NIHVIVO-3877 and NIHVIVO-3872 using RDFService for aspects of import and export

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

@@ -3,7 +3,10 @@
 package edu.cornell.mannlib.vitro.webapp.controller.jena;
 
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.OutputStream;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -11,6 +14,7 @@ import javax.servlet.RequestDispatcher;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -28,6 +32,11 @@ 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.dao.jena.RDFServiceModelMaker;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 
 public class JenaExportController extends BaseEditController {
@@ -116,12 +125,10 @@ public class JenaExportController extends BaseEditController {
 						getServletContext()).getABoxModel();
 			}
 			else if("full".equals(assertedOrInferredParam)){
-				model = ModelContext.getUnionOntModelSelector(
+			    outputSparqlConstruct(ABOX_FULL_CONSTRUCT, formatParam, response);
-						getServletContext()).getABoxModel();
 			}
 			else if("asserted".equals(assertedOrInferredParam)){
-				model = ModelContext.getBaseOntModelSelector(
+			    outputSparqlConstruct(ABOX_ASSERTED_CONSTRUCT, formatParam, response);
-						getServletContext()).getABoxModel();
 			}
 		}
 		else if("tbox".equals(subgraphParam)){
@@ -161,46 +168,16 @@ public class JenaExportController extends BaseEditController {
 						getServletContext()).getTBoxModel());
 			}
 			else if("full".equals(assertedOrInferredParam)){
-				ontModel = xutil.extractTBox(dataset, ontologyURI, FULL_GRAPH);
+			    outputSparqlConstruct(FULL_FULL_CONSTRUCT, formatParam, response);
-				ontModel.addSubModel(ModelContext.getUnionOntModelSelector(
-						getServletContext()).getABoxModel());
-				ontModel.addSubModel(ModelContext.getUnionOntModelSelector(
-						getServletContext()).getTBoxModel());
-				ontModel.addSubModel(ModelContext.getUnionOntModelSelector(
-						getServletContext()).getApplicationMetadataModel());
 			}
 			else{
-				ontModel = xutil.extractTBox(
+			    outputSparqlConstruct(FULL_ASSERTED_CONSTRUCT, formatParam, response);
-						dataset, ontologyURI, ASSERTIONS_GRAPH);
-				ontModel.addSubModel(ModelContext.getBaseOntModelSelector(
-						getServletContext()).getABoxModel());
-				ontModel.addSubModel(ModelContext.getBaseOntModelSelector(
-						getServletContext()).getTBoxModel());
-				ontModel.addSubModel(ModelContext.getBaseOntModelSelector(
-						getServletContext()).getApplicationMetadataModel());
 			}
 			
 		}
 		
 		JenaOutputUtils.setNameSpacePrefixes(model,vreq.getWebappDaoFactory());
-		
+		setHeaders(response, formatParam);
-		if ( formatParam == null ) {
-			formatParam = "RDF/XML-ABBREV";  // default
-		}
-		String mime = formatToMimetype.get( formatParam );
-		if ( mime == null ) {
-			throw new RuntimeException( "Unsupported RDF format " + formatParam);
-		}
-		
-		response.setContentType( mime );
-		if(mime.equals("application/rdf+xml"))
-			response.setHeader("content-disposition", "attachment; filename=" + "export.rdf");
-		else if(mime.equals("text/n3"))
-			response.setHeader("content-disposition", "attachment; filename=" + "export.n3");
-		else if(mime.equals("text/plain"))
-			response.setHeader("content-disposition", "attachment; filename=" + "export.txt");
-		else if(mime.equals("application/x-turtle"))
-			response.setHeader("content-disposition", "attachment; filename=" + "export.ttl");
 
 		try {
 			OutputStream outStream = response.getOutputStream();
@@ -237,6 +214,50 @@ public class JenaExportController extends BaseEditController {
 		
 	}
 	
+	private void setHeaders(HttpServletResponse response, String formatParam) {
+	       if ( formatParam == null ) {
+	            formatParam = "RDF/XML-ABBREV";  // default
+	        }
+	        String mime = formatToMimetype.get( formatParam );
+	        if ( mime == null ) {
+	            throw new RuntimeException( "Unsupported RDF format " + formatParam);
+	        }
+	        
+	        response.setContentType( mime );
+	        if(mime.equals("application/rdf+xml"))
+	            response.setHeader("content-disposition", "attachment; filename=" + "export.rdf");
+	        else if(mime.equals("text/n3"))
+	            response.setHeader("content-disposition", "attachment; filename=" + "export.n3");
+	        else if(mime.equals("text/plain"))
+	            response.setHeader("content-disposition", "attachment; filename=" + "export.txt");
+	        else if(mime.equals("application/x-turtle"))
+	            response.setHeader("content-disposition", "attachment; filename=" + "export.ttl");
+	}
+	
+	private void outputSparqlConstruct(String queryStr, String formatParam, 
+	        HttpServletResponse response) {
+	    RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(getServletContext()).getRDFService();
+	    try {
+	        setHeaders(response, formatParam);
+	        OutputStream out = response.getOutputStream();
+            if ( formatParam.startsWith("RDF/XML") ) {
+                out.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>".getBytes());
+            }
+	        InputStream in = rdfService.sparqlConstructQuery(
+	                queryStr, RDFServiceUtils.getSerializationFormatFromJenaString(
+	                        formatParam));
+	        IOUtils.copy(in, out);
+	        out.flush();
+	        out.close();
+	    } catch (RDFServiceException e) {
+	        throw new RuntimeException(e);
+	    } catch (IOException ioe) {
+	        throw new RuntimeException(ioe);
+	    } finally {
+	        rdfService.close();
+	    }	    
+	}
+	
 	private void prepareExportSelectionPage( VitroRequest vreq, HttpServletResponse response ) {
 		vreq.setAttribute( "bodyJsp", Controllers.EXPORT_SELECTION_JSP );
 		RequestDispatcher dispatcher = vreq.getRequestDispatcher( Controllers.BASIC_JSP );
@@ -278,16 +299,35 @@ public class JenaExportController extends BaseEditController {
 		formatToExtension.put("RDF/XML",".rdf");
 		formatToExtension.put("RDF/XML-ABBREV",".rdf");
 		formatToExtension.put("N3",".n3");
-		formatToExtension.put("N-TRIPLES",".nt");
+		formatToExtension.put("N-TRIPLE",".nt");
 		formatToExtension.put("TURTLE",".ttl");
 		
 		formatToMimetype = new HashMap<String,String>();
 		formatToMimetype.put("RDF/XML","application/rdf+xml");
 		formatToMimetype.put("RDF/XML-ABBREV","application/rdf+xml");
 		formatToMimetype.put("N3","text/n3");
-		formatToMimetype.put("N-TRIPLES", "text/plain");
+		formatToMimetype.put("N-TRIPLE", "text/plain");
 		formatToMimetype.put("TURTLE", "application/x-turtle");
 		
 	}
 	
+	private static final String ABOX_FULL_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
+	        "WHERE { GRAPH ?g { ?s ?p ?o } FILTER (!regex(str(?g), \"tbox\")) " +
+            "FILTER (?g != <" + JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL + ">) " +
+            "FILTER (?g != <" + RDFServiceModelMaker.METADATA_MODEL_URI + ">) }";
+	
+	private static final String ABOX_ASSERTED_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
+            "WHERE { GRAPH ?g { ?s ?p ?o } FILTER (!regex(str(?g), \"tbox\")) " + 
+	        "FILTER (?g != <" + JenaDataSourceSetupBase.JENA_INF_MODEL + ">) " +
+	        "FILTER (?g != <" + JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL + ">) " +
+	        "FILTER (?g != <" + RDFServiceModelMaker.METADATA_MODEL_URI + ">) }";
+	
+	private static final String FULL_FULL_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
+            "WHERE { ?s ?p ?o }";
+
+    private static final String FULL_ASSERTED_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
+            "WHERE { GRAPH ?g { ?s ?p ?o } " + 
+            "FILTER (?g != <" + JenaDataSourceSetupBase.JENA_INF_MODEL + ">) " +
+            "FILTER (?g != <" + JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL + ">) }";
+    
 }

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

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.jena;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
+import java.net.URL;
 import java.util.List;
 import java.util.Map;
 
@@ -41,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.filestorage.uploadrequest.FileUploadServ
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 public class RDFUploadController extends JenaIngestController {
@@ -239,7 +241,13 @@ public class RDFUploadController extends JenaIngestController {
         ModelMaker maker = getVitroJenaModelMaker(request);
         
         if (docLoc!=null && modelName != null) {
-            doLoadRDFData(modelName, docLoc, filePath, languageStr, maker);
+            RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(
+                    getServletContext()).getRDFService();
+            try {
+                doLoadRDFData(modelName, docLoc, filePath, languageStr, rdfService);
+            } finally {
+                rdfService.close();
+            }
             String modelType = getModelType(request, maker);
             showModelList(request, maker, modelType);
         } else {
@@ -319,12 +327,12 @@ public class RDFUploadController extends JenaIngestController {
                                String docLoc, 
                                String filePath, 
                                String language, 
-                               ModelMaker modelMaker) {
+                               RDFService rdfService) {
-        Model m = modelMaker.getModel(modelName);
-        m.enterCriticalSection(Lock.WRITE);
         try {
             if ( (docLoc != null) && (docLoc.length()>0) ) {
-                m.read(docLoc, language);
+                URL docLocURL = new URL(docLoc);
+                InputStream in = docLocURL.openStream();
+                readIntoModel(in, language, rdfService, modelName);
             } else if ( (filePath != null) && (filePath.length()>0) ) {
                 File file = new File(filePath);
                 File[] files;
@@ -338,7 +346,8 @@ public class RDFUploadController extends JenaIngestController {
                     File currentFile = files[i];
                     log.debug("Reading file " + currentFile.getName());
                     try {
-                        m.read(fileStream.getInputStream(), null, language);
+                        readIntoModel(fileStream.getInputStream(), language, 
+                                rdfService, modelName);
                         fileStream.delete();
                     } catch (IOException ioe) {
                         String errMsg = "Error loading RDF from " + 
@@ -348,8 +357,20 @@ public class RDFUploadController extends JenaIngestController {
                     }
                 }
             }
-        } finally { 
+        } catch (IOException e) {
-            m.leaveCriticalSection();
+            throw new RuntimeException(e);
+        }
+    }
+    
+    private void readIntoModel(InputStream in, String language, 
+            RDFService rdfService, String modelName) {
+        ChangeSet cs = rdfService.manufactureChangeSet();
+        cs.addAddition(in, RDFServiceUtils.getSerializationFormatFromJenaString(
+                        language), modelName);
+        try {
+            rdfService.changeSetUpdate(cs);
+        } catch (RDFServiceException e) {
+            throw new RuntimeException(e);
         }
     }
     

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceUtils.java

@@ -30,8 +30,6 @@ public class RDFServiceUtils {
 	
     private static final String RDFSERVICEFACTORY_ATTR = 
             RDFServiceUtils.class.getName() + ".RDFServiceFactory";
-    private static final String RDFSERVICEFACTORY_FILTERING_ATTR = 
-            RDFServiceUtils.class.getName() + ".RDFServiceFactory.Filtering";
     
        
     public static RDFServiceFactory getRDFServiceFactory(ServletContext context) {
@@ -80,11 +78,27 @@ public class RDFServiceUtils {
                 return "RDF/XML";
             case N3: 
                 return "N3";
+            case NTRIPLE:
+                return "N-TRIPLE";
             default: 
                 throw new RuntimeException("unexpected format in getSerializationFormatString");
         }
     }
     
+    public static ModelSerializationFormat getSerializationFormatFromJenaString(String jenaString) {
+        if ("N3".equals(jenaString) || "TTL".equals(jenaString) 
+                || "TURTLE".equals(jenaString)) {
+            return ModelSerializationFormat.N3;
+        } else if ("N-TRIPLE".equals(jenaString)) {
+            return ModelSerializationFormat.NTRIPLE;
+        } else if ("RDF/XML".equals(jenaString) 
+                || "RDF/XML-ABBREV".equals(jenaString)) {
+            return ModelSerializationFormat.RDFXML;
+        } else {
+            throw new RuntimeException("unrecognized format " + jenaString);
+        }
+    }
+    
     public static RDFService getRDFService(VitroRequest vreq) {
         return getRDFServiceFactory(
                 vreq.getSession().getServletContext()).getRDFService();

webapp/web/jenaIngest/exportSelection.jsp

@@ -39,7 +39,7 @@
     <option value="RDF/XML">RDF/XML</option>
     <option value="RDF/XML-ABBREV">RDF/XML abbrev.</option>
     <option value="N3">N3</option>
-    <option value="N-TRIPLES">N-Triples</option>
+    <option value="N-TRIPLE">N-Triples</option>
     <option value="TURTLE">Turtle</option>
 </select>
 

webapp/web/templates/edit/specific/ontologies_edit.jsp

@@ -62,7 +62,7 @@
 	                <input type="radio" name="format" value="RDF/XML-ABBREV" checked="checked" selected="selected"/> RDF/XML abbreviated
 	                <input type="radio" name="format" value="RDF/XML"/> RDF/XML
 	                <input type="radio" name="format" value="N3"/> N3
-	                <input type="radio" name="format" value="N-TRIPLES"/> N-Triples
+	                <input type="radio" name="format" value="N-TRIPLE"/> N-Triples
 	                <input type="radio" name="format" value="TURTLE"/> Turtle
                 </div>
             </form>