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Merge branch 'develop' of github.com:vivo-project/VIVO into develop

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This commit is contained in:
Stephen V. Williams 2013-08-26 09:41:23 -06:00
commit 957b6345e7
15 changed files with 554 additions and 82 deletions
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3
.gitignore vendored
View file

@ -6,4 +6,5 @@
/deploy.properties
/build.properties
/runtime.properties
catalog-v001.xml
/ontology/public/catalog-v0001.xml

47
productMods/WEB-INF/filegraph/tbox/ConceptSemanticType.owl Normal file
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@ -0,0 +1,47 @@
<rdf:RDF
xmlns:vitro-public="http://vitro.mannlib.cornell.edu/ns/vitro/public#"
xmlns:c4o="http://purl.org/spar/c4o/"
xmlns:ero="http://purl.obolibrary.org/obo/"
xmlns:pvs="http://vivoweb.org/ontology/provenance-support#"
xmlns:owl2="http://www.w3.org/2006/12/owl2-xml#"
xmlns:scirr="http://vivoweb.org/ontology/scientific-research-resource#"
xmlns:vivo="http://vivoweb.org/ontology/core#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:scires="http://vivoweb.org/ontology/scientific-research#"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:geo="http://aims.fao.org/aos/geopolitical.owl#"
xmlns:skco="http://www.w3.org/2004/02/skos/core#"
xmlns:event="http://purl.org/NET/c4dm/event.owl#"
xmlns:dcelem="http://purl.org/dc/elements/1.1/"
xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
xmlns:vann="http://purl.org/vocab/vann/"
xmlns:skos="http://www.w3.org/2008/05/skos#"
xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:fabio="http://purl.org/spar/fabio/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal"
>0.7</owl:versionInfo>
<owl:Class rdf:about="http://vivoweb.org/ontology/core#ConceptSemanticType">
<vitro:exampleAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Semantic Type for given concept, for example UMLS's type returned for concepts</vitro:exampleAnnot>
<vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Semantic Type for given concept, for example UMLS's type returned for concepts.</vitro:descriptionAnnot>
<vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Concept Semantic Type</vitro:shortDef>
</owl:Class>
<owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#hasConceptSemanticType">
<rdfs:range rdf:resource="http://vivoweb.org/ontology/core#ConceptSemanticType"/>
<owl:inverseOf rdf:resource="http://vivoweb.org/ontology/core#isConceptSemanticTypeOf"/>
</owl:ObjectProperty>
</rdf:RDF>

14
productMods/js/homePageMaps.js
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@ -9,6 +9,7 @@ $(document).ready(function(){
$.extend(this, urlsBase);
$.extend(this, i18nStrings);
$.extend(this, geoResearcherCount);
getGeoJsonForMaps();
@ -368,7 +369,7 @@ $(document).ready(function(){
function getResearcherCount(area) {
var researcherCount = 0;
var researcherCount = this.geoResearcherCount;
var areaCount = 0;
var text = "";
if ( area == "global" ) {
@ -383,7 +384,6 @@ $(document).ready(function(){
$.each(researchAreas.features, function() {
if ( this.properties.mapType == area ) {
researcherCount = researcherCount + this.properties.html ;
areaCount = areaCount + 1;
}
});
@ -391,10 +391,16 @@ $(document).ready(function(){
if ( areaCount == 1 && text == " states.") {
text = " " + i18nStrings.stateString;
}
if ( researcherCount == 1 ) {
researcherText = " " + i18nStrings.researcherString + " " + i18nStrings.inString;
}
else {
researcherText = " " + i18nStrings.researcherInString
}
$('div#researcherTotal').html("<font style='font-size:1.05em;color:#167093'>"
+ researcherCount.toString().replace(/(\d+)(\d{3})/, '$1'+','+'$2')
+ "</font> " + i18nStrings.researchersInString + " <font style='font-size:1.05em;color:#167093'>"
+ researcherCount
+ "</font> " + researcherText + " <font style='font-size:1.05em;color:#167093'>"
+ areaCount + "</font>" + text);
}
function appendLegendToLeafletContainer() {

35
productMods/js/individual/propertyGroupControls.js
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@ -69,22 +69,25 @@ $(document).ready(function(){
location.hash = location.hash.replace(/\s+/g, '');
if ( location.hash.indexOf("map") >= 0 ) {
// get the name of the group that contains the geographicFocusOf property.
var tabName = $('h3#geographicFocusOf').parent('article').parent('div').attr("id");
tabName = tabName.replace("Group","");
tabNameCapped = tabName.charAt(0).toUpperCase() + tabName.slice(1);
// if the name of the first tab section = tabName we don't have to do anything;
// otherwise, select the correct tab and deselect the first one
var $firstTab = $('li.clickable').first();
if ( $firstTab.text() != tabNameCapped ) {
// select the correct tab
$('li[groupName="' + tabName + '"]').removeClass("nonSelectedGroupTab clickable");
$('li[groupName="' + tabName + '"]').addClass("selectedGroupTab clickable");
// deselect the first tab
$firstTab.removeClass("selectedGroupTab clickable");
$firstTab.addClass("nonSelectedGroupTab clickable");
$('section.property-group:visible').hide();
// show the selected tab section
$('section#' + tabName).show();
// if it doesn't exist, don't do anything.
if ( $('h3#geographicFocusOf').length ) {
var tabName = $('h3#geographicFocusOf').parent('article').parent('div').attr("id");
tabName = tabName.replace("Group","");
tabNameCapped = tabName.charAt(0).toUpperCase() + tabName.slice(1);
// if the name of the first tab section = tabName we don't have to do anything;
// otherwise, select the correct tab and deselect the first one
var $firstTab = $('li.clickable').first();
if ( $firstTab.text() != tabNameCapped ) {
// select the correct tab
$('li[groupName="' + tabName + '"]').removeClass("nonSelectedGroupTab clickable");
$('li[groupName="' + tabName + '"]').addClass("selectedGroupTab clickable");
// deselect the first tab
$firstTab.removeClass("selectedGroupTab clickable");
$firstTab.addClass("nonSelectedGroupTab clickable");
$('section.property-group:visible').hide();
// show the selected tab section
$('section#' + tabName).show();
}
}
// if there is a more link, "click" more to show all the researchers
// we need the timeout delay so that the more link can get rendered

2
productMods/js/latLongJson.js
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2
productMods/templates/freemarker/body/partials/individual/individual-positions.ftl
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@ -1,6 +1,6 @@
<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
<#-- List of positions for the individual --> <h3>Positions!${core}personInPosition</h3>
<#-- List of positions for the individual -->
<#assign positions = propertyGroups.pullProperty("${core}personInPosition")!>
<#if positions?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
<#assign localName = positions.localName>

4
productMods/templates/freemarker/body/partials/individual/individual-researchAreas.ftl
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@ -3,8 +3,6 @@
<#-- List of research areas for the individual -->
<#assign researchAreas = propertyGroups.pullProperty("${core}hasResearchArea")!>
<#assign concepts = propertyGroups.pullProperty("${core}hasAssociatedConcept")!>
<#if concepts?has_content> concepts has content <#else> concepts dont have content</#if>
<h2>RESEARCH AREAS: ${core}hasResearchArea</h2>
<#if researchAreas?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
<#assign localName = researchAreas.localName>
<h2 id="${localName}" class="mainPropGroup">
@ -14,5 +12,5 @@
</h2>
<ul id="individual-${localName}" role="list" >
<@p.objectProperty researchAreas editable />
</ul> <#else> Research areas does not have content
</ul>
</#if>

2
productMods/templates/freemarker/edit/forms/js/addConcept.js
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@ -281,7 +281,7 @@ var addConceptForm = {
generateIndividualLabelsDisplay:function(label, altLabels) {
var labelDisplay = label;
if(altLabels != null && altLabels.length > 0) {
labelDisplay += "<br>(" + altLabels + ")";
labelDisplay += "<br> [" + altLabels + "]";
}
return labelDisplay;
},

13
productMods/templates/freemarker/lib/lib-home-page.ftl
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@ -205,3 +205,16 @@ var urlsBase = "${urls.base}";
</section>
</#macro>
<#-- retrieves a count, the number of researchers with a geographic focus, -->
<#-- and saves it as a js variable to be used by the homePageMaps.js file -->
<#macro getGeoResearcherCount>
<script>
<#if researcherCountDG?has_content>
<#assign theCount = researcherCountDG[0].count />
<#else>
<#assign theCount = 0 />
</#if>
var geoResearcherCount = ${theCount};
</script>
</#macro>

102
rdf/abox/filegraph/us-states.rdf
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@ -6,201 +6,303 @@
<rdf:Description rdf:about="http://dbpedia.org/resource/Alabama">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Alabama</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Alaska">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Alaska</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Arizona">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Arizona</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Arkansas">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Arkansas</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/California">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">California</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Colorado">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Colorado</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Connecticut">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Connecticut</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Delaware">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Delaware</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Florida">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Florida</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Georgia">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Georgia</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Hawaii">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Hawaii</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Idaho">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Idaho</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Illinois">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Illinois</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Indiana">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Indiana</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Iowa">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Iowa</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Kansas">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Kansas</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Kentucky">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Kentucky</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Louisiana">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Louisiana</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Maine">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Maine</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Maryland">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Maryland</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Massachusetts">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Massachusetts</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Michigan">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Michigan</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Minnesota">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Minnesota</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Mississipi">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Mississipi</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Missouri">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Missouri</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Montana">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Montana</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Nebraska">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Nebraska</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Nevada">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Nevada</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/New_Hampshire">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">New Hampshire</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/New_Jersey">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">New Jersey</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/New_Mexico">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">New Mexico</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/New_York">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">New York</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/North_Carolina">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">North Carolina</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/North_Dakota">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">North Dakota</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Ohio">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Ohio</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Oklahoma">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Oklahoma</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Oregon">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Oregon</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Pennsylvania">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Pennsylvania</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Rhode_Island">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Rhode Island</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/South_Carolina">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">South Carolina</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/South_Dakota">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">South Dakota</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Tennessee">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Tennessee</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Texas">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Texas</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Utah">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Utah</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Vermont">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Vermont</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Virginia">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Virginia</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Washington">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Washington</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/West_Virginia">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">West Virginia</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Wisconsin">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Wisconsin</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://dbpedia.org/resource/Wyoming">
<rdf:type rdf:resource="http://vivoweb.org/ontology/core#StateOrProvince"/>
<rdfs:label xml:lang="en">Wyoming</rdfs:label>
<vivo:geographicallyWithin rdf:resource="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America"/>
</rdf:Description>
<rdf:Description rdf:about="http://aims.fao.org/aos/geopolitical.owl#United_States_of_America">
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Alabama"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Alaska"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Arizona"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Arkansas"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/California"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Colorado"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Connecticut"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Delaware"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Florida"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Georgia"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Hawaii"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Idaho"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Illinois"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Indiana"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Iowa"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Kansas"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Kentucky"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Louisiana"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Maine"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Maryland"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Massachusetts"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Michigan"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Minnesota"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Mississipi"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Missouri"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Montana"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Nebraska"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Nevada"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/New_Hampshire"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/New_Jersey"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/New_Mexico"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/New_York"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/North_Carolina"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/North_Dakota"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Ohio"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Oklahoma"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Oregon"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Pennsylvania"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Rhode_Island"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/South_Carolina"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/South_Dakota"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Tennessee"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Texas"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Utah"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Vermont"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Virginia"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Washington"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/West_Virginia"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Wisconsin"/>
<vivo:geographicallyContains rdf:resource="http://dbpedia.org/resource/Wyoming"/>
</rdf:Description>
</rdf:RDF>

20
rdf/display/everytime/homePageDataGetters.n3
View file

@ -29,3 +29,23 @@ display:academicDeptsDataGetter
""" .
<freemarker:lib-home-page.ftl> display:hasDataGetter display:researcherCountDataGetter .
display:researcherCountDataGetter
a <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter> ;
display:saveToVar "researcherCountDG" ;
display:query """
PREFIX geo: <http://aims.fao.org/aos/geopolitical.owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX core: <http://vivoweb.org/ontology/core#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX vivoc: <http://vivo.library.cornell.edu/ns/0.1#>
SELECT DISTINCT (COUNT(?person) AS ?count)
WHERE {
?person rdf:type foaf:Person .
FILTER (EXISTS {?person core:geographicFocus ?focus})
}
""" .

2
src/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusMapLocations.java
View file

@ -36,7 +36,7 @@ public class GeoFocusMapLocations extends AbstractAjaxResponder {
+ "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
+ "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
+ "PREFIX vivoc: <http://vivo.library.cornell.edu/ns/0.1#> \n"
+ "SELECT DISTINCT ?label ?location (COUNT(?person) AS ?count) \n"
+ "SELECT DISTINCT ?label ?location (COUNT(DISTINCT ?person) AS ?count) \n"
+ "WHERE { { \n"
+ " ?location rdf:type core:GeographicRegion . \n"
+ " ?location rdfs:label ?label . \n"

37
src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java
View file

@ -16,6 +16,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.vocabulary.RDF;
@ -27,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -85,7 +87,7 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
setTemplate(editConfiguration, vreq);
// No validators required here
// Add preprocessors
addPreprocessors(editConfiguration, vreq.getWebappDaoFactory());
addPreprocessors(editConfiguration, ModelAccess.on(vreq).getJenaOntModel());
// Adding additional data, specifically edit mode
addFormSpecificData(editConfiguration, vreq);
// One override for basic functionality, changing url pattern
@ -174,8 +176,10 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
private List<String> generateN3Optional() {
return list("?conceptNode <" + RDFS.label.getURI() + "> ?conceptLabel .\n" +
"?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?conceptSource .",
"?conceptNode <" + VIVOCore + "conceptSemanticType> ?conceptSemanticTypeURI ." +
"?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ."
"?conceptNode <" + VIVOCore + "hasConceptSemanticType> ?conceptSemanticTypeURI ." +
"?conceptSemanticTypeURI <" + VIVOCore + "isConceptSemanticTypeOf> ?conceptNode ." +
"?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ." +
"?conceptSemanticTypeURI <" + RDF.type.getURI() + "> <" + VIVOCore + "ConceptSemanticType> ."
);
}
@ -190,7 +194,7 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
//There are no new resources here, the concept node uri doesn't
//get created but already exists, and vocab uri should already exist as well
//Adding concept semantic type uri just to test - note this isn't really on the form at all
//newResources.put("conceptSemanticTypeURI", null);
newResources.put("conceptSemanticTypeURI", null);
return newResources;
}
@ -239,11 +243,11 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
//The URI of the node that defines the concept
urisOnForm.add("conceptNode");
urisOnForm.add("conceptSource");
// urisOnForm.add("conceptSemanticTypeURI");
urisOnForm.add("conceptSemanticTypeURI");
editConfiguration.setUrisOnform(urisOnForm);
//Also need to add the label of the concept
literalsOnForm.add("conceptLabel");
// literalsOnForm.add("conceptSemanticTypeLabel");
literalsOnForm.add("conceptSemanticTypeLabel");
editConfiguration.setLiteralsOnForm(literalsOnForm);
}
@ -272,8 +276,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
setConceptNodeField(editConfiguration, vreq);
setConceptLabelField(editConfiguration, vreq);
setVocabURIField(editConfiguration, vreq);
//setConceptSemanticTypeURIField(editConfiguration,vreq);
//setConceptSemanticTypeLabelField(editConfiguration,vreq);
setConceptSemanticTypeURIField(editConfiguration,vreq);
setConceptSemanticTypeLabelField(editConfiguration,vreq);
}
//this field will be hidden and include the concept node URI
@ -321,11 +325,14 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
//Add preprocessor
private void addPreprocessors(EditConfigurationVTwo editConfiguration, WebappDaoFactory wadf) {
private void addPreprocessors(EditConfigurationVTwo editConfiguration, OntModel ontModel) {
//An Edit submission preprocessor for enabling addition of multiple terms for a single search
//TODO: Check if this is the appropriate way of getting model
//Passing model to check for any URIs that are present
editConfiguration.addEditSubmissionPreprocessor(
new AddAssociatedConceptsPreprocessor(editConfiguration, wadf));
new AddAssociatedConceptsPreprocessor(editConfiguration, ontModel));
}
@ -411,13 +418,13 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
String conceptSemanticTypeURI = null;
String conceptSemanticTypeLabel = null;
//Can a concept have multiple semantic types? Currently we are only returning the first one
/*
List<ObjectPropertyStatement> semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "conceptSemanticType");
List<ObjectPropertyStatement> semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "hasConceptSemanticType");
if(semanticTypeStatements.size() > 0) {
conceptSemanticTypeURI = semanticTypeStatements.get(0).getObjectURI();
Individual conceptSemanticTypeIndividual = EditConfigurationUtils.getIndividual(vreq, conceptSemanticTypeURI);
conceptSemanticTypeLabel = conceptSemanticTypeIndividual.getName();
}*/
}
//get label
//Assuming this is from an external vocabulary source
@ -442,8 +449,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
this.vocabURI = inputVocabURI;
this.vocabLabel = inputVocabLabel;
this.type = inputType;
//this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
//this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
}
//Getters

346
src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java
View file

@ -3,19 +3,29 @@
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
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.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.BaseEditSubmissionPreprocessorVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -27,13 +37,18 @@ public class AddAssociatedConceptsPreprocessor extends
protected static final Log log = LogFactory
.getLog(AddAssociatedConceptsPreprocessor.class.getName());
protected WebappDaoFactory wadf = null;
//TODO: Check if better way to do this?
protected OntModel ontModel = null;
// Field names/variables names for n3 - these will have numbers added as
// suffix if more than one term
private static String conceptNodeBase = "conceptNode";
private static String sourceBase = "conceptSource";
private static String labelBase = "conceptLabel";
private static String conceptSemanticTypeLabelBase = "conceptSemanticTypeLabel";
private static String conceptSemanticTypeURIBase = "conceptSemanticTypeURI";
//keyed off label variable, specifies which uri variable should be used, useful if same label repeated twice
private HashMap<String, String> labelVarToUriVarHash = null;
private HashMap<String, List<String>> conceptSemanticTypeURIVarToValueMap = null;
//Also storing submission values
private static String conceptNodeValues = null;
private static String conceptLabelValues = null;
@ -46,9 +61,12 @@ public class AddAssociatedConceptsPreprocessor extends
// Will be editing the edit configuration as well as edit submission here
public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig, WebappDaoFactory wadf) {
public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig, OntModel ontModel) {
super(editConfig);
this.wadf = wadf;
this.ontModel = ontModel;
this.labelVarToUriVarHash = new HashMap<String, String>();
//Saves values of concept type uris
this.conceptSemanticTypeURIVarToValueMap = new HashMap<String, List<String>>();
}
public void preprocess(MultiValueEditSubmission inputSubmission) {
@ -57,12 +75,14 @@ public class AddAssociatedConceptsPreprocessor extends
// as vocab uri (which is based on thge
// For query parameters, check whether CUI
copySubmissionValues();
//This will put the URI value in scope for the first semantic type label
//and generate the rest if need be
//processConceptSemanticValues();
if (conceptNodeValues != null) {
String[] conceptNodes = convertDelimitedStringToArray(conceptNodeValues);
int numberConcepts = conceptNodes.length;
//This will put the URI value in scope for the first semantic type label
//and generate the rest if need be
processConceptSemanticValues();
if (numberConcepts > 1) {
processConceptNodes(numberConcepts);
}
@ -80,6 +100,7 @@ public class AddAssociatedConceptsPreprocessor extends
conceptLabelValues = getConceptLabelValues();
conceptNodeValues = getConceptNodeValues();
conceptSourceValues = getConceptSourceValues();
log.debug("concept label values are " + conceptLabelValues);
}
@ -94,14 +115,11 @@ public class AddAssociatedConceptsPreprocessor extends
}
//This is for additional concept nodes (i.e. if user selects more than one concept)
private void processConceptNodes(int numberConcepts) {
//There are no "new" resources b/c the concept nodes are URIs from external vocabularies
//New resources for concept semantic type uris
addNewResources(numberConcepts);
// Add N3Required
addN3Required(numberConcepts);
//Add N3 Optional as well
@ -115,6 +133,42 @@ public class AddAssociatedConceptsPreprocessor extends
}
//This is specifically for concept semantic type URIs which may need to be generated
private void addNewResources(int numberConcepts) {
// TODO Auto-generated method stub
addConceptSemanticTypeURIResources(numberConcepts);
}
private void addConceptSemanticTypeURIResources(int numberConcepts) {
//Iterate through the labels and get the corresponding uris
HashSet<String> urisToAdd = new HashSet<String>();
String[] conceptSemanticTypeLabels= convertDelimitedStringToArray(conceptSemanticTypeLabelValues);
//the number of existing values may not match up, or at least existing populated ones
//Now we can't determine whether all concepts will have semantic types - at some point what if
//we ran a search across all external vocabularies? So we can't compare labels to number of concepts
//but we can ensure that it isn't greater than then number of concepts
if(conceptSemanticTypeLabels != null && conceptSemanticTypeLabels.length <= numberConcepts) {
int i;
for(i = 0; i < numberConcepts; i++) {
int suffix = i + 1;
String conceptSemanticTypeLabelVar = conceptSemanticTypeLabelBase + suffix;
if(this.labelVarToUriVarHash.containsKey(conceptSemanticTypeLabelVar)) {
String newResourceName = this.labelVarToUriVarHash.get(conceptSemanticTypeLabelVar);
if(!urisToAdd.contains(newResourceName)) {
urisToAdd.add(newResourceName);
editConfiguration.addNewResource(newResourceName, null);
}
}
}
} else if(conceptSemanticTypeLabels != null && conceptSemanticTypeLabels.length > numberConcepts){
log.error("Number of concept semantic type labels is greater than number of concepts");
} else{
log.error("Concept semantic type labels returned are null");
}
}
//This is where the actual values will be submitted as if they were separate input fields
//Each field name will correspond to the names of the fileds/uris on form/literals on form
//generated here
@ -126,7 +180,8 @@ public class AddAssociatedConceptsPreprocessor extends
addConceptSourceInputs(numberConcepts);
addConceptLabelInputs(numberConcepts);
//for concept semantic type labels and uris where they exist
//addConceptSemanticTypeLabelInputs(numberConcepts);
//TODO: Make into single method as URIs depend on labels
addConceptSemanticTypeLabelAndURIInputs(numberConcepts);
//addConceptSemanticTypeURIInputs(numberConcepts);
}
@ -198,12 +253,73 @@ public class AddAssociatedConceptsPreprocessor extends
}
}
private void addConceptSemanticTypeLabelInputs(int numberConcepts) {
private void addConceptSemanticTypeLabelAndURIInputs(int numberConcepts) {
String[] labels = convertDelimitedStringToArray(conceptSemanticTypeLabelValues);
HashSet<String> uniqueLabelValues = new HashSet<String>();
if(labels != null && labels.length == numberConcepts) {
int i;
for(i = 0; i < numberConcepts; i++) {
String thisLabel = labels[i];
int suffix = i + 1;
String labelInputName = conceptSemanticTypeLabelBase + suffix;
String[] labelValues = new String[1];
labelValues[0] = thisLabel;
//TODO: Check if there are no funky typed information also stored
//At this point the field should already have been added to edit configuration
FieldVTwo labelField = editConfiguration.getField(labelInputName);
//TODO: Also check to see whether the label is actually populate or will n3 editing take care of that?
if(labelField != null) {
submission.addLiteralToForm(editConfiguration, labelField, labelInputName, labelValues);
//Associate URI
if(!uniqueLabelValues.contains(thisLabel)) {
uniqueLabelValues.add(thisLabel);
this.addConceptSemanticTypeURIInputForLabel(labelInputName, suffix);
}
} else {
log.error("Corresponding field for " + labelInputName + " was not added to edit configuration");
}
}
} else if(labels != null && labels.length != numberConcepts){
log.error("Number of concept semantic type labels did not match the number of concepts to be added");
} else{
log.error("Concept labels returned were null");
}
}
private void addConceptSemanticTypeURIInputs(int numberConcepts) {
private void addConceptSemanticTypeURIInputForLabel(String conceptSemanticTypeLabel, int suffix) {
//String[] conceptSemanticTypeURIs= convertDelimitedStringToArray(conceptSemanticTypeURIValues);
//Get the semantic type URI variable name associated with this label
String uriInputName = this.getConceptSemanticTypeURIFieldName(conceptSemanticTypeLabel, suffix);
//List<>
if(this.conceptSemanticTypeURIVarToValueMap.containsKey(uriInputName)) {
List<String> uriVals = this.conceptSemanticTypeURIVarToValueMap.get(uriInputName);
String[] uriValuesArray = uriVals.toArray(new String[uriVals.size()]);
submission.addUriToForm(editConfiguration, uriInputName, uriValuesArray);
}
//the number of existing values may not match up, or at least existing populated ones
/*
if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length == numberConcepts) {
int i;
for(i = 0; i < numberConcepts; i++) {
int suffix = i + 1;
String conceptInputName = conceptSemanticTypeURIBase + suffix;
String[] uriValues = new String[1];
uriValues[0] = conceptSemanticTypeURIs[i];
//Add value for uri to form
//TODO: Check if value is empty in which case don't add to submission
submission.addUriToForm(editConfiguration, conceptInputName, uriValues);
}
} else if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length != numberConcepts){
log.error("Number of concept nodes did not match the number of concepts to be added");
} else{
log.error("Concept nodes returned were null");
}
*/
}
//Fields
@ -212,16 +328,26 @@ public class AddAssociatedConceptsPreprocessor extends
//Clear out all fields in edit configuration first
editConfiguration.setFields(new HashMap<String, FieldVTwo>());
int index;
HashSet<String> conceptSemanticTypeUris = new HashSet<String>();
// First one already included in generator so add additional ones here
for (index = 1; index <= numberConcepts; index++) {
int suffix = index;
String conceptNode = conceptNodeBase + suffix;
String label = labelBase + suffix;
String source = sourceBase + suffix;
String conceptSemanticTypeLabel = conceptSemanticTypeLabelBase + suffix;
String conceptSemanticTypeURI = this.getConceptSemanticTypeURIFieldName(conceptSemanticTypeLabel, suffix);
addConceptNodeField(conceptNode);
addLabelField(label);
addSourceField(source);
//Also add fields for concept semantic type label
addConceptSemanticTypeLabelField(conceptSemanticTypeLabel);
//and concept semantic type URI
if(!conceptSemanticTypeUris.contains(conceptSemanticTypeURI)) {
conceptSemanticTypeUris.add(conceptSemanticTypeURI);
addConceptSemanticTypeURIField(conceptSemanticTypeURI);
}
}
}
@ -247,6 +373,25 @@ public class AddAssociatedConceptsPreprocessor extends
}
//TODO: Do we need to check if label is empty string?
private void addConceptSemanticTypeLabelField(String label) {
if(label != null) {
editConfiguration.addField(new FieldVTwo().
setName(label).
setRangeDatatypeUri(XSD.xstring.toString())
);
}
}
private void addConceptSemanticTypeURIField(String conceptSemanticTypeURI) {
if(conceptSemanticTypeURI != null) {
editConfiguration.addField(new FieldVTwo().
setName(conceptSemanticTypeURI));
}
}
//original literals on form: label, uris on form: conceptNode and conceptSource
//This will overwrite the original values in the edit configuration
private void addLiteralsAndUrisOnForm(int numberTerms) {
@ -254,16 +399,24 @@ public class AddAssociatedConceptsPreprocessor extends
List<String> literalsOnForm = new ArrayList<String>();
int index;
HashSet<String> conceptSemanticTypeURIs = new HashSet<String>();
// First one already included so add new ones here
for (index = 1; index <= numberTerms; index++) {
int suffix = index;
String conceptNode = conceptNodeBase + suffix;
String label = labelBase + suffix;
String source = sourceBase + suffix;
String conceptSemanticTypeLabel = conceptSemanticTypeLabelBase + suffix;
//String conceptSemanticTypeURI = conceptSemanticTypeURIBase + suffix;
String conceptSemanticTypeURI = this.getConceptSemanticTypeURIFieldName(conceptSemanticTypeLabel, suffix);
urisOnForm.add(conceptNode);
urisOnForm.add(source);
if(!conceptSemanticTypeURIs.contains(conceptSemanticTypeURI)) {
conceptSemanticTypeURIs.add(conceptSemanticTypeURI);
urisOnForm.add(conceptSemanticTypeURI);
}
literalsOnForm.add(label);
literalsOnForm.add(conceptSemanticTypeLabel);
}
editConfiguration.setUrisOnform(urisOnForm);
editConfiguration.setLiteralsOnForm(literalsOnForm);
@ -279,8 +432,7 @@ public class AddAssociatedConceptsPreprocessor extends
List<String> n3Required = new ArrayList<String>();
int index;
String nodeBase = "?" + conceptNodeBase;
String labelVar = "?" + labelBase;
String sourceVar = "?" + sourceBase;
String prefixStr = "@prefix core: <http://vivoweb.org/ontology/core#> .";
// First one already included so add new ones here
for (index = 1; index <= numberConcepts; index++) {
@ -293,30 +445,61 @@ public class AddAssociatedConceptsPreprocessor extends
editConfiguration.setN3Required(n3Required);
}
//Add n3 optional
//TODO: Rewrite optional N3
private void addN3Optional(int numberConcepts) {
List<String> n3Optional = new ArrayList<String>();
int index;
String nodeBase = "?" + conceptNodeBase;
String labelVar = "?" + labelBase;
String sourceVar = "?" + sourceBase;
String conceptSemanticTypeLabelVar = "?" + conceptSemanticTypeLabelBase;
String prefixStr = "@prefix core: <http://vivoweb.org/ontology/core#> .";
// First one already included so add new ones here
//We already have a label var to uri var setup
for (index = 1; index <= numberConcepts; index++) {
int suffix = index;
String node = nodeBase + suffix;
String label = labelVar + suffix;
String source = sourceVar + suffix;
String conceptSemanticTypeLabel = conceptSemanticTypeLabelVar + suffix;
//get the URI appropriate for the concept semantic type label var
String conceptSemanticTypeURI = getConceptSemanticTypeURIVar(conceptSemanticTypeLabelBase + suffix, suffix);
//onceptSemanticTypeURIVar + suffix;
String n3String = prefixStr;
n3String += node + " <" + RDFS.label.getURI() + "> " + label + " .\n" +
node + " <" + RDFS.isDefinedBy.getURI() + "> " + source + " .";
node + " <" + RDFS.isDefinedBy.getURI() + "> " + source + " .";
String n3ConceptTypeString = prefixStr;
n3ConceptTypeString += node + " core:hasConceptSemanticType " + conceptSemanticTypeURI + " ." +
conceptSemanticTypeURI + " core:isConceptSemanticTypeOf " + node + ". " +
conceptSemanticTypeURI + " <" + RDFS.label.getURI() + "> " + conceptSemanticTypeLabel + " .\n" +
conceptSemanticTypeURI + " <" + RDF.type.getURI() + "> core:ConceptSemanticType .\n" ;
n3Optional.add(n3String);
//adding separately so their resolution does not depend on each other
n3Optional.add(n3ConceptTypeString);
}
//Already have n3 required so need to add to that
editConfiguration.setN3Optional(n3Optional);
}
//get the URI variable that is associated with this concept type URI, which might not be
//the same suffix because the same label value might be repeated and we need to use the same URI
//representing that concept semantic type
private String getConceptSemanticTypeURIVar(String labelVar, int suffix) {
// TODO Auto-generated method stub
return "?" + this.getConceptSemanticTypeURIFieldName(labelVar, suffix);
}
private String getConceptSemanticTypeURIFieldName(String labelVar, int suffix) {
// TODO Auto-generated method stub
if(this.labelVarToUriVarHash.containsKey(labelVar)) {
return this.labelVarToUriVarHash.get(labelVar);
}
return this.conceptSemanticTypeURIBase + suffix;
}
private String[] convertDelimitedStringToArray(String inputString) {
String[] inputArray = new String[1];
if (inputString.indexOf(",") != -1) {
@ -357,31 +540,122 @@ public class AddAssociatedConceptsPreprocessor extends
//This will either generate or retrieve URIs for the concept semantic type labels if they exist
//We will then update the submission to include this
private String getConceptSemanticTypeURIValues() {
List<String> conceptSemanticTypeURIs = new ArrayList<String>();
String[] conceptSemanticTypeLabels = convertDelimitedStringToArray(conceptSemanticTypeLabelValues);
//keep track of what label values already exist and to which label variables they map
HashMap<String, List<Integer>> labelValueToVarSuffix = new HashMap<String, List<Integer>>();
int numberLabels = conceptSemanticTypeLabels.length;
String pseudoInputString = "";
for(int i = 0; i < numberLabels; i++) {
String label = conceptSemanticTypeLabels[i];
//Make or retrieve URI for this label
//The rest of this code is really only relevant for multiple values, so we could break out the old code above
//as we don't need to set up hashes etc. if there is only one concept node being added
if(numberLabels == 1) {
String label = conceptSemanticTypeLabels[0];
String uri = getURIForSemanticTypeLabel(label);
conceptSemanticTypeURIs.add(uri);
}
if(uri != "") {
String[] urisToAdd = new String[1];
urisToAdd[0] = uri;
pseudoInputString = uri;
log.debug("uris to add" + uri);
submission.addUriToForm(this.editConfiguration, "conceptSemanticTypeURI", urisToAdd);
}
//Set uris as string
//Essentially this will allow the URI to be put in scope
return conceptSemanticTypeURIs.toString();
}
//if there is more than one concept node, we may have duplicate semantic types
//which will need to be referred to by the same semantic type uri
else if (numberLabels > 1){
for(int i = 0; i < numberLabels; i++) {
int suffix = i + 1;
String label = conceptSemanticTypeLabels[i];
String labelVar = this.conceptSemanticTypeLabelBase + suffix;
//if label has not already been encountered, create entry for label value
//and list with the label variables that would refer to it
//for unique values, the uri variable will be the same as label
Integer thisSuffix = new Integer(suffix);
if(!labelValueToVarSuffix.containsKey(label)) {
labelValueToVarSuffix.put(label, new ArrayList<Integer>());
//Add suffix to list if not already there
labelValueToVarSuffix.get(label).add(thisSuffix);
} else {
//in this case, the label already exists, get the very first element in the list
//and use that as the uri variable
List<Integer> suffixList = labelValueToVarSuffix.get(label);
if(suffixList != null && suffixList.size() > 0) {
thisSuffix = suffixList.get(0);
}
}
//Now add the uri var to the hash mapping label variable to uri variable
String uriVar = this.conceptSemanticTypeURIBase + thisSuffix.intValue();
this.labelVarToUriVarHash.put(labelVar, uriVar);
//Make or retrieve URI for this label
//TODO: Do we create this string with empty inputs ?
String uri = getURIForSemanticTypeLabel(label);
if(uri != "") {
//uri var shouldn't be repeated?
if(!this.conceptSemanticTypeURIVarToValueMap.containsKey(uriVar)) {
this.conceptSemanticTypeURIVarToValueMap.put(uriVar, new ArrayList<String>());
this.conceptSemanticTypeURIVarToValueMap.get(uriVar).add(uri);
}
}
if(i != 0) {
pseudoInputString += ",";
}
pseudoInputString += uri;
}
//Add this string to the uris for the form
String[] urisToAdd = new String[1];
urisToAdd[0] = pseudoInputString;
log.debug("uris to add" + pseudoInputString);
submission.addUriToForm(this.editConfiguration, "conceptSemanticTypeURI", urisToAdd);
}
return pseudoInputString;
}
private String getURIForSemanticTypeLabel(String label) {
//Check if system has an individual with this URI
//
List<Individual> individualsWithLabel = this.wadf.getIndividualDao().getIndividualsByDataProperty(RDFS.label.getURI(), label);
//We are only interested in concepts
return null;
String existingURI = this.getExistingSemanticTypeURI(label);
if(existingURI != null) {
return existingURI;
}
//if we leave this as null, we should be able to generate a new resource
//empty string because there may be more than one value returned for labels
else return "";
}
private String getExistingSemanticTypeURI(String label) {
String queryStr = "SELECT ?semanticType WHERE { ?semanticType <" + RDF.type.getURI() + "> <http://vivoweb.org/ontology/core#ConceptSemanticType> . " +
"?semanticType <" + RDFS.label.getURI() + "> \"" + label + "\"^^<http://www.w3.org/2001/XMLSchema#string> . }";
QueryExecution qe = null;
try{
Query query = QueryFactory.create(queryStr);
qe = QueryExecutionFactory.create(query, this.ontModel);
ResultSet results = null;
results = qe.execSelect();
while( results.hasNext()){
QuerySolution qs = results.nextSolution();
if(qs.get("semanticType") != null) {
Resource semanticTypeURI = qs.getResource("semanticType");
log.debug("Semantic Type URI returned " + semanticTypeURI.getURI());
return semanticTypeURI.getURI();
}
}
}catch(Exception ex){
throw new Error("Error in executing query string: \n" + queryStr + '\n' + ex.getMessage());
}finally{
if( qe != null)
qe.close();
}
return null;
}
private Object getFirstElement(List inputList) {
if(inputList == null || inputList.size() == 0)
return null;

3
themes/wilma/templates/page-home.ftl
View file

@ -97,6 +97,7 @@
stateString: '${i18n().map_state_string}',
statewideLocations: '${i18n().statewide_locations}',
researchersInString: '${i18n().researchers_in}',
inString: '${i18n().in}',
noFacultyFound: '${i18n().no_faculty_found}',
placeholderImage: '${i18n().placeholder_image}',
viewAllFaculty: '${i18n().view_all_faculty}',
@ -108,7 +109,7 @@
if ( $('input.search-homepage').css('text-align') == "right" ) {
$('input.search-homepage').attr("value","${i18n().limit_search} \u2192");
}
</script>
<@lh.getGeoResearcherCount/>
</body>
</html>