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Genesys PGR
Genesys Backend
Commits
39102ce9
Commit
39102ce9
authored
Jun 07, 2016
by
Aleksandr Sharaban
Committed by
Matija Obreza
Jun 07, 2016
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Feature #32756 - Taxonomy2: Cleanup.
Created service method which removes all obsolete Taxonomy2 records.
parent
e8b0c725
Changes
5
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5 changed files
with
53 additions
and
6 deletions
+53
-6
src/main/java/org/genesys2/server/persistence/domain/Taxonomy2Repository.java
...nesys2/server/persistence/domain/Taxonomy2Repository.java
+18
-0
src/main/java/org/genesys2/server/service/TaxonomyService.java
...ain/java/org/genesys2/server/service/TaxonomyService.java
+1
-0
src/main/java/org/genesys2/server/service/impl/TaxonomyServiceImpl.java
...org/genesys2/server/service/impl/TaxonomyServiceImpl.java
+16
-0
src/main/java/org/genesys2/server/servlet/controller/admin/AdminController.java
...sys2/server/servlet/controller/admin/AdminController.java
+11
-6
src/main/webapp/WEB-INF/jsp/admin/index.jsp
src/main/webapp/WEB-INF/jsp/admin/index.jsp
+7
-0
No files found.
src/main/java/org/genesys2/server/persistence/domain/Taxonomy2Repository.java
View file @
39102ce9
...
...
@@ -16,12 +16,15 @@
package
org.genesys2.server.persistence.domain
;
import
java.math.BigInteger
;
import
java.util.List
;
import
java.util.Set
;
import
org.genesys2.server.model.genesys.Taxonomy2
;
import
org.genesys2.server.model.impl.Crop
;
import
org.springframework.data.domain.Pageable
;
import
org.springframework.data.jpa.repository.JpaRepository
;
import
org.springframework.data.jpa.repository.Modifying
;
import
org.springframework.data.jpa.repository.Query
;
public
interface
Taxonomy2Repository
extends
JpaRepository
<
Taxonomy2
,
Long
>
{
...
...
@@ -68,4 +71,19 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
List
<
Taxonomy2
>
findByGenusAndSpeciesAndSubtaxa
(
String
genus
,
String
species
,
String
subtaxa
);
@Query
(
nativeQuery
=
true
,
value
=
"SELECT ct.taxonomyId FROM croptaxonomy ct "
+
"UNION ALL SELECT t2.taxGenus FROM taxonomy2 t2 "
+
"UNION ALL SELECT t3.taxSpecies FROM taxonomy2 t3 "
+
"UNION ALL SELECT a.taxonomyId2 FROM accession a "
+
"UNION ALL SELECT a2.taxGenus FROM accession a2 "
+
"UNION ALL SELECT ah.taxGenus FROM accessionhistoric ah "
+
"UNION ALL SELECT ah2.taxonomyId2 FROM accessionhistoric ah2;"
)
Set
<
BigInteger
>
findTaxonomyReferencedIds
();
@Query
(
"select t.id from Taxonomy2 t"
)
Set
<
Long
>
findTaxonomyIds
();
@Query
(
"delete from Taxonomy2 t where t.id in (?1)"
)
@Modifying
void
removeUnusedIds
(
Set
<
Long
>
ids
);
}
src/main/java/org/genesys2/server/service/TaxonomyService.java
View file @
39102ce9
...
...
@@ -47,4 +47,5 @@ public interface TaxonomyService {
List
<
String
>
autocompleteSubtaxa
(
String
ac
,
Crop
crop
,
List
<
String
>
genus
,
List
<
String
>
species
);
void
cleanupTaxonomies
();
}
src/main/java/org/genesys2/server/service/impl/TaxonomyServiceImpl.java
View file @
39102ce9
...
...
@@ -16,7 +16,9 @@
package
org.genesys2.server.service.impl
;
import
java.math.BigInteger
;
import
java.util.List
;
import
java.util.Set
;
import
org.apache.commons.lang.StringUtils
;
import
org.apache.commons.logging.Log
;
...
...
@@ -199,4 +201,18 @@ public class TaxonomyServiceImpl implements TaxonomyService {
public
Taxonomy2
get
(
String
genus
)
{
return
find
(
genus
,
"sp."
,
""
,
""
,
""
);
}
@Override
@Transactional
public
void
cleanupTaxonomies
()
{
Set
<
BigInteger
>
referencedIds
=
taxonomy2Repository
.
findTaxonomyReferencedIds
();
Set
<
Long
>
allIds
=
taxonomy2Repository
.
findTaxonomyIds
();
for
(
BigInteger
integer:
referencedIds
)
{
allIds
.
remove
(
integer
.
longValue
());
}
if
(
allIds
.
size
()
>
0
)
{
taxonomy2Repository
.
removeUnusedIds
(
allIds
);
}
}
}
src/main/java/org/genesys2/server/servlet/controller/admin/AdminController.java
View file @
39102ce9
...
...
@@ -31,12 +31,7 @@ import org.apache.commons.lang.StringUtils;
import
org.apache.commons.logging.Log
;
import
org.apache.commons.logging.LogFactory
;
import
org.genesys2.server.persistence.domain.GenesysLowlevelRepository
;
import
org.genesys2.server.service.CountryNamesUpdater
;
import
org.genesys2.server.service.ElasticService
;
import
org.genesys2.server.service.GenesysService
;
import
org.genesys2.server.service.GeoRegionService
;
import
org.genesys2.server.service.GeoService
;
import
org.genesys2.server.service.InstituteService
;
import
org.genesys2.server.service.*
;
import
org.genesys2.server.service.impl.ContentSanitizer
;
import
org.genesys2.server.service.worker.ElasticUpdater
;
import
org.genesys2.server.service.worker.ITPGRFAStatusUpdater
;
...
...
@@ -98,6 +93,9 @@ public class AdminController {
@Autowired
private
GeoRegionService
geoRegionService
;
@Autowired
private
TaxonomyService
taxonomyService
;
ObjectMapper
mapper
=
new
ObjectMapper
();
@RequestMapping
(
"/"
)
...
...
@@ -355,4 +353,11 @@ public class AdminController {
elasticService
.
regenerateAccessionSequentialNumber
();
return
"redirect:/admin/"
;
}
@RequestMapping
(
value
=
"/cleanup-taxonomies"
,
method
=
RequestMethod
.
POST
)
public
String
cleanupTaxonomies
()
{
taxonomyService
.
cleanupTaxonomies
();
return
"redirect:/admin/"
;
}
}
src/main/webapp/WEB-INF/jsp/admin/index.jsp
View file @
39102ce9
...
...
@@ -116,5 +116,12 @@
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Taxonomy
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/cleanup-taxonomies"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Cleanup taxonomies"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
</body>
</html>
\ No newline at end of file
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