Update commons-lang to 3.4 (same as used by Jena 3.1.1)

grahamtriggs · Dec 17, 2016 · 06200d3 · 06200d3
1 parent 319e136
commit 06200d3
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Showing 36 changed files with 44 additions and 44 deletions.
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
@@ -25,7 +25,7 @@
 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;

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
@@ -18,7 +18,7 @@
 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
@@ -14,7 +14,7 @@
 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/...ornell/mannlib/vitro/webapp/controller/visualization/ShortURLVisualizationController.java b/...ornell/mannlib/vitro/webapp/controller/visualization/ShortURLVisualizationController.java
@@ -9,7 +9,7 @@
 
 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 @@ private Map<String, String> getParamatersForVis(List<String> matchedPatternGroup
 							+ 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 @@ private List<String> extractShortURLParameters(VitroRequest vitroRequest) {
 
 		List<String> matchedGroups = new ArrayList<String>(); 
 		String subURIString = vitroRequest.getRequestURI().substring(vitroRequest.getContextPath().length()+1);
-		String[] urlParams = StringEscapeUtils.escapeHtml(subURIString).split("/");
+		String[] urlParams = StringEscapeUtils.ESCAPE_HTML4.translate(subURIString).split("/");
 
 		if (urlParams.length > 1 
 				&& urlParams[0].equalsIgnoreCase("vis")) {

diff --git a/...n/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PersonHasPublicationValidator.java b/...n/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PersonHasPublicationValidator.java
@@ -6,7 +6,7 @@
 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/...n/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PublicationHasAuthorValidator.java b/...n/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/PublicationHasAuthorValidator.java
@@ -8,7 +8,7 @@
 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/...itro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java b/...itro/webapp/edit/n3editing/configuration/generators/AddRoleToPersonTwoStageGenerator.java
@@ -11,7 +11,7 @@
 
 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/...tro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java b/...tro/webapp/edit/n3editing/configuration/generators/SubjectHasPhoneFaxNumberGenerator.java
@@ -13,7 +13,7 @@
 
 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/.../webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java b/.../webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java
@@ -12,7 +12,7 @@
 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/...ebapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java b/...ebapp/edit/n3editing/configuration/preprocessors/RoleToActivityPredicatePreprocessor.java
@@ -9,7 +9,7 @@
 
 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/.../vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java b/.../vitro/webapp/edit/n3editing/configuration/preprocessors/RoleToPredicatePreprocessor.java
@@ -9,7 +9,7 @@
 
 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
@@ -11,7 +11,7 @@
 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/.../edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java b/.../edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java
@@ -22,7 +22,7 @@
 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/...u/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java b/...u/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipRequestHandler.java
@@ -8,8 +8,8 @@
 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/...itro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java b/...itro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java
@@ -8,7 +8,7 @@
 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/...mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java b/...mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java
@@ -17,7 +17,7 @@
 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/...nlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java b/...nlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountRequestHandler.java
@@ -6,8 +6,8 @@
 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/...nlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java b/...nlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java
@@ -22,8 +22,8 @@
 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/...nell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java b/...nell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java
@@ -18,7 +18,7 @@
 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/...l/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java b/...l/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountRequestHandler.java
@@ -8,7 +8,7 @@
 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/.../mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java b/.../mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java
@@ -14,7 +14,7 @@
 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 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/...nnlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java b/...nnlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountRequestHandler.java
@@ -7,8 +7,8 @@
 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/...ornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java b/...ornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java
@@ -4,7 +4,7 @@
 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/...ib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java b/...ib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java
@@ -15,8 +15,8 @@
 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/...ro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java b/...ro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java
@@ -15,8 +15,8 @@
 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
@@ -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/...ava/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java b/...ava/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java
@@ -7,7 +7,7 @@
 
 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/.../edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/ConstructedModelTracker.java b/.../edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/ConstructedModelTracker.java
@@ -4,7 +4,7 @@
 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/...ava/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java b/...ava/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java
@@ -5,7 +5,7 @@
 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 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/...c/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java b/...c/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java
@@ -12,7 +12,7 @@
 
 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/.../cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividual.java b/.../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/...nell/mannlib/vitro/webapp/web/templatemodels/searchresult/VIVOIndividualSearchResult.java b/...nell/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
@@ -21,7 +21,7 @@
 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/startup/JSONWrapperSetup.java b/api/src/main/java/org/vivoweb/webapp/startup/JSONWrapperSetup.java
@@ -11,7 +11,7 @@
 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/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/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;