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Genesys PGR
Genesys Backend
Commits
4543c36b
Commit
4543c36b
authored
Oct 13, 2018
by
Matija Obreza
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Admin: update tileIndex, pdci without modifying Accession @LastModifiedDate
parent
ebb86823
Changes
2
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2 changed files
with
74 additions
and
34 deletions
+74
-34
src/main/java/org/genesys2/server/mvc/admin/AdminController.java
...n/java/org/genesys2/server/mvc/admin/AdminController.java
+64
-26
src/main/java/org/genesys2/server/service/impl/AccessionServiceImpl.java
...rg/genesys2/server/service/impl/AccessionServiceImpl.java
+10
-8
No files found.
src/main/java/org/genesys2/server/mvc/admin/AdminController.java
View file @
4543c36b
...
...
@@ -28,11 +28,15 @@ import javax.persistence.PersistenceContext;
import
javax.xml.parsers.ParserConfigurationException
;
import
org.apache.commons.lang.time.StopWatch
;
import
org.apache.commons.lang3.ObjectUtils
;
import
org.genesys.catalog.service.DatasetService
;
import
org.genesys.worldclim.WorldClimUtil
;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.genesys.AccessionGeo
;
import
org.genesys2.server.model.genesys.AccessionId
;
import
org.genesys2.server.model.genesys.PDCI
;
import
org.genesys2.server.model.genesys.QAccession
;
import
org.genesys2.server.model.genesys.QAccessionId
;
import
org.genesys2.server.model.impl.FaoInstitute
;
import
org.genesys2.server.persistence.AccessionRepository
;
import
org.genesys2.server.persistence.PDCIRepository
;
...
...
@@ -45,6 +49,7 @@ import org.genesys2.server.service.GeoService;
import
org.genesys2.server.service.InstituteService
;
import
org.genesys2.server.service.TaxonomyService
;
import
org.genesys2.server.service.filter.AccessionFilter
;
import
org.genesys2.server.service.worker.AccessionCounter
;
import
org.genesys2.server.service.worker.AccessionProcessor
;
import
org.genesys2.server.service.worker.ITPGRFAStatusUpdater
;
import
org.genesys2.server.service.worker.InstituteUpdater
;
...
...
@@ -67,12 +72,13 @@ import org.xml.sax.SAXException;
import
com.fasterxml.jackson.core.JsonParseException
;
import
com.fasterxml.jackson.databind.JsonMappingException
;
import
com.fasterxml.jackson.databind.ObjectMapper
;
import
com.querydsl.jpa.impl.JPAQueryFactory
;
@Controller
@RequestMapping
(
"/admin"
)
@PreAuthorize
(
"hasRole('ADMINISTRATOR')"
)
public
class
AdminController
{
public
static
final
Logger
LOG
=
LoggerFactory
.
getLogger
(
AdminController
.
class
);
@Autowired
...
...
@@ -114,6 +120,12 @@ public class AdminController {
@PersistenceContext
private
EntityManager
entityManager
;
@Autowired
private
JPAQueryFactory
jpaQueryFactory
;
@Autowired
private
AccessionCounter
accessionCounter
;
ObjectMapper
mapper
=
new
ObjectMapper
();
@Autowired
...
...
@@ -124,10 +136,10 @@ public class AdminController {
@Autowired
private
AccessionProcessor
accessionProcessor
;
@Autowired
private
PDCIRepository
pdciRepository
;
@RequestMapping
(
"/"
)
public
String
root
(
Model
model
)
{
return
"/admin/index"
;
...
...
@@ -231,9 +243,9 @@ public class AdminController {
@RequestMapping
(
value
=
"/pdci"
,
method
=
RequestMethod
.
POST
,
params
=
"action=institute-pdci"
)
public
String
updatePDCI
()
{
for
(
FaoInstitute
institute:
instituteService
.
listActive
(
new
PageRequest
(
0
,
Integer
.
MAX_VALUE
)))
{
for
(
FaoInstitute
institute
:
instituteService
.
listActive
(
new
PageRequest
(
0
,
Integer
.
MAX_VALUE
)))
{
LOG
.
info
(
"Updating PDCI for {}"
,
institute
.
getCode
());
genesysService
.
updatePDCI
(
institute
);
accessionCounter
.
recountInstitute
(
institute
);
}
return
"redirect:/admin/"
;
...
...
@@ -241,12 +253,12 @@ public class AdminController {
@RequestMapping
(
value
=
"/pdci"
,
method
=
RequestMethod
.
POST
,
params
=
"action=filtered-pdci"
)
public
String
updateFilteredPDCI
(
@RequestParam
(
name
=
"filter"
)
String
filters
)
throws
JsonParseException
,
JsonMappingException
,
IOException
{
AccessionFilter
filter
=
mapper
.
readValue
(
filters
,
AccessionFilter
.
class
);
LOG
.
warn
(
"Recalculating PDCI for accessions matching filter: {}"
,
filter
);
accessionProcessor
.
apply
(
filter
,
(
accessions
)
->
{
// Everything here is executed within a @Transaction(readOnly = false) context
if
(
accessions
==
null
)
{
return
accessions
;
...
...
@@ -257,28 +269,37 @@ public class AdminController {
PDCI
pdci
=
accessionId
.
getPdci
();
// create new PDCI if missing
PDCI
resultingPdci
=
PDCICalculator
.
updatePdci
(
pdci
==
null
?
new
PDCI
()
:
pdci
,
accession
);
// if PDCI was missing, link it with accession
if
(
pdci
==
null
)
{
LOG
.
trace
(
"Assigning new PDCI for {}"
,
accession
);
resultingPdci
.
setAccession
(
accessionId
);
accessionId
.
setPdci
(
resultingPdci
);
}
else
{
LOG
.
trace
(
"Updating PDCI for {}"
,
accession
);
accessionId
.
setPdci
(
pdciRepository
.
save
(
resultingPdci
));
}
updateAccessionPDCI
(
accession
,
resultingPdci
);
accessionCounter
.
recountInstitute
(
accession
.
getInstitute
());
});
LOG
.
debug
(
"Updated {} PDCI entries"
,
accessions
.
size
());
return
accession
Repository
.
save
(
accessions
)
;
return
accession
s
;
});
return
"redirect:/admin/"
;
}
private
void
updateAccessionPDCI
(
Accession
accession
,
PDCI
pdci
)
{
AccessionId
accessionId
=
accession
.
getAccessionId
();
pdci
.
setAccession
(
accessionId
);
pdciRepository
.
save
(
pdci
);
if
(
accessionId
.
getPdci
()
==
null
)
{
accessionId
.
setPdci
(
pdci
);
LOG
.
trace
(
"Assigning new PDCI for {}"
,
accession
);
jpaQueryFactory
.
update
(
QAccessionId
.
accessionId
).
where
(
QAccessionId
.
accessionId
.
eq
(
accessionId
)).
set
(
QAccessionId
.
accessionId
.
pdci
,
pdci
).
execute
();
// jpaQueryFactory.update(QAccession.accession).where(QAccession.accession.eq(accession)).set(QAccession.accession.pdci,
// pdci).execute();
}
}
@RequestMapping
(
value
=
"/admin-action"
,
method
=
RequestMethod
.
POST
,
params
=
"action=tile-index"
)
public
String
updateTileIndex
(
@RequestParam
(
name
=
"filter"
)
String
filters
)
throws
JsonParseException
,
JsonMappingException
,
IOException
{
AccessionFilter
filter
=
mapper
.
readValue
(
filters
,
AccessionFilter
.
class
);
LOG
.
warn
(
"Recalculating tileIndex for accessions matching filter: {}"
,
filter
);
...
...
@@ -288,19 +309,35 @@ public class AdminController {
}
accessions
.
forEach
(
accession
->
{
AccessionGeo
geo
=
accession
.
getAccessionId
().
getGeo
();
if
(
geo
!=
null
)
{
accession
.
setTileIndex
(
WorldClimUtil
.
getTileIndex
(
5
,
geo
.
getLongitude
(),
geo
.
getLatitude
()));
Long
index
=
WorldClimUtil
.
getTileIndex
(
5
,
geo
.
getLongitude
(),
geo
.
getLatitude
());
if
(
ObjectUtils
.
compare
(
index
,
accession
.
getTileIndex
())
!=
0
)
{
updateAccessionTileIndex
(
accession
,
index
);
}
}
else
{
if
(
accession
.
getTileIndex
()
!=
null
)
{
updateAccessionTileIndex
(
accession
,
null
);
}
}
});
LOG
.
debug
(
"Regenerated {} tileIndexes"
,
accessions
.
size
());
return
accession
Repository
.
save
(
accessions
)
;
return
accession
s
;
});
return
"redirect:/admin/"
;
}
private
void
updateAccessionTileIndex
(
Accession
accession
,
Long
index
)
{
if
(
index
==
null
)
{
jpaQueryFactory
.
update
(
QAccession
.
accession
).
where
(
QAccession
.
accession
.
eq
(
accession
)).
setNull
(
QAccession
.
accession
.
tileIndex
).
execute
();
}
else
{
jpaQueryFactory
.
update
(
QAccession
.
accession
).
where
(
QAccession
.
accession
.
eq
(
accession
)).
set
(
QAccession
.
accession
.
tileIndex
,
index
).
execute
();
}
}
@RequestMapping
(
value
=
"/admin-action"
,
method
=
RequestMethod
.
POST
,
params
=
"georegion"
)
public
String
updateGeoReg
()
throws
IOException
,
ParserConfigurationException
,
SAXException
{
geoRegionService
.
updateGeoRegionData
();
...
...
@@ -308,7 +345,8 @@ public class AdminController {
}
/**
* Scan AccessionData table and convert ACCENUMB to ACCENUMBNUMB (extract the number from the ACCNUMB)
* Scan AccessionData table and convert ACCENUMB to ACCENUMBNUMB (extract the
* number from the ACCNUMB)
*
* @return
*/
...
...
@@ -364,7 +402,7 @@ public class AdminController {
}
@PostMapping
(
value
=
"/clear-dois"
)
public
String
clearDois
(){
public
String
clearDois
()
{
LOG
.
info
(
"Clear DOIs"
);
genesysService
.
removeDOIs
();
return
"redirect:/admin/"
;
...
...
src/main/java/org/genesys2/server/service/impl/AccessionServiceImpl.java
View file @
4543c36b
...
...
@@ -15,9 +15,16 @@
*/
package
org.genesys2.server.service.impl
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.Collections
;
import
java.util.HashMap
;
import
java.util.HashSet
;
import
java.util.List
;
import
java.util.Map
;
import
java.util.Optional
;
import
java.util.Set
;
import
java.util.UUID
;
import
com.querydsl.core.BooleanBuilder
;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.genesys.AccessionData
;
import
org.genesys2.server.model.genesys.AccessionId
;
...
...
@@ -27,7 +34,6 @@ import org.genesys2.server.persistence.AccessionRepository;
import
org.genesys2.server.service.AccessionService
;
import
org.genesys2.server.service.ElasticsearchService
;
import
org.genesys2.server.service.filter.AccessionFilter
;
import
org.genesys2.server.service.worker.AccessionCounter
;
import
org.slf4j.Logger
;
import
org.slf4j.LoggerFactory
;
import
org.springframework.beans.factory.annotation.Autowired
;
...
...
@@ -39,6 +45,7 @@ import org.springframework.stereotype.Service;
import
org.springframework.transaction.annotation.Propagation
;
import
org.springframework.transaction.annotation.Transactional
;
import
com.querydsl.core.BooleanBuilder
;
import
com.querydsl.core.Tuple
;
import
com.querydsl.jpa.impl.JPAQuery
;
import
com.querydsl.jpa.impl.JPAQueryFactory
;
...
...
@@ -59,9 +66,6 @@ public class AccessionServiceImpl implements AccessionService {
@Autowired
private
ElasticsearchService
elasticsearchService
;
@Autowired
private
AccessionCounter
accessionCounter
;
@Autowired
private
JPAQueryFactory
jpaQueryFactory
;
...
...
@@ -212,7 +216,6 @@ public class AccessionServiceImpl implements AccessionService {
@Transactional
(
readOnly
=
false
,
propagation
=
Propagation
.
REQUIRES_NEW
)
public
List
<
Accession
>
processAccessions
(
List
<
Long
>
accessionIds
,
IAccessionAction
action
)
{
List
<
Accession
>
accessions
=
accessionRepository
.
findAll
(
accessionIds
);
accessions
.
stream
().
map
(
a
->
a
.
getInstitute
()).
distinct
().
forEach
(
institute
->
accessionCounter
.
recountInstitute
(
institute
));
LOG
.
debug
(
"Processing {} accessions of {} IDs provided"
,
accessions
.
size
(),
accessionIds
.
size
());
accessions
.
forEach
(
accession
->
{
try
{
...
...
@@ -228,7 +231,6 @@ public class AccessionServiceImpl implements AccessionService {
@Transactional
(
readOnly
=
false
,
propagation
=
Propagation
.
REQUIRES_NEW
)
public
List
<
Accession
>
processAccessions
(
List
<
Long
>
accessionIds
,
IAccessionBatchAction
action
)
{
List
<
Accession
>
accessions
=
accessionRepository
.
findAll
(
accessionIds
);
accessions
.
stream
().
map
(
a
->
a
.
getInstitute
()).
distinct
().
forEach
(
institute
->
accessionCounter
.
recountInstitute
(
institute
));
LOG
.
debug
(
"Processing {} accessions of {} IDs provided"
,
accessions
.
size
(),
accessionIds
.
size
());
try
{
return
action
.
apply
(
accessions
);
...
...
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