Updated dependencies

api/src/main/java/edu/cornell/mannlib/vedit/tags/OptionTag.java

@@ -2,8 +2,8 @@
 
 package edu.cornell.mannlib.vedit.tags;
 
-import org.apache.commons.collections.map.ListOrderedMap;
+import org.apache.commons.collections4.map.ListOrderedMap;
-import org.apache.commons.collections.OrderedMapIterator;
+import org.apache.commons.collections4.OrderedMapIterator;
 import java.util.List;
 import java.util.Iterator;
 import java.io.IOException;
@@ -51,7 +51,7 @@ public class OptionTag extends EditTag {
             } catch (ClassCastException e){
                 // maybe it's a ListOrderedMap of optgroups
                 optGroups = (ListOrderedMap) getFormObject().getOptionLists().get(name);
-                OrderedMapIterator ogKey = optGroups.orderedMapIterator();
+                OrderedMapIterator ogKey = optGroups.mapIterator();
                 while (ogKey.hasNext()) {
                     String optGroupName = (String) ogKey.next();
                     out.println("<optgroup label=\""+StringEscapeUtils.ESCAPE_HTML4.translate(optGroupName)+"\">");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/EntityRetryController.java

@@ -19,7 +19,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import edu.cornell.mannlib.vitro.webapp.utils.JSPPageHandler;
-import org.apache.commons.collections.map.ListOrderedMap;
+import org.apache.commons.collections4.map.ListOrderedMap;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -230,7 +230,7 @@ public class EntityRetryController extends BaseEditController {
             }
 
             List<DynamicField> dynamicFields = new ArrayList();
-            Iterator<String> dpHashIt = dpMap.orderedMapIterator();
+            Iterator<String> dpHashIt = dpMap.mapIterator();
             while (dpHashIt.hasNext()) {
                 String uri = dpHashIt.next();
                 DataProperty dp = (DataProperty) dpMap.get(uri);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaXMLFileUpload.java

@@ -207,7 +207,7 @@ public class JenaXMLFileUpload  extends JenaIngestController  {
 				XsltTransformer t = xsltExec.load();
 				//this is how to set parameters:
 				//t.setParameter(new QName("someparametername"), new XdmAtomicValue(10));				
-				Serializer out = new Serializer();
+				Serializer out = new Processor(false).newSerializer();
 				out.setOutputProperty(Serializer.Property.METHOD, "xml");
 				out.setOutputProperty(Serializer.Property.INDENT, "yes");
 				File outFile = new File(file.getAbsolutePath() + ".rdfxml");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filters/CachingResponseFilter.java

@@ -19,7 +19,7 @@ import javax.servlet.annotation.WebFilter;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.EnumerationUtils;
+import org.apache.commons.collections4.EnumerationUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/test/java/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRdfAssemblerTest.java

@@ -18,7 +18,7 @@ import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
 
-import org.apache.commons.collections.IteratorUtils;
+import org.apache.commons.collections4.IteratorUtils;
 import org.apache.log4j.Level;
 import org.junit.Before;
 import org.junit.Test;

dependencies/pom.xml

@@ -111,20 +111,10 @@
             <artifactId>commons-lang3</artifactId>
             <version>3.4</version>
         </dependency>
-        <dependency>
-            <groupId>commons-collections</groupId>
-            <artifactId>commons-collections</artifactId>
-            <version>3.2.2</version>
-        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
-            <artifactId>commons-csv</artifactId>
+            <artifactId>commons-collections4</artifactId>
-            <version>1.4</version>
+            <version>4.1</version>
-        </dependency>
-        <dependency>
-            <groupId>commons-logging</groupId>
-            <artifactId>commons-logging</artifactId>
-            <version>1.1.1</version>
         </dependency>
         <dependency>
             <groupId>mysql</groupId>
@@ -145,7 +135,7 @@
         <dependency>
             <groupId>net.sf.saxon</groupId>
             <artifactId>Saxon-HE</artifactId>
-            <version>9.6.0-7</version>
+            <version>9.8.0-4</version>
         </dependency>
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
@@ -159,6 +149,7 @@
                 </exclusion>
             </exclusions>
         </dependency>
+        <!-- OWLAPI should match the version used by JFact -->
         <!-- Include all OWALPI JARs that are in the OSGi bundle -->
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
@@ -180,12 +171,12 @@
         <dependency>
             <groupId>org.semarglproject</groupId>
             <artifactId>semargl-core</artifactId>
-            <version>0.6.1</version>
+            <version>0.7</version>
         </dependency>
         <dependency>
             <groupId>org.semarglproject</groupId>
             <artifactId>semargl-rdfa</artifactId>
-            <version>0.6.1</version>
+            <version>0.7</version>
         </dependency>
         <!-- Needed for ORCID? -->
         <dependency>
@@ -226,7 +217,7 @@
         <dependency>
             <groupId>org.apache.solr</groupId>
             <artifactId>solr-solrj</artifactId>
-            <version>4.7.2</version>
+            <version>4.10.4</version>
         </dependency>
         <dependency>
             <groupId>org.directwebremoting</groupId>

solr/pom.xml

@@ -38,7 +38,7 @@
         <dependency>
             <groupId>org.apache.solr</groupId>
             <artifactId>solr</artifactId>
-            <version>4.7.2</version>
+            <version>4.10.4</version>
             <type>war</type>
         </dependency>
         <dependency>