Rebranded to org.genesys2.server

.project

 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>org.crophub.rest</name>
+	<name>org.genesys2.server</name>
 	<comment></comment>
 	<projects>
 	</projects>

build.gradle

-apply plugin: "java"
-
-//dependencies versions
-def version = [
-        "commons" : [
-                "beanutils" : "1.8.3",
-                "collections" : "3.2.1",
-                "fileupload" : "1.2.2",
-                "io" : "2.4",
-                "lang" : "2.6",
-                "logging" : "1.1.1"
-        ],
-        "slf4j" : "1.7.5",
-        "log4j" : "1.2.17",
-        "spring" : [
-                "core" : "3.2.2.RELEASE",
-                "security" : "3.1.4.RELEASE",
-                "data" : [
-                        "core" : "1.5.1.RELEASE",
-                        "jpa" : "1.3.2.RELEASE"
-                ]
-        ],
-        "hibernate" : [
-                "core" : "4.2.1.Final",
-                "annotations" : "4.0.1.Final"
-        ],
-        "aspectj" : "1.7.2",
-        "c3p0" : "0.9.2.1",
-        "hsqldb" : "2.2.9",
-        "mysql" : "5.1.25",
-        "jackson" : "2.2.1",
-        "oval" : "1.81",
-        "ehcache" : "2.7.0",
-        "jetty" : "9.0.3.v20130506"
-]
-
-repositories {
-    mavenCentral()
-}
-
-dependencies {
-    //commons dependencies
-    compile "commons-beanutils:commons-beanutils:${version.commons.beanutils}"
-    compile "commons-collections:commons-collections:${version.commons.collections}"
-    compile "commons-fileupload:commons-fileupload:${version.commons.fileupload}"
-    compile "commons-io:commons-io:${version.commons.io}"
-    compile "commons-lang:commons-lang:${version.commons.lang}"
-    compile "commons-logging:commons-logging:${version.commons.logging}"
-
-    //logging dependencies
-    compile "org.slf4j:slf4j-api:${version.slf4j}"
-    compile "org.slf4j:slf4j-log4j12:${version.slf4j}"
-    compile "log4j:log4j:${version.log4j}"
-
-    //Spring dependencies
-    compile "org.springframework:spring-context-support:${version.spring.core}"
-    compile "org.springframework:spring-jdbc:${version.spring.core}"
-    compile "org.springframework:spring-jms:${version.spring.core}"
-    compile "org.springframework:spring-orm:${version.spring.core}"
-    compile "org.springframework:spring-oxm:${version.spring.core}"
-    compile "org.springframework:spring-test:${version.spring.core}"
-    compile "org.springframework:spring-tx:${version.spring.core}"
-    compile "org.springframework:spring-web:${version.spring.core}"
-    compile "org.springframework:spring-webmvc:${version.spring.core}"
-    compile "org.springframework.security:spring-security-config:${version.spring.security}"
-    compile "org.springframework.security:spring-security-crypto:${version.spring.security}"
-    compile "org.springframework.security:spring-security-taglibs:${version.spring.security}"
-    compile "org.springframework.data:spring-data-commons:${version.spring.data.core}"
-    compile "org.springframework.data:spring-data-jpa:${version.spring.data.jpa}"
-
-    compile "org.aspectj:aspectjweaver:${version.aspectj}"
-
-    //hibernate dependencies
-    compile "org.hibernate:hibernate-core:${version.hibernate.core}"
-    compile "org.hibernate.common:hibernate-commons-annotations:${version.hibernate.annotations}"
-    compile("org.hibernate:hibernate-c3p0:${version.hibernate.core}"){
-        //We have newer version of c3p0
-        exclude module: "c3p0:c3p0"
-    }
-    compile "org.hibernate:hibernate-entitymanager:${version.hibernate.core}"
-
-    //DB dependencies
-    compile "com.mchange:c3p0:${version.c3p0}"
-    compile "org.hsqldb:hsqldb:${version.hsqldb}"
-    compile "mysql:mysql-connector-java:${version.mysql}"
-
-    //other dependencies
-    compile "com.fasterxml.jackson.core:jackson-databind:${version.jackson}"
-    compile "net.sf.oval:oval:${version.oval}"
-    compile "net.sf.ehcache:ehcache:${version.ehcache}"
-
-    //jetty container dependencies
-    compile "org.eclipse.jetty:jetty-deploy:${version.jetty}"
-    compile "org.eclipse.jetty:jetty-jsp:${version.jetty}"
-
-}
-
-compileJava {
-    sourceCompatibility "1.6"
-    targetCompatibility "1.6"
-}
-
-task startJetty(type: JavaExec, dependsOn: 'compileJava') {
-    classpath = sourceSets.main.runtimeClasspath
-    main = "com.crophub.JettyMain"
-}
-
-defaultTasks 'startJetty'
\ No newline at end of file

gradle.properties

-version=0.0.4
\ No newline at end of file

pom.xml

@@ -2,7 +2,7 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
-	<groupId>org.crophub</groupId>
+	<groupId>org.genesys2</groupId>
 	<artifactId>crophub</artifactId>
 	<version>0.0.1</version>
 
@@ -390,7 +390,7 @@
 						<version>1.2.1</version>
 
 						<configuration>
-							<mainClass>org.crophub.JettyMain</mainClass>
+							<mainClass>org.genesys2.JettyMain</mainClass>
 						</configuration>
 						<executions>
 							<execution>

src/main/java/org/crophub/JettyMain.java → src/main/java/org/genesys2/JettyMain.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.crophub;
+package org.genesys2;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;

src/main/java/org/croptrust/geo/sources/CountryInfo.java → src/main/java/org/genesys2/geo/sources/CountryInfo.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.croptrust.geo.sources;
+package org.genesys2.geo.sources;
 
 import java.io.Serializable;
 import java.text.MessageFormat;

src/main/java/org/croptrust/geo/sources/DavrosCountrySource.java → src/main/java/org/genesys2/geo/sources/DavrosCountrySource.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.croptrust.geo.sources;
+package org.genesys2.geo.sources;
 
 import java.io.BufferedReader;
 import java.io.IOException;

src/main/java/org/croptrust/geo/sources/GeoNamesCountrySource.java → src/main/java/org/genesys2/geo/sources/GeoNamesCountrySource.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.croptrust.geo.sources;
+package org.genesys2.geo.sources;
 
 import java.io.BufferedReader;
 import java.io.IOException;

src/main/java/org/crophub/rest/ApplicationException.java → src/main/java/org/genesys2/rest/ApplicationException.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest;
+package org.genesys2.rest;
 
 public class ApplicationException extends Exception {
 	private static final long serialVersionUID = 7077761656242902954L;

src/main/java/org/crophub/rest/common/aspect/AsAdmin.java → src/main/java/org/genesys2/rest/common/aspect/AsAdmin.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.aspect;
+package org.genesys2.rest.common.aspect;
 
 import java.lang.annotation.Documented;
 import java.lang.annotation.ElementType;

src/main/java/org/crophub/rest/common/aspect/AsAdminAspect.java → src/main/java/org/genesys2/rest/common/aspect/AsAdminAspect.java

@@ -15,14 +15,14 @@
  **/
 
 
-package org.crophub.rest.common.aspect;
+package org.genesys2.rest.common.aspect;
 
 import java.util.Arrays;
 
 import org.aspectj.lang.ProceedingJoinPoint;
 import org.aspectj.lang.annotation.Around;
 import org.aspectj.lang.annotation.Aspect;
-import org.crophub.rest.common.model.UserRole;
+import org.genesys2.rest.common.model.UserRole;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.security.core.Authentication;
@@ -43,8 +43,8 @@ public class AsAdminAspect {
             Arrays.asList(new SimpleGrantedAuthority(UserRole.ADMINISTRATOR.getName()))
     );
 
-    @Around("org.crophub.rest.common.aspect.SystemArchitecture.allServices()" +
-            " && @annotation(org.crophub.rest.common.aspect.AsAdmin)")
+    @Around("org.genesys2.rest.common.aspect.SystemArchitecture.allServices()" +
+            " && @annotation(org.genesys2.rest.common.aspect.AsAdmin)")
     public Object authenticateAsAdmin(ProceedingJoinPoint pjp) throws Throwable {
         //store previous version of auth (if any exists)
         Authentication prevAuth = SecurityContextHolder.getContext().getAuthentication();

src/main/java/org/crophub/rest/common/aspect/SystemArchitecture.java → src/main/java/org/genesys2/rest/common/aspect/SystemArchitecture.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.aspect;
+package org.genesys2.rest.common.aspect;
 
 import org.aspectj.lang.annotation.Aspect;
 import org.aspectj.lang.annotation.Pointcut;
@@ -31,19 +31,19 @@ public class SystemArchitecture {
     public void allServices(){
     }
 
-    @Pointcut("execution(* org.crophub.rest.common.service.*.*(..))")
+    @Pointcut("execution(* org.genesys2.rest.common.service.*.*(..))")
     public void businessServices(){
     }
 
-    @Pointcut("execution(* org.crophub.rest.common.listener.sample.*.*(..))")
+    @Pointcut("execution(* org.genesys2.rest.common.listener.sample.*.*(..))")
     public void sampleServices(){
     }
 
-    @Pointcut("execution(* org.crophub.rest.common.security.*.*(..))")
+    @Pointcut("execution(* org.genesys2.rest.common.security.*.*(..))")
     public void securityServices(){
     }
 
-    @Pointcut("execution(* org.crophub.rest.servlet.controller.*.*(..))")
+    @Pointcut("execution(* org.genesys2.rest.servlet.controller.*.*(..))")
     public void controllers(){
     }
 
@@ -52,15 +52,15 @@ public class SystemArchitecture {
      */
 
     //USER
-    @Pointcut("execution(* org.crophub.rest.common.service.impl.UserServiceImpl.addUser(..))")
+    @Pointcut("execution(* org.genesys2.rest.common.service.impl.UserServiceImpl.addUser(..))")
     public void addUserModel(){
     }
 
-    @Pointcut("execution(* org.crophub.rest.common.service.impl.UserServiceImpl.updateUser(..))")
+    @Pointcut("execution(* org.genesys2.rest.common.service.impl.UserServiceImpl.updateUser(..))")
     public void changeUserModel(){
     }
 
-    @Pointcut("execution(* org.crophub.rest.common.service.impl.UserServiceImpl.removeUser(..))")
+    @Pointcut("execution(* org.genesys2.rest.common.service.impl.UserServiceImpl.removeUser(..))")
     public void removeUserModel(){
     }
 

src/main/java/org/crophub/rest/common/config/ApplicationProps.java → src/main/java/org/genesys2/rest/common/config/ApplicationProps.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.config;
+package org.genesys2.rest.common.config;
 
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;

src/main/java/org/crophub/rest/common/exception/NoUserFoundException.java → src/main/java/org/genesys2/rest/common/exception/NoUserFoundException.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.exception;
+package org.genesys2.rest.common.exception;
 
 public class NoUserFoundException extends UserException {
 

src/main/java/org/crophub/rest/common/exception/NotUniqueUserException.java → src/main/java/org/genesys2/rest/common/exception/NotUniqueUserException.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.exception;
+package org.genesys2.rest.common.exception;
 
 public class NotUniqueUserException extends UserException {
 

src/main/java/org/crophub/rest/common/exception/UserException.java → src/main/java/org/genesys2/rest/common/exception/UserException.java

@@ -15,9 +15,9 @@
  **/
 
 
-package org.crophub.rest.common.exception;
+package org.genesys2.rest.common.exception;
 
-import org.crophub.rest.ApplicationException;
+import org.genesys2.rest.ApplicationException;
 
 public class UserException extends ApplicationException {
     /**

src/main/java/org/crophub/rest/common/factory/ObjectFactory.java → src/main/java/org/genesys2/rest/common/factory/ObjectFactory.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.factory;
+package org.genesys2.rest.common.factory;
 
 import org.springframework.beans.BeansException;
 import org.springframework.context.ApplicationContext;

src/main/java/org/crophub/rest/common/listener/RunAsAdminListener.java → src/main/java/org/genesys2/rest/common/listener/RunAsAdminListener.java

@@ -15,11 +15,11 @@
  **/
 
 
-package org.crophub.rest.common.listener;
+package org.genesys2.rest.common.listener;
 
 import java.util.concurrent.Callable;
 
-import org.crophub.rest.common.security.AsAdminInvoker;
+import org.genesys2.rest.common.security.AsAdminInvoker;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;

src/main/java/org/crophub/rest/common/listener/sample/CreateAdminListener.java → src/main/java/org/genesys2/rest/common/listener/sample/CreateAdminListener.java

@@ -14,15 +14,15 @@
  * limitations under the License.
  **/
 
-package org.crophub.rest.common.listener.sample;
+package org.genesys2.rest.common.listener.sample;
 
 import java.util.HashSet;
 import java.util.Set;
 
-import org.crophub.rest.common.listener.RunAsAdminListener;
-import org.crophub.rest.common.model.UserRole;
-import org.crophub.rest.common.model.impl.User;
-import org.crophub.rest.common.service.UserService;
+import org.genesys2.rest.common.listener.RunAsAdminListener;
+import org.genesys2.rest.common.model.UserRole;
+import org.genesys2.rest.common.model.impl.User;
+import org.genesys2.rest.common.service.UserService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 

src/main/java/org/crophub/rest/common/lucene/genesys/AccessionBridge.java → src/main/java/org/genesys2/rest/common/lucene/genesys/AccessionBridge.java

-package org.crophub.rest.common.lucene.genesys;
+package org.genesys2.rest.common.lucene.genesys;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.document.Field;
-import org.crophub.rest.common.model.genesys.Accession;
-import org.crophub.rest.common.model.genesys.AllAccnames;
-import org.crophub.rest.common.model.genesys.AllAcqBreeding;
-import org.crophub.rest.common.model.genesys.AllAcqCollect;
-import org.crophub.rest.common.model.genesys.AllAcqExchange;
-import org.crophub.rest.common.model.genesys.Taxonomy;
-import org.crophub.rest.common.model.impl.Country;
-import org.crophub.rest.common.model.impl.FaoInstitute;
+import org.genesys2.rest.common.model.genesys.Accession;
+import org.genesys2.rest.common.model.genesys.AllAccnames;
+import org.genesys2.rest.common.model.genesys.AllAcqBreeding;
+import org.genesys2.rest.common.model.genesys.AllAcqCollect;
+import org.genesys2.rest.common.model.genesys.AllAcqExchange;
+import org.genesys2.rest.common.model.genesys.Taxonomy;
+import org.genesys2.rest.common.model.impl.Country;
+import org.genesys2.rest.common.model.impl.FaoInstitute;
 import org.hibernate.search.bridge.FieldBridge;
 import org.hibernate.search.bridge.LuceneOptions;
 

src/main/java/org/crophub/rest/common/lucene/genesys/FaoInstituteBridge.java → src/main/java/org/genesys2/rest/common/lucene/genesys/FaoInstituteBridge.java

-package org.crophub.rest.common.lucene.genesys;
+package org.genesys2.rest.common.lucene.genesys;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.document.Field;
-import org.crophub.rest.common.model.impl.FaoInstitute;
+import org.genesys2.rest.common.model.impl.FaoInstitute;
 import org.hibernate.search.bridge.FieldBridge;
 import org.hibernate.search.bridge.LuceneOptions;
 

src/main/java/org/crophub/rest/common/lucene/genesys/StringDocument.java → src/main/java/org/genesys2/rest/common/lucene/genesys/StringDocument.java

-package org.crophub.rest.common.lucene.genesys;
+package org.genesys2.rest.common.lucene.genesys;
 
 import org.apache.commons.lang.StringUtils;
 

src/main/java/org/crophub/rest/common/model/AuditedModel.java → src/main/java/org/genesys2/rest/common/model/AuditedModel.java

@@ -14,13 +14,13 @@
  * limitations under the License.
  **/
 
-package org.crophub.rest.common.model;
+package org.genesys2.rest.common.model;
 
 import java.util.Date;
 
 import javax.persistence.MappedSuperclass;
 
-import org.crophub.rest.common.model.impl.User;
+import org.genesys2.rest.common.model.impl.User;
 
 @MappedSuperclass
 public abstract class AuditedModel extends OwnedModel {

src/main/java/org/crophub/rest/common/model/BusinessModel.java → src/main/java/org/genesys2/rest/common/model/BusinessModel.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.model;
+package org.genesys2.rest.common.model;
 
 import javax.persistence.Column;
 import javax.persistence.GeneratedValue;

src/main/java/org/crophub/rest/common/model/HibernateModel.java → src/main/java/org/genesys2/rest/common/model/HibernateModel.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.model;
+package org.genesys2.rest.common.model;
 
 import java.io.Serializable;
 

src/main/java/org/crophub/rest/common/model/OwnedModel.java → src/main/java/org/genesys2/rest/common/model/OwnedModel.java

@@ -14,12 +14,12 @@
  * limitations under the License.
  **/
 
-package org.crophub.rest.common.model;
+package org.genesys2.rest.common.model;
 
 import javax.persistence.ManyToOne;
 import javax.persistence.MappedSuperclass;
 
-import org.crophub.rest.common.model.impl.User;
+import org.genesys2.rest.common.model.impl.User;
 
 @MappedSuperclass
 public abstract class OwnedModel extends BusinessModel {

src/main/java/org/crophub/rest/common/model/Permissions.java → src/main/java/org/genesys2/rest/common/model/Permissions.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.model;
+package org.genesys2.rest.common.model;
 
 public enum Permissions {
     CREATE("Create"),

src/main/java/org/crophub/rest/common/model/UserRole.java → src/main/java/org/genesys2/rest/common/model/UserRole.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.model;
+package org.genesys2.rest.common.model;
 
 public enum  UserRole {
     USER("User"),

src/main/java/org/crophub/rest/common/model/genesys/Accession.java → src/main/java/org/genesys2/rest/common/model/genesys/Accession.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.crophub.rest.common.model.genesys;
+package org.genesys2.rest.common.model.genesys;
 
 // Generated Apr 24, 2013 10:08:59 AM by Hibernate Tools 4.0.0
 
@@ -29,9 +29,9 @@ import javax.persistence.ManyToOne;
 import javax.persistence.OneToOne;
 import javax.persistence.Table;
 
-import org.crophub.rest.common.lucene.genesys.AccessionBridge;
-import org.crophub.rest.common.model.impl.Country;
-import org.crophub.rest.common.model.impl.FaoInstitute;
+import org.genesys2.rest.common.lucene.genesys.AccessionBridge;
+import org.genesys2.rest.common.model.impl.Country;
+import org.genesys2.rest.common.model.impl.FaoInstitute;
 import org.hibernate.search.annotations.ClassBridge;
 import org.hibernate.search.annotations.DocumentId;
 import org.hibernate.search.annotations.Indexed;

src/main/java/org/crophub/rest/common/model/genesys/AccessionTrait.java → src/main/java/org/genesys2/rest/common/model/genesys/AccessionTrait.java

@@ -15,7 +15,7 @@
  **/
 
 
-package org.crophub.rest.common.model.genesys;
+package org.genesys2.rest.common.model.genesys;
 
 import java.io.Serializable;
 

src/main/java/org/crophub/rest/common/model/genesys/AllAccnames.java → src/main/java/org/genesys2/rest/common/model/genesys/AllAccnames.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.crophub.rest.common.model.genesys;
+package org.genesys2.rest.common.model.genesys;
 
 // Generated Apr 24, 2013 10:08:59 AM by Hibernate Tools 4.0.0
 

src/main/java/org/crophub/rest/common/model/genesys/AllAcqBreeding.java → src/main/java/org/genesys2/rest/common/model/genesys/AllAcqBreeding.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.crophub.rest.common.model.genesys;
+