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

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This commit is contained in:
Jim Blake 2017-01-03 13:03:20 -05:00
commit b87bf74e4b
86 changed files with 158 additions and 359 deletions
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5
.travis.yml
View file

@ -8,6 +8,11 @@ env:
# Give Maven 1GB of memory to work with
- MAVEN_OPTS=-Xmx1024M
cache:
directories:
- .autoconf
- $HOME/.m2
install:
- git clone https://github.com/vivo-project/Vitro.git ../Vitro

20
api/pom.xml
View file

@ -30,16 +30,6 @@
<type>pom</type>
</dependency>
<dependency>
<groupId>axis</groupId>
<artifactId>axis</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>com.itextpdf</groupId>
<artifactId>itextpdf</artifactId>
@ -56,11 +46,6 @@
<version>2.5.6</version>
</dependency>
<dependency>
<groupId>org.vivoweb.dependencies</groupId>
<artifactId>agrovocws</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>org.vivoweb.dependencies</groupId>
<artifactId>oim.vivo.scimapcore</artifactId>
@ -84,6 +69,11 @@
<version>2.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.xml</groupId>
<artifactId>jaxrpc</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>junit</groupId>

184
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java
View file

@ -17,6 +17,7 @@ import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.concurrent.TimeUnit;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.rpc.ServiceException;
@ -25,11 +26,9 @@ import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.fao.www.webservices.AgrovocWS.ACSWWebService;
import org.fao.www.webservices.AgrovocWS.ACSWWebServiceServiceLocator;
import org.w3c.dom.Attr;
import org.w3c.dom.Document;
import org.w3c.dom.NamedNodeMap;
@ -56,7 +55,6 @@ import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
public class AgrovocService implements ExternalConceptService {
protected final Log logger = LogFactory.getLog(getClass());
private java.lang.String AgrovocWS_address = "http://agrovoc.fao.org/axis/services/SKOSWS";
private final String schemeUri = "http://aims.fao.org/aos/agrovoc/agrovocScheme";
private final String ontologyName = "agrovoc";
private final String format = "SKOS";
@ -136,9 +134,8 @@ public class AgrovocService implements ExternalConceptService {
if (closeMatch.startsWith("http://dbpedia.org")) {
try {
String description = getDbpediaDescription(closeMatch);
// System.out.println("description: "+ description);
c.setDefinition(description);
String description = getDbpediaDescription(closeMatch);
c.setDefinition(description);
} catch (Exception ex) {
logger.error("An error occurred in the process of retrieving dbpedia description", ex);
}
@ -190,153 +187,6 @@ public class AgrovocService implements ExternalConceptService {
return concept;
}
@Deprecated
protected String getTermcodeByTerm(String term) throws Exception {
String result = new String();
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
try {
URL url = new URL(AgrovocWS_address);
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
result = agrovoc_service.getTermcodeByTerm(term);
} catch (ServiceException e) {
logger.error("service exception", e);
throw e;
} catch (RemoteException e) {
logger.error("remote exception", e);
throw e;
} catch (MalformedURLException e) {
logger.error("malformed URL exception", e);
throw e;
}
return result;
}
protected String getTermCodeByTermAndLangXML(String ontologyName,
String searchString, String lang, String codeName, String format) {
String result = new String();
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
try {
URL url = new URL(AgrovocWS_address);
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
result = agrovoc_service.getTermCodeByTermAndLangXML(ontologyName,
searchString, lang, codeName, format);
} catch (ServiceException e) {
logger.error("service exception", e);
e.printStackTrace();
} catch (RemoteException e) {
e.printStackTrace();
} catch (MalformedURLException e) {
e.printStackTrace();
}
return result;
}
protected String getURIByTermAndLangXML(String ontologyName, String term,
String searchMode, String format, String lang) {
String result = new String();
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
try {
URL url = new URL(AgrovocWS_address);
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
result = agrovoc_service.getURIByTermAndLangXML(ontologyName, term,
searchMode, format, lang);
} catch (ServiceException e) {
e.printStackTrace();
} catch (RemoteException e) {
e.printStackTrace();
} catch (MalformedURLException e) {
e.printStackTrace();
}
return result;
}
// Creating method for term expansion
protected String getTermExpansion(String ontologyName, String term,
String searchMode, String format, String lang) {
String result = new String();
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
try {
URL url = new URL(AgrovocWS_address);
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
result = agrovoc_service.getTermExpansion(ontologyName, term,
format, searchMode, lang); // the actual call has this order
// for parameters
} catch (ServiceException e) {
e.printStackTrace();
} catch (RemoteException e) {
e.printStackTrace();
} catch (MalformedURLException e) {
e.printStackTrace();
}
return result;
}
protected String getConceptInfoByTermcodeXML(String termcode, String format) {
String result = new String();
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
try {
URL url = new URL(AgrovocWS_address);
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
result = agrovoc_service.getConceptInfoByTermcodeXML(termcode,
format);
} catch (ServiceException e) {
logger.error("service exception", e);
e.printStackTrace();
} catch (RemoteException e) {
e.printStackTrace();
} catch (MalformedURLException e) {
e.printStackTrace();
}
return result;
}
protected String getConceptByKeyword(String ontologyName,
String searchString, String format, String searchMode, String lang) {
String result = new String();
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
try {
URL url = new URL(AgrovocWS_address);
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
result = agrovoc_service.getConceptByKeyword(ontologyName,
searchString, format, searchMode, lang);
} catch (ServiceException e) {
logger.error("service exception", e);
e.printStackTrace();
} catch (RemoteException e) {
e.printStackTrace();
} catch (MalformedURLException e) {
e.printStackTrace();
}
return result;
}
protected String getWsdl() {
String result = new String();
try {
StringWriter sw = new StringWriter();
URL rss = new URL(this.AgrovocWS_address + "?wsdl");
BufferedReader in = new BufferedReader(new InputStreamReader(
rss.openStream()));
String inputLine;
while ((inputLine = in.readLine()) != null) {
sw.write(inputLine);
}
in.close();
result = sw.toString();
} catch (Exception ex) {
logger.error("error occurred in servlet", ex);
}
return result;
}
public List<Concept> getConceptsByURIWithSparql(String uri)
throws Exception {
// deprecating this method...just return an empty list
@ -440,8 +290,8 @@ public class AgrovocService implements ExternalConceptService {
try {
Query query = QueryFactory.create(qs);
qexec = QueryExecutionFactory.sparqlService(this.dbpedia_endpoint,
query);
qexec = QueryExecutionFactory.sparqlService(this.dbpedia_endpoint, query);
qexec.setTimeout(5000, TimeUnit.MILLISECONDS);
resultList = new ArrayList<HashMap>();
ResultSet resultSet = qexec.execSelect();
int resultSetSize = 0;
@ -501,28 +351,6 @@ public class AgrovocService implements ExternalConceptService {
}
}
// Get concept using agrovoc service
protected String getConceptInfoByURI(String ontologyName,
String conceptURI, String format) {
String result = new String();
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
try {
URL url = new URL(AgrovocWS_address);
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
result = agrovoc_service.getConceptByURI(ontologyName, conceptURI,
format);
} catch (ServiceException e) {
logger.error("service exception", e);
e.printStackTrace();
} catch (RemoteException e) {
e.printStackTrace();
} catch (MalformedURLException e) {
e.printStackTrace();
}
return result;
}
/**
* The code here utilizes the SKOSMOS REST API for Agrovoc
* This returns JSON LD so we would parse JSON instead of RDF

2
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/GemetService.java
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@ -24,7 +24,7 @@ import edu.cornell.mannlib.semservices.service.ExternalConceptService;
public class GemetService implements ExternalConceptService {
protected final Log logger = LogFactory.getLog(getClass());
private final String GemetWS_address = "http://www.eionet.europa.eu/gemet/";
private final String GemetWS_address = "https://www.eionet.europa.eu/gemet/";
private final String narrowerUri = "http://www.w3.org/2004/02/skos/core%23narrower";
private final String broaderUri = "http://www.w3.org/2004/02/skos/core%23broader";
private final String relatedUri = "http://www.w3.org/2004/02/skos/core%23related";

2
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/LCSHService.java
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@ -18,7 +18,7 @@ import javax.xml.parsers.ParserConfigurationException;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.w3c.dom.Attr;

2
api/src/main/java/edu/cornell/mannlib/semservices/util/SKOSUtils.java
View file

@ -14,7 +14,7 @@ import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/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"
+ "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> "
+ "PREFIX afn: <http://jena.apache.org/ARQ/function#> "
+ "SELECT DISTINCT ?label ?location (afn:localname(?location) AS ?localName) (COUNT(DISTINCT ?person) AS ?count) \n"
+ "WHERE { { \n"
+ " ?location rdf:type core:GeographicRegion . \n"

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java
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@ -66,7 +66,7 @@ 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.hpl.hp.com/ARQ/function#> \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"

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java
View file

@ -66,7 +66,7 @@ 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.hpl.hp.com/ARQ/function#> \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"

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java
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@ -66,7 +66,7 @@ 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.hpl.hp.com/ARQ/function#> \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"

99
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/harvester/CsvFileHarvestJob.java
View file

@ -6,18 +6,20 @@ import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.skife.csv.SimpleReader;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
/**
* An implementation of FileHarvestJob that can be used for any CSV file harvest.
*/
@ -214,75 +216,48 @@ class CsvFileHarvestJob implements FileHarvestJob {
@SuppressWarnings("rawtypes")
public String validateUpload(File file) {
try {
SimpleReader reader = new SimpleReader();
List templateCsv = reader.parse(this.templateFile);
String[] templateFirstLine = (String[])templateCsv.get(0);
//if a line ends in a comma (absolutely a comma, no whitespace), SimpleReader will not consider the part after the comma to be a blank section.
List csv = reader.parse(file);
boolean[] linesEndingInComma = getLinesEndingInComma(file);
int length = csv.size();
if(length == 0)
return "No data in file";
for(int i = 0; i < length; i++) {
String[] line = (String[])csv.get(i);
boolean endsInComma = linesEndingInComma[i];
if(i == 0) {
String errorMessage = validateCsvFirstLine(templateFirstLine, line);
if(errorMessage != null)
return errorMessage;
}
else if(line.length != 0) {
int actualLineLength = line.length + (endsInComma ? 1 : 0);
if(actualLineLength != templateFirstLine.length) {
return "Mismatch in number of entries in row " + i + ": expected " + templateFirstLine.length + ", found " + actualLineLength;
String message = "No data in file";
CSVParser cReader = new CSVParser(new FileReader(file), CSVFormat.DEFAULT);
try {
int rowNum = 0;
int numberFields = 0;
String errorMsg = "File header does not match template";
for (CSVRecord cRecord : cReader) {
rowNum++;
if (false) {
numberFields = cRecord.size();
errorMsg += "file header items: ";
for(int i = 0; i < cRecord.size(); i++) {
errorMsg += cRecord.get(i) + ", ";
}
} else {
if (cRecord.size() > 0) {
if(cRecord.size() != numberFields) {
if (errorMsg != null) {
errorMsg += "template items: ";
for(int i = 0; i < cRecord.size(); i++) {
errorMsg += cRecord.get(i) + ", ";
}
return errorMsg;
}
return "Mismatch in number of entries in row " + rowNum + ": expected " + numberFields + ", found " + cRecord.size();
}
}
message = null;
errorMsg = null;
}
}
}
return message;
} finally {
cReader.close();
}
} catch (IOException e) {
log.error(e, e);
return e.getMessage();
}
return null;
}
/**
* Makes sure that the first line of the CSV file is identical to the first line of the template file. This is
* assuming we are expecting all user CSV files to contain an initial header line. If this is not the case, then
* this method is unnecessary.
* @param templateFirstLine the parsed-out contents of the first line of the template file
* @param line the parsed-out contents of the first line of the input file
* @return an error message if the two lines don't match, or null if they do
*/
private String validateCsvFirstLine(String[] templateFirstLine, String[] line) {
String errorMessage = "File header does not match template";
if(line.length != templateFirstLine.length) {
//return errorMessage + ": " + "file header columns = " + line.length + ", template columns = " + templateFirstLine.length;
String errorMsg = "";
errorMsg += "file header items: ";
for(int i = 0; i < line.length; i++) {
errorMsg += line[i] + ", ";
}
errorMsg += "template items: ";
for(int i = 0; i < templateFirstLine.length; i++) {
errorMsg += templateFirstLine[i] + ", ";
}
return errorMsg;
}
for(int i = 0; i < line.length; i++)
{
if(!line[i].equals(templateFirstLine[i]))
return errorMessage + ": file header column " + (i + 1) + " = " + line[i] + ", template column " + (i + 1) + " = " + templateFirstLine[i];
}
return null;
}
/*
private void prepareWorkspaceDirectory() {
String path = FileHarvestController.getFileHarvestRootPath() + "workspaces/" + this.sessionId;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/visualization/ShortURLVisualizationController.java
View file

@ -9,7 +9,7 @@ import java.util.Map;
import javax.servlet.ServletContext;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -168,7 +168,7 @@ public class ShortURLVisualizationController extends FreemarkerHttpServlet {
+ matchedPatternGroups.get(1);
}
subjectURI = StringEscapeUtils.escapeHtml(subjectURI);
subjectURI = StringEscapeUtils.ESCAPE_HTML4.translate(subjectURI);
parameters.put(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY, subjectURI);
if (VisualizationFrameworkConstants.COAUTHORSHIP_VIS_SHORT_URL
@ -243,7 +243,7 @@ public class ShortURLVisualizationController extends FreemarkerHttpServlet {
List<String> matchedGroups = new ArrayList<String>();
String subURIString = vitroRequest.getRequestURI().substring(vitroRequest.getContextPath().length()+1);
String[] urlParams = StringEscapeUtils.escapeHtml(subURIString).split("/");
String[] urlParams = StringEscapeUtils.ESCAPE_HTML4.translate(subURIString).split("/");
if (urlParams.length > 1
&& urlParams[0].equalsIgnoreCase("vis")) {

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PersonHasPublicationValidator.java
View file

@ -6,7 +6,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PublicationHasAuthorValidator.java
View file

@ -8,7 +8,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.rdf.model.Literal;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAuthorsToInformationResourceGenerator.java
View file

@ -352,7 +352,7 @@ public class AddAuthorsToInformationResourceGenerator extends VivoBaseGenerator
private static String AUTHORSHIPS_MODEL = " \n"
+ "PREFIX core: <http://vivoweb.org/ontology/core#>\n"
+ "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#>\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"
@ -418,7 +418,7 @@ public class AddAuthorsToInformationResourceGenerator extends VivoBaseGenerator
private static String AUTHORSHIPS_QUERY = " \n"
+ "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
+ "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \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"

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorsToInformationResourceGenerator.java
View file

@ -315,7 +315,7 @@ public class AddEditorsToInformationResourceGenerator extends VivoBaseGenerator
private static String EDITORSHIPS_MODEL = ""
+ "PREFIX core: <http://vivoweb.org/ontology/core#>\n"
+ "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#>\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"
@ -353,7 +353,7 @@ public class AddEditorsToInformationResourceGenerator extends VivoBaseGenerator
private static String EDITORSHIPS_QUERY = ""
+ "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
+ "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \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"

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java
View file

@ -11,7 +11,7 @@ import java.util.Map;
import javax.servlet.http.HttpSession;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.vivoweb.webapp.util.ModelUtils;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java
View file

@ -13,7 +13,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java
View file

@ -12,7 +12,7 @@ import net.sf.json.JSON;
import net.sf.json.JSONArray;
import net.sf.json.JSONSerializer;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java
View file

@ -9,7 +9,7 @@ import java.util.HashMap;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java
View file

@ -9,7 +9,7 @@ import java.util.HashMap;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/ConceptSearchServlet.java
View file

@ -11,7 +11,7 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/capabilitymap/CapabilityMapRequestHandler.java
View file

@ -3,6 +3,7 @@
package edu.cornell.mannlib.vitro.webapp.visualization.capabilitymap;
import com.google.gson.Gson;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
@ -24,7 +25,6 @@ import edu.cornell.mannlib.vitro.webapp.visualization.model.ConceptPeopleMap;
import edu.cornell.mannlib.vitro.webapp.visualization.model.OrganizationPeopleMap;
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
import org.apache.axis.utils.StringUtils;
import org.apache.commons.logging.Log;
import java.util.HashMap;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java
View file

@ -22,7 +22,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java
View file

@ -8,8 +8,8 @@ import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeMap;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.query.Dataset;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryConstants.java
View file

@ -41,7 +41,7 @@ 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.hpl.hp.com/ARQ/function#");
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#");

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java
View file

@ -8,7 +8,7 @@ import java.util.Set;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.jena.iri.IRI;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java
View file

@ -17,7 +17,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.jena.iri.IRI;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java
View file

@ -6,8 +6,8 @@ import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.query.Dataset;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java
View file

@ -22,8 +22,8 @@ import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCac
import mapping.ScienceMapping;
import mapping.ScienceMappingResult;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import com.google.gson.Gson;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java
View file

@ -18,7 +18,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java
View file

@ -8,7 +8,7 @@ import java.util.Map.Entry;
import java.util.Set;
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.query.Dataset;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java
View file

@ -14,7 +14,7 @@ import org.apache.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java
View file

@ -7,8 +7,8 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.query.Dataset;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java
View file

@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.temporalgraph;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java
View file

@ -15,8 +15,8 @@ import edu.cornell.mannlib.vitro.webapp.visualization.model.OrganizationPeopleMa
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.CounterUtils;
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.OrgUtils;
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import com.google.gson.Gson;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java
View file

@ -15,8 +15,8 @@ import edu.cornell.mannlib.vitro.webapp.visualization.model.OrganizationPeopleMa
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.CounterUtils;
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.OrgUtils;
import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import com.google.gson.Gson;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/OrgUtils.java
View file

@ -2,7 +2,7 @@
package edu.cornell.mannlib.vitro.webapp.visualization.utilities;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import java.util.HashSet;
import java.util.Map;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java
View file

@ -7,7 +7,7 @@ import java.util.Map;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/ConstructedModelTracker.java
View file

@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.rdf.model.Model;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java
View file

@ -5,7 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.visutils;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.jena.iri.IRI;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java
View file

@ -12,7 +12,7 @@ import java.util.TreeMap;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.joda.time.DateTime;
import org.joda.time.format.DateTimeFormatter;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividual.java
View file

@ -2,7 +2,7 @@
package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/VIVOIndividualSearchResult.java
View file

@ -2,7 +2,7 @@
package edu.cornell.mannlib.vitro.webapp.web.templatemodels.searchresult;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/edu/cornell/mannlib/vivo/orcid/OrcidContextSetup.java
View file

@ -21,7 +21,7 @@ import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

2
api/src/main/java/org/vivoweb/webapp/sitemap/SiteMapServlet.java
View file

@ -2,6 +2,7 @@
package org.vivoweb.webapp.sitemap;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.query.QuerySolution;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -9,7 +10,6 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import org.apache.axis.utils.StringUtils;
import org.apache.commons.io.IOUtils;
import javax.servlet.ServletException;

2
api/src/main/java/org/vivoweb/webapp/startup/JSONWrapperSetup.java
View file

@ -11,7 +11,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.individuallist.IndividualJson
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONException;

2
home/src/main/resources/rdf/abox/firsttime/geopolitical.ver1.1-11-18-11-individual-labels.rdf
View file

@ -13,7 +13,7 @@
xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:j.2="http://www.w3.org/2008/05/skos#"
xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
xmlns:afn="http://jena.apache.org/ARQ/function#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:j.3="http://www.w3.org/2003/06/sw-vocab-status/ns#"

2
home/src/main/resources/rdf/display/everytime/vivoQrCodeDataGetter.n3
View file

@ -6,7 +6,7 @@
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix core: <http://vivoweb.org/ontology/core#> .
@prefix vivoweb: <http://vivoweb.org/ontology#> .
@prefix afn: <http://jena.hpl.hp.com/ARQ/function#> .
@prefix afn: <http://jena.apache.org/ARQ/function#> .
#### Check to see if the person being viewed has a first and last name. ####

2
home/src/main/resources/rdf/tbox/filegraph/appControls-temp.n3
View file

@ -1,5 +1,5 @@
@prefix hr: <http://vivo.cornell.edu/ns/hr/0.9/hr.owl#> .
@prefix afn: <http://jena.hpl.hp.com/ARQ/function#> .
@prefix afn: <http://jena.apache.org/ARQ/function#> .
@prefix : <http://vivoweb.org/ontology/activity-insight#> .
@prefix scires: <http://vivoweb.org/ontology/scientific-research#> .
@prefix aka: <http://vivoweb.org/ontology/aka#> .

2
home/src/main/resources/rdf/tbox/filegraph/dataDomains.rdf
View file

@ -9,7 +9,7 @@
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
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:afn="http://jena.apache.org/ARQ/function#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:scires="http://vivoweb.org/ontology/scientific-research#"

2
home/src/main/resources/rdf/tbox/filegraph/objectDomains.rdf
View file

@ -9,7 +9,7 @@
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
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:afn="http://jena.apache.org/ARQ/function#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:scires="http://vivoweb.org/ontology/scientific-research#"

2
home/src/main/resources/rdf/tbox/filegraph/objectRanges.rdf
View file

@ -9,7 +9,7 @@
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
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:afn="http://jena.apache.org/ARQ/function#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:scires="http://vivoweb.org/ontology/scientific-research#"

2
home/src/main/resources/rdf/tbox/filegraph/personTypes.n3
View file

@ -1,4 +1,4 @@
@prefix afn: <http://jena.hpl.hp.com/ARQ/function#> .
@prefix afn: <http://jena.apache.org/ARQ/function#> .
@prefix : <http://purl.obolibrary.org/obo/arg/app-views/vivo/vivo-app.owl#> .
@prefix hr: <http://vivo.cornell.edu/ns/hr/0.9/hr.owl#> .
@prefix ns: <http://www.w3.org/2003/06/sw-vocab-status/ns#> .

2
home/src/main/resources/rdf/tbox/filegraph/relationshipAxioms.n3
View file

@ -1,5 +1,5 @@
@prefix hr: <http://vivo.cornell.edu/ns/hr/0.9/hr.owl#> .
@prefix afn: <http://jena.hpl.hp.com/ARQ/function#> .
@prefix afn: <http://jena.apache.org/ARQ/function#> .
@prefix : <http://vivoweb.org/ontology/activity-insight#> .
@prefix scires: <http://vivoweb.org/ontology/scientific-research#> .
@prefix aka: <http://vivoweb.org/ontology/aka#> .

4
installer/pom.xml
View file

@ -21,8 +21,8 @@
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.7</source>
<target>1.7</target>
<source>1.8</source>
<target>1.8</target>
<encoding>UTF-8</encoding>
</configuration>
</plugin>

2
installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties
View file

@ -46,4 +46,4 @@ log4j.logger.org.apache.jena.sdb.layout2.LoaderTuplesNodes=FATAL
log4j.logger.org.apache.jena.sdb.sql.SDBConnection=ERROR
log4j.logger.org.openjena.riot=FATAL
log4j.logger.org.apache.jena.riot=FATAL
log4j.logger.org.directwebremoting=FATAL
log4j.logger.org.directwebremoting=WARN

4
pom.xml
View file

@ -230,8 +230,8 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.7</source>
<target>1.7</target>
<source>1.8</source>
<target>1.8</target>
<encoding>UTF-8</encoding>
</configuration>
</plugin>

2
selenium/src/test/java/org/vivoweb/vivo/selenium/WebAppTester.java
View file

@ -1,7 +1,7 @@
package org.vivoweb.vivo.selenium;
import com.sun.tools.internal.xjc.Driver;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang33.StringUtils;
import org.junit.Assert;
import org.openqa.selenium.Alert;
import org.openqa.selenium.By;

2
webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/geopolitical-ver1.1-11-18-11-annotations.rdf
View file

@ -12,7 +12,7 @@
xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:j.2="http://www.w3.org/2008/05/skos#"
xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
xmlns:afn="http://jena.apache.org/ARQ/function#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:j.3="http://www.w3.org/2003/06/sw-vocab-status/ns#"

2
webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/isDefinedBy-1.5-annotations.rdf
View file

@ -13,7 +13,7 @@
xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:j.2="http://www.w3.org/2008/05/skos#"
xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
xmlns:afn="http://jena.apache.org/ARQ/function#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:j.3="http://www.w3.org/2003/06/sw-vocab-status/ns#"

2
webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/scires-1.5-annotations.rdf
View file

@ -13,7 +13,7 @@
xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:skos="http://www.w3.org/2008/05/skos#"
xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
xmlns:afn="http://jena.apache.org/ARQ/function#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#"

2
webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/vivo-core-1.5-annotations.rdf
View file

@ -13,7 +13,7 @@
xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:skos="http://www.w3.org/2008/05/skos#"
xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
xmlns:afn="http://jena.apache.org/ARQ/function#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#"

2
webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/isDefinedBy-1.5.owl
View file

@ -11,7 +11,7 @@
xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
xmlns:skos="http://www.w3.org/2008/05/skos#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
xmlns:afn="http://jena.apache.org/ARQ/function#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#"

2
webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/scires-1.5.owl
View file

@ -8,7 +8,7 @@
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:afn="http://jena.apache.org/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/"

2
webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/vivo-core-1.5.owl
View file

@ -8,7 +8,7 @@
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:afn="http://jena.apache.org/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/"

13
webapp/src/main/webapp/WEB-INF/web.xml
View file

@ -1060,7 +1060,7 @@
<servlet>
<servlet-name>dwr-invoker</servlet-name>
<servlet-class>uk.ltd.getahead.dwr.DWRServlet</servlet-class>
<servlet-class>org.directwebremoting.servlet.DwrServlet</servlet-class>
<init-param>
<param-name>debug</param-name>
<param-value>true</param-value>
@ -1475,6 +1475,17 @@
<url-pattern>/orcid/*</url-pattern>
</servlet-mapping>
<servlet>
<display-name>TpfServlet</display-name>
<servlet-name>TpfServlet</servlet-name>
<servlet-class>org.vivoweb.linkeddatafragments.servlet.VitroLinkedDataFragmentServlet</servlet-class>
</servlet>
<servlet-mapping>
<servlet-name>TpfServlet</servlet-name>
<url-pattern>/tpf/*</url-pattern>
</servlet-mapping>
<!-- ==================== mime types ============================== -->
<mime-mapping>

2
webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml
View file

@ -6,7 +6,7 @@
<list-view-config>
<query-select>
PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&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;

2
webapp/src/main/webapp/config/listViewConfig-advisorIn.xml
View file

@ -6,7 +6,7 @@
<list-view-config>
<query-select>
PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&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;

2
webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml
View file

@ -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.hpl.hp.com/ARQ/function#&gt;
PREFIX afn: &lt;http://jena.apache.org/ARQ/function#&gt;
SELECT DISTINCT ?dateTimeInterval ?label
?valueStart ?valueStartName

2
webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml
View file

@ -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.hpl.hp.com/ARQ/function#&gt;
PREFIX afn: &lt;http://jena.apache.org/ARQ/function#&gt;
SELECT DISTINCT ?dateTimeValue
(afn:localname(?dateTimePrecision) AS ?precision)

2
webapp/src/main/webapp/config/listViewConfig-default.xml
View file

@ -7,7 +7,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml
View file

@ -7,7 +7,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml
View file

@ -8,7 +8,7 @@
PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
PREFIX vivo: &lt;http://vivoweb.org/ontology/core#&gt;
PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
PREFIX afn: &lt;http://jena.apache.org/ARQ/function#&gt;
SELECT ?concept ?conceptLabel ?conceptName ?vocabularySource ?vocabularySourceName
WHERE {

2
webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml
View file

@ -5,7 +5,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml
View file

@ -5,7 +5,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml
View file

@ -5,7 +5,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml
View file

@ -5,7 +5,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml
View file

@ -8,7 +8,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-hasPrincipalInvestigatorRole.xml
View file

@ -5,7 +5,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-hasReviewerRole.xml
View file

@ -5,7 +5,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-issuedCredential.xml
View file

@ -6,7 +6,7 @@
<list-view-config>
<query-select>
PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt;
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&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;

2
webapp/src/main/webapp/config/listViewConfig-rangeUnion.xml
View file

@ -7,7 +7,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

2
webapp/src/main/webapp/config/listViewConfig-relatedRole.xml
View file

@ -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.hpl.hp.com/ARQ/function#&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;

2
webapp/src/main/webapp/config/listViewConfig-webpage.xml
View file

@ -7,7 +7,7 @@
<list-view-config>
<query-select>
PREFIX afn: &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
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;

10
webapp/src/main/webapp/js/individual/individualQtipBubble.js
View file

@ -7,11 +7,6 @@ $(document).ready(function(){
$.extend(this, i18nStrings);
$('head').append('<style id="researchAreaCSS">.qtip { font-size: 14px; max-width: none !important; } .researchAreaTip { background: url(' + imagesPath + '/individual/researchAreaBubble.png) no-repeat; } </style>');
padding: '0em',
// textAlign: 'center',
// fontSize: '0.7em',
// lineHeight: '15px',
// border: 'none',
$('#researchAreaIcon').each(function()
{
@ -38,11 +33,6 @@ $(document).ready(function(){
});
$('head').append('<style id="bubbleCSS">.qtip { font-size: 14px; max-width: none !important; } .bubbleTip { url(' + imagesPath + '/individual/toolTipBubble.png) no-repeat; } </style>');
// padding: '0em',
// textAlign: 'center',
// fontSize: '0.7em',
// lineHeight: '15px',
// border: 'none',
$('#fullViewIcon').each(function()
{