Fix commons-lang3 errors

Using org.genesys-pgr:pgr-ontology-model

pom.xml

@@ -410,18 +410,7 @@
 			<version>${hazelcast.version}</version>
 		</dependency>
 
-		<dependency>
-			<groupId>org.apache.jena</groupId>
-			<artifactId>apache-jena-libs</artifactId>
-			<type>pom</type>
-			<version>2.10.1</version>
-		</dependency>
 
-		<dependency>
-			<groupId>org.bioversityinternational</groupId>
-			<artifactId>org.bioversityinternational.ontology</artifactId>
-			<version>0.6.2</version>
-		</dependency>
 
 		<dependency>
 			<groupId>org.jamel.dbf</groupId>
@@ -504,6 +493,11 @@
 		 	<artifactId>worldclim-reader</artifactId>
 		 	<version>0.0.3-SNAPSHOT</version>
 		 </dependency>
+		 <dependency>
+		 	<groupId>org.genesys-pgr</groupId>
+		 	<artifactId>pgr-ontology-model</artifactId>
+		 	<version>0.7.1-SNAPSHOT</version>
+		 </dependency>
 	</dependencies>
 
 	<build>

src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java

@@ -29,7 +29,7 @@ import javax.persistence.PrePersist;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 import org.genesys2.server.model.GlobalVersionedAuditedModel;
 import org.genesys2.server.model.impl.CropTaxonomy;
 import org.hibernate.annotations.Type;

src/main/java/org/genesys2/server/model/json/GenesysJsonFactory.java

@@ -19,7 +19,7 @@ package org.genesys2.server.model.json;
 import java.util.List;
 
 import org.apache.commons.lang.ArrayUtils;
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;

src/main/java/org/genesys2/server/service/impl/DirectMysqlQuery.java

@@ -22,7 +22,7 @@ import java.util.List;
 import java.util.Set;
 
 import org.apache.commons.lang.ArrayUtils;
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Method;
@@ -42,6 +42,7 @@ import org.springframework.data.domain.Sort.Order;
 
 public class DirectMysqlQuery {
 	private static final Log LOG = LogFactory.getLog(DirectMysqlQuery.class);
+	private static final String SPACE = " ";
 
 	final Set<String> tables = new HashSet<String>();
 	final List<Object> params = new ArrayList<Object>();
@@ -49,7 +50,7 @@ public class DirectMysqlQuery {
 
 	public DirectMysqlQuery(String baseTable, String baseAlias) {
 		sb = new StringBuffer(300);
-		sb.append(" from ").append(baseTable).append(StringUtils.SPACE).append(baseAlias);
+		sb.append(" from ").append(baseTable).append(SPACE).append(baseAlias);
 		tables.add(baseTable);
 	}
 
@@ -62,13 +63,13 @@ public class DirectMysqlQuery {
 		if (LOG.isDebugEnabled()) {
 			LOG.debug("Inner-joining " + table + " " + alias + " on " + onExpr);
 		}
-		sb.append(" inner join ").append(table).append(StringUtils.SPACE);
+		sb.append(" inner join ").append(table).append(SPACE);
 		tables.add(table);
 
 		if (StringUtils.isNotBlank(alias)) {
-			sb.append(alias).append(StringUtils.SPACE);
+			sb.append(alias).append(SPACE);
 		}
-		sb.append("on ").append(onExpr).append(StringUtils.SPACE);
+		sb.append("on ").append(onExpr).append(SPACE);
 		return this;
 	}
 
@@ -80,14 +81,14 @@ public class DirectMysqlQuery {
 		if (LOG.isDebugEnabled()) {
 			LOG.debug("Leftouter-joining " + table + " " + alias + " on " + onExpr);
 		}
-		sb.append(" left outer join ").append(table).append(StringUtils.SPACE);
+		sb.append(" left outer join ").append(table).append(SPACE);
 		tables.add(table);
 
 		if (StringUtils.isNotBlank(alias)) {
-			sb.append(alias).append(StringUtils.SPACE);
+			sb.append(alias).append(SPACE);
 		}
 		if (StringUtils.isNotBlank(onExpr)) {
-			sb.append("on ").append(onExpr).append(StringUtils.SPACE);
+			sb.append("on ").append(onExpr).append(SPACE);
 		}
 		return this;
 	}

src/main/java/org/genesys2/server/service/impl/DownloadServiceImpl.java

@@ -26,7 +26,7 @@ import java.util.List;
 
 import javax.persistence.EntityManager;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.poi.ss.usermodel.Cell;

src/main/java/org/genesys2/server/service/impl/FilterHandler.java

@@ -27,8 +27,8 @@ import java.util.Set;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.Predicate;
+import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang.StringUtils;
-import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.filters.AutocompleteFilter;

src/main/java/org/genesys2/server/service/impl/GenesysRESTServiceImpl.java

@@ -20,7 +20,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;

src/main/java/org/genesys2/server/service/impl/RequestServiceImpl.java

@@ -26,7 +26,7 @@ import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Accession;

src/main/java/org/genesys2/server/service/impl/TaxonomyManager.java

@@ -21,7 +21,7 @@ import java.util.concurrent.TimeUnit;
 import javax.annotation.Resource;
 
 import org.apache.commons.lang.StringUtils;
-import org.apache.commons.lang3.text.WordUtils;
+import org.apache.commons.lang.WordUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Taxonomy2;

src/main/java/org/genesys2/server/servlet/controller/ExplorerController.java

@@ -29,8 +29,8 @@ import java.util.Map;
 import javax.imageio.ImageIO;
 import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang.StringUtils;
-import org.apache.commons.lang3.ArrayUtils;
 import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.filters.GenesysFilter;
 import org.genesys2.server.model.genesys.Accession;

src/main/java/org/genesys2/server/servlet/controller/rdf/CropControllerRdf.java

@@ -19,8 +19,8 @@ package org.genesys2.server.servlet.controller.rdf;
 import java.util.List;
 import java.util.Map;
 
-import org.bioversityinternational.model.germplasm.CCO;
-import org.bioversityinternational.model.rdf.dwc.DarwinCore;
+import org.genesys2.rdf.model.dwc.DarwinCore;
+import org.genesys2.rdf.model.germplasm.CCO;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.CropRule;
 import org.genesys2.server.service.CropService;

src/main/java/org/genesys2/server/servlet/controller/rdf/DescriptorControllerRdf.java

@@ -21,8 +21,8 @@ import java.util.Map;
 
 import javax.servlet.http.HttpServletResponse;
 
-import org.bioversityinternational.model.germplasm.CCO;
-import org.bioversityinternational.model.rdf.skos.SKOS;
+import org.genesys2.rdf.model.germplasm.CCO;
+import org.genesys2.rdf.model.skos.SKOS;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.genesys.ParameterCategory;

src/main/java/org/genesys2/server/servlet/controller/rdf/RdfBaseController.java

@@ -21,10 +21,9 @@ import java.io.PrintStream;
 import java.io.UnsupportedEncodingException;
 import java.util.Date;
 
-import org.bioversityinternational.model.germplasm.CCO;
-import org.bioversityinternational.model.rdf.dc.DublinCore;
-import org.bioversityinternational.model.rdf.dwc.DarwinCore;
-import org.bioversityinternational.model.rdf.skos.SKOS;
+import org.genesys2.rdf.model.dc.DublinCore;
+import org.genesys2.rdf.model.dwc.DarwinCore;
+import org.genesys2.rdf.model.skos.SKOS;
 import org.genesys2.server.exception.UserException;
 import org.genesys2.server.model.VersionedAuditedModel;
 import org.genesys2.server.model.impl.User;
@@ -86,7 +85,6 @@ public abstract class RdfBaseController extends BaseController {
 		model.setNsPrefix("dcterms", DublinCore.getURI());
 		model.setNsPrefix("dwc", DarwinCore.getURI());
 		model.setNsPrefix("skos", SKOS.getURI());
-		model.setNsPrefix("cco", CCO.getURI());
 		model.setNsPrefix("genesys", getBaseUri() + "/");
 		return model;
 	}

src/main/java/org/genesys2/server/servlet/controller/rest/LookupController.java

@@ -21,7 +21,7 @@ import java.util.Locale;
 import java.util.Map;
 import java.util.TreeMap;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;

src/test/java/org/genesys2/transifex/client/TransifexClientTest.java

@@ -21,7 +21,7 @@ import static org.junit.Assert.assertTrue;
 
 import java.io.IOException;
 
-import org.apache.commons.lang3.RandomStringUtils;
+import org.apache.commons.lang.RandomStringUtils;
 import org.genesys2.server.test.PropertyPlacholderInitializer;
 import org.junit.Ignore;
 import org.junit.Test;