NIHVIVO-707 Set hidden rank field value based on existing webpage ranks

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java

@@ -27,6 +27,7 @@ import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
@@ -783,7 +784,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
         }                     
         log.debug("Data property query string:\n" + query);         
      
-        Iterator<QuerySolution> results = getPropertyQueryResults(query);
+        ResultSet results = getPropertyQueryResults(query);
         List<DataProperty> properties = new ArrayList<DataProperty>();
         while (results.hasNext()) {
             QuerySolution sol = results.next();

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyStatementDaoJena.java

@@ -338,8 +338,9 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         DatasetWrapper w = dwf.getDatasetWrapper();
         Dataset dataset = w.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
+        QueryExecution qexec = null;
         try {
-            QueryExecution qexec = QueryExecutionFactory.create(
+            qexec = QueryExecutionFactory.create(
                     queryString, dataset);
             ResultSet results = qexec.execSelect(); 
     
@@ -351,6 +352,9 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         } finally {
             dataset.getLock().leaveCriticalSection();
             w.close();
+            if (qexec != null) {
+                qexec.close();
+            }
         }
         return values;         
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java

@@ -871,7 +871,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         } 
         log.debug("Object property query:\n" + query);
         
-        Iterator<QuerySolution> results = getPropertyQueryResults(query);
+        ResultSet results = getPropertyQueryResults(query);
         List<ObjectProperty> properties = new ArrayList<ObjectProperty>();
         while (results.hasNext()) {
             QuerySolution soln = results.next();
@@ -917,6 +917,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 String filename = soln.getLiteral("filename").getLexicalForm();
                 customListViewConfigFileMap.put(prop, filename);                
             }       
+            qexec.close();
         }        
         return customListViewConfigFileMap.get(op);
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyStatementDaoJena.java

@@ -302,9 +302,10 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         DatasetWrapper w = dwf.getDatasetWrapper();
         Dataset dataset = w.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
+        QueryExecution qexec = null;
         try {
 
-            QueryExecution qexec = (constructedModel == null) 
+            qexec = (constructedModel == null) 
                     ? QueryExecutionFactory.create(
                             query, dataset, initialBindings)
                     : QueryExecutionFactory.create(
@@ -323,6 +324,9 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         } finally {
             dataset.getLock().leaveCriticalSection();
             w.close();
+            if (qexec != null) {
+                qexec.close();
+            }
         }
         return list;
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyDaoJena.java

@@ -20,15 +20,13 @@ import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.QuerySolutionMap;
 import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
@@ -404,7 +402,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         return classSet;
     }
      
-    protected Iterator<QuerySolution> getPropertyQueryResults(Query query) {        
+    protected ResultSet getPropertyQueryResults(Query query) {        
         log.debug("SPARQL query:\n" + query.toString());
         
         // RY Removing prebinding due to Jena bug: when isLiteral(?object) or 
@@ -417,17 +415,12 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         DatasetWrapper w = dwf.getDatasetWrapper();
         Dataset dataset = w.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
+        ResultSet rs = null;
         try {
             QueryExecution qexec = QueryExecutionFactory.create(
                     query, dataset); //, subjectBinding);
             try {
-                ResultSet rs = qexec.execSelect();
+                rs = new ResultSetMem(qexec.execSelect());
-                // consume iterator before wrapper w is closed in finally block
-                List<QuerySolution> results = new ArrayList<QuerySolution>();
-                while (rs.hasNext()) {
-                    results.add(rs.next());
-                }
-                return results.iterator();
             } finally {
                 qexec.close();
             }
@@ -435,6 +428,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
             dataset.getLock().leaveCriticalSection();
             w.close();
         }
+        return rs;
     }
     
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/QueryUtils.java

@@ -18,6 +18,7 @@ import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
 
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 
@@ -30,6 +31,8 @@ public class QueryUtils {
     
     private static final Log log = LogFactory.getLog(QueryUtils.class);
     
+    private QueryUtils() { }
+    
     protected static Map<String,Object> querySolutionToObjectValueMap( QuerySolution soln){
         Map<String,Object> map = new HashMap<String,Object>();
         Iterator<String> varNames = soln.varNames();
@@ -110,12 +113,11 @@ public class QueryUtils {
         
         Dataset dataset = vreq.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
-queryStr = " SELECT ?x WHERE { ?x ?p ?y } LIMIT 10";
         QueryExecution qexec = null;
         ResultSet results = null;
         try {
             qexec = QueryExecutionFactory.create(queryStr, dataset);                    
-            results = qexec.execSelect();
+            results = new ResultSetMem(qexec.execSelect());
         } catch (Exception e) {
             log.error(e, e);
         } finally {
@@ -124,32 +126,8 @@ queryStr = " SELECT ?x WHERE { ?x ?p ?y } LIMIT 10";
                 qexec.close();
             }
         } 
-         try {
-        /* DEBUGGING */
-        int maxRank = 0;
-        if (results.hasNext()) { // there is at most one result
-            log.debug("found a rank");
-            QuerySolution soln = results.next(); 
-            RDFNode node = soln.get("rank");
-            if (node != null && node.isLiteral()) {
-                log.debug("node value =" + node.asLiteral().getLexicalForm());
-                try {
-                    int rank = node.asLiteral().getInt(); 
-                    if (rank > maxRank) {  
-                        log.debug("setting maxRank to " + rank);
-                        maxRank = rank;
-                    }
-                } catch (Exception e) {
-                    log.error("Error getting int value for rank: " + e.getMessage());
-                }
-            }
-        }
-         } catch (Exception e) {
-             log.error(e, e);
-         }
         
         return results;
     }
 
-
 }

webapp/web/edit/forms/addMissingWithMonikerAndLink.jsp

@@ -1,264 +0,0 @@
-<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
-
-<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.VitroRequest" %>
-<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory" %>
-<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty" %>
-<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.VClass" %>
-<%@ page import="com.hp.hpl.jena.rdf.model.Literal" %>
-<%@ page import="com.hp.hpl.jena.rdf.model.Model" %>
-<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.Individual" %>
-<%@ page import="edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfiguration" %>
-<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
-<%@ taglib prefix="v" uri="http://vitro.mannlib.cornell.edu/vitro/tags" %>
-<%
-    Individual subject = (Individual)request.getAttribute("subject");
-    ObjectProperty prop = (ObjectProperty)request.getAttribute("predicate");
-    if (prop == null) throw new Error("no object property specified via incoming predicate attribute in defaultAddMissingIndividualForm.jsp");
-    String propDomainPublic = (prop.getDomainPublic() == null) ? "affiliation" : prop.getDomainPublic();
-
-    VitroRequest vreq = new VitroRequest(request);
-    //String contextPath = vreq.getContextPath();
-    WebappDaoFactory wdf = vreq.getWebappDaoFactory();
-    if( prop.getRangeVClassURI() == null )throw new Error("Property has null for its range class URI");
-
-    VClass rangeClass = wdf.getVClassDao().getVClassByURI(prop.getRangeVClassURI());
-    if( rangeClass == null ) throw new Error ("Cannot find class for range for property.  Looking for " + prop.getRangeVClassURI() );
-    //vreq.setAttribute("rangeClassLocalName",rangeClass.getLocalName());
-    //vreq.setAttribute("rangeClassNamespace",rangeClass.getNamespace());
-    vreq.setAttribute("rangeClassUri",prop.getRangeVClassURI());
-    vreq.setAttribute("curatorReviewUri","http://vivo.library.cornell.edu/ns/0.1#CuratorReview");
-    
-%>
-
-<v:jsonset var="queryForInverse" >
-    PREFIX owl:  <http://www.w3.org/2002/07/owl#>
-    SELECT ?inverse_property
-    WHERE { ?inverse_property owl:inverseOf ?predicate }
-</v:jsonset>
-
-<%-- Enter here the class names to be used for constructing MONIKERS_VIA_VCLASS pick lists
-     These are then referenced in the field's ObjectClassUri but not elsewhere.
-     Note that you can't reference a jsonset variable inside another jsonset expression
-     or you get double escaping problems --%>
-<v:jsonset var="newIndividualVClassUri">${rangeClassUri}</v:jsonset>
-
-<%-- Then enter a SPARQL query for each field, by convention concatenating the field id with "Existing"
-     to convey that the expression is used to retrieve any existing value for the field in an existing individual.
-     Each of these must then be referenced in the sparqlForExistingLiterals section of the JSON block below
-     and in the literalsOnForm --%>
-<v:jsonset var="nameExisting" >
-    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-    SELECT ?existingName
-    WHERE { ?newIndividual rdfs:label ?existingName }
-</v:jsonset>
-<%-- Pair the "existing" query with the skeleton of what will be asserted for a new statement involving this field.
-     the actual assertion inserted in the model will be created via string substitution into the ? variables.
-     NOTE the pattern of punctuation (a period after the prefix URI and after the ?field) --%> 
-<v:jsonset var="nameAssertion" >
-    @prefix vivo: <http://vivo.library.cornell.edu/ns/0.1#> .
-    ?newIndividual rdfs:label ?name .
-</v:jsonset>
-
-<v:jsonset var="monikerExisting" >
-    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-    SELECT ?existingMoniker
-    WHERE { ?newIndividual vitro:moniker ?existingMoniker }
-</v:jsonset>
-<v:jsonset var="monikerAssertion" >
-    @prefix vivo: <http://vivo.library.cornell.edu/ns/0.1#> .
-    ?newIndividual vitro:moniker ?moniker .
-</v:jsonset>
-
-<v:jsonset var="linkUrlExisting" >
-    PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>
-    SELECT ?existingLinkUrl
-    WHERE { ?newIndividual vitro:primaryLink ?newLink ;
-            ?newLink vitro:linkURL ?existingLinkUrl .            
-    }
-</v:jsonset>
-<v:jsonset var="linkUrlAssertion" >
-    @prefix vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> .
-    ?newLink vitro:linkURL ?linkUrl .
-</v:jsonset>
-
-<v:jsonset var="n3ForEdit"  >
-    @prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-    @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-    @prefix vivo: <http://vivo.library.cornell.edu/ns/0.1#> .
-    @prefix vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> .
-
-    ?newIndividual rdf:type <${curatorReviewUri}> .
-    ?newIndividual rdf:type <${rangeClassUri}> .
-    ?subject ?predicate ?newIndividual .
-    
-    ?newIndividual rdfs:label ?name .
-</v:jsonset>
-
-<v:jsonset var="n3Inverse" >
-    ?newIndividual ?inverseProp ?subject .
-</v:jsonset>
-
-<%-- make sure you have all the @prefix entries to cover the statements in each block --%>
-<v:jsonset var="n3optional" >
-    @prefix vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> .
-    ?newIndividual vitro:moniker ?moniker .
-</v:jsonset>
-
-<%-- note that it's safer to have multiple distinct optional blocks so that a failure in one
-     will not prevent correct sections from being inserted --%>
-<v:jsonset var="n3link" >
-    @prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-    @prefix vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> .
-    ?newLink
-        rdf:type vitro:Link ;
-        vitro:linkURL ?linkUrl ;
-        vitro:linkAnchor ?name ;
-        vitro:linkDisplayRank "1" .
-    
-    ?newIndividual vitro:primaryLink ?newLink .
-</v:jsonset>
-
-
-<c:set var="editjson" scope="request">
-  {
-    "formUrl" : "${formUrl}",
-    "editKey" : "${editKey}",
-    "urlPatternToReturnTo" : "/entity",
-
-    "subject"   : [ "subject", "${subjectUriJson}" ],
-    "predicate" : [ "predicate", "${predicateUriJson}" ],
-    "object"    : [ "newIndividual", "${objectUriJson}", "URI" ],
-    
-    "n3required"                : [ "${n3ForEdit}" ],
-    "n3optional"                : [ "${n3optional}", "${n3Inverse}", "${n3link}" ],
-    "newResources" : {
-        "newIndividual"         : "http://vivo.library.cornell.edu/ns/0.1#individual",
-        "newLink"               : "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#Link"
-    },
-    "urisInScope"               : { },
-    "literalsInScope"           : { },
-    "urisOnForm"                : [ ],
-    "literalsOnForm"            : [ "name","moniker","linkUrl" ],
-    "filesOnForm"               : [ ],
-    "sparqlForLiterals"         : { },
-    "sparqlForUris"             : { "inverseProp" : "${queryForInverse}" },
-    "sparqlForExistingLiterals" : {
-        "name"                  : "${nameExisting}",
-        "moniker"               : "${monikerExisting}",
-        "linkUrl"               : "${linkUrlExisting}"
-    },
-    "sparqlForExistingUris"     : { },
-    "fields" : {
-        "name" : {
-            "newResource"       : "false",
-            "validators"        : [ "nonempty" ],
-            "optionsType"       : "UNDEFINED",
-            "literalOptions"    : [ ],
-            "predicateUri"      : "",
-            "objectClassUri"    : "",
-            "rangeDatatypeUri"  : "",
-            "rangeLang"         : "",
-            "assertions"        : [ "${nameAssertion}" ]
-        },
-        "moniker" : {
-            "newResource"       : "false",
-            "validators"        : [ ],
-            "optionsType"       : "MONIKERS_VIA_VCLASS",
-            "literalOptions"    : [ ],
-            "predicateUri"      : "",
-            "objectClassUri"    : "${newIndividualVClassUri}",
-            "rangeDatatypeUri"  : "",
-            "rangeLang"         : "",
-            "assertions"        : [ "${monikerAssertion}" ]
-        },
-        "linkUrl" : {
-            "newResource"       : "false",
-            "validators"        : [],
-            "optionsType"       : "UNDEFINED",
-            "literalOptions"    : [],
-            "predicateUri"      : "",
-            "objectClassUri"    : "",
-            "rangeDatatypeUri"  : "",
-            "rangeLang"         : "",
-            "assertions"        : [ "${linkUrlAssertion}" ]
-        }
-     }
-  }
-</c:set>
-<%
-    EditConfiguration editConfig = EditConfiguration.getConfigFromSession(session,request);
-    if( editConfig == null ){
-        editConfig = new EditConfiguration((String)request.getAttribute("editjson"));
-        EditConfiguration.putConfigInSession(editConfig, session);
-    }
-
-    Model model =  (Model)application.getAttribute("jenaOntModel");
-    String objectUri = (String)request.getAttribute("objectUri");    
-    if( objectUri != null ){        
-        editConfig.prepareForObjPropUpdate(model);            
-    }else{
-        editConfig.prepareForNonUpdate(model);
-    }
-
-    String submitButtonLabel=""; // don't put local variables into the request
-    /* title is used by pre and post form fragments */
-    //set title to Edit to maintain functionality from 1.1.1 and avoid updates to Selenium tests
-    request.setAttribute("title", "Edit");
-    if (objectUri != null) {
-    	request.setAttribute("formTitle", "Edit \""+propDomainPublic+"\" entry for " + subject.getName());
-        submitButtonLabel = "Save changes";
-    } else {
-        request.setAttribute("formTitle","Create \""+propDomainPublic+"\" entry for " + subject.getName());
-        submitButtonLabel = "Create \""+propDomainPublic+"\" entry";
-    }
-
-%>
-
-<jsp:include page="${preForm}">
-    <jsp:param name="useTinyMCE" value="false"/>
-    <jsp:param name="useAutoComplete" value="true"/>
-</jsp:include>
-
-<script type="text/javascript" language="javascript">
-$(this).load($(this).parent().children('a').attr('src')+" .editForm");
-
-$(document).ready(function() {
-    var key = $("input[name='editKey']").attr("value");
-    $.getJSON("<c:url value="/dataservice"/>", {getN3EditOptionList:"1", field: "moniker", editKey: key}, function(json){
-
-    $("select#moniker").replaceWith("<input type='text' id='moniker' name='moniker' />");
-
-    $("#moniker").autocomplete(json, {
-            minChars: 0,
-            width: 320,
-            matchContains: true,
-            mustMatch: 0,
-            autoFill: false,
-            formatItem: function(row, i, max) {
-                return row[0];
-            },
-            formatMatch: function(row, i, max) {
-                return row[0];
-            },
-            formatResult: function(row) {
-                return row[0];
-            }
-           
-        }).result(function(event, data, formatted) {
-             $("input#moniker").attr("value", data[1]);
-           });
-}
-);
-})
-</script>
-
-<h2>${formTitle}</h2>
-<form action="<c:url value="/edit/processRdfForm2.jsp"/>" >
-    <v:input type="text" label="name (required)" id="name" size="30"/>
-    <hr/>
-    <v:input type="select" label="label (optional)" id="moniker"/> <em>start typing to see existing choices, or add a new label</em>
-    <v:input type="text" label="associated web page (optional)" id="linkUrl" size="50"/>
-    <v:input type="submit" id="submit" value="<%=submitButtonLabel%>" cancel="true"/>
-</form>
-
-<jsp:include page="${postForm}"/>