various dev work on language filtering and querying from a generic endpoint
This commit is contained in:
brianjlowe
parent
65c0898997
commit
d1db16b0b4
4 changed files with 964 additions and 3 deletions
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@ -0,0 +1,63 @@
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import com.hp.hpl.jena.graph.Graph;
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import com.hp.hpl.jena.graph.GraphEvents;
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import com.hp.hpl.jena.graph.GraphUtil;
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import com.hp.hpl.jena.graph.Node;
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import com.hp.hpl.jena.graph.Triple;
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import com.hp.hpl.jena.graph.impl.GraphWithPerform;
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import com.hp.hpl.jena.graph.impl.SimpleBulkUpdateHandler;
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import com.hp.hpl.jena.util.iterator.ExtendedIterator;
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public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
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public SparqlGraphBulkUpdater(GraphWithPerform graph) {
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super(graph);
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}
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@Override
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public void removeAll() {
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removeAll(graph);
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notifyRemoveAll();
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}
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protected void notifyRemoveAll() {
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manager.notifyEvent(graph, GraphEvents.removeAll);
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}
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@Override
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public void remove(Node s, Node p, Node o) {
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removeAll(graph, s, p, o);
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manager.notifyEvent(graph, GraphEvents.remove(s, p, o));
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}
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public static void removeAll(Graph g, Node s, Node p, Node o)
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{
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ExtendedIterator<Triple> it = g.find( s, p, o );
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try {
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while (it.hasNext()) {
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Triple t = it.next();
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g.delete(t);
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it.remove();
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}
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}
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finally {
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it.close();
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}
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}
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public static void removeAll( Graph g )
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{
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ExtendedIterator<Triple> it = GraphUtil.findAll(g);
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try {
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while (it.hasNext()) {
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Triple t = it.next();
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g.delete(t);
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it.remove();
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}
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} finally {
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it.close();
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}
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}
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}
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@ -102,9 +102,8 @@ public class SparqlGraphMultilingual extends SparqlGraph implements GraphWithPer
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}
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}
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return WrappedIterator.create(tripl.iterator());
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return WrappedIterator.create(tripl.iterator());
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} else {
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} else {
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long filterTime = System.currentTimeMillis() - rawTime - startTime;
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if (rawTime > 9) {
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if (rawTime > 9) {
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log.info("raw time " + rawTime + " ; filter time " + filterTime);
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log.info("raw time " + rawTime);
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log.info("^ " + subject + " : " + predicate + " : " + object);
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log.info("^ " + subject + " : " + predicate + " : " + object);
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}
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}
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return WrappedIterator.create(tripList.iterator());
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return WrappedIterator.create(tripList.iterator());
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@ -0,0 +1,207 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.filters;
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import java.io.IOException;
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import java.sql.Connection;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Enumeration;
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import java.util.List;
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import java.util.Locale;
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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.Filter;
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import javax.servlet.FilterChain;
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import javax.servlet.FilterConfig;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletException;
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import javax.servlet.ServletRequest;
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import javax.servlet.ServletResponse;
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import javax.servlet.http.HttpServletRequest;
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import org.apache.commons.dbcp.BasicDataSource;
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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.graph.Graph;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.query.DataSource;
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import com.hp.hpl.jena.query.Dataset;
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import com.hp.hpl.jena.query.DatasetFactory;
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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.sdb.SDBFactory;
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import com.hp.hpl.jena.sdb.Store;
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import com.hp.hpl.jena.sdb.StoreDesc;
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import com.hp.hpl.jena.sdb.sql.SDBConnection;
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import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.SingleContentOntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraphMultilingual;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
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import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
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public class WebappDaoFactorySparqlPrep implements Filter {
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private final static Log log = LogFactory.getLog(WebappDaoFactorySparqlPrep.class);
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ServletContext _ctx;
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/**
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* The filter will be applied to all incoming urls,
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this is a list of URI patterns to skip. These are
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matched against the requestURI sans query parameters,
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* e.g.
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* "/vitro/index.jsp"
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* "/vitro/themes/enhanced/css/edit.css"
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*
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* These patterns are from VitroRequestPrep.java
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*/
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Pattern[] skipPatterns = {
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Pattern.compile(".*\\.(gif|GIF|jpg|jpeg)$"),
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Pattern.compile(".*\\.css$"),
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Pattern.compile(".*\\.js$"),
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Pattern.compile("/.*/themes/.*/site_icons/.*"),
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Pattern.compile("/.*/images/.*")
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};
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@Override
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public void doFilter(ServletRequest request, ServletResponse response,
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FilterChain filterChain) throws IOException, ServletException {
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if ( request.getAttribute("WebappDaoFactorySDBPrep.setup") != null ) {
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// don't run multiple times
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filterChain.doFilter(request, response);
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return;
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}
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for( Pattern skipPattern : skipPatterns){
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Matcher match =skipPattern.matcher( ((HttpServletRequest)request).getRequestURI() );
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if( match.matches() ){
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log.debug("request matched a skipPattern, skipping VitroRequestPrep");
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filterChain.doFilter(request, response);
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return;
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}
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}
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BasicDataSource bds = JenaDataSourceSetupBase.getApplicationDataSource(_ctx);
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StoreDesc storeDesc = (StoreDesc) _ctx.getAttribute("storeDesc");
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OntModelSelector oms = (OntModelSelector) _ctx.getAttribute("unionOntModelSelector");
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String defaultNamespace = (String) _ctx.getAttribute("defaultNamespace");
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Connection sqlConn = null;
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SDBConnection conn = null;
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Store store = null;
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Dataset dataset = null;
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WebappDaoFactory wadf = null;
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try {
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if (bds == null || storeDesc == null || oms == null) {
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throw new RuntimeException("SDB store not property set up");
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}
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try {
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sqlConn = bds.getConnection();
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conn = new SDBConnection(sqlConn) ;
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} catch (SQLException sqe) {
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throw new RuntimeException("Unable to connect to database", sqe);
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}
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if (conn != null) {
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store = SDBFactory.connectStore(conn, storeDesc);
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dataset = SDBFactory.connectDataset(store);
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VitroRequest vreq = new VitroRequest((HttpServletRequest) request);
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log.info("---------");
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Enumeration<String> headStrs = vreq.getHeaderNames();
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while (headStrs.hasMoreElements()) {
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String head = headStrs.nextElement();
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log.info(head + " : " + vreq.getHeader(head));
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}
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List<String> langs = new ArrayList<String>();
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log.info("Accept-Language: " + vreq.getHeader("Accept-Language"));
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Enumeration<Locale> locs = vreq.getLocales();
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while (locs.hasMoreElements()) {
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Locale locale = locs.nextElement();
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langs.add(locale.toString().replace("_", "-"));
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log.info(locale.toString() + " / " + locale.getLanguage() + " + " + locale.getCountry() + " : " + locale.getDisplayCountry() + " | " + locale.getLanguage() + " : " + locale.getDisplayLanguage());
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}
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WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
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config.setDefaultNamespace(defaultNamespace);
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config.setPreferredLanguages(langs);
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//okay let's make a graph-backed model
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String endpointURI = ConfigurationProperties.getBean(
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request).getProperty("VitroConnection.DataSource.endpointURI");
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Graph g = new SparqlGraphMultilingual(endpointURI, langs);
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//Graph g = new SparqlGraph(endpointURI);
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Model m = ModelFactory.createModelForGraph(g);
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OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, m);
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oms = new SingleContentOntModelSelector(om, oms.getDisplayModel(), oms.getUserAccountsModel());
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DataSource datasource = DatasetFactory.create();
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datasource.addNamedModel("fake:fake", m);
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dataset = datasource;
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wadf = new WebappDaoFactoryJena(oms, config);
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//wadf = new WebappDaoFactorySDB(oms, dataset, config);
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vreq.setWebappDaoFactory(wadf);
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vreq.setFullWebappDaoFactory(wadf);
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vreq.setUnfilteredWebappDaoFactory(wadf);
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vreq.setWebappDaoFactory(wadf);
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vreq.setAssertionsWebappDaoFactory(wadf);
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vreq.setDataset(dataset);
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vreq.setJenaOntModel(om);
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vreq.setOntModelSelector(oms);
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}
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} catch (Throwable t) {
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log.error("Unable to filter request to set up SDB connection", t);
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}
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request.setAttribute("WebappDaoFactorySDBPrep.setup", 1);
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try {
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filterChain.doFilter(request, response);
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return;
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} finally {
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if (conn != null) {
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conn.close();
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}
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if (dataset != null) {
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dataset.close();
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}
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if (store != null) {
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store.close();
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}
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if (wadf != null) {
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wadf.close();
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}
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}
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}
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@Override
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public void init(FilterConfig filterConfig) throws ServletException {
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try {
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_ctx = filterConfig.getServletContext();
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} catch (Throwable t) {
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log.error("Unable to initialize WebappDaoFactorySDBPrep", t);
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}
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}
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@Override
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public void destroy() {
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// no destroy actions
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}
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}
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@ -0,0 +1,692 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.servlet.setup;
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import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.List;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletContextEvent;
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import org.apache.commons.dbcp.BasicDataSource;
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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.graph.Graph;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.query.Query;
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import com.hp.hpl.jena.query.QueryExecution;
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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.query.Syntax;
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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.ResIterator;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.sdb.SDB;
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import com.hp.hpl.jena.sdb.SDBFactory;
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import com.hp.hpl.jena.sdb.Store;
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import com.hp.hpl.jena.sdb.StoreDesc;
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import com.hp.hpl.jena.sdb.sql.SDBConnection;
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import com.hp.hpl.jena.sdb.store.DatabaseType;
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import com.hp.hpl.jena.sdb.store.LayoutType;
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import com.hp.hpl.jena.sdb.util.StoreUtils;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.util.ResourceUtils;
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import com.hp.hpl.jena.util.iterator.ClosableIterator;
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import com.hp.hpl.jena.vocabulary.RDF;
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import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.SingleContentOntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
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import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
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public class JenaDataSourceSetupSparql extends JenaDataSourceSetupBase
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|
implements javax.servlet.ServletContextListener {
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(JenaDataSourceSetupSparql.class);
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void contextInitialized(ServletContextEvent sce) {
|
||||||
|
ServletContext ctx = sce.getServletContext();
|
||||||
|
StartupStatus ss = StartupStatus.getBean(ctx);
|
||||||
|
|
||||||
|
try {
|
||||||
|
long startTime = System.currentTimeMillis();
|
||||||
|
setUpJenaDataSource(ctx);
|
||||||
|
log.info((System.currentTimeMillis() - startTime) / 1000 +
|
||||||
|
" seconds to set up SDB store");
|
||||||
|
} catch (SQLException sqle) {
|
||||||
|
// SQL exceptions are fatal and should halt startup
|
||||||
|
log.error("Error using SQL database; startup aborted.", sqle);
|
||||||
|
ss.fatal(this, "Error using SQL database; startup aborted.", sqle);
|
||||||
|
} catch (Throwable t) {
|
||||||
|
log.error("Throwable in " + this.getClass().getName(), t);
|
||||||
|
ss.fatal(this, "Throwable in " + this.getClass().getName(), t);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private void setUpJenaDataSource(ServletContext ctx) throws SQLException {
|
||||||
|
|
||||||
|
OntModelSelector baseOms = new OntModelSelectorImpl();
|
||||||
|
OntModelSelector inferenceOms = new OntModelSelectorImpl();
|
||||||
|
OntModelSelector unionOms = new OntModelSelectorImpl();
|
||||||
|
|
||||||
|
OntModel userAccountsModel = ontModelFromContextAttribute(
|
||||||
|
ctx, "userAccountsOntModel");
|
||||||
|
// baseOms.setUserAccountsModel(userAccountsModel);
|
||||||
|
// inferenceOms.setUserAccountsModel(userAccountsModel);
|
||||||
|
// unionOms.setUserAccountsModel(userAccountsModel);
|
||||||
|
|
||||||
|
OntModel displayModel = ontModelFromContextAttribute(
|
||||||
|
ctx,DISPLAY_ONT_MODEL);
|
||||||
|
// baseOms.setDisplayModel(displayModel);
|
||||||
|
// inferenceOms.setDisplayModel(displayModel);
|
||||||
|
// unionOms.setDisplayModel(displayModel);
|
||||||
|
|
||||||
|
//okay let's make a graph-backed model
|
||||||
|
String endpointURI = ConfigurationProperties.getBean(
|
||||||
|
ctx).getProperty("VitroConnection.DataSource.endpointURI");
|
||||||
|
|
||||||
|
Graph g = new SparqlGraph(endpointURI);
|
||||||
|
|
||||||
|
Model m = ModelFactory.createModelForGraph(g);
|
||||||
|
OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, m);
|
||||||
|
baseOms = new SingleContentOntModelSelector(om, displayModel, userAccountsModel);
|
||||||
|
inferenceOms = baseOms;
|
||||||
|
unionOms = baseOms;
|
||||||
|
|
||||||
|
// SDB setup
|
||||||
|
|
||||||
|
// union default graph
|
||||||
|
SDB.getContext().set(SDB.unionDefaultGraph, true) ;
|
||||||
|
|
||||||
|
StoreDesc storeDesc = makeStoreDesc(ctx);
|
||||||
|
setApplicationStoreDesc(storeDesc, ctx);
|
||||||
|
|
||||||
|
BasicDataSource bds = getApplicationDataSource(ctx);
|
||||||
|
if (bds == null) {
|
||||||
|
bds = makeDataSourceFromConfigurationProperties(ctx);
|
||||||
|
setApplicationDataSource(bds, ctx);
|
||||||
|
}
|
||||||
|
|
||||||
|
Store store = connectStore(bds, storeDesc);
|
||||||
|
setApplicationStore(store, ctx);
|
||||||
|
|
||||||
|
// if (!isSetUp(store)) {
|
||||||
|
// log.info("Initializing SDB store");
|
||||||
|
// if (isFirstStartup()) {
|
||||||
|
// setupSDB(ctx, store);
|
||||||
|
// } else {
|
||||||
|
// migrateToSDBFromExistingRDBStore(ctx, store);
|
||||||
|
// }
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// // The code below, which sets up the OntModelSelectors, controls whether
|
||||||
|
// // each model is maintained in memory, in the DB, or both while the
|
||||||
|
// // application is running.
|
||||||
|
//
|
||||||
|
// // Populate the three OntModelSelectors (BaseOntModel = assertions,
|
||||||
|
// // InferenceOntModel = inferences and JenaOntModel = union of assertions
|
||||||
|
// // and inferences) with the post-SDB-conversion models.
|
||||||
|
//
|
||||||
|
// // ABox assertions
|
||||||
|
// Model aboxAssertions = makeDBModel(
|
||||||
|
// bds, JenaDataSourceSetupBase.JENA_DB_MODEL, DB_ONT_MODEL_SPEC,
|
||||||
|
// TripleStoreType.SDB, ctx);
|
||||||
|
// Model listenableAboxAssertions = ModelFactory.createUnion(
|
||||||
|
// aboxAssertions, ModelFactory.createDefaultModel());
|
||||||
|
// baseOms.setABoxModel(
|
||||||
|
// ModelFactory.createOntologyModel(
|
||||||
|
// OntModelSpec.OWL_MEM, listenableAboxAssertions));
|
||||||
|
//
|
||||||
|
// // ABox inferences
|
||||||
|
// Model aboxInferences = makeDBModel(
|
||||||
|
// bds, JenaDataSourceSetupBase.JENA_INF_MODEL, DB_ONT_MODEL_SPEC,
|
||||||
|
// TripleStoreType.SDB, ctx);
|
||||||
|
// Model listenableAboxInferences = ModelFactory.createUnion(
|
||||||
|
// aboxInferences, ModelFactory.createDefaultModel());
|
||||||
|
// inferenceOms.setABoxModel(ModelFactory.createOntologyModel(
|
||||||
|
// OntModelSpec.OWL_MEM, listenableAboxInferences));
|
||||||
|
//
|
||||||
|
//
|
||||||
|
// // Since the TBox models are in memory, they do not have timeout issues
|
||||||
|
// // like the like the ABox models do (and so don't need the extra step
|
||||||
|
// // to make them listenable.)
|
||||||
|
//
|
||||||
|
// // TBox assertions
|
||||||
|
// try {
|
||||||
|
// Model tboxAssertionsDB = makeDBModel(
|
||||||
|
// bds, JENA_TBOX_ASSERTIONS_MODEL, DB_ONT_MODEL_SPEC,
|
||||||
|
// TripleStoreType.SDB, ctx);
|
||||||
|
// OntModel tboxAssertions = ModelFactory.createOntologyModel(
|
||||||
|
// MEM_ONT_MODEL_SPEC);
|
||||||
|
//
|
||||||
|
// if (tboxAssertionsDB != null) {
|
||||||
|
// long startTime = System.currentTimeMillis();
|
||||||
|
// System.out.println(
|
||||||
|
// "Copying cached tbox assertions into memory");
|
||||||
|
// tboxAssertions.add(tboxAssertionsDB);
|
||||||
|
// System.out.println((System.currentTimeMillis() - startTime)
|
||||||
|
// / 1000 + " seconds to load tbox assertions");
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// tboxAssertions.getBaseModel().register(new ModelSynchronizer(
|
||||||
|
// tboxAssertionsDB));
|
||||||
|
// baseOms.setTBoxModel(tboxAssertions);
|
||||||
|
// } catch (Throwable e) {
|
||||||
|
// log.error("Unable to load tbox assertion cache from DB", e);
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// // TBox inferences
|
||||||
|
// try {
|
||||||
|
// Model tboxInferencesDB = makeDBModel(
|
||||||
|
// bds, JENA_TBOX_INF_MODEL, DB_ONT_MODEL_SPEC,
|
||||||
|
// TripleStoreType.SDB, ctx);
|
||||||
|
// OntModel tboxInferences = ModelFactory.createOntologyModel(
|
||||||
|
// MEM_ONT_MODEL_SPEC);
|
||||||
|
//
|
||||||
|
// if (tboxInferencesDB != null) {
|
||||||
|
// long startTime = System.currentTimeMillis();
|
||||||
|
// System.out.println(
|
||||||
|
// "Copying cached tbox inferences into memory");
|
||||||
|
// tboxInferences.add(tboxInferencesDB);
|
||||||
|
// System.out.println((System.currentTimeMillis() - startTime)
|
||||||
|
// / 1000 + " seconds to load tbox inferences");
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// tboxInferences.getBaseModel().register(new ModelSynchronizer(
|
||||||
|
// tboxInferencesDB));
|
||||||
|
// inferenceOms.setTBoxModel(tboxInferences);
|
||||||
|
// } catch (Throwable e) {
|
||||||
|
// log.error("Unable to load tbox inference cache from DB", e);
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// // union ABox
|
||||||
|
// OntModel unionABoxModel = ModelFactory.createOntologyModel(
|
||||||
|
// MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
|
||||||
|
// baseOms.getABoxModel(), inferenceOms.getABoxModel()));
|
||||||
|
// unionOms.setABoxModel(unionABoxModel);
|
||||||
|
//
|
||||||
|
// // union TBox
|
||||||
|
// OntModel unionTBoxModel = ModelFactory.createOntologyModel(
|
||||||
|
// MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
|
||||||
|
// baseOms.getTBoxModel(), inferenceOms.getTBoxModel()));
|
||||||
|
// unionOms.setTBoxModel(unionTBoxModel);
|
||||||
|
//
|
||||||
|
//
|
||||||
|
// // Application metadata model is cached in memory.
|
||||||
|
// try {
|
||||||
|
//
|
||||||
|
// Model applicationMetadataModelDB = makeDBModel(
|
||||||
|
// bds, JENA_APPLICATION_METADATA_MODEL, DB_ONT_MODEL_SPEC,
|
||||||
|
// TripleStoreType.SDB, ctx);
|
||||||
|
// OntModel applicationMetadataModel =
|
||||||
|
// ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
|
||||||
|
//
|
||||||
|
// long startTime = System.currentTimeMillis();
|
||||||
|
// System.out.println(
|
||||||
|
// "Copying cached application metadata model into memory");
|
||||||
|
// applicationMetadataModel.add(applicationMetadataModelDB);
|
||||||
|
// System.out.println((System.currentTimeMillis() - startTime)
|
||||||
|
// / 1000 + " seconds to load application metadata model " +
|
||||||
|
// "assertions of size " + applicationMetadataModel.size());
|
||||||
|
// applicationMetadataModel.getBaseModel().register(
|
||||||
|
// new ModelSynchronizer(applicationMetadataModelDB));
|
||||||
|
//
|
||||||
|
// if (isFirstStartup()) {
|
||||||
|
// applicationMetadataModel.add(
|
||||||
|
// InitialJenaModelUtils.loadInitialModel(
|
||||||
|
// ctx, getDefaultNamespace(ctx)));
|
||||||
|
//
|
||||||
|
// } else if (applicationMetadataModelDB.size() == 0) {
|
||||||
|
// repairAppMetadataModel(
|
||||||
|
// applicationMetadataModel, aboxAssertions,
|
||||||
|
// aboxInferences);
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// baseOms.setApplicationMetadataModel(applicationMetadataModel);
|
||||||
|
// inferenceOms.setApplicationMetadataModel(
|
||||||
|
// baseOms.getApplicationMetadataModel());
|
||||||
|
// unionOms.setApplicationMetadataModel(
|
||||||
|
// baseOms.getApplicationMetadataModel());
|
||||||
|
//
|
||||||
|
// } catch (Throwable e) {
|
||||||
|
// log.error("Unable to load application metadata model cache from DB"
|
||||||
|
// , e);
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
|
||||||
|
//
|
||||||
|
// if (isFirstStartup()) {
|
||||||
|
// loadDataFromFilesystem(baseOms, ctx);
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// log.info("Setting up union models and DAO factories");
|
||||||
|
//
|
||||||
|
// // create TBox + ABox union models and set up webapp DAO factories
|
||||||
|
// OntModel baseUnion = ModelFactory.createOntologyModel(
|
||||||
|
// OntModelSpec.OWL_MEM,
|
||||||
|
// ModelFactory.createUnion(baseOms.getABoxModel(),
|
||||||
|
// baseOms.getTBoxModel()));
|
||||||
|
// baseOms.setFullModel(baseUnion);
|
||||||
|
ModelContext.setBaseOntModel(baseOms.getFullModel(), ctx);
|
||||||
|
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
|
||||||
|
config.setDefaultNamespace(getDefaultNamespace(ctx));
|
||||||
|
// revert this
|
||||||
|
WebappDaoFactory baseWadf = new WebappDaoFactoryJena(
|
||||||
|
baseOms, config
|
||||||
|
);
|
||||||
|
ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
|
||||||
|
|
||||||
|
OntModel inferenceUnion = ModelFactory.createOntologyModel(
|
||||||
|
OntModelSpec.OWL_MEM,
|
||||||
|
ModelFactory.createUnion(
|
||||||
|
inferenceOms.getABoxModel(),
|
||||||
|
inferenceOms.getTBoxModel()));
|
||||||
|
// inferenceOms.setFullModel(inferenceUnion);
|
||||||
|
ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), ctx);
|
||||||
|
WebappDaoFactory infWadf = new WebappDaoFactorySDB(
|
||||||
|
inferenceOms, bds, storeDesc, config,
|
||||||
|
WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
|
||||||
|
ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
|
||||||
|
|
||||||
|
OntModel masterUnion = unionOms.getFullModel();
|
||||||
|
|
||||||
|
// ModelFactory.createOntologyModel(
|
||||||
|
// DB_ONT_MODEL_SPEC, makeDBModel(
|
||||||
|
// bds, WebappDaoFactorySDB.UNION_GRAPH,
|
||||||
|
// DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx));
|
||||||
|
|
||||||
|
// unionOms.setFullModel(masterUnion);
|
||||||
|
ctx.setAttribute("jenaOntModel", masterUnion);
|
||||||
|
WebappDaoFactory wadf = new WebappDaoFactorySDB(
|
||||||
|
unionOms, bds, storeDesc, config);
|
||||||
|
ctx.setAttribute("webappDaoFactory",wadf);
|
||||||
|
|
||||||
|
ModelContext.setOntModelSelector(unionOms, ctx);
|
||||||
|
ModelContext.setUnionOntModelSelector(unionOms, ctx);
|
||||||
|
// assertions and inferences
|
||||||
|
ModelContext.setBaseOntModelSelector(baseOms, ctx);
|
||||||
|
// assertions
|
||||||
|
ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);
|
||||||
|
// inferences
|
||||||
|
|
||||||
|
ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
|
||||||
|
|
||||||
|
log.info("SDB store ready for use");
|
||||||
|
|
||||||
|
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
|
||||||
|
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
|
||||||
|
setVitroJenaModelMaker(vjmm, ctx);
|
||||||
|
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
||||||
|
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
|
||||||
|
setVitroJenaSDBModelMaker(vsmm, ctx);
|
||||||
|
|
||||||
|
//bdc34: I have no reason for vsmm vs vjmm.
|
||||||
|
//I don't know what are the implications of this choice.
|
||||||
|
setVitroModelSource( new VitroModelSource(vsmm,ctx), ctx);
|
||||||
|
|
||||||
|
log.info("Model makers set up");
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* If we find a "portal1" portal (and we should), its URI should use the
|
||||||
|
* default namespace.
|
||||||
|
*/
|
||||||
|
private void checkForNamespaceMismatch(OntModel model, ServletContext ctx) {
|
||||||
|
String expectedNamespace = getDefaultNamespace(ctx);
|
||||||
|
|
||||||
|
List<Resource> portals = getPortal1s(model);
|
||||||
|
|
||||||
|
if(!portals.isEmpty() && noPortalForNamespace(
|
||||||
|
portals, expectedNamespace)) {
|
||||||
|
// There really should be only one portal 1, but if there happen to
|
||||||
|
// be multiple, just arbitrarily pick the first in the list.
|
||||||
|
Resource portal = portals.get(0);
|
||||||
|
String oldNamespace = portal.getNameSpace();
|
||||||
|
renamePortal(portal, expectedNamespace, model);
|
||||||
|
StartupStatus ss = StartupStatus.getBean(ctx);
|
||||||
|
ss.warning(this, "\nThe default namespace has been changed \n" +
|
||||||
|
"from " + oldNamespace +
|
||||||
|
"\nto " + expectedNamespace + ".\n" +
|
||||||
|
"The application will function normally, but " +
|
||||||
|
"any individuals in the \n" + oldNamespace + " " +
|
||||||
|
"namespace will need to have their URIs \n" +
|
||||||
|
"changed in order to be served as linked data. " +
|
||||||
|
"You can use the Ingest Tools \nto change the " +
|
||||||
|
"URIs for a batch of resources.");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private List<Resource> getPortal1s(Model model) {
|
||||||
|
List<Resource> portals = new ArrayList<Resource>();
|
||||||
|
try {
|
||||||
|
model.enterCriticalSection(Lock.READ);
|
||||||
|
ResIterator portalIt = model.listResourcesWithProperty(
|
||||||
|
RDF.type, PORTAL);
|
||||||
|
while (portalIt.hasNext()) {
|
||||||
|
Resource portal = portalIt.nextResource();
|
||||||
|
if ("portal1".equals(portal.getLocalName())) {
|
||||||
|
portals.add(portal);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} finally {
|
||||||
|
model.leaveCriticalSection();
|
||||||
|
}
|
||||||
|
return portals;
|
||||||
|
}
|
||||||
|
|
||||||
|
private boolean noPortalForNamespace(List<Resource> portals,
|
||||||
|
String expectedNamespace) {
|
||||||
|
for (Resource portal : portals) {
|
||||||
|
if(expectedNamespace.equals(portal.getNameSpace())) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
private void renamePortal(Resource portal, String namespace, Model model) {
|
||||||
|
model.enterCriticalSection(Lock.WRITE);
|
||||||
|
try {
|
||||||
|
ResourceUtils.renameResource(
|
||||||
|
portal, namespace + portal.getLocalName());
|
||||||
|
} finally {
|
||||||
|
model.leaveCriticalSection();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ===================================================================== */
|
||||||
|
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void contextDestroyed(ServletContextEvent sce) {
|
||||||
|
// Nothing to do.
|
||||||
|
}
|
||||||
|
|
||||||
|
private OntModel ontModelFromContextAttribute(ServletContext ctx,
|
||||||
|
String attribute) {
|
||||||
|
OntModel ontModel;
|
||||||
|
Object attributeValue = ctx.getAttribute(attribute);
|
||||||
|
if (attributeValue != null && attributeValue instanceof OntModel) {
|
||||||
|
ontModel = (OntModel) attributeValue;
|
||||||
|
} else {
|
||||||
|
ontModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
|
||||||
|
ctx.setAttribute(attribute, ontModel);
|
||||||
|
}
|
||||||
|
return ontModel;
|
||||||
|
}
|
||||||
|
|
||||||
|
private boolean isEmpty(Model model) {
|
||||||
|
ClosableIterator<Statement> closeIt = model.listStatements(
|
||||||
|
null, RDF.type, ResourceFactory.createResource(
|
||||||
|
VitroVocabulary.PORTAL));
|
||||||
|
try {
|
||||||
|
if (closeIt.hasNext()) {
|
||||||
|
return false;
|
||||||
|
} else {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
} finally {
|
||||||
|
closeIt.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void loadDataFromFilesystem(OntModelSelector baseOms,
|
||||||
|
ServletContext ctx) {
|
||||||
|
Long startTime = System.currentTimeMillis();
|
||||||
|
log.debug("Initializing models from RDF files");
|
||||||
|
readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseOms.getABoxModel());
|
||||||
|
readOntologyFilesInPathSet(USER_TBOX_PATH, ctx, baseOms.getTBoxModel());
|
||||||
|
readOntologyFilesInPathSet(
|
||||||
|
USER_APPMETA_PATH, ctx, baseOms.getApplicationMetadataModel());
|
||||||
|
log.debug(((System.currentTimeMillis() - startTime) / 1000)
|
||||||
|
+ " seconds to read RDF files ");
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void getTBoxModel(Model fullModel,
|
||||||
|
Model submodels,
|
||||||
|
Model tboxModel) {
|
||||||
|
|
||||||
|
JenaModelUtils modelUtils = new JenaModelUtils();
|
||||||
|
|
||||||
|
Model tempModel = ModelFactory.createUnion(fullModel, submodels);
|
||||||
|
Model tempTBoxModel = modelUtils.extractTBox(tempModel);
|
||||||
|
|
||||||
|
// copy intersection of tempTBoxModel and fullModel to tboxModel.
|
||||||
|
StmtIterator iter = tempTBoxModel.listStatements();
|
||||||
|
|
||||||
|
while (iter.hasNext()) {
|
||||||
|
Statement stmt = iter.next();
|
||||||
|
if (fullModel.contains(stmt)) {
|
||||||
|
tboxModel.add(stmt);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
/*
|
||||||
|
* Copy all statements from model 1 that are not in model 2 to model 3.
|
||||||
|
*/
|
||||||
|
private static void copyDifference(Model model1,
|
||||||
|
Model model2,
|
||||||
|
Model model3) {
|
||||||
|
|
||||||
|
StmtIterator iter = model1.listStatements();
|
||||||
|
|
||||||
|
while (iter.hasNext()) {
|
||||||
|
Statement stmt = iter.next();
|
||||||
|
if (!model2.contains(stmt)) {
|
||||||
|
model3.add(stmt);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void getAppMetadata(Model source, Model target) {
|
||||||
|
|
||||||
|
String amdQuery = "DESCRIBE ?x WHERE { " +
|
||||||
|
"{?x a <" + VitroVocabulary.PORTAL +"> } UNION " +
|
||||||
|
"{?x a <" + VitroVocabulary.PROPERTYGROUP +"> } UNION " +
|
||||||
|
"{?x a <" + VitroVocabulary.CLASSGROUP +"> } } ";
|
||||||
|
|
||||||
|
try {
|
||||||
|
Query q = QueryFactory.create(amdQuery, Syntax.syntaxARQ);
|
||||||
|
QueryExecution qe = QueryExecutionFactory.create(q, source);
|
||||||
|
qe.execDescribe(target);
|
||||||
|
} catch (Exception e) {
|
||||||
|
log.error("unable to create the application metadata model",e);
|
||||||
|
}
|
||||||
|
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void repairAppMetadataModel(Model applicationMetadataModel,
|
||||||
|
Model aboxAssertions,
|
||||||
|
Model aboxInferences) {
|
||||||
|
|
||||||
|
log.info("Moving application metadata from ABox to dedicated model");
|
||||||
|
getAppMetadata(aboxAssertions, applicationMetadataModel);
|
||||||
|
getAppMetadata(aboxInferences, applicationMetadataModel);
|
||||||
|
aboxAssertions.remove(applicationMetadataModel);
|
||||||
|
aboxInferences.remove(applicationMetadataModel);
|
||||||
|
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static StoreDesc makeStoreDesc(ServletContext ctx) {
|
||||||
|
String layoutStr = ConfigurationProperties.getBean(ctx).getProperty(
|
||||||
|
"VitroConnection.DataSource.sdb.layout", "layout2/hash");
|
||||||
|
String dbtypeStr = ConfigurationProperties.getBean(ctx).getProperty(
|
||||||
|
"VitroConnection.DataSource.dbtype", "MySQL");
|
||||||
|
return new StoreDesc(
|
||||||
|
LayoutType.fetch(layoutStr),
|
||||||
|
DatabaseType.fetch(dbtypeStr) );
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Store connectStore(BasicDataSource bds, StoreDesc storeDesc)
|
||||||
|
throws SQLException {
|
||||||
|
SDBConnection conn = new SDBConnection(bds.getConnection()) ;
|
||||||
|
return SDBFactory.connectStore(conn, storeDesc);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static void setupSDB(ServletContext ctx, Store store) {
|
||||||
|
setupSDB(ctx,
|
||||||
|
store,
|
||||||
|
ModelFactory.createDefaultModel(),
|
||||||
|
ModelFactory.createDefaultModel());
|
||||||
|
}
|
||||||
|
|
||||||
|
public static void setupSDB(ServletContext ctx,
|
||||||
|
Store store,
|
||||||
|
Model memModel,
|
||||||
|
Model inferenceModel) {
|
||||||
|
|
||||||
|
store.getTableFormatter().create();
|
||||||
|
store.getTableFormatter().truncate();
|
||||||
|
|
||||||
|
store.getTableFormatter().dropIndexes(); // improve load performance
|
||||||
|
|
||||||
|
try {
|
||||||
|
|
||||||
|
// This is a one-time copy of stored KB data - from a Jena RDB store
|
||||||
|
// to a Jena SDB store. In the process, we will also separate out
|
||||||
|
// the TBox from the Abox; these are in the same graph in pre-1.2
|
||||||
|
// VIVO versions and will now be stored and maintained in separate
|
||||||
|
// models. Access to the Jena RDB data is through the
|
||||||
|
// OntModelSelectors that have been set up earlier in the current
|
||||||
|
// session by JenaPersistentDataSourceSetup.java. In the code
|
||||||
|
// below, note that the current getABoxModel() methods on the
|
||||||
|
// OntModelSelectors return a graph with both ABox and TBox data.
|
||||||
|
|
||||||
|
OntModel submodels = ModelFactory.createOntologyModel(
|
||||||
|
MEM_ONT_MODEL_SPEC);
|
||||||
|
readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
|
||||||
|
|
||||||
|
Model tboxAssertions = SDBFactory.connectNamedModel(
|
||||||
|
store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
|
||||||
|
// initially putting the results in memory so we have a
|
||||||
|
// cheaper way of computing the difference when we copy the ABox
|
||||||
|
Model memTboxAssertions = ModelFactory.createDefaultModel();
|
||||||
|
getTBoxModel(memModel, submodels, memTboxAssertions);
|
||||||
|
tboxAssertions.add(memTboxAssertions);
|
||||||
|
|
||||||
|
Model tboxInferences = SDBFactory.connectNamedModel(
|
||||||
|
store, JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL);
|
||||||
|
// initially putting the results in memory so we have a
|
||||||
|
// cheaper way of computing the difference when we copy the ABox
|
||||||
|
Model memTboxInferences = ModelFactory.createDefaultModel();
|
||||||
|
getTBoxModel(inferenceModel, submodels, memTboxInferences);
|
||||||
|
tboxInferences.add(memTboxInferences);
|
||||||
|
|
||||||
|
Model aboxAssertions = SDBFactory.connectNamedModel(
|
||||||
|
store, JenaDataSourceSetupBase.JENA_DB_MODEL);
|
||||||
|
copyDifference(memModel, memTboxAssertions, aboxAssertions);
|
||||||
|
|
||||||
|
Model aboxInferences = SDBFactory.connectNamedModel(
|
||||||
|
store, JenaDataSourceSetupBase.JENA_INF_MODEL);
|
||||||
|
copyDifference(inferenceModel, memTboxInferences, aboxInferences);
|
||||||
|
|
||||||
|
// Set up the application metadata model
|
||||||
|
Model applicationMetadataModel = SDBFactory.connectNamedModel(
|
||||||
|
store,
|
||||||
|
JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
|
||||||
|
getAppMetadata(memModel, applicationMetadataModel);
|
||||||
|
log.info("During initial SDB setup, created an application " +
|
||||||
|
"metadata model of size " +
|
||||||
|
applicationMetadataModel.size());
|
||||||
|
|
||||||
|
// remove application metadata from ABox model
|
||||||
|
aboxAssertions.remove(applicationMetadataModel);
|
||||||
|
aboxInferences.remove(applicationMetadataModel);
|
||||||
|
|
||||||
|
// Make sure the reasoner takes into account the newly-set-up data.
|
||||||
|
SimpleReasonerSetup.setRecomputeRequired(ctx);
|
||||||
|
|
||||||
|
} finally {
|
||||||
|
log.info("Adding indexes to SDB database tables.");
|
||||||
|
store.getTableFormatter().addIndexes();
|
||||||
|
log.info("Indexes created.");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void migrateToSDBFromExistingRDBStore(ServletContext ctx,
|
||||||
|
Store store) {
|
||||||
|
Model rdbAssertionsModel = makeDBModelFromConfigurationProperties(
|
||||||
|
JENA_DB_MODEL, DB_ONT_MODEL_SPEC, ctx);
|
||||||
|
Model rdbInferencesModel = makeDBModelFromConfigurationProperties(
|
||||||
|
JENA_INF_MODEL, DB_ONT_MODEL_SPEC, ctx);
|
||||||
|
setupSDB(ctx, store, rdbAssertionsModel, rdbInferencesModel);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Tests whether an SDB store has been formatted and populated for use.
|
||||||
|
* @param store
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
private boolean isSetUp(Store store) throws SQLException {
|
||||||
|
if (!(StoreUtils.isFormatted(store))) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
// even if the store exists, it may be empty
|
||||||
|
|
||||||
|
try {
|
||||||
|
return (SDBFactory.connectNamedModel(
|
||||||
|
store,
|
||||||
|
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL))
|
||||||
|
.size() > 0;
|
||||||
|
} catch (Exception e) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static final String STOREDESC_ATTR = "storeDesc";
|
||||||
|
private static final String STORE_ATTR = "kbStore";
|
||||||
|
|
||||||
|
public static void setApplicationStoreDesc(StoreDesc storeDesc,
|
||||||
|
ServletContext ctx) {
|
||||||
|
ctx.setAttribute(STOREDESC_ATTR, storeDesc);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static StoreDesc getApplicationStoreDesc(ServletContext ctx) {
|
||||||
|
return (StoreDesc) ctx.getAttribute(STOREDESC_ATTR);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static void setApplicationStore(Store store,
|
||||||
|
ServletContext ctx) {
|
||||||
|
ctx.setAttribute(STORE_ATTR, store);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Store getApplicationStore(ServletContext ctx) {
|
||||||
|
return (Store) ctx.getAttribute(STORE_ATTR);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue