NIHVIVO-15 Merge three configuration properties files into one. Create ConfigProperties as a central mechanism for reading configuration properties.

webapp/build.xml

@@ -161,9 +161,7 @@
 
       <!-- copy properties files -->        
       <copy todir="${webapp.build}/WEB-INF/classes">
-        <fileset dir="${webapp.dir}/config" includes="connection.properties" />
+        <fileset dir="${webapp.dir}/config" includes="deploy.properties" />
-        <fileset file="${webapp.dir}/config/upload.properties" />
-        <fileset file="${webapp.dir}/config/LuceneSetup.properties" />
       </copy>
      
       <copy todir="${webapp.build}/WEB-INF/tlds">
@@ -208,6 +206,9 @@
           	<exclude name="servlet-api.jar"/>
           </fileset>
         </copy>
+
+		<copy file="${webapp.dir}/context.xml"
+              tofile="${webapp.build}/META-INF/context.xml" />
     </target>
 
     <!-- ==================== Local Modifications ============================ -->

webapp/config/default.log4j.properties

@@ -19,10 +19,11 @@ log4j.appender.AllAppender.MaxBackupIndex=10
 log4j.appender.AllAppender.layout=org.apache.log4j.PatternLayout 
 log4j.appender.AllAppender.layout.ConversionPattern=%p %t %c - %m%n 
 
-log4j.logger.org.apache.catalina=INFO, AllAppender
+log4j.logger.org.apache.catalina=INFO
-log4j.logger.org.diretwebremoting=ERROR, AllAppender
+log4j.logger.org.diretwebremoting=ERROR
 
-#log4j.logger.edu.cornell.mannlib.vitro.webapp.auth=INFO, AllAppender
+log4j.logger.edu.cornell.mannlib.vitro.webapp.ConfigurationProperties=INFO
+#log4j.logger.edu.cornell.mannlib.vitro.webapp.auth=INFO
 
 #### setup a debugging logger
 log4j.appender.DebuggingAppender=org.apache.log4j.FileAppender

webapp/config/example.LuceneSetup.properties

@@ -1,11 +0,0 @@
-#this is an example of what needs to be in this 
-#file to setup the lucene index directory
-#
-# The default location is /usr/local/lucene/vitrodefault
-
-#You could hard code the location like this:
-#LuceneSetup.indexDir=/usr/local/lucene/example
-
-#this line will be setup by ant to work for clones
-#if you hardcode the dir, this line should be commented out
-LuceneSetup.indexDir=${luceneIndexDir}

webapp/config/example.connection.properties

@@ -1,80 +0,0 @@
-################################################################################
-# DataSource properties file
-################################################################################
-
-######################### DataSource Properties ################################
-
-VitroConnection.DataSource.url=jdbc:mysql://localhost/vitro
-VitroConnection.DataSource.username=vitroweb
-VitroConnection.DataSource.password=vitrovitro
-
-####################### Other Important Properties #############################
-
-# CHANGE the following property unless you're using Cornell's VIVO ontology
-Vitro.defaultNamespace=http://vivo.library.cornell.edu/ns/0.1#
-
-# Uncomment this next line and specify an SMTP host to activate the Contact Us form
-#Vitro.smtpHost=
-
-################################################################################
-
-
-
-
-
-
-
-
-
-
-
-
-
-# maximum number of connections to the db server
-# This must not be greater than the mysql max_connection parameter.
-# defaults to 40
-#VitroConnection.DataSource.MaxActive=40
-
-# maximum number of connections to the db server to keep
-# around when nothing is happening.
-# defaults to 10
-#VitroConnection.DataSource.MaxIdle=10
-
-# Time to wait in msec for a result from the sql server
-# defaults to 10000 
-#VitroConnection.DataSource.MaxWait=10000
-
-# query to use to test to see if a connection to the db server is live.
-# defaults to SELECT 1
-#VitroConnection.DataSource.ValidationQuery=SELECT 1
-
-# should the connection pool test the connections it gets from the pool?
-#defaults to true
-#VitroConnection.DataSource.TestOnBorrow=true
-
-# should the connection pool test connections it puts back in pool?
-#defaults to true
-#VitroConnection.DataSource.TestOnReturn=true
-
-# Nnumber of milliseconds to sleep between runs of the idle object
-# evictor thread. When non-positive, no idle object evictor thread will
-# be run. defaults to 30min
-#VitroConnection.DataSource.TimeBetweenEvictions=
-
-# The number of objects to examine during each
-# run of the idle object evictor thread (if any).
-# defaults to 3
-#VitroConnection.DataSource.TestsPerEviction=3
-
-# The minimum amount of time
-# an object may sit idle in the pool before it is eligable for eviction
-# by the idle object evictor (if any).
-# defaults to 30min
-#VitroConnection.DataSource.MinEvictionIdleTime=
-
-################################################ # other notes:
-# The file checked into source control is example.connection.properties so
-# that if you have a connection.properties on your machine it will not be
-# under source control.  This is useful so that your customizations for your
-# database setup are less likely to be checked into source control and then
-# overwrite other folks' customizations.

webapp/config/example.deploy.properties

@@ -0,0 +1,48 @@
+# -----------------------------------------------------------------------------
+#
+# VIVO deployment properties
+#
+# This file is provided as example.deploy.properties.
+#
+# Save a copy of this file as deploy.properties, and edit the properties as 
+# needed for your deployment.
+#
+# -----------------------------------------------------------------------------
+
+#
+# The location where the VIVO application will store uploaded files 
+# (usually images). You should arrange for these files to be backed up in some
+# way.
+#
+UploadImagesServlet.sourceDirName = /usr/local/vivo/data/uploads
+
+#
+# The location where the VIVO application will create its Lucene search 
+# index. 
+#
+LuceneSetup.indexDir = /usr/local/vivo/data/luceneIndex
+
+# 
+# This namespace will be used when generating URIs for objects created in the 
+# editor. Change it to reflect your own domain. For example, Cornell's 
+# namespace is http://vivo.cornell.edu/individual/
+#
+# Note: it is essential that this namespace end with a trailing slash.
+#
+Vitro.defaultNamespace = http://vitro.mydomain.edu/individual/
+
+#
+# SMTP host which the "Contact Us" form can use to send mail. If this is left 
+# empty, the "Contact Us" form will be disabled.
+#
+#Vitro.smtpHost =
+
+#
+# The basic parameters for a MySQL database connection. Change the end of the 
+# URL to reflect your database name (if it is not "vitro"). Change the username 
+# and password to match the authorized user you created in MySQL.
+#
+VitroConnection.DataSource.url = jdbc:mysql://localhost/vitro
+VitroConnection.DataSource.username = vitroweb
+VitroConnection.DataSource.password = vitrovitro
+

webapp/config/example.upload.properties

@@ -1,26 +0,0 @@
-# The UploadImagesServlet will upload the images to a directory
-# that is under tomcat and serve them from there.
-# This causes a problem when the tomcat/webapps dir is deleted
-# or deployed because you will lose all the images that the
-# curators have uploaded. We deal with this by copying
-# the files to another directory, one that is under version control.
-
-# This property indicates which non-tomcat directory to save the images in.
-# ${uploadDir} is defined in the main build.xml via the following statements:
-#
-# <!-- defined in globalbuild.properties -->
-# <property name="source.dir" value="{source.home}"/>
-# <property name="uploadDir" value="{source.dir}/webapp/web" />
-#
-# But, this value will be replaced by the Vitro/clones/build.xml
-# to point to the clones/{clone}/modifications directory based on the following
-# <property file="./config/globalbuild.properties"/>
-# <property name="source.dir" value="{source.home}"/>
-# <property name="uploadDir" value="${source.dir}/clones/${clone}/modifications"/>
-#
-# The UploadImagesServlet.getSourceDirName() method then looks at this parameter
-# in the upload.properties file, which file is stuck by the clones/build.xml file
-# into the clone's modifications/WEB-INF/classes directory:
-UploadImagesServlet.sourceDirName=${uploadDir}
-
-

webapp/config/web.xml

@@ -17,12 +17,13 @@
   <env-entry>
     <env-entry-name>jdbc/vitro/connectionType</env-entry-name>
     <!--
-           				How to get a DataSource, Valid valies:
+    How to get a DataSource, Valid values:
-                        SERVER_XML_POOL gets a named DataSource connection from the
+        SERVER_XML_POOL gets a named DataSource connection from the JNDI context, 
-                        JNDI context, most likely that was set up tomcat/conf/server.xml
+                most likely that was set up tomcat/conf/server.xml
-                        PROPERTIES_FILE_POOL makes a DataSource using properties from
+        PROPERTIES_FILE_POOL makes a DataSource using properties from a file that
-                        a file in the classpath at /beans/connection.properties
+                is pointed to by the JNDI name "java:comp/env/path.configuration"
-           -->
+                (set in the Tomcat context).
+    -->
     <!--            <env-entry-value>SERVER_XML_POOL</env-entry-value> -->
     <env-entry-type>java.lang.String</env-entry-type>
     <env-entry-value>PROPERTIES_FILE_POOL</env-entry-value>

webapp/context.xml

@@ -0,0 +1,14 @@
+<Context override="true">
+    <!--
+        Vitro will interpret this as either a file path or a resource path. So,
+        if a simple resource path is used, such as "deploy.properties", Vitro 
+        will find the file at: 
+            ${Tomcat}/webapps/vitro/WEB-INF/classes/deploy.properties
+        For an external file, specify a full file path, like
+            "/usr/local/vitro/deploy.properties".   
+    -->
+    <Environment type="java.lang.String" override="false" 
+        name="path.configuration" 
+        value="deploy.properties"
+        />
+</Context>

webapp/src/edu/cornell/mannlib/vitro/webapp/ConfigurationProperties.java

@@ -0,0 +1,144 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.naming.Context;
+import javax.naming.InitialContext;
+import javax.naming.NamingException;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Loads the configuration properties from a properties file. The path to the
+ * file is specified an an Environment name in the Context, like this:
+ * 
+ * <pre>
+ * &lt;Context override="true">
+ *     &lt;Environment name="path.configuration" 
+ *         value="/wherever/the/file/lives/deploy.properties"
+ *         type="java.lang.String" 
+ *         override="false" />
+ * &lt;/Context>
+ * </pre>
+ * 
+ * This initializer will look for a file at this path. If it does not find one,
+ * it will look for a resource at this path. So, one might reasonable set this
+ * to a value like <code>/usr/local/vitro/stuff/deploy.properties</code> for a
+ * file, or like <code>deploy.properties</code> for a resource in the classpath.
+ * 
+ * @author jeb228
+ */
+public class ConfigurationProperties {
+	private static final Logger LOG = Logger
+			.getLogger(ConfigurationProperties.class);
+	
+	/**
+	 * The name of the JNDI environment mapping for the path to the
+	 * configuration file (or resource).
+	 */
+	private static final String PATH_CONFIGURATION = "path.configuration";
+	private static volatile Map<String, String> theMap;
+
+	static {
+		try {
+			// Obtain our environment naming context
+			Context initCtx = new InitialContext();
+			Context envCtx = (Context) initCtx.lookup("java:comp/env");
+
+			// Get the name of the configuration properties file.
+			String configPath = (String) envCtx.lookup(PATH_CONFIGURATION);
+			if (configPath == null) {
+				throw new IllegalStateException(
+						"Could not find a JNDI Environment naming for '"
+								+ PATH_CONFIGURATION + "'.");
+			}
+
+			InputStream inStream = null;
+			// Try to find this as a file.
+			File file = new File(configPath);
+			try {
+				inStream = new FileInputStream(file);
+			} catch (FileNotFoundException e) {
+				inStream = null;
+			}
+			
+			// If no file, try to find it as a resource.
+			if (inStream == null) {
+				inStream = ConfigurationProperties.class.getClassLoader()
+						.getResourceAsStream(configPath);
+			}
+			
+			// If neither file nor resource, give up.
+			if (inStream == null) {
+				throw new IllegalArgumentException(
+						"Failed to find a configuration properties file at '"
+								+ file.getAbsolutePath()
+								+ "', or a resource at '" + configPath + "'");
+			}
+
+			// Load a properties object - it will handle the syntax of the file.
+			Properties props = new Properties();
+			try {
+				props.load(inStream);
+			} catch (IOException e) {
+				throw new IllegalStateException("Problem while reading the "
+						+ "configuration properties file at '" + configPath
+						+ "'", e);
+			}
+
+			// It's awkward to copy from Properties to a Map.
+			Map<String, String> newMap = new HashMap<String, String>();
+			for (Enumeration<?> keys = props.keys(); keys.hasMoreElements();) {
+				String key = (String) keys.nextElement();
+				newMap.put(key, props.getProperty(key));
+			}
+			
+			LOG.info("Configuration properties are: " + newMap);
+
+			// Save an unmodifiable version of the Map
+			theMap = Collections.unmodifiableMap(newMap);
+		} catch (NamingException e) {
+			throw new IllegalStateException(e);
+		}
+
+	}
+
+	/**
+	 * Get an unmodifiable copy of the map of configuration properties.
+	 */
+	public static Map<String, String> getMap() {
+		return theMap;
+	}
+
+	/**
+	 * Get the value of the specified property, or <code>null</code> if the
+	 * property has not been assigned a value.
+	 */
+	public static String getProperty(String key) {
+		return theMap.get(key);
+	}
+
+	/**
+	 * Get the value of the specified property, or use the default value if the
+	 * property has not been assigned a value.
+	 */
+	public static String getProperty(String key, String defaultValue) {
+		String value = theMap.get(key);
+		if (value == null) {
+			return defaultValue;
+		} else {
+			return value;
+		}
+	}
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/CommentsController.java

@@ -33,7 +33,8 @@ public class CommentsController extends VitroHttpServlet{
             if (!ContactMailServlet.isSmtpHostConfigured()) {
                 request.setAttribute("title", "Comments and Feedback Form");
                 request.setAttribute("bodyJsp", "/contact_err.jsp");// <<< this is where the body gets set
-                request.setAttribute("ERR","This application has not yet been configured to send mail -- smtp host has not been specified in connection.properties");
+                request.setAttribute("ERR","This application has not yet been configured to send mail -- " +
+                		"smtp host has not been specified in the configuration properties file.");
                 RequestDispatcher errd = request.getRequestDispatcher(Controllers.BASIC_JSP);
                 errd.forward(request, response);
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/ContactMailServlet.java

@@ -2,12 +2,8 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.FileWriter;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.PrintWriter;
 import java.util.Calendar;
 import java.util.Date;
@@ -22,31 +18,29 @@ import javax.mail.internet.AddressException;
 import javax.mail.internet.InternetAddress;
 import javax.mail.internet.MimeMessage;
 import javax.servlet.ServletConfig;
-import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.apache.log4j.Logger;
 
-import com.hp.hpl.jena.ontology.OntModel;
 
-import edu.cornell.mannlib.vitro.webapp.auth.policy.JenaNetidPolicy.ContextSetup;
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
-import edu.cornell.mannlib.vitro.webapp.controller.BrowseController.RebuildGroupCacheThread;
 
 public class ContactMailServlet extends VitroHttpServlet {
+	private static final Logger LOG = Logger.getLogger(ContactMailServlet.class);
+	
     public static HttpServletRequest request;
     public static HttpServletRequest response;
-    protected final static String CONNECTION_PROP_LOCATION = "/WEB-INF/classes/connection.properties";
     private static String smtpHost = null;
     private static final Log log = LogFactory.getLog(ContactMailServlet.class.getName());
 
     public void init(ServletConfig servletConfig) throws javax.servlet.ServletException {
         super.init(servletConfig);
-        ServletContext sContext = servletConfig.getServletContext();
+        smtpHost = getSmtpHostFromProperties();
-        smtpHost = getSmtpHostFromPropertiesFile(sContext.getRealPath(CONNECTION_PROP_LOCATION));
     }
     
     public static boolean isSmtpHostConfigured() {
@@ -56,43 +50,15 @@ public class ContactMailServlet extends VitroHttpServlet {
         return true;
     }
 
-    private String getSmtpHostFromPropertiesFile(final String filename){
+	private String getSmtpHostFromProperties() {
-
+		String host = ConfigurationProperties.getProperty("Vitro.smtpHost");
-        if (filename == null || filename.length() <= 0) {
+		if (host != null && !host.equals("")) {
-            throw new Error(
+			LOG.info("Found Vitro.smtpHost value of " + host);
-                    "To establish the Contact Us mail capability you must  "
+		} else {
-                    + "specify an SMTP server host name in the "
+			System.out.println("No Vitro.smtpHost specified");
-                    + "connection.properties file along with the "
+		}
-                    + "database connection parameters.");
+		return (host != null && host.length() > 0) ? host : null;
-                    		
+	}
-        }
-
-        File propF = new File(filename );
-        InputStream is;
-        try {
-            is = new FileInputStream(propF);
-        } catch (FileNotFoundException e) {
-            log.error("Could not load file "+filename);
-            throw new Error("Could not load file " + filename
-                    + '\n' + e.getMessage());
-        }
-
-        Properties dbProps = new Properties();
-        try {
-            dbProps.load(is);
-            String host = dbProps.getProperty("Vitro.smtpHost");
-            /* doesn't display in catalina.out, not sure why
-if (host!=null && !host.equals("")){
-    System.out.println("Found Vitro.smtpHost value of "+host+" in "+filename);
-} else {
-    System.out.println("No Vitro.smtpHost specified in "+filename);
-}           */
-            return (host != null && host.length()>0) ? host : null;
-        } catch (IOException e) {
-            throw new Error("Could not load any properties from file " + filename + '\n'
-                    + e.getMessage());
-        }
-    }
     
     public void doGet( HttpServletRequest request, HttpServletResponse response )
         throws ServletException, IOException {
@@ -104,7 +70,8 @@ if (host!=null && !host.equals("")){
         String status = null; // holds the error status
         
         if (smtpHost==null || smtpHost.equals("")){
-            status = "This application has not yet been configured to send mail -- smtp host has not been identified in connection.properties";
+            status = "This application has not yet been configured to send mail " +
+            		"-- smtp host has not been identified in the Configuration Properties file.";
             response.sendRedirect( "test?bodyJsp=" + errpage + "&ERR=" + status + "&home=" + portal.getPortalId() );
             return;
         }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/FedoraDatastreamController.java

@@ -4,7 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.controller;
 
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.MalformedURLException;
@@ -31,12 +30,11 @@ import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
 
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.controller.edit.N3MultiPartUpload;
-import edu.cornell.mannlib.vitro.webapp.controller.edit.N3MultiPartUpload.PostUpload;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
@@ -54,7 +52,6 @@ import fedora.server.types.gen.Datastream;
  */
 public class FedoraDatastreamController extends VitroHttpServlet implements Constants{
     private static String FEDORA_PROPERTIES = "/WEB-INF/fedora.properties";
-    private static String FEDORA_FOXML_1_1 = "info:fedora/fedora-system:FOXML-1.1";
     private static String DEFAULT_DSID = "DS1";
     
     private String fedoraUrl = null;
@@ -71,7 +68,6 @@ public class FedoraDatastreamController extends VitroHttpServlet implements Cons
     private static String fileUriPrefix = DEFAULT_FILE_URI_PREFIX;
     private static String baseDirectoryForFiles = DEFAULT_BASE_DIR;
     private static int maxFileSize = DEFAULT_MAX_SIZE;
-    private static PostUpload postUpload = null;
     
     /**
      * The get will present a form to the user. 
@@ -394,59 +390,23 @@ public class FedoraDatastreamController extends VitroHttpServlet implements Cons
         }
     }
     
-    public void init() throws ServletException {
+	public void init() throws ServletException {
-        super.init();
+		super.init();
-        String realPropFile = getServletContext().getRealPath(
-                N3MultiPartUpload.FILE_UPLOAD_PROP_FILE);
-        File propF = new File(realPropFile);
-        if (propF != null && propF.exists() && propF.isFile()) {
-            if (!propF.canRead()) {
-                log.error("There is a file upload configuration file at "
-                        + realPropFile + " but is is not readable");
-                return;
-            }
 
-            InputStream is;
+		fileUriPrefix = ConfigurationProperties.getProperty(
-            try {
+				"n3.defaultUriPrefix", DEFAULT_FILE_URI_PREFIX);
-                is = new FileInputStream(propF);
+		baseDirectoryForFiles = ConfigurationProperties.getProperty(
-            } catch (FileNotFoundException e) {
+				"n3.baseDirectoryForFiles", DEFAULT_BASE_DIR);
-                log.error("Could not load file " + realPropFile, e);
-                return;
-            }
 
-            Properties props = new Properties();
+		String maxSize = ConfigurationProperties.getProperty("n3.maxSize", Long
-            try {
+				.toString(DEFAULT_MAX_SIZE));
-                props.load(is);
+		try {
-                is.close();
+			maxFileSize = Integer.parseInt(maxSize);
-            } catch (IOException e) {
+		} catch (NumberFormatException nfe) {
-                log.error(
+			log.error(nfe);
-                        "could not load properties from file " + realPropFile,
+			maxFileSize = DEFAULT_MAX_SIZE;
-                        e);
+		}
-            }
+	}
-            fileUriPrefix = props.getProperty("defaultUriPrefix",
-                    DEFAULT_FILE_URI_PREFIX);
-            baseDirectoryForFiles = props.getProperty("baseDirectoryForFiles",
-                    DEFAULT_BASE_DIR);
-
-//            String postUploadProcess = props.getProperty("postUploadProcess");
-//            System.out.println("Attempting to load postUploadProcess "
-//                    + postUploadProcess);
-//            postUpload = getPostUpload(postUploadProcess);
-
-            String maxSize = props.getProperty("maxSize", Long
-                    .toString(DEFAULT_MAX_SIZE));
-            try {
-                maxFileSize = Integer.parseInt(maxSize);
-            } catch (NumberFormatException nfe) {
-                log.error(nfe);
-                maxFileSize = DEFAULT_MAX_SIZE;
-            }
-        } else {
-            System.out
-                    .println("No properties file found for N3MultiPartUpload at "
-                            + realPropFile);
-        }
-    }
     
     private void setup(OntModel model, ServletContext context) {
         this.configurationStatus = "";

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/N3MultiPartUpload.java

@@ -9,8 +9,6 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
@@ -45,7 +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.controller.FedoraDatastreamController;
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
@@ -96,44 +94,18 @@ public class N3MultiPartUpload extends VitroHttpServlet {
     @Override
     public void init() throws ServletException {
         super.init();
-        String realPropFile = getServletContext().getRealPath(
-                FILE_UPLOAD_PROP_FILE);
-        File propF = new File(realPropFile);
-        if (propF != null && propF.exists() && propF.isFile()) {
-            if (!propF.canRead()) {
-                log.error("There is a file upload configuration file at "
-                        + realPropFile + " but is is not readable");
-                return;
-            }
         
-            InputStream is;
+            fileUriPrefix = ConfigurationProperties.getProperty("n3.defaultUriPrefix",
-            try {
-                is = new FileInputStream(propF);
-            } catch (FileNotFoundException e) {
-                log.error("Could not load file " + realPropFile, e);
-                return;
-            }
-
-            Properties props = new Properties();
-            try {
-                props.load(is);
-                is.close();
-            } catch (IOException e) {
-                log.error(
-                        "could not load properties from file " + realPropFile,
-                        e);
-            }
-            fileUriPrefix = props.getProperty("defaultUriPrefix",
                     DEFAULT_FILE_URI_PREFIX);
-            baseDirectoryForFiles = props.getProperty("baseDirectoryForFiles",
+            baseDirectoryForFiles = ConfigurationProperties.getProperty("n3.baseDirectoryForFiles",
                     DEFAULT_BASE_DIR);
 
-            String postUploadProcess = props.getProperty("postUploadProcess");
+            String postUploadProcess = ConfigurationProperties.getProperty("n3.postUploadProcess");
             System.out.println("Attempting to load postUploadProcess "
                     + postUploadProcess);
             postUpload = getPostUpload(postUploadProcess);
 
-            String maxSize = props.getProperty("maxSize", Long
+            String maxSize = ConfigurationProperties.getProperty("n3.maxSize", Long
                     .toString(DEFAULT_MAX_SIZE));
             try {
                 maxFileSize = Integer.parseInt(maxSize);
@@ -141,11 +113,6 @@ public class N3MultiPartUpload extends VitroHttpServlet {
                 log.error(nfe);
                 maxFileSize = DEFAULT_MAX_SIZE;
             }
-        } else {
-            System.out
-                    .println("No properties file found for N3MultiPartUpload at "
-                            + realPropFile);
-        }
     }
 
     @Override
@@ -624,8 +591,6 @@ public class N3MultiPartUpload extends VitroHttpServlet {
 
     static Random random = new Random();
 
-    public static final String FILE_UPLOAD_PROP_FILE = "/WEB-INF/N3MultiPartUpload.properties";
-
     private static Property FILE_LOCATION_PROP = ResourceFactory
             .createProperty(VitroVocabulary.FILE_LOCATION);
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/UploadImagesServlet.java

@@ -31,6 +31,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import edu.cornell.mannlib.vedit.beans.LoginFormBean;
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@@ -42,10 +43,6 @@ public class UploadImagesServlet extends VitroHttpServlet {
     private static final Log log = LogFactory.getLog(UploadImagesServlet.class.getName());
     private String sourceDirName;  // all uploaded images are copied to the source directory, not just the application context
     private String websiteDirName; // the application context
-    private String webAppName;     // the name of the application context (e.g., vivo, usaep)
-
-    private static String UPLOAD_SERVLET_PROPERTIES = "/upload.properties";
-    private static String UPLOAD_SERVLET_PROPERTIES_WIN="\\upload.properties";
 
     /**
      * Notice that init() gets called the first time the servlet is requested,
@@ -57,15 +54,6 @@ public class UploadImagesServlet extends VitroHttpServlet {
         // something like: /usr/local/tomcat/webapps/vivo
         websiteDirName = getServletContext().getRealPath("");
 
-        //get the last directory, which should be the webapp name.
-        String[] dirs = new String[0];
-        if (File.separator.equals("\\")) {
-            dirs =  websiteDirName.split("\\\\");
-        } else {
-            dirs =  websiteDirName.split(File.separator);
-        }
-        webAppName = dirs[dirs.length-1];
-
         // something like: /usr/local/src/Vitro/dream/common/web
         try{
             sourceDirName = getSourceDirName();
@@ -546,24 +534,9 @@ public class UploadImagesServlet extends VitroHttpServlet {
      * @throws IOException
      */
     private  String getSourceDirName() throws IOException{
-        Properties props = new Properties();
+        String dirName = ConfigurationProperties.getProperty("UploadImagesServlet.sourceDirName");
-        InputStream raw = this.getClass().getResourceAsStream( UPLOAD_SERVLET_PROPERTIES );
-        if (raw == null) {
-            raw = this.getClass().getResourceAsStream( UPLOAD_SERVLET_PROPERTIES_WIN );
-            if (raw == null)
-                throw new IOException("UploadImagesServlet.getSourceDirName()" +
-                        " Failed to find resource: " + UPLOAD_SERVLET_PROPERTIES );
-        }
-        try{
-            props.load( raw );
-        } catch (Exception ex){
-            throw new IOException("unable to load upload.properties file: " + ex.getMessage());
-        } finally {
-            raw.close();
-        }
-        String dirName = props.getProperty("UploadImagesServlet.sourceDirName");
         if( dirName == null ) {
-            log.error("getSourceDirName(): property sourceDirName not defined in upload.properties");
+            log.error("getSourceDirName(): property sourceDirName not defined in configuration properties");
         } else {
             File dir = new File(dirName);
             if(!dir.exists()) {

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/LuceneSetup.java

@@ -4,11 +4,9 @@ package edu.cornell.mannlib.vitro.webapp.search.lucene;
 
 import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Properties;
 
 import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
@@ -18,6 +16,7 @@ import org.apache.commons.logging.LogFactory;
 import org.apache.lucene.analysis.Analyzer;
 import org.apache.lucene.search.BooleanQuery;
 
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
@@ -55,13 +54,13 @@ public class LuceneSetup implements javax.servlet.ServletContextListener {
         /**
          * Gets run to set up DataSource when the webapp servlet context gets created.
          */
-        @SuppressWarnings({ "static-access", "unchecked" })
+        @SuppressWarnings("unchecked")
         public void contextInitialized(ServletContextEvent sce) {
         	try {
 	            ServletContext context = sce.getServletContext();
 	            log.info("**** Running "+this.getClass().getName()+".contextInitialized()");
 	
-	            indexDir = getIndexDirName(sce.getServletContext());
+	            indexDir = getIndexDirName();
 	            log.info("Directory of full text index: " + indexDir );
 	
 	            setBoolMax();
@@ -135,62 +134,40 @@ public class LuceneSetup implements javax.servlet.ServletContextListener {
             BooleanQuery.setMaxClauseCount(16384);
         }
         
-        /** Directory to store lucene index use when none is specified. */ 
+	/**
-        private String DEFAULT_INDEX_DIR = "/fullTextIndex";
+	 * Gets the name of the directory to store the lucene index in. The
+	 * {@link ConfigurationProperties} should have a property named
+	 * 'LuceneSetup.indexDir' which has the directory to store the lucene index
+	 * for this clone in. If the property is not found, an exception will be
+	 * thrown.
+	 * 
+	 * @return a string that is the directory to store the lucene index.
+	 * @throws IllegalStateException
+	 *             if the property is not found.
+	 * @throws IOException
+	 *             if the directory doesn't exist and we fail to create it.
+	 */
+	private String getIndexDirName()
+			throws IOException {
+		String dirName = ConfigurationProperties
+				.getProperty("LuceneSetup.indexDir");
+		if (dirName == null) {
+			throw new IllegalStateException(
+					"LuceneSetup.indexDir not found in properties file.");
+		}
 
-        /** name of the properties file to look for in the 'resources' */
+		File dir = new File(dirName);
-        private String LUCENE_PROPERTIES = "/LuceneSetup.properties";
+		if (!dir.exists()) {
+			boolean created = dir.mkdir();
+			if (!created) {
+				throw new IOException(
+						"Unable to create Lucene index directory at '" + dir
+								+ "'");
+			}
+		}
 
-        /**
+		return dirName;
-         * Gets the name of the directory to store the lucene index in.
+	}
-         * This is stored in a file named LuceneSetup.properties
-         * which should be on the classpath in the default package.
-         * That file should have a property named 'LuceneSetup.indexDir'
-         * which has the directory to store the lucene index for this
-         * clone in.  If the property file is not found or the 
-         * LuceneSetup.indexDir is not found, then DEFAULT_INDEX_DIR will 
-         * be used.
-         * @param servletContext 
-         * @return a string that is the directory to store the lucene
-         * index.
-         *
-         * @throws IOException
-         */
-        private  String getIndexDirName(ServletContext servletContext) {
-            String dirName = null;
-            
-            // Check if we can get the properties file
-            Properties props = new Properties();
-            InputStream raw = this.getClass().getResourceAsStream( LUCENE_PROPERTIES );
-            if (raw != null){                     
-                try{ 
-                    props.load( raw ); 
-                }catch (Exception ex){
-                    log.info("Could not load properties file " + LUCENE_PROPERTIES);
-                    props = null;
-                }finally { 
-                    try{ raw.close(); } 
-                    catch(Exception ex){} 
-                }
-
-                // Check if we can get the indexDir property from the file
-                if( props != null ){
-                    dirName = props.getProperty("LuceneSetup.indexDir");
-                    if( dirName == null ){
-                        log.info("LuceneSetup.indexDir not found in file " + LUCENE_PROPERTIES + " using default.");                                          
-                    }
-                }
-            }
-            
-            if( dirName == null ){
-                dirName = servletContext.getRealPath(DEFAULT_INDEX_DIR);
-                File dir = new File( dirName);
-                if( !dir.exists() )
-                    dir.mkdir();
-            }
-            
-            return dirName;
-        }
 
     /**
      * Gets the analyzer that will be used when building the indexing
@@ -198,7 +175,6 @@ public class LuceneSetup implements javax.servlet.ServletContextListener {
      *
      * @return
      */
-    @SuppressWarnings("static-access")
     private Analyzer getAnalyzer() {
         return new VitroAnalyzer();
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/LuceneSetupCJK.java

@@ -2,12 +2,11 @@
 
 package edu.cornell.mannlib.vitro.webapp.search.lucene;
 
+import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Properties;
 
 import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
@@ -18,6 +17,7 @@ import org.apache.lucene.analysis.Analyzer;
 import org.apache.lucene.analysis.cjk.CJKAnalyzer;
 import org.apache.lucene.search.BooleanQuery;
 
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
@@ -55,7 +55,7 @@ public class LuceneSetupCJK implements javax.servlet.ServletContextListener {
         /**
          * Gets run to set up DataSource when the webapp servlet context gets created.
          */
-        @SuppressWarnings({ "static-access", "unchecked" })
+        @SuppressWarnings("unchecked")
         public void contextInitialized(ServletContextEvent sce) {
             ServletContext context = sce.getServletContext();
             log.info("**** Running "+this.getClass().getName()+".contextInitialized()");
@@ -130,53 +130,40 @@ public class LuceneSetupCJK implements javax.servlet.ServletContextListener {
             BooleanQuery.setMaxClauseCount(16384);
         }
 
-        /** directory to use when none is specified */
+    	/**
-        private String DEFAULT_INDEX_DIR = "/usr/local/lucene/vitrodefault";
+    	 * Gets the name of the directory to store the lucene index in. The
+    	 * {@link ConfigurationProperties} should have a property named
+    	 * 'LuceneSetup.indexDir' which has the directory to store the lucene index
+    	 * for this clone in. If the property is not found, an exception will be
+    	 * thrown.
+    	 * 
+    	 * @return a string that is the directory to store the lucene index.
+    	 * @throws IllegalStateException
+    	 *             if the property is not found.
+    	 * @throws IOException
+    	 *             if the directory doesn't exist and we fail to create it.
+    	 */
+    	private String getIndexDirName()
+    			throws IOException {
+    		String dirName = ConfigurationProperties
+    				.getProperty("LuceneSetup.indexDir");
+    		if (dirName == null) {
+    			throw new IllegalStateException(
+    					"LuceneSetup.indexDir not found in properties file.");
+    		}
 
-        /** name of the properties file to look for in the 'resources' */
+    		File dir = new File(dirName);
-        private String LUCENE_PROPERTIES = "/LuceneSetup.properties";
+    		if (!dir.exists()) {
+    			boolean created = dir.mkdir();
+    			if (!created) {
+    				throw new IOException(
+    						"Unable to create Lucene index directory at '" + dir
+    								+ "'");
+    			}
+    		}
 
-        /**
+    		return dirName;
-         * Gets the name of the directory to store the lucene index in.
+    	}
-         * This is stored in a file named LuceneSetup.properties
-         * which should be on the classpath in the default package.
-         * That file should have a property named 'LuceneSetup.indexDir'
-         * which has the directory to store the lucene index for this
-         * clone in.  If the property file is not found or the 
-         * LuceneSetup.indexDir is not found, then DEFAULT_INDEX_DIR will 
-         * be used.
-         * @return a string that is the directory to store the lucene
-         * index.
-         *
-         * @throws IOException
-         */
-        private  String getIndexDirName() {
-            Properties props = new Properties();
-            InputStream raw = this.getClass().getResourceAsStream( LUCENE_PROPERTIES );
-            if (raw == null){
-                    log.warn("LuceneSetup.getIndexDirName()" +
-                            " Failed to find resource: " + LUCENE_PROPERTIES +
-                            ". Using default directory " + DEFAULT_INDEX_DIR);
-                    return DEFAULT_INDEX_DIR;
-            }
-
-            try{ props.load( raw ); }
-            catch (Exception ex){
-                log.error("LuceneSetup.getIndexDirName()" +
-                        "unable to load properties: \n" + ex.getMessage() +
-                        "\nUsing default directory " + DEFAULT_INDEX_DIR);
-                return DEFAULT_INDEX_DIR;
-            }
-            finally { try{raw.close();} catch(Exception ex){} }
-
-            String dirName = props.getProperty("LuceneSetup.indexDir");
-            if( dirName == null ){
-                log.error("LuceneSetup.getIndexDir:  " +
-                        "indexDir not found.  Using default directory "+DEFAULT_INDEX_DIR );
-                return DEFAULT_INDEX_DIR;
-            }
-            return dirName;
-        }
 
     /**
      * Gets the analyzer that will be used when building the indexing
@@ -184,7 +171,6 @@ public class LuceneSetupCJK implements javax.servlet.ServletContextListener {
      *
      * @return
      */
-    @SuppressWarnings("static-access")
     private Analyzer getAnalyzer() {
         return new CJKAnalyzer();        
     }

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

@@ -2,29 +2,21 @@
 
 package edu.cornell.mannlib.vitro.webapp.servlet.setup;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
 import java.io.InputStream;
-import java.util.Iterator;
-import java.util.Properties;
 import java.util.Set;
 
 import javax.servlet.ServletContext;
-import javax.servlet.ServletContextEvent;
 
 import org.apache.commons.dbcp.BasicDataSource;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.graph.Graph;
-import com.hp.hpl.jena.ontology.OntModel;
 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.auth.policy.JenaNetidPolicy.ContextSetup;
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDBGraphGenerator;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RegeneratingGraph;
 
@@ -42,8 +34,6 @@ public class JenaDataSourceSetupBase {
     DEFAULT_TESTONRETURN = true,
     DEFAULT_TESTWHILEIDLE = true;
 
-   protected final static String CONNECTION_PROP_LOCATION = "/WEB-INF/classes/connection.properties";
-
    protected static String BASE = "/WEB-INF/ontologies/";
    protected static String USERPATH = BASE+"user/";
    protected static String SYSTEMPATH = BASE+"system/";
@@ -53,73 +43,43 @@ public class JenaDataSourceSetupBase {
    String DB_PASSWD = "jenatest";                          // database password
    String DB =        "MySQL";                             // database type
    String DB_DRIVER_CLASS_NAME = "com.mysql.jdbc.Driver";
-   String JENA_DB_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-2";
+   static final String JENA_DB_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-2";
-   String JENA_AUDIT_MODEL = "http://vitro.mannlib.cornell.edu/ns/db/experimental/audit";
+   static final String JENA_AUDIT_MODEL = "http://vitro.mannlib.cornell.edu/ns/db/experimental/audit";
-   String JENA_INF_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-inf";
+   static final String JENA_INF_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-inf";
-   String JENA_USER_ACCOUNTS_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts";
+   static final String JENA_USER_ACCOUNTS_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts";
-   String JENA_APPLICATION_METADATA_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadata";
+   static final String JENA_APPLICATION_METADATA_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadata";
 
    static final String DEFAULT_DEFAULT_NAMESPACE = "http://vitro.mannlib.cornell.edu/ns/default#";
    
    static String defaultNamespace = DEFAULT_DEFAULT_NAMESPACE; // TODO: improve this
    
    // use OWL models with no reasoning
-   OntModelSpec DB_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
+   static final OntModelSpec DB_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
-   OntModelSpec MEM_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM; 
+   static final OntModelSpec MEM_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM; 
    
    private static final Log log = LogFactory.getLog(JenaDataSourceSetupBase.class.getName());   
    
-   /**
-    * Sets up a Model and DB connection using values from 
-    * a properties file.
-    */
-   public final Model makeDBModelFromPropertiesFile(final String filename) {
-	   return makeDBModelFromPropertiesFile(filename, null, null);
-   }
-   
     /**
     * Sets up a Model and DB connection using values from
     * a properties file.
     */
-   public final Model makeDBModelFromPropertiesFile(final String filename, String jenaDbModelName, OntModelSpec jenaDbOntModelSpec){
+   public final Model makeDBModelFromConfigurationProperties(String jenaDbModelName, OntModelSpec jenaDbOntModelSpec){
+       String dbDriverClassname = ConfigurationProperties.getProperty("VitroConnection.DataSource.driver", DB_DRIVER_CLASS_NAME);
+	   String jdbcUrl = ConfigurationProperties.getProperty("VitroConnection.DataSource.url") + "?useUnicode=yes&characterEncoding=utf8";
+	   String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
+	   String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
+	   BasicDataSource ds = makeBasicDataSource(dbDriverClassname, jdbcUrl, username, password);
 	
-       if (filename == null || filename.length() <= 0) {
+       String dns = ConfigurationProperties.getProperty("Vitro.defaultNamespace");
-           throw new Error(
+       defaultNamespace = (dns != null && dns.length()>0) ? dns : null;
-                   "To establish the DB model you MUST set the "
-                   + "filename to the location of a "
-                   + "connection.properties file with the database connection parameters.");
-       }
        
-       File propF = new File(filename );
+       jenaDbOntModelSpec = (jenaDbOntModelSpec != null) ? jenaDbOntModelSpec : DB_ONT_MODEL_SPEC;
-       InputStream is;
+	   return makeDBModel(ds, jenaDbModelName, jenaDbOntModelSpec);
-       try {
-           is = new FileInputStream(propF);
-       } catch (FileNotFoundException e) {
-           log.error("Could not load file "+filename);
-           throw new Error("Could not load file " + filename
-                   + '\n' + e.getMessage());
-       }
-
-       Properties dbProps = new Properties();
-       try {
-           dbProps.load(is);
-           if (jenaDbModelName == null) {
-        	   String specifiedModelName = dbProps.getProperty("Jena.modelName");
-        	   jenaDbModelName = (specifiedModelName != null) ? specifiedModelName : JENA_DB_MODEL;
-           }
-           jenaDbOntModelSpec = (jenaDbOntModelSpec != null) ? jenaDbOntModelSpec : DB_ONT_MODEL_SPEC;
-           String dns = dbProps.getProperty("Vitro.defaultNamespace");
-           defaultNamespace = (dns != null && dns.length()>0) ? dns : null;
-           return makeDBModelFromProperties(dbProps, jenaDbModelName, jenaDbOntModelSpec);
-       } catch (IOException e) {
-           throw new Error("Could not load properties from file " + filename + '\n'
-                   + e.getMessage());
-       }
    }
 
    protected BasicDataSource makeBasicDataSource(String dbDriverClassname, String jdbcUrl, String username, String password) {
 	   BasicDataSource ds = new BasicDataSource();
-       ds.setDriverClassName( (dbDriverClassname==null) ? DB_DRIVER_CLASS_NAME : dbDriverClassname );
+       ds.setDriverClassName(dbDriverClassname);
        ds.setUrl(jdbcUrl);
        ds.setUsername(username);
        ds.setPassword(password);
@@ -139,14 +99,6 @@ public class JenaDataSourceSetupBase {
            e.printStackTrace();
        }
 
-       //Class.forName(DB_DRIVER_CLASS_NAME);
-       //Create database connection
-       //IDBConnection conn = new DBConnection ( jdbcUrl, username, password, DB );
-       //IDBConnection conn = new DBConnection(ds.getConnection(),DB);
-       //ModelMaker maker = ModelFactory.createModelRDBMaker(conn) ;
-
-       //ReconnectingGraphRDBMaker maker = new ReconnectingGraphRDBMaker(jdbcUrl, username, password, DB, null, ReificationStyle.Convenient);
-
        return ds;
    }
    
@@ -174,15 +126,6 @@ public class JenaDataSourceSetupBase {
        return dbModel;
    }
 
-   private Model makeDBModelFromProperties(Properties dbProps, String jenaDbModelName, OntModelSpec jenaDbOntModelSpec) {
-       String dbDriverClassname = dbProps.getProperty("VitroConnection.DataSource.driver");
-       String jdbcUrl = dbProps.getProperty("VitroConnection.DataSource.url") + "?useUnicode=yes&characterEncoding=utf8";
-       String username = dbProps.getProperty("VitroConnection.DataSource.username");
-       String password = dbProps.getProperty("VitroConnection.DataSource.password");
-       BasicDataSource ds = makeBasicDataSource(dbDriverClassname, jdbcUrl, username, password);
-       return makeDBModel(ds, jenaDbModelName, jenaDbOntModelSpec);
-   }
-   
    public static void readOntologyFilesInPathSet(String path, ServletContext ctx, Model model) {
 	   Set<String> paths = ctx.getResourcePaths(path);
 	   for(String p : paths) {

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

@@ -27,7 +27,7 @@ public class JenaPersistentDBOnlyDataSourceSetup extends JenaDataSourceSetupBase
 		OntModel memModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
 		OntModel dbModel = null;
         try {
-            Model dbPlainModel = makeDBModelFromPropertiesFile(sce.getServletContext().getRealPath(CONNECTION_PROP_LOCATION), JENA_DB_MODEL, DB_ONT_MODEL_SPEC);
+            Model dbPlainModel = makeDBModelFromConfigurationProperties(JENA_DB_MODEL, DB_ONT_MODEL_SPEC);
             dbModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,dbPlainModel);
             boolean isEmpty = true;
             ClosableIterator stmtIt = dbModel.listStatements();
@@ -57,7 +57,7 @@ public class JenaPersistentDBOnlyDataSourceSetup extends JenaDataSourceSetupBase
         } catch (Throwable t) {
 			System.out.println("**** ERROR *****");
             System.out.println("Vitro unable to open Jena database model.");
-			System.out.println("Check that connection.properties has been created WEB-INF/classes, ");
+			System.out.println("Check that the configuration properties file has been created in WEB-INF/classes, ");
 			System.out.println("and that the database connection parameters are accurate. ");
 			System.out.println("****************");
         }
@@ -77,7 +77,7 @@ public class JenaPersistentDBOnlyDataSourceSetup extends JenaDataSourceSetupBase
         
         // default inference graph
         try {
-        	Model infDbPlainModel = makeDBModelFromPropertiesFile(sce.getServletContext().getRealPath(CONNECTION_PROP_LOCATION), JENA_INF_MODEL, DB_ONT_MODEL_SPEC);
+        	Model infDbPlainModel = makeDBModelFromConfigurationProperties(JENA_INF_MODEL, DB_ONT_MODEL_SPEC);
         	OntModel infDbModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,infDbPlainModel);
         	sce.getServletContext().setAttribute("inferenceOntModel",infDbModel);
         } catch (Throwable e) {

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

@@ -27,7 +27,7 @@ public class JenaPersistentDataSourceSetup extends JenaDataSourceSetupBase imple
 		boolean firstStartup = false;
 		
         try {
-            dbModel = makeDBModelFromPropertiesFile(sce.getServletContext().getRealPath(CONNECTION_PROP_LOCATION), JENA_DB_MODEL, DB_ONT_MODEL_SPEC);
+            dbModel = makeDBModelFromConfigurationProperties(JENA_DB_MODEL, DB_ONT_MODEL_SPEC);
             
             ClosableIterator stmtIt = dbModel.listStatements();
             try {
@@ -63,14 +63,14 @@ public class JenaPersistentDataSourceSetup extends JenaDataSourceSetupBase imple
         } catch (Throwable t) {
 			System.out.println("**** ERROR *****");
             System.out.println("Vitro unable to open Jena database model.");
-			System.out.println("Check that connection.properties has been created WEB-INF/classes, ");
+			System.out.println("Check that the configuration properties file has been created in WEB-INF/classes, ");
 			System.out.println("and that the database connection parameters are accurate. ");
 			System.out.println("****************");
         }        
         
         // default inference graph
         try {
-        	Model infDbModel = makeDBModelFromPropertiesFile(sce.getServletContext().getRealPath(CONNECTION_PROP_LOCATION), JENA_INF_MODEL, DB_ONT_MODEL_SPEC);
+        	Model infDbModel = makeDBModelFromConfigurationProperties(JENA_INF_MODEL, DB_ONT_MODEL_SPEC);
         	OntModel infModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
         	if (infDbModel != null) {
         		long startTime = System.currentTimeMillis();
@@ -86,7 +86,7 @@ public class JenaPersistentDataSourceSetup extends JenaDataSourceSetupBase imple
         
         // user accounts Model
         try {
-        	Model userAccountsDbModel = makeDBModelFromPropertiesFile(sce.getServletContext().getRealPath(CONNECTION_PROP_LOCATION), JENA_USER_ACCOUNTS_MODEL, DB_ONT_MODEL_SPEC);
+        	Model userAccountsDbModel = makeDBModelFromConfigurationProperties(JENA_USER_ACCOUNTS_MODEL, DB_ONT_MODEL_SPEC);
         	if (firstStartup) {
         		readOntologyFilesInPathSet(AUTHPATH, sce.getServletContext(), userAccountsDbModel);
         	}

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

@@ -32,7 +32,7 @@ public class ModelAuditorSetup extends JenaDataSourceSetupBase implements Servle
         	Model baseModel = ontModel.getBaseModel();
         	OntModel dynamicUnionModel = (OntModel) sce.getServletContext().getAttribute("jenaOntModel");
             log.debug("Setting model auditor database...");
-            OntModel auditModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,makeDBModelFromPropertiesFile(sce.getServletContext().getRealPath(CONNECTION_PROP_LOCATION), JENA_AUDIT_MODEL, DB_ONT_MODEL_SPEC));
+            OntModel auditModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,makeDBModelFromConfigurationProperties(JENA_AUDIT_MODEL, DB_ONT_MODEL_SPEC));
             sce.getServletContext().setAttribute("jenaAuditModel", auditModel);
             ModelAuditor ma = new ModelAuditor(auditModel,ontModel);
             baseModel.register(ma);

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

@@ -2,29 +2,22 @@
 
 package edu.cornell.mannlib.vitro.webapp.servlet.setup;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Properties;
-
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
-import org.apache.commons.logging.Log;
+import org.apache.log4j.Logger;
-import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.db.DBConnection;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.ModelMaker;
 
-import edu.cornell.mannlib.vitro.webapp.auth.policy.JenaNetidPolicy.ContextSetup;
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
 
 public class VitroJenaModelMakerSetup implements ServletContextListener {
+	private static final Logger LOG = Logger
+			.getLogger(VitroJenaModelMakerSetup.class);
 
-	protected final static String CONNECTION_PROP_LOCATION = "/WEB-INF/classes/connection.properties";
 	protected final static String DB_TYPE = "MySQL";
 	
 	public void contextDestroyed(ServletContextEvent arg0) {
@@ -32,78 +25,19 @@ public class VitroJenaModelMakerSetup implements ServletContextListener {
 	}
 
 	public void contextInitialized(ServletContextEvent arg0) {
-		
-		/* Sometimes this class fails for no apparent reason and stops
-		the context from loading.  Trying to eliminate all uncaught errors. */
-		Log log = null;
-		
 		try {		
-			log = LogFactory.getLog(VitroJenaModelMakerSetup.class.getName());
+			String jdbcUrl = ConfigurationProperties.getProperty("VitroConnection.DataSource.url")
+					+ "?useUnicode=yes&characterEncoding=utf8";
+			String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
+			String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
+				
+			DBConnection dbConn = new DBConnection(jdbcUrl, username, password, DB_TYPE);
+			ModelMaker mMaker = ModelFactory.createModelRDBMaker(dbConn);
+			VitroJenaModelMaker vjmm = new VitroJenaModelMaker(mMaker);
+			arg0.getServletContext().setAttribute("vitroJenaModelMaker", vjmm);
+			LOG.debug("VitroJenaModelMaker set up");
 		} catch (Throwable t) {
-			System.out.println("Unable to use error log for "+this.getClass().getName());
+			LOG.error("Unable to set up default VitroJenaModelMaker", t);
-		}
-		
-		try {		
-			String filename = arg0.getServletContext().getRealPath(CONNECTION_PROP_LOCATION);
-		    if (filename == null || filename.length() <= 0) {
-		    	if (log != null) {
-		           log.error(
-		        		   "Error setting up VitroModelMaker:\n" +
-		                   "To establish the DB model you MUST set the "
-		                   + "filename to the location of a "
-		                   + "connection.properties file with the database connection parameters.");
-		    	}
-  	        }
-	
-	       File propF = new File(filename );
-	       InputStream is = null;
-	       try {
-	           is = new FileInputStream(propF);
-	       } catch (FileNotFoundException e) {
-	    	   String msg = "Error setting up VitroJenaModelMaker:\nCould not load file "+filename;
-	    	   if (log != null) {
-	    		   log.error(msg);
-	    	   } else {
-	    		   System.out.println(msg);
-	    	   }
-	       }
-
-	       Properties dbProps = new Properties();
-	       try {
-	           dbProps.load(is);
-	           String dns = dbProps.getProperty("Vitro.defaultNamespace");
-	           String dbDriverClassname = dbProps.getProperty("VitroConnection.DataSource.driver");
-	           String jdbcUrl = dbProps.getProperty("VitroConnection.DataSource.url") + "?useUnicode=yes&characterEncoding=utf8";
-	           String username = dbProps.getProperty("VitroConnection.DataSource.username");
-	           String password = dbProps.getProperty("VitroConnection.DataSource.password"); 	   
-	           DBConnection dbConn = new DBConnection(jdbcUrl,username,password,DB_TYPE);
-	           ModelMaker mMaker = ModelFactory.createModelRDBMaker(dbConn);
-	           VitroJenaModelMaker vjmm = new VitroJenaModelMaker(mMaker);
-	           arg0.getServletContext().setAttribute("vitroJenaModelMaker",vjmm);
-	           String msg = "VitroJenaModelMaker set up";
-	           if (log != null) {
-	        	   log.debug(msg);
-	           } else {
-	        	   System.out.println(msg);
-	           }
-	       } catch (IOException e) {
-	    	   String msg = "Error setting up VitroJenaModelMaker:\nCould not load properties from file " + filename + '\n'
-               + e.getMessage();
-	    	   if (log != null) { 
-	    		   log.error(msg); 
-	    	   } else { 
-	    		   System.out.println(msg);
-	    	   }
-	       } 
-	       
-		} catch (Throwable t) {
-			String msg = "Unable to set up default VitroJenaModelMaker";
-			if (log != null) {
-				log.error(msg);
-				log.error(t);
-			} else {
-				System.out.println(msg);
-			}
 		}
 
 	}