NIHVIVO-3198 - include namespace prefixes defined via VIVO admin interface in the RDF output from VIVO

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

@@ -27,6 +27,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.shared.Lock;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
+import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 import edu.cornell.mannlib.vitro.webapp.web.ContentType;
 
 public class OntologyController extends VitroHttpServlet{
@@ -161,7 +162,8 @@ public class OntologyController extends VitroHttpServlet{
             //respond to HTTP outside of critical section
             doNotFound(req,res);
             return;
-        } else {		
+        } else {	
+        	JenaOutputUtils.setNameSpacePrefixes(newModel,vreq.getWebappDaoFactory());
             res.setContentType(rdfFormat.getMediaType());
             String format = ""; 
             if ( RDFXML_MIMETYPE.equals(rdfFormat.getMediaType()))

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

@@ -57,6 +57,7 @@ import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
 import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
 import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapperFactory;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.ExtendedLinkedDataUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 import edu.cornell.mannlib.vitro.webapp.web.ContentType;
 import edu.cornell.mannlib.vitro.webapp.web.beanswrappers.ReadOnlyBeansWrapper;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModel;
@@ -354,7 +355,7 @@ public class IndividualController extends FreemarkerHttpServlet {
                 
         String[] includes = vreq.getParameterValues("include");
 		Model newModel = getRDF(individual,ontModel,ModelFactory.createDefaultModel(),0,includes);		
-		
+		JenaOutputUtils.setNameSpacePrefixes(newModel, vreq.getWebappDaoFactory());
 		return new RdfResponseValues(rdfFormat, newModel);
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaExportController.java

@@ -13,20 +13,19 @@ import javax.servlet.http.HttpServletResponse;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.DatasetFactory;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.shared.Lock;
 
 import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.EditOntology;
+import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
-import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
+import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 
 public class JenaExportController extends BaseEditController {
 	private static final Actions REQUIRED_ACTIONS = new Actions(
@@ -177,6 +176,8 @@ public class JenaExportController extends BaseEditController {
 			
 		}
 		
+		JenaOutputUtils.setNameSpacePrefixes(model,vreq.getWebappDaoFactory());
+		
 		if ( formatParam == null ) {
 			formatParam = "RDF/XML-ABBREV";  // default
 		}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java

@@ -78,6 +78,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetup;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestWorkflowProcessor;
+import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.WorkflowOntology;
 
 public class JenaIngestController extends BaseEditController {
@@ -324,6 +325,7 @@ public class JenaIngestController extends BaseEditController {
 			                               String modelType) {
 		String modelNameStr = vreq.getParameter("modelName");
 		Model model = getModel(modelNameStr,vreq);
+		JenaOutputUtils.setNameSpacePrefixes(model,vreq.getWebappDaoFactory());
 		model.enterCriticalSection(Lock.READ);
 		try {
 			OutputStream out = response.getOutputStream();

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaOutputUtils.java

@@ -0,0 +1,52 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.utils.jena;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import com.hp.hpl.jena.rdf.model.Model;
+
+import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+
+public class JenaOutputUtils {
+	
+	private static final Log log = LogFactory.getLog(JenaOutputUtils.class.getName());
+		
+	public static void setNameSpacePrefixes(Model model, WebappDaoFactory wadf) {
+		
+		Map<String,String> prefixes = new HashMap<String,String>();
+		List<Ontology> ontologies = wadf.getOntologyDao().getAllOntologies();
+		Iterator<Ontology> iter = ontologies.iterator();
+		String namespace = null;
+		String prefix = null;
+		
+		prefixes.put("vitro", "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#");
+		while (iter.hasNext()) {
+			Ontology ontology = iter.next();
+            			
+			namespace = ontology.getURI(); // this method returns the namespace
+            if (namespace == null || namespace.isEmpty()) {
+            	log.warn("ontology with empty namespace found");
+            	continue;
+            }
+            
+            prefix = ontology.getPrefix();
+            if (prefix == null || prefix.isEmpty()) {
+            	log.info("no prefix found for namespace: " + namespace);
+            	continue;
+            }
+            
+			prefixes.put(prefix,namespace);
+		}
+	    
+		model.setNsPrefixes(prefixes);
+		return;
+	}	
+}