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Genesys PGR
Genesys Backend
Commits
9ae8d169
Commit
9ae8d169
authored
Sep 09, 2015
by
Matija Obreza
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Java 8
parent
4295ea57
Changes
6
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6 changed files
with
11 additions
and
8 deletions
+11
-8
.classpath
.classpath
+1
-1
.settings/org.eclipse.jdt.core.prefs
.settings/org.eclipse.jdt.core.prefs
+3
-3
pom.xml
pom.xml
+2
-2
src/main/java/org/genesys2/server/persistence/domain/AccessionRepository.java
...nesys2/server/persistence/domain/AccessionRepository.java
+4
-0
src/main/java/org/genesys2/server/service/worker/ElasticUpdater.java
...va/org/genesys2/server/service/worker/ElasticUpdater.java
+0
-2
src/main/java/org/genesys2/server/servlet/controller/AccessionController.java
...nesys2/server/servlet/controller/AccessionController.java
+1
-0
No files found.
.classpath
View file @
9ae8d169
...
...
@@ -29,7 +29,7 @@
<attribute
name=
"maven.pomderived"
value=
"true"
/>
</attributes>
</classpathentry>
<classpathentry
kind=
"con"
path=
"org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.
7
"
>
<classpathentry
kind=
"con"
path=
"org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.
8
"
>
<attributes>
<attribute
name=
"maven.pomderived"
value=
"true"
/>
</attributes>
...
...
.settings/org.eclipse.jdt.core.prefs
View file @
9ae8d169
...
...
@@ -25,9 +25,9 @@ org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annota
org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.
7
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.
8
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.
7
org.eclipse.jdt.core.compiler.compliance=1.
8
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
...
...
@@ -116,7 +116,7 @@ org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
org.eclipse.jdt.core.compiler.source=1.
7
org.eclipse.jdt.core.compiler.source=1.
8
org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0
...
...
pom.xml
View file @
9ae8d169
...
...
@@ -52,8 +52,8 @@
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
<jdk.target>
1.
7
</jdk.target>
<jdk.source>
1.
7
</jdk.source>
<jdk.target>
1.
8
</jdk.target>
<jdk.source>
1.
8
</jdk.source>
<show.deprecations>
false
</show.deprecations>
<junit.version>
4.11
</junit.version>
...
...
src/main/java/org/genesys2/server/persistence/domain/AccessionRepository.java
View file @
9ae8d169
...
...
@@ -20,6 +20,7 @@ import java.util.Collection;
import
java.util.List
;
import
java.util.Set
;
import
java.util.UUID
;
import
java.util.stream.Stream
;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.genesys.Taxonomy2
;
...
...
@@ -120,4 +121,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
public
Accession
findOneByUuid
(
UUID
uuid
);
public
List
<
Accession
>
findByAccessionName
(
String
acceNumb
);
@Query
(
"select a from Accession a"
)
Stream
<
Accession
>
streamAll
();
}
src/main/java/org/genesys2/server/service/worker/ElasticUpdater.java
View file @
9ae8d169
...
...
@@ -168,7 +168,6 @@ public class ElasticUpdater {
}
int
page
=
0
,
size
=
100
;
List
<
IndexQuery
>
queries
=
new
ArrayList
<
IndexQuery
>();
do
{
if
((
page
*
size
)
%
10000
==
0
)
{
LOG
.
info
(
"Full reindex enqueue progress "
+
(
page
*
size
));
...
...
@@ -178,7 +177,6 @@ public class ElasticUpdater {
}
catch
(
InterruptedException
e
)
{
}
}
queries
.
clear
();
List
<
Long
>
accessions
=
genesysService
.
listAccessionsIds
(
new
PageRequest
(
page
,
size
));
if
(
accessions
.
isEmpty
())
{
LOG
.
info
(
"No more content"
);
...
...
src/main/java/org/genesys2/server/servlet/controller/AccessionController.java
View file @
9ae8d169
...
...
@@ -108,6 +108,7 @@ public class AccessionController extends BaseController {
// PDCI
if
(
pdciCalculator
!=
null
)
{
try
{
// FIXME Duplicated loading of all accession information
PDCI
pdci
=
pdciCalculator
.
makePDCI
(
accession
.
getId
());
PDCI
existingPdci
=
genesysService
.
loadPDCI
(
accession
.
getId
());
...
...
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