NIHVIVO-437 adding new controller to serve local ontology extensions as linked data
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package edu.cornell.mannlib.vitro.webapp.controller;
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import java.io.IOException;
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import java.io.UnsupportedEncodingException;
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import java.net.URLEncoder;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import javax.servlet.RequestDispatcher;
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import javax.servlet.ServletException;
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import javax.servlet.ServletOutputStream;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import javax.servlet.http.HttpSession;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.OntClass;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntProperty;
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import com.hp.hpl.jena.ontology.OntResource;
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import com.hp.hpl.jena.query.QueryExecutionFactory;
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import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
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import edu.cornell.mannlib.vitro.webapp.beans.Individual;
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import edu.cornell.mannlib.vitro.webapp.beans.Portal;
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import edu.cornell.mannlib.vitro.webapp.beans.VClass;
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import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
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import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
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import edu.cornell.mannlib.vitro.webapp.web.ContentType;
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public class OntologyController extends VitroHttpServlet{
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private static final Log log = LogFactory.getLog(OntologyController.class.getName());
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private String default_jsp = Controllers.BASIC_JSP;
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private String default_body_jsp = Controllers.ENTITY_JSP;
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private ApplicationBean appBean;
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public void doPost(HttpServletRequest request, HttpServletResponse response)
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throws ServletException,IOException{
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doGet(request, response);
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}
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public void doGet(HttpServletRequest req, HttpServletResponse res)
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throws ServletException,IOException{
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super.doGet(req, res);
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//get URL without hostname or servlet context
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String url = req.getRequestURI().substring(req.getContextPath().length());
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String redirectURL = checkForRedirect ( url, req.getHeader("accept") );
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if( redirectURL != null ){
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doRedirect( req, res, redirectURL );
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return;
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}
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ContentType rdfFormat = checkForLinkedDataRequest(url,req.getHeader("accept"));
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if( rdfFormat != null ){
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doRdf(req, res, rdfFormat );
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return;
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}
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}
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private static Pattern RDF_REQUEST = Pattern.compile("^/ontology/([^/]*)/([^/]*).rdf$");
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private static Pattern N3_REQUEST = Pattern.compile("^/ontology/([^/]*)/([^/]*).n3$");
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private static Pattern TTL_REQUEST = Pattern.compile("^/ontology/([^/]*)/([^/]*).ttl$");
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private static Pattern HTML_REQUEST = Pattern.compile("^/ontology/([^/]*)$");
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protected ContentType checkForLinkedDataRequest(String url, String acceptHeader) {
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try {
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//check the accept header
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if (acceptHeader != null) {
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List<ContentType> actualContentTypes = new ArrayList<ContentType>();
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actualContentTypes.add(new ContentType( XHTML_MIMETYPE ));
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actualContentTypes.add(new ContentType( HTML_MIMETYPE ));
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actualContentTypes.add(new ContentType( RDFXML_MIMETYPE ));
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actualContentTypes.add(new ContentType( N3_MIMETYPE ));
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actualContentTypes.add(new ContentType( TTL_MIMETYPE ));
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ContentType best = ContentType.getBestContentType(acceptHeader,actualContentTypes);
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if (best!=null && (
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RDFXML_MIMETYPE.equals(best.getMediaType()) ||
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N3_MIMETYPE.equals(best.getMediaType()) ||
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TTL_MIMETYPE.equals(best.getMediaType()) ))
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return best;
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}
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/*
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* check for parts of URL that indicate request for RDF
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http://vivo.cornell.edu/ontology/(ontologyname)/n23.rdf
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http://vivo.cornell.edu/ontology/(ontologyname)/n23.n3
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http://vivo.cornell.edu/ontology/(ontologyname)/n23.ttl
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*/
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Matcher m = RDF_REQUEST.matcher(url);
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if( m.matches() ){
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return new ContentType(RDFXML_MIMETYPE);}
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m = N3_REQUEST.matcher(url);
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if( m.matches() ){
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return new ContentType(N3_MIMETYPE);}
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m = TTL_REQUEST.matcher(url);
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if( m.matches() ){
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return new ContentType(TTL_MIMETYPE);}
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} catch (Throwable th) {
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log.error("problem while checking accept header " , th);
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}
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return null;
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}
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private void doRdf(HttpServletRequest req, HttpServletResponse res,
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ContentType rdfFormat) throws IOException, ServletException {
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VitroRequest vreq = new VitroRequest(req);
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int index = vreq.getRequestURL().lastIndexOf("/");
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String ontology = vreq.getRequestURL().substring(0, index);
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String classOrProperty = vreq.getRequestURL().substring(index+1);
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if(classOrProperty.lastIndexOf(".")!= -1){
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int indexx = classOrProperty.lastIndexOf(".");
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classOrProperty = classOrProperty.substring(0, indexx);
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}
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String url = ontology;
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System.out.println(url);
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OntModel ontModel = null;
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HttpSession session = vreq.getSession(false);
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if( session != null )
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ontModel =(OntModel)session.getAttribute("jenaOntModel");
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if( ontModel == null)
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ontModel = (OntModel)getServletContext().getAttribute("jenaOntModel");
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ontModel.enterCriticalSection(Lock.READ);
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OntResource ontResource = ontModel.getOntResource(url);
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if(ontResource == null)
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ontResource = ontModel.getOntResource(url + "/");
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Model newModel = ModelFactory.createDefaultModel();
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if(ontResource != null){
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Resource resource = (Resource)ontResource;
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try{
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String queryString = "Describe <" + resource.getURI() + ">";
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newModel = QueryExecutionFactory.create(QueryFactory.create(queryString), ontModel).execDescribe();
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}
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finally{
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ontModel.leaveCriticalSection();
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}
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}
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else{
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ontModel.leaveCriticalSection();
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doNotFound(vreq,res);
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return;
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}
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res.setContentType(rdfFormat.getMediaType());
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String format = "";
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if ( RDFXML_MIMETYPE.equals(rdfFormat.getMediaType()))
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format = "RDF/XML";
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else if( N3_MIMETYPE.equals(rdfFormat.getMediaType()))
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format = "N3";
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else if ( TTL_MIMETYPE.equals(rdfFormat.getMediaType()))
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format ="TTL";
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newModel.write( res.getOutputStream(), format );
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}
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private static Pattern URI_PATTERN = Pattern.compile("^/ontology/([^/]*)/([^/]*)$");
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//Redirect if the request is for http://hostname/individual/localname
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// if accept is nothing or text/html redirect to ???
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// if accept is some RDF thing redirect to the URL for RDF
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private String checkForRedirect(String url, String acceptHeader) {
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ContentType c = checkForLinkedDataRequest(url, acceptHeader);
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Matcher m = URI_PATTERN.matcher(url);
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if( m.matches() && m.groupCount() <=2 ){
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String group2="";
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if(m.group(2).indexOf(".")!=-1){
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group2 = m.group(2).substring(0, m.group(2).indexOf("."));
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System.out.println("group2 " + group2);
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System.out.println("group1 " + m.group(1));}
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if( c != null && !group2.trim().equals(m.group(1).trim()) ){
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String redirectUrl = null;
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if(m.group(2).isEmpty() || m.group(2) == null){
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redirectUrl = "/ontology/" + m.group(1) + "/" + m.group(1); }
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else{
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redirectUrl = "/ontology/" + m.group(1) + "/" + m.group(2) + "/" + m.group(2) ; }
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if( RDFXML_MIMETYPE.equals( c.getMediaType()) ){
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return redirectUrl + ".rdf";
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}else if( N3_MIMETYPE.equals( c.getMediaType() )){
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return redirectUrl + ".n3";
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}else if( TTL_MIMETYPE.equals( c.getMediaType() )){
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return redirectUrl + ".ttl";
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}//else send them to html
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}
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//else redirect to HTML representation
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return null;
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}else{
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return null;
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}
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}
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private void doRedirect(HttpServletRequest req, HttpServletResponse res,
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String redirectURL) throws IOException {
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//It seems like there must be a more standard way to do a redirect in tomcat.
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String hn = req.getHeader("Host");
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if (req.isSecure()) {
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res.setHeader("Location", res.encodeURL("https://" + hn
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+ req.getContextPath() + redirectURL));
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log.info("doRedirect by using HTTPS");
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} else {
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res.setHeader("Location", res.encodeURL("http://" + hn
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+ req.getContextPath() + redirectURL));
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log.info("doRedirect by using HTTP");
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}
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res.setStatus(res.SC_SEE_OTHER);
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}
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private void doNotFound(HttpServletRequest req, HttpServletResponse res)
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throws IOException, ServletException {
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VitroRequest vreq = new VitroRequest(req);
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Portal portal = vreq.getPortal();
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ApplicationBean appBean = ApplicationBean.getAppBean(getServletContext());
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int allPortalId = appBean.getAllPortalFlagNumeric();
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//If an Individual is not found, there is possibility that it
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//was requested from a portal where it was not visible.
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//In this case redirect to the all portal.
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try{
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Portal allPortal =
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vreq.getWebappDaoFactory().getPortalDao().getPortal(allPortalId);
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// there must be a portal defined with the ID of the all portal
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// for this to work
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if( portal.getPortalId() != allPortalId && allPortal != null ) {
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//bdc34:
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// this is hard coded to get the all portal
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// I didn't find a way to get the id of the all portal
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// it is likely that redirecting will not work in non VIVO clones
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String portalPrefix = null;
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String portalParam = null;
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if( allPortal != null && allPortal.getUrlprefix() != null )
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portalPrefix = allPortal.getUrlprefix();
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else
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portalParam = "home=" + allPortalId;
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String queryStr = req.getQueryString();
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if( queryStr == null && portalParam != null && !"".equals(portalParam)){
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queryStr = portalParam;
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} else {
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if( portalParam != null && !"".equals(portalParam))
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queryStr = queryStr + "&" + portalParam;
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}
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if( queryStr != null && !queryStr.startsWith("?") )
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queryStr = "?" + queryStr;
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StringBuilder url = new StringBuilder();
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url.append( req.getContextPath() );
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if( req.getContextPath() != null && !req.getContextPath().endsWith("/"))
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url.append('/');
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if( portalPrefix != null && !"".equals(portalPrefix))
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url.append( portalPrefix ).append('/');
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String servletPath = req.getServletPath();
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String spath = "";
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if( servletPath != null ){
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if( servletPath.startsWith("/") )
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spath = servletPath.substring(1);
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else
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spath = servletPath;
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}
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if( spath != null && !"".equals(spath))
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url.append( spath );
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if( req.getPathInfo() != null )
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url.append( req.getPathInfo() );
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if( queryStr != null && !"".equals(queryStr ))
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url.append( queryStr );
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res.sendRedirect(url.toString());
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return;
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}
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}catch(Throwable th){
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log.error("could not do a redirect", th);
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}
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//set title before we do the highlighting so we don't get markup in it.
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req.setAttribute("title","not found");
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res.setStatus(HttpServletResponse.SC_NOT_FOUND);
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String css = "<link rel=\"stylesheet\" type=\"text/css\" media=\"screen\" href=\""
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+ portal.getThemeDir() + "css/entity.css\"/>"
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+ "<script language='JavaScript' type='text/javascript' src='js/toggle.js'></script>";
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req.setAttribute("css",css);
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req.setAttribute("bodyJsp","/"+Controllers.ENTITY_NOT_FOUND_JSP);
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RequestDispatcher rd = req.getRequestDispatcher(Controllers.BASIC_JSP);
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rd.forward(req,res);
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}
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}
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