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

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This commit is contained in:
stellamit 2011-09-29 19:06:47 +00:00
parent 1d321f6c83
commit cc639de7f4
5 changed files with 63 additions and 5 deletions
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2
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/OntologyController.java
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@ -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{
@ -162,6 +163,7 @@ public class OntologyController extends VitroHttpServlet{
doNotFound(req,res);
return;
} else {
JenaOutputUtils.setNameSpacePrefixes(newModel,vreq.getWebappDaoFactory());
res.setContentType(rdfFormat.getMediaType());
String format = "";
if ( RDFXML_MIMETYPE.equals(rdfFormat.getMediaType()))

3
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/IndividualController.java
View file

@ -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);
}

7
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaExportController.java
View file

@ -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
}

2
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
View file

@ -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();

52
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaOutputUtils.java Normal file
View file

@ -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;
}
}