diff --git a/.travis.yml b/.travis.yml index bcd16f88..cf8ba95d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,6 +8,11 @@ env: # Give Maven 1GB of memory to work with - MAVEN_OPTS=-Xmx1024M +cache: + directories: + - .autoconf + - $HOME/.m2 + install: - git clone https://github.com/vivo-project/Vitro.git ../Vitro diff --git a/api/pom.xml b/api/pom.xml index 5e15d44e..cfafdc23 100644 --- a/api/pom.xml +++ b/api/pom.xml @@ -30,16 +30,6 @@ pom - - axis - axis - 1.3 - - - com.google.code.gson - gson - 1.4 - com.itextpdf itextpdf @@ -56,11 +46,6 @@ 2.5.6 - - org.vivoweb.dependencies - agrovocws - 3.0 - org.vivoweb.dependencies oim.vivo.scimapcore @@ -84,6 +69,11 @@ 2.0 provided + + javax.xml + jaxrpc + 1.1 + junit diff --git a/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java b/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java index c8ab50f8..17b719f6 100644 --- a/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java +++ b/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java @@ -17,6 +17,7 @@ import java.util.HashSet; import java.util.Iterator; import java.util.LinkedHashSet; import java.util.List; +import java.util.concurrent.TimeUnit; import javax.xml.parsers.ParserConfigurationException; import javax.xml.rpc.ServiceException; @@ -25,11 +26,9 @@ import net.sf.json.JSONArray; import net.sf.json.JSONObject; import net.sf.json.JSONSerializer; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.fao.www.webservices.AgrovocWS.ACSWWebService; -import org.fao.www.webservices.AgrovocWS.ACSWWebServiceServiceLocator; import org.w3c.dom.Attr; import org.w3c.dom.Document; import org.w3c.dom.NamedNodeMap; @@ -56,7 +55,6 @@ import edu.cornell.mannlib.vitro.webapp.web.URLEncoder; public class AgrovocService implements ExternalConceptService { protected final Log logger = LogFactory.getLog(getClass()); - private java.lang.String AgrovocWS_address = "http://agrovoc.fao.org/axis/services/SKOSWS"; private final String schemeUri = "http://aims.fao.org/aos/agrovoc/agrovocScheme"; private final String ontologyName = "agrovoc"; private final String format = "SKOS"; @@ -136,9 +134,8 @@ public class AgrovocService implements ExternalConceptService { if (closeMatch.startsWith("http://dbpedia.org")) { try { - String description = getDbpediaDescription(closeMatch); - // System.out.println("description: "+ description); - c.setDefinition(description); + String description = getDbpediaDescription(closeMatch); + c.setDefinition(description); } catch (Exception ex) { logger.error("An error occurred in the process of retrieving dbpedia description", ex); } @@ -190,153 +187,6 @@ public class AgrovocService implements ExternalConceptService { return concept; } - @Deprecated - protected String getTermcodeByTerm(String term) throws Exception { - String result = new String(); - ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator(); - try { - URL url = new URL(AgrovocWS_address); - ACSWWebService agrovoc_service = locator.getACSWWebService(url); - result = agrovoc_service.getTermcodeByTerm(term); - } catch (ServiceException e) { - logger.error("service exception", e); - throw e; - } catch (RemoteException e) { - logger.error("remote exception", e); - throw e; - } catch (MalformedURLException e) { - logger.error("malformed URL exception", e); - throw e; - } - return result; - } - - protected String getTermCodeByTermAndLangXML(String ontologyName, - String searchString, String lang, String codeName, String format) { - String result = new String(); - ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator(); - try { - URL url = new URL(AgrovocWS_address); - ACSWWebService agrovoc_service = locator.getACSWWebService(url); - result = agrovoc_service.getTermCodeByTermAndLangXML(ontologyName, - searchString, lang, codeName, format); - } catch (ServiceException e) { - logger.error("service exception", e); - e.printStackTrace(); - } catch (RemoteException e) { - e.printStackTrace(); - } catch (MalformedURLException e) { - e.printStackTrace(); - } - return result; - } - - protected String getURIByTermAndLangXML(String ontologyName, String term, - String searchMode, String format, String lang) { - String result = new String(); - ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator(); - try { - URL url = new URL(AgrovocWS_address); - ACSWWebService agrovoc_service = locator.getACSWWebService(url); - result = agrovoc_service.getURIByTermAndLangXML(ontologyName, term, - searchMode, format, lang); - } catch (ServiceException e) { - e.printStackTrace(); - } catch (RemoteException e) { - e.printStackTrace(); - } catch (MalformedURLException e) { - e.printStackTrace(); - } - - return result; - } - - // Creating method for term expansion - protected String getTermExpansion(String ontologyName, String term, - String searchMode, String format, String lang) { - String result = new String(); - ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator(); - try { - URL url = new URL(AgrovocWS_address); - ACSWWebService agrovoc_service = locator.getACSWWebService(url); - result = agrovoc_service.getTermExpansion(ontologyName, term, - format, searchMode, lang); // the actual call has this order - // for parameters - } catch (ServiceException e) { - e.printStackTrace(); - } catch (RemoteException e) { - e.printStackTrace(); - } catch (MalformedURLException e) { - e.printStackTrace(); - } - - return result; - } - - protected String getConceptInfoByTermcodeXML(String termcode, String format) { - String result = new String(); - ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator(); - try { - URL url = new URL(AgrovocWS_address); - ACSWWebService agrovoc_service = locator.getACSWWebService(url); - result = agrovoc_service.getConceptInfoByTermcodeXML(termcode, - format); - } catch (ServiceException e) { - logger.error("service exception", e); - e.printStackTrace(); - } catch (RemoteException e) { - e.printStackTrace(); - } catch (MalformedURLException e) { - e.printStackTrace(); - } - - return result; - } - - protected String getConceptByKeyword(String ontologyName, - String searchString, String format, String searchMode, String lang) { - String result = new String(); - ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator(); - try { - URL url = new URL(AgrovocWS_address); - ACSWWebService agrovoc_service = locator.getACSWWebService(url); - result = agrovoc_service.getConceptByKeyword(ontologyName, - searchString, format, searchMode, lang); - } catch (ServiceException e) { - logger.error("service exception", e); - e.printStackTrace(); - } catch (RemoteException e) { - e.printStackTrace(); - } catch (MalformedURLException e) { - e.printStackTrace(); - } - - return result; - } - - protected String getWsdl() { - String result = new String(); - try { - - StringWriter sw = new StringWriter(); - URL rss = new URL(this.AgrovocWS_address + "?wsdl"); - - BufferedReader in = new BufferedReader(new InputStreamReader( - rss.openStream())); - String inputLine; - while ((inputLine = in.readLine()) != null) { - sw.write(inputLine); - } - in.close(); - - result = sw.toString(); - - } catch (Exception ex) { - logger.error("error occurred in servlet", ex); - } - return result; - } - public List getConceptsByURIWithSparql(String uri) throws Exception { // deprecating this method...just return an empty list @@ -440,8 +290,8 @@ public class AgrovocService implements ExternalConceptService { try { Query query = QueryFactory.create(qs); - qexec = QueryExecutionFactory.sparqlService(this.dbpedia_endpoint, - query); + qexec = QueryExecutionFactory.sparqlService(this.dbpedia_endpoint, query); + qexec.setTimeout(5000, TimeUnit.MILLISECONDS); resultList = new ArrayList(); ResultSet resultSet = qexec.execSelect(); int resultSetSize = 0; @@ -501,28 +351,6 @@ public class AgrovocService implements ExternalConceptService { } } - // Get concept using agrovoc service - protected String getConceptInfoByURI(String ontologyName, - String conceptURI, String format) { - String result = new String(); - ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator(); - try { - URL url = new URL(AgrovocWS_address); - ACSWWebService agrovoc_service = locator.getACSWWebService(url); - result = agrovoc_service.getConceptByURI(ontologyName, conceptURI, - format); - } catch (ServiceException e) { - logger.error("service exception", e); - e.printStackTrace(); - } catch (RemoteException e) { - e.printStackTrace(); - } catch (MalformedURLException e) { - e.printStackTrace(); - } - - return result; - } - /** * The code here utilizes the SKOSMOS REST API for Agrovoc * This returns JSON LD so we would parse JSON instead of RDF diff --git a/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/GemetService.java b/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/GemetService.java index d3911fbf..843baab6 100644 --- a/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/GemetService.java +++ b/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/GemetService.java @@ -24,7 +24,7 @@ import edu.cornell.mannlib.semservices.service.ExternalConceptService; public class GemetService implements ExternalConceptService { protected final Log logger = LogFactory.getLog(getClass()); - private final String GemetWS_address = "http://www.eionet.europa.eu/gemet/"; + private final String GemetWS_address = "https://www.eionet.europa.eu/gemet/"; private final String narrowerUri = "http://www.w3.org/2004/02/skos/core%23narrower"; private final String broaderUri = "http://www.w3.org/2004/02/skos/core%23broader"; private final String relatedUri = "http://www.w3.org/2004/02/skos/core%23related"; diff --git a/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/LCSHService.java b/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/LCSHService.java index a8cec31f..ed38ab52 100644 --- a/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/LCSHService.java +++ b/api/src/main/java/edu/cornell/mannlib/semservices/service/impl/LCSHService.java @@ -18,7 +18,7 @@ import javax.xml.parsers.ParserConfigurationException; import net.sf.json.JSONObject; import net.sf.json.JSONSerializer; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.w3c.dom.Attr; diff --git a/api/src/main/java/edu/cornell/mannlib/semservices/util/SKOSUtils.java b/api/src/main/java/edu/cornell/mannlib/semservices/util/SKOSUtils.java index 73243fcb..1afe4896 100644 --- a/api/src/main/java/edu/cornell/mannlib/semservices/util/SKOSUtils.java +++ b/api/src/main/java/edu/cornell/mannlib/semservices/util/SKOSUtils.java @@ -14,7 +14,7 @@ import java.net.URL; import java.util.ArrayList; import java.util.List; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusMapLocations.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusMapLocations.java index c0c1412c..3ddf3a39 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusMapLocations.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusMapLocations.java @@ -36,7 +36,7 @@ public class GeoFocusMapLocations extends AbstractAjaxResponder { + "PREFIX core: \n" + "PREFIX foaf: \n" + "PREFIX vivoc: \n" - + "PREFIX afn: " + + "PREFIX afn: " + "SELECT DISTINCT ?label ?location (afn:localname(?location) AS ?localName) (COUNT(DISTINCT ?person) AS ?count) \n" + "WHERE { { \n" + " ?location rdf:type core:GeographicRegion . \n" diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java index 531a9d01..d8eb047a 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java @@ -66,7 +66,7 @@ public class ManageGrantsForIndividualController extends FreemarkerHttpServlet { + "PREFIX core: \n" + "PREFIX rdfs: \n" + "PREFIX vitro: \n" - + "PREFIX afn: \n" + + "PREFIX afn: \n" + "SELECT DISTINCT ?subclass ?role (str(?label2) as ?label) ?activity ?hideThis WHERE { \n" + " ?subject ?role . \n" + " ?role a core:ResearcherRole . \n" diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java index c87a2b4a..483acde6 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java @@ -66,7 +66,7 @@ public class ManagePeopleForOrganizationController extends FreemarkerHttpServlet + "PREFIX core: \n" + "PREFIX rdfs: \n" + "PREFIX vitro: \n" - + "PREFIX afn: \n" + + "PREFIX afn: \n" + "PREFIX foaf: \n" + "SELECT DISTINCT ?subclass ?position ?positionLabel (str(?label) as ?name) ?person ?hideThis WHERE { \n" + " ?subject core:relatedBy ?position . \n" diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java index 7fba5e83..74b193b1 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java @@ -66,7 +66,7 @@ public class ManagePublicationsForIndividualController extends FreemarkerHttpSer + "PREFIX core: \n" + "PREFIX rdfs: \n" + "PREFIX vitro: \n" - + "PREFIX afn: \n" + + "PREFIX afn: \n" + "SELECT DISTINCT ?subclass ?authorship (str(?label) as ?title) ?pub ?hideThis WHERE { \n" + " ?subject core:relatedBy ?authorship . \n" + " ?authorship a core:Authorship . \n" diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/harvester/CsvFileHarvestJob.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/harvester/CsvFileHarvestJob.java index 28869704..10efd694 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/harvester/CsvFileHarvestJob.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/harvester/CsvFileHarvestJob.java @@ -6,18 +6,20 @@ import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; +import java.io.InputStreamReader; import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVParser; +import org.apache.commons.csv.CSVRecord; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.skife.csv.SimpleReader; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; - /** * An implementation of FileHarvestJob that can be used for any CSV file harvest. */ @@ -214,75 +216,48 @@ class CsvFileHarvestJob implements FileHarvestJob { @SuppressWarnings("rawtypes") public String validateUpload(File file) { try { - SimpleReader reader = new SimpleReader(); - - List templateCsv = reader.parse(this.templateFile); - String[] templateFirstLine = (String[])templateCsv.get(0); - - //if a line ends in a comma (absolutely a comma, no whitespace), SimpleReader will not consider the part after the comma to be a blank section. - List csv = reader.parse(file); - boolean[] linesEndingInComma = getLinesEndingInComma(file); - - int length = csv.size(); - - if(length == 0) - return "No data in file"; - - for(int i = 0; i < length; i++) { - String[] line = (String[])csv.get(i); - boolean endsInComma = linesEndingInComma[i]; - if(i == 0) { - String errorMessage = validateCsvFirstLine(templateFirstLine, line); - if(errorMessage != null) - return errorMessage; - } - else if(line.length != 0) { - int actualLineLength = line.length + (endsInComma ? 1 : 0); - if(actualLineLength != templateFirstLine.length) { - return "Mismatch in number of entries in row " + i + ": expected " + templateFirstLine.length + ", found " + actualLineLength; + String message = "No data in file"; + CSVParser cReader = new CSVParser(new FileReader(file), CSVFormat.DEFAULT); + try { + int rowNum = 0; + int numberFields = 0; + String errorMsg = "File header does not match template"; + for (CSVRecord cRecord : cReader) { + rowNum++; + if (false) { + numberFields = cRecord.size(); + errorMsg += "file header items: "; + for(int i = 0; i < cRecord.size(); i++) { + errorMsg += cRecord.get(i) + ", "; + } + } else { + if (cRecord.size() > 0) { + if(cRecord.size() != numberFields) { + if (errorMsg != null) { + errorMsg += "template items: "; + for(int i = 0; i < cRecord.size(); i++) { + errorMsg += cRecord.get(i) + ", "; + } + return errorMsg; + } + return "Mismatch in number of entries in row " + rowNum + ": expected " + numberFields + ", found " + cRecord.size(); + } + } + message = null; + errorMsg = null; } } - } + return message; + } finally { + cReader.close(); + } } catch (IOException e) { log.error(e, e); return e.getMessage(); } - return null; } - /** - * Makes sure that the first line of the CSV file is identical to the first line of the template file. This is - * assuming we are expecting all user CSV files to contain an initial header line. If this is not the case, then - * this method is unnecessary. - * @param templateFirstLine the parsed-out contents of the first line of the template file - * @param line the parsed-out contents of the first line of the input file - * @return an error message if the two lines don't match, or null if they do - */ - private String validateCsvFirstLine(String[] templateFirstLine, String[] line) { - String errorMessage = "File header does not match template"; - if(line.length != templateFirstLine.length) { - //return errorMessage + ": " + "file header columns = " + line.length + ", template columns = " + templateFirstLine.length; - String errorMsg = ""; - errorMsg += "file header items: "; - for(int i = 0; i < line.length; i++) { - errorMsg += line[i] + ", "; - } - errorMsg += "template items: "; - for(int i = 0; i < templateFirstLine.length; i++) { - errorMsg += templateFirstLine[i] + ", "; - } - return errorMsg; - } - for(int i = 0; i < line.length; i++) - { - if(!line[i].equals(templateFirstLine[i])) - return errorMessage + ": file header column " + (i + 1) + " = " + line[i] + ", template column " + (i + 1) + " = " + templateFirstLine[i]; - } - return null; - } - - /* private void prepareWorkspaceDirectory() { String path = FileHarvestController.getFileHarvestRootPath() + "workspaces/" + this.sessionId; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/visualization/ShortURLVisualizationController.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/visualization/ShortURLVisualizationController.java index 376bc3c2..d9d4c84f 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/visualization/ShortURLVisualizationController.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/visualization/ShortURLVisualizationController.java @@ -9,7 +9,7 @@ import java.util.Map; import javax.servlet.ServletContext; -import org.apache.commons.lang.StringEscapeUtils; +import org.apache.commons.lang3.StringEscapeUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -168,7 +168,7 @@ public class ShortURLVisualizationController extends FreemarkerHttpServlet { + matchedPatternGroups.get(1); } - subjectURI = StringEscapeUtils.escapeHtml(subjectURI); + subjectURI = StringEscapeUtils.ESCAPE_HTML4.translate(subjectURI); parameters.put(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY, subjectURI); if (VisualizationFrameworkConstants.COAUTHORSHIP_VIS_SHORT_URL @@ -243,7 +243,7 @@ public class ShortURLVisualizationController extends FreemarkerHttpServlet { List matchedGroups = new ArrayList(); String subURIString = vitroRequest.getRequestURI().substring(vitroRequest.getContextPath().length()+1); - String[] urlParams = StringEscapeUtils.escapeHtml(subURIString).split("/"); + String[] urlParams = StringEscapeUtils.ESCAPE_HTML4.translate(subURIString).split("/"); if (urlParams.length > 1 && urlParams[0].equalsIgnoreCase("vis")) { diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PersonHasPublicationValidator.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PersonHasPublicationValidator.java index de09dcf5..e9202b73 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PersonHasPublicationValidator.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PersonHasPublicationValidator.java @@ -6,7 +6,7 @@ import java.util.HashMap; import java.util.List; import java.util.Map; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PublicationHasAuthorValidator.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PublicationHasAuthorValidator.java index ea511435..b84005a3 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PublicationHasAuthorValidator.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PublicationHasAuthorValidator.java @@ -8,7 +8,7 @@ import java.util.HashMap; import java.util.List; import java.util.Map; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.jena.rdf.model.Literal; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAuthorsToInformationResourceGenerator.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAuthorsToInformationResourceGenerator.java index ee2dd1e5..f2d541ff 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAuthorsToInformationResourceGenerator.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAuthorsToInformationResourceGenerator.java @@ -352,7 +352,7 @@ public class AddAuthorsToInformationResourceGenerator extends VivoBaseGenerator private static String AUTHORSHIPS_MODEL = " \n" + "PREFIX core: \n" - + "PREFIX afn: \n" + + "PREFIX afn: \n" + "PREFIX rdfs: \n" + "PREFIX foaf: \n" + "PREFIX vcard: \n" @@ -418,7 +418,7 @@ public class AddAuthorsToInformationResourceGenerator extends VivoBaseGenerator private static String AUTHORSHIPS_QUERY = " \n" + "PREFIX core: \n" - + "PREFIX afn: \n" + + "PREFIX afn: \n" + "PREFIX rdfs: \n" + "PREFIX foaf: \n" + "PREFIX vcard: \n" diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorsToInformationResourceGenerator.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorsToInformationResourceGenerator.java index a3a50620..f37d0363 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorsToInformationResourceGenerator.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditorsToInformationResourceGenerator.java @@ -315,7 +315,7 @@ public class AddEditorsToInformationResourceGenerator extends VivoBaseGenerator private static String EDITORSHIPS_MODEL = "" + "PREFIX core: \n" - + "PREFIX afn: \n" + + "PREFIX afn: \n" + "PREFIX rdfs: \n" + "PREFIX foaf: \n" + "CONSTRUCT\n" @@ -353,7 +353,7 @@ public class AddEditorsToInformationResourceGenerator extends VivoBaseGenerator private static String EDITORSHIPS_QUERY = "" + "PREFIX core: \n" - + "PREFIX afn: \n" + + "PREFIX afn: \n" + "PREFIX rdfs: \n" + "PREFIX foaf: \n" + "SELECT ?editorshipURI (afn:localname(?editorshipURI) AS ?editorshipName) ?editorURI ?editorName ?rank \n" diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java index 8f51aaf1..6ca72b64 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java @@ -11,7 +11,7 @@ import java.util.Map; import javax.servlet.http.HttpSession; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.vivoweb.webapp.util.ModelUtils; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java index 74bafa69..3f366408 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java @@ -13,7 +13,7 @@ import javax.servlet.http.HttpSession; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.jena.rdf.model.Literal; import org.apache.jena.rdf.model.Model; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java index df9b9f94..04d8acf6 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java @@ -12,7 +12,7 @@ import net.sf.json.JSON; import net.sf.json.JSONArray; import net.sf.json.JSONSerializer; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java index e0c4f4bb..7ff66758 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java @@ -9,7 +9,7 @@ import java.util.HashMap; import javax.servlet.http.HttpServletRequest; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java index 2831cba1..7fa8599e 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java @@ -9,7 +9,7 @@ import java.util.HashMap; import javax.servlet.http.HttpServletRequest; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/ConceptSearchServlet.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/ConceptSearchServlet.java index 38bdf751..cf076989 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/ConceptSearchServlet.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/ConceptSearchServlet.java @@ -11,7 +11,7 @@ import javax.servlet.ServletException; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/capabilitymap/CapabilityMapRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/capabilitymap/CapabilityMapRequestHandler.java index c2eea52e..0588e0f4 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/capabilitymap/CapabilityMapRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/capabilitymap/CapabilityMapRequestHandler.java @@ -3,6 +3,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.capabilitymap; import com.google.gson.Gson; +import org.apache.commons.lang3.StringUtils; import org.apache.jena.query.Dataset; import org.apache.jena.query.QueryExecution; import org.apache.jena.query.QueryExecutionFactory; @@ -24,7 +25,6 @@ import edu.cornell.mannlib.vitro.webapp.visualization.model.ConceptPeopleMap; import edu.cornell.mannlib.vitro.webapp.visualization.model.OrganizationPeopleMap; import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches; import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler; -import org.apache.axis.utils.StringUtils; import org.apache.commons.logging.Log; import java.util.HashMap; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java index 29e5646f..30acced1 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java @@ -22,7 +22,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer; import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches; import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.iri.IRI; import org.apache.jena.iri.IRIFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java index 74ccca76..32dd0fad 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java @@ -8,8 +8,8 @@ import java.util.Map.Entry; import java.util.Set; import java.util.TreeMap; -import org.apache.commons.lang.StringEscapeUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringEscapeUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.query.Dataset; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryConstants.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryConstants.java index abfc9e51..53898382 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryConstants.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryConstants.java @@ -41,7 +41,7 @@ public class QueryConstants { put("vivo", "http://vivo.library.cornell.edu/ns/0.1#"); put("geo", "http://aims.fao.org/aos/geopolitical.owl#"); put("public", "http://vitro.mannlib.cornell.edu/ns/vitro/public#"); - put("afn", "http://jena.hpl.hp.com/ARQ/function#"); + put("afn", "http://jena.apache.org/ARQ/function#"); put("vivosocnet", "http://vivo.cns.iu.edu/ns/#"); put("obo", "http://purl.obolibrary.org/obo/"); put("vcard", "http://www.w3.org/2006/vcard/ns#"); diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java index 4b34e32a..b3674764 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java @@ -8,7 +8,7 @@ import java.util.Set; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.jena.iri.IRI; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java index f237bba8..49e42073 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java @@ -17,7 +17,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer; import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.jena.iri.IRI; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java index cc995fba..818dd96a 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java @@ -6,8 +6,8 @@ import java.util.Map; import java.util.Set; import java.util.TreeMap; -import org.apache.commons.lang.StringEscapeUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringEscapeUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.query.Dataset; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java index b109a0aa..941bc6c3 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java @@ -22,8 +22,8 @@ import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCac import mapping.ScienceMapping; import mapping.ScienceMappingResult; -import org.apache.commons.lang.StringEscapeUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringEscapeUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import com.google.gson.Gson; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java index 0df6afc2..c2899521 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java @@ -18,7 +18,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants; import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException; import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity; import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.iri.IRI; import org.apache.jena.iri.IRIFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java index 41c692b1..20454dbd 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java @@ -8,7 +8,7 @@ import java.util.Map.Entry; import java.util.Set; import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner; -import org.apache.commons.lang.StringEscapeUtils; +import org.apache.commons.lang3.StringEscapeUtils; import org.apache.commons.logging.Log; import org.apache.jena.query.Dataset; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java index 208b4f84..8af4dbb9 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java @@ -14,7 +14,7 @@ import org.apache.jena.vocabulary.RDFS; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.iri.IRI; import org.apache.jena.iri.IRIFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java index a851cb43..52782528 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java @@ -7,8 +7,8 @@ import java.util.Map; import java.util.Map.Entry; import java.util.Set; -import org.apache.commons.lang.StringEscapeUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringEscapeUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.query.Dataset; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java index b2357427..56beb5e5 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java @@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.temporalgraph; import java.util.HashMap; import java.util.Map; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.iri.IRI; import org.apache.jena.iri.IRIFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java index efead735..16e15873 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java @@ -15,8 +15,8 @@ import edu.cornell.mannlib.vitro.webapp.visualization.model.OrganizationPeopleMa import edu.cornell.mannlib.vitro.webapp.visualization.utilities.CounterUtils; import edu.cornell.mannlib.vitro.webapp.visualization.utilities.OrgUtils; import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches; -import org.apache.commons.lang.StringEscapeUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringEscapeUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import com.google.gson.Gson; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java index fc734fdc..e40f846a 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java @@ -15,8 +15,8 @@ import edu.cornell.mannlib.vitro.webapp.visualization.model.OrganizationPeopleMa import edu.cornell.mannlib.vitro.webapp.visualization.utilities.CounterUtils; import edu.cornell.mannlib.vitro.webapp.visualization.utilities.OrgUtils; import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches; -import org.apache.commons.lang.StringEscapeUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringEscapeUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import com.google.gson.Gson; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/OrgUtils.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/OrgUtils.java index e052ecc4..2f8dbc29 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/OrgUtils.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/OrgUtils.java @@ -2,7 +2,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.utilities; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import java.util.HashSet; import java.util.Map; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java index 337d82a7..7facc943 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java @@ -7,7 +7,7 @@ import java.util.Map; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.jena.iri.IRI; import org.apache.jena.iri.IRIFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/ConstructedModelTracker.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/ConstructedModelTracker.java index 6f3be4d8..549131a1 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/ConstructedModelTracker.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/ConstructedModelTracker.java @@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects; import java.util.HashMap; import java.util.Map; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.jena.rdf.model.Model; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java index b80ca037..2be8094d 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java @@ -5,7 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.visualization.visutils; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.jena.iri.IRI; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java index 247ea0cb..f981bd66 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java @@ -12,7 +12,7 @@ import java.util.TreeMap; import javax.servlet.http.HttpServletResponse; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.joda.time.DateTime; import org.joda.time.format.DateTimeFormatter; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividual.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividual.java index b7e71d71..93f8ffd8 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividual.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividual.java @@ -2,7 +2,7 @@ package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/VIVOIndividualSearchResult.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/VIVOIndividualSearchResult.java index d254fa6e..b9316816 100644 --- a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/VIVOIndividualSearchResult.java +++ b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/VIVOIndividualSearchResult.java @@ -2,7 +2,7 @@ package edu.cornell.mannlib.vitro.webapp.web.templatemodels.searchresult; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/edu/cornell/mannlib/vivo/orcid/OrcidContextSetup.java b/api/src/main/java/edu/cornell/mannlib/vivo/orcid/OrcidContextSetup.java index 4eca45f1..6a07d5f8 100644 --- a/api/src/main/java/edu/cornell/mannlib/vivo/orcid/OrcidContextSetup.java +++ b/api/src/main/java/edu/cornell/mannlib/vivo/orcid/OrcidContextSetup.java @@ -21,7 +21,7 @@ import javax.servlet.ServletContext; import javax.servlet.ServletContextEvent; import javax.servlet.ServletContextListener; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/api/src/main/java/org/vivoweb/webapp/sitemap/SiteMapServlet.java b/api/src/main/java/org/vivoweb/webapp/sitemap/SiteMapServlet.java index 480d4edf..eb4ec0fb 100644 --- a/api/src/main/java/org/vivoweb/webapp/sitemap/SiteMapServlet.java +++ b/api/src/main/java/org/vivoweb/webapp/sitemap/SiteMapServlet.java @@ -2,6 +2,7 @@ package org.vivoweb.webapp.sitemap; +import org.apache.commons.lang3.StringUtils; import org.apache.jena.query.QuerySolution; import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; @@ -9,7 +10,6 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer; import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants; -import org.apache.axis.utils.StringUtils; import org.apache.commons.io.IOUtils; import javax.servlet.ServletException; diff --git a/api/src/main/java/org/vivoweb/webapp/startup/JSONWrapperSetup.java b/api/src/main/java/org/vivoweb/webapp/startup/JSONWrapperSetup.java index f1543482..7244fd34 100644 --- a/api/src/main/java/org/vivoweb/webapp/startup/JSONWrapperSetup.java +++ b/api/src/main/java/org/vivoweb/webapp/startup/JSONWrapperSetup.java @@ -11,7 +11,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.individuallist.IndividualJson import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao; import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils; -import org.apache.commons.lang.StringUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.json.JSONException; diff --git a/home/src/main/resources/rdf/abox/firsttime/geopolitical.ver1.1-11-18-11-individual-labels.rdf b/home/src/main/resources/rdf/abox/firsttime/geopolitical.ver1.1-11-18-11-individual-labels.rdf index afae26b8..6d34e7a7 100644 --- a/home/src/main/resources/rdf/abox/firsttime/geopolitical.ver1.1-11-18-11-individual-labels.rdf +++ b/home/src/main/resources/rdf/abox/firsttime/geopolitical.ver1.1-11-18-11-individual-labels.rdf @@ -13,7 +13,7 @@ xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:j.2="http://www.w3.org/2008/05/skos#" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:j.3="http://www.w3.org/2003/06/sw-vocab-status/ns#" diff --git a/home/src/main/resources/rdf/display/everytime/vivoQrCodeDataGetter.n3 b/home/src/main/resources/rdf/display/everytime/vivoQrCodeDataGetter.n3 index 88aa0673..55abd9f3 100644 --- a/home/src/main/resources/rdf/display/everytime/vivoQrCodeDataGetter.n3 +++ b/home/src/main/resources/rdf/display/everytime/vivoQrCodeDataGetter.n3 @@ -6,7 +6,7 @@ @prefix rdfs: . @prefix core: . @prefix vivoweb: . -@prefix afn: . +@prefix afn: . #### Check to see if the person being viewed has a first and last name. #### diff --git a/home/src/main/resources/rdf/tbox/filegraph/appControls-temp.n3 b/home/src/main/resources/rdf/tbox/filegraph/appControls-temp.n3 index d5566035..f30c9c37 100644 --- a/home/src/main/resources/rdf/tbox/filegraph/appControls-temp.n3 +++ b/home/src/main/resources/rdf/tbox/filegraph/appControls-temp.n3 @@ -1,5 +1,5 @@ @prefix hr: . -@prefix afn: . +@prefix afn: . @prefix : . @prefix scires: . @prefix aka: . diff --git a/home/src/main/resources/rdf/tbox/filegraph/dataDomains.rdf b/home/src/main/resources/rdf/tbox/filegraph/dataDomains.rdf index 9526dba1..1209eff0 100644 --- a/home/src/main/resources/rdf/tbox/filegraph/dataDomains.rdf +++ b/home/src/main/resources/rdf/tbox/filegraph/dataDomains.rdf @@ -9,7 +9,7 @@ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:scires="http://vivoweb.org/ontology/scientific-research#" diff --git a/home/src/main/resources/rdf/tbox/filegraph/objectDomains.rdf b/home/src/main/resources/rdf/tbox/filegraph/objectDomains.rdf index d50bbf34..77d76ec4 100644 --- a/home/src/main/resources/rdf/tbox/filegraph/objectDomains.rdf +++ b/home/src/main/resources/rdf/tbox/filegraph/objectDomains.rdf @@ -9,7 +9,7 @@ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:scires="http://vivoweb.org/ontology/scientific-research#" diff --git a/home/src/main/resources/rdf/tbox/filegraph/objectRanges.rdf b/home/src/main/resources/rdf/tbox/filegraph/objectRanges.rdf index a4431cc6..01251b82 100644 --- a/home/src/main/resources/rdf/tbox/filegraph/objectRanges.rdf +++ b/home/src/main/resources/rdf/tbox/filegraph/objectRanges.rdf @@ -9,7 +9,7 @@ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:scires="http://vivoweb.org/ontology/scientific-research#" diff --git a/home/src/main/resources/rdf/tbox/filegraph/personTypes.n3 b/home/src/main/resources/rdf/tbox/filegraph/personTypes.n3 index 034472e7..8b056165 100644 --- a/home/src/main/resources/rdf/tbox/filegraph/personTypes.n3 +++ b/home/src/main/resources/rdf/tbox/filegraph/personTypes.n3 @@ -1,4 +1,4 @@ -@prefix afn: . +@prefix afn: . @prefix : . @prefix hr: . @prefix ns: . diff --git a/home/src/main/resources/rdf/tbox/filegraph/relationshipAxioms.n3 b/home/src/main/resources/rdf/tbox/filegraph/relationshipAxioms.n3 index b97a3062..8e80ffe1 100644 --- a/home/src/main/resources/rdf/tbox/filegraph/relationshipAxioms.n3 +++ b/home/src/main/resources/rdf/tbox/filegraph/relationshipAxioms.n3 @@ -1,5 +1,5 @@ @prefix hr: . -@prefix afn: . +@prefix afn: . @prefix : . @prefix scires: . @prefix aka: . diff --git a/installer/pom.xml b/installer/pom.xml index 8ff31d23..100397fe 100644 --- a/installer/pom.xml +++ b/installer/pom.xml @@ -21,8 +21,8 @@ maven-compiler-plugin - 1.7 - 1.7 + 1.8 + 1.8 UTF-8 diff --git a/installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties b/installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties index eef3874e..a7e18ae2 100644 --- a/installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties +++ b/installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties @@ -46,4 +46,4 @@ log4j.logger.org.apache.jena.sdb.layout2.LoaderTuplesNodes=FATAL log4j.logger.org.apache.jena.sdb.sql.SDBConnection=ERROR log4j.logger.org.openjena.riot=FATAL log4j.logger.org.apache.jena.riot=FATAL -log4j.logger.org.directwebremoting=FATAL +log4j.logger.org.directwebremoting=WARN diff --git a/pom.xml b/pom.xml index 98280fab..1dcda272 100644 --- a/pom.xml +++ b/pom.xml @@ -230,8 +230,8 @@ org.apache.maven.plugins maven-compiler-plugin - 1.7 - 1.7 + 1.8 + 1.8 UTF-8 diff --git a/selenium/src/test/java/org/vivoweb/vivo/selenium/WebAppTester.java b/selenium/src/test/java/org/vivoweb/vivo/selenium/WebAppTester.java index bf8efb8a..f23a2158 100644 --- a/selenium/src/test/java/org/vivoweb/vivo/selenium/WebAppTester.java +++ b/selenium/src/test/java/org/vivoweb/vivo/selenium/WebAppTester.java @@ -1,7 +1,7 @@ package org.vivoweb.vivo.selenium; import com.sun.tools.internal.xjc.Driver; -import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang33.StringUtils; import org.junit.Assert; import org.openqa.selenium.Alert; import org.openqa.selenium.By; diff --git a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/geopolitical-ver1.1-11-18-11-annotations.rdf b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/geopolitical-ver1.1-11-18-11-annotations.rdf index 82cbce85..97282f05 100644 --- a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/geopolitical-ver1.1-11-18-11-annotations.rdf +++ b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/geopolitical-ver1.1-11-18-11-annotations.rdf @@ -12,7 +12,7 @@ xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:j.2="http://www.w3.org/2008/05/skos#" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:j.3="http://www.w3.org/2003/06/sw-vocab-status/ns#" diff --git a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/isDefinedBy-1.5-annotations.rdf b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/isDefinedBy-1.5-annotations.rdf index 27938d1f..392a90b1 100644 --- a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/isDefinedBy-1.5-annotations.rdf +++ b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/isDefinedBy-1.5-annotations.rdf @@ -13,7 +13,7 @@ xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:j.2="http://www.w3.org/2008/05/skos#" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:j.3="http://www.w3.org/2003/06/sw-vocab-status/ns#" diff --git a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/scires-1.5-annotations.rdf b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/scires-1.5-annotations.rdf index 4eda8a12..683eae33 100644 --- a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/scires-1.5-annotations.rdf +++ b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/scires-1.5-annotations.rdf @@ -13,7 +13,7 @@ xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:skos="http://www.w3.org/2008/05/skos#" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#" diff --git a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/vivo-core-1.5-annotations.rdf b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/vivo-core-1.5-annotations.rdf index 88df4862..f39f09dd 100644 --- a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/vivo-core-1.5-annotations.rdf +++ b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldAnnotations/vivo-core-1.5-annotations.rdf @@ -13,7 +13,7 @@ xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:skos="http://www.w3.org/2008/05/skos#" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#" diff --git a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/isDefinedBy-1.5.owl b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/isDefinedBy-1.5.owl index df14801a..7020407f 100644 --- a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/isDefinedBy-1.5.owl +++ b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/isDefinedBy-1.5.owl @@ -11,7 +11,7 @@ xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#" xmlns:skos="http://www.w3.org/2008/05/skos#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#" diff --git a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/scires-1.5.owl b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/scires-1.5.owl index 1d58e2f2..91121913 100644 --- a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/scires-1.5.owl +++ b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/scires-1.5.owl @@ -8,7 +8,7 @@ xmlns:vivo="http://vivoweb.org/ontology/core#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:scires="http://vivoweb.org/ontology/scientific-research#" xmlns:dcterms="http://purl.org/dc/terms/" diff --git a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/vivo-core-1.5.owl b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/vivo-core-1.5.owl index 70cbb052..3226faa0 100644 --- a/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/vivo-core-1.5.owl +++ b/webapp/src/main/webapp/WEB-INF/ontologies/update15to16/oldVersion/vivo-core-1.5.owl @@ -8,7 +8,7 @@ xmlns:vivo="http://vivoweb.org/ontology/core#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" - xmlns:afn="http://jena.hpl.hp.com/ARQ/function#" + xmlns:afn="http://jena.apache.org/ARQ/function#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:scires="http://vivoweb.org/ontology/scientific-research#" xmlns:dcterms="http://purl.org/dc/terms/" diff --git a/webapp/src/main/webapp/WEB-INF/web.xml b/webapp/src/main/webapp/WEB-INF/web.xml index da650712..61cd93fe 100644 --- a/webapp/src/main/webapp/WEB-INF/web.xml +++ b/webapp/src/main/webapp/WEB-INF/web.xml @@ -1060,7 +1060,7 @@ dwr-invoker - uk.ltd.getahead.dwr.DWRServlet + org.directwebremoting.servlet.DwrServlet debug true @@ -1474,7 +1474,18 @@ OrcidIntegrationController /orcid/* - + + + + TpfServlet + TpfServlet + org.vivoweb.linkeddatafragments.servlet.VitroLinkedDataFragmentServlet + + + TpfServlet + /tpf/* + + diff --git a/webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml b/webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml index b4a908e2..6666a089 100644 --- a/webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml +++ b/webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml @@ -6,7 +6,7 @@ PREFIX foaf: <http://xmlns.com/foaf/0.1/> - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX owl: <http://www.w3.org/2002/07/owl#> diff --git a/webapp/src/main/webapp/config/listViewConfig-advisorIn.xml b/webapp/src/main/webapp/config/listViewConfig-advisorIn.xml index ae2ef824..320d319c 100644 --- a/webapp/src/main/webapp/config/listViewConfig-advisorIn.xml +++ b/webapp/src/main/webapp/config/listViewConfig-advisorIn.xml @@ -6,7 +6,7 @@ PREFIX foaf: <http://xmlns.com/foaf/0.1/> - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX owl: <http://www.w3.org/2002/07/owl#> diff --git a/webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml b/webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml index fbd8d1ee..ddd3ed86 100644 --- a/webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml +++ b/webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml @@ -7,7 +7,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX core: <http://vivoweb.org/ontology/core#> - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> SELECT DISTINCT ?dateTimeInterval ?label ?valueStart ?valueStartName diff --git a/webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml b/webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml index 1281a801..8b73336a 100644 --- a/webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml +++ b/webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml @@ -7,7 +7,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX core: <http://vivoweb.org/ontology/core#> - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> SELECT DISTINCT ?dateTimeValue (afn:localname(?dateTimePrecision) AS ?precision) diff --git a/webapp/src/main/webapp/config/listViewConfig-default.xml b/webapp/src/main/webapp/config/listViewConfig-default.xml index 3aaa19f1..533eb1c9 100644 --- a/webapp/src/main/webapp/config/listViewConfig-default.xml +++ b/webapp/src/main/webapp/config/listViewConfig-default.xml @@ -7,7 +7,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> diff --git a/webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml b/webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml index d4ae97cb..3efd7236 100644 --- a/webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml +++ b/webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml @@ -7,7 +7,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> diff --git a/webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml b/webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml index 2de65f00..885cf6e7 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml @@ -8,7 +8,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX vivo: <http://vivoweb.org/ontology/core#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> SELECT ?concept ?conceptLabel ?conceptName ?vocabularySource ?vocabularySourceName WHERE { diff --git a/webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml index 373f4e0d..378b56e0 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml @@ -5,7 +5,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX vivo: <http://vivoweb.org/ontology/core#> PREFIX owl: <http://www.w3.org/2002/07/owl#> diff --git a/webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml index 4648fca4..231cb255 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml @@ -5,7 +5,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> diff --git a/webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml index 4f503a7e..d48fd321 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml @@ -5,7 +5,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> diff --git a/webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml index 7e01c265..4188b905 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml @@ -5,7 +5,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> diff --git a/webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml index 9f34aabf..8b0e88a6 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml @@ -8,7 +8,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX vivo: <http://vivoweb.org/ontology/core#> PREFIX owl: <http://www.w3.org/2002/07/owl#> diff --git a/webapp/src/main/webapp/config/listViewConfig-hasPrincipalInvestigatorRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasPrincipalInvestigatorRole.xml index 88f37a91..3730e9c6 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasPrincipalInvestigatorRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasPrincipalInvestigatorRole.xml @@ -5,7 +5,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> diff --git a/webapp/src/main/webapp/config/listViewConfig-hasReviewerRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasReviewerRole.xml index 0de20953..4f3197a6 100644 --- a/webapp/src/main/webapp/config/listViewConfig-hasReviewerRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-hasReviewerRole.xml @@ -5,7 +5,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> diff --git a/webapp/src/main/webapp/config/listViewConfig-issuedCredential.xml b/webapp/src/main/webapp/config/listViewConfig-issuedCredential.xml index bb1deb4b..b5d5d40b 100644 --- a/webapp/src/main/webapp/config/listViewConfig-issuedCredential.xml +++ b/webapp/src/main/webapp/config/listViewConfig-issuedCredential.xml @@ -6,7 +6,7 @@ PREFIX foaf: <http://xmlns.com/foaf/0.1/> - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX owl: <http://www.w3.org/2002/07/owl#> diff --git a/webapp/src/main/webapp/config/listViewConfig-rangeUnion.xml b/webapp/src/main/webapp/config/listViewConfig-rangeUnion.xml index 92dbccdb..745edf03 100644 --- a/webapp/src/main/webapp/config/listViewConfig-rangeUnion.xml +++ b/webapp/src/main/webapp/config/listViewConfig-rangeUnion.xml @@ -7,7 +7,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> diff --git a/webapp/src/main/webapp/config/listViewConfig-relatedRole.xml b/webapp/src/main/webapp/config/listViewConfig-relatedRole.xml index dca9ffad..f3d86c04 100644 --- a/webapp/src/main/webapp/config/listViewConfig-relatedRole.xml +++ b/webapp/src/main/webapp/config/listViewConfig-relatedRole.xml @@ -8,7 +8,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX core: <http://vivoweb.org/ontology/core#> - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> PREFIX vcard: <http://www.w3.org/2006/vcard/ns#> diff --git a/webapp/src/main/webapp/config/listViewConfig-webpage.xml b/webapp/src/main/webapp/config/listViewConfig-webpage.xml index 184e8182..406f281e 100644 --- a/webapp/src/main/webapp/config/listViewConfig-webpage.xml +++ b/webapp/src/main/webapp/config/listViewConfig-webpage.xml @@ -7,7 +7,7 @@ - PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> + PREFIX afn: <http://jena.apache.org/ARQ/function#> PREFIX core: <http://vivoweb.org/ontology/core#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX vcard: <http://www.w3.org/2006/vcard/ns#> diff --git a/webapp/src/main/webapp/js/individual/individualQtipBubble.js b/webapp/src/main/webapp/js/individual/individualQtipBubble.js index 567c4f2b..661a25cb 100644 --- a/webapp/src/main/webapp/js/individual/individualQtipBubble.js +++ b/webapp/src/main/webapp/js/individual/individualQtipBubble.js @@ -7,11 +7,6 @@ $(document).ready(function(){ $.extend(this, i18nStrings); $('head').append(''); - padding: '0em', -// textAlign: 'center', -// fontSize: '0.7em', -// lineHeight: '15px', -// border: 'none', $('#researchAreaIcon').each(function() { @@ -38,11 +33,6 @@ $(document).ready(function(){ }); $('head').append(''); -// padding: '0em', -// textAlign: 'center', -// fontSize: '0.7em', -// lineHeight: '15px', -// border: 'none', $('#fullViewIcon').each(function() {