EVA-685 Minor updates based on the requirements for eva-pipeline

variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AnnotationMetadata.java

@@ -33,7 +33,7 @@ public class AnnotationMetadata implements IAnnotationMetadata {
 
     public AnnotationMetadata(IAnnotationMetadata annotationMetadata) {
         this(annotationMetadata.getVepVersion(), annotationMetadata.getCacheVersion(),
-             annotationMetadata.isDefaultVersion());
+                annotationMetadata.isDefaultVersion());
     }
 
     public AnnotationMetadata(String vepVersion, String cacheVersion) {
@@ -61,6 +61,10 @@ public boolean isDefaultVersion() {
         return defaultVersion;
     }
 
+    public void setDefaultVersion(boolean defaultVersion) {
+        this.defaultVersion = defaultVersion;
+    }
+
     @Override
     public String toString() {
         return "AnnotationMetadata{" +

variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/VariantStatistics.java

@@ -250,7 +250,7 @@ private Genotype normalizeGenotypeAlleles(Genotype g) {
         }
     }
 
-    void setGenotypesCount(Map<Genotype, Integer> genotypesCount) {
+    public void setGenotypesCount(Map<Genotype, Integer> genotypesCount) {
         this.genotypesCount = genotypesCount;
     }
 

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/AnnotationMongo.java

@@ -212,11 +212,11 @@ public AnnotationMongo concatenate(AnnotationMongo annotation) {
         return temp;
     }
 
-    private void addConsequenceTypes(Set<ConsequenceTypeMongo> consequenceTypes) {
+    public void addConsequenceTypes(Set<ConsequenceTypeMongo> consequenceTypes) {
         consequenceTypes.forEach(this::addConsequenceType);
     }
 
-    private void addConsequenceType(ConsequenceTypeMongo consequenceType) {
+    public void addConsequenceType(ConsequenceTypeMongo consequenceType) {
         consequenceTypes.add(consequenceType);
         xrefs.addAll(generateXrefsFromConsequenceType(consequenceType));
     }

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/VariantMongo.java

@@ -321,14 +321,35 @@ public Set<VariantSourceEntryMongo> getSourceEntries() {
         return variantSourceEntries;
     }
 
+    public void setSourceEntries(Set<VariantSourceEntryMongo> variantSourceEntries) {
+        this.variantSourceEntries = new HashSet<>();
+        if (variantSourceEntries != null && !variantSourceEntries.isEmpty()) {
+            this.variantSourceEntries.addAll(variantSourceEntries);
+        }
+    }
+
     public Set<VariantStatisticsMongo> getVariantStatsMongo() {
         return variantStatsMongo;
     }
 
+    public void setVariantStatsMongo(Set<VariantStatisticsMongo> variantStatsMongo) {
+        this.variantStatsMongo = new HashSet<>();
+        if (variantStatsMongo != null && !variantStatsMongo.isEmpty()) {
+            this.variantStatsMongo.addAll(variantStatsMongo);
+        }
+    }
+
     public Set<AnnotationIndexMongo> getIndexedAnnotations() {
         return indexedAnnotations;
     }
 
+    public void setIndexedAnnotations(Set<AnnotationIndexMongo> indexedAnnotations) {
+        this.indexedAnnotations = new HashSet<>();
+        if (indexedAnnotations != null && !indexedAnnotations.isEmpty()) {
+            this.indexedAnnotations.addAll(indexedAnnotations);
+        }
+    }
+
     public Set<String> getAnnotationIds() {
         Set<String> ids = new HashSet<>();
         for (AnnotationIndexMongo indexedAnnotation : indexedAnnotations) {

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/VariantSourceMongo.java

@@ -21,7 +21,6 @@
 import uk.ac.ebi.eva.commons.core.models.IVariantGlobalStats;
 import uk.ac.ebi.eva.commons.core.models.IVariantSource;
 import uk.ac.ebi.eva.commons.core.models.StudyType;
-import uk.ac.ebi.eva.commons.core.models.stats.VariantGlobalStats;
 import uk.ac.ebi.eva.commons.mongodb.entities.subdocuments.VariantGlobalStatsMongo;
 
 import java.util.Calendar;

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/projections/SimplifiedVariant.java

@@ -97,4 +97,43 @@ public SimplifiedVariant(VariantType variantType, String chromosome, long start,
         }
     }
 
+    public String getId() {
+        return id;
+    }
+
+    public VariantType getVariantType() {
+        return variantType;
+    }
+
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    public long getStart() {
+        return start;
+    }
+
+    public long getEnd() {
+        return end;
+    }
+
+    public int getLength() {
+        return length;
+    }
+
+    public String getReference() {
+        return reference;
+    }
+
+    public String getAlternate() {
+        return alternate;
+    }
+
+    public VariantAtMongo getAt() {
+        return at;
+    }
+
+    public Set<HgvsMongo> getHgvs() {
+        return hgvs;
+    }
 }

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/subdocuments/ConsequenceTypeMongo.java

@@ -96,7 +96,7 @@ public class ConsequenceTypeMongo implements IConsequenceType {
     @Field(value = RELATIVE_POS_FIELD)
     private Integer relativePosition;
 
-    ConsequenceTypeMongo() {
+    public ConsequenceTypeMongo() {
         this(null, null, null, null, null, null, null, null, null, null, null, null, null, null);
     }
 

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantMongoWriter.java

@@ -15,7 +15,6 @@
  */
 package uk.ac.ebi.eva.commons.mongodb.writers;
 
-import com.mongodb.BulkWriteOperation;
 import com.mongodb.client.model.IndexOptions;
 import com.mongodb.client.model.UpdateOneModel;
 import com.mongodb.client.model.UpdateOptions;
@@ -104,7 +103,7 @@ private void createIndexes() {
     }
 
     @Override
-    protected void doWrite(List<? extends IVariant> variants) {
+    public void doWrite(List<? extends IVariant> variants) {
         List<UpdateOneModel<Document>> updates = new ArrayList<>();
         for (IVariant variant : variants) {
             updates.add(new UpdateOneModel<>(generateQuery(variant), generateUpdate(variant),