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Genesys PGR
Genesys Backend
Commits
3b06011f
Commit
3b06011f
authored
Jan 15, 2014
by
Matija Obreza
Browse files
REST API updated for donorCode, donorNumb, donorName
parent
5fd3b72c
Changes
5
Hide whitespace changes
Inline
Side-by-side
src/main/java/org/genesys2/server/model/genesys/A
llAcq
Exchange.java
→
src/main/java/org/genesys2/server/model/genesys/A
ccession
Exchange.java
View file @
3b06011f
...
...
@@ -31,7 +31,7 @@ import org.genesys2.server.model.BusinessModel;
*/
@Entity
@Table
(
name
=
"accessionexchange"
)
public
class
A
llAcq
Exchange
extends
BusinessModel
{
public
class
A
ccession
Exchange
extends
BusinessModel
{
@Version
private
long
version
=
0
;
...
...
@@ -43,10 +43,13 @@ public class AllAcqExchange extends BusinessModel{
@Column
(
name
=
"donorInst"
,
length
=
8
)
private
String
donorInstitute
;
@Column
(
name
=
"donorName"
,
length
=
200
)
private
String
donorName
;
@Column
(
name
=
"acceNumb"
,
length
=
36
)
private
String
accNumbDonor
;
public
A
llAcq
Exchange
()
{
public
A
ccession
Exchange
()
{
}
public
long
getVersion
()
{
...
...
@@ -82,4 +85,11 @@ public class AllAcqExchange extends BusinessModel{
this
.
accNumbDonor
=
accNumbDonor
;
}
public
String
getDonorName
()
{
return
donorName
;
}
public
void
setDonorName
(
String
donorName
)
{
this
.
donorName
=
donorName
;
}
}
src/main/java/org/genesys2/server/persistence/domain/AccessionExchangeRepository.java
View file @
3b06011f
...
...
@@ -17,11 +17,11 @@
package
org.genesys2.server.persistence.domain
;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.genesys.A
llAcq
Exchange
;
import
org.genesys2.server.model.genesys.A
ccession
Exchange
;
import
org.springframework.data.jpa.repository.JpaRepository
;
public
interface
AccessionExchangeRepository
extends
JpaRepository
<
A
llAcq
Exchange
,
Long
>
{
public
interface
AccessionExchangeRepository
extends
JpaRepository
<
A
ccession
Exchange
,
Long
>
{
A
llAcq
Exchange
findByAccession
(
Accession
accession
);
A
ccession
Exchange
findByAccession
(
Accession
accession
);
}
src/main/java/org/genesys2/server/service/GenesysService.java
View file @
3b06011f
...
...
@@ -29,7 +29,7 @@ import org.genesys2.server.model.genesys.AccessionGeo;
import
org.genesys2.server.model.genesys.AllAccnames
;
import
org.genesys2.server.model.genesys.AccessionBreeding
;
import
org.genesys2.server.model.genesys.AccessionCollect
;
import
org.genesys2.server.model.genesys.A
llAcq
Exchange
;
import
org.genesys2.server.model.genesys.A
ccession
Exchange
;
import
org.genesys2.server.model.genesys.ExperimentTrait
;
import
org.genesys2.server.model.genesys.Metadata
;
import
org.genesys2.server.model.genesys.Method
;
...
...
@@ -63,7 +63,7 @@ public interface GenesysService {
List
<
AccessionAlias
>
listAccessionAliases
(
Accession
accession
);
A
llAcq
Exchange
listAccessionExchange
(
Accession
accession
);
A
ccession
Exchange
listAccessionExchange
(
Accession
accession
);
AccessionCollect
listAccessionCollect
(
Accession
accession
);
...
...
@@ -134,6 +134,7 @@ public interface GenesysService {
void
saveCollecting
(
List
<
AccessionCollect
>
all
);
void
saveGeo
(
List
<
AccessionGeo
>
all
);
void
saveBreeding
(
List
<
AccessionBreeding
>
all
);
void
saveExchange
(
List
<
AccessionExchange
>
all
);
void
refreshMetadataMethods
();
...
...
@@ -146,4 +147,5 @@ public interface GenesysService {
void
removeAliases
(
List
<
AccessionAlias
>
aliases
);
}
src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java
View file @
3b06011f
...
...
@@ -28,11 +28,12 @@ import org.apache.commons.logging.Log;
import
org.apache.commons.logging.LogFactory
;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.genesys.AccessionAlias
;
import
org.genesys2.server.model.genesys.AccessionGeo
;
import
org.genesys2.server.model.genesys.AccessionCollect
;
import
org.genesys2.server.model.genesys.AccessionAlias.AliasType
;
import
org.genesys2.server.model.genesys.AccessionBreeding
;
import
org.genesys2.server.model.genesys.AccessionCollect
;
import
org.genesys2.server.model.genesys.AccessionExchange
;
import
org.genesys2.server.model.genesys.AccessionGeo
;
import
org.genesys2.server.model.genesys.Taxonomy
;
import
org.genesys2.server.model.genesys.AccessionAlias.AliasType
;
import
org.genesys2.server.model.impl.Country
;
import
org.genesys2.server.model.impl.FaoInstitute
;
import
org.genesys2.server.service.BatchRESTService
;
...
...
@@ -42,8 +43,8 @@ import org.genesys2.server.service.InstituteService;
import
org.genesys2.server.service.OrganizationService
;
import
org.genesys2.server.service.TaxonomyService
;
import
org.genesys2.server.servlet.controller.rest.model.AccessionAliasJson
;
import
org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson
;
import
org.genesys2.server.servlet.controller.rest.model.AccessionJson
;
import
org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.security.access.prepost.PreAuthorize
;
import
org.springframework.stereotype.Service
;
...
...
@@ -82,6 +83,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
List
<
AccessionCollect
>
toSaveColl
=
new
ArrayList
<
AccessionCollect
>();
List
<
AccessionGeo
>
toSaveGeo
=
new
ArrayList
<
AccessionGeo
>();
List
<
AccessionBreeding
>
toSaveBreed
=
new
ArrayList
<
AccessionBreeding
>();
List
<
AccessionExchange
>
toSaveExch
=
new
ArrayList
<
AccessionExchange
>();
for
(
AccessionJson
dataJson
:
batch
.
keySet
())
{
if
(
LOG
.
isDebugEnabled
())
...
...
@@ -325,6 +327,27 @@ public class BatchRESTServiceImpl implements BatchRESTService {
toSaveBreed
.
add
(
accnBred
);
}
if
(
accnJson
.
has
(
"donorCode"
)
||
accnJson
.
has
(
"donorNumb"
)
||
accnJson
.
has
(
"donorName"
))
{
AccessionExchange
accnExch
=
genesysService
.
listAccessionExchange
(
accession
);
if
(
accnExch
==
null
)
{
accnExch
=
new
AccessionExchange
();
accnExch
.
setAccession
(
accession
);
}
value
=
accnJson
.
get
(
"donorCode"
);
if
(
value
!=
null
)
{
accnExch
.
setDonorInstitute
(
value
.
isTextual
()
?
value
.
asText
()
:
null
);
}
value
=
accnJson
.
get
(
"donorNumb"
);
if
(
value
!=
null
)
{
accnExch
.
setAccNumbDonor
(
value
.
isTextual
()
?
value
.
asText
()
:
null
);
}
value
=
accnJson
.
get
(
"donorName"
);
if
(
value
!=
null
)
{
accnExch
.
setDonorName
(
value
.
isTextual
()
?
value
.
asText
()
:
null
);
}
toSaveExch
.
add
(
accnExch
);
}
if
(
updated
)
{
toSave
.
add
(
accession
);
}
...
...
@@ -347,8 +370,12 @@ public class BatchRESTServiceImpl implements BatchRESTService {
if
(
toSaveBreed
.
size
()
>
0
)
{
genesysService
.
saveBreeding
(
toSaveBreed
);
}
if
(
toSaveExch
.
size
()
>
0
)
{
genesysService
.
saveExchange
(
toSaveExch
);
}
return
toSave
.
size
()
>
0
||
toSaveColl
.
size
()
>
0
||
toSaveGeo
.
size
()
>
0
||
toSaveBreed
.
size
()
>
0
;
return
toSave
.
size
()
>
0
||
toSaveColl
.
size
()
>
0
||
toSaveGeo
.
size
()
>
0
||
toSaveBreed
.
size
()
>
0
||
toSaveExch
.
size
()
>
0
;
}
@Override
...
...
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @
3b06011f
...
...
@@ -41,7 +41,7 @@ import org.genesys2.server.model.genesys.AccessionTrait;
import
org.genesys2.server.model.genesys.AllAccnames
;
import
org.genesys2.server.model.genesys.AccessionBreeding
;
import
org.genesys2.server.model.genesys.AccessionCollect
;
import
org.genesys2.server.model.genesys.A
llAcq
Exchange
;
import
org.genesys2.server.model.genesys.A
ccession
Exchange
;
import
org.genesys2.server.model.genesys.ExperimentAccessionTrait
;
import
org.genesys2.server.model.genesys.ExperimentTrait
;
import
org.genesys2.server.model.genesys.Metadata
;
...
...
@@ -253,7 +253,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
}
@Override
public
A
llAcq
Exchange
listAccessionExchange
(
Accession
accession
)
{
public
A
ccession
Exchange
listAccessionExchange
(
Accession
accession
)
{
if
(
accession
==
null
||
accession
.
getId
()
==
null
)
return
null
;
return
accessionExchangeRepository
.
findByAccession
(
accession
);
...
...
@@ -470,12 +470,18 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
public
void
saveGeo
(
List
<
AccessionGeo
>
all
)
{
accessionGeoRepository
.
save
(
all
);
}
@Override
@Transactional
(
readOnly
=
false
)
public
void
saveBreeding
(
List
<
AccessionBreeding
>
all
)
{
accessionBreedingRepository
.
save
(
all
);
}
@Override
@Transactional
(
readOnly
=
false
)
public
void
saveExchange
(
List
<
AccessionExchange
>
all
)
{
accessionExchangeRepository
.
save
(
all
);
}
@Override
public
long
countAvailable
(
Set
<
Long
>
accessionIds
)
{
...
...
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