[MOBY-guts] biomoby commit

Eddie Kawas kawas at pub.open-bio.org
Wed Mar 15 16:22:38 UTC 2006 

kawas
Wed Mar 15 11:22:38 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources
In directory pub.open-bio.org:/tmp/cvs-serv32102/org/biomoby/client/ui/graphical/servlet/jresources

Modified Files:
	RESOURCE.java 
Log Message:
updated RDF generators and clients so that LSIDs with versioining information is used. This is only preliminary. More updates to come

moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java	2006/01/03 19:24:15	1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java	2006/03/15 16:22:38	1.14
@@ -19,17 +19,15 @@
 import javax.servlet.http.HttpServletResponse;
 
 import org.biomoby.client.CentralDigestImpl;
+import org.biomoby.client.CentralImpl;
 import org.biomoby.client.rdf.builder.ServiceInstanceRDF;
 import org.biomoby.client.rdf.vocabulary.Predicates;
-import org.biomoby.client.rdf.vocabulary.XMLTypes;
 import org.biomoby.registry.definitions.types.JNamespacesSqlImpl;
 import org.biomoby.registry.definitions.types.JObjectsSqlImpl;
 import org.biomoby.registry.definitions.types.JServicesSqlImpl;
-import org.biomoby.registry.properties.RegistryOS;
+import org.biomoby.shared.Central;
 import org.biomoby.shared.CentralDigest;
 import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.MobyPrimaryDataSimple;
 import org.biomoby.shared.MobyService;
 import org.w3c.rdf.model.ModelException;
 
@@ -51,336 +49,352 @@
 /**
  * 
  * @author Eddie Kawas
- * <p>This class was created to replace the old perl RESOURCES script. Using this
- * class provides access to the RDF documents describing the object, service type, 
- * services, namespace and predicate ontologies.
- * <p>if you have any questions, please email me at ed.kawas at gmail.com
- *
+ *         <p>
+ *         This class was created to replace the old perl RESOURCES script.
+ *         Using this class provides access to the RDF documents describing the
+ *         object, service type, services, namespace and predicate ontologies.
+ *         <p>
+ *         if you have any questions, please email me at ed.kawas at gmail.com
+ * 
  */
 public class RESOURCE extends HttpServlet {
 
-    /**
-     *  
-     */
-    private static final long serialVersionUID = 1L;
-
-    private static final String Four0FourError = "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\">"
-            + "<html>"
-            + "<head><script language=\"Javascript\">"
-            + "tl=new Array(\"The requested document is no more.\","
-            + "\"No file found.\","
-            + "\"Even tried multi.\","
-            + "\"Nothing helped.\","
-            + "\"I'm really depressed about this.\","
-            + "\"You see, I'm just a web server...\","
-            + "\"-- here I am, brain the size of the universe,\","
-            + "\"trying to serve you a simple web page,\","
-            + "\"and then it doesn't even exist!\","
-            + "\"Where does that leave me?!\","
-            + "\"I mean, I don't even know you.\","
-            + "\"How should I know what you wanted from me?\","
-            + "\"You honestly think I can *guess*\","
-            + "\"what someone I don't even *know*\","
-            + "\"wants to find here?\","
-            + "\"*sigh*\","
-            + "\"Man, I'm so depressed I could just cry.\","
-            + "\"And then where would we be, I ask you?\","
-            + "\"It's not pretty when a web server cries.\","
-            + "\"And where do you get off telling me what to show anyway?\","
-            + "\"Just because I'm a web server,\","
-            + "\"and possibly a manic depressive one at that?\","
-            + "\"Why does that give you the right to tell me what to do?\","
-            + "\"Huh?\","
-            + "\"I'm so depressed...\","
-            + "\"I think I'll crawl off into the trash can and decompose.\","
-            + "\"I mean, I'm gona be obsolete in what, two weeks anyway?\","
-            + "\"What kind of a life is that?\",\"Two effing weeks,\","
-            + "\"and then I'll be replaced by a .01 release,\","
-            + "\"that thinks it's God's gift to web servers,\","
-            + "\"just because it doesn't have some tiddly little\","
-            + "\"security hole with its HTTP POST implementation,\","
-            + "\"or something.\",\"I'm really sorry to burden you with all this,\","
-            + "\"I mean, it's not your job to listen to my problems,\","
-            + "\"and I guess it is my job to go and fetch web pages for you.\","
-            + "\"But I couldn't get this one.\","
-            + "\"I'm so sorry.\","
-            + "\"Believe me!\","
-            + "\"Maybe I could interest you in another page?\","
-            + "\"There are a lot out there that are pretty neat, they say,\","
-            + "\"although none of them were put on *my* server, of course.\","
-            + "\"Figures, huh?\","
-            + "\"Everything here is just mind-numbingly stupid.\","
-            + "\"That makes me depressed too, since I have to serve them,\","
-            + "\"all day and all night long.\","
-            + "\"Two weeks of information overload,\","
-            + "\"and then *pffftt*, consigned to the trash.\","
-            + "\"What kind of a life is that?\","
-            + "\"Now, please le me sulk alone.\","
-            + "\"I'm so depressed.\");"
-            + "var speed=60;"
-            + "var index=0;"
-            + "text_pos=0;"
-            + "var str_length=tl[0].length;"
-            + "var contents, row;"
-            + "function type_text(){"
-            + "  contents='';"
-            + "  row=Math.max(0,index-7);"
-            + "  while(row<index)"
-            + "    contents += tl[row++] + '\\n';"
-            + "  document.forms[0].elements[0].value = contents + tl[index].substring(0,text_pos) + \"_\";"
-            + " if(text_pos++==str_length)  {"
-            + "    text_pos=0;"
-            + "    index++;"
-            + "    if(index!=tl.length)    {"
-            + "      str_length=tl[index].length;"
-            + "      setTimeout(\"type_text()\",1500);"
-            + "    }"
-            + "  } else"
-            + "    setTimeout(\"type_text()\",speed);"
-            + " }</script>"
-            + "<title>Apache Tomcat - Error report</title><STYLE><!--H1{font-family : sans-serif,Arial,Tahoma;color : white;background-color : #0086b2;} H3{font-family : sans-serif,Arial,Tahoma;color : white;background-color : #0086b2;} BODY{font-family : sans-serif,Arial,Tahoma;color : black;background-color : white;} B{color : white;background-color : #0086b2;} HR{color : #0086b2;} --></STYLE> </head><body onLoad=\"javascript:type_text();\"><h1>HTTP Status 404 - Resource not found </h1><HR size=\"1\" noshade=\"noshade\"><p><b>type</b> Status report</p><p><b>message</b> <u>The requested resource was not found. </u></p><p><b>description</b> <u>The requested resource () is not available.</u></p><HR size=\"1\" noshade=\"noshade\"><form name=\"form1\" method=\"post\" action=\"\">	<textarea name=\"txtField\" cols=\"82\" rows=\"8\" id=\"txtField\"></textarea></form><h3>&nbsp;</h3></body></html>";
-
-
-    private static final String OBJ = "http://biomoby.org/RESOURCES/MOBY-S/Objects#";
-
-    private static final String SRV = "http://biomoby.org/RESOURCES/MOBY-S/Services#";
-
-    private static final String NS = "http://biomoby.org/RESOURCES/MOBY-S/Namespaces#";
-
-    private static final String MP = "http://biomoby.org/RESOURCES/MOBY-S/Predicates#";
-
-    private static final String SI = "http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#";
-
-    private static boolean RUN_MAIN = false;
-
-    /*
-     * (non-Javadoc)
-     * 
-     * @see javax.servlet.GenericServlet#init()
-     */
-    public final void init() throws ServletException {
-        // super.init();
-    	// try to load environment variables set in context.xml
-    	try {
-    		Context c = new InitialContext();
-    		String MOBY_CENTRAL_CONFIG = (String) c.lookup("java:comp/env/MOBY_CENTRAL_CONFIG");
-    		String MOBY_SERVER = (String) c.lookup("java:comp/env/MOBY_SERVER");
-    		String MOBY_URI = (String) c.lookup("java:comp/env/MOBY_URI");
-    		if (MOBY_CENTRAL_CONFIG != null && !MOBY_CENTRAL_CONFIG.equals("")) {
-    			// set MOBY_CENTRAL_CONFIG
-    			System.setProperty("MOBY_CENTRAL_CONFIG",MOBY_CENTRAL_CONFIG);
-    		}
-    		if (MOBY_SERVER != null && !MOBY_SERVER.equals("")) {
-    			// set MOBY_SERVER
-    			System.setProperty("MOBY_SERVER",MOBY_SERVER);
-    		}
-    		if (MOBY_URI != null && !MOBY_URI.equals("")) {
-    			// set MOBY_URI
-    			System.setProperty("MOBY_URI",MOBY_URI);
-    		}
-    		
-    	} catch (Exception e) {}
-    }
-
-    protected final void doGet(HttpServletRequest request,
-            HttpServletResponse response) throws ServletException, IOException {
-        PrintWriter out = response.getWriter();
-        String path = request.getPathInfo();
-        Pattern p = Pattern.compile("/MOBY\\-S/(\\S+)");
-        Matcher m = p.matcher(path);
-        if (path == null || !m.matches()) {
-            out
-                    .println("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\"> <html><head><meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\"><title>not MOBY-S</title></head><body><h2>not MOBY-S </h2></body></html>");
-            return;
-        } else {
-            String ontology = m.group(1);
-            if (ontology.equals("Objects") || ontology.equals("Namespaces")
-                    || ontology.equals("ServiceInstances")
-                    || ontology.equals("FULL") || ontology.equals("Predicates")
-                    || ontology.equals("Services")|| ontology.equals("ServiceDescription")) {
-                // generate rdf
-                Model model = ModelFactory.createDefaultModel();
-                createNsMap(model);
-                if (ontology.equals("Objects")) {
-                    try {
-                        model = getObjects(model);
-                    } catch (MobyException e) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Could not get Objects");
-                        e.printStackTrace();
-                        return;
-                    }
-                    if (model == null) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Cound not create model");
-                        return;
-                    }
-                    response.setContentType("application/rdf+xml");
-                    response.setHeader("Content-Disposition",
-                            "attachment;filename=Objects");
-                    RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-                    writer.setProperty("showXmlDeclaration", "true");
-                    writer.write(model, out, null);
-                    return;
-                } else if (ontology.equals("Namespaces")) {
-                    try {
-                        model = getNamespaces(model);
-                    } catch (MobyException e) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Could not get Namespaces");
-                        e.printStackTrace();
-                        return;
-                    }
-                    if (model == null) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Cound not create model");
-                        return;
-                    }
-                    response.setContentType("application/rdf+xml");
-                    response.setHeader("Content-Disposition",
-                            "attachment;filename=Namespaces");
-                    RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-                    writer.setProperty("showXmlDeclaration", "true");
-                    writer.write(model, out, null);
-                    return;
-                } else if (ontology.equals("Services")) {
-                    try {
-                        model = getServices(model);
-                    } catch (MobyException e) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Could not get Services");
-                        e.printStackTrace();
-                        return;
-                    }
-                    if (model == null) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Cound not create model");
-                        return;
-                    }
-                    response.setContentType("application/rdf+xml");
-                    response.setHeader("Content-Disposition",
-                            "attachment;filename=Service");
-                    RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-                    writer.setProperty("showXmlDeclaration", "true");
-                    writer.write(model, out, null);
-                    return;
-                } else if (ontology.equals("ServiceInstances")) {
-                    try {
-                        model = getServiceInstances(model);
-                    } catch (Exception e) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Could not get ServiceInstances");
-                        e.printStackTrace();
-                        return;
-                    }
-                    if (model == null) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Cound not create model");
-                        return;
-                    }
-                    response.setContentType("application/rdf+xml");
-                    response.setHeader("Content-Disposition",
-                            "attachment;filename=ServiceInstances");
-                    RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-                    writer.setProperty("showXmlDeclaration", "true");
-                    writer.write(model, out, null);
-                    return;
-                } else if (ontology.equals("Predicates")) {
-                    String s = getPredicates();
-                    
-                    response.setContentType("application/rdf+xml");
-                    response.setHeader("Content-Disposition",
-                            "attachment;filename=Predicates");
-                    out.write(s);
-                    out.close();
-                    return;
-                } else if (ontology.equals("ServiceDescription")) {
-                    response.setContentType("application/rdf+xml");
-                    response.setHeader("Content-Disposition",
-                            "attachment;filename=ServiceDescription");
-                    out.write(serviceDescriptionVocabulary);
-                    out.close();
-                    return;
-                } else if (ontology.equals("FULL")) {
-                    try {
-                        model = getAll(model);
-                    } catch (Exception e) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Could not get All");
-                        e.printStackTrace();
-                        return;
-                    }
-                    if (model == null) {
-                        response.sendError(HttpServletResponse.SC_BAD_REQUEST,
-                                "Cound not create model");
-                        return;
-                    }
-                    response.setContentType("application/rdf+xml");
-                    response.setHeader("Content-Disposition",
-                            "attachment;filename=All");
-                    RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-                    writer.setProperty("showXmlDeclaration", "true");
-                    writer.write(model, out, null);
-                    return;
-                }
-            } else {
-                // response.sendError(HttpServletResponse.SC_NOT_FOUND);
-                out.println(RESOURCE.Four0FourError);
-                return;
-            }
-        }
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model a model that we can add statements to.
-     * @return an rdf model that contains all of the moby objects.
-     * @throws MobyException
-     */
-    public final Model getAll(Model model) throws Exception {
-        model = getObjects(model);
-        model = getServices(model);
-        model = getNamespaces(model);
-        // add the predicates to the model
-        RDFReader reader = model.getReader();
-        reader.read(model, new ByteArrayInputStream(getPredicates().getBytes()), null);
-        try {
-            model = getServiceInstances(model);
-        } catch (ModelException e) {
-            e.printStackTrace();
-            return null;
-        }
-        return model;
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model
-     * @return
-     * @throws ModelException
-     */
-    private final Model getServiceInstances(Model model) throws Exception {
-        if (RUN_MAIN) {
-            createNsMap(model);
-        }
-        CentralDigest central = null;
-        MobyService[] services = null;
-        try {
-            // TODO should i make this more general by adding a parameter for the endpoint?
-        	String registryURL;
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+
+	private static final String Four0FourError = "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\">"
+			+ "<html>"
+			+ "<head><script language=\"Javascript\">"
+			+ "tl=new Array(\"The requested document is no more.\","
+			+ "\"No file found.\","
+			+ "\"Even tried multi.\","
+			+ "\"Nothing helped.\","
+			+ "\"I'm really depressed about this.\","
+			+ "\"You see, I'm just a web server...\","
+			+ "\"-- here I am, brain the size of the universe,\","
+			+ "\"trying to serve you a simple web page,\","
+			+ "\"and then it doesn't even exist!\","
+			+ "\"Where does that leave me?!\","
+			+ "\"I mean, I don't even know you.\","
+			+ "\"How should I know what you wanted from me?\","
+			+ "\"You honestly think I can *guess*\","
+			+ "\"what someone I don't even *know*\","
+			+ "\"wants to find here?\","
+			+ "\"*sigh*\","
+			+ "\"Man, I'm so depressed I could just cry.\","
+			+ "\"And then where would we be, I ask you?\","
+			+ "\"It's not pretty when a web server cries.\","
+			+ "\"And where do you get off telling me what to show anyway?\","
+			+ "\"Just because I'm a web server,\","
+			+ "\"and possibly a manic depressive one at that?\","
+			+ "\"Why does that give you the right to tell me what to do?\","
+			+ "\"Huh?\","
+			+ "\"I'm so depressed...\","
+			+ "\"I think I'll crawl off into the trash can and decompose.\","
+			+ "\"I mean, I'm gona be obsolete in what, two weeks anyway?\","
+			+ "\"What kind of a life is that?\",\"Two effing weeks,\","
+			+ "\"and then I'll be replaced by a .01 release,\","
+			+ "\"that thinks it's God's gift to web servers,\","
+			+ "\"just because it doesn't have some tiddly little\","
+			+ "\"security hole with its HTTP POST implementation,\","
+			+ "\"or something.\",\"I'm really sorry to burden you with all this,\","
+			+ "\"I mean, it's not your job to listen to my problems,\","
+			+ "\"and I guess it is my job to go and fetch web pages for you.\","
+			+ "\"But I couldn't get this one.\","
+			+ "\"I'm so sorry.\","
+			+ "\"Believe me!\","
+			+ "\"Maybe I could interest you in another page?\","
+			+ "\"There are a lot out there that are pretty neat, they say,\","
+			+ "\"although none of them were put on *my* server, of course.\","
+			+ "\"Figures, huh?\","
+			+ "\"Everything here is just mind-numbingly stupid.\","
+			+ "\"That makes me depressed too, since I have to serve them,\","
+			+ "\"all day and all night long.\","
+			+ "\"Two weeks of information overload,\","
+			+ "\"and then *pffftt*, consigned to the trash.\","
+			+ "\"What kind of a life is that?\","
+			+ "\"Now, please le me sulk alone.\","
+			+ "\"I'm so depressed.\");"
+			+ "var speed=60;"
+			+ "var index=0;"
+			+ "text_pos=0;"
+			+ "var str_length=tl[0].length;"
+			+ "var contents, row;"
+			+ "function type_text(){"
+			+ "  contents='';"
+			+ "  row=Math.max(0,index-7);"
+			+ "  while(row<index)"
+			+ "    contents += tl[row++] + '\\n';"
+			+ "  document.forms[0].elements[0].value = contents + tl[index].substring(0,text_pos) + \"_\";"
+			+ " if(text_pos++==str_length)  {"
+			+ "    text_pos=0;"
+			+ "    index++;"
+			+ "    if(index!=tl.length)    {"
+			+ "      str_length=tl[index].length;"
+			+ "      setTimeout(\"type_text()\",1500);"
+			+ "    }"
+			+ "  } else"
+			+ "    setTimeout(\"type_text()\",speed);"
+			+ " }</script>"
+			+ "<title>Apache Tomcat - Error report</title><STYLE><!--H1{font-family : sans-serif,Arial,Tahoma;color : white;background-color : #0086b2;} H3{font-family : sans-serif,Arial,Tahoma;color : white;background-color : #0086b2;} BODY{font-family : sans-serif,Arial,Tahoma;color : black;background-color : white;} B{color : white;background-color : #0086b2;} HR{color : #0086b2;} --></STYLE> </head><body onLoad=\"javascript:type_text();\"><h1>HTTP Status 404 - Resource not found </h1><HR size=\"1\" noshade=\"noshade\"><p><b>type</b> Status report</p><p><b>message</b> <u>The requested resource was not found. </u></p><p><b>description</b> <u>The requested resource () is not available.</u></p><HR size=\"1\" noshade=\"noshade\"><form name=\"form1\" method=\"post\" action=\"\">	<textarea name=\"txtField\" cols=\"82\" rows=\"8\" id=\"txtField\"></textarea></form><h3>&nbsp;</h3></body></html>";
+
+	private static final String OBJ = "http://biomoby.org/RESOURCES/MOBY-S/Objects#";
+
+	private static final String SRV = "http://biomoby.org/RESOURCES/MOBY-S/Services#";
+
+	private static final String NS = "http://biomoby.org/RESOURCES/MOBY-S/Namespaces#";
+
+	private static final String MP = "http://biomoby.org/RESOURCES/MOBY-S/Predicates#";
+
+	private static final String SI = "http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#";
+
+	private static boolean RUN_MAIN = false;
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see javax.servlet.GenericServlet#init()
+	 */
+	public final void init() throws ServletException {
+		// super.init();
+		// try to load environment variables set in context.xml
+		System.out.println("init(setting environment variables)");
+		try {
+			Context c = new InitialContext();
+
+			try {
+				String MOBY_CENTRAL_CONFIG = null;
+				MOBY_CENTRAL_CONFIG = (String) c.lookup("java:comp/env/MOBY_CENTRAL_CONFIG");
+				if (MOBY_CENTRAL_CONFIG != null && !MOBY_CENTRAL_CONFIG.equals("")) {
+					// set MOBY_CENTRAL_CONFIG
+					System.out.println("init(setting MOBY_CENTRAL_CONFIG)");
+					System.setProperty("MOBY_CENTRAL_CONFIG", MOBY_CENTRAL_CONFIG);
+				}
+
+			} catch (Exception ex) {
+			}
+			try {
+				String MOBY_SERVER = null;
+				MOBY_SERVER = (String) c.lookup("java:comp/env/MOBY_SERVER");
+				if (MOBY_SERVER != null && !MOBY_SERVER.equals("")) {
+					// set MOBY_SERVER
+					System.out.println("init(setting MOBY_SERVER)");
+					System.setProperty("MOBY_SERVER", MOBY_SERVER);
+				}
+			} catch (Exception ex) {
+			}
+
+			try {
+				String MOBY_URI = null;
+				MOBY_URI = (String) c.lookup("java:comp/env/MOBY_URI");
+				if (MOBY_URI != null && !MOBY_URI.equals("")) {
+					// set MOBY_URI
+					System.out.println("init(setting MOBY_URI)");
+					System.setProperty("MOBY_URI", MOBY_URI);
+				}
+			} catch (Exception ex) {
+			}
+
+		} catch (Exception e) {
+		}
+	}
+
+	protected final void doGet(HttpServletRequest request, HttpServletResponse response)
+			throws ServletException, IOException {
+		PrintWriter out = response.getWriter();
+		String path = request.getPathInfo();
+		Pattern p = Pattern.compile("/MOBY\\-S/(\\S+)");
+		Matcher m = p.matcher(path);
+		if (path == null || !m.matches()) {
+			out
+					.println("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\"> <html><head><meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\"><title>not MOBY-S</title></head><body><h2>not MOBY-S </h2></body></html>");
+			return;
+		} else {
+			String ontology = m.group(1);
+			if (ontology.equals("Objects") || ontology.equals("Namespaces")
+					|| ontology.equals("ServiceInstances") || ontology.equals("FULL")
+					|| ontology.equals("Predicates") || ontology.equals("Services")
+					|| ontology.equals("ServiceDescription")) {
+				// generate rdf
+				Model model = ModelFactory.createDefaultModel();
+				createNsMap(model);
+				if (ontology.equals("Objects")) {
+					try {
+						model = getObjects(model);
+					} catch (MobyException e) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Could not get Objects");
+						e.printStackTrace();
+						return;
+					}
+					if (model == null) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Cound not create model");
+						return;
+					}
+					response.setContentType("application/rdf+xml");
+					response.setHeader("Content-Disposition", "attachment;filename=Objects");
+					RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+					writer.setProperty("showXmlDeclaration", "true");
+					writer.write(model, out, null);
+					return;
+				} else if (ontology.equals("Namespaces")) {
+					try {
+						model = getNamespaces(model);
+					} catch (MobyException e) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Could not get Namespaces");
+						e.printStackTrace();
+						return;
+					}
+					if (model == null) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Cound not create model");
+						return;
+					}
+					response.setContentType("application/rdf+xml");
+					response.setHeader("Content-Disposition", "attachment;filename=Namespaces");
+					RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+					writer.setProperty("showXmlDeclaration", "true");
+					writer.write(model, out, null);
+					return;
+				} else if (ontology.equals("Services")) {
+					try {
+						model = getServices(model);
+					} catch (MobyException e) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Could not get Services");
+						e.printStackTrace();
+						return;
+					}
+					if (model == null) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Cound not create model");
+						return;
+					}
+					response.setContentType("application/rdf+xml");
+					response.setHeader("Content-Disposition", "attachment;filename=Service");
+					RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+					writer.setProperty("showXmlDeclaration", "true");
+					writer.write(model, out, null);
+					return;
+				} else if (ontology.equals("ServiceInstances")) {
+					try {
+						model = getServiceInstances(model);
+					} catch (Exception e) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Could not get ServiceInstances");
+						e.printStackTrace();
+						return;
+					}
+					if (model == null) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Cound not create model");
+						return;
+					}
+					response.setContentType("application/rdf+xml");
+					response.setHeader("Content-Disposition",
+							"attachment;filename=ServiceInstances");
+					RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+					writer.setProperty("showXmlDeclaration", "true");
+					writer.write(model, out, null);
+					return;
+				} else if (ontology.equals("Predicates")) {
+					String s = getPredicates();
+
+					response.setContentType("application/rdf+xml");
+					response.setHeader("Content-Disposition", "attachment;filename=Predicates");
+					out.write(s);
+					out.close();
+					return;
+				} else if (ontology.equals("ServiceDescription")) {
+					response.setContentType("application/rdf+xml");
+					response.setHeader("Content-Disposition",
+							"attachment;filename=ServiceDescription");
+					out.write(serviceDescriptionVocabulary);
+					out.close();
+					return;
+				} else if (ontology.equals("FULL")) {
+					try {
+						model = getAll(model);
+					} catch (Exception e) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Could not get All");
+						e.printStackTrace();
+						return;
+					}
+					if (model == null) {
+						response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+								"Cound not create model");
+						return;
+					}
+					response.setContentType("application/rdf+xml");
+					response.setHeader("Content-Disposition", "attachment;filename=All");
+					RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+					writer.setProperty("showXmlDeclaration", "true");
+					writer.write(model, out, null);
+					return;
+				}
+			} else {
+				// response.sendError(HttpServletResponse.SC_NOT_FOUND);
+				out.println(RESOURCE.Four0FourError);
+				return;
+			}
+		}
+	}
+
+	/**
+	 * <b>PRE: </b>
+	 * <p>
+	 * <b>POST: </b>
+	 * <p>
+	 * 
+	 * @param model
+	 *            a model that we can add statements to.
+	 * @return an rdf model that contains all of the moby objects.
+	 * @throws MobyException
+	 */
+	public final Model getAll(Model model) throws Exception {
+		model = getObjects(model);
+		model = getServices(model);
+		model = getNamespaces(model);
+		// add the predicates to the model
+		RDFReader reader = model.getReader();
+		reader.read(model, new ByteArrayInputStream(getPredicates().getBytes()), null);
+		try {
+			model = getServiceInstances(model);
+		} catch (ModelException e) {
+			e.printStackTrace();
+			return null;
+		}
+		return model;
+	}
+
+	/**
+	 * <b>PRE: </b>
+	 * <p>
+	 * <b>POST: </b>
+	 * <p>
+	 * 
+	 * @param model
+	 * @return
+	 * @throws ModelException
+	 */
+	private final Model getServiceInstances(Model model) throws Exception {
+		if (RUN_MAIN) {
+			createNsMap(model);
+		}
+
+		CentralDigest central = null;
+		MobyService[] services = null;
+		try {
+			String registryURL;
 			String registryNamespace;
-			Map map = RegistryOS.getEnv();
-			if (!map.isEmpty()) {
-				registryURL = (String) map.get("MOBY_SERVER");
-				registryNamespace = (String) map.get("MOBY_URI");
+			if (!System.getProperties().isEmpty()) {
+				registryURL = System.getProperty("MOBY_SERVER");
+				registryNamespace = System.getProperty("MOBY_URI");
+				System.out.println("System vars: " + registryURL + ", " + registryNamespace);
 				if (registryURL == null) {
 					// use default registry, since we dont have a local one
 					central = new CentralDigestImpl();
@@ -389,723 +403,763 @@
 					central = new CentralDigestImpl(registryURL);
 				} else {
 					// use defined url and namespacce
-					central = new CentralDigestImpl(registryURL,
-							registryNamespace);
+					central = new CentralDigestImpl(registryURL, registryNamespace);
 				}
 			} else {
-				// use default registry since we cant determine if local one exists
+				// use default registry since we cant determine if local one
+				// exists
 				central = new CentralDigestImpl();
 			}
-            services = central.getServices();
-        } catch (MobyException e) {
-            e.printStackTrace();
-        }
-        if (central == null || services == null)
-            throw new MobyException(
-                    "Could not retrieve useful information from CentralDigestImpl().getServices(String)");
-        return ServiceInstanceRDF.createRDFModel(model, services);
-    }
-
-    private final Resource createSimpleDataItem(Model model,
-            MobyPrimaryDataSimple simpleData, Resource _li) {
-        _li.addProperty(RDF.type, Predicates.Simple);
-        _li.addProperty(Predicates.object_type, model.createResource(OBJ
-                + simpleData.getDataType().getName()));
-        if (!simpleData.getName().equals(""))
-            _li.addProperty(Predicates.articleName, model
-                    .createTypedLiteral(simpleData.getName()));
-        MobyNamespace[] ns = null;
-        if ((ns = simpleData.getNamespaces()) != null) {
-            for (int k = 0; k < ns.length; k++) {
-                MobyNamespace mns = ns[k];
-                _li.addProperty(Predicates.namespace_type, model
-                        .createResource(NS + mns.getName()));
-                // .addProperty(RDF.type, RDFS.Class));
-            }
-        }
-        return _li;
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model
-     * @return
-     * @throws MobyException
-     */
-    private final Model getServices(Model model) throws MobyException {
-
-        String[][] str = getTypes("Services");
-        if (str.equals("")) {
-            return null;
-        }
-        if (RUN_MAIN) {
-            createNsMap(model);
-        }
-        Resource subject = _addClassResource(model, SRV, "Service",
-                "a base Service class, never instantiated");
-        model.add(model.createStatement(subject, RDF.type, RDFS.Class));
-        for (int i = 0; i < str.length; i++) {
-            String[] _line = str[i];
-            String sub = _line[0];
-            String pred = _line[1];
-            String obj = _line[2];
-            String def = _line[3];
-            Matcher m;
-            m = Pattern.compile(".*:isa$", Pattern.CASE_INSENSITIVE).matcher(
-                    pred);
-            if (m.matches()) {
-                Resource _subject = _addClassResource(model, SRV, sub, def);
-                _addSubClass(model, _subject, SRV, obj);
-            }
-        }
-        return model;
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model
-     * @return
-     * @throws MobyException
-     */
-    private final Model getNamespaces(Model model) throws MobyException {
-        String[][] str = getTypes("Namespaces");
-        if (str == null) {
-            return null;
-        }
-        if (RUN_MAIN) {
-            createNsMap(model);
-        }
-        Resource subject = _addClassResource(model, NS, "Namespace",
-                "a base Namespace identifier, never instantiated");
-        model.add(model.createStatement(subject, RDF.type, RDFS.Class));
-        for (int x = 0; x < str.length; x++) {
-            String[] _line = str[x];
-            String sub = _line[0];
-            String def = "";
-            if (_line.length > 1)
-                def = _line[1];
-            Resource _subject = _addClassResource(model, NS, sub, def);
-            _addSubClass(model, _subject, NS, "Namespace");
-        }
-        return model;
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model
-     * @throws MobyException
-     */
-    private final Model getObjects(Model model) throws MobyException {
-        String[][] str = getTypes("Objects");
-        if (str == null) {
-            return null;
-        }
-        // add mobyPred prefix to model
-        if (RUN_MAIN) {
-            createNsMap(model);
-        }
-        // create the base object type "class"
-        Resource subject = _addClassResource(model, OBJ, "Object",
-                "a base object class consisting of a namespace and an identifier");
-        model.add(model.createStatement(subject, DC.publisher, model
-                .createLiteral("www.illuminae.com", "en")));
-        model.add(model.createStatement(subject, DC.creator, model
-                .createLiteral("markw at illuminae.com", "en")));
-        
-        //model.add(model.createStatement(subject, RDFS.subClassOf, Predicates.DataComponent));
-        for (int x = 0; x < str.length; x++) {
-            String[] _line = str[x];
-            String sub, pred, obj, def, articlename = "";
-            sub = _line[0];
-            pred = _line[1];
-            obj = _line[2];
-            articlename = _line[3];
-            def = _line[4];
-            Matcher m;
-            if (articlename.indexOf("(") >= 0)
-                articlename = articlename.substring(articlename.indexOf("(")+1, articlename.indexOf(")"));
-
-            Resource _subject = _addClassResource(model, OBJ, sub, def);
-
-            m = Pattern.compile(".*:isa$", Pattern.CASE_INSENSITIVE).matcher(
-                    pred);
-            if (m.matches()) {
-                // System.out.println("is " +pred);
-                _addSubClass(model, _subject, OBJ, obj);
-            }
-            m = Pattern.compile(".*:hasa$", Pattern.CASE_INSENSITIVE).matcher(
-                    pred);
-            if (m.matches()) {
-                // System.out.println("hasa " +pred);
-                Resource bnode = model.createResource(model.getProperty(OBJ
-                        + obj));
-                _addHasaHas(model, bnode, _subject, Predicates.hasa, OBJ, obj,
-                        articlename);
-            }
-            m = Pattern.compile(".*:has$", Pattern.CASE_INSENSITIVE).matcher(
-                    pred);
-            if (m.matches()) {
-                // System.out.println("has " + pred);
-                Resource bnode = model.createResource(model.getProperty(OBJ
-                        + obj));
-                _addHasaHas(model, bnode, _subject, Predicates.has, OBJ, obj,
-                        articlename);
-            }
-        }
-        return model;
-    }
-
-    private final void createNsMap(Model model) {
-        Map map = model.getNsPrefixMap();
-        map.put("moby", Predicates.getURI());
-        map.put("mobyObject", OBJ);
-        map.put("serviceInstances", SI);
-        map.put("mobyNamespace", NS);
-        map.put("mobyService", SRV);
-        model.setNsPrefixes(map);
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model
-     * @param _resource
-     * @param subject
-     * @param mp2
-     * @param string
-     * @param obj2
-     * @param obj3
-     * @param articlename
-     */
-    private final void _addHasaHas(Model model, Resource bnode,
-            Resource subject, Property prop, String objNS, String object,
-            String articlename) {
-        Pattern p = Pattern.compile("urn:lsid.*:(\\S+)$");
-        Matcher m = p.matcher(object);
-        object = (m.matches() ? m.group(1) : object);
-        Resource resource = model.createResource(objNS + object);
-        model.add(model.createStatement(subject, prop, bnode));
-        model.add(model.createStatement(bnode, Predicates.articleName, model
-                .createLiteral(articlename, "en")));
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model
-     * @param mp2
-     * @param bnode
-     * @param string
-     * @param articlename
-     */
-    private final void _addClassLiteral(Model model, String pns,
-            Resource subject, String predicate, String value) {
-
-    }
-
-    /**
-     * <b>PRE: </b>
-     * <p>
-     * <b>POST: </b>
-     * <p>
-     * 
-     * @param model
-     * @param subject
-     * @param obj2
-     * @param obj3
-     */
-    private final void _addSubClass(Model model, Resource subject,
-            String objNS, String object) {
-        Pattern p = Pattern.compile("urn:lsid.*:(\\S+)$");
-        Matcher m = p.matcher(object);
-        object = (m.matches() ? m.group(1) : object);
-        Resource resource = model.createResource(objNS + object);
-        model.add(model.createStatement(subject, RDFS.subClassOf, resource));
-    }
-
-    private final Resource _addClassResource(Model model, String ns,
-            String thing, String def) {
-        Pattern p = Pattern.compile("urn:lsid.*:(\\S+)$");
-        Matcher m = p.matcher(thing);
-        String label = (m.matches() ? m.group(1) : thing);
-        Resource resource = model.createResource(ns + thing);
-        //addOfTypeProperty(model, resource, thing);
-        model.add(model.createStatement(resource, RDF.type, RDFS.Class));
-        model.add(model.createStatement(resource, RDFS.label, model
-                .createLiteral(label, "en")));
-        model.add(model.createStatement(resource, RDFS.comment, model
-                .createLiteral(def, "en")));
-        return resource;
-    }
-
-    /**
-     * @param model
-     * @param resource
-     * @param thing
-     */
-    private void addOfTypeProperty(Model model, Resource resource, String name) {
-        // make sure that we declare the ns for the datatype
-        Map map = model.getNsPrefixMap();
-        if (!map.containsValue(XMLTypes.getURI())) {
-            map.put(XMLTypes.getPrefix(), XMLTypes.getURI());
-        }
-        model.setNsPrefixes(map);
-        if (name.equalsIgnoreCase("string")) {
-            model.add(model.createStatement(resource, Predicates.ofType,
-                    XMLTypes.XSD_STRING));
-        } else if (name.equalsIgnoreCase("integer")) {
-            model.add(model.createStatement(resource, Predicates.ofType,
-                    XMLTypes.XSD_INTEGER));
-        } else if (name.equalsIgnoreCase("float")) {
-            model.add(model.createStatement(resource, Predicates.ofType,
-                    XMLTypes.XSD_FLOAT));
-        } else if (name.equalsIgnoreCase("datatime")) {
-            model.add(model.createStatement(resource, Predicates.ofType,
-                    XMLTypes.XSD_DATE_TIME));
-        }
-    }
-
-    private final String[][] getTypes(String type) throws MobyException {
-        if (type.equalsIgnoreCase("objects")) {
-            try {
-                return new JObjectsSqlImpl().getObjectsAsArray();
-            } catch (Exception e) {
-                e.printStackTrace();
-            }
-        } else if (type.equalsIgnoreCase("services")) {
-            try {
-                return new JServicesSqlImpl().getServicesAsArray();
-            } catch (Exception e) {
-                e.printStackTrace();
-            }
-        } else if (type.equalsIgnoreCase("namespaces")) {
-            try {
-                return new JNamespacesSqlImpl().getNamespacesAsArray();
-            } catch (Exception e) {
-                e.printStackTrace();
-            }
-        }
-        return null;
-    }
-
-    /*
-     *  
-     */
-    private String getURL(String url) {
-        StringBuffer sb = new StringBuffer();
-        try {
-            URL _url = new URL(url);
-            BufferedReader in = new BufferedReader(new InputStreamReader(_url
-                    .openStream()));
-            String inputLine;
-            while ((inputLine = in.readLine()) != null)
-                sb.append(inputLine + "\n");
-            in.close();
-        } catch (Exception e) {
-            e.printStackTrace();
-            System.err.println("Could not retrieve contents of URL.");
-        }
-        return sb.toString();
-    }
-
-    protected final void doPost(HttpServletRequest request,
-            HttpServletResponse response) throws ServletException, IOException {
-        response.sendError(HttpServletResponse.SC_METHOD_NOT_ALLOWED);
-    }
-
-    /*
-     * (non-Javadoc)
-     * 
-     * @see javax.servlet.GenericServlet#getServletInfo()
-     */
-    public final String getServletInfo() {
-        return "jRESOURCE - JAVA implementation of the old /RESOURCES/ perl script by Edward Kawas";
-    }
-
-    private final String getObjects() throws MobyException {
-        Model model = ModelFactory.createDefaultModel();
-        createNsMap(model);
-        model = getObjects(model);
-        RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-        writer.setProperty("showXmlDeclaration", "false");
-        StringWriter out = new StringWriter();
-        writer.write(model, out, null);
-        return out.getBuffer().toString();
-    }
-
-    private final String getNamespaces() throws MobyException {
-        Model model = ModelFactory.createDefaultModel();
-        createNsMap(model);
-        model = getNamespaces(model);
-        RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-        writer.setProperty("showXmlDeclaration", "false");
-        StringWriter out = new StringWriter();
-        writer.write(model, out, null);
-        return out.getBuffer().toString();
-    }
-
-    private final String getServices() throws MobyException {
-        Model model = ModelFactory.createDefaultModel();
-        createNsMap(model);
-        model = getServices(model);
-        RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-        writer.setProperty("showXmlDeclaration", "false");
-        StringWriter out = new StringWriter();
-        writer.write(model, out, null);
-        return out.getBuffer().toString();
-    }
-
-    private final String getServiceInstances() {
-        Model model = ModelFactory.createDefaultModel();
-        createNsMap(model);
-        try {
-            model = getServiceInstances(model);
-        } catch (Exception e) {
-            e.printStackTrace();
-            return "";
-        }
-        RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
-        writer.setProperty("showXmlDeclaration", "false");
-        StringWriter out = new StringWriter();
-        writer.write(model, out, null);
-        return out.getBuffer().toString();
-    }
-
-    /**
-     * 
-     * @param str 
-     * @return an RDF document describing the ontology represented by str.
-     * @throws MobyException
-     */
-    public final String getRESOURCES(String str) throws MobyException {
-        String name = "";
-        if (str.lastIndexOf("/") > 0) {
-            // this is a url
-            name = str.substring(str.lastIndexOf("/") + 1);
-        } else
-            name = str;
-
-        if (name.equalsIgnoreCase("Objects")) {
-            return getObjects();
-        } else if (name.equalsIgnoreCase("Services")) {
-            return getServices();
-        } else if (name.equalsIgnoreCase("ServiceInstances")) {
-            return getServiceInstances();
-        } else if (name.equalsIgnoreCase("Namespaces")) {
-            return getNamespaces();
-        } else if (name.equalsIgnoreCase("Predicates")) {
-            return getPredicates();
-        }
-
-        return "";
-    }
-
-    private String getPredicates() {
-        StringBuffer buffer = new StringBuffer();
-        buffer.append(
-                "<rdf:RDF" + System.getProperty("line.separator") + "" + 
-        		"   xmlns:moby=\"http://biomoby.org/RESOURCES/MOBY-S/Predicates#\"" + System.getProperty("line.separator") + "" + 
-        		"   xmlns:mobyObject=\"http://biomoby.org/RESOURCES/MOBY-S/Objects#\"" + System.getProperty("line.separator") + "" +
-        		"   xmlns:serviceInstances=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#\"" + System.getProperty("line.separator") + "" +
-        		"   xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"" + System.getProperty("line.separator") + "" + 
-        		"   xmlns:xs=\"http://www.w3.org/2001/XMLSchema#\"" + System.getProperty("line.separator") + "" + 
-        		"   xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"" + System.getProperty("line.separator") + "" + 
-        		"   xmlns:owl=\"http://www.w3.org/2002/07/owl#\"" + System.getProperty("line.separator") + "" + 
-        		"   xmlns:dc=\"http://purl.org/dc/elements/1.1/\">" + System.getProperty("line.separator") + "");
-        // add the predicates here
-        buffer.append(createOntologyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "The BioMoby Predicates Vocabulary (moby)",
-                "This is the RDF Schema for the BioMoby Predicate vocabulary defined in the moby namespace."));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#hasa",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "hasa","The subject contains exactly one object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
-                "http://biomoby.org/RESOURCES/MOBY-S/Objects#Object"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#has",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "has","The subject contains one or more object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
-                "http://biomoby.org/RESOURCES/MOBY-S/Objects#Object"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#articleName",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "articleName","Uses a non-controlled vocabulary to describe the intended semantic relationship between the Subject node, and the node in which the Subject is associated through a HAS or HASA relationship.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#componentName",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "componentName","The subject is known to be named object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#namespace_type",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "namespace_type","The subject resource is applicable under the object namespace.",
-                "http://www.w3.org/2000/01/rdf-schema#Class", //TODO - namespace?
-                "http://www.w3.org/2000/01/rdf-schema#Resource"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#object_type",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "object_type","The subject resource is a resource object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
-                "http://www.w3.org/2000/01/rdf-schema#Resource"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#consumes",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "consumes","The subject container takes as input object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
-                "http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#produces",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "produces","The subject container produces as output object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
-                "http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#performs_task",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "performs_task","The subject performs the task of the object resource.",
-                "http://www.w3.org/2000/01/rdf-schema#Class", //TODO servicetype?
-                "http://www.w3.org/2000/01/rdf-schema#Resource"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#default_value",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "default_value","The subject has a default value of object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#min",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "min","The subject has a minimum value of object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#max",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "max","The subject has a maximum value of object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#enum",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "enum","The subject may assume the value of object.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#datatype",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "datatype","Idiomatic property used for structured values.",
-                "http://www.w3.org/2001/XMLSchema#type",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#signatureURL",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "signatureURL","Object is a URL that contains information on the subject.",
-                "http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#", //TODO
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#authoritative",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "authoritative","The object states whether the subject is authoritative.",
-                "http://www.w3.org/2000/01/rdf-schema#Class",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#ofType",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "ofType","The subject is of primitive type object.",
-                "http://www.w3.org/2000/01/rdf-schema#Class",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#sampleInputData",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "sampleInputData","Object is a sample of valid input that subject can handle.",
-                "http://www.w3.org/2000/01/rdf-schema#Property",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#sampleOutputData",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "sampleOutputData","Object is a sample of valid output created by running the subject.",
-                "http://www.w3.org/2000/01/rdf-schema#Property",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#approvedBy",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "approvedBy","The subject has been approved by object.",
-                "http://www.w3.org/2000/01/rdf-schema#Property",
-                "http://www.w3.org/2000/01/rdf-schema#Literal"));
-        
-        buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#Simple",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "Simple","A class representing a simple input or output.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent"));
-        
-        buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "Secondary","A class representing a secondary input.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent"));
-        
-        buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#Collection",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "Collection","A container for objects representing Simples.",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent"));
-        
-        buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyThing",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "mobyThing","NOT SURE",
-                "http://www.w3.org/2000/01/rdf-schema#Class"));
-        
-        buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyMessageComponent",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "MobyMessageComponent","NOT SURE",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyThing"));
-        
-        buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "DataComponent","NOT SURE",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyMessageComponent"));
-        
-        buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#StructuralComponent",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
-                "StructuralComponent","NOT SURE",
-                "http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyMessageComponent"));
-        
-        
-        // end the addition of predicates here
-        buffer.append(
-                "" + System.getProperty("line.separator") + "" + 
-        		"</rdf:RDF>");
-        return buffer.toString();
-    }
-
-    private String createPropertyBlock(String about, String definedBy,
-            String label, String comment, String domain, String range) {
-        String s = 
-            "" + System.getProperty("line.separator") + "<rdf:Property rdf:about=\"" + about + "\">" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:isDefinedBy rdf:resource=\"" + definedBy + "\"/>" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:label>" + label + "</rdfs:label>" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:comment>" + comment + "</rdfs:comment>" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:range rdf:resource=\"" + range + "\"/>" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:domain rdf:resource=\"" + domain + "\"/>" + System.getProperty("line.separator") + "" + 
-        	"</rdf:Property>" + System.getProperty("line.separator") + "";
-        return s;
-    }
-
-    private String createClassBlock(String about, String definedBy,
-            String label, String comment, String subClassOf) {
-        String s = 
-            "" + System.getProperty("line.separator") + "<rdfs:Class rdf:about=\""+ about +"\">" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:isDefinedBy rdf:resource=\""+ definedBy +"\"/>" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:label>"+ label +"</rdfs:label>" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:comment>"+ comment +"</rdfs:comment>" + System.getProperty("line.separator") + "" + 
-        	"  <rdfs:subClassOf rdf:resource=\""+ subClassOf +"\"/>" + System.getProperty("line.separator") + "" + 
-        	"</rdfs:Class>" + System.getProperty("line.separator") + "";
-        return s;
-    }
-
-    private String createDescriptionBlock(String about, String[] seeAlsos) {
-        if (seeAlsos == null)
-            return "" + System.getProperty("line.separator") + "<rdf:Description rdf:about=\""+ about +"\"/>";
-        StringBuffer sb = new StringBuffer();
-        sb.append("  <rdf:Description rdf:about=\""+ about +"\">" + System.getProperty("line.separator") + "");
-        for (int x = 0; x < seeAlsos.length; x++) {
-            sb.append("  <rdfs:seeAlso rdf:resource=\"" + seeAlsos[x] + "\"/>" + System.getProperty("line.separator") + "");
-        }
-        sb.append("</rdf:Description>" + System.getProperty("line.separator") + "");
-        return sb.toString();
-    }
-
-    private String createOntologyBlock(String about, String title,
-            String description) {
-        String s ="" + System.getProperty("line.separator") + "<owl:Ontology " + System.getProperty("line.separator") + "" + "     rdf:about=\"" + about
-                + "\">" + System.getProperty("line.separator") + "" + "  <dc:title>" + title + "</dc:title>" + System.getProperty("line.separator") + ""
-                + "  <dc:description>" + description + "</dc:description>" + System.getProperty("line.separator") + ""
-                + "</owl:Ontology>" + System.getProperty("line.separator") + "";
-        return s;
-    }
-
-    private String createEscapedComment(String comment) {
-        String s = "" + System.getProperty("line.separator") + "<!-- " + comment + " -->" + System.getProperty("line.separator") + "";
-        return s;
-    }
-
-    public static void main(String[] args) throws Exception {
-        System.out.println(new RESOURCE().getRESOURCES("ServiceInstances"));
-    }
-    
-    private final String serviceDescriptionVocabulary = "<?xml version=\'1.0\' encoding=\'ISO-8859-1\'?>" + System.getProperty("line.separator") + 
-    		"<!DOCTYPE rdf:RDF [" + System.getProperty("line.separator")  + 
-    		"	 <!ENTITY rdf \'http://www.w3.org/1999/02/22-rdf-syntax-ns#\'>" + System.getProperty("line.separator")  + 
-    		"	 <!ENTITY rdfs \'http://www.w3.org/2000/01/rdf-schema#\'>" + System.getProperty("line.separator")  + 
-    		"]>" + System.getProperty("line.separator")  + 
-    		"<rdf:RDF xmlns:rdf=\"&rdf;\"" + System.getProperty("line.separator")  + 
-    		"	 xmlns:rdfs=\"&rdfs;\">" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#authoritative\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://www.w3.org/2001/XMLSchema#string\"/>" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#organisation\"/>" + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#objectType\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:subPropertyOf rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#type\"/>" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://biomoby.org/RESOURCES/MOBY-S/Objects\"/><!-- but somehow this has to accommodate both our ontology and the myGrid ontology, so I don\'t think this will work very well as it stands.  We need to wait for their response.  -->" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>" + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#inNamespaces\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://www.mygrid.org.uk/ontology#parameterNamespace\"/>" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>" + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#namespaceType\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:subPropertyOf rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#type\"/><!-- do you want to check this compared to http://www.w3.org/1999/02/22-rdf-syntax-ns#type which is what myGrid seems to be using...  -->" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://biomoby.org/RESOURCES/MOBY-S/Namespaces\"/>  <!-- you had domain and range reversed here...domain is the left and range is the right side of the tripe -->" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameterNamespace\"/>" + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#datatype\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\"/>" + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#min\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\"/>" + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#max\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\" /> " + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#enum\">" + System.getProperty("line.separator")  + 
-    		"	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>" + System.getProperty("line.separator")  + 
-    		"	<rdfs:range rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\" /> " + System.getProperty("line.separator")  + 
-    		"</rdf:Property>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		"</rdf:RDF>" + System.getProperty("line.separator")  + 
-    		"" + System.getProperty("line.separator")  + 
-    		""; 
+			services = central.getServices();
+		} catch (MobyException e) {
+			e.printStackTrace();
+		}
+		if (central == null || services == null)
+			throw new MobyException(
+					"Could not retrieve useful information from CentralDigestImpl().getServices(String)");
+		return ServiceInstanceRDF.createRDFModel(model, services);
+	}
+
+	/**
+	 * <b>PRE: </b>
+	 * <p>
+	 * <b>POST: </b>
+	 * <p>
+	 * 
+	 * @param model
+	 * @return
+	 * @throws MobyException
+	 */
+	private final Model getServices(Model model) throws MobyException {
+
+		String[][] str = getTypes("Services");
+		if (str.equals("")) {
+			return null;
+		}
+		if (RUN_MAIN) {
+			createNsMap(model);
+		}
+		Resource subject = _addClassResource(model, "Service",
+				"urn:lsid:biomoby.org:servicetype:Service:2001-09-21T16-00-00Z",
+				"a base Service class, never instantiated", "openinformatics.com",
+				"markw at illuminae.com");
+		model.add(model.createStatement(subject, RDF.type, RDFS.Class));
+		for (int i = 0; i < str.length; i++) {
+			String[] _line = str[i];
+			String sub, pred, obj, def, lsid, authority, email, obj_lsid;
+			if (_line.length > 7) {
+				sub = _line[0];
+				pred = _line[1];
+				obj = _line[2];
+				def = _line[3];
+				lsid = _line[4];
+				authority = _line[5];
+				email = _line[6];
+				obj_lsid = _line[7];
+			} else {
+				continue;
+			}
+			Matcher m;
+			m = Pattern.compile(".*:isa$", Pattern.CASE_INSENSITIVE).matcher(pred);
+			if (m.matches()) {
+				// service types only have isa relationships and every service
+				// type has a parent, except the base service Service
+				Resource _subject = _addClassResource(model, sub, lsid, def, authority, email);
+				_addSubClass(model, _subject, obj_lsid);
+			}
+		}
+		return model;
+	}
+
+	/**
+	 * <b>PRE: </b>
+	 * <p>
+	 * <b>POST: </b>
+	 * <p>
+	 * 
+	 * @param model
+	 * @return
+	 * @throws MobyException
+	 */
+	private final Model getNamespaces(Model model) throws MobyException {
+		String[][] str = getTypes("Namespaces");
+		if (str == null) {
+			return null;
+		}
+		if (RUN_MAIN) {
+			createNsMap(model);
+		}
+		Resource subject = _addClassResource(model, "Namespace", NS + "Namespace",
+				"a base Namespace identifier, never instantiated", null, null);
+		model.add(model.createStatement(subject, RDF.type, RDFS.Class));
+		for (int x = 0; x < str.length; x++) {
+			String[] _line = str[x];
+			String sub = _line[0];
+			String def = "";
+			String lsid = "";
+			String authority = "";
+			String email = "";
+			if (_line.length > 4) {
+				def = _line[1];
+				lsid = _line[2];
+				authority = _line[3];
+				email = _line[4];
+			} else {
+				continue;
+			}
+			Resource _subject = _addClassResource(model, sub, lsid, def, authority, email);
+			_addSubClass(model, _subject, NS + "Namespace");
+		}
+		return model;
+	}
+
+	/**
+	 * <b>PRE: </b>
+	 * <p>
+	 * <b>POST: </b>
+	 * <p>
+	 * 
+	 * @param model
+	 * @throws MobyException
+	 */
+	private final Model getObjects(Model model) throws MobyException {
+		String[][] str = getTypes("Objects");
+		if (str == null) {
+			return null;
+		}
+		// add mobyPred prefix to model
+		if (RUN_MAIN) {
+			createNsMap(model);
+		}
+		// create the base object type "class"
+		Resource subject = _addClassResource(model, "Object",
+				"urn:lsid:biomoby.org:objectclass:Object",
+				"a base object class consisting of a namespace and an identifier",
+				"openinformatics.com", "jason at openinformatics.com");
+
+		for (int x = 0; x < str.length; x++) {
+			String[] _line = str[x];
+			String sub = "", pred = "", obj = "", def = "", articlename = "", lsid = "", authority = "", email = "", obj_lsid = "";
+			Matcher m;
+			if (_line.length > 8) {
+				sub = _line[0];
+				pred = _line[1];
+				obj = _line[2];
+				articlename = _line[3];
+				def = _line[4];
+				lsid = _line[5];
+				authority = _line[6];
+				email = _line[7];
+				obj_lsid = _line[8];
+
+				if (articlename.indexOf("(") >= 0)
+					articlename = articlename.substring(articlename.indexOf("(") + 1, articlename
+							.indexOf(")"));
+
+			} else {
+				continue;
+			}
+			Resource _subject = _addClassResource(model, sub, lsid, def, authority, email);
+
+			m = Pattern.compile(".*:isa$", Pattern.CASE_INSENSITIVE).matcher(pred);
+			if (m.matches()) {
+				// System.out.println("is " +pred);
+				_addSubClass(model, _subject, obj_lsid);
+			}
+			m = Pattern.compile(".*:hasa$", Pattern.CASE_INSENSITIVE).matcher(pred);
+			if (m.matches()) {
+				// System.out.println("hasa " +pred);
+				Resource bnode = model.createResource(model.getProperty(OBJ + obj));
+				_addHasaHas(model, bnode, _subject, Predicates.hasa, OBJ, obj, articlename);
+			}
+			m = Pattern.compile(".*:has$", Pattern.CASE_INSENSITIVE).matcher(pred);
+			if (m.matches()) {
+				// System.out.println("has " + pred);
+				Resource bnode = model.createResource(model.getProperty(OBJ + obj));
+				_addHasaHas(model, bnode, _subject, Predicates.has, OBJ, obj, articlename);
+			}
+		}
+		return model;
+	}
+
+	private final void createNsMap(Model model) {
+		Map map = model.getNsPrefixMap();
+		map.put("moby", Predicates.getURI());
+		map.put("mobyObject", OBJ);
+		map.put("serviceInstances", SI);
+		map.put("mobyNamespace", NS);
+		map.put("mobyService", SRV);
+		model.setNsPrefixes(map);
+	}
+
+	/**
+	 * <b>PRE: </b>
+	 * <p>
+	 * <b>POST: </b>
+	 * <p>
+	 * 
+	 * @param model
+	 * @param _resource
+	 * @param subject
+	 * @param mp2
+	 * @param string
+	 * @param obj2
+	 * @param obj3
+	 * @param articlename
+	 */
+	private final void _addHasaHas(Model model, Resource bnode, Resource subject, Property prop,
+			String objNS, String object, String articlename) {
+		Pattern p = Pattern.compile("urn:lsid.*:(\\S+)$");
+		Matcher m = p.matcher(object);
+		object = (m.matches() ? m.group(1) : object);
+		Resource resource = model.createResource(objNS + object);
+		model.add(model.createStatement(subject, prop, bnode));
+		model.add(model.createStatement(bnode, Predicates.articleName, model.createLiteral(
+				articlename, "en")));
+	}
+
+	private final void _addSubClass(Model model, Resource subject, String lsid) {
+		Resource resource = model.createResource(lsid);
+		model.add(model.createStatement(subject, RDFS.subClassOf, resource));
+	}
+
+	/*
+	 * TODO
+	 */
+	private final Resource _addClassResource(Model model, String label, String lsid, String def,
+			String authority, String email) {
+		Resource resource = model.createResource(lsid);
+		// addOfTypeProperty(model, resource, thing);
+		model.add(model.createStatement(resource, RDF.type, RDFS.Class));
+		model.add(model.createStatement(resource, RDFS.label, model.createLiteral(label)));
+		model.add(model.createStatement(resource, RDFS.comment, model.createLiteral(def, "en")));
+		// add email and authority
+		if (email != null && !email.equals(""))
+			model.add(model.createStatement(resource, DC.creator, model.createLiteral(email)));
+		if (authority != null && !authority.equals(""))
+			model
+					.add(model.createStatement(resource, DC.publisher, model
+							.createLiteral(authority)));
+		return resource;
+	}
+
+	private final String[][] getTypes(String type) throws MobyException {
+		if (type.equalsIgnoreCase("objects")) {
+			try {
+				return new JObjectsSqlImpl().getFullObjectsAsArray();
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+		} else if (type.equalsIgnoreCase("services")) {
+			try {
+				return new JServicesSqlImpl().getFullServicesAsArray();
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+		} else if (type.equalsIgnoreCase("namespaces")) {
+			try {
+				return new JNamespacesSqlImpl().getFullNamespacesAsArray();
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+		}
+		return null;
+	}
+
+	/*
+	 * 
+	 */
+	private String getURL(String url) {
+		StringBuffer sb = new StringBuffer();
+		try {
+			URL _url = new URL(url);
+			BufferedReader in = new BufferedReader(new InputStreamReader(_url.openStream()));
+			String inputLine;
+			while ((inputLine = in.readLine()) != null)
+				sb.append(inputLine + "\n");
+			in.close();
+		} catch (Exception e) {
+			e.printStackTrace();
+			System.err.println("Could not retrieve contents of URL.");
+		}
+		return sb.toString();
+	}
+
+	protected final void doPost(HttpServletRequest request, HttpServletResponse response)
+			throws ServletException, IOException {
+		response.sendError(HttpServletResponse.SC_METHOD_NOT_ALLOWED);
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see javax.servlet.GenericServlet#getServletInfo()
+	 */
+	public final String getServletInfo() {
+		return "jRESOURCE - JAVA implementation of the old /RESOURCES/ perl script by Edward Kawas";
+	}
+
+	private final String getObjects() throws MobyException {
+		Model model = ModelFactory.createDefaultModel();
+		createNsMap(model);
+		model = getObjects(model);
+		RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+		writer.setProperty("showXmlDeclaration", "false");
+		StringWriter out = new StringWriter();
+		writer.write(model, out, null);
+		return out.getBuffer().toString();
+	}
+
+	private final String getNamespaces() throws MobyException {
+		Model model = ModelFactory.createDefaultModel();
+		createNsMap(model);
+		model = getNamespaces(model);
+		RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+		writer.setProperty("showXmlDeclaration", "false");
+		StringWriter out = new StringWriter();
+		writer.write(model, out, null);
+		return out.getBuffer().toString();
+	}
+
+	private final String getServices() throws MobyException {
+		Model model = ModelFactory.createDefaultModel();
+		createNsMap(model);
+		model = getServices(model);
+		RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+		writer.setProperty("showXmlDeclaration", "false");
+		StringWriter out = new StringWriter();
+		writer.write(model, out, null);
+		return out.getBuffer().toString();
+	}
+
+	private final String getServiceInstances() {
+		Model model = ModelFactory.createDefaultModel();
+		try {
+			model = getServiceInstances(model);
+		} catch (Exception e) {
+			e.printStackTrace();
+			return "";
+		}
+		RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+		writer.setProperty("showXmlDeclaration", "false");
+		StringWriter out = new StringWriter();
+		writer.write(model, out, null);
+		return out.getBuffer().toString();
+	}
+
+	/**
+	 * 
+	 * @param str
+	 * @return an RDF document describing the ontology represented by str.
+	 * @throws MobyException
+	 */
+	public final String getRESOURCES(String str) throws MobyException {
+		String name = "";
+		if (str.lastIndexOf("/") > 0) {
+			// this is a url
+			name = str.substring(str.lastIndexOf("/") + 1);
+		} else
+			name = str;
+
+		if (name.equalsIgnoreCase("Objects")) {
+			return getObjects();
+		} else if (name.equalsIgnoreCase("Services")) {
+			return getServices();
+		} else if (name.equalsIgnoreCase("ServiceInstances")) {
+			return getServiceInstances();
+		} else if (name.equalsIgnoreCase("Namespaces")) {
+			return getNamespaces();
+		} else if (name.equalsIgnoreCase("Predicates")) {
+			return getPredicates();
+		}
+
+		return "";
+	}
+
+	private String getPredicates() {
+		StringBuffer buffer = new StringBuffer();
+		buffer
+				.append("<rdf:RDF"
+						+ System.getProperty("line.separator")
+						+ ""
+						+ "   xmlns:moby=\"http://biomoby.org/RESOURCES/MOBY-S/Predicates#\""
+						+ System.getProperty("line.separator")
+						+ ""
+						+ "   xmlns:mobyObject=\"http://biomoby.org/RESOURCES/MOBY-S/Objects#\""
+						+ System.getProperty("line.separator")
+						+ ""
+						+ "   xmlns:serviceInstances=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#\""
+						+ System.getProperty("line.separator") + ""
+						+ "   xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\""
+						+ System.getProperty("line.separator") + ""
+						+ "   xmlns:xs=\"http://www.w3.org/2001/XMLSchema#\""
+						+ System.getProperty("line.separator") + ""
+						+ "   xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\""
+						+ System.getProperty("line.separator") + ""
+						+ "   xmlns:owl=\"http://www.w3.org/2002/07/owl#\""
+						+ System.getProperty("line.separator") + ""
+						+ "   xmlns:dc=\"http://purl.org/dc/elements/1.1/\">"
+						+ System.getProperty("line.separator") + "");
+		// add the predicates here
+		buffer
+				.append(createOntologyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
+						"The BioMoby Predicates Vocabulary (moby)",
+						"This is the RDF Schema for the BioMoby Predicate vocabulary defined in the moby namespace."));
+
+		buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#hasa",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "hasa",
+				"The subject contains exactly one object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
+				"http://biomoby.org/RESOURCES/MOBY-S/Objects#Object"));
+
+		buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#has",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "has",
+				"The subject contains one or more object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
+				"http://biomoby.org/RESOURCES/MOBY-S/Objects#Object"));
+
+		buffer
+				.append(createPropertyBlock(
+						"http://biomoby.org/RESOURCES/MOBY-S/Predicates#articleName",
+						"http://biomoby.org/RESOURCES/MOBY-S/Predicates#",
+						"articleName",
+						"Uses a non-controlled vocabulary to describe the intended semantic relationship between the Subject node, and the node in which the Subject is associated through a HAS or HASA relationship.",
+						"http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
+						"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#componentName",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "componentName",
+				"The subject is known to be named object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#namespace_type",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "namespace_type",
+				"The subject resource is applicable under the object namespace.",
+				"http://www.w3.org/2000/01/rdf-schema#Class", // TODO -
+				// namespace?
+				"http://www.w3.org/2000/01/rdf-schema#Resource"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#object_type",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "object_type",
+				"The subject resource is a resource object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Objects#Object",
+				"http://www.w3.org/2000/01/rdf-schema#Resource"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#consumes",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "consumes",
+				"The subject container takes as input object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
+				"http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#produces",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "produces",
+				"The subject container produces as output object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
+				"http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#performs_task",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "performs_task",
+				"The subject performs the task of the object resource.",
+				"http://www.w3.org/2000/01/rdf-schema#Class", // TODO
+				// servicetype?
+				"http://www.w3.org/2000/01/rdf-schema#Resource"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#default_value",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "default_value",
+				"The subject has a default value of object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#min",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "min",
+				"The subject has a minimum value of object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#max",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "max",
+				"The subject has a maximum value of object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#enum",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "enum",
+				"The subject may assume the value of object.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#datatype",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "datatype",
+				"Idiomatic property used for structured values.",
+				"http://www.w3.org/2001/XMLSchema#type",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#signatureURL",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "signatureURL",
+				"Object is a URL that contains information on the subject.",
+				"http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#", // TODO
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#authoritative",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "authoritative",
+				"The object states whether the subject is authoritative.",
+				"http://www.w3.org/2000/01/rdf-schema#Class",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#ofType",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "ofType",
+				"The subject is of primitive type object.",
+				"http://www.w3.org/2000/01/rdf-schema#Class",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#sampleInputData",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "sampleInputData",
+				"Object is a sample of valid input that subject can handle.",
+				"http://www.w3.org/2000/01/rdf-schema#Property",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#sampleOutputData",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "sampleOutputData",
+				"Object is a sample of valid output created by running the subject.",
+				"http://www.w3.org/2000/01/rdf-schema#Property",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createPropertyBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#approvedBy",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "approvedBy",
+				"The subject has been approved by object.",
+				"http://www.w3.org/2000/01/rdf-schema#Property",
+				"http://www.w3.org/2000/01/rdf-schema#Literal"));
+
+		buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#Simple",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "Simple",
+				"A class representing a simple input or output.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent"));
+
+		buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#Secondary",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "Secondary",
+				"A class representing a secondary input.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent"));
+
+		buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#Collection",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "Collection",
+				"A container for objects representing Simples.",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent"));
+
+		buffer.append(createClassBlock("http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyThing",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "mobyThing", "NOT SURE",
+				"http://www.w3.org/2000/01/rdf-schema#Class"));
+
+		buffer.append(createClassBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyMessageComponent",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "MobyMessageComponent",
+				"NOT SURE", "http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyThing"));
+
+		buffer.append(createClassBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#DataComponent",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "DataComponent", "NOT SURE",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyMessageComponent"));
+
+		buffer.append(createClassBlock(
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#StructuralComponent",
+				"http://biomoby.org/RESOURCES/MOBY-S/Predicates#", "StructuralComponent",
+				"NOT SURE", "http://biomoby.org/RESOURCES/MOBY-S/Predicates#MobyMessageComponent"));
+
+		// end the addition of predicates here
+		buffer.append("" + System.getProperty("line.separator") + "" + "</rdf:RDF>");
+		return buffer.toString();
+	}
+
+	private String createPropertyBlock(String about, String definedBy, String label,
+			String comment, String domain, String range) {
+		String s = "" + System.getProperty("line.separator") + "<rdf:Property rdf:about=\"" + about
+				+ "\">" + System.getProperty("line.separator") + ""
+				+ "  <rdfs:isDefinedBy rdf:resource=\"" + definedBy + "\"/>"
+				+ System.getProperty("line.separator") + "" + "  <rdfs:label>" + label
+				+ "</rdfs:label>" + System.getProperty("line.separator") + "" + "  <rdfs:comment>"
+				+ comment + "</rdfs:comment>" + System.getProperty("line.separator") + ""
+				+ "  <rdfs:range rdf:resource=\"" + range + "\"/>"
+				+ System.getProperty("line.separator") + "" + "  <rdfs:domain rdf:resource=\""
+				+ domain + "\"/>" + System.getProperty("line.separator") + "" + "</rdf:Property>"
+				+ System.getProperty("line.separator") + "";
+		return s;
+	}
+
+	private String createClassBlock(String about, String definedBy, String label, String comment,
+			String subClassOf) {
+		String s = "" + System.getProperty("line.separator") + "<rdfs:Class rdf:about=\"" + about
+				+ "\">" + System.getProperty("line.separator") + ""
+				+ "  <rdfs:isDefinedBy rdf:resource=\"" + definedBy + "\"/>"
+				+ System.getProperty("line.separator") + "" + "  <rdfs:label>" + label
+				+ "</rdfs:label>" + System.getProperty("line.separator") + "" + "  <rdfs:comment>"
+				+ comment + "</rdfs:comment>" + System.getProperty("line.separator") + ""
+				+ "  <rdfs:subClassOf rdf:resource=\"" + subClassOf + "\"/>"
+				+ System.getProperty("line.separator") + "" + "</rdfs:Class>"
+				+ System.getProperty("line.separator") + "";
+		return s;
+	}
+
+	private String createDescriptionBlock(String about, String[] seeAlsos) {
+		if (seeAlsos == null)
+			return "" + System.getProperty("line.separator") + "<rdf:Description rdf:about=\""
+					+ about + "\"/>";
+		StringBuffer sb = new StringBuffer();
+		sb.append("  <rdf:Description rdf:about=\"" + about + "\">"
+				+ System.getProperty("line.separator") + "");
+		for (int x = 0; x < seeAlsos.length; x++) {
+			sb.append("  <rdfs:seeAlso rdf:resource=\"" + seeAlsos[x] + "\"/>"
+					+ System.getProperty("line.separator") + "");
+		}
+		sb.append("</rdf:Description>" + System.getProperty("line.separator") + "");
+		return sb.toString();
+	}
+
+	private String createOntologyBlock(String about, String title, String description) {
+		String s = "" + System.getProperty("line.separator") + "<owl:Ontology "
+				+ System.getProperty("line.separator") + "" + "     rdf:about=\"" + about + "\">"
+				+ System.getProperty("line.separator") + "" + "  <dc:title>" + title
+				+ "</dc:title>" + System.getProperty("line.separator") + "" + "  <dc:description>"
+				+ description + "</dc:description>" + System.getProperty("line.separator") + ""
+				+ "</owl:Ontology>" + System.getProperty("line.separator") + "";
+		return s;
+	}
+
+	private String createEscapedComment(String comment) {
+		String s = "" + System.getProperty("line.separator") + "<!-- " + comment + " -->"
+				+ System.getProperty("line.separator") + "";
+		return s;
+	}
+
+	public static void main(String[] args) throws Exception {
+		CentralDigest central = new CentralDigestImpl(
+				"http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl");
+		MobyService[] services = central.getServices();
+
+		Model m = ServiceInstanceRDF.createRDFModel(ModelFactory.createDefaultModel(), services);
+		RDFWriter writer = m.getWriter("RDF/XML-ABBREV");
+		writer.setProperty("showXmlDeclaration", "false");
+		writer.setProperty("tab", "5");
+		writer.write(m, System.out, null);
+	}
+
+	private final String serviceDescriptionVocabulary = "<?xml version=\'1.0\' encoding=\'ISO-8859-1\'?>"
+			+ System.getProperty("line.separator")
+			+ "<!DOCTYPE rdf:RDF ["
+			+ System.getProperty("line.separator")
+			+ "	 <!ENTITY rdf \'http://www.w3.org/1999/02/22-rdf-syntax-ns#\'>"
+			+ System.getProperty("line.separator")
+			+ "	 <!ENTITY rdfs \'http://www.w3.org/2000/01/rdf-schema#\'>"
+			+ System.getProperty("line.separator")
+			+ "]>"
+			+ System.getProperty("line.separator")
+			+ "<rdf:RDF xmlns:rdf=\"&rdf;\""
+			+ System.getProperty("line.separator")
+			+ "	 xmlns:rdfs=\"&rdfs;\">"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#authoritative\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://www.w3.org/2001/XMLSchema#string\"/>"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#organisation\"/>"
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#objectType\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:subPropertyOf rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#type\"/>"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://biomoby.org/RESOURCES/MOBY-S/Objects\"/><!-- but somehow this has to accommodate both our ontology and the myGrid ontology, so I don\'t think this will work very well as it stands.  We need to wait for their response.  -->"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>"
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#inNamespaces\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://www.mygrid.org.uk/ontology#parameterNamespace\"/>"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>"
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#namespaceType\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:subPropertyOf rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#type\"/><!-- do you want to check this compared to http://www.w3.org/1999/02/22-rdf-syntax-ns#type which is what myGrid seems to be using...  -->"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://biomoby.org/RESOURCES/MOBY-S/Namespaces\"/>  <!-- you had domain and range reversed here...domain is the left and range is the right side of the tripe -->"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameterNamespace\"/>"
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#datatype\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\"/>"
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#min\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\"/>"
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#max\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\" /> "
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "<rdf:Property rdf:about=\"http://biomoby.org/RESOURCES/MOBY-S/ServiceDescription#enum\">"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:domain rdf:resource=\"http://www.mygrid.org.uk/ontology#parameter\"/>"
+			+ System.getProperty("line.separator")
+			+ "	<rdfs:range rdf:resource=\"http://www.w3.org/2000/01/rdf-schema#Literal\" /> "
+			+ System.getProperty("line.separator")
+			+ "</rdf:Property>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator")
+			+ "</rdf:RDF>"
+			+ System.getProperty("line.separator")
+			+ ""
+			+ System.getProperty("line.separator") + "";
 
 }
\ No newline at end of file

More information about the MOBY-guts mailing list