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Genesys PGR
Genesys Backend
Commits
322bf2d9
Commit
322bf2d9
authored
Mar 17, 2015
by
Matija Obreza
Browse files
Fix commons-lang3 errors
Using org.genesys-pgr:pgr-ontology-model
parent
bcff1971
Changes
15
Hide whitespace changes
Inline
Side-by-side
pom.xml
View file @
322bf2d9
...
...
@@ -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
View file @
322bf2d9
...
...
@@ -29,7 +29,7 @@ import javax.persistence.PrePersist;
import
javax.persistence.Table
;
import
javax.persistence.UniqueConstraint
;
import
org.apache.commons.lang
3
.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
View file @
322bf2d9
...
...
@@ -19,7 +19,7 @@ package org.genesys2.server.model.json;
import
java.util.List
;
import
org.apache.commons.lang.ArrayUtils
;
import
org.apache.commons.lang
3
.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
View file @
322bf2d9
...
...
@@ -22,7 +22,7 @@ import java.util.List;
import
java.util.Set
;
import
org.apache.commons.lang.ArrayUtils
;
import
org.apache.commons.lang
3
.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
View file @
322bf2d9
...
...
@@ -26,7 +26,7 @@ import java.util.List;
import
javax.persistence.EntityManager
;
import
org.apache.commons.lang
3
.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
View file @
322bf2d9
...
...
@@ -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
View file @
322bf2d9
...
...
@@ -20,7 +20,7 @@ import java.util.ArrayList;
import
java.util.Collection
;
import
java.util.List
;
import
org.apache.commons.lang
3
.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
View file @
322bf2d9
...
...
@@ -26,7 +26,7 @@ import java.util.Locale;
import
java.util.Map
;
import
java.util.Set
;
import
org.apache.commons.lang
3
.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
View file @
322bf2d9
...
...
@@ -21,7 +21,7 @@ import java.util.concurrent.TimeUnit;
import
javax.annotation.Resource
;
import
org.apache.commons.lang.StringUtils
;
import
org.apache.commons.lang
3.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
View file @
322bf2d9
...
...
@@ -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
View file @
322bf2d9
...
...
@@ -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
View file @
322bf2d9
...
...
@@ -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
View file @
322bf2d9
...
...
@@ -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
View file @
322bf2d9
...
...
@@ -21,7 +21,7 @@ import java.util.Locale;
import
java.util.Map
;
import
java.util.TreeMap
;
import
org.apache.commons.lang
3
.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
View file @
322bf2d9
...
...
@@ -21,7 +21,7 @@ import static org.junit.Assert.assertTrue;
import
java.io.IOException
;
import
org.apache.commons.lang
3
.RandomStringUtils
;
import
org.apache.commons.lang.RandomStringUtils
;
import
org.genesys2.server.test.PropertyPlacholderInitializer
;
import
org.junit.Ignore
;
import
org.junit.Test
;
...
...
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