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Genesys PGR
Genesys Backend
Commits
5b88da74
Commit
5b88da74
authored
Sep 18, 2013
by
Matija Obreza
Browse files
Rebranded to org.genesys2.server
parent
c9db3e18
Changes
159
Hide whitespace changes
Inline
Side-by-side
.project
View file @
5b88da74
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>
org.
crophub.rest
</name>
<name>
org.
genesys2.server
</name>
<comment></comment>
<projects>
</projects>
...
...
build.gradle
deleted
100644 → 0
View file @
c9db3e18
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
deleted
100644 → 0
View file @
c9db3e18
version
=
0.0.4
\ No newline at end of file
pom.xml
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
...
...
@@ -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
View file @
5b88da74
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
;
...
...
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