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Genesys PGR
Genesys Backend
Commits
bcba3ad5
Commit
bcba3ad5
authored
Dec 27, 2018
by
Matija Obreza
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Plain Diff
AccessionRef relinking after addAccessionRefs requires a delay
parent
8585cf19
Changes
6
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6 changed files
with
78 additions
and
33 deletions
+78
-33
src/main/java/org/genesys/catalog/persistence/dataset/DatasetAccessionRefRepository.java
...og/persistence/dataset/DatasetAccessionRefRepository.java
+7
-0
src/main/java/org/genesys/catalog/persistence/dataset/DatasetAccessionRefRepositoryCustomImpl.java
...ence/dataset/DatasetAccessionRefRepositoryCustomImpl.java
+18
-0
src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java
.../org/genesys/catalog/service/impl/DatasetServiceImpl.java
+14
-17
src/main/java/org/genesys2/server/persistence/SubsetAccessionRefRepository.java
...sys2/server/persistence/SubsetAccessionRefRepository.java
+7
-0
src/main/java/org/genesys2/server/persistence/SubsetAccessionRefRepositoryCustomImpl.java
...r/persistence/SubsetAccessionRefRepositoryCustomImpl.java
+18
-0
src/main/java/org/genesys2/server/service/impl/SubsetServiceImpl.java
...a/org/genesys2/server/service/impl/SubsetServiceImpl.java
+14
-16
No files found.
src/main/java/org/genesys/catalog/persistence/dataset/DatasetAccessionRefRepository.java
View file @
bcba3ad5
...
...
@@ -48,6 +48,13 @@ public interface DatasetAccessionRefRepository {
* @param entities the existing DatasetAccessionRefs to update
*/
void
update
(
Iterable
<
DatasetAccessionRef
>
entities
);
/**
* Update safely: check if records exist before persisting.
*
* @param entities the entities
*/
void
updateSafely
(
Iterable
<
DatasetAccessionRef
>
entities
);
/**
* Delete for dataset.
...
...
src/main/java/org/genesys/catalog/persistence/dataset/DatasetAccessionRefRepositoryCustomImpl.java
View file @
bcba3ad5
...
...
@@ -71,6 +71,24 @@ public class DatasetAccessionRefRepositoryCustomImpl implements DatasetAccession
em
.
merge
(
entity
);
}
}
@Override
@Transactional
public
void
updateSafely
(
Iterable
<
DatasetAccessionRef
>
entities
)
{
for
(
DatasetAccessionRef
entity:
entities
)
{
if
(
exists
(
entity
))
{
em
.
merge
(
entity
);
}
else
{
LOG
.
warn
(
"Record is gone {}"
,
entity
);
}
}
}
private
boolean
exists
(
DatasetAccessionRef
ref
)
{
return
jpaQueryFactory
.
selectFrom
(
QDatasetAccessionRef
.
datasetAccessionRef
).
where
(
QDatasetAccessionRef
.
datasetAccessionRef
.
dataset
.
eq
(
ref
.
getDataset
()).
and
(
QDatasetAccessionRef
.
datasetAccessionRef
.
instCode
.
eq
(
ref
.
getInstCode
()).
and
(
QDatasetAccessionRef
.
datasetAccessionRef
.
genus
.
eq
(
ref
.
getGenus
()).
and
(
QDatasetAccessionRef
.
datasetAccessionRef
.
acceNumb
.
eq
(
ref
.
getAcceNumb
()))))).
fetchCount
()
==
1
;
}
/* (non-Javadoc)
* @see org.genesys.catalog.persistence.dataset.DatasetAccessionRefRepository#save(java.lang.Iterable)
...
...
src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java
View file @
bcba3ad5
...
...
@@ -92,7 +92,9 @@ import org.springframework.transaction.TransactionStatus;
import
org.springframework.transaction.annotation.Isolation
;
import
org.springframework.transaction.annotation.Propagation
;
import
org.springframework.transaction.annotation.Transactional
;
import
org.springframework.transaction.support.DefaultTransactionDefinition
;
import
org.springframework.transaction.interceptor.DefaultTransactionAttribute
;
import
org.springframework.transaction.support.TransactionCallbackWithoutResult
;
import
org.springframework.transaction.support.TransactionTemplate
;
import
org.springframework.validation.annotation.Validated
;
import
org.springframework.web.multipart.MultipartFile
;
...
...
@@ -617,22 +619,17 @@ public class DatasetServiceImpl implements DatasetService {
datasetRepository
.
save
(
loadedDataset
);
threadPoolTaskExecutor
.
execute
(()
->
{
DefaultTransactionDefinition
def
=
new
DefaultTransactionDefinition
();
// explicitly setting the transaction name is something that can only be done
// programmatically
def
.
setName
(
"SomeTxName"
);
def
.
setPropagationBehavior
(
TransactionDefinition
.
PROPAGATION_REQUIRED
);
TransactionStatus
status
=
transactionManager
.
getTransaction
(
def
);
try
{
// execute your business logic here
rematchDatasetAccessions
(
dArs
);
}
catch
(
Throwable
ex
)
{
LOG
.
error
(
"Rolling back rematch. Exception: {}"
,
ex
.
getMessage
(),
ex
);
transactionManager
.
rollback
(
status
);
throw
ex
;
Thread
.
sleep
(
500
);
TransactionDefinition
transactionDefinition
=
new
DefaultTransactionAttribute
(
TransactionDefinition
.
PROPAGATION_REQUIRED
);
new
TransactionTemplate
(
transactionManager
,
transactionDefinition
).
execute
(
new
TransactionCallbackWithoutResult
()
{
@Override
protected
void
doInTransactionWithoutResult
(
TransactionStatus
status
)
{
rematchDatasetAccessions
(
dArs
);
}
});
}
catch
(
InterruptedException
e
)
{
}
transactionManager
.
commit
(
status
);
});
return
lazyLoad
(
loadedDataset
);
}
...
...
@@ -1048,7 +1045,7 @@ public class DatasetServiceImpl implements DatasetService {
@Transactional
(
readOnly
=
false
)
@PreAuthorize
(
"hasRole('ADMINISTRATOR')"
)
private
List
<
DatasetAccessionRef
>
rematchDatasetAccessions
(
List
<
DatasetAccessionRef
>
accessionRefs
)
{
LOG
.
warn
(
"Re-linking {} accessions refs with accessions"
,
accessionRefs
.
size
());
LOG
.
debug
(
"Re-linking {} accessions refs with accessions"
,
accessionRefs
.
size
());
final
AtomicInteger
batchCounter
=
new
AtomicInteger
(
0
);
...
...
@@ -1058,7 +1055,7 @@ public class DatasetServiceImpl implements DatasetService {
lookupMatchingAccessions
(
batch
);
});
// Save in this transaction
accessionRefRepository
.
update
(
accessionRefs
);
accessionRefRepository
.
update
Safely
(
accessionRefs
);
LOG
.
warn
(
"Done relinking {} accession refs."
,
accessionRefs
.
size
());
return
accessionRefs
;
}
...
...
src/main/java/org/genesys2/server/persistence/SubsetAccessionRefRepository.java
View file @
bcba3ad5
...
...
@@ -50,6 +50,13 @@ public interface SubsetAccessionRefRepository {
* @param entities the existing SubsetAccessionRefs to update
*/
void
update
(
Iterable
<
SubsetAccessionRef
>
entities
);
/**
* Update safely: check if records exist before persisting.
*
* @param entities the entities
*/
void
updateSafely
(
Iterable
<
SubsetAccessionRef
>
entities
);
/**
* Delete for subset.
...
...
src/main/java/org/genesys2/server/persistence/SubsetAccessionRefRepositoryCustomImpl.java
View file @
bcba3ad5
...
...
@@ -75,6 +75,24 @@ public class SubsetAccessionRefRepositoryCustomImpl implements SubsetAccessionRe
}
}
@Override
@Transactional
public
void
updateSafely
(
Iterable
<
SubsetAccessionRef
>
entities
)
{
for
(
SubsetAccessionRef
entity:
entities
)
{
if
(
exists
(
entity
))
{
em
.
merge
(
entity
);
}
else
{
LOG
.
warn
(
"Record is gone {}"
,
entity
);
}
}
}
private
boolean
exists
(
SubsetAccessionRef
ref
)
{
return
jpaQueryFactory
.
selectFrom
(
QSubsetAccessionRef
.
subsetAccessionRef
).
where
(
QSubsetAccessionRef
.
subsetAccessionRef
.
subset
.
eq
(
ref
.
getSubset
()).
and
(
QSubsetAccessionRef
.
subsetAccessionRef
.
instCode
.
eq
(
ref
.
getInstCode
()).
and
(
QSubsetAccessionRef
.
subsetAccessionRef
.
genus
.
eq
(
ref
.
getGenus
()).
and
(
QSubsetAccessionRef
.
subsetAccessionRef
.
acceNumb
.
eq
(
ref
.
getAcceNumb
()))))).
fetchCount
()
==
1
;
}
/* (non-Javadoc)
* @see org.genesys2.server.persistence.SubsetAccessionRefRepository#save(java.lang.Iterable)
*/
...
...
src/main/java/org/genesys2/server/service/impl/SubsetServiceImpl.java
View file @
bcba3ad5
...
...
@@ -73,7 +73,9 @@ import org.springframework.transaction.TransactionStatus;
import
org.springframework.transaction.annotation.Isolation
;
import
org.springframework.transaction.annotation.Propagation
;
import
org.springframework.transaction.annotation.Transactional
;
import
org.springframework.transaction.support.DefaultTransactionDefinition
;
import
org.springframework.transaction.interceptor.DefaultTransactionAttribute
;
import
org.springframework.transaction.support.TransactionCallbackWithoutResult
;
import
org.springframework.transaction.support.TransactionTemplate
;
import
org.springframework.validation.annotation.Validated
;
import
com.google.common.collect.Iterables
;
...
...
@@ -368,23 +370,19 @@ public class SubsetServiceImpl implements SubsetService {
LOG
.
info
(
"Done saving {} accession refs, have {} in subset"
,
accessionRefs
.
size
(),
loadedSubset
.
getAccessionCount
());
subsetRepository
.
save
(
loadedSubset
);
threadPoolTaskExecutor
.
execute
(()
->
{
DefaultTransactionDefinition
def
=
new
DefaultTransactionDefinition
();
// explicitly setting the transaction name is something that can only be done
// programmatically
def
.
setName
(
"SomeTxName"
);
def
.
setPropagationBehavior
(
TransactionDefinition
.
PROPAGATION_REQUIRED
);
TransactionStatus
status
=
transactionManager
.
getTransaction
(
def
);
try
{
// execute your business logic here
rematchSubsetAccessions
(
sArs
);
}
catch
(
Throwable
ex
)
{
LOG
.
error
(
"Rolling back rematch. Exception: {}"
,
ex
.
getMessage
(),
ex
);
transactionManager
.
rollback
(
status
);
throw
ex
;
Thread
.
sleep
(
500
);
TransactionDefinition
transactionDefinition
=
new
DefaultTransactionAttribute
(
TransactionDefinition
.
PROPAGATION_REQUIRES_NEW
);
new
TransactionTemplate
(
transactionManager
,
transactionDefinition
).
execute
(
new
TransactionCallbackWithoutResult
()
{
@Override
protected
void
doInTransactionWithoutResult
(
TransactionStatus
status
)
{
rematchSubsetAccessions
(
sArs
);
}
});
}
catch
(
InterruptedException
e
)
{
}
transactionManager
.
commit
(
status
);
});
return
lazyLoad
(
loadedSubset
);
...
...
@@ -623,7 +621,7 @@ public class SubsetServiceImpl implements SubsetService {
lookupMatchingAccessions
(
batch
);
});
// Save in this transaction
accessionRefRepository
.
update
(
accessionRefs
);
accessionRefRepository
.
update
Safely
(
accessionRefs
);
LOG
.
info
(
"Done relinking {} accession refs."
,
accessionRefs
.
size
());
return
accessionRefs
;
}
...
...
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