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Genesys PGR
Genesys Backend
Commits
6642332d
Commit
6642332d
authored
Oct 23, 2018
by
Matija Obreza
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Removed unused statisticsPheno in WIEWS details
parent
ff0767f5
Changes
6
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6 changed files
with
50 additions
and
103 deletions
+50
-103
src/main/java/org/genesys2/server/mvc/WiewsController.java
src/main/java/org/genesys2/server/mvc/WiewsController.java
+20
-8
src/main/java/org/genesys2/server/service/GenesysService.java
...main/java/org/genesys2/server/service/GenesysService.java
+0
-3
src/main/java/org/genesys2/server/service/StatisticsService.java
...n/java/org/genesys2/server/service/StatisticsService.java
+0
-2
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
.../org/genesys2/server/service/impl/GenesysServiceImpl.java
+30
-41
src/main/java/org/genesys2/server/service/impl/StatisticsServiceImpl.java
...g/genesys2/server/service/impl/StatisticsServiceImpl.java
+0
-13
src/main/java/org/genesys2/spring/config/ApplicationStartup.java
...n/java/org/genesys2/spring/config/ApplicationStartup.java
+0
-36
No files found.
src/main/java/org/genesys2/server/mvc/WiewsController.java
View file @
6642332d
...
...
@@ -35,6 +35,7 @@ import java.util.stream.Stream;
import
javax.servlet.http.HttpServletRequest
;
import
javax.servlet.http.HttpServletResponse
;
import
org.apache.commons.lang3.time.StopWatch
;
import
org.genesys.filerepository.InvalidRepositoryFileDataException
;
import
org.genesys.filerepository.InvalidRepositoryPathException
;
import
org.genesys.filerepository.NoSuchRepositoryFileException
;
...
...
@@ -51,6 +52,7 @@ import org.genesys2.server.service.CRMException;
import
org.genesys2.server.service.ContentService
;
import
org.genesys2.server.service.DownloadService
;
import
org.genesys2.server.service.ElasticsearchService
;
import
org.genesys2.server.service.ElasticsearchService.TermResult
;
import
org.genesys2.server.service.FilterConstants
;
import
org.genesys2.server.service.GenesysService
;
import
org.genesys2.server.service.GeoService
;
...
...
@@ -165,6 +167,7 @@ public class WiewsController extends BaseController {
@RequestMapping
(
"/{wiewsCode}"
)
public
String
view
(
ModelMap
model
,
@PathVariable
(
value
=
"wiewsCode"
)
String
wiewsCode
)
{
StopWatch
stopWatch
=
StopWatch
.
createStarted
();
LOG
.
debug
(
"Viewing institute {}"
,
wiewsCode
);
if
(!
wiewsCode
.
toUpperCase
().
equals
(
wiewsCode
))
{
...
...
@@ -177,12 +180,15 @@ public class WiewsController extends BaseController {
}
model
.
addAttribute
(
"faoInstitute"
,
faoInstitute
);
model
.
addAttribute
(
"organizations"
,
organizationService
.
getOrganizations
(
faoInstitute
));
LOG
.
trace
(
"organizations after {}ms"
,
stopWatch
.
getTime
());
model
.
addAttribute
(
"blurp"
,
contentService
.
getArticle
(
faoInstitute
,
"blurp"
,
getLocale
()));
LOG
.
trace
(
"blurp after {}ms"
,
stopWatch
.
getTime
());
model
.
addAttribute
(
"countByInstitute"
,
faoInstitute
.
getAccessionCount
());
LOG
.
trace
(
"countByInstitute after {}ms"
,
stopWatch
.
getTime
());
long
datasetCount
=
genesysService
.
countDatasets
(
faoInstitute
);
model
.
addAttribute
(
"datasetCount"
,
datasetCount
);
LOG
.
trace
(
"datasetCount after {}ms"
,
stopWatch
.
getTime
());
{
AccessionFilter
af
=
new
AccessionFilter
();
...
...
@@ -190,23 +196,29 @@ public class WiewsController extends BaseController {
af
.
historic
=
false
;
try
{
model
.
addAttribute
(
"statisticsCrops"
,
elasticService
.
termStatisticsAuto
(
Accession
.
class
,
af
,
5
,
AppliedFiltersConverter
Map
<
String
,
TermResult
>
esStats
=
elasticService
.
termStatisticsAuto
(
Accession
.
class
,
af
,
5
,
AppliedFiltersConverter
.
convertTerm
(
FilterConstants
.
CROPS
),
AppliedFiltersConverter
.
convertTerm
(
FilterConstants
.
CROPNAME
),
AppliedFiltersConverter
.
convertTerm
(
FilterConstants
.
TAXONOMY_GENUS
));
LOG
.
trace
(
"ES statistics after {}ms"
,
stopWatch
.
getTime
());
model
.
addAttribute
(
"statisticsCrops"
,
esStats
.
get
(
AppliedFiltersConverter
.
convertTerm
(
FilterConstants
.
CROPS
)));
model
.
addAttribute
(
"statisticsCropName"
,
e
lasticService
.
termStatisticsAuto
(
Accession
.
class
,
af
,
5
,
AppliedFiltersConverter
model
.
addAttribute
(
"statisticsCropName"
,
e
sStats
.
get
(
AppliedFiltersConverter
.
convertTerm
(
FilterConstants
.
CROPNAME
)));
model
.
addAttribute
(
"statisticsGenus"
,
e
lasticService
.
termStatisticsAuto
(
Accession
.
class
,
af
,
5
,
AppliedFiltersConverter
model
.
addAttribute
(
"statisticsGenus"
,
e
sStats
.
get
(
AppliedFiltersConverter
.
convertTerm
(
FilterConstants
.
TAXONOMY_GENUS
)));
}
catch
(
SearchException
e
)
{
LOG
.
warn
(
e
.
getMessage
());
}
}
model
.
addAttribute
(
"statisticsTaxonomy"
,
genesysService
.
statisticsSpeciesByInstituteES
(
faoInstitute
,
5
));
LOG
.
trace
(
"statisticsTaxonomy after {}ms"
,
stopWatch
.
getTime
());
model
.
addAttribute
(
"statisticsPDCI"
,
faoInstitute
.
getStatisticsPDCI
());
LOG
.
trace
(
"statisticsPDCI after {}ms"
,
stopWatch
.
getTime
());
model
.
addAttribute
(
"updates"
,
genesysService
.
getLastUpdatedStatistics
(
faoInstitute
));
if
(
datasetCount
>
0
)
{
model
.
addAttribute
(
"statisticsPheno"
,
statisticsService
.
statisticsPheno
(
faoInstitute
));
}
LOG
.
trace
(
"updates after {}ms"
,
stopWatch
.
getTime
());
return
"/wiews/details"
;
}
...
...
src/main/java/org/genesys2/server/service/GenesysService.java
View file @
6642332d
...
...
@@ -40,7 +40,6 @@ import org.genesys2.server.model.genesys.Metadata;
import
org.genesys2.server.model.genesys.Method
;
import
org.genesys2.server.model.genesys.PDCI
;
import
org.genesys2.server.model.genesys.PDCIStatistics
;
import
org.genesys2.server.model.genesys.PhenoStatistics
;
import
org.genesys2.server.model.genesys.SvalbardDeposit
;
import
org.genesys2.server.model.genesys.Taxonomy2
;
import
org.genesys2.server.model.impl.AccessionIdentifier3
;
...
...
@@ -233,8 +232,6 @@ public interface GenesysService {
PDCIStatistics
statisticsPDCI
(
Organization
organization
);
PhenoStatistics
statisticsPheno
(
FaoInstitute
faoInstitute
);
void
regenerateAccessionSequentialNumber
();
List
<
SvalbardDeposit
>
saveSvalbards
(
List
<
SvalbardDeposit
>
svalbards
);
...
...
src/main/java/org/genesys2/server/service/StatisticsService.java
View file @
6642332d
...
...
@@ -37,6 +37,4 @@ public interface StatisticsService {
PDCIStatistics
statisticsPDCI
(
Organization
organization
);
PhenoStatistics
statisticsPheno
(
FaoInstitute
faoInstitute
);
}
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @
6642332d
...
...
@@ -22,23 +22,47 @@ import java.io.OutputStream;
import
java.io.OutputStreamWriter
;
import
java.sql.ResultSet
;
import
java.sql.SQLException
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.Arrays
;
import
java.util.Collection
;
import
java.util.Collections
;
import
java.util.Date
;
import
java.util.HashMap
;
import
java.util.HashSet
;
import
java.util.List
;
import
java.util.Map
;
import
java.util.Set
;
import
java.util.UUID
;
import
java.util.stream.Collectors
;
import
java.util.zip.ZipEntry
;
import
java.util.zip.ZipOutputStream
;
import
javax.persistence.EntityManager
;
import
com.google.common.collect.Sets
;
import
com.querydsl.jpa.impl.JPAQueryFactory
;
import
org.apache.commons.collections4.CollectionUtils
;
import
org.genesys.blocks.security.SecurityContextUtil
;
import
org.genesys.blocks.security.model.AclSid
;
import
org.genesys.blocks.security.service.CustomAclService
;
import
org.genesys2.server.api.model.AccessionHeaderJson
;
import
org.genesys2.server.model.elastic.AccessionDetails
;
import
org.genesys2.server.model.genesys.
*
;
import
org.genesys2.server.model.genesys.
Accession
;
import
org.genesys2.server.model.genesys.AccessionAlias.AliasType
;
import
org.genesys2.server.model.genesys.AccessionData
;
import
org.genesys2.server.model.genesys.AccessionGeo
;
import
org.genesys2.server.model.genesys.AccessionHistoric
;
import
org.genesys2.server.model.genesys.AccessionId
;
import
org.genesys2.server.model.genesys.AccessionTrait
;
import
org.genesys2.server.model.genesys.AllAccnames
;
import
org.genesys2.server.model.genesys.ExperimentAccessionTrait
;
import
org.genesys2.server.model.genesys.ExperimentTrait
;
import
org.genesys2.server.model.genesys.Metadata
;
import
org.genesys2.server.model.genesys.Method
;
import
org.genesys2.server.model.genesys.PDCI
;
import
org.genesys2.server.model.genesys.PDCIStatistics
;
import
org.genesys2.server.model.genesys.SelfCopy
;
import
org.genesys2.server.model.genesys.SvalbardDeposit
;
import
org.genesys2.server.model.genesys.Taxonomy2
;
import
org.genesys2.server.model.genesys.TraitCode
;
import
org.genesys2.server.model.impl.AccessionIdentifier3
;
import
org.genesys2.server.model.impl.Country
;
import
org.genesys2.server.model.impl.Crop
;
...
...
@@ -90,9 +114,11 @@ import org.springframework.transaction.annotation.Isolation;
import
org.springframework.transaction.annotation.Propagation
;
import
org.springframework.transaction.annotation.Transactional
;
import
com.google.common.collect.Sets
;
import
com.opencsv.CSVWriter
;
import
com.opencsv.ResultSetHelper
;
import
com.opencsv.ResultSetHelperService
;
import
com.querydsl.jpa.impl.JPAQueryFactory
;
@Service
@Transactional
(
readOnly
=
true
)
...
...
@@ -1447,43 +1473,6 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
return
stats
;
}
@Override
public
PhenoStatistics
statisticsPheno
(
FaoInstitute
faoInstitute
)
{
List
<
Object
[]>
metadatas
=
accessionTraitRepository
.
statisticsAccessionMetadata
(
faoInstitute
);
List
<
Object
[]>
methods
=
accessionTraitRepository
.
statisticsAccessionMethod
(
faoInstitute
);
long
count
=
countByInstitute
(
faoInstitute
);
PhenoStatistics
stats
=
new
PhenoStatistics
();
stats
.
setCount
(
count
);
{
long
withMetadata
=
0
,
metadatasTotal
=
0
;
for
(
Object
[]
m
:
metadatas
)
{
// Long accessionId = (Long) m[0];
Long
metadataCount
=
(
Long
)
m
[
1
];
if
(
metadataCount
!=
null
&&
metadataCount
>
0
)
{
withMetadata
++;
metadatasTotal
+=
metadataCount
;
}
}
stats
.
setWithMetadata
(
withMetadata
);
stats
.
setAvgMetadatas
((
float
)
metadatasTotal
/
withMetadata
);
}
{
long
withMethod
=
0
,
methodsTotal
=
0
;
for
(
Object
[]
m
:
methods
)
{
// Long accessionId = (Long) m[0];
Long
methodCount
=
(
Long
)
m
[
1
];
if
(
methodCount
!=
null
&&
methodCount
>
0
)
{
withMethod
++;
methodsTotal
+=
methodCount
;
}
}
stats
.
setWithMethod
(
withMethod
);
stats
.
setAvgMethods
((
float
)
methodsTotal
/
withMethod
);
}
return
stats
;
}
@Transactional
(
readOnly
=
false
)
@Override
...
...
src/main/java/org/genesys2/server/service/impl/StatisticsServiceImpl.java
View file @
6642332d
...
...
@@ -21,8 +21,6 @@ import org.genesys.catalog.service.DatasetService;
import
org.genesys2.server.model.PublishState
;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.genesys.PDCIStatistics
;
import
org.genesys2.server.model.genesys.PhenoStatistics
;
import
org.genesys2.server.model.impl.FaoInstitute
;
import
org.genesys2.server.model.impl.Organization
;
import
org.genesys2.server.service.ElasticsearchService
;
import
org.genesys2.server.service.GenesysService
;
...
...
@@ -109,15 +107,4 @@ public class StatisticsServiceImpl implements StatisticsService {
}
}
@Override
@Cacheable
(
unless
=
"#result == null"
,
value
=
"statistics"
,
key
=
"'stats.' + #root.methodName + '-' + #faoInstitute.id"
)
public
PhenoStatistics
statisticsPheno
(
FaoInstitute
faoInstitute
)
{
synchronized
(
this
)
{
if
(
LOG
.
isDebugEnabled
())
{
LOG
.
debug
(
"Regenerating C&E statistics for {}"
,
faoInstitute
);
}
return
genesysService
.
statisticsPheno
(
faoInstitute
);
}
}
}
src/main/java/org/genesys2/spring/config/ApplicationStartup.java
View file @
6642332d
...
...
@@ -26,10 +26,6 @@ import org.genesys.blocks.security.UserException;
import
org.genesys.blocks.security.model.BasicUser
;
import
org.genesys.blocks.security.service.CustomAclService
;
import
org.genesys.blocks.security.service.PasswordPolicy.PasswordPolicyException
;
import
org.genesys.catalog.persistence.PartnerRepository
;
import
org.genesys.catalog.persistence.dataset.DatasetRepository
;
import
org.genesys.catalog.persistence.traits.DescriptorListRepository
;
import
org.genesys.catalog.persistence.traits.DescriptorRepository
;
import
org.genesys2.server.model.UserRole
;
import
org.genesys2.server.model.impl.User
;
import
org.genesys2.server.persistence.UserRepository
;
...
...
@@ -99,12 +95,6 @@ public class ApplicationStartup implements InitializingBean, ApplicationListener
}
startup
();
asAdminInvoker
.
invoke
(()
->
{
aclForCatalog
();
// aclParentObject();
return
null
;
});
}
/**
...
...
@@ -178,32 +168,6 @@ public class ApplicationStartup implements InitializingBean, ApplicationListener
LOG
.
info
(
"Startup initializer done."
);
}
@Autowired
private
PartnerRepository
partnerRepository
;
@Autowired
private
DatasetRepository
datasetRepository
;
@Autowired
private
DescriptorRepository
descriptorRepository
;
@Autowired
private
DescriptorListRepository
descriptorListRepository
;
// TODO Remove after first deployment to sandbox
private
void
aclForCatalog
()
{
partnerRepository
.
findAll
().
stream
().
forEach
(
partner
->
aclService
.
addCreatorPermissions
(
partner
));
// datasetRepository.findAll().stream().forEach(dataset ->
// aclService.removeAclAwareModel(dataset));
datasetRepository
.
findAll
().
stream
().
forEach
(
dataset
->
aclService
.
addCreatorPermissions
(
dataset
));
// descriptorListRepository.findAll().stream().forEach(descriptorList ->
// aclService.removeAclAwareModel(descriptorList));
descriptorListRepository
.
findAll
().
stream
().
forEach
(
descriptorList
->
aclService
.
addCreatorPermissions
(
descriptorList
));
// descriptorRepository.findAll().stream().forEach(descriptor ->
// aclService.removeAclAwareModel(descriptor));
descriptorRepository
.
findAll
().
stream
().
forEach
(
descriptor
->
aclService
.
addCreatorPermissions
(
descriptor
));
}
@Autowired
private
ElasticsearchService
elasticsearch
;
...
...
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