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Genesys PGR
Genesys Backend
Commits
5fd3b72c
Commit
5fd3b72c
authored
Jan 15, 2014
by
Matija Obreza
Browse files
REST API updated for bredCode, ancest
parent
0eb2e7e5
Changes
5
Hide whitespace changes
Inline
Side-by-side
src/main/java/org/genesys2/server/model/genesys/A
llAcq
Breeding.java
→
src/main/java/org/genesys2/server/model/genesys/A
ccession
Breeding.java
View file @
5fd3b72c
...
...
@@ -32,7 +32,7 @@ import org.genesys2.server.model.BusinessModel;
*/
@Entity
@Table
(
name
=
"accessionbreeding"
)
public
class
A
llAcq
Breeding
extends
BusinessModel
{
public
class
A
ccession
Breeding
extends
BusinessModel
{
@Version
private
long
version
=
0
;
...
...
@@ -48,7 +48,7 @@ public class AllAcqBreeding extends BusinessModel{
@Lob
private
String
pedigree
;
public
A
llAcq
Breeding
()
{
public
A
ccession
Breeding
()
{
}
public
long
getVersion
()
{
...
...
src/main/java/org/genesys2/server/persistence/domain/AccessionBreedingRepository.java
View file @
5fd3b72c
...
...
@@ -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
Breeding
;
import
org.genesys2.server.model.genesys.A
ccession
Breeding
;
import
org.springframework.data.jpa.repository.JpaRepository
;
public
interface
AccessionBreedingRepository
extends
JpaRepository
<
A
llAcq
Breeding
,
Long
>
{
public
interface
AccessionBreedingRepository
extends
JpaRepository
<
A
ccession
Breeding
,
Long
>
{
A
llAcq
Breeding
findByAccession
(
Accession
accession
);
A
ccession
Breeding
findByAccession
(
Accession
accession
);
}
src/main/java/org/genesys2/server/service/GenesysService.java
View file @
5fd3b72c
...
...
@@ -27,7 +27,7 @@ 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.AllAccnames
;
import
org.genesys2.server.model.genesys.A
llAcq
Breeding
;
import
org.genesys2.server.model.genesys.A
ccession
Breeding
;
import
org.genesys2.server.model.genesys.AccessionCollect
;
import
org.genesys2.server.model.genesys.AllAcqExchange
;
import
org.genesys2.server.model.genesys.ExperimentTrait
;
...
...
@@ -67,7 +67,7 @@ public interface GenesysService {
AccessionCollect
listAccessionCollect
(
Accession
accession
);
A
llAcq
Breeding
listAccessionBreeding
(
Accession
accession
);
A
ccession
Breeding
listAccessionBreeding
(
Accession
accession
);
AccessionGeo
listAccessionGeo
(
Accession
accession
);
...
...
@@ -132,8 +132,8 @@ public interface GenesysService {
SvalbardData
getSvalbardData
(
Accession
accession
);
void
saveCollecting
(
List
<
AccessionCollect
>
all
);
void
saveGeo
(
List
<
AccessionGeo
>
all
);
void
saveBreeding
(
List
<
AccessionBreeding
>
all
);
void
refreshMetadataMethods
();
...
...
@@ -145,4 +145,5 @@ public interface GenesysService {
void
removeAliases
(
List
<
AccessionAlias
>
aliases
);
}
src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java
View file @
5fd3b72c
...
...
@@ -30,6 +30,7 @@ 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.AccessionBreeding
;
import
org.genesys2.server.model.genesys.Taxonomy
;
import
org.genesys2.server.model.genesys.AccessionAlias.AliasType
;
import
org.genesys2.server.model.impl.Country
;
...
...
@@ -80,6 +81,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
List
<
Accession
>
toSave
=
new
ArrayList
<
Accession
>();
List
<
AccessionCollect
>
toSaveColl
=
new
ArrayList
<
AccessionCollect
>();
List
<
AccessionGeo
>
toSaveGeo
=
new
ArrayList
<
AccessionGeo
>();
List
<
AccessionBreeding
>
toSaveBreed
=
new
ArrayList
<
AccessionBreeding
>();
for
(
AccessionJson
dataJson
:
batch
.
keySet
())
{
if
(
LOG
.
isDebugEnabled
())
...
...
@@ -127,7 +129,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
updated
=
true
;
}
}
/* Allow updating Genus */
value
=
accnJson
.
get
(
"newGenus"
);
if
(
value
!=
null
)
{
...
...
@@ -306,6 +308,23 @@ public class BatchRESTServiceImpl implements BatchRESTService {
toSaveGeo
.
add
(
accnGeo
);
}
if
(
accnJson
.
has
(
"bredCode"
)
||
accnJson
.
has
(
"ancest"
))
{
AccessionBreeding
accnBred
=
genesysService
.
listAccessionBreeding
(
accession
);
if
(
accnBred
==
null
)
{
accnBred
=
new
AccessionBreeding
();
accnBred
.
setAccession
(
accession
);
}
value
=
accnJson
.
get
(
"bredCode"
);
if
(
value
!=
null
)
{
accnBred
.
setBreederCode
(
value
.
isTextual
()
?
value
.
asText
()
:
null
);
}
value
=
accnJson
.
get
(
"ancest"
);
if
(
value
!=
null
)
{
accnBred
.
setPedigree
(
value
.
isTextual
()
?
value
.
asText
()
:
null
);
}
toSaveBreed
.
add
(
accnBred
);
}
if
(
updated
)
{
toSave
.
add
(
accession
);
}
...
...
@@ -325,7 +344,11 @@ public class BatchRESTServiceImpl implements BatchRESTService {
genesysService
.
saveGeo
(
toSaveGeo
);
}
return
toSave
.
size
()
>
0
||
toSaveColl
.
size
()
>
0
||
toSaveGeo
.
size
()
>
0
;
if
(
toSaveBreed
.
size
()
>
0
)
{
genesysService
.
saveBreeding
(
toSaveBreed
);
}
return
toSave
.
size
()
>
0
||
toSaveColl
.
size
()
>
0
||
toSaveGeo
.
size
()
>
0
||
toSaveBreed
.
size
()
>
0
;
}
@Override
...
...
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @
5fd3b72c
...
...
@@ -39,7 +39,7 @@ import org.genesys2.server.model.genesys.AccessionAlias;
import
org.genesys2.server.model.genesys.AccessionGeo
;
import
org.genesys2.server.model.genesys.AccessionTrait
;
import
org.genesys2.server.model.genesys.AllAccnames
;
import
org.genesys2.server.model.genesys.A
llAcq
Breeding
;
import
org.genesys2.server.model.genesys.A
ccession
Breeding
;
import
org.genesys2.server.model.genesys.AccessionCollect
;
import
org.genesys2.server.model.genesys.AllAcqExchange
;
import
org.genesys2.server.model.genesys.ExperimentAccessionTrait
;
...
...
@@ -225,7 +225,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
}
@Override
public
A
llAcq
Breeding
listAccessionBreeding
(
Accession
accession
)
{
public
A
ccession
Breeding
listAccessionBreeding
(
Accession
accession
)
{
if
(
accession
==
null
||
accession
.
getId
()
==
null
)
return
null
;
return
accessionBreedingRepository
.
findByAccession
(
accession
);
...
...
@@ -470,6 +470,12 @@ 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
public
long
countAvailable
(
Set
<
Long
>
accessionIds
)
{
...
...
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