Java 8

.classpath

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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());