Merge branch 'master' of github.com:Mark-de-Haan/molgenis into featur…

…e/l3-cache

Conflicts:
	molgenis-data-platform/src/main/java/org/molgenis/data/platform/decorators/MolgenisRepositoryDecoratorFactory.java

molgenis-data-annotators/src/main/java/org/molgenis/data/annotation/core/effects/EffectsMetaData.java

@@ -21,22 +21,22 @@ public class EffectsMetaData implements AnnotatorEntityMetaData
 	public static String ID = "id";
 	public static String VARIANT = VcfWriterUtils.VARIANT;
 
-	public static String ALT = "Alt_Allele";
-	public static String ANNOTATION = "Annotation";
-	public static String PUTATIVE_IMPACT = "Putative_impact";
-	public static String GENE_NAME = "Gene_Name";
-	public static String GENE_ID = "Gene_ID";
-	public static String FEATURE_TYPE = "Feature_type";
-	public static String FEATURE_ID = "Feature_ID";
-	public static String TRANSCRIPT_BIOTYPE = "Transcript_biotype";
-	public static String RANK_TOTAL = "Rank_total";
-	public static String HGVS_C = "HGVS_c";
-	public static String HGVS_P = "HGVS_p";
-	public static String C_DNA_POSITION = "cDNA_position";
-	public static String CDS_POSITION = "CDS_position";
-	public static String PROTEIN_POSITION = "Protein_position";
-	public static String DISTANCE_TO_FEATURE = "Distance_to_feature";
-	public static String ERRORS = "Errors";
+	public static final String ALT = "Alt_Allele";
+	public static final String ANNOTATION = "Annotation";
+	public static final String PUTATIVE_IMPACT = "Putative_impact";
+	public static final String GENE_NAME = "Gene_Name";
+	public static final String GENE_ID = "Gene_ID";
+	public static final String FEATURE_TYPE = "Feature_type";
+	public static final String FEATURE_ID = "Feature_ID";
+	public static final String TRANSCRIPT_BIOTYPE = "Transcript_biotype";
+	public static final String RANK_TOTAL = "Rank_total";
+	public static final String HGVS_C = "HGVS_c";
+	public static final String HGVS_P = "HGVS_p";
+	public static final String C_DNA_POSITION = "cDNA_position";
+	public static final String CDS_POSITION = "CDS_position";
+	public static final String PROTEIN_POSITION = "Protein_position";
+	public static final String DISTANCE_TO_FEATURE = "Distance_to_feature";
+	public static final String ERRORS = "Errors";
 
 	public LinkedList<AttributeMetaData> getOrderedAttributes()
 	{

molgenis-data-annotators/src/main/java/org/molgenis/data/annotation/core/entity/impl/gavin/GavinEntry.java

@@ -49,12 +49,12 @@ public GavinEntry(String lineFromFile) throws Exception
 		this.gene = split[0];
 		this.category = Category.valueOf(split[1]);
 		this.chromosome = split[2];
-		this.start = Integer.valueOf(split[3]);
-		this.end = Integer.valueOf(split[4]);
-		this.NrOfPopulationVariants = Integer.valueOf(split[5]);
-		this.NrOfPathogenicVariants = Integer.valueOf(split[6]);
-		this.NrOfOverlappingVariants = Integer.valueOf(split[7]);
-		this.NrOfFilteredPopVariants = Integer.valueOf(split[8]);
+		this.start = Integer.parseInt(split[3]);
+		this.end = Integer.parseInt(split[4]);
+		this.NrOfPopulationVariants = Integer.parseInt(split[5]);
+		this.NrOfPathogenicVariants = Integer.parseInt(split[6]);
+		this.NrOfOverlappingVariants = Integer.parseInt(split[7]);
+		this.NrOfFilteredPopVariants = Integer.parseInt(split[8]);
 		this.PathoMAFThreshold = split[9].isEmpty() ? null : Double.parseDouble(split[9]);
 
 		this.PopImpactHighPerc = split[10].isEmpty() ? null : Double.parseDouble(split[10]);

molgenis-data-annotators/src/main/java/org/molgenis/data/annotation/web/meta/AnnotationJobExecutionMetaData.java

@@ -31,6 +31,7 @@ public class AnnotationJobExecutionMetaData extends SystemEntityMetaData
 	@Override
 	public void init()
 	{
+		setLabel("Annotation job execution");
 		setExtends(jobExecutionMetaData);
 		addAttribute(TARGET_NAME).setDataType(STRING).setLabel("target name")
 				.setDescription("Fully qualified name of the entity that is being annotated.").setNillable(false);

molgenis-data-annotators/src/main/java/org/molgenis/data/annotation/web/settings/ThousendGenomesAnnotatorSettings.java

@@ -33,6 +33,7 @@ public Meta()
 		public void init()
 		{
 			super.init();
+			setLabel("1000 Genomes annotator settings");
 			addAttribute(CHROMOSOMES).setLabel("Chromosomes")
 					.setDefaultValue("1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22");
 			addAttribute(FILEPATTERN).setLabel("Filepattern")

molgenis-data-cache/src/main/java/org/molgenis/data/cache/l1/L1Cache.java

@@ -92,6 +92,7 @@ public void evictAll(String entityName)
 	 * @return the retrieved {@link Entity} or Optional.empty() if deletion of this entity is stored in the cache or
 	 * null if no information available about this entity in the cache
 	 */
+	@edu.umd.cs.findbugs.annotations.SuppressWarnings(value = "NP_OPTIONAL_RETURN_NULL", justification = "Intentional behavior")
 	public Optional<Entity> get(String entityName, Object id, EntityMetaData entityMetaData)
 	{
 		CombinedEntityCache cache = caches.get();

molgenis-data-cache/src/main/java/org/molgenis/data/cache/l1/L1CacheRepositoryDecorator.java

@@ -28,7 +28,7 @@
  * Delegates to the underlying repository when an action is not supported by the cache or when the cache doesn't contain
  * the needed entity.
  */
-public class L1CacheRepositoryDecorator extends AbstractRepositoryDecorator
+public class L1CacheRepositoryDecorator extends AbstractRepositoryDecorator<Entity>
 {
 	private static final int ID_BATCH_SIZE = 1000;
 

molgenis-data-cache/src/main/java/org/molgenis/data/cache/l2/L2CacheRepositoryDecorator.java

@@ -32,7 +32,7 @@
  * Delegates to the underlying repository when an action is not supported by the cache or when the cache doesn't contain
  * the needed entity.
  */
-public class L2CacheRepositoryDecorator extends AbstractRepositoryDecorator
+public class L2CacheRepositoryDecorator extends AbstractRepositoryDecorator<Entity>
 {
 	private static final int ID_BATCH_SIZE = 1000;
 

molgenis-data-cache/src/main/java/org/molgenis/data/cache/l2/settings/L2CacheSettingsMetaData.java

@@ -46,8 +46,8 @@ public L2CacheSettingsMetaData(RootSystemPackage rootSystemPackage, EntityMetaDa
 	@Override
 	public void init()
 	{
+		setLabel("L2 cache settings");
 		setPackage(rootSystemPackage);
-		setDescription("L2 Cache settings");
 		addAttribute(ID, ROLE_ID).setAuto(true).setVisible(false)
 				.setDescription("automatically generated internal id, only for internal use.");
 		addAttribute(CACHED_ENTITY).setDescription("Name of the entity whose L2 Cache settings these are.")

molgenis-data-cache/src/main/java/org/molgenis/data/cache/utils/CombinedEntityCache.java

@@ -60,6 +60,7 @@ public void evictAll(String entityName)
 	 * @return Optional {@link Entity} with the result from the cache,
 	 * or null if no record of the entity is present in the cache
 	 */
+	@edu.umd.cs.findbugs.annotations.SuppressWarnings(value = "NP_OPTIONAL_RETURN_NULL", justification = "Intentional behavior")
 	public Optional<Entity> getIfPresent(EntityMetaData entityMetaData, Object id)
 	{
 		Optional<Map<String, Object>> optionalDehydratedEntity = cache

molgenis-data-elasticsearch/src/main/java/org/molgenis/data/elasticsearch/reindex/meta/ReindexJobExecutionMeta.java

@@ -42,6 +42,7 @@ public ReindexJobExecutionMeta(IndexPackage indexPackage, JobExecutionMetaData j
 	@Override
 	public void init()
 	{
+		setLabel("Index job execution");
 		setPackage(indexPackage);
 
 		setExtends(jobExecutionMetaData);

molgenis-data-idcard/src/main/java/org/molgenis/data/idcard/model/IdCardIndexingEventMetaData.java

@@ -36,6 +36,7 @@ public class IdCardIndexingEventMetaData extends SystemEntityMetaData
 	@Override
 	public void init()
 	{
+		setLabel("ID-Card indexing event");
 		setPackage(idCardPackage);
 
 		addAttribute(ID, ROLE_ID).setVisible(false).setAuto(true).setLabel("Id");