From b8fd17ba1ec3bcf805c47fc326df3a52d49b2063 Mon Sep 17 00:00:00 2001
From: "Huda J. Khan" <hjk54@cornell.edu>
Date: Wed, 7 Feb 2018 18:39:58 -0500
Subject: [PATCH] Revert "integrating related term info in skos utils"

This reverts commit 8f66b10323ffb14bc5d622502d7dd12b8b6f3934.
---
 .../mannlib/semservices/util/SKOSUtils.java   |  21 +--
 dependencies/pom.xml                          | 164 ++++++------------
 2 files changed, 56 insertions(+), 129 deletions(-)

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 fb29b3f0b..5b8955a87 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
@@ -1,4 +1,4 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+/* $This file is distributed under the terms of the license in LICENSE$ */
 
 /* We are no longer using the SKOS API since Vitro has moved to V 4.0 of OWL API which does not appear to be compatible.
  This file will contain methods used for reading SKOS as XML and parsing it for the properties
@@ -160,19 +160,13 @@ public class SKOSUtils {
 			// conceptURI);
 			concept.setCloseMatchURIList(closeMatchURIList);
 
-		 
 			// Notes may exist, in which case they should be employed
 			if (addNotes) {
-				List<String> notes = getNotesFromModel(conceptURI, model, langTagValue);
+				List<String> notes = getNotesFromModel(conceptURI, model,
+						langTagValue);
 				if (notes.size() > 0) {
 					concept.setDefinition(notes.get(0));
 				}
-			} else { // get definitions from skos:definition
-
-				List<String> definitions = getDefinitionFromModel(conceptURI, model, langTagValue);
-				if (definitions.size() > 0) {
-					concept.setDefinition(definitions.get(0));
-				}
 			}
 
 		} catch (Exception e) {
@@ -225,17 +219,12 @@ public class SKOSUtils {
 		String propertyURI = "http://www.w3.org/2004/02/skos/core#note";
 		return getLabelsFromModel(conceptURI, propertyURI, model, langTagValue);
 	}
-	
-	private static List<String> getDefinitionFromModel(String conceptURI,
-			Model model, String langTagValue) {
-		String propertyURI = "http://www.w3.org/2004/02/skos/core#definition";
-		return getLabelsFromModel(conceptURI, propertyURI, model, langTagValue);
-	}
 
 	private static List<String> getCloseMatchURIsFromModel(String conceptURI,
 			Model model) {
 		String propertyURI = "http://www.w3.org/2004/02/skos/core#closeMatch";
-		return getRelatedURIsFromModel(conceptURI, propertyURI, model); 
+		return getRelatedURIsFromModel(conceptURI, propertyURI, model);
+
 	}
 
 	private static List<String> getExactMatchURIsFromModel(String conceptURI,
diff --git a/dependencies/pom.xml b/dependencies/pom.xml
index eb18519c1..77bc41c76 100644
--- a/dependencies/pom.xml
+++ b/dependencies/pom.xml
@@ -7,37 +7,37 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vitro-dependencies</artifactId>
-    <version>1.10.0-beta2</version>
+    <version>2.0.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vitro-project</artifactId>
-        <version>1.10.0-beta2</version>
+        <version>2.0.0-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
     <name>Vitro Dependencies</name>
 
     <dependencies>
-        <dependency>
-            <!-- Added for runtime -->
+        <!-- Added for runtime, or just EasyMock -->
+        <!-- dependency>
             <groupId>asm</groupId>
             <artifactId>asm</artifactId>
             <version>3.1</version>
-        </dependency>
-        <dependency>
-            <!-- Added for runtime, was 1.6 -->
+        </dependency -->
+        <!-- Added for runtime, was 1.6 - was used by Pellet, still needed? -->
+        <!-- dependency>
             <groupId>com.github.ansell.aterms</groupId>
             <artifactId>aterm-java</artifactId>
             <version>1.8.2</version>
-        </dependency>
-        <dependency>
-            <!-- Added for runtime -->
+        </dependency -->
+        <!-- Added for runtime, used by Jackson databind, was used by EasyMock -->
+        <!-- dependency>
             <groupId>cglib</groupId>
             <artifactId>cglib</artifactId>
             <version>2.2</version>
-        </dependency>
+        </dependency -->
             <!-- Added for runtime -->
         <!-- dependency>
             <groupId>com.servlets</groupId>
@@ -68,37 +68,32 @@
         <dependency>
             <groupId>com.ibm.icu</groupId>
             <artifactId>icu4j</artifactId>
-            <version>3.4.4</version>
-        </dependency>
-        <dependency>
-            <groupId>com.mchange</groupId>
-            <artifactId>c3p0</artifactId>
-            <version>0.9.5.2</version>
+            <version>59.1</version>
         </dependency>
         <dependency>
             <groupId>com.twelvemonkeys.imageio</groupId>
             <artifactId>imageio-jpeg</artifactId>
-            <version>3.3.1</version>
+            <version>3.3.2</version>
         </dependency>
         <dependency>
             <groupId>com.twelvemonkeys.imageio</groupId>
             <artifactId>imageio-tiff</artifactId>
-            <version>3.3.1</version>
+            <version>3.3.2</version>
         </dependency>
         <dependency>
             <groupId>com.twelvemonkeys.servlet</groupId>
             <artifactId>servlet</artifactId>
-            <version>3.3.1</version>
+            <version>3.3.2</version>
         </dependency>
         <dependency>
-            <groupId>commons-dbcp</groupId>
-            <artifactId>commons-dbcp</artifactId>
-            <version>1.4</version>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-dbcp2</artifactId>
+            <version>2.1.1</version>
         </dependency>
         <dependency>
             <groupId>commons-fileupload</groupId>
             <artifactId>commons-fileupload</artifactId>
-            <version>1.3.2</version>
+            <version>1.3.3</version>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>
@@ -111,30 +106,15 @@
             <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>
-            <version>1.4</version>
-        </dependency>
-        <dependency>
-            <groupId>commons-logging</groupId>
-            <artifactId>commons-logging</artifactId>
-            <version>1.1.1</version>
-        </dependency>
-        <dependency>
-            <groupId>joda-time</groupId>
-            <artifactId>joda-time</artifactId>
-            <version>1.4</version>
+            <artifactId>commons-collections4</artifactId>
+            <version>4.1</version>
         </dependency>
         <dependency>
             <groupId>mysql</groupId>
             <artifactId>mysql-connector-java</artifactId>
-            <version>5.1.42</version>
+            <version>6.0.6</version>
         </dependency>
         <dependency>
             <groupId>net.sf.jga</groupId>
@@ -150,7 +130,7 @@
         <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>
@@ -164,16 +144,17 @@
                 </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>
             <artifactId>owlapi-api</artifactId>
-            <version>5.0.4</version>
+            <version>5.1.1</version>
         </dependency>
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-apibinding</artifactId>
-            <version>5.0.4</version>
+            <version>5.1.1</version>
             <!-- Exclude rio binding as we don't use Sesame -->
             <exclusions>
                 <exclusion>
@@ -182,67 +163,51 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.semarglproject</groupId>
-            <artifactId>semargl-core</artifactId>
-            <version>0.6.1</version>
-        </dependency>
-        <dependency>
-            <groupId>org.semarglproject</groupId>
-            <artifactId>semargl-rdfa</artifactId>
-            <version>0.6.1</version>
-        </dependency>
-        <dependency>
-            <groupId>com.github.jsonld-java</groupId>
-            <artifactId>jsonld-java</artifactId>
-            <version>0.8.3</version>
-        </dependency>
-        <!-- Force updated Jackson core used by dependencies, otherwise we get an incompatible version -->
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-core</artifactId>
-            <version>2.7.4</version>
-        </dependency>
-        <!-- Needed for ORCID? -->
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>fluent-hc</artifactId>
-            <version>4.5.2</version>
-        </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
-            <version>4.5.2</version>
+            <version>4.5.3</version>
         </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpmime</artifactId>
-            <version>4.5.2</version>
+            <version>4.5.3</version>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-arq</artifactId>
-            <version>3.3.0</version>
+            <version>3.4.0</version>
+            <exclusions>
+                <!-- Exclude OSGi bundles from jsonld-java -->
+                <exclusion>
+                    <groupId>org.apache.httpcomponents</groupId>
+                    <artifactId>httpclient-osgi</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.httpcomponents</groupId>
+                    <artifactId>httpcore-osgi</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
-            <version>3.3.0</version>
+            <version>3.4.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-sdb</artifactId>
-            <version>3.3.0</version>
+            <version>3.4.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-tdb</artifactId>
-            <version>3.3.0</version>
+            <version>3.4.0</version>
         </dependency>
         <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>
@@ -254,30 +219,15 @@
             <artifactId>freemarker</artifactId>
             <version>2.3.23</version>
         </dependency>
-        <dependency>
-            <groupId>org.glassfish</groupId>
-            <artifactId>javax.json</artifactId>
-            <version>1.0.4</version>
-        </dependency>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>jtidy</artifactId>
-            <version>r8-20060801</version>
-        </dependency>
         <dependency>
             <groupId>org.jsoup</groupId>
             <artifactId>jsoup</artifactId>
-            <version>1.10.1</version>
+            <version>1.10.3</version>
         </dependency>
         <dependency>
             <groupId>org.owasp.antisamy</groupId>
             <artifactId>antisamy</artifactId>
-            <version>1.5.3</version>
-        </dependency>
-        <dependency>
-            <groupId>com.google.code.gson</groupId>
-            <artifactId>gson</artifactId>
-            <version>2.5</version>
+            <version>1.5.6</version>
         </dependency>
 
         <!-- Used for JSP runtime -->
@@ -289,30 +239,18 @@
         <dependency>
             <groupId>org.apache.taglibs</groupId>
             <artifactId>taglibs-standard-spec</artifactId>
-            <version>1.2.1</version>
+            <version>1.2.5</version>
         </dependency>
         <dependency>
             <groupId>org.apache.taglibs</groupId>
             <artifactId>taglibs-standard-impl</artifactId>
-            <version>1.2.1</version>
+            <version>1.2.5</version>
         </dependency>
 
-        <!-- dependency>
-            <groupId>javax.json</groupId>
-            <artifactId>javax.json-api</artifactId>
-            <version>1.0</version>
-        </dependency -->
         <dependency>
-            <groupId>javax.mail</groupId>
-            <artifactId>mail</artifactId>
-            <version>1.4</version>
-        </dependency>
-        <!-- Data Distribution API -->
-        <dependency>
-          <groupId>edu.cornell.library.scholars</groupId>
-          <artifactId>DataDistributionAPI_VIVO_1.10.0</artifactId>
-          <version>1.0</version>
-          <type>jar</type>
+            <groupId>com.sun.mail</groupId>
+            <artifactId>javax.mail</artifactId>
+            <version>1.6.0</version>
         </dependency>
     </dependencies>
 </project>