7 @@ public class ContactMailController extends FreemarkerHttpServlet {
 	    
 	    try {
 	    	// Write the message to the journal file
-	    	FileWriter fw = new FileWriter(locateTheJournalFile(vreq),true);
+	    	FileWriter fw = new FileWriter(locateTheJournalFile(), true);
 	        PrintWriter outFile = new PrintWriter(fw); 
 	        writeBackupCopy(outFile, msgText, vreq);
   
@@ -159,21 +158,8 @@ public class ContactMailController extends FreemarkerHttpServlet {
 	 * The journal file belongs in a sub-directory of the Vitro home directory.
 	 * If the sub-directory doesn't exist, create it.
 	 */
-	private File locateTheJournalFile(VitroRequest vreq) {
-		String homeDirPath = ConfigurationProperties.getBean(vreq).getProperty(
-				PROPERTY_VITRO_HOME_DIR);
-		if (homeDirPath == null) {
-			throw new IllegalArgumentException(
-					"Configuration properties must contain a value for '"
-							+ PROPERTY_VITRO_HOME_DIR + "'");
-		}
-
-		File homeDir = new File(homeDirPath);
-		if (!homeDir.exists()) {
-			throw new IllegalStateException("Vitro home directory '"
-					+ homeDir.getAbsolutePath() + "' does not exist.");
-		}
-
+	private File locateTheJournalFile() {
+		File homeDir = ApplicationUtils.instance().getHomeDirectory().getPath().toFile();
 		File journalDir = new File(homeDir, EMAIL_JOURNAL_FILE_DIR);
 		if (!journalDir.exists()) {
 			boolean created = journalDir.mkdir();

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/impl/FileStorageImplWrapper.java

@@ -11,6 +11,7 @@ import java.util.Collections;
 
 import javax.servlet.ServletContext;
 
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.modules.Application;
 import edu.cornell.mannlib.vitro.webapp.modules.ComponentStartupStatus;
@@ -22,7 +23,6 @@ import edu.cornell.mannlib.vitro.webapp.modules.fileStorage.FileStorage;
  */
 public class FileStorageImplWrapper implements FileStorage {
 	public static final String PROPERTY_DEFAULT_NAMESPACE = "Vitro.defaultNamespace";
-	public static final String PROPERTY_VITRO_HOME_DIR = "vitro.home";
 	public static final String FILE_STORAGE_SUBDIRECTORY = "uploads";
 
 	private FileStorageImpl fs;
@@ -35,7 +35,7 @@ public class FileStorageImplWrapper implements FileStorage {
 		ServletContext ctx = application.getServletContext();
 
 		try {
-			File baseDirectory = figureBaseDir(ctx);
+			File baseDirectory = figureBaseDir();
 			Collection<String> fileNamespace = confirmDefaultNamespace(ctx);
 			fs = new FileStorageImpl(baseDirectory, fileNamespace);
 		} catch (Exception e) {
@@ -47,21 +47,8 @@ public class FileStorageImplWrapper implements FileStorage {
 	 * Get the configuration property for the file storage base directory, and
 	 * check that it points to an existing, writeable directory.
 	 */
-	private File figureBaseDir(ServletContext ctx) throws IOException {
-		String homeDirPath = ConfigurationProperties.getBean(ctx).getProperty(
-				PROPERTY_VITRO_HOME_DIR);
-		if (homeDirPath == null) {
-			throw new IllegalArgumentException(
-					"Configuration properties must contain a value for '"
-							+ PROPERTY_VITRO_HOME_DIR + "'");
-		}
-
-		File homeDir = new File(homeDirPath);
-		if (!homeDir.exists()) {
-			throw new IllegalStateException("Vitro home directory '"
-					+ homeDir.getAbsolutePath() + "' does not exist.");
-		}
-
+	private File figureBaseDir() throws IOException {
+		File homeDir = ApplicationUtils.instance().getHomeDirectory().getPath().toFile();
 		File baseDir = new File(homeDir, FILE_STORAGE_SUBDIRECTORY);
 		if (!baseDir.exists()) {
 			boolean created = baseDir.mkdir();

webapp/src/edu/cornell/mannlib/vitro/webapp/modules/Application.java

@@ -4,9 +4,12 @@ package edu.cornell.mannlib.vitro.webapp.modules;
 
 import javax.servlet.ServletContext;
 
+import edu.cornell.mannlib.vitro.webapp.application.VitroHomeDirectory;
 import edu.cornell.mannlib.vitro.webapp.modules.fileStorage.FileStorage;
 import edu.cornell.mannlib.vitro.webapp.modules.imageProcessor.ImageProcessor;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine;
+import edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ConfigurationTripleSource;
+import edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ContentTripleSource;
 
 /**
  * The interface that holds the modules and extensions together.
@@ -14,12 +17,20 @@ import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine;
 public interface Application {
 	ServletContext getServletContext();
 	
+	VitroHomeDirectory getHomeDirectory();
+
 	SearchEngine getSearchEngine();
 
 	ImageProcessor getImageProcessor();
 	
 	FileStorage getFileStorage();
 	
+	ContentTripleSource getContentTripleSource();
+	
+	ConfigurationTripleSource getConfigurationTripleSource();
+	
+	void shutdown();
+
 	public interface Component {
 		enum LifecycleState {
 			NEW, ACTIVE, STOPPED

webapp/src/edu/cornell/mannlib/vitro/webapp/searchengine/InstrumentedSearchEngineWrapper.java

@@ -18,6 +18,8 @@ import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngineExcepti
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchInputDocument;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchQuery;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchResponse;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.Property;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.Validation;
 
 /**
  * Manages the life-cycle of the SearchEngine. Adds logging, controlled by
@@ -27,17 +29,30 @@ public class InstrumentedSearchEngineWrapper implements SearchEngine {
 	private static final Log log = LogFactory
 			.getLog(InstrumentedSearchEngineWrapper.class);
 
-	private final SearchEngine innerEngine;
+	private SearchEngine innerEngine;
 
 	private volatile LifecycleState lifecycleState = NEW;
 
-	public InstrumentedSearchEngineWrapper(SearchEngine innerEngine) {
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#wraps")
+	public void setInnerEngine(SearchEngine inner) {
 		if (innerEngine == null) {
-			throw new NullPointerException("innerEngine may not be null.");
+			innerEngine = inner;
+		} else {
+			throw new IllegalStateException(
+					"Configuration includes multiple SearchEngine instancess: "
+							+ innerEngine + ", and " + inner);
 		}
-		this.innerEngine = innerEngine;
 	}
 
+	@Validation
+	public void validate() throws Exception {
+		if (innerEngine == null) {
+			throw new IllegalStateException(
+					"Configuration did not include a wrapped SearchEngine.");
+		}
+	}
+
+
 	/**
 	 * Complain unless ACTIVE.
 	 */

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ConfigurationModelsSetup.java

@@ -52,13 +52,12 @@ public class ConfigurationModelsSetup implements ServletContextListener {
 
 	private void loadFirstTimeFiles(ServletContext ctx, String modelPath,
 			OntModel baseModel) {
-		RDFFilesLoader.loadFirstTimeFiles(ctx, modelPath, baseModel,
-				baseModel.isEmpty());
+		RDFFilesLoader.loadFirstTimeFiles(modelPath, baseModel, baseModel.isEmpty());
 	}
 
 	private void loadEveryTimeFiles(ServletContext ctx, String modelPath,
 			OntModel memoryModel) {
-		RDFFilesLoader.loadEveryTimeFiles(ctx, modelPath, memoryModel);
+		RDFFilesLoader.loadEveryTimeFiles(modelPath, memoryModel);
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ContentModelSetup.java

@@ -62,13 +62,13 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
         
         if (isFirstStartup()) {
         	initializeApplicationMetadata(ctx, applicationMetadataModel);
-        	RDFFilesLoader.loadFirstTimeFiles(ctx, "abox", baseABoxModel, true);
-        	RDFFilesLoader.loadFirstTimeFiles(ctx, "tbox", baseTBoxModel, true);
+        	RDFFilesLoader.loadFirstTimeFiles("abox", baseABoxModel, true);
+        	RDFFilesLoader.loadFirstTimeFiles("tbox", baseTBoxModel, true);
         } else {
         	checkForNamespaceMismatch( applicationMetadataModel, ctx );
         }
-    	RDFFilesLoader.loadEveryTimeFiles(ctx, "abox", baseABoxModel);
-    	RDFFilesLoader.loadEveryTimeFiles(ctx, "tbox", baseTBoxModel);
+    	RDFFilesLoader.loadEveryTimeFiles("abox", baseABoxModel);
+    	RDFFilesLoader.loadEveryTimeFiles("tbox", baseTBoxModel);
     	
 		log.info("Setting up DAO factories");
     }
@@ -89,7 +89,7 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
 	private void initializeApplicationMetadata(ServletContext ctx,
 			Model applicationMetadataModel) {
 		OntModel temporaryAMModel = VitroModelFactory.createOntologyModel();
-    	RDFFilesLoader.loadFirstTimeFiles(ctx, "applicationMetadata", temporaryAMModel, true);
+    	RDFFilesLoader.loadFirstTimeFiles("applicationMetadata", temporaryAMModel, true);
     	setPortalUriOnFirstTime(temporaryAMModel, ctx);
     	applicationMetadataModel.add(temporaryAMModel);
 	}

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

@@ -33,6 +33,7 @@ import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.ModelMaker;
 
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.BlankNodeFilteringModelMaker;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
@@ -49,7 +50,6 @@ public class FileGraphSetup implements ServletContextListener {
     private static final String ABOX = "abox";
     private static final String TBOX = "tbox";
     private static final String FILEGRAPH = "filegraph";
-    private static final String PROPERTY_VITRO_HOME = "vitro.home";
 
     public static final String FILEGRAPH_URI_ROOT = "http://vitro.mannlib.cornell.edu/filegraph/";
     
@@ -119,7 +119,7 @@ public class FileGraphSetup implements ServletContextListener {
 		StartupStatus ss = StartupStatus.getBean(ctx);
 
 		ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
-		String homeDirProperty = props.getProperty(PROPERTY_VITRO_HOME);
+		String homeDirProperty = ApplicationUtils.instance().getHomeDirectory().getPath().toString();
 		Path filegraphDir = Paths.get(homeDirProperty, strings);
 
 		Set<Path> paths = new TreeSet<>();

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

@@ -13,8 +13,6 @@ import java.nio.file.Paths;
 import java.util.Set;
 import java.util.TreeSet;
 
-import javax.servlet.ServletContext;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -23,7 +21,7 @@ import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 
-import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 
 /**
  * Help to load RDF files on first time and on every startup.
@@ -31,7 +29,6 @@ import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 public class RDFFilesLoader {
 	private static final Log log = LogFactory.getLog(RDFFilesLoader.class);
 
-	private static final String PROPERTY_VITRO_HOME = "vitro.home";
 	private static final String DEFAULT_RDF_FORMAT = "RDF/XML";
 	private static final String RDF = "rdf";
 	private static final String FIRST_TIME = "firsttime";
@@ -61,10 +58,10 @@ public class RDFFilesLoader {
 	 * 
 	 * The files from the directory are added to the model.
 	 */
-	public static void loadFirstTimeFiles(ServletContext ctx, String modelPath,
-			Model model, boolean firstTime) {
+	public static void loadFirstTimeFiles(String modelPath, Model model,
+			boolean firstTime) {
 		if (firstTime) {
-			Set<Path> paths = getPaths(locateHomeDirectory(ctx), RDF,
+			Set<Path> paths = getPaths(locateHomeDirectory(), RDF,
 					modelPath, FIRST_TIME);
 			for (Path p : paths) {
 				readOntologyFileIntoModel(p, model);
@@ -83,11 +80,10 @@ public class RDFFilesLoader {
 	 * 
 	 * The files from the directory become a sub-model of the model.
 	 */
-	public static void loadEveryTimeFiles(ServletContext ctx, String modelPath,
-			OntModel model) {
+	public static void loadEveryTimeFiles(String modelPath, OntModel model) {
 		OntModel everytimeModel = ModelFactory
 				.createOntologyModel(OntModelSpec.OWL_MEM);
-		String home = locateHomeDirectory(ctx);
+		String home = locateHomeDirectory();
 		Set<Path> paths = getPaths(home, RDF, modelPath, EVERY_TIME);
 		for (Path p : paths) {
 			log.info("Loading " + relativePath(p, home));
@@ -177,9 +173,9 @@ public class RDFFilesLoader {
 			return DEFAULT_RDF_FORMAT;
 	}
 
-	private static String locateHomeDirectory(ServletContext ctx) {
-		return ConfigurationProperties.getBean(ctx).getProperty(
-				PROPERTY_VITRO_HOME);
+	private static String locateHomeDirectory() {
+		return ApplicationUtils.instance().getHomeDirectory().getPath()
+				.toString();
 	}
 
 	/**

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

@@ -13,7 +13,6 @@ import java.io.IOException;
 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;
@@ -44,6 +43,7 @@ import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
@@ -98,7 +98,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			settings.setUnionOntModelSelector(ModelAccess.on(ctx).getOntModelSelector());
 			
 		    ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
-		    Path homeDir = Paths.get(props.getProperty("vitro.home"));
+		    Path homeDir = ApplicationUtils.instance().getHomeDirectory().getPath();
 			settings.setDisplayModel(ModelAccess.on(ctx).getOntModel(DISPLAY));
 			OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
 			settings.setOldTBoxModel(oldTBoxModel);
@@ -202,8 +202,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 	 * Put the paths for the directories and files into the settings object.
 	 */
 	private void putReportingPathsIntoSettings(ServletContext ctx, UpdateSettings settings) throws IOException {
-		ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
-		Path homeDir = Paths.get(props.getProperty("vitro.home"));
+	    Path homeDir = ApplicationUtils.instance().getHomeDirectory().getPath();
 		
 		Path dataDir = createDirectory(homeDir, "upgrade", "knowledgeBase");
 		settings.setDataDir(dataDir.toString());

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/rdfsetup/RDFSetup.java

@@ -1,113 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup;
-
-import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService.CONFIGURATION;
-import static edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.sparql.ContentDataStructuresProviderSPARQL.PROPERTY_SPARQL_ENDPOINT_URI;
-import static edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.tdb.ContentDataStructuresProviderTDB.PROPERTY_CONTENT_TDB_PATH;
-
-import javax.servlet.ServletContext;
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.ontology.OntDocumentManager;
-
-import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
-import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.BasicDataStructuresProvider;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.ConfigurationDataStructuresProvider;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.ContentDataStructuresProvider;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.sdb.ContentDataStructuresProviderSDB;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.sparql.ContentDataStructuresProviderSPARQL;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.tdb.ConfigurationDataStructuresProviderTDB;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.impl.tdb.ContentDataStructuresProviderTDB;
-
-/**
- * Create the RDFServiceFactories and ModelMakers for the application to use.
- */
-public class RDFSetup implements ServletContextListener {
-	private static final Log log = LogFactory.getLog(RDFSetup.class);
-
-	private ServletContext ctx;
-	private ConfigurationProperties configProps;
-
-	private ContentDataStructuresProvider contentProvider;
-	private ConfigurationDataStructuresProvider configurationProvider;
-	private BasicDataStructuresProvider provider;
-
-	@Override
-	public void contextInitialized(ServletContextEvent sce) {
-		this.ctx = sce.getServletContext();
-		this.configProps = ConfigurationProperties.getBean(ctx);
-
-		configureJena();
-
-		createProviders();
-
-		RDFServiceUtils.setRDFServiceFactory(ctx,
-				contentProvider.getRDFServiceFactory());
-		RDFServiceUtils.setRDFServiceFactory(ctx,
-				configurationProvider.getRDFServiceFactory(), CONFIGURATION);
-
-		ModelAccess.setDataStructuresProvider(provider);
-	}
-
-	private void configureJena() {
-		// we do not want to fetch imports when we wrap Models in OntModels
-		OntDocumentManager.getInstance().setProcessImports(false);
-	}
-
-	/**
-	 * For now, these steps are hard-coded. They should be driven by a
-	 * configuration file.
-	 */
-	private void createProviders() {
-		if (isSparqlEndpointContentConfigured()) {
-			contentProvider = new ContentDataStructuresProviderSPARQL(ctx, this);
-		} else if (isTdbConfigured()) {
-			contentProvider = new ContentDataStructuresProviderTDB(ctx, this);
-		} else {
-			contentProvider = new ContentDataStructuresProviderSDB(ctx, this);
-		}
-
-		configurationProvider = new ConfigurationDataStructuresProviderTDB(ctx,
-				this);
-
-		provider = new BasicDataStructuresProvider(contentProvider,
-				configurationProvider);
-	}
-
-	private boolean isSparqlEndpointContentConfigured() {
-		return StringUtils.isNotBlank(configProps
-				.getProperty(PROPERTY_SPARQL_ENDPOINT_URI));
-	}
-
-	private boolean isTdbConfigured() {
-		return StringUtils.isNotBlank(configProps
-				.getProperty(PROPERTY_CONTENT_TDB_PATH));
-	}
-
-	@Override
-	public void contextDestroyed(ServletContextEvent sce) {
-		if (contentProvider != null) {
-			try {
-				contentProvider.close();
-			} catch (Exception e) {
-				log.error("Problem when closing content provider", e);
-			}
-		}
-		if (configurationProvider != null) {
-			try {
-				configurationProvider.close();
-			} catch (Exception e) {
-				log.error("Problem when closing configuration provider", e);
-			}
-		}
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/developer/DeveloperSettings.java

@@ -5,7 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.utils.developer;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
-import java.nio.file.Paths;
+import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.EnumMap;
 import java.util.HashMap;
@@ -20,7 +20,7 @@ import javax.servlet.ServletContextListener;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
@@ -194,12 +194,10 @@ public class DeveloperSettings {
 		public void contextInitialized(ServletContextEvent sce) {
 			ServletContext ctx = sce.getServletContext();
 			StartupStatus ss = StartupStatus.getBean(ctx);
-			ConfigurationProperties props = ConfigurationProperties
-					.getBean(ctx);
 			DeveloperSettings devSettings = DeveloperSettings.getInstance();
 
-			String home = props.getProperty("vitro.home");
-			File dsFile = Paths.get(home, "developer.properties").toFile();
+			Path homeDir = ApplicationUtils.instance().getHomeDirectory().getPath();
+			File dsFile = homeDir.resolve("developer.properties").toFile();
 
 			try (FileReader reader = new FileReader(dsFile)) {
 				Properties dsProps = new Properties();

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/developer/loggers/StackTraceUtility.java

@@ -124,8 +124,9 @@ public class StackTraceUtility {
 		StringBuilder sb = new StringBuilder();
 		if (requested) {
 			for (StackTraceElement ste : stackTrace) {
-				sb.append(String.format("   line %4d, %s \n",
-						ste.getLineNumber(), ste.getClassName()));
+				sb.append(String.format("   %s.%s(%s:%d) \n",
+						ste.getClassName(), ste.getMethodName(),
+						ste.getFileName(), ste.getLineNumber()));
 			}
 			sb.append("   ...\n");
 		}

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/modules/ApplicationStub.java

@@ -7,10 +7,13 @@ import java.lang.reflect.Field;
 import javax.servlet.ServletContext;
 
 import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
+import edu.cornell.mannlib.vitro.webapp.application.VitroHomeDirectory;
 import edu.cornell.mannlib.vitro.webapp.modules.Application;
 import edu.cornell.mannlib.vitro.webapp.modules.fileStorage.FileStorage;
 import edu.cornell.mannlib.vitro.webapp.modules.imageProcessor.ImageProcessor;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine;
+import edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ConfigurationTripleSource;
+import edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ContentTripleSource;
 
 /**
  * TODO
@@ -61,6 +64,12 @@ public class ApplicationStub implements Application {
 	// Un-implemented methods
 	// ----------------------------------------------------------------------
 
+	@Override
+	public VitroHomeDirectory getHomeDirectory() {
+		throw new RuntimeException(
+				"ApplicationStub.getHomeDirectory() not implemented.");
+	}
+
 	@Override
 	public ImageProcessor getImageProcessor() {
 		throw new RuntimeException(
@@ -74,4 +83,22 @@ public class ApplicationStub implements Application {
 				"ApplicationStub.getFileStorage() not implemented.");
 	}
 
+	@Override
+	public void shutdown() {
+		throw new RuntimeException(
+				"ApplicationStub.shutdown() not implemented.");
+	}
+
+	@Override
+	public ContentTripleSource getContentTripleSource() {
+		throw new RuntimeException(
+				"ApplicationStub.getContentTripleSource() not implemented.");
+	}
+
+	@Override
+	public ConfigurationTripleSource getConfigurationTripleSource() {
+		throw new RuntimeException(
+				"ApplicationStub.getConfigurationTripleSource() not implemented.");
+	}
+
 }

webapp/web/WEB-INF/resources/startup_listeners.txt

@@ -7,6 +7,8 @@
 
 edu.cornell.mannlib.vitro.webapp.servlet.setup.JvmSmokeTests
 
+edu.cornell.mannlib.vitro.webapp.application.ApplicationSetup
+
 edu.cornell.mannlib.vitro.webapp.config.ConfigurationPropertiesSetup
 
 edu.cornell.mannlib.vitro.webapp.config.ConfigurationPropertiesSmokeTests
@@ -16,15 +18,12 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.GuardAgainstUnmigratedRDB
 
 edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings$Setup
 
-edu.cornell.mannlib.vitro.webapp.application.ApplicationImpl$Setup
+edu.cornell.mannlib.vitro.webapp.application.ApplicationImpl$ComponentsSetup
 
 edu.cornell.mannlib.vitro.webapp.config.RevisionInfoSetup
 
 edu.cornell.mannlib.vitro.webapp.email.FreemarkerEmailFactory$Setup
 
-# In 1.8, this should replace JenaPersistentDataSourceSetup, RDFServiceSetup, and maybe more.
-edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.RDFSetup
-
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ConfigurationModelsSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ContentModelSetup