Merge branch 'develop' of github.com:vivo-project/Vitro into develop
This commit is contained in:
Brian Caruso
commit
08dab8e52f
27 changed files with 627 additions and 158 deletions
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@ -15,6 +15,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.display.DisplayObje
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import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAction;
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import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
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import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
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import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
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import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
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import edu.cornell.mannlib.vitro.webapp.beans.Property;
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@ -112,11 +113,12 @@ public class DisplayByRolePermission extends Permission {
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*/
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private boolean isAuthorized(DisplayObjectPropertyStatement action) {
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ObjectPropertyStatement stmt = action.getObjectPropertyStatement();
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String subjectUri = stmt.getSubjectURI();
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String predicateUri = stmt.getPropertyURI();
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String subjectUri = stmt.getSubjectURI();
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String objectUri = stmt.getObjectURI();
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Property op = (stmt.getProperty() != null)
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? stmt.getProperty() : new Property(stmt.getPropertyURI());
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return canDisplayResource(subjectUri)
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&& canDisplayPredicate(new Property(predicateUri))
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&& canDisplayPredicate(op)
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&& canDisplayResource(objectUri);
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}
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@ -0,0 +1,59 @@
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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.controller.json;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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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 org.json.JSONObject;
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import edu.cornell.mannlib.vitro.webapp.beans.VClass;
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import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupsForRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VClassGroupCache;
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/**
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*This class will get all the vclasses in the system.
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*/
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public class GetAllVClasses extends JsonObjectProducer {
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private static final Log log = LogFactory
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.getLog(GetAllVClasses.class);
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public GetAllVClasses(VitroRequest vreq) {
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super(vreq);
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}
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@Override
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protected JSONObject process() throws Exception {
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JSONObject map = new JSONObject();
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//Get all VClassGroups
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List<VClass> vclasses = new ArrayList<VClass>();
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VClassGroupsForRequest vcgc = VClassGroupCache.getVClassGroups(vreq);
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List<VClassGroup> groups = vcgc.getGroups();
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for(VClassGroup vcg: groups) {
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for( VClass vc : vcg){
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vclasses.add(vc);
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}
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}
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//Sort vclass by name
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Collections.sort(vclasses);
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ArrayList<JSONObject> classes = new ArrayList<JSONObject>(vclasses.size());
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for(VClass vc: vclasses) {
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JSONObject vcObj = new JSONObject();
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vcObj.put("name", vc.getName());
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vcObj.put("URI", vc.getURI());
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classes.add(vcObj);
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}
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map.put("classes", classes);
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return map;
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}
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}
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@ -83,6 +83,8 @@ public class JsonServlet extends VitroHttpServlet {
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new GetRenderedSolrIndividualsByVClass(vreq).process(resp);
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}else if( vreq.getParameter("getRandomSolrIndividualsByVClass") != null ){
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new GetRandomSolrIndividualsByVClass(vreq).process(resp);
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} else if( vreq.getParameter("getAllVClasses") != null ){
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new GetAllVClasses(vreq).process(resp);
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}
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}
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@ -104,8 +104,10 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
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// funny business because it needs to be able to retrieve anonymous union
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// classes by their "pseudo-bnode URIs".
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// Someday we'll need to figure out a different way of doing this.
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WebappDaoFactory ctxDaoFact = ModelAccess.on(
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vreq.getSession().getServletContext()).getWebappDaoFactory();
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//WebappDaoFactory ctxDaoFact = ModelAccess.on(
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// vreq.getSession().getServletContext()).getWebappDaoFactory();
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WebappDaoFactory ctxDaoFact = vreq.getLanguageNeutralWebappDaoFactory();
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List<VClass> types = new ArrayList<VClass>();
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Individual subject = EditConfigurationUtils.getSubjectIndividual(vreq);
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String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
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@ -4,6 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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@ -30,10 +31,14 @@ 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.vocabulary.XSD;
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import edu.cornell.mannlib.vitro.webapp.beans.VClass;
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import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
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import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupsForRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VClassGroupCache;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
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@ -521,6 +526,8 @@ private String getExistingIsSelfContainedTemplateQuery() {
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MenuManagementDataUtils.includeRequiredSystemData(vreq.getSession().getServletContext(), data);
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data.put("classGroup", new ArrayList<String>());
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data.put("classGroups", DataGetterUtils.getClassGroups(vreq));
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//for solr individuals data get getter
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data.put("classes", this.getAllVClasses(vreq));
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data.put("availablePermissions", this.getAvailablePermissions(vreq));
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data.put("availablePermissionOrderedList", this.getAvailablePermissonsOrderedURIs());
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}
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@ -664,4 +671,33 @@ private String getExistingIsSelfContainedTemplateQuery() {
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return query;
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}
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//Get all vclasses for the list of vclasses for solr
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//Originally considered using an ajax request to get the vclasses list which is fine for adding a new content type
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//but for an existing solr content type, would need to make yet another ajax request which seems too much
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private List<HashMap<String, String>> getAllVClasses(VitroRequest vreq) {
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List<VClass> vclasses = new ArrayList<VClass>();
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VClassGroupsForRequest vcgc = VClassGroupCache.getVClassGroups(vreq);
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List<VClassGroup> groups = vcgc.getGroups();
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for(VClassGroup vcg: groups) {
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for( VClass vc : vcg){
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vclasses.add(vc);
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}
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}
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//Sort vclass by name
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Collections.sort(vclasses);
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ArrayList<HashMap<String, String>> classes = new ArrayList<HashMap<String, String>>(vclasses.size());
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for(VClass vc: vclasses) {
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HashMap<String, String> vcObj = new HashMap<String, String>();
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vcObj.put("name", vc.getName());
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vcObj.put("URI", vc.getURI());
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classes.add(vcObj);
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}
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return classes;
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}
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}
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@ -18,6 +18,7 @@ public class ProcessDataGetterN3Map {
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessClassGroupDataGetterN3");
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessIndividualsForClassesDataGetterN3");
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessFixedHTMLN3");
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SolrIndividualsDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessSolrIndividualsDataGetterN3");
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return map;
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}
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@ -0,0 +1,179 @@
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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.edit.n3editing.configuration.preprocessors.utils;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import javax.servlet.ServletContext;
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import net.sf.json.JSONObject;
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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.OntModel;
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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.QuerySolution;
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import com.hp.hpl.jena.query.ResultSet;
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import com.hp.hpl.jena.rdf.model.Literal;
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import com.hp.hpl.jena.rdf.model.Resource;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
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//Returns the appropriate n3 based on data getter
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public class ProcessSolrIndividualsDataGetterN3 extends ProcessDataGetterAbstract {
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private static String classType = "java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SolrIndividualsDataGetter";
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private Log log = LogFactory.getLog(ProcessFixedHTMLN3.class);
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public ProcessSolrIndividualsDataGetterN3(){
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}
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//Pass in variable that represents the counter
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//TODO: ensure correct model returned
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//We shouldn't use the ACTUAL values here but generate the n3 required
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//?dataGetter a FixedHTMLDataGetter ; display:saveToVar ?saveToVar; display:htmlValue ?htmlValue .
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public List<String> retrieveN3Required(int counter) {
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String dataGetterVar = getDataGetterVar(counter);
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//UPDATE: Using variable for class type
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String classTypeVar = getN3VarName(classTypeVarBase, counter);
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String n3 = dataGetterVar + " a " + classTypeVar + "; \n" +
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"display:saveToVar " + getN3VarName("saveToVar", counter) + "; \n" +
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"display:hasVClassId " + getN3VarName("vclassUri", counter) + " .";
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List<String> requiredList = new ArrayList<String>();
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requiredList.add(getPrefixes() + n3);
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return requiredList;
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}
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public List<String> retrieveN3Optional(int counter) {
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return null;
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}
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public List<String> retrieveLiteralsOnForm(int counter) {
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List<String> literalsOnForm = new ArrayList<String>();
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literalsOnForm.add(getVarName("saveToVar",counter));
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return literalsOnForm;
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}
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public List<String> retrieveUrisOnForm(int counter) {
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List<String> urisOnForm = new ArrayList<String>();
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//UPDATE: adding class type as uri on form
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urisOnForm.add(getVarName("vclassUri", counter));
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urisOnForm.add(getVarName(classTypeVarBase, counter));
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return urisOnForm;
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}
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public List<FieldVTwo> retrieveFields(int counter) {
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List<FieldVTwo> fields = new ArrayList<FieldVTwo>();
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//fields.add(new FieldVTwo().setName(getVarName("dataGetter", counter)));
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fields.add(new FieldVTwo().setName(getVarName("saveToVar", counter)));
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fields.add(new FieldVTwo().setName(getVarName("vclassUri", counter)));
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//UPDATE: adding class type to the uris on the form
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fields.add(new FieldVTwo().setName(getVarName(classTypeVarBase, counter)));
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return fields;
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}
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public List<String> getLiteralVarNamesBase() {
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return Arrays.asList("saveToVar");
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}
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//these are for the fields ON the form
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public List<String> getUriVarNamesBase() {
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return Arrays.asList(classTypeVarBase, "vclassUri");
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}
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//For Existing Values in case of editing
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//Execute populate before retrieval
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public void populateExistingValues(String dataGetterURI, int counter, OntModel queryModel) {
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//First, put dataGetterURI within scope as well
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this.populateExistingDataGetterURI(dataGetterURI, counter);
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//Put in type
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this.populateExistingClassType(this.getClassType(), counter);
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//Sparql queries for values to be executed
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//And then placed in the correct place/literal or uri
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String querystr = getExistingValuesSparqlQuery(dataGetterURI);
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QueryExecution qe = null;
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try{
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Query query = QueryFactory.create(querystr);
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qe = QueryExecutionFactory.create(query, queryModel);
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ResultSet results = qe.execSelect();
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while( results.hasNext()){
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QuerySolution qs = results.nextSolution();
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Literal saveToVarLiteral = qs.getLiteral("saveToVar");
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Resource vclassUriResource = qs.getResource("vclassUri");
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//Put both literals in existing literals
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existingLiteralValues.put(this.getVarName("saveToVar", counter),
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new ArrayList<Literal>(Arrays.asList(saveToVarLiteral)));
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existingUriValues.put(this.getVarName("vclassUri", counter),
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new ArrayList<String>(Arrays.asList(vclassUriResource.getURI())));
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}
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} catch(Exception ex) {
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log.error("Exception occurred in retrieving existing values with query " + querystr, ex);
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}
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}
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//?dataGetter a FixedHTMLDataGetter ; display:saveToVar ?saveToVar; display:htmlValue ?htmlValue .
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protected String getExistingValuesSparqlQuery(String dataGetterURI) {
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String query = this.getSparqlPrefix() + " SELECT ?saveToVar ?vclassUri WHERE {" +
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"<" + dataGetterURI + "> display:saveToVar ?saveToVar . \n" +
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"<" + dataGetterURI + "> display:hasVClassId ?vclassUri . \n" +
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"}";
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return query;
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}
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//Method to create a JSON object with existing values to return to form
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//There may be a better way to do this without having to run the query twice
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//TODO: Refactor code if required
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public JSONObject getExistingValuesJSON(String dataGetterURI, OntModel queryModel, ServletContext context) {
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JSONObject jObject = new JSONObject();
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jObject.element("dataGetterClass", classType);
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jObject.element(classTypeVarBase, classType);
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String querystr = getExistingValuesSparqlQuery(dataGetterURI);
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QueryExecution qe = null;
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try{
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Query query = QueryFactory.create(querystr);
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qe = QueryExecutionFactory.create(query, queryModel);
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ResultSet results = qe.execSelect();
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while( results.hasNext()){
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QuerySolution qs = results.nextSolution();
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Literal saveToVarLiteral = qs.getLiteral("saveToVar");
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Resource vclassUriResource = qs.getResource("vclassUri");
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String vclassUriString = vclassUriResource.getURI();
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jObject.element("saveToVar", saveToVarLiteral.getString());
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//TODO: Handle single and double quotes within string and escape properlyu
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jObject.element("vclassUri", vclassUriString);
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}
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} catch(Exception ex) {
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log.error("Exception occurred in retrieving existing values with query " + querystr, ex);
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}
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return jObject;
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}
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//Escape single and double quotes for html string to be returned to form
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public String replaceQuotes(String inputStr) {
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return inputStr.replaceAll("\'", "'").replaceAll("\"", """);
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}
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//This class can be extended so returning type here
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public String getClassType() {
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return classType;
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}
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}
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@ -64,7 +64,7 @@ public class KnowledgeBaseUpdater {
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}
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long startTime = System.currentTimeMillis();
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log.info("Migrating the knowledge base");
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log.info("Performing any necessary data migration");
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logger.log("Started knowledge base migration");
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try {
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@ -93,24 +93,6 @@ public class KnowledgeBaseUpdater {
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List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
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AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
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// Only modify the TBox and migration metadata the first time
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if(updateRequired(servletContext)) {
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//process the TBox before the ABox
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try {
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log.debug("\tupdating tbox annotations");
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updateTBoxAnnotations();
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} catch (Exception e) {
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log.error(e,e);
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}
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try {
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migrateMigrationMetadata(servletContext);
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logger.log("Migrated migration metadata");
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||||
} catch (Exception e) {
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log.error("unable to migrate migration metadata " + e.getMessage());
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}
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}
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// update ABox data any time
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log.info("performing SPARQL CONSTRUCT additions");
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@ -130,6 +112,18 @@ public class KnowledgeBaseUpdater {
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performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/",
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settings.getRDFService(), RETRACT);
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||||
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// Only modify the TBox and migration metadata the first time
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||||
if(updateRequired(servletContext)) {
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||||
//process the TBox before the ABox
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try {
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log.debug("\tupdating tbox annotations");
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||||
updateTBoxAnnotations();
|
||||
} catch (Exception e) {
|
||||
log.error(e,e);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -264,39 +258,6 @@ public class KnowledgeBaseUpdater {
|
|||
aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
|
||||
}
|
||||
|
||||
// special for 1.5 - temporary code
|
||||
// migrate past migration indicators to not use blank nodes and move them to app metadata model
|
||||
// changing structure for pre 1.5 ones in the process
|
||||
private void migrateMigrationMetadata(ServletContext servletContext) throws Exception {
|
||||
|
||||
String baseResourceURI = "http://vitro.mannlib.cornell.edu/ns/vitro/metadata/migration/";
|
||||
String queryFile = "MigrationData.sparql";
|
||||
|
||||
RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(servletContext).getRDFService();
|
||||
|
||||
String fmQuery = FileUtils.readFileToString(new File(settings.getSparqlConstructDeletionsDir() + "/" + queryFile));
|
||||
Model toRemove = ModelFactory.createDefaultModel();
|
||||
toRemove.read(rdfService.sparqlConstructQuery(fmQuery, RDFService.ModelSerializationFormat.RDFXML), null);
|
||||
|
||||
String cmQuery = FileUtils.readFileToString(new File(settings.getSparqlConstructAdditionsDir() + "/" + queryFile));
|
||||
Model toAdd = ModelFactory.createDefaultModel();
|
||||
toAdd.read(rdfService.sparqlConstructQuery(cmQuery, RDFService.ModelSerializationFormat.RDFXML), null);
|
||||
|
||||
ByteArrayOutputStream outAdd = new ByteArrayOutputStream();
|
||||
toAdd.write(outAdd);
|
||||
InputStream inAdd = new ByteArrayInputStream(outAdd.toByteArray());
|
||||
ChangeSet addChangeSet = rdfService.manufactureChangeSet();
|
||||
addChangeSet.addAddition(inAdd, RDFService.ModelSerializationFormat.RDFXML, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
|
||||
rdfService.changeSetUpdate(addChangeSet);
|
||||
|
||||
ByteArrayOutputStream outRemove = new ByteArrayOutputStream();
|
||||
toRemove.write(outRemove);
|
||||
InputStream inRemove = new ByteArrayInputStream(outRemove.toByteArray());
|
||||
ChangeSet removeChangeSet = rdfService.manufactureChangeSet();
|
||||
removeChangeSet.addRemoval(inRemove, RDFService.ModelSerializationFormat.RDFXML, JenaDataSourceSetupBase.JENA_DB_MODEL);
|
||||
rdfService.changeSetUpdate(removeChangeSet);
|
||||
}
|
||||
|
||||
private void updateTBoxAnnotations() {
|
||||
TBoxUpdater tboxUpdater = new TBoxUpdater(settings, logger, record);
|
||||
try {
|
||||
|
|
|
|||
|
|
@ -88,10 +88,6 @@ public class TBoxUpdater {
|
|||
public void modifyPropertyQualifications() throws IOException {
|
||||
|
||||
}
|
||||
|
||||
private Model mergeConfigurations(Model oldConfig, Model newConfig) {
|
||||
return null;
|
||||
}
|
||||
|
||||
public void updateDefaultAnnotationValues() throws IOException {
|
||||
updateDefaultAnnotationValues(null);
|
||||
|
|
@ -454,89 +450,69 @@ public class TBoxUpdater {
|
|||
}
|
||||
|
||||
public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
|
||||
Dataset dataset = new RDFServiceDataset(settings.getRDFService());
|
||||
Model userAnnotationsModel = dataset.getNamedModel(
|
||||
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
|
||||
if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
|
||||
mergePropertyAnnotationsToPropertyConfig(changeObj, userAnnotationsModel);
|
||||
mergePropertyAnnotationsToPropertyConfig(changeObj, siteModel);
|
||||
}
|
||||
Resource renamedProperty = userAnnotationsModel.getResource(changeObj.getSourceURI());
|
||||
userAnnotationsModel.removeAll(renamedProperty, null, (RDFNode) null);
|
||||
userAnnotationsModel.removeAll(null, null, renamedProperty);
|
||||
Resource renamedProperty = siteModel.getResource(changeObj.getSourceURI());
|
||||
siteModel.removeAll(renamedProperty, null, (RDFNode) null);
|
||||
siteModel.removeAll(null, null, renamedProperty);
|
||||
}
|
||||
|
||||
private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj,
|
||||
Model userAnnotationsModel) throws IOException {
|
||||
String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3);
|
||||
String oldPropertyURI = changeObj.getSourceURI();
|
||||
|
||||
Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel();
|
||||
|
||||
String propertyAnnotationsQuery =
|
||||
"PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
|
||||
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
|
||||
"CONSTRUCT { \n" +
|
||||
" <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
|
||||
" <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
|
||||
" <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
|
||||
" <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
|
||||
" <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
|
||||
" <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
|
||||
" <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
|
||||
"} WHERE { \n" +
|
||||
" { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
|
||||
" UNION { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
|
||||
" UNION { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
|
||||
" UNION { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
|
||||
" UNION { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
|
||||
" UNION { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
|
||||
" { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
|
||||
" UNION { <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
|
||||
" FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
|
||||
"} \n" ;
|
||||
|
||||
Model userChangesModel = construct(
|
||||
propertyAnnotationsQuery, userAnnotationsModel).difference(
|
||||
construct(propertyAnnotationsQuery, oldAnnotationsModel));
|
||||
|
||||
String addQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
|
||||
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
|
||||
"CONSTRUCT { \n" +
|
||||
" ?configuration config:propertyGroup ?group . \n" +
|
||||
" ?configuration config:displayName ?label . \n" +
|
||||
" ?configuration vitro:displayRankAnnot ?displayRank . \n" +
|
||||
" ?configuration vitro:customEntryFormAnnot ?customForm . \n" +
|
||||
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
|
||||
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
|
||||
"} WHERE { \n" +
|
||||
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
|
||||
"} \n" ;
|
||||
if(userChangesModel.size() == 0) {
|
||||
return;
|
||||
} else {
|
||||
log.info("Updating PropertyConfig.n3 to include locally-changed " +
|
||||
"settings from old property " + oldPropertyURI);
|
||||
}
|
||||
|
||||
String retractQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
|
||||
String newQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
|
||||
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
|
||||
"CONSTRUCT { \n" +
|
||||
" <" + oldPropertyURI + "> config:propertyGroup ?rgroup . \n" +
|
||||
" ?configuration config:displayName ?rlabel . \n" +
|
||||
" ?configuration vitro:displayRankAnnot ?rdisplayRank . \n" +
|
||||
" ?configuration vitro:customEntryFormAnnot ?rcustomForm . \n" +
|
||||
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel . \n" +
|
||||
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?rupdateLevel . \n " +
|
||||
" ?configuration config:propertyGroup ?group . \n" +
|
||||
" ?configuration config:displayName ?label . \n" +
|
||||
" ?configuration ?vitroProp ?vitroValue . \n" +
|
||||
"} WHERE { \n" +
|
||||
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
|
||||
" ?configuration config:propertyGroup ?rgroup } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
|
||||
" ?configuration config:displayName ?rlabel } \n " +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
|
||||
" ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
|
||||
" ?configuration vitro:customEntryFormAnnot ?rcustomForm } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
|
||||
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
|
||||
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } " +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
|
||||
" OPTIONAL { <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
|
||||
" FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
|
||||
"} \n" ;
|
||||
|
||||
String existingQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
|
||||
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
|
||||
"CONSTRUCT { \n" +
|
||||
" ?configuration config:propertyGroup ?group . \n" +
|
||||
" ?configuration config:displayName ?label . \n" +
|
||||
" ?configuration ?vitroProp ?vitroValue . \n" +
|
||||
"} WHERE { \n" +
|
||||
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
|
||||
" OPTIONAL { ?configuration config:propertyGroup ?group } \n" +
|
||||
" OPTIONAL { ?configuration config:displayName ?label } \n" +
|
||||
" OPTIONAL { ?configuration ?vitroProp ?vitroValue \n" +
|
||||
" FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
|
||||
"} \n" ;
|
||||
|
||||
Model configModel = ModelFactory.createDefaultModel();
|
||||
|
|
@ -545,17 +521,31 @@ public class TBoxUpdater {
|
|||
FileInputStream fis = new FileInputStream(file);
|
||||
configModel.read(fis, null, "N3");
|
||||
|
||||
Model union = ModelFactory.createUnion(configModel,
|
||||
userChangesModel);
|
||||
Model currentUnion = ModelFactory.createUnion(configModel,
|
||||
userAnnotationsModel);
|
||||
|
||||
Model additions = construct(addQuery, union);
|
||||
Model retractions = construct(retractQuery, union);
|
||||
Model userAnnotationsAsConfig = construct(newQuery, currentUnion);
|
||||
Model currentDefaultConfig = construct(existingQuery, currentUnion);
|
||||
|
||||
if (additions.size() > 0 || retractions.size() > 0) {
|
||||
configModel.remove(retractions);
|
||||
log.info("Removing " + retractions.size() + " statements from " + contextURI);
|
||||
Model additions = userAnnotationsAsConfig.difference(currentDefaultConfig);
|
||||
Model retractions = currentDefaultConfig.difference(userAnnotationsAsConfig);
|
||||
|
||||
// filter the retractions so we won't remove a value for a given predicate
|
||||
// unless the additions model contains at least one value for the same predicate
|
||||
Model filteredRetractions = ModelFactory.createDefaultModel();
|
||||
StmtIterator retractIt = retractions.listStatements();
|
||||
while(retractIt.hasNext()) {
|
||||
Statement candidate = retractIt.nextStatement();
|
||||
if(additions.contains(null, candidate.getPredicate(), (RDFNode) null)) {
|
||||
filteredRetractions.add(candidate);
|
||||
}
|
||||
}
|
||||
|
||||
if (additions.size() > 0 || filteredRetractions.size() > 0) {
|
||||
configModel.remove(filteredRetractions);
|
||||
log.debug("Removing " + filteredRetractions.size() + " statements from " + contextURI);
|
||||
configModel.add(additions);
|
||||
log.info("Adding " + additions.size() + " statements from " + contextURI);
|
||||
log.debug("Adding " + additions.size() + " statements from " + contextURI);
|
||||
FileOutputStream fos = new FileOutputStream(file);
|
||||
configModel.write(fos, "N3");
|
||||
}
|
||||
|
|
|
|||
|
|
@ -81,6 +81,8 @@ public class SimpleReasonerSetup implements ServletContextListener {
|
|||
|
||||
log.info("Pellet reasoner connected for the TBox");
|
||||
|
||||
waitForTBoxReasoning(sce);
|
||||
|
||||
// set up simple reasoning for the ABox
|
||||
|
||||
RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService();
|
||||
|
|
@ -131,7 +133,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
|
|||
int sleeps = 0;
|
||||
// sleep at least once to make sure the TBox reasoning gets started
|
||||
while ((0 == sleeps) || ((sleeps < 1000) && pelletListener.isReasoning())) {
|
||||
if ((sleeps % 10) == 0) { // print message at 10 second intervals
|
||||
if (((sleeps - 1) % 10) == 0) { // print message at 10 second intervals
|
||||
log.info("Waiting for initial TBox reasoning to complete");
|
||||
}
|
||||
Thread.sleep(1000);
|
||||
|
|
|
|||
|
|
@ -141,7 +141,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
|
|||
if(!JenaDataSourceSetupBase.isFirstStartup()) {
|
||||
try {
|
||||
ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
|
||||
log.info("Data migration required");
|
||||
migrationChangesMade = ontologyUpdater.update(ctx);
|
||||
if (tryMigrateDisplay) {
|
||||
try {
|
||||
|
|
@ -221,8 +220,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
|
|||
StartupStatus.getBean(ctx).info(this, "Updating knowledge base: reports are in '" + dataDir + "'");
|
||||
|
||||
Path changedDir = createDirectory(dataDir, "changedData");
|
||||
settings.setAddedDataFile(changedDir.resolve("addedData.n3").toString());
|
||||
settings.setRemovedDataFile(changedDir.resolve("removedData.n3").toString());
|
||||
settings.setAddedDataFile(changedDir.resolve(timestampedFileName("addedData", "n3")).toString());
|
||||
settings.setRemovedDataFile(changedDir.resolve(timestampedFileName("removedData", "n3")).toString());
|
||||
|
||||
Path logDir = createDirectory(dataDir, "logs");
|
||||
settings.setLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate", "log")).toString());
|
||||
|
|
|
|||
|
|
@ -108,9 +108,9 @@ public class GroupedPropertyList extends BaseTemplateModel {
|
|||
|
||||
if (editing) {
|
||||
mergeAllPossibleDataProperties(propertyList);
|
||||
propertyList = correctLanguageForProperties(propertyList);
|
||||
}
|
||||
|
||||
propertyList = correctLanguageForProperties(propertyList);
|
||||
sort(propertyList);
|
||||
|
||||
// Put the list into groups
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue