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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 2016-12-14 11:19:58 -05:00
commit 67f771fecf
287 changed files with 21445 additions and 23879 deletions
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5
api/pom.xml
View file

@ -7,13 +7,13 @@
<groupId>org.vivoweb</groupId>
<artifactId>vivo-api</artifactId>
<version>1.9.0-SNAPSHOT</version>
<version>1.10.0-SNAPSHOT</version>
<packaging>jar</packaging>
<parent>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-project</artifactId>
<version>1.9.0-SNAPSHOT</version>
<version>1.10.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
@ -27,7 +27,6 @@
<dependency>
<groupId>org.vivoweb</groupId>
<artifactId>vitro-dependencies</artifactId>
<version>1.9.0-SNAPSHOT</version>
<type>pom</type>
</dependency>

3
api/src/main/java/edu/cornell/mannlib/semservices/bo/BaseObject.java
View file

@ -5,9 +5,6 @@ public class BaseObject {
/**
* Simple JavaBean domain object with an id property.
* Used as a base class for objects needing this property.
*
* @author Ken Krebs
* @author Juergen Hoeller
*/
private Integer id;

6
api/src/main/java/edu/cornell/mannlib/semservices/bo/SemanticServicesError.java
View file

@ -17,9 +17,9 @@ public class SemanticServicesError {
/**
* @param exception
* @param message
* @param severity
* @param exception Exception description
* @param message Error message
* @param severity Severity
*/
public SemanticServicesError(String exception, String message, String severity) {
super();

9
api/src/main/java/edu/cornell/mannlib/semservices/service/ExternalConceptService.java
View file

@ -9,21 +9,18 @@ import edu.cornell.mannlib.semservices.bo.Concept;
public interface ExternalConceptService {
/**
* @param term
* @return
* @param term Term
*/
List<Concept> processResults(String term) throws Exception;
/**
* @param term
* @return
* @param term Term
* @throws Exception
*/
List<Concept> getConcepts(String term) throws Exception;
/**
* @param uri
* @return
* @param uri URI
*/
List<Concept> getConceptsByURIWithSparql(String uri) throws Exception;

24
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java
View file

@ -37,15 +37,15 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import edu.cornell.mannlib.semservices.bo.Concept;
import edu.cornell.mannlib.semservices.service.ExternalConceptService;
@ -481,8 +481,7 @@ public class AgrovocService implements ExternalConceptService {
}
/**
* @param uri
* @return
* @param uri The URI
*/
protected String stripConceptId(String uri) {
String conceptId = new String();
@ -492,8 +491,7 @@ public class AgrovocService implements ExternalConceptService {
}
/**
* @param str
* @return
* @param str The String
*/
protected String extractConceptId(String str) {
try {

30
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/GemetService.java
View file

@ -75,8 +75,7 @@ public class GemetService implements ExternalConceptService {
}
/**
* @param results
* @return
* @param results Results to process
*/
private List<Concept> processOutput(String results) throws Exception {
@ -145,9 +144,8 @@ public class GemetService implements ExternalConceptService {
/**
* Get a string from a json object or an empty string if there is no value for the given key
* @param obj
* @param key
* @return
* @param obj JSON Object
* @param key Key to retrieve
*/
protected String getJsonValue(JSONObject obj, String key) {
if (obj.has(key)) {
@ -159,8 +157,7 @@ public class GemetService implements ExternalConceptService {
/**
* @param concept_uri
* @return
* @param concept_uri Concept URI
* @throws Exception
*/
protected String getAvailableLangs(String concept_uri) throws Exception {
@ -177,8 +174,7 @@ public class GemetService implements ExternalConceptService {
}
/**
* @param concept_uri
* @return
* @param concept_uri concept URI
* @throws Exception
*/
protected String getConcept(String concept_uri) throws Exception {
@ -196,9 +192,8 @@ public class GemetService implements ExternalConceptService {
}
/**
* @param concept_uri
* @param property
* @return
* @param concept_uri Concept URI
* @param property Property
* @throws Exception
*/
protected String getAllTranslationsForConcept(String concept_uri, String property) throws Exception {
@ -235,9 +230,8 @@ public class GemetService implements ExternalConceptService {
/**
* @param concept_uri
* @param relation
* @return
* @param concept_uri Concept URI
* @param relation Relations
* @throws Exception
*/
protected String getRelatedConcepts(String concept_uri, String relation) throws Exception {
@ -266,8 +260,7 @@ public class GemetService implements ExternalConceptService {
/**
* @param keyword
* @return
* @param keyword Keyword
* @throws Exception
*/
protected String getConceptsMatchingKeyword(String keyword) throws Exception {
@ -288,8 +281,7 @@ public class GemetService implements ExternalConceptService {
}
/**
* @param url
* @return
* @param url URI
*/
protected String getGemetResults(String url) throws Exception {
String results = new String();

58
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/LCSHService.java
View file

@ -49,7 +49,7 @@ public class LCSHService implements ExternalConceptService {
String results = null;
String dataUrl = baseUri + "?q=" + URLEncoder.encode(term, "UTF-8")
+ "&q=cs%3Ahttp%3A%2F%2Fid.loc.gov%2Fauthorities%2Fsubjects"
+ "&format=XML";
+ "&format=atom";
log.debug("dataURL " + dataUrl);
try {
@ -81,7 +81,7 @@ public class LCSHService implements ExternalConceptService {
return conceptList;
}
// Results are in json format (atom) - atom entries need to be extracted
// Results are in XML format (atom) - atom entries need to be extracted
// retrieve the URIs and get the SKOS version of the entry, getting broader
// and narrower terms as applicable as well as any description (skos:note)
// that might exist
@ -99,7 +99,7 @@ public class LCSHService implements ExternalConceptService {
//This is the URL for retrieving the concept - the pattern is http://id.loc.gov/authorities/subjects/sh85014203.skos.rdf
//This is not the URI itself which would be http://id.loc.gov/authorities/subjects/sh85014203
String conceptURLString = getSKOSURL(uri);
String baseConceptURI = getConceptURI(uri);
String baseConceptURI = uri;
URL conceptURL = null;
try {
conceptURL = new URL(conceptURLString);
@ -154,23 +154,12 @@ public class LCSHService implements ExternalConceptService {
private String getSKOSURL(String uri) {
// Strip .xml at the end and replace with .skos.rdf
String skosURI = uri;
if (uri.endsWith(".xml")) {
skosURI = uri.substring(0, uri.length() - 4);
skosURI += skosSuffix;
}
return hostUri + skosURI;
String skosURI = uri + skosSuffix;
return skosURI;
}
//Given the URI from the xml, get just the base URI
private String getConceptURI(String uri) {
String skosURI = uri;
if (uri.endsWith(".xml")) {
skosURI = uri.substring(0, uri.length() - 4);
}
return hostUri + skosURI;
}
public List<String> getConceptURISFromJSON(String results) {
List<String> uris = new ArrayList<String>();
@ -192,14 +181,25 @@ public class LCSHService implements ExternalConceptService {
String conceptUri = new String();
try {
Document doc = XMLUtils.parse(rdf);
NodeList nodes = doc.getElementsByTagName("search:result");
NodeList nodes = doc.getElementsByTagName("entry");
int len = nodes.getLength();
int i;
int i, j;
for (i = 0; i < len; i++) {
Node node = nodes.item(i);
NamedNodeMap attrs = node.getAttributes();
Attr idAttr = (Attr) attrs.getNamedItem("uri");
conceptUri = idAttr.getTextContent();
NodeList childNodes = node.getChildNodes();
for(j = 0; j < childNodes.getLength(); j++) {
Node childNode = childNodes.item(j);
if(childNode.getNodeName().equals("link")) {
NamedNodeMap attrs = childNode.getAttributes();
Attr hrefAttr = (Attr) attrs.getNamedItem("href");
//if type doesn't exist, this is the direct URL without extension
if((hrefAttr != null) && ((Attr)attrs.getNamedItem("type") == null)) {
conceptUri = hrefAttr.getTextContent();
}
}
}
log.debug("concept uri is " + conceptUri);
uris.add(conceptUri);
}
@ -221,8 +221,7 @@ public class LCSHService implements ExternalConceptService {
}
/**
* @param uri
* @return
* @param uri URI
*/
protected String stripConceptId(String uri) {
String conceptId = new String();
@ -232,8 +231,7 @@ public class LCSHService implements ExternalConceptService {
}
/**
* @param str
* @return
* @param str String with concept id
*/
protected String extractConceptId(String str) {
try {
@ -251,11 +249,5 @@ public class LCSHService implements ExternalConceptService {
return null;
}
}

11
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/UMLSService.java
View file

@ -97,8 +97,7 @@ public class UMLSService implements ExternalConceptService {
}
/**
* @param uri
* @return
* @param uri URI
*/
public List<Concept> getConceptsByURIWithSparql(String uri)
throws Exception {
@ -108,8 +107,7 @@ public class UMLSService implements ExternalConceptService {
}
/**
* @param results
* @return
* @param results Results to process
*/
private List<Concept> processOutput(String results) throws Exception {
@ -193,9 +191,8 @@ public class UMLSService implements ExternalConceptService {
/**
* Get a string from a json object or an empty string if there is no value for the given key
* @param obj
* @param key
* @return
* @param obj JSON Object
* @param key Key to retrieve
*/
protected String getJsonValue(JSONObject obj, String key) {
if (obj.has(key)) {

14
api/src/main/java/edu/cornell/mannlib/semservices/util/SKOSUtils.java
View file

@ -18,13 +18,13 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.NodeIterator;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.semservices.bo.Concept;

28
api/src/main/java/edu/cornell/mannlib/semservices/util/XMLUtils.java
View file

@ -50,7 +50,6 @@ public class XMLUtils {
/**
* @return
* @throws ParserConfigurationException
*/
public static DocumentBuilder getDocumentBuilder()
@ -68,8 +67,7 @@ public class XMLUtils {
}
/**
* @param xmlString
* @return
* @param xmlString XML String
* @throws IOException
* @throws SAXException
* @throws ParserConfigurationException
@ -82,8 +80,7 @@ public class XMLUtils {
}
/**
* @param stream
* @return
* @param stream Input stream
* @throws IOException
* @throws SAXException
* @throws ParserConfigurationException
@ -94,9 +91,8 @@ public class XMLUtils {
}
/**
* @param document
* @param name
* @return
* @param document DOM Document
* @param name Name
*/
public static String getElementByName(Document document, String name) {
NodeList nodes = document.getElementsByTagName(name);
@ -109,7 +105,7 @@ public class XMLUtils {
}
/**
* @param doc
* @param doc DOM Document
* @throws IOException
*/
@SuppressWarnings("deprecation")
@ -130,7 +126,7 @@ public class XMLUtils {
}
/**
* @param xml
* @param xml XML String
*/
public static void prettyPrint(String xml) {
Source xmlInput = new StreamSource(new StringReader(xml));
@ -160,7 +156,7 @@ public class XMLUtils {
}
/**
* @param xml
* @param xml XML String
*/
public static String prettyPrintToString(String xml) {
Source xmlInput = new StreamSource(new StringReader(xml));
@ -190,7 +186,7 @@ public class XMLUtils {
}
/**
* @param node
* @param node DOM Node
*/
public static void displayNodeInfo(Node node) {
switch (node.getNodeType()) {
@ -222,7 +218,7 @@ public class XMLUtils {
}
/**
* @param node
* @param node DOM Node
* @throws IOException
*/
public static void serializeNode(Node node) throws IOException {
@ -308,7 +304,7 @@ public class XMLUtils {
}
/**
* @param s
* @param s String
* @throws IOException
*/
private static void print(String s) throws IOException {
@ -336,8 +332,8 @@ public class XMLUtils {
}
/**
* @param doc (either a Document or a Node)
* @param expression
* @param obj (either a Document or a Node)
* @param expression Expression
* @return string contents
*/
public static Node getNodeWithXpath(Object obj, String expression) {

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ExportQrCodeController.java
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@ -11,8 +11,8 @@ import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.Individual
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusMapLocations.java
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@ -16,9 +16,9 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONException;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusResearcherCount.java
View file

@ -16,9 +16,9 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONException;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/QrCodeDetails.java
View file

@ -13,8 +13,8 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONException;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

12
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/InstitutionalInternalClassController.java
View file

@ -12,12 +12,12 @@ import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.rdf.model.StmtIterator;
import org.apache.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java
View file

@ -10,9 +10,9 @@ import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java
View file

@ -10,9 +10,9 @@ import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java
View file

@ -10,9 +10,9 @@ import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;

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

@ -12,9 +12,9 @@ import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

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

@ -12,9 +12,9 @@ import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

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

@ -13,9 +13,9 @@ import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

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

@ -7,9 +7,9 @@ import javax.servlet.ServletContext;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

3
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/visualization/VisualizationsDependencyInjector.java
View file

@ -19,8 +19,7 @@ public class VisualizationsDependencyInjector {
* This method is used to inject vis dependencies i.e. the vis algorithms that are
* being implemented into the vis controller. Modified Dependency Injection pattern is
* used here. XML file containing the location of all the vis is saved in accessible folder.
* @param servletContext
* @return
* @param servletContext Servlet context
*/
private synchronized static Map<String, VisualizationRequestHandler> initVisualizations(
ServletContext servletContext) {

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

@ -6,7 +6,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import com.hp.hpl.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.N3ValidatorVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;

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

@ -6,7 +6,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import com.hp.hpl.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.N3ValidatorVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;

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

@ -10,7 +10,7 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.N3ValidatorVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;

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

@ -10,7 +10,7 @@ import java.util.Map;
import org.apache.commons.lang.StringUtils;
import com.hp.hpl.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.N3ValidatorVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;

26
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java
View file

@ -16,19 +16,19 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;

20
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAuthorsToInformationResourceGenerator.java
View file

@ -12,20 +12,20 @@ import java.util.Map.Entry;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyComparator;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;

14
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditWebpageFormGenerator.java
View file

@ -10,13 +10,13 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

20
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorsToInformationResourceGenerator.java
View file

@ -12,20 +12,20 @@ import java.util.Map.Entry;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyComparator;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;

16
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorshipToPersonGenerator.java
View file

@ -8,14 +8,14 @@ import java.util.List;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.sparql.resultset.ResultSetMem;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

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

@ -14,7 +14,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

16
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddGrantRoleToPersonGenerator.java
View file

@ -14,11 +14,11 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.vivoweb.webapp.util.ModelUtils;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -556,9 +556,9 @@ public class AddGrantRoleToPersonGenerator implements EditConfigurationGenerator
/**
* Prepare edit configuration for update
* @param vreq
* @param session
* @param editConfiguration
* @param vreq - current VitroRequest
* @param session - the HTTP session
* @param editConfiguration - Edit configuration
*/
private void prepareForUpdate(VitroRequest vreq, HttpSession session, EditConfigurationVTwo editConfiguration) {

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

@ -14,7 +14,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -6,7 +6,7 @@ import java.util.Arrays;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

18
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddPublicationToPersonGenerator.java
View file

@ -9,15 +9,15 @@ import java.util.Map;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.sparql.resultset.ResultSetMem;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

8
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java
View file

@ -16,9 +16,9 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.vivoweb.webapp.util.ModelUtils;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -436,7 +436,6 @@ public abstract class AddRoleToPersonTwoStageGenerator extends BaseEditConfigura
/**
* Utility method for subclasses to make a query for type from a ChildVClassesOptions object.
* @throws Exception
*/
protected String getActivityTypeQueryForChildVClassOptions(VitroRequest vreq, ChildVClassesOptions opts){
log.debug("objectClassUri = " + opts.getClassUri());
@ -447,7 +446,6 @@ public abstract class AddRoleToPersonTwoStageGenerator extends BaseEditConfigura
/**
* Utility method for subclasses to make a query for type from a IndividualsViaClassGroupOptions object.
* @throws Exception
*/
protected String getActivityTypeQueryForIndividualsViaClassGroupOptions(VitroRequest vreq, IndividualsViaClassGroupOptions opts){
log.debug("ClassGroupUri = " + opts.getClassGroupUri());

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

@ -13,8 +13,8 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;

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

@ -8,7 +8,7 @@ import java.util.Map;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -8,7 +8,7 @@ import java.util.List;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

8
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForPersonGenerator.java
View file

@ -21,9 +21,9 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AddDataPropertyStatement;
@ -556,6 +556,6 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
}
}
private String N3_PREFIX = "@prefix foaf:<http://xmlns.com/foaf/0.1/> .\n";
private String N3_PREFIX = "@prefix foaf: <http://xmlns.com/foaf/0.1/> .\n";
}

14
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageWebpagesForIndividualGenerator.java
View file

@ -7,17 +7,17 @@ import java.util.Map;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

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

@ -8,7 +8,7 @@ import java.util.Map;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -8,7 +8,7 @@ import java.util.List;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -5,7 +5,7 @@ import java.util.Arrays;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -7,7 +7,7 @@ import java.util.HashMap;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -7,7 +7,7 @@ import java.util.HashMap;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -6,7 +6,7 @@ import java.util.Arrays;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -8,7 +8,7 @@ import java.util.List;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -14,7 +14,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -8,7 +8,7 @@ import java.util.Map;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -9,7 +9,7 @@ import java.util.List;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/PersonHasPreferredTitleGenerator.java
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@ -14,7 +14,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -8,7 +8,7 @@ import java.util.List;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -14,7 +14,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

8
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java
View file

@ -15,11 +15,11 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.commons.lang.StringUtils;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

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

@ -35,11 +35,11 @@ public class VIVODefaultAddMissingIndividualFormGenerator extends DefaultAddMiss
protected List<String> getN3Prefixes() {
List<String> prefixStrings = super.getN3Prefixes();
prefixStrings.add("@prefix vcard:<http://www.w3.org/2006/vcard/ns#> .");
prefixStrings.add("@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .");
return prefixStrings;
}
private String getN3ForName() {
protected String getN3ForName() {
return "?" + objectVarName + " rdfs:label ?label .";
}

12
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/VIVONewIndividualFormGenerator.java
View file

@ -9,9 +9,9 @@ import java.util.List;
import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -43,7 +43,7 @@ public class VIVONewIndividualFormGenerator extends BaseEditConfigurationGenerat
//Person uses first name and last name whereas individual of other class would use label
//middle name is also optional
config.setN3Optional(list(
N3_PREFIX + "@prefix vcard:<http://www.w3.org/2006/vcard/ns#> .\n"
N3_PREFIX + "@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .\n"
+ " ?newInd <http://purl.obolibrary.org/obo/ARG_2000028> ?newVcardInd . \n"
+ " ?newVcardInd <http://purl.obolibrary.org/obo/ARG_2000029> ?newInd . \n"
+ " ?newVcardInd a vcard:Individual . \n"
@ -52,7 +52,7 @@ public class VIVONewIndividualFormGenerator extends BaseEditConfigurationGenerat
+ " ?newVcardName vcard:givenName ?firstName . \n"
+ " ?newVcardName vcard:familyName ?lastName . \n",
N3_PREFIX + " ?newInd <" + RDFS.label.getURI() + "> ?label .",
N3_PREFIX + "@prefix vcard:<http://www.w3.org/2006/vcard/ns#> .\n"
N3_PREFIX + "@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .\n"
+ " ?newInd <http://purl.obolibrary.org/obo/ARG_2000028> ?newVcardInd . \n"
+ " ?newVcardInd a vcard:Individual . \n"
+ " ?newVcardInd vcard:hasName ?newVcardName . \n"
@ -204,5 +204,5 @@ public class VIVONewIndividualFormGenerator extends BaseEditConfigurationGenerat
editConfiguration.setLiteralsInScope(new HashMap<String, List<Literal>>());
}
private String N3_PREFIX = "@prefix foaf:<http://xmlns.com/foaf/0.1/> .\n";
private String N3_PREFIX = "@prefix foaf: <http://xmlns.com/foaf/0.1/> .\n";
}

26
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java
View file

@ -16,19 +16,19 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.vocabulary.OWL;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;

22
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/ConceptSemanticTypesPreprocessor.java
View file

@ -7,17 +7,17 @@ import javax.servlet.http.HttpServletRequest;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.shared.Lock;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;

14
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/ManageLabelsForPersonPreprocessor.java
View file

@ -9,13 +9,13 @@ import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.ResIterator;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.rdf.model.ResIterator;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.Statement;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;

28
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java
View file

@ -13,20 +13,20 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.shared.Lock;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.vocabulary.XSD;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

28
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java
View file

@ -13,20 +13,20 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.vocabulary.XSD;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.shared.Lock;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.vocabulary.XSD;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

20
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessInternalClassDataGetterN3.java
View file

@ -12,16 +12,16 @@ import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;

28
api/src/main/java/edu/cornell/mannlib/vitro/webapp/searchindex/documentBuilding/CalculateParameters.java
View file

@ -11,20 +11,20 @@ import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.DatasetFactory;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.shared.Lock;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.DatasetFactory;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.QuerySolutionMap;
import org.apache.jena.query.ResultSet;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ContextModelAccess;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/searchindex/extensions/LabelsAcrossContextNodes.java
View file

@ -16,9 +16,9 @@ import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.vocabulary.RDFS;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;

24
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/InternalClassesDataGetter.java
View file

@ -12,18 +12,18 @@ import javax.servlet.ServletContext;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.QuerySolutionMap;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;

10
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/menuManagement/ProcessInternalClasses.java
View file

@ -7,11 +7,11 @@ import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.vocabulary.RDF;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;

8
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/menuManagement/VIVOMenuManagementDataUtils.java
View file

@ -11,10 +11,10 @@ import javax.servlet.ServletContext;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;

22
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/capabilitymap/CapabilityMapRequestHandler.java
View file

@ -3,13 +3,13 @@
package edu.cornell.mannlib.vitro.webapp.visualization.capabilitymap;
import com.google.gson.Gson;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
@ -50,10 +50,10 @@ public class CapabilityMapRequestHandler implements VisualizationRequestHandler
@Override
public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log, Dataset dataSource) throws MalformedQueryParametersException {
ConceptLabelMap conceptLabelMap = VisualizationCaches.conceptToLabel.get(vitroRequest.getRDFService());
ConceptPeopleMap conceptPeopleMap = VisualizationCaches.conceptToPeopleMap.get(vitroRequest.getRDFService());
OrganizationPeopleMap organizationPeopleMap = VisualizationCaches.organisationToPeopleMap.get(vitroRequest.getRDFService());
Map<String, String> organizationLabels = VisualizationCaches.organizationLabels.get(vitroRequest.getRDFService());
ConceptLabelMap conceptLabelMap = VisualizationCaches.conceptToLabel.getNoWait(vitroRequest.getRDFService());
ConceptPeopleMap conceptPeopleMap = VisualizationCaches.conceptToPeopleMap.getNoWait(vitroRequest.getRDFService());
OrganizationPeopleMap organizationPeopleMap = VisualizationCaches.organisationToPeopleMap.getNoWait(vitroRequest.getRDFService());
Map<String, String> organizationLabels = VisualizationCaches.organizationLabels.getNoWait(vitroRequest.getRDFService());
String data = vitroRequest.getParameter("data");
if (!StringUtils.isEmpty(data)) {

14
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java
View file

@ -12,10 +12,10 @@ import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
@ -28,9 +28,9 @@ import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;
import org.apache.jena.iri.Violation;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CoAuthorshipData;
import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CollaboratorComparator;

11
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java
View file

@ -12,7 +12,7 @@ import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -177,8 +177,7 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
/**
* Provides response when a csv file containing number & names of unique co-authors per
* year is requested.
* @param authorNodesAndEdges
* @param response
* @param authorNodesAndEdges Author nodes and edges
*/
private Map<String, String> prepareCoauthorsCountPerYearDataResponse(
CollaborationData authorNodesAndEdges) {
@ -214,8 +213,7 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
/**
* Provides response when a csv file containing number & names of unique co-authors per
* year is requested.
* @param authorNodesAndEdges
* @param response
* @param coAuthorshipData Co authorship data
*/
private Map<String, String> prepareCoauthorsListDataResponse(
CollaborationData coAuthorshipData) {
@ -246,8 +244,7 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
/**
* Provides a response when graphml formatted co-authorship network is requested, typically by
* the flash vis.
* @param authorNodesAndEdges
* @param response
* @param authorNodesAndEdges Author nodes and edges
*/
private Map<String, String> prepareNetworkStreamDataResponse(
CollaborationData authorNodesAndEdges) {

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

@ -62,8 +62,8 @@ public class CoAuthorshipVisCodeGenerator {
/**
* This method is used to setup parameters for the sparkline value object. These parameters
* will be used in the template to construct the actual html/javascript code.
* @param visMode
* @param visContainer
* @param visMode Visualization mode
* @param providedVisContainerID Container ID
*/
private SparklineData setupSparklineParameters(String visMode,
String providedVisContainerID) {

16
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java
View file

@ -15,14 +15,14 @@ import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;
import org.apache.jena.iri.Violation;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java
View file

@ -24,9 +24,9 @@ import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;
import org.apache.jena.iri.Violation;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CoInvestigationData;
import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CollaborationData;

13
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java
View file

@ -10,8 +10,8 @@ import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.query.Dataset;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -174,8 +174,7 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
/**
* Provides response when a csv file containing number & names of unique co-pis per
* year is requested.
* @param piNodesAndEdges
* @param response
* @param piNodesAndEdges PI nodes and edges
*/
private Map<String, String> prepareCoPIsCountPerYearDataResponse(
CollaborationData piNodesAndEdges) {
@ -211,8 +210,7 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
/**
* Provides response when a csv file containing number & names of unique co-pis per
* year is requested.
* @param coPIData
* @param response
* @param coPIData Co Principal Investigator Data
*/
private Map<String, String> prepareCoPIsListDataResponse(CollaborationData coPIData) {
@ -242,8 +240,7 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
/**
* Provides a response when graphml formatted co-pi network is requested, typically by
* the flash vis.
* @param coPIData
* @param response
* @param coPIData Co Investigator data
*/
private Map<String, String> prepareNetworkStreamDataResponse(CollaborationData coPIData) {

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

@ -69,8 +69,8 @@ public class CoPIVisCodeGenerator {
/**
* This method is used to setup parameters for the sparkline value object. These parameters
* will be used in the template to construct the actual html/javascript code.
* @param visMode
* @param visContainer
* @param visMode Visualization mode
* @param providedVisContainerID Container ID
*/
private SparklineData setupSparklineParameters(String visMode,
String providedVisContainerID) {

15
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java
View file

@ -9,8 +9,9 @@ import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import com.hp.hpl.jena.query.QuerySolution;
import org.apache.jena.query.QuerySolution;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
@ -26,7 +27,7 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.google.gson.Gson;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -450,7 +451,15 @@ public class MapOfScienceVisualizationRequestHandler implements VisualizationReq
body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory().getDefaultNamespace());
ConfigurationProperties properties = ConfigurationProperties.getBean(vreq);
if (properties != null) {
String key = properties.getProperty("google.maps.key");
if (!StringUtils.isEmpty(key)) {
body.put("googleMapsKey", key);
}
}
return new TemplateResponseValues(standaloneTemplate, body);
}

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/ModelConstructorRequestHandler.java
View file

@ -13,7 +13,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCac
import org.apache.commons.logging.Log;
import com.google.gson.Gson;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/ModelConstructorUtilities.java
View file

@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor;
import java.util.HashMap;
import java.util.Map;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/PersonToGrantsModelConstructor.java
View file

@ -8,9 +8,9 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/factory/ModelFactoryInterface.java
View file

@ -1,7 +1,7 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.visualization.modelconstructor.factory;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;

18
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java
View file

@ -2,15 +2,15 @@
package edu.cornell.mannlib.vitro.webapp.visualization.persongrantcount;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;

19
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java
View file

@ -11,7 +11,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -199,9 +199,8 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
/**
* Provides response when csv file containing the grant count over the years
* is requested.
* @param investigator
* @param yearToGrantCount
* @return
* @param investigator Investigator entiry
* @param yearToGrantCount Year / grant counts
*/
private Map<String, String> prepareDataResponse(
SubEntity investigator,
@ -225,9 +224,8 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
/**
* Provides response when an entire page dedicated to grant sparkline is requested.
* @param vreq
* @param valueObjectContainer
* @return
* @param vreq Vitro Request
* @param valueObjectContainer Sparkline data
*/
private TemplateResponseValues prepareStandaloneResponse(VitroRequest vreq,
SparklineData valueObjectContainer) {
@ -245,10 +243,9 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
/**
* Provides response when the grant sparkline has to be rendered in already existing
* page, e.g. profile page.
* @param vreq
* @param valueObjectContainer
* @param shouldVIVOrenderVis
* @return
* @param vreq Vitro Request
* @param valueObjectContainer Sparkline data
* @param shouldVIVOrenderVis Flag to render visualization
*/
private TemplateResponseValues prepareDynamicResponse(
VitroRequest vreq,

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountVisCodeGenerator.java
View file

@ -60,10 +60,8 @@ public class PersonGrantCountVisCodeGenerator {
/**
* This method is used to setup parameters for the sparkline value object. These parameters
* will be used in the template to construct the actual html/javascript code.
* @param visMode
* @param visContainer
* @param authorDocuments
* @return
* @param visMode Visualisation mode
* @param providedVisContainerID Container ID
*/
private SparklineData setupSparklineParameters(String visMode,
String providedVisContainerID) {

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personlevel/PersonLevelRequestHandler.java
View file

@ -11,7 +11,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CoInves
import edu.cornell.mannlib.vitro.webapp.visualization.visutils.CollaborationDataViewHelper;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

30
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java
View file

@ -5,12 +5,12 @@ package edu.cornell.mannlib.vitro.webapp.visualization.personpubcount;
import java.util.HashSet;
import java.util.Set;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.vocabulary.RDFS;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.rdf.model.Statement;
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;
@ -20,15 +20,15 @@ import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;
import org.apache.jena.iri.Violation;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;

21
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java
View file

@ -11,7 +11,7 @@ import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -217,10 +217,8 @@ VisualizationRequestHandler {
* Provides response when csv file containing the publication count over the
* years is requested.
*
* @param author
* @param authorDocuments
* @param yearToPublicationCount
* @return
* @param authorName Name of author
* @param yearToPublicationCount Year / publication counts
*/
private Map<String, String> prepareDataResponse(String authorName,
Map<String, Integer> yearToPublicationCount) {
@ -251,9 +249,8 @@ VisualizationRequestHandler {
* Provides response when an entire page dedicated to publication sparkline
* is requested.
*
* @param vreq
* @param valueObjectContainer
* @return
* @param vreq Vitro Request
* @param valueObjectContainer Sparkline Data
*/
private TemplateResponseValues prepareStandaloneResponse(VitroRequest vreq,
SparklineData valueObjectContainer) {
@ -272,10 +269,10 @@ VisualizationRequestHandler {
* Provides response when the publication sparkline has to be rendered in
* already existing page, e.g. profile page.
*
* @param vreq
* @param valueObjectContainer
* @param yearToPublicationCount
* @return
* @param vreq Vitro Request
* @param valueObjectContainer Sparkline data
* @param shouldVIVOrenderVis Flag to render visualization
* @param requestingTemplate Requesting template name
*/
private TemplateResponseValues prepareDynamicResponse(VitroRequest vreq,
SparklineData valueObjectContainer, boolean shouldVIVOrenderVis, String requestingTemplate) {

5
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountVisCodeGenerator.java
View file

@ -62,9 +62,8 @@ public class PersonPublicationCountVisCodeGenerator {
/**
* This method is used to setup parameters for the sparkline value object. These parameters
* will be used in the template to construct the actual html/javascript code.
* @param visMode
* @param visContainer
* @return
* @param visMode Visualization mode
* @param providedVisContainerID container id
*/
private SparklineData setupSparklineParameters(String visMode,
String providedVisContainerID) {

8
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java
View file

@ -9,10 +9,10 @@ import org.apache.commons.logging.Log;
import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;

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

@ -20,7 +20,7 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.google.gson.Gson;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

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

@ -20,7 +20,7 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import com.google.gson.Gson;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/tools/ToolsRequestHandler.java
View file

@ -7,7 +7,7 @@ import java.util.Map;
import org.apache.commons.logging.Log;
import com.hp.hpl.jena.query.Dataset;
import org.apache.jena.query.Dataset;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;

167
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/CachingRDFServiceExecutor.java
View file

@ -5,20 +5,20 @@ package edu.cornell.mannlib.vitro.webapp.visualization.utilities;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Callable;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.FutureTask;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.TimeoutException;
/**
* Utilicy class that populates and returns a cache.
* Utility class that populates and returns a cache.
* Once the cache is populated, it can return the cached results whilst refreshing in the background.
*
* @param <T>
@ -30,7 +30,7 @@ public class CachingRDFServiceExecutor<T> {
private T cachedResults;
private long lastCacheTime;
private RDFServiceCallable<T> resultBuilder;
private final RDFServiceCallable<T> resultBuilder;
/**
* Background task tracker
@ -59,9 +59,28 @@ public class CachingRDFServiceExecutor<T> {
* Will wait for completion if the cache is not already populated, otherwise the refresh will happen in the background.
*
* @param rdfService an RDF service to use, in foreground mode, if the background service is missing
* @return
*/
public synchronized T get(RDFService rdfService) {
return get(rdfService, false);
}
/**
* Return the cached results if present, or start the task.
* Will wait for completion if the cache is not already populated, otherwise the refresh will happen in the background.
*
* @param rdfService an RDF service to use, in foreground mode, if the background service is missing
*/
public synchronized T getNoWait(RDFService rdfService) {
return get(rdfService, true);
}
/**
* Return the cached results if present, or start the task.
* Will wait for completion if the cache is not already populated, otherwise the refresh will happen in the background.
*
* @param rdfService an RDF service to use, in foreground mode, if the background service is missing
*/
public synchronized T get(RDFService rdfService, boolean allowWaits) {
// First, check if there are results from the previous background task, and update the cache
if (backgroundTask != null && backgroundTask.isDone()) {
completeBackgroundTask();
@ -71,19 +90,24 @@ public class CachingRDFServiceExecutor<T> {
if (cachedResults != null) {
// If the background service exists, and the cache is considered invalid
if (backgroundRDFService != null && resultBuilder.invalidateCache(System.currentTimeMillis() - lastCacheTime)) {
// Determine how long we are prepared to wait for an answer
long waitFor = (backgroundTask == null ? 1000 : 500);
// In most cases, only wait for half a second
long waitFor = 500;
// Start the background task to refresh the cache
startBackgroundTask(rdfService);
if (backgroundTask == null) {
// Start the background task to refresh the cache
startBackgroundTask(backgroundRDFService);
// As we've just started the background task, allow a wait time of 1 second
waitFor = 1000;
}
// See if we expect it to complete in time, and if so, wait for it
if (isExpectedToCompleteIn(waitFor)) {
if (allowWaits && isExpectedToCompleteIn(waitFor)) {
completeBackgroundTask(waitFor);
}
}
} else {
// No cached results, so fetch the results using any availabe RDF service
// No cached results, so fetch the results using any available RDF service
if (rdfService != null) {
startBackgroundTask(rdfService);
} else if (backgroundRDFService != null) {
@ -126,8 +150,8 @@ public class CachingRDFServiceExecutor<T> {
startBackgroundTask(backgroundRDFService);
completeBackgroundTaskAsync();
} else if (rdfService != null) {
// No background service, so use the paassed RDF service, and wait for completion
startBackgroundTask(backgroundRDFService);
// No background service, so use the passed RDF service, and wait for completion
startBackgroundTask(rdfService);
completeBackgroundTask();
}
}
@ -171,7 +195,7 @@ public class CachingRDFServiceExecutor<T> {
/**
* Create and start a background thread using the configured task
* @param rdfService
* @param rdfService An RDFService
*/
private void startBackgroundTask(RDFService rdfService) {
// Ensure that there isn't already a task
@ -211,11 +235,7 @@ public class CachingRDFServiceExecutor<T> {
backgroundCompletion = new Thread(new Runnable() {
@Override
public void run() {
try {
Thread.sleep(500);
completeBackgroundTask(-1);
} catch (InterruptedException e) {
}
completeBackgroundTask(-1);
}
});
backgroundCompletion.setDaemon(true);
@ -259,11 +279,8 @@ public class CachingRDFServiceExecutor<T> {
abortBackgroundTask();
} catch (ExecutionException e) {
// There was a problem inside the task, so abort and throw an exception
try {
abortBackgroundTask();
} finally {
throw new RuntimeException("Background RDF thread through an exception", e.getCause());
}
abortBackgroundTask();
throw new RuntimeException("Background RDF thread through an exception", e.getCause());
} catch (TimeoutException e) {
// Ignore a timeout waiting for the results
}
@ -271,7 +288,7 @@ public class CachingRDFServiceExecutor<T> {
/**
* Set the RDF service to be used for background threads (called from a startup servlet)
* @param rdfService
* @param rdfService An RDFService
*/
public static void setBackgroundRDFService(RDFService rdfService) {
backgroundRDFService = rdfService;
@ -299,13 +316,13 @@ public class CachingRDFServiceExecutor<T> {
/**
* Constructor that allows an affinity object to be supplied
* @param affinity
* @param affinity Affinity
*/
public RDFServiceCallable(Affinity affinity) { this.affinity = affinity; }
/**
* Set the RDF service to be used
* @param rdfService
* @param rdfService An RDFService
*/
final void setRDFService(RDFService rdfService) {
this.rdfService = rdfService;
@ -313,8 +330,7 @@ public class CachingRDFServiceExecutor<T> {
/**
* Entry point for the background threads, ensuring the right start / cleanup is done
* @return
* @throws Exception
* @throws Exception Any exception
*/
@Override
final public T call() throws Exception {
@ -349,17 +365,15 @@ public class CachingRDFServiceExecutor<T> {
/**
* Method for users to implement, to return the results
* @param rdfService
* @return
* @throws Exception
* @param rdfService An RDFService
* @throws Exception Any exception
*/
protected abstract T callWithService(RDFService rdfService) throws Exception;
/**
* Method to determine if the cache should be invalidated for the current results
* Default implementation dynamically adjusts the cache time based on the efficiency of creating results
* @param timeCached
* @return
* @param timeCached The time of caching
*/
boolean invalidateCache(long timeCached) {
if (executionTime > -1) {
@ -390,50 +404,64 @@ public class CachingRDFServiceExecutor<T> {
* Affinity class that serializes background processing for tasks given the same affinity
*/
public static class Affinity {
private int maxThreads = 1;
private final int maxThreads = 1;
static class ThreadControl {
ThreadControl(long started, long expectedDuration) {
this.started = started;
this.expectedDuration = expectedDuration;
}
final long started;
final long expectedDuration;
final CountDownLatch latch = new CountDownLatch(1);
}
// Map of executing threads, and the time they expect to need to execute
private Map<Thread, Long> threadToExecutionTime = new HashMap<>();
private Set<Thread> executingThreads = new HashSet<>();
private final Map<Thread, ThreadControl> threadToExecutionTime = new HashMap<>();
private final Set<Thread> executingThreads = new HashSet<>();
/**
* Called by a background thread to determine if it is allowed to start
* @param expectedExecutionTime time that the thread expects to take (usualling the last execution time)
* @param expectedExecutionTime time that the thread expects to take (usually the last execution time)
*/
private void requestStart(long expectedExecutionTime) {
Thread executingThread = Thread.currentThread();
// Ask if the task needs to be queued
if (queueThis(Thread.currentThread(), expectedExecutionTime)) {
// Synchronize the thread to call wait
synchronized (Thread.currentThread()) {
try {
// Make the thread wait until it is notified to continue
Thread.currentThread().wait();
} catch(InterruptedException e) {
}
CountDownLatch latch = queueThis(executingThread, expectedExecutionTime);
// We got a latch from the queue, so wait for it to clear
if (latch != null) {
try {
latch.await();
} catch (InterruptedException e) {
}
}
}
/**
* Adds a thread to the map, returns whether the thread needs to wait
* @param thread
* @param time
* @param thread The thread to add
* @param time start time of the thread
* @return true if the thread needs to wait, false if it can continue
*/
private synchronized boolean queueThis(Thread thread, Long time) {
private synchronized CountDownLatch queueThis(Thread thread, Long time) {
// If we have fewer that the max threads running
if (executingThreads.size() < maxThreads) {
// Add thread to executing set
executingThreads.add(thread);
// Not queued - we can continue
return false;
return null;
} else {
// Add the thread to the map
threadToExecutionTime.put(thread, time);
ThreadControl control = new ThreadControl(System.currentTimeMillis(), time);
// Let the caller know that we are queued
return true;
// Add the thread to the map
threadToExecutionTime.put(thread, control);
// Give the caller a handle to the latch for the queued thread
return control.latch;
}
}
@ -450,26 +478,41 @@ public class CachingRDFServiceExecutor<T> {
// If there are still threads to execute, and we have not exhausted maximum threads
while (threadToExecutionTime.size() > 0 && executingThreads.size() < maxThreads) {
Thread nextToRelease = null;
long executionTime = -1;
ThreadControl nextToReleaseControl = null;
long current = System.currentTimeMillis();
boolean favourStartTime = false;
// Find the thread that expects to take the least time
for (Thread thread : threadToExecutionTime.keySet()) {
long thisTime = threadToExecutionTime.get(thread);
ThreadControl threadControl = threadToExecutionTime.get(thread);
// If there are threads that have been waiting over 2 seconds, favour the oldest thread
if (threadControl.started + 2000 < current) {
favourStartTime = true;
}
if (nextToRelease == null) {
nextToRelease = thread;
executionTime = thisTime;
} else if (thisTime < executionTime) {
nextToRelease = thread;
executionTime = thisTime;
nextToReleaseControl = threadControl;
} else {
if (favourStartTime) {
// Find the oldest thread
if (threadControl.started < nextToReleaseControl.started) {
nextToRelease = thread;
nextToReleaseControl = threadControl;
}
} else if (threadControl.expectedDuration < nextToReleaseControl.expectedDuration) {
nextToRelease = thread;
nextToReleaseControl = threadControl;
}
}
}
// Synchronize on the thread we are releasing, and notify it to continue
synchronized (nextToRelease) {
// Notify the Thread we are releasing to continue
if (nextToRelease != null) {
threadToExecutionTime.remove(nextToRelease);
executingThreads.add(nextToRelease);
nextToRelease.notify();
nextToReleaseControl.latch.countDown();
}
}
}

8
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java
View file

@ -15,10 +15,10 @@ import org.apache.jena.iri.Violation;
import org.vivoweb.webapp.util.ModelUtils;
import com.google.gson.Gson;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;

18
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/VisualizationCaches.java
View file

@ -2,14 +2,14 @@
package edu.cornell.mannlib.vitro.webapp.visualization.utilities;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
@ -82,7 +82,7 @@ final public class VisualizationCaches {
/**
* Rebuild the specifield caches
* @param executors
* @param executors Caching RDF executors
*/
public static void rebuild(CachingRDFServiceExecutor... executors) {
if (executors != null) {

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

@ -36,7 +36,6 @@ public class Activity extends Individual {
* The 2 choices, in order, are,
* 1. parsed year from xs:DateTime object saved in core:dateTimeValue
* 2. Default Publication Year
* @return
*/
public String getParsedActivityYear() {
@ -47,7 +46,6 @@ public class Activity extends Individual {
/**
* This method should be used to get the raw date & not the parsed publication year.
* For the later use getParsedPublicationYear.
* @return
*/
public String getActivityDate() {
return activityDate;

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

@ -6,7 +6,7 @@ import java.util.Map;
import org.apache.commons.lang.StringUtils;
import com.hp.hpl.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Model;
import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.IllegalConstructedModelIdentifierException;

18
api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java
View file

@ -12,15 +12,15 @@ import org.apache.jena.iri.IRI;
import org.apache.jena.iri.IRIFactory;
import org.apache.jena.iri.Violation;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.RDFNode;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;

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