Merge pull request #124 from awoods/sprint-search

Update sprint-search to current develop branch

README.md

@@ -1,5 +1,7 @@
 # VIVO: Connect, Share, Discover
 
+[![Build Status](https://travis-ci.org/vivo-project/VIVO.png?branch=develop)](https://travis-ci.org/vivo-project/VIVO)
+
 VIVO is an open source semantic web tool for research discovery -- finding people and the research they do.
 
 VIVO supports editing, searching, browsing and visualizing research activity in order to discover people, programs, 

api/src/main/java/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java

@@ -58,12 +58,12 @@ public class AgrovocService implements ExternalConceptService {
 	protected final String dbpedia_endpoint = " http://dbpedia.org/sparql";
 	// URL to get all the information for a concept
 	
-	protected final String conceptSkosMosBase = "http://artemide.art.uniroma2.it:8081/skosmos/rest/v1/";
+	protected final String conceptSkosMosBase = "http://agrovoc.uniroma2.it/agrovoc/rest/v1/";
 	protected final String conceptsSkosMosSearch = conceptSkosMosBase + "search?";
 	protected final String conceptSkosMosURL = conceptSkosMosBase + "data?";
 	@Override
 	public List<Concept> getConcepts(String term) throws Exception {
-		List<Concept> conceptList = new ArrayList<Concept>();
+		List<Concept> conceptList = new ArrayList<>();
 		
 		//For the RDF webservices mechanism, utilize the following
 		/*
@@ -86,7 +86,7 @@ public class AgrovocService implements ExternalConceptService {
 			return conceptList;
 		int conceptCounter = 0;
 		
-		HashSet<String> encounteredURI = new HashSet<String>();
+		HashSet<String> encounteredURI = new HashSet<>();
 		
 		// Loop through each of these URIs and load using the SKOSManager
 		for (String conceptUri : conceptUris) {
@@ -185,7 +185,7 @@ public class AgrovocService implements ExternalConceptService {
 	public List<Concept> getConceptsByURIWithSparql(String uri)
 			throws Exception {
 		// deprecating this method...just return an empty list
-		List<Concept> conceptList = new ArrayList<Concept>();
+		List<Concept> conceptList = new ArrayList<>();
 		return conceptList;
 	}
 
@@ -227,7 +227,7 @@ public class AgrovocService implements ExternalConceptService {
 	// When utilizing the getTermExpansion method, will get a list of URIs back
 	// and not just one URI
 	protected List<String> getConceptURIsListFromRDF(String rdf) {
-		List<String> conceptUris = new ArrayList<String>();
+		List<String> conceptUris = new ArrayList<>();
 		try {
 			Document doc = XMLUtils.parse(rdf);
 				NodeList nodes = doc.getElementsByTagName("skos:Concept");
@@ -262,21 +262,21 @@ public class AgrovocService implements ExternalConceptService {
 				+ "> rdfs:comment ?description . \n"
 				+ "FILTER (LANG(?description)='en' ) \n" + "}";
 		// System.out.println(qs);
-		List<HashMap> resultList = new ArrayList<HashMap>();
+		List<HashMap> resultList = new ArrayList<>();
 		QueryExecution qexec = null;
 		try {
 
 			Query query = QueryFactory.create(qs);
 			qexec = QueryExecutionFactory.sparqlService(this.dbpedia_endpoint, query);
 			qexec.setTimeout(5000, TimeUnit.MILLISECONDS);
-			resultList = new ArrayList<HashMap>();
+			resultList = new ArrayList<>();
 			ResultSet resultSet = qexec.execSelect();
 			int resultSetSize = 0;
 			while (resultSet.hasNext()) {
 				resultSetSize++;
 				QuerySolution solution = resultSet.nextSolution();
 				Iterator varnames = solution.varNames();
-				HashMap<String, String> hm = new HashMap<String, String>();
+				HashMap<String, String> hm = new HashMap<>();
 				while (varnames.hasNext()) {
 					String name = (String) varnames.next();
 					RDFNode rdfnode = solution.get(name);
@@ -374,7 +374,7 @@ public class AgrovocService implements ExternalConceptService {
 		
 		//JSON-LD array
 		private List<String> getConceptURIsListFromSkosMosResult(String results) {
-			List<String> conceptURIs = new ArrayList<String>();
+			List<String> conceptURIs = new ArrayList<>();
 			ObjectNode json = (ObjectNode) JacksonUtils.parseJson(results);
 			//Format should be: { ..."results":["uri":uri...]
 			if (json.has("results")) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusMapLocations.java

@@ -31,8 +31,7 @@ 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"
-        + "PREFIX afn:  <http://jena.apache.org/ARQ/function#> "
+        + "SELECT DISTINCT ?label ?location (REPLACE(STR(?location),\"^.*(#)(.*)$\", \"$2\") AS ?localName) (COUNT(DISTINCT ?person) AS ?count)  \n"
-        + "SELECT DISTINCT ?label ?location (afn:localname(?location) AS ?localName) (COUNT(DISTINCT ?person) AS ?count)  \n"
         + "WHERE { { \n"
         + "    ?location rdf:type core:GeographicRegion .  \n"
         + "    ?location rdfs:label ?label .   \n"

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java

@@ -69,7 +69,6 @@ public class ManageGrantsForIndividualController extends FreemarkerHttpServlet {
         + "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
         + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
         + "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n"
-        + "PREFIX afn:  <http://jena.apache.org/ARQ/function#> \n"
         + "SELECT DISTINCT ?subclass ?role (str(?label2) as ?label) ?activity ?hideThis WHERE { \n"
         + "    ?subject <http://purl.obolibrary.org/obo/RO_0000053> ?role . \n"
         + "    ?role a core:ResearcherRole . \n"

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java

@@ -69,7 +69,6 @@ public class ManagePeopleForOrganizationController extends FreemarkerHttpServlet
         + "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
         + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
         + "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n"
-        + "PREFIX afn: <http://jena.apache.org/ARQ/function#> \n"
         + "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
         + "SELECT DISTINCT ?subclass ?position ?positionLabel (str(?label) as ?name) ?person ?hideThis WHERE { \n"
         + "    ?subject core:relatedBy ?position . \n"

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java

@@ -69,7 +69,6 @@ public class ManagePublicationsForIndividualController extends FreemarkerHttpSer
         + "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
         + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
         + "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n"
-        + "PREFIX afn: <http://jena.apache.org/ARQ/function#> \n"
         + "SELECT DISTINCT ?subclass ?authorship (str(?label) as ?title) ?pub ?hideThis WHERE { \n"
         + "    ?subject core:relatedBy ?authorship . \n"
         + "    ?authorship a core:Authorship  . \n"

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAuthorsToInformationResourceGenerator.java

@@ -346,7 +346,6 @@ public class AddAuthorsToInformationResourceGenerator extends VivoBaseGenerator
 
 	private static String AUTHORSHIPS_MODEL = " \n"
 			+ "PREFIX core: <http://vivoweb.org/ontology/core#>\n"
-			+ "PREFIX afn:  <http://jena.apache.org/ARQ/function#>\n"
 			+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n"
 			+ "PREFIX foaf: <http://xmlns.com/foaf/0.1/>\n"
 			+ "PREFIX vcard:  <http://www.w3.org/2006/vcard/ns#>\n"
@@ -412,11 +411,10 @@ public class AddAuthorsToInformationResourceGenerator extends VivoBaseGenerator
 
     private static String AUTHORSHIPS_QUERY = " \n"
         + "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
-        + "PREFIX afn:  <http://jena.apache.org/ARQ/function#> \n"
         + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
         + "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
         + "PREFIX vcard:  <http://www.w3.org/2006/vcard/ns#> \n"
-        + "SELECT ?authorshipURI (afn:localname(?authorshipURI) AS ?authorshipName) ?authorURI ?authorName ?rank \n"
+        + "SELECT ?authorshipURI (REPLACE(STR(?authorshipURI),\"^.*(#)(.*)$\", \"$2\") AS ?authorshipName) ?authorURI ?authorName ?rank \n"
         + "WHERE { { \n"
         + "  ?subject core:relatedBy ?authorshipURI . \n"
         + "  ?authorshipURI a core:Authorship . \n"

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorsToInformationResourceGenerator.java

@@ -309,7 +309,6 @@ public class AddEditorsToInformationResourceGenerator extends VivoBaseGenerator
 
 	private static String EDITORSHIPS_MODEL = ""
 			+ "PREFIX core: <http://vivoweb.org/ontology/core#>\n"
-			+ "PREFIX afn:  <http://jena.apache.org/ARQ/function#>\n"
 			+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n"
 			+ "PREFIX foaf: <http://xmlns.com/foaf/0.1/>\n"
 			+ "CONSTRUCT\n"
@@ -347,10 +346,9 @@ public class AddEditorsToInformationResourceGenerator extends VivoBaseGenerator
 
     private static String EDITORSHIPS_QUERY = ""
         + "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
-        + "PREFIX afn:  <http://jena.apache.org/ARQ/function#> \n"
         + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
         + "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
-        + "SELECT ?editorshipURI (afn:localname(?editorshipURI) AS ?editorshipName) ?editorURI ?editorName ?rank \n"
+        + "SELECT ?editorshipURI (REPLACE(STR(?editorshipURI),\"^.*(#)(.*)$\", \"$2\") AS ?editorshipName) ?editorURI ?editorName ?rank \n"
         + "WHERE { \n"
         + "?subject core:relatedBy ?editorshipURI . \n"
         + "?editorshipURI a core:Editorship . \n"

api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryConstants.java

@@ -41,7 +41,6 @@ public class QueryConstants {
 			put("vivo", "http://vivo.library.cornell.edu/ns/0.1#");
 			put("geo", "http://aims.fao.org/aos/geopolitical.owl#");
 			put("public", "http://vitro.mannlib.cornell.edu/ns/vitro/public#");
-			put("afn", "http://jena.apache.org/ARQ/function#");
 			put("vivosocnet", "http://vivo.cns.iu.edu/ns/#");
 			put("obo", "http://purl.obolibrary.org/obo/");
 			put("vcard", "http://www.w3.org/2006/vcard/ns#");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personlevel/PersonLevelRequestHandler.java

@@ -8,6 +8,7 @@ import java.util.Map;
 import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CoAuthorshipData;
 import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CoInvestigationData;
 import edu.cornell.mannlib.vitro.webapp.visualization.visutils.CollaborationDataViewHelper;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 
 import org.apache.jena.query.Dataset;
@@ -74,8 +75,15 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
         String visMode = vitroRequest.getParameter(
         							VisualizationFrameworkConstants.VIS_MODE_KEY);
 
-        return generateStandardVisualizationForPersonLevelVis(vitroRequest,
+        if (!StringUtils.isEmpty(egoURI)) {
-				log, dataset, egoURI, visMode);
+			return generateStandardVisualizationForPersonLevelVis(vitroRequest,
+					log, dataset, egoURI, visMode);
+		} else {
+			return UtilityFunctions.handleMalformedParameters(
+					"Visualization Query Error",
+					"Inappropriate query parameters were submitted.",
+					vitroRequest);
+		}
 
 	}
 
@@ -84,12 +92,22 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
 			Map<String, String> parameters, VitroRequest vitroRequest, Log log,
 			Dataset dataset) throws MalformedQueryParametersException {
 
-        return generateStandardVisualizationForPersonLevelVis(
+		String egoURI = parameters.get(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
-        				vitroRequest,
+		String visMode = parameters.get(VisualizationFrameworkConstants.VIS_MODE_KEY);
-        				log, 
+
-        				dataset, 
+		if (!StringUtils.isEmpty(egoURI)) {
-        				parameters.get(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY), 
+			return generateStandardVisualizationForPersonLevelVis(
-        				parameters.get(VisualizationFrameworkConstants.VIS_MODE_KEY));
+							vitroRequest,
+							log,
+							dataset,
+							egoURI,
+							visMode);
+		} else {
+			return UtilityFunctions.handleMalformedParameters(
+					"Visualization Query Error",
+					"Inappropriate query parameters were submitted.",
+					vitroRequest);
+		}
 	}
 
 	private ResponseValues generateStandardVisualizationForPersonLevelVis(

home/src/main/resources/config/example.runtime.properties

@@ -7,6 +7,11 @@
 # Save a copy of this file as runtime.properties in your VIVO home directory, 
 # and edit the properties as needed for your installation.
 #
+# For more information on specific properties, see the configuration reference
+# or installation options section of the technical documentation for the
+# version of VIVO you are running:
+# https://wiki.duraspace.org/display/VIVO/VIVO+Technical+Documentation 
+#
 # -----------------------------------------------------------------------------
 
 
@@ -295,8 +300,6 @@ VitroConnection.DataSource.validationQuery = SELECT 1
   #  
   # When the following flag is set to enabled, the VIVO home page displays a 
   # global map highlighting the geographical focus of foaf:person individuals. 
-  # For information on the maps, refer to this wiki page:
-  # https://wiki.duraspace.org/x/c4XVAw
   #
 #homePage.geoFocusMaps=enabled
 
@@ -307,9 +310,6 @@ VitroConnection.DataSource.validationQuery = SELECT 1
   # Implementing this feature requires an installation to develop a web service
   # that captures images of web pages or to use an existing service outside of VIVO. 
   #
-  # For more information on implementing multiple profile pages, refer to this 
-  # wiki page: https://wiki.duraspace.org/x/doXVAw
-  #
 #multiViews.profilePageTypes=enabled
 
 
@@ -317,9 +317,6 @@ VitroConnection.DataSource.validationQuery = SELECT 1
   # Tell VIVO to generate HTTP headers on its responses to facilitate caching the 
   # profile pages that it creates. 
   #
-  # For more information, see this wiki page: 
-  # https://wiki.duraspace.org/x/5sQQAg
-  #
   # Developers will likely want to leave caching disabled, since a change to a
   # Freemarker template or to a Java class would not cause the page to be 
   # considered stale.

home/src/main/resources/rdf/display/everytime/searchIndexerConfigurationVivo.n3

@@ -23,6 +23,7 @@
         searchIndex:documentBuilding.DocumentModifier ,
         searchIndex:extensions.LabelsAcrossContextNodes ;
     rdfs:label "Labels across relatedBy/relates" ;
+    :hasTypeRestriction "http://vivoweb.org/ontology/core#Relationship" ;
     :hasIncomingProperty "http://vivoweb.org/ontology/core#relatedBy" ;
     :hasOutgoingProperty "http://vivoweb.org/ontology/core#relates" .
 
@@ -150,4 +151,3 @@
 			?emailHolder vcard:email ?email .
 		}
         """ .
-

home/src/main/resources/rdf/tbox/filegraph/vivo.owl

@@ -1911,13 +1911,17 @@ there is a measurement process p that has specified output m, a measurement datu
     <!-- http://vivoweb.org/ontology/core#hasCollaborator -->
 
     <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#hasCollaborator">
-        <rdfs:label xml:lang="en">has collaborator</rdfs:label>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
-        <rdfs:range rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
         <rdfs:domain rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
+        <rdfs:range rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
+        <rdfs:label xml:lang="en">has collaborator</rdfs:label>
+        <obo:IAO_0000112 xml:lang="en">Fran has collaborator Jim, they work together regularly.</obo:IAO_0000112>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+        <obo:IAO_0000115 xml:lang="en">Two agents are collaborators if they work together to produce common results.</obo:IAO_0000115>
+        <obo:IAO_0000117 xml:lang="en">PERSON: Michael Conlon</obo:IAO_0000117>
+        <obo:IAO_0000119 xml:lang="en">Merriam Webster (https://www.merriam-webster.com/dictionary/collaborator)</obo:IAO_0000119>
     </owl:ObjectProperty>
 
-
-
     <!-- http://vivoweb.org/ontology/core#hasEquipment -->
 
     <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#hasEquipment">

home/src/main/resources/rdf/tbox/firsttime/vitroAnnotations.n3

@@ -1,107 +1,107 @@
 @prefix bibo:    <http://purl.org/ontology/bibo/> .
 @prefix cito:    <http://purl.org/spar/cito/> .
 @prefix c4o:     <http://purl.org/spar/c4o/> .
-@prefix dcterms:   <http://purl.org/dc/terms/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix event:   <http://purl.org/NET/c4dm/event.owl> .
+@prefix event:   <http://purl.org/NET/c4dm/event.owl#> .
 @prefix fabio:   <http://purl.org/spar/fabio/> .
 @prefix foaf:    <http://xmlns.com/foaf/0.1/> .
-@prefix geo:     <http://aims.fao.org/aos/geopolitical.owl> .
+@prefix geo:     <http://aims.fao.org/aos/geopolitical.owl#> .
 @prefix obo:     <http://purl.obolibrary.org/obo/> .
-@prefix ocrer:   <http://purl.org/net/OCRe/research.owl> .
+@prefix ocrer:   <http://purl.org/net/OCRe/research.owl#> .
-@prefix ocresd:   <http://purl.org/net/OCRe/study_design.owl> .
+@prefix ocresd:  <http://purl.org/net/OCRe/study_design.owl#> .
-@prefix ocresp:   <http://purl.org/net/OCRe/study_protocol.owl> .
+@prefix ocresp:  <http://purl.org/net/OCRe/study_protocol.owl#> .
-@prefix ocrest:   <http://purl.org/net/OCRe/statistics.owl> .
+@prefix ocrest:  <http://purl.org/net/OCRe/statistics.owl#> .
 @prefix owl:     <http://www.w3.org/2002/07/owl#> .
 @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix ro:      <http://purl.obolibrary.org/obo/ro.owl> .
+@prefix ro:      <http://purl.obolibrary.org/obo/ro.owl#> .
-@prefix scires:  <http://vivoweb.org/ontology/scientific-research> .
+@prefix scires:  <http://vivoweb.org/ontology/scientific-research#> .
-@prefix skos:    <http://www.w3.org/2004/02/skos/core> .
+@prefix skos:    <http://www.w3.org/2004/02/skos/core#> .
 @prefix swo:     <http://www.ebi.ac.uk/efo/swo/> .
 @prefix vann:    <http://purl.org/vocab/vann/> .
-@prefix vcard:   <http://www.w3.org/2006/vcard/ns> .
+@prefix vcard:   <http://www.w3.org/2006/vcard/ns#> .
 @prefix vitro:   <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> .
 @prefix vitro-public:  <http://vitro.mannlib.cornell.edu/ns/vitro/public#> .
 @prefix vivo:    <http://vivoweb.org/ontology/core#> .
 @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
 
-bibo:
+<http://purl.org/ontology/bibo/>
       rdfs:label "Bibliographic Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "bibo" .
 
-skos:
+<http://www.w3.org/2004/02/skos/core>
       rdfs:label "SKOS (Simple Knowledge Organization System)"@en-US ;
       vitro:ontologyPrefixAnnot "skos" .
       
-vivo:
+<http://vivoweb.org/ontology/core>
       rdfs:label "VIVO Core Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "vivo" .
 
-ocrer:
+<http://purl.org/net/OCRe/research.owl>
       rdfs:label "OCRe Research"@en-US ;
       vitro:ontologyPrefixAnnot "ocrer" .
       
-ocresd:
+<http://purl.org/net/OCRe/study_design.owl>
       rdfs:label "OCRe Study Design"@en-US ;
       vitro:ontologyPrefixAnnot "ocresd" .
       
-ocresp:
+<http://purl.org/net/OCRe/study_protocol.owl>
       rdfs:label "OCRe Study Protocol"@en-US ;
       vitro:ontologyPrefixAnnot "ocresp" .
       
-ocrest:
+<http://purl.org/net/OCRe/statistics.owl>
       rdfs:label "OCRe Statistics"@en-US ;
       vitro:ontologyPrefixAnnot "ocresst" .
       
-geo:
+<http://aims.fao.org/aos/geopolitical.owl>
       rdfs:label "Geopolitical Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "geo" .
       
-event:
+<http://purl.org/NET/c4dm/event.owl>
       rdfs:label "Event Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "event" .
 
-obo:  
+<http://purl.obolibrary.org/obo/>  
       rdfs:label "OBO Foundry"@en-US ;
       vitro:ontologyPrefixAnnot "obo" .
               
-vcard:
+<http://www.w3.org/2006/vcard/ns>
       rdfs:label "VCard"@en-US ;
       vitro:ontologyPrefixAnnot "vcard" .
               
-foaf:
+<http://xmlns.com/foaf/0.1/>
       rdfs:label "FOAF (Friend of a Friend)"@en-US ;
       vitro:ontologyPrefixAnnot "foaf" .
 
-scires:
+<http://vivoweb.org/ontology/scientific-research>
       rdfs:label "VIVO Scientific Research Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "scires" .
 
-fabio:
+<http://purl.org/spar/fabio/>
       rdfs:label "FaBiO (FRBR-Aligned Bibliographic Ontology)"@en-US ;
       vitro:ontologyPrefixAnnot "fabio" .
 
-c4o:
+<http://purl.org/spar/c4o/>
       rdfs:label "Citation Counting and Context Characterization Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "c4o" .
 
-cito:
+<http://purl.org/spar/cito/>
       rdfs:label "CiTO (Citation Typing Ontology)"@en-US ;
       vitro:ontologyPrefixAnnot "cito" .
     
-dcterms:
+<http://purl.org/dc/terms/>
       rdfs:label "Dublin Core Terms"@en-US ;
       vitro:ontologyPrefixAnnot "dcterms" .  
     
-vann:
+<http://purl.org/vocab/vann/>
       rdfs:label "Vocabulary for Annotating Vocabulary Descriptions"@en-US ;
       vitro:ontologyPrefixAnnot "vann" .
       
-ro:
+<http://purl.obolibrary.org/obo/ro.owl>
       rdfs:label "Relations Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "ro" .    
       
-swo:
+<http://www.ebi.ac.uk/efo/swo/>
       rdfs:label "Software Ontology"@en-US ;
       vitro:ontologyPrefixAnnot "swo" . 
 
@@ -1730,7 +1730,9 @@ vivo:outreachOverview
       vitro:prohibitedFromUpdateBelowRoleLevelAnnot
               <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
       vitro:publicDescriptionAnnot
-              "Please enter a single summary narrative of your outreach goals and/or contributions"^^xsd:string .
+              "Please enter a single summary narrative of your outreach goals and/or contributions"^^xsd:string ;
+      vitro:editing
+              "HTML"^^xsd:string .
 
 obo:ERO_0000031
       vitro:hiddenFromDisplayBelowRoleLevelAnnot
@@ -1912,7 +1914,9 @@ bibo:abstract
       vitro:prohibitedFromUpdateBelowRoleLevelAnnot
               <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
       vitro:publicDescriptionAnnot
-              "A summary of the resource."^^xsd:string .
+              "A summary of the resource."^^xsd:string ;
+      vitro:editing
+              "HTML"^^xsd:string .
 
 vivo:PrincipalInvestigatorRole
       vitro:displayLimitAnnot
@@ -2141,7 +2145,9 @@ vivo:teachingOverview
       vitro:prohibitedFromUpdateBelowRoleLevelAnnot
               <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
       vitro:publicDescriptionAnnot
-              "Please enter a single narrative summary description of your teaching activities, goals, and/or experience"^^xsd:string .
+              "Please enter a single narrative summary description of your teaching activities, goals, and/or experience"^^xsd:string ;
+      vitro:editing
+              "HTML"^^xsd:string .
 
 vivo:rank
       vitro:hiddenFromDisplayBelowRoleLevelAnnot
@@ -2268,7 +2274,9 @@ vivo:overview
       vitro:prohibitedFromUpdateBelowRoleLevelAnnot
               <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
       vitro:publicDescriptionAnnot
-              "A short narrative summary to be used as a single descriptive overview statement."^^xsd:string .
+              "A short narrative summary to be used as a single descriptive overview statement."^^xsd:string ;
+      vitro:editing
+              "HTML"^^xsd:string .
 
 vivo:description
       vitro:displayLimitAnnot
@@ -5405,7 +5413,9 @@ vivo:researchOverview
       vitro:inPropertyGroupAnnot
               <http://vivoweb.org/ontology#vitroPropertyGroupresearch> ;
       vitro:prohibitedFromUpdateBelowRoleLevelAnnot
-              <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> .
+              <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
+      vitro:editing
+              "HTML"^^xsd:string .
 
 obo:ERO_0000390
       vitro:displayLimitAnnot

installer/home/pom.xml

@@ -58,9 +58,9 @@
                                     <goal>run</goal>
                                 </goals>
                                 <configuration>
-                                    <tasks>
+                                    <target>
                                         <delete dir="${vivo-dir}/rdf" />
-                                    </tasks>
+                                    </target>
                                 </configuration>
                             </execution>
                         </executions>

installer/pom.xml

@@ -64,7 +64,7 @@
                 </plugin>
                 <plugin>
                     <artifactId>maven-compiler-plugin</artifactId>
-                    <version>3.5.1</version>
+                    <version>3.8.0</version>
                 </plugin>
                 <plugin>
                     <artifactId>maven-dependency-plugin</artifactId>

installer/webapp/pom.xml

@@ -84,9 +84,9 @@
                                     <goal>run</goal>
                                 </goals>
                                 <configuration>
-                                    <tasks>
+                                    <target>
                                         <delete dir="${tomcat-dir}/webapps/${project.build.finalName}" />
-                                    </tasks>
+                                    </target>
                                 </configuration>
                             </execution>
                         </executions>

pom.xml

@@ -151,6 +151,18 @@
             </activation>
             <build>
                 <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-source-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>attach-sources</id>
+                                <goals>
+                                    <goal>jar-no-fork</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-javadoc-plugin</artifactId>
@@ -167,18 +179,6 @@
                             <additionalparam>${javadoc.opts}</additionalparam>
                         </configuration>
                     </plugin>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-source-plugin</artifactId>
-                        <executions>
-                            <execution>
-                                <id>attach-sources</id>
-                                <goals>
-                                    <goal>jar-no-fork</goal>
-                                </goals>
-                            </execution>
-                        </executions>
-                    </plugin>
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-gpg-plugin</artifactId>
@@ -202,22 +202,28 @@
                             <autoReleaseAfterClose>true</autoReleaseAfterClose>
                         </configuration>
                     </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <profile>
+            <!-- JDK 8 profile for the Error Prone plugin -->
+            <id>jdk8</id>
+            <activation>
+                <jdk>1.8</jdk>
+            </activation>
+            <properties>
+                <javac.version>9+181-r4173-1</javac.version>
+            </properties>
+            <build>
+                <plugins>
                     <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
+                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>buildnumber-maven-plugin</artifactId>
+                        <artifactId>maven-compiler-plugin</artifactId>
-                        <executions>
-                            <execution>
-                                <phase>validate</phase>
-                                <goals>
-                                    <goal>create</goal>
-                                </goals>
-                            </execution>
-                        </executions>
                         <configuration>
-                            <doCheck>false</doCheck>
+                            <fork>true</fork>
-                            <doUpdate>false</doUpdate>
+                            <compilerArgs combine.children="append">
-                            <shortRevisionLength>7</shortRevisionLength>
+                                <arg>-J-Xbootclasspath/p:${settings.localRepository}/com/google/errorprone/javac/${javac.version}/javac-${javac.version}.jar</arg>
-                            <revisionOnScmFailure>Detached</revisionOnScmFailure>
+                            </compilerArgs>
                         </configuration>
                     </plugin>
                 </plugins>
@@ -269,23 +275,36 @@
                     <source>1.8</source>
                     <target>1.8</target>
                     <encoding>UTF-8</encoding>
-                    <compilerId>javac-with-errorprone</compilerId>
+                    <compilerArgs>
-                    <forceJavacCompilerUse>true</forceJavacCompilerUse>
+                        <arg>-XDcompilePolicy=simple</arg>
+                        <arg>-Xplugin:ErrorProne</arg>
+                    </compilerArgs>
+                    <annotationProcessorPaths>
+                        <path>
+                            <groupId>com.google.errorprone</groupId>
+                            <artifactId>error_prone_core</artifactId>
+                            <version>2.3.2</version>
+                        </path>
+                    </annotationProcessorPaths>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>buildnumber-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <phase>validate</phase>
+                        <goals>
+                            <goal>create</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <doCheck>false</doCheck>
+                    <doUpdate>false</doUpdate>
+                    <shortRevisionLength>7</shortRevisionLength>
+                    <revisionOnScmFailure>Detached</revisionOnScmFailure>
                 </configuration>
-                <dependencies>
-                    <dependency>
-                        <groupId>org.codehaus.plexus</groupId>
-                        <artifactId>plexus-compiler-javac-errorprone</artifactId>
-                        <version>2.8</version>
-                    </dependency>
-                    <!-- override plexus-compiler-javac-errorprone's dependency on
-                         Error Prone with the latest version -->
-                    <dependency>
-                        <groupId>com.google.errorprone</groupId>
-                        <artifactId>error_prone_core</artifactId>
-                        <version>2.1.1</version>
-                    </dependency>
-                </dependencies>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -314,7 +333,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-compiler-plugin</artifactId>
-                    <version>3.5.1</version>
+                    <version>3.8.0</version>
                 </plugin>
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>

webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml

@@ -6,7 +6,7 @@
 <list-view-config>
     <query-select>
         PREFIX foaf:  &lt;http://xmlns.com/foaf/0.1/&gt;
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX bibo:  &lt;http://purl.org/ontology/bibo/&gt;
         PREFIX core:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX owl:   &lt;http://www.w3.org/2002/07/owl#&gt;
@@ -31,7 +31,7 @@
             ?adviseeRole a core:AdviseeRole .
             ?adviseeRole core:relatedBy ?advisingRel .
             ?advisingRel a core:AdvisingRelationship .
-            LET ( ?localName := afn:localname(?advisingRel) )
+            LET ( ?localName := REPLACE(STR(?advisingRel),"^.*(#)(.*)$", "$2") )
             OPTIONAL {
                 <precise-subquery>?subject ?property ?adviseeRole .
                 ?adviseeRole a core:AdviseeRole .

webapp/src/main/webapp/config/listViewConfig-advisorIn.xml

@@ -6,7 +6,6 @@
 <list-view-config>
     <query-select>
         PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
-        PREFIX afn: &lt;http://jena.apache.org/ARQ/function#&gt;
         PREFIX bibo: &lt;http://purl.org/ontology/bibo/&gt;
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
@@ -31,7 +30,7 @@
             ?advisorRole a core:AdvisorRole .
             ?advisorRole core:relatedBy ?advisingRel .
             ?advisingRel a core:AdvisingRelationship .
-            LET ( ?localName := afn:localname(?advisingRel) )
+            LET ( ?localName := REPLACE(STR(?advisingRel),"^.*(#)(.*)$", "$2") )
             OPTIONAL {
                 <precise-subquery>?subject ?property ?advisorRole .
                 ?advisorRole a core:AdvisorRole .

webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml

@@ -7,7 +7,7 @@
     <query-select>
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
-        PREFIX afn:  &lt;http://jena.apache.org/ARQ/function#&gt;
+        
 
         SELECT DISTINCT ?dateTimeInterval ?label
             ?valueStart ?valueStartName
@@ -24,7 +24,7 @@
             OPTIONAL {
                 <precise-subquery>?subject ?property ?dateTimeInterval .</precise-subquery>
                 ?dateTimeInterval core:start ?valueStart .
-                LET (?valueStartName := afn:localname(?valueStart))
+                LET (?valueStartName := REPLACE(STR(?valueStart),"^.*(#)(.*)$", "$2"))
 
                 OPTIONAL {
                     <precise-subquery>?subject ?property ?dateTimeInterval .
@@ -35,13 +35,13 @@
                     <precise-subquery>?subject ?property ?dateTimeInterval .
                     ?dateTimeInterval core:start ?valueStart .</precise-subquery>
                     ?valueStart core:dateTimePrecision ?dateTimePrecisionStart .
-                    LET (?precisionStart := afn:localname(?dateTimePrecisionStart))
+                    LET (?precisionStart := REPLACE(STR(?dateTimePrecisionStart),"^.*(#)(.*)$", "$2"))
                 }
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?dateTimeInterval .</precise-subquery>
                 ?dateTimeInterval core:end ?valueEnd .
-                LET (?valueEndName := afn:localname(?valueEnd))
+                LET (?valueEndName := REPLACE(STR(?valueEnd),"^.*(#)(.*)$", "$2"))
                 OPTIONAL {
                     <precise-subquery>?subject ?property ?dateTimeInterval .
                     ?dateTimeInterval core:end ?valueEnd .</precise-subquery>
@@ -51,7 +51,7 @@
                     <precise-subquery>?subject ?property ?dateTimeInterval .
                     ?dateTimeInterval core:end ?valueEnd .</precise-subquery>
                     ?valueEnd core:dateTimePrecision ?dateTimePrecisionEnd .
-                    LET (?precisionEnd := afn:localname(?dateTimePrecisionEnd))
+                    LET (?precisionEnd := REPLACE(STR(?dateTimePrecisionEnd),"^.*(#)(.*)$", "$2"))
                 }
             }
             OPTIONAL {

webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml

@@ -7,10 +7,10 @@
     <query-select>     
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;    
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
-        PREFIX afn:  &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         
         SELECT DISTINCT ?dateTimeValue 
-                        (afn:localname(?dateTimePrecision) AS ?precision) 
+                        (REPLACE(STR(?dateTimePrecision),"^.*(#)(.*)$", "$2") AS ?precision) 
                         ?dateTime
         WHERE {
             ?subject ?property ?dateTimeValue .

webapp/src/main/webapp/config/listViewConfig-default.xml

@@ -7,7 +7,7 @@
 
 <list-view-config>
     <query-select>
-        PREFIX afn:  &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
@@ -25,7 +25,7 @@
         WHERE
         {
             ?subject ?property ?object .
-            LET (?localName := afn:localname(?object))
+            LET (?localName := REPLACE(STR(?object), "^.*(#)(.*)$", "$2"))
 
             OPTIONAL {
                 <precise-subquery>?subject ?property ?object .</precise-subquery>
@@ -57,7 +57,7 @@
             }
 
         <collated>
-            FILTER ( afn:namespace(?subclass) != "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" )
+            FILTER ( REPLACE(STR(?subclass),"^(.*)(#)(.*)$", "$1$2") != "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" )
         </collated>
 
         # Order by ?type is important, because if the object has more than one mostSpecificType,

webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml

@@ -7,7 +7,7 @@
 
 <list-view-config>
     <query-select>
-        PREFIX afn:  &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
@@ -26,7 +26,7 @@
         {
             ?subject ?property ?object .
             ?object a ?objectType .
-            LET (?localName := afn:localname(?object))
+            LET (?localName := REPLACE(STR(?object),"^.*(#)(.*)$", "$2"))
 
             OPTIONAL {
                 <precise-subquery>?subject ?property ?object .
@@ -63,7 +63,7 @@
                 ?object a ?objectType .</precise-subquery>
                 ?object a ?subclass .
             }
-            FILTER ( afn:namespace(?subclass) != "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" )
+            FILTER ( REPLACE(STR(?subclass),"^(.*)(#)(.*)$", "$1$2") != "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" )
         </collated>
 
         # Order by ?type is important, because if the object has more than one mostSpecificType,

webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml

@@ -8,12 +8,12 @@
         PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>    
         PREFIX vivo: <http://vivoweb.org/ontology/core#>
         PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-        PREFIX afn:  <http://jena.apache.org/ARQ/function#>
+        
         
         SELECT ?concept ?conceptLabel ?conceptName ?vocabularySource ?vocabularySourceName
         WHERE {
          	?subject ?property ?concept .
-         	LET (?conceptName := afn:localname(?concept)) 
+         	LET (?conceptName := REPLACE(STR(?concept),"^.*(#)(.*)$", "$2")) 
          	OPTIONAL {
                 <precise-subquery>?subject ?property ?concept .</precise-subquery>
                 ?concept rdfs:label ?conceptLabel .

webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml

@@ -5,7 +5,7 @@
 
 <list-view-config>
     <query-select>
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX bibo:  &lt;http://purl.org/ontology/bibo/&gt;
         PREFIX vivo:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX owl:   &lt;http://www.w3.org/2002/07/owl#&gt;
@@ -55,7 +55,7 @@
                 }
                 </collated>
 
-                LET (?event1Name := afn:localname(?event1))
+                LET (?event1Name := REPLACE(STR(?event1),"^.*(#)(.*)$", "$2"))
 
                 OPTIONAL {
                     <precise-subquery>

webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml

@@ -5,7 +5,7 @@
 
 <list-view-config>
     <query-select>
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
         PREFIX rdfs:  &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
@@ -32,7 +32,7 @@
                 ?role core:relatedBy ?activity .
                 ?activity a core:Contract .
                 ?activity rdfs:label ?activityLabel .
-                LET (?activityName := afn:localname(?activity)) .
+                LET (?activityName := REPLACE(STR(?activity),"^.*(#)(.*)$", "$2")) .
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?role .
@@ -40,7 +40,7 @@
                 ?role core:relatedBy ?activity .
                 ?activity a core:Grant .
                 ?activity rdfs:label ?activityLabel .
-                LET (?activityName := afn:localname(?activity)) .
+                LET (?activityName := REPLACE(STR(?activity),"^.*(#)(.*)$", "$2")) .
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?role .

webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml

@@ -5,7 +5,7 @@
 
 <list-view-config>
     <query-select>    
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX rdfs:  &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
         PREFIX vitro: &lt;http://vitro.mannlib.cornell.edu/ns/vitro/0.7#&gt;
@@ -14,7 +14,7 @@
                         ?role
                         ?subclassLabel
                         ?activity 
-                        (afn:localname(?activity) AS ?activityLocal)
+                        (REPLACE(STR(?activity),"^.*(#)(.*)$", "$2") AS ?activityLocal)
                         ?activityName
                         ?dateTimeStart 
                         ?dateTimeEnd 

webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml

@@ -5,7 +5,7 @@
 
 <list-view-config>
     <query-select>
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
         PREFIX rdfs:  &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
@@ -32,7 +32,7 @@
                 ?role &lt;http://vivoweb.org/ontology/core#relatedBy&gt; ?activity .
                 ?activity a core:Contract .
                 ?activity rdfs:label ?activityLabel .
-                LET (?activityName := afn:localname(?activity))
+                LET (?activityName := REPLACE(STR(?activity),"^.*(#)(.*)$", "$2"))
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?role .
@@ -57,7 +57,7 @@
                 ?role &lt;http://vivoweb.org/ontology/core#relatedBy&gt; ?activity .
                 ?activity a core:Grant .
                 ?activity rdfs:label ?activityLabel .
-                LET (?activityName := afn:localname(?activity))
+                LET (?activityName := REPLACE(STR(?activity),"^.*(#)(.*)$", "$2"))
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?role .

webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml

@@ -8,7 +8,7 @@
 
 <list-view-config>
     <query-select>    
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX bibo:  &lt;http://purl.org/ontology/bibo/&gt;
         PREFIX vivo:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX owl:   &lt;http://www.w3.org/2002/07/owl#&gt;
@@ -38,7 +38,7 @@
                 ?role &lt;http://purl.obolibrary.org/obo/BFO_0000054&gt; ?presentation .
                 ?presentation a vivo:Presentation .
                 ?presentation rdfs:label ?presentationLabel .
-                LET (?presentationName := afn:localname(?presentation))
+                LET (?presentationName := REPLACE(STR(?presentation),"^.*(#)(.*)$", "$2"))
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?role .

webapp/src/main/webapp/config/listViewConfig-hasPrincipalInvestigatorRole.xml

@@ -5,7 +5,7 @@
 
 <list-view-config>
     <query-select>
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
         PREFIX rdfs:  &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
@@ -34,7 +34,7 @@
                 ?role core:relatedBy ?activity .
                 ?activity a core:Contract .
                 ?activity rdfs:label ?activityLabel .
-                LET (?activityName := afn:localname(?activity)) .
+                LET (?activityName := REPLACE(STR(?activity),"^.*(#)(.*)$", "$2")) .
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?role .
@@ -59,7 +59,7 @@
                 ?role core:relatedBy ?activity .
                 ?activity a core:Grant .
                 ?activity rdfs:label ?activityLabel .
-                LET (?activityName := afn:localname(?activity)) .
+                LET (?activityName := REPLACE(STR(?activity),"^.*(#)(.*)$", "$2")) .
             }
             OPTIONAL {
                 <precise-subquery>?subject ?property ?role .

webapp/src/main/webapp/config/listViewConfig-hasReviewerRole.xml

@@ -5,7 +5,7 @@
 
 <list-view-config>
     <query-select>    
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX rdfs:  &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
         PREFIX vitro: &lt;http://vitro.mannlib.cornell.edu/ns/vitro/0.7#&gt;
@@ -14,7 +14,7 @@
                         ?role
                         ?subclassLabel
                         ?activity 
-                        (afn:localname(?activity) AS ?activityLocal)
+                        (REPLACE(STR(?activity),"^.*(#)(.*)$", "$2") AS ?activityLocal)
                         ?activityName
                         ?dateTimeStart 
                         ?dateTimeEnd 

webapp/src/main/webapp/config/listViewConfig-informationResourceInAuthorship.xml

@@ -64,7 +64,7 @@
                 bind ( COALESCE(?firstName, "") As ?firstName1) .
                 bind ( COALESCE(?middleName, "") As ?middleName1) .
                 bind ( COALESCE(?lastName, "") As ?lastName1) .
-                bind (concat(str(?lastName1 + ", "),str(?firstName1 + " "),str(?middleName1)) as ?authorName) .
+                bind (concat(str(?lastName1),", ",str(?firstName1)," ",str(?middleName1)) as ?authorName) .
 
                 OPTIONAL {
                     <precise-subquery>?subject ?property ?authorship .

webapp/src/main/webapp/config/listViewConfig-issuedCredential.xml

@@ -6,7 +6,7 @@
 <list-view-config>
     <query-select>    
         PREFIX foaf:  &lt;http://xmlns.com/foaf/0.1/&gt;
-        PREFIX afn:   &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX bibo:  &lt;http://purl.org/ontology/bibo/&gt;
         PREFIX core:  &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX owl:   &lt;http://www.w3.org/2002/07/owl#&gt;
@@ -26,7 +26,7 @@
         WHERE {
             ?subject ?property ?issuedCredential .
             ?issuedCredential a core:IssuedCredential .
-            LET (?issuedCredentialLocal := afn:localname(?issuedCredential))
+            LET (?issuedCredentialLocal := REPLACE(STR(?issuedCredential),"^.*(#)(.*)$", "$2"))
             OPTIONAL {
                 <precise-subquery>?subject ?property ?issuedCredential .
                 ?issuedCredential a core:IssuedCredential .</precise-subquery>
@@ -39,7 +39,7 @@
                 ?credential a core:Credential .
                 ?credential core:relatedBy ?issuedCredential .
                 ?credential rdfs:label ?credentialLabel .
-                LET (?credentialLocal := afn:localname(?credential))
+                LET (?credentialLocal := REPLACE(STR(?credential),"^.*(#)(.*)$", "$2"))
             }
              OPTIONAL {
                 <precise-subquery>?subject ?property ?issuedCredential .

webapp/src/main/webapp/config/listViewConfig-rangeUnion.xml

@@ -7,7 +7,7 @@
 
 <list-view-config>
     <query-select>
-        PREFIX afn:  &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
@@ -24,7 +24,7 @@
         WHERE
         {
             ?subject ?property ?object .
-            LET (?localName := afn:localname(?object))
+            LET (?localName := REPLACE(STR(?object),"^.*(#)(.*)$", "$2"))
 
             OPTIONAL {
                 <precise-subquery>?subject ?property ?object .</precise-subquery>
@@ -50,7 +50,7 @@
             }
 
         <collated>
-            FILTER ( afn:namespace(?subclass) != "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" )
+            FILTER ( REPLACE(STR(?subclass),"^(.*)(#)(.*)$", "$1$2") != "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" )
         </collated>
 
         # Order by ?type is important, because if the object has more than one mostSpecificType,

webapp/src/main/webapp/config/listViewConfig-relatedRole.xml

@@ -8,7 +8,7 @@
     <query-select>    
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
-        PREFIX afn:  &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX vitro: &lt;http://vitro.mannlib.cornell.edu/ns/vitro/0.7#&gt;
         PREFIX vcard:  &lt;http://www.w3.org/2006/vcard/ns#&gt;
         
@@ -18,7 +18,7 @@
                         ?property
                         ?role   
                         ?roleLabel ?roleTypeLabel                          
-                        ?indivInRole (afn:localname(?indivInRole) AS ?indivName)
+                        ?indivInRole (REPLACE(STR(?indivInRole),"^.*(#)(.*)$", "$2") AS ?indivName)
                         ?indivLabel
                         ?dateTimeInterval ?dateTimeStart ?dateTimeEnd ?objectType
         WHERE {

webapp/src/main/webapp/config/listViewConfig-webpage.xml

@@ -7,13 +7,13 @@
 
 <list-view-config>
     <query-select>            
-        PREFIX afn:  &lt;http://jena.apache.org/ARQ/function#&gt;
+        
         PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
         PREFIX vcard: &lt;http://www.w3.org/2006/vcard/ns#&gt;
 
         SELECT ?vcard ?link 
-               (afn:localname(?link) AS ?linkName) 
+               (REPLACE(STR(?link),"^.*(#)(.*)$", "$2") AS ?linkName) 
                (group_concat(distinct ?linkLabel;separator="/") as ?label)
                ?url 
                ?rank

webapp/src/main/webapp/templates/freemarker/body/partials/individual/propStatement-authorInAuthorship.ftl

@@ -137,8 +137,10 @@
                 <#assign plumIdParam = "isbn=${statement.isbn13}">
             <#elseif statement.oclc??>
                 <#assign plumIdParam = "oclc=${statement.oclc}">
+            <#else>
+                <#assign plumIdParam = "">
             </#if>
-            <#if plumIdParam??>
+            <#if plumIdParam?has_content>
                 <div class="plum-print-wrapper" style="display: inline-block; vertical-align: top">
                     <a class="plumx-plum-print-popup"
                        href="https://plu.mx/plum/a/?${plumIdParam}"

webapp/src/main/webapp/templates/freemarker/body/partials/individual/propStatement-dataDefault.ftl

@@ -1,108 +0,0 @@
-<#-- $This file is distributed under the terms of the license in LICENSE$ -->
-
-<#-- VIVO-specific default data property statement template. 
-    
-     This template must be self-contained and not rely on other variables set for the individual page, because it
-     is also used to generate the property statement during a deletion.  
- -->
-<#import "lib-datetime.ftl" as dt>
-<#import "lib-meta-tags.ftl" as lmt>
-<#if property.rangeDatatypeURI?? && property.rangeDatatypeURI?contains("#")>
-	<#assign datatype = property.rangeDatatypeURI?substring(property.rangeDatatypeURI?last_index_of("#")+1) />
-<#else>
-	<#assign datatype = "none" />
-</#if>
-<@showStatement statement property datatype />
-
-<#macro showStatement statement property datatype>
-    <#assign theValue = statement.value />
-	
-    <#if theValue?contains("<ul>") >
-        <#assign theValue = theValue?replace("<ul>","<ul class='tinyMCEDisc'>") />
-    </#if>
-    <#if theValue?contains("<ol>") >
-        <#assign theValue = theValue?replace("<ol>","<ol class='tinyMCENumeric'>") />
-    </#if>
-    <#if theValue?contains("<p>") >
-        <#assign theValue = theValue?replace("<p>","<p style='margin-bottom:.6em'>") />
-    </#if>
-	<#if theValue?matches("([0-9]{4})-([0-9]{1,2})-([0-9]{1,2})") >
-		<#assign theValue = theValue + "T00:00:00" />
-		${dt.formatXsdDateTimeLong(theValue, "yearMonthDayPrecision")}
-	<#elseif theValue?matches("^([0-9]{4})-((0[1-9])|(1[0-2]))-((0[1-9])|([1-2][0-9])|(3[0-1]))(T|\\s)(([0-1][0-9])|(2[0-3])):([0-5][0-9]):([0-5][0-9])")>
-		<#if theValue?contains("T00:00:00") >
-			${dt.formatXsdDateTimeLong(theValue, "yearMonthDayPrecision")}
-		<#else>
-			${dt.formatXsdDateTimeLong(theValue, "yearMonthDayTimePrecision")}
-		</#if>
-	<#elseif theValue?matches("^([0-9]{4})-(0[1-9]|1[012])")>
-		<#assign theValue = theValue + "-01T00:00:00" />
-		${dt.formatXsdDateTimeLong(theValue, "yearMonthPrecision")}
-	<#elseif theValue?matches("^--(0[1-9]|1[012])")>
-		<#assign theValue = "2000" + theValue?substring(1) + "-01T00:00:00" />
-		${dt.formatXsdDateTimeLong(theValue, "monthPrecision")}
-	<#else>
-    	${theValue} <#if !datatype?contains("none")> <@validateFormat theValue datatype/> </#if>
-	</#if>
-	<@lmt.addCitationMetaTag uri=(property.uri!) content=(theValue!) />
-</#macro>
-<#macro validateFormat value datatype >
-	<#if datatype?? >
-		<#switch datatype>
-			<#case "date">
-				<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt="${i18n().invalid_format}" title=" ${i18n().invalid_format}"> <#-- validated above -->
-		     	<span class="invalidFormatText">invalid format</span>
-				<#break>
-		    <#case "dateTime">
-				<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}"> <#-- validated above -->
-		     	<span class="invalidFormatText">invalid format</span>
-				<#break>
-		  	<#case "time">
-		     	<#if !value?matches("(([0-1][0-9])|(2[0-3])):([0-5][0-9]):([0-5][0-9])") >
-					<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}">
-					<span class="invalidFormatText">invalid format</span>
-			 	</#if>
-		     	<#break>
-		  	<#case "gYear">
-		     	<#if !value?matches("^\\d{4}") >
-					<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}">
-					<span class="invalidFormatText">invalid format</span>
-			 	</#if>
-		     	<#break>
-		    <#case "gMonth">
-		     	<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}"> <#-- validated above -->
-		     	<span class="invalidFormatText">invalid format</span>
-				<#break>
-		    <#case "gYearMonth">
-		     	<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}"> <#-- validated above -->
-		     	<span class="invalidFormatText">invalid format</span>
-				<#break>
-		  	<#case "float">
-				<#if !value?matches("^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?.") >
-		     		<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}">
-			     	<span class="invalidFormatText">invalid format</span>
-				</#if>
-				<#break>
-		  	<#case "integer">
-				<#if !value?matches("^-?\\d+$") >
-		     		<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}">
-			     	<span class="invalidFormatText">invalid format</span>
-				</#if>
-				<#break>
-		  	<#case "int">
-				<#if !value?matches("^-?\\d+$") >
-	     			<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}">
-			     	<span class="invalidFormatText">invalid format</span>
-				</#if>
-				<#break>
-		  	<#case "boolean">
-				<#if !value?matches("false") && !value?matches("true") >
-		     		<img class="invalidFormatImg" src="${urls.base}/images/iconAlert.png" width="18" alt=" ${i18n().invalid_format}" title=" ${i18n().invalid_format}">
-			     	<span class="invalidFormatText">invalid format</span>
-				</#if>
-				<#break>
-		  	<#default>
-		</#switch>
-	</#if>
-</#macro>
-

webapp/src/main/webapp/templates/freemarker/body/partials/individual/propStatement-informationResourceInAuthorship.ftl

@@ -19,7 +19,7 @@
 			<#if statement.authorName?replace(" ","")?length == statement.authorName?replace(" ","")?last_index_of(",") + 1 >
         		${statement.authorName?replace(",","")}
 			<#else>
-				${statement.authorName}
+				${statement.authorName!i18n().missing_author}
 			</#if>
     	<#else>
         	<a href="${profileUrl(statement.uri("author"))}" title="${i18n().author_name}">${statement.authorName}</a>

webapp/src/main/webapp/templates/freemarker/edit/forms/addServiceProviderRoleToPerson.ftl

@@ -25,6 +25,8 @@ roleExamples-->
 <#assign acMultipleTypes = "'true'" />
 <#assign acTypes = "{activity: 'http://xmlns.com/foaf/0.1/Organization,http://xmlns.com/foaf/0.1/Group,http://purl.obolibrary.org/obo/OBI_0000835,http://purl.org/NET/c4dm/event.owl#Event'}" />
 
+<#assign editTitle = "${i18n().edit_entry_for_service_provider_role}"/>
+<#assign createTitle = "${i18n().create_entry_for_service_provider_role}"/>
 
 <#--Each of the two stage forms will include the form below-->
 <#include "addRoleToPersonTwoStage.ftl">

webapp/src/main/webapp/templates/freemarker/edit/forms/personHasAdvisorRelationship.ftl

@@ -114,7 +114,7 @@ Set this flag on the input acUriReceiver where you would like this behavior to o
         </#list>
       <#else>
         <select id="selector" name="advisingRelType"  ${disabledVal} >
-            <option value="${blankSentinel}" selected="selected">${i18n().select_one}</option>                
+            <option value="" selected="selected">${i18n().select_one}</option>
             <#list advisingRelTypeOpts?keys as key>             
                 <option value="${key}"  <#if advisingRelTypeValue = key>selected</#if>>${advisingRelTypeOpts[key]}</option>            
             </#list>

webapp/src/main/webapp/templates/freemarker/visualization/mapOfScience/mapOfScienceSetup.ftl

@@ -110,7 +110,7 @@ var i18nStrings = {
 <#if googleMapsKey??>
     ${scripts.add('<script type="text/javascript" src="https://maps.googleapis.com/maps/api/js?key=${googleMapsKey}"></script>')}
 <#else>
-    ${scripts.add('<script type="text/javascript" src="http://maps.google.com/maps/api/js?sensor=false"></script>')}
+    ${scripts.add('<script type="text/javascript" src="https://maps.google.com/maps/api/js?sensor=false"></script>')}
 </#if>
 ${scripts.add('<script type="text/javascript" src="${urls.base}/js/jquery-ui/js/jquery-ui-1.12.1.min.js"></script>',
 			  '<script type="text/javascript" src="${urls.base}/js/jquery_plugins/jquery.blockUI.js"></script>',